Books by Subject
- Accurate methods for ancestry and relatedness inference — Epigenetics protocols. 2nd ed. (153)
- Epigenetics, the environment, and children's health across lifespans — Introduction to genomic signal processing with control (153)
- Investigations in yeast functional genomics and molecular biology — Protein engineering protocols (153)
- Proteins and proteomics of Leishmania and Trypanosoma — Zebrafish-- genetics, genomics, and transcriptomics. Fourth edition. [4th ed.] (152)
- 2016 SpringerDavid Hollar, editor.Epigenetics and Development: A Natural Process -- Cause and Effect in Epigenetic Disease Epidemiology -- Epigenetics and Health -- Molecular Basis of Epigenetics -- Trans-generational Epigenetics -- Maternal Exposure to Pharmaceuticals -- Maternal Exposure to Poor Nutrition -- Maternal Exposure to Alcohol, Tobacco, and Drugs -- Maternal Exposure to Lead and Mercury -- Maternal Exposure to Stress -- Paternal Exposure to Environmental Mutagens and Stressors -- Protective Nutrition Before and During Pregnancy -- Protective Behaviors Before and During Pregnancy -- Impact of Dental Mercury on Lifespan Health -- Children's Exposure to Stress -- Children's Exposure to Lead and Mercury -- Children's Exposure to Alcohol, Tobacco, and Drugs -- Children's Exposure to Violence -- Children's Exposure to Traumatic Events -- Children's Exposure to Poor Nutrition -- Infection Impact on Child Development and Epigenetics -- HLA and Immune Response -- Allostatic Load -- Latent Periods and Cardiovascular/Cancer Risks -- Dynamics of Life Experiences on Polygenic Gene Regulation -- Food Chain Impact of Pesticides on Human Health -- Sun and Artificial Radiation Exposure on Skin Health -- Medical Imaging Radiation Risk on Health -- Naturopathic Approaches to Epigenetic Health -- Reprogramming Epigenetic Effects -- An Ecological Systems Approach to Epigenetic Health -- The Health Leader's Guide to Promoting Epigenetic Health .
- 2015 Springer Protocolsedited by Jason H. Moore, Scott M. Williams.Long-term selection experiments : epistasis and the response to selection / Charles Goodnight -- Finding the epistasis needles in the genome-wide haystack / Marylyn D. Ritchie -- Biological knowledge-driven analysis of epistasis in human GWAS with application to lipid traits / Li Ma, Alon Keinan, and Andrew G. Clark -- Epistasis for quantitative traits in Drosophila / Trudy F. C. Mackay -- Epistasis in the risk of human neuropsychiatric disease / Scott M. Williams -- On the partitioning of genetic variance with epistasis / José M. Álvarez-Castro and Arnaud Le Rouzic -- Measuring gene interactions / Thomas F. Hansen -- Two rules for the detection and quantification of epistasis and other interaction effects / Günter P. Wagner -- Direct approach to modeling epistasis / Rong-Cai Yang -- Capacitating epistasis -- detection and role in the genetic architecture of complex traits / Mats E. Pettersson and Örjan Carlborg -- Compositional epistasis : an epidemiologic perspective / Etsuji Suzuki and Tyler J. VanderWeele -- Identification of genome-wide SNP-SNP and SNP-clinical boolean interactions in age-related macular degeneration / Carlos Riveros [and eight others] -- Epistasis analysis using information theory / Jason H. Moore and Ting Hu -- Genome-wide epistasis and pleiotropy characterized by the bipartite human phenotype network / Christian Darabos and Jason H. Moore -- Network theory for data-driven epistasis networks / Caleb A. Lareau and Brett A. McKinney -- Epistasis analysis using multifactor dimensionality reduction / Jason H. Moore and Peter C. Andrews -- Epistasis analysis using ReliefF / Jason H. Moore -- Epistasis analysis using artificial intelligence / Jason H. Moore and Doug P. Hill.
- 2008 Springer Protocolsedited by Donna L. Mendrick, William B. Mattes.Toxicogenomics and classical toxicology, how to improve prediction and mechanistic understanding of human toxicity / Donna L. Mendrick -- Use of traditional endpoints and gene dysregulation to understand mechanisms of toxicity / Wayne R. Buck, Jeffrey F. Waring, Eric A. Blomme -- Quality control of microarray assays for toxicogenomic and in vitro diagnostic applications / Karol L. Thompson and Joseph Hackett -- Role of statistics in toxicogenomics / Michael Elashoff -- Predictive toxicogenomics in preclinical discovery / Scott A. Barros and Rory B. Martin -- In vivo predictive toxicogenomics / Mark W. Porter -- Bioinformatics, databasing and gene annotation / Lyle D. Burgoon and Timothy R. Zacharewski -- Microarray probe mapping and annotation in cross - species comparative toxicogenomics / John N Calley, William B Mattes, Timothy P. Ryan -- Toxicogenomics in biomarker discovery -- Marc F. DeCristofaro, Kellye K. Daniels -- From pharmacogenomics to translational biomarkers / Donna L. Mendrick -- Public consortium efforts in toxicogenomics / William B. Mattes -- Applications of toxicogenomics to nonclinical drug development / Frank D. Sistare, Joseph J. DeGeorge.
- 2012 SpringerPaula Boddington.The "Ethics Job" -- Why Research Ethics? Why Ethics in Genetics? The Case of Genomics Research -- What Ethics Is, What It Is Not, and How We Are Going to Proceed -- Starting Analysis in Ethics: A Practical Guide -- An Overview of Research Ethics and Challenges from Genomics -- Autonomy and Its Limits: The View from Genomics -- The Social and Institutional Setting of Ethics -- Respect for Persons in Research and in Genetics -- Responsibilities of Researchers in Genetics -- Data Sharing in Genomics.
- 2015 SpringerDeborah Mascalzoni, editor.Biobank research and genomic information are changing the way we look at health and medicine. Genomics challenges our values and has always been controversial and difficult to regulate. In the future lies the promise of tailored medical treatments and pharmacogenomics but the borders between medical research and clinical practice are becoming blurred. We see sequencing platforms for research that can have diagnostic value for patients. Clinical applications and research have been kept separate, but the blurring lines challenges existing regulations and ethical frameworks.Then how do we regulate it? This book contains an overview of the existing regulatory landscape for biobank research in the Western world and some critical chapters to show how regulations and ethical frameworks are developed and work. How should international sharing work? How design an ethical informed consent? An underlying critique: the regulatory systems are becoming increasingly complex and opaque. The international community is building systems that should respond to that. According to the authors in fact, it is time to turn the ship around. Biobank researchers have a moral responsibility to look at and assess their work in relation to the bigger picture: the shared norms and values of current society. Research ethics shouldn?t only be a matter of bioethicists writing guidelines that professionals have to follow. Ethics should be practiced through discourse and regulatory frameworks need to be part of that public discourse. Ethics review should be then not merely application of bureaucracy and a burden for researchers but an arena where researchers discuss their projects, receive advice and practice their ethics skills.
- 2012Amanda Morgan Casto.Population geneticists have used genome-wide single nucleotide polymorphism (SNP) datasets to investigate the demographic history of humans and to identify regions of the human genome subject to selection. While some general statements can be made about genome as a whole, every genomic locus has its own evolutionary history. The work contained in this dissertation is aimed at elucidating this history for two particular SNP subsets. The first two chapters explore the effects of selection on the X chromosome. Chapter 1 presents evidence that the X chromosome is more frequently a target of selection than the autosomes and identifies regions of the chromosome where selection may have acted. Chapter 2 explores the evolutionary history of one of these regions in depth through haplotype analyses. Chapter 3 investigates the role of selection in the evolution of SNPs with phenotypic associations and finds evidence for selection on SNPs associated with pigmentation, blood pressure, autoimmune disease, and infectious disease susceptibility. Overall, this work as a whole reinforces the conclusion that natural selection acts unevenly throughout the genome and presents evidence for selection on two subsets of genome-wide SNP datasets: X-linked SNPs and SNPs with phenotypic associations.
- 2007 MyiLibraryMichael L. Arnold.History of investigations -- The role of species concepts -- Testing the hypothesis -- Barriers to gene flow -- Hybrid fitness -- Gene duplication -- Origin of new evolutionary lineages -- Implications for endangered taxa -- Humans and associated lineages -- Emergent properties.
- 2012 Springer ProtocolsFulltext v. 2 (2012) Springer Protocolsedited by Maria Anisimova.Vol. 1. -- pt. I. Introduction: Bioinformactician's primers: 1. Introduction to genome biology: features, processes, and structures / Aidan Budd ; 2. Diversity of genome organisation / Aidan Budd ; 3. Probability, statistics, and computational science / Niko Beerenwinkel and Juliane Siebourg ; 4. The essentials of computational molecular evolution / Stéphane Aris-Brosou and Nicolas Rodrigue ; -- pt. II. Genomic data assembly, alignment, and homology inference: 5. Next-generation sequencing technologies and fragment assembly algorithms / Heewook Lee and Haixu Tang ; 6. Gene prediction / Tyler Alioto ; 7. Alignment methods: strategies, challenges, benchmarking, and comparative overview / Ari Lötynoja ; 8. Whole-genome alignment / Colin N. Dewey ; 9. Inferring orthology and paralogy / Adrian M. Altenhoff and Christophe Dessimoz ; 10. Detecting laterally transferred genes / Rajeev K. Azad and Jeffrey G. Lawrence ; -- pt. III. Genome evolution: insights from statistical analyses: 11. Genome evolution in outcrossing versus selfing versus asexual species / Sylvain Glémin and Nicolas Galtier ; 12. Transposable elements and their identification / Wojciech Makałowski, Amit Pande, Valer Gotea, and Izabela Makałowska ; 13. Evolution of genome content: population dynamics of transposable elements in flies and humans / Josefa González and Dmitri Petrov ; 14. Detection and phylogenetic assessment of conserved synteny derived from whole genome duplications / Shigehiro Kuraku and Axel Meyer ; 15. Analysis of gene order evolution beyond single-copy genes / Nadia El-Mabrouk and David Sankoff ; 16. Discovering patterns in gene order / Laxmi Parida and Niina Haiminen -- Vol. 2. -- pt. I. Phylogenomics: 1. Tangled trees: the challenge of inferring species trees from coalescent and noncoalescent genes / Christian N.K. Anderson, Liang Liu, Dennis Pearl, and Scott V. Edwards ; 2. Modeling gene family evolution and reconciling phylogenetic discord / Gergely J. Szöllősi and Vincent Daubin ; 3. Genome-wide comparative analysis comparative analysis of phylogenetic trees: the Prokaryotic forest of life / Pere Puigbó, Yuri I. Wolf, and Eugene V. Koonin ; 4. Philosophy and evolution: minding the gap between evolutionary patterns and tree-like patterns / Eric Bapteste, Frédéric Bouchard, and Richard M. Burian ; -- pt. II. Natural selection, recombination, and innovation in genomic sequences: 5. Selection on the protein-coding genome / Carolin Kosiol and Maria Anisimova ; 6. Methods to detect selection on noncoding DNA / Ying Zhen and Peter Andolfatto ; 7. The origin and evolution of new genes / Margarida Cardoso-Moreiera and Manyuan Long ; 8. Evolution of protein domain architectures / Kristoffer Forslund and Erik L.L. Sonnhammer ; 9. Estimating recombination rates from genetic variation in humans / Adam Auton and Gil McVean ; 10. Evolution of viral genomes: interplay between selection, recombination and other forces / Sergei L. Kosakovsky Pond, Ben Murrell, and Art F.Y. Poon ; -- pt. III. Population genomics: 11. Association mapping and disease: evolutionary perspectives / Soren Besenbacher, Thomas Mailund, and Mikkel H. Schierup ; 12. Ancestral population genomics / Julien Y. Dutheil and Asger Hobolth ; 13. Nonredundant representation of ancestral recombinations graphs / Laxmi Parida ; -- pt. IV: The "-OMICS". 14. Using Genomic tools to study regulatory evolution / Yoav Gilad ; 15. Characterization and evolutionary analysis of protein-protein interaction networks / Gabriel Musso, Andrew Emili, and Zhaolei Zhang ; 16. Statistical methods in metabolomics / Alexander Korman, Amy Oh, Alexander Raskind, and David Banks ; 17. Introduction the analysis of environmental sequences: metagenomics with MEGAN / Daniel H. Huson and Suparna Mitra ; 18. Analyzing epigenome data in context of genome evolution and human diseases / Lars Feuerbach, Konstantin Halachev, Yassen Assenov, Fabian Müller, Cahristoph Bock, and Thomas Lengauer ; 19. Genetical genomics for evolutionary studies / Pjotr Prins, Geert Smant, and Ritsert C. Jansen ; -- pt. V. Handling genomic data: resources and computation: 20. Genomics data resources: frameworks and standards / Mark D. Wilkinson ; 21. Sharing programming resources between bio* projects through remote procedure call and native call stack strategies / Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scotter Willis, Christopher Fields, and Toshiaki Katayama ; 22. Scaleable computing for evoluntionart genomics / Pjotr Prins, Dominique Belhachemi, Steffen Möller, and Geert Smant.
- 2012 SpringerOrkun S. Soyer, editor.Also available: Print – 2012
- 2011 SpringerLinda S. Pescatello, Stephen M. Roth, editors.Fundamental Concepts in Exercise Genomics -- Statistical and Methodological Considerations in Exercise Genomics -- Can You Be Born a Couch Potato? The Genomic Regulation of Physical Activity -- Interaction Between Exercise and Genetics in Type 2 Diabetes Mellitus: An Epidemiological Perspective -- The Interaction Between Genetic Variation and Exercise and Physical Activity in the Determination of Body Composition and Obesity Status -- Interactive Effects of Genetics and Acute Exercise and Exercise Training on Plasma Lipoprotein-Lipid and Blood Pressure Phenotypes -- Genetic Aspects of Muscular Strength and Size -- Genomics of Aerobic Capacity and Endurance Performance: Clinical Implications -- A Synopsis of Exercise Genomics Research and a Vision for its Future Translation into Practice.
- 2012 Springer Protocolsedited by Annemieke Aartsma-Rus.DNA diagnostics and exon skipping / Umasuthan Srirangalingam and Shern L. Chew -- Bioinformatics and mutations leading to exon skipping / F.O. Desmet and C. Béroud -- Minigenes to confirm exon skipping mutations / Lourdes R. Desviat, Belén Pérez, and Magdalena Ugarte -- Analysis and interpretation of RNA splicing alterations in genes involved in genetic disorders / Maaike P.G. Vreeswijk and Heleen M. van der Klift -- Exon skipping mutations in neurofibromatosis / Emanuele Buratti and Diana Baralle -- Overview on applications of antisense-mediated exon skipping / Willeke M.C. van Roon-Mom and Annemieke Aartsma-Rus -- Overview on DMD exon skipping / Annemieke Aartsma-Rus -- Overview on AON design / Annemieke Aartsma-Rus -- Optimizing RNA/ENA chimeric antisense oligonucleotides using in vitro splicing / Yasuhiro Takeshima, Mariko Yagi, and Masafumi Matsuo -- Optimizing antisense oligonucleotides using phophorodiamidate morpholino oligomers / Linda J. Popplewell, Alberto Malerba, and George Dickson -- Optimizing splice-switching oligomer sequences using 2'-O-methyl phosphorothioate chemistry / Carl Adkin, Sue Fletcher, and Steve D. Wilton -- Exon skipping quantification by real-time PCR / Alessandra Ferlini and Paola Rimessi -- Antisense-mediated exon skipping to shift alternative splicing to treat cancer / Jing Wan -- Antisense-mediated exon skipping to generate soluble receptors / A. Seda Yilmaz-Elis and J. Sjef Verbeek -- Antisense-mediated exon skipping to reframe transcripts / Sandrina Turczynski [and others] -- U1 snRNA as an effective vector for stable expression of antisense molecules and for the inhibition of the splicing reaction / Julie Martone, Fernanda Gabriella De Angelis, and Irene Bozzoni -- Engineering U7snRNA gene to reframe transcripts / Aurélie Goyenvalle -- Dynamic fluorescent and luminescent reporters for cell-based splicing screens / Claude C. Warzecha, Ruben Hovhannisyan, and Russ P. Carstens -- Antisense-mediated exon-skipping to induce gene knockdown / Petra Disterer and Bernard Khoo -- Antisense-mediated exon inclusion / Yimin Hua and Adrian R. Krainer -- Antisense genes to induce exon inclusion / Rachel Nlend Nlend and Daniel Schümperli -- Using mini-genes to identify factors that modulate alternative splicing / Robert Morse, Adrian G. Todd, and Philip J. Young -- Overview of alternative oligonucleotide chemistries for exon skipping / Amer F. Saleh, Andrey A. Arzumanov, and Michael J. Gait -- Identification of peptides for tissue-specific delivery / Hans Heemskerk -- Systemic delivery of antisense oligomer in animal models and its implications for treating DMD / Qi Long Lu and Bo Wu -- Cell-penetrating peptides enhance systemic delivery of antisense morpholino oligomers / Hong M. Moulton -- Optimizing tissue-specific antisense oligonucleotide-peptide conjugates / Corinne A. Betts [and others].
- 2009 Springer Protocolsedited by John Parkinson.Expressed sequence tags : an overview / John Parkinson and Mark Blaxter --Strategies for undertaking expressed sequence tag (EST) projects / Sandra W. Clifton and Makedonka Mitreva -- Construction of cDNA libraries : focus on protists and fungi / Naiara Rodríguez-Ezpeleta ... [et al.] -- Generation of full-length cDNA libraries : focus on plants / Motoaki Seki ... [et al.] -- Preparation of full-length cDNA libraries : focus on metazoans / Masako Harada and Yoshihide Hayashizaki -- Expressed sequence tags : normalization and subtraction of cDNA libraries / Marcelo Bento Soares ... [et al.] -- Generating EST libraries : trans-spliced cDNAs / Cecilia Fernández and Rick M. Maizels -- Large-scale sequencing and analytical processing of ESTs / Makedonka Mitreva and Elaine R. Mardis -- EST processing : from trace to sequence / Ralf Schmid and Mark Blaxter -- Obtaining accurate translations from expressed sequence tags / James Wasmuth and Mark Blaxter -- EST databases and web tools for EST projects /Yao-Qing Shen ... [et al.] -- Phylogenomic analysis of EST datasets / José M. Peregrín-Alvarez and John Parkinson -- Statistical analysis of expressed sequence tags / Edward Susko and Andrew J. Roger -- Application of ESTs in microarray analysis / Weizhong Li ... [et al.] -- Exploiting ESTs in human health / Sandro José de Souza.
- 2012 Springer Protocolsedited by Yannis Karamanos.1. DNA microarrays for gene expression analysis in brain tissue and cell lines / Gustavo A. Barisone and Elva Diaz -- 2. Gene expression profiling using the terminal continuation RNA amplification method for small input samples in neuroscience / Stephen D. Ginsberg, Melissa J. Alldred, and Shaoli Che -- 3. Expression profiling in brain disorders / Peter J. Gebicke-Haerter -- 4. Endothelial cell heterogeneity of blood-brain barrier gene expression: analysis by LCM/qRT-PCR / Tyler Demarest, Nivetha Murugesan, Jennifer A. Macdonald, and Joel S. Pachter -- 5. Gene expression profiling using 3' tag digital approach / Yan W. Asmann, E. Aubrey Thompson, and Jean-Pierre A. Kocher -- 6. Sharing expression profiling data with gemma / Anton Zoubarev and Paul Pavlidis -- 7. Two-dimensional protein analysis of neural stem cells / Martin H. Maurer -- 8. iTRAQ proteomics profiling of regulartory proteins during oligodendrocyte differentiation / Mohit Raja Jain, Tong Liu, Teresa L. Wood, and Hong Li -- 9. Protein profiling of the brain: proteomics of isolated tissues and cells / Nicole Haverland and Pawel Ciborowski -- 10. The proteome of brain capillary endothelial cells: toward a molecular characterization of an in vitro blood-brain barrier model / Sophie Duban-Deweer, Christophe Flahaut, and Yannis Karamanos -- 11. MALDI imaging technology applications in neurosciences: from history to perspectives / Michael Salzet, Céline Mériaux, Julien Franck, Maxence Wistorsi, and Isabelle Fournier -- 12. Profiling of HIV proteins in cerebrospinal fluid / Melinda Wojtkiewicz and Pawel Ciborowski -- 13. Proteomic profiling of cerebrospinal fluid / Gwenael Pottiez and Pawel Ciboroski -- 14. New nanotechnology applications in single cell analysis: why and how? / Gradimir N. Misevic, Gerard BenAssaya, Bernard Rasser, Philippe Sales, Jovana Simic-Krstic, Nikola Misevic, and Octavian Popescu.
- 2013Ronald Chen.Lung cancer is the deadliest cancer worldwide. Survival rates for the most common histological subtype, non-small cell lung cancer (NSCLC), have remained 15% over the past several decades. New molecular understandings and treatments are required to advance NSCLC patient care. Here we use several gene expression-based methods to uncover novel dependencies within NSCLC. First, we use cross-species functional genomics to identify TCEB1 (Elongin C) as a novel synthetic lethal partner with mutant KRAS. Secondly, we use gene expression meta-analysis to identify PTK7 as a survival gene in a subset of lung adenocarcinoma, the major type of NSCLC. Our work demonstrates the utility of analyzing gene expression data sets to expose functionally relevant genes within NSCLC, which may lead to effective therapies.
- 2007 Kargervolume editors, Detlev Schindler, Holger Hoehn.Why, what, and how can we learn from a rare disease like Fanconi anemia? / Schroeder-Kurth, T. -- Fanconi anemia: a disease with many faces / Dietrich, R., Velleuer, E. -- Milestones in Fanconi anemia research / Digweed, M., Hoehn, H., Sperling K. -- Fanconi anemia genes: structure, mutations, and genotype-phenotype correlations / Kalb, R. ... [et al.] -- Cancer in Fanconi anemia and Fanconi anemia genes in cancer / Neveling, K., Kalb, R., Schindler, D. -- Clonal chromosomal aberrations in bone marrow cells of Fanconi anemia patients: results and implications / Neitzel H. ... [et al.] -- Interphase FISH-assay for the detection of MDS- and AML-associated chromosomal imbalances in native bone marrow and peripheral blood cells / Tönnies, H. ... [et al.] -- Applications of cell cycle testing in Fanconi anemia / Schindler, D. ... [et al.] -- Prenatal diagnosis of Fanconi anemia: functional and molecular testing / Bechtold, A. ... [et al.] -- Revertant mosaicism in Fanconi anemia: natural gene therapy at work / Hoehn, H. ... [et al.] -- Stem cell transplantation in Fanconi anemia, recent advances with alternative donors / Eyrich, M., Winkler, B., Schlegel, P.G. -- Fanconi anemia genes in vertebrates: evolutionary conservation, sex-linkage, and embryonic expression of FANCC and FANCG in avian cells / Nanda, I. ... [et al.] -- Studying homologous recombination in Fanconi anemia / Demuth, I., Digweed, M. -- Functional knock-down of human RAD51 for testing the Fanconi anemia-BRCA connection / Rio, P., Hanenberg, H.
- 2006 Springer Protocolsedited by Vladimir V. Didenko.
- 2014 CRCnetBASEedited by Dragan Primorac, M.D., Ph.D., Adjunct Professor of Forensic Science, Eberly College of Science, Pennsylvania State University, University Park, PA, USA, and Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT, USA, Professor of Pediatric Medicine, School of Medicine, University of Split, Split, Croatia and School of Medicine, University of Osijek, Osijek, Croatia; Moses Schanfield, Ph.D., Professor of Science and Anthropology, Department of Forensic Science, George Washington University, Mount Vernon Campus, Washington, D.C., USA.
- 2010 SpringerFlora Tassone, Elizabeth M. Berry-Kravis, editors.Clinical Neurological Phenotype of FXTAS / Maureen A. Leehey, Elizabeth Berry-Kravis, Christopher G. Goetz and Randi J. Hagerman -- The Epidemiology of FXTAS / Deborah A. Hall and Sebastien Jacquemont -- FXTAS: Neuropsychological/Neuropsychiatric Phenotypes / Jim Grigsby, Angela G. Brega, Andreea L. Seritan and James A. Bourgeois -- Radiological Findings in FXTAS / Susan M. Rivera, Glenn T. Stebbins and Jim Grigsby -- The Pathology of FXTAS / Claudia M. Greco, Michael R. Hunsaker and Robert F. Berman -- The Molecular Biology of FXTAS / Flora Tassone and Paul J. Hagerman -- Genotype/Phenotype Relationships in FXTAS / Emily Allen, Maureen A. Leehey, Flora Tassone and Stephanie Sherman -- Animal Models for FXTAS / Rob Willemsen, Yujing Li, Robert F. Berman, Judith R. Brouwer and Ben A. Oostra, et al. -- Treatment and Management of FXTAS / Elizabeth Berry-Kravis, Deborah A. Hall, Maureen A. Leehey and Randi J. Hagerman -- Genetic Counseling for FXTAS and FMR1-Associated Disorders / Louise W. Gane, Katherine Howard and Liane Abrams.
- 2012 SpringerVolker A. Erdmann, Jan Barciszewski, editors.RNAissance / Juergen Brosius -- Nucleic Acids as Therapeutics / Saraswat Pushpendra, Pareek Arvind and Bhandari Anil -- Thio Effects as a Tool for Mechanistic Studies of the Cleavage of RNA Phosphodiester Bonds: The Chemical Basis / Mikko Ora, Tuomas Lönnberg and Harri Lönnberg -- Off-Target Effects and Safety Aspects of Phosphorothioate Oligonucleotides / Martina Stessl, Christian R. Noe and Johannes Winkler -- Oligonucleotide Conjugates: Rationale, Synthesis, and Applications / Yashveer Singh, Pierre Murat, Nicolas Spinelli and Eric Defrancq -- CRISPR: A Bacterial Immunity System Based on Small RNAs / Rolf Wagner and Ümit Pul -- Antisense Technology: From Unique Laboratory Tool to Novel Anticancer Treatments / Christine Di Cresce, Colin Way, Mateusz Rytelewski, Saman Maleki Vareki and Supritha Nilam, et al. -- Antisense-Mediated Reduction of Eukaryotic Noncoding RNAs / Xue-hai Liang, Timothy A. Vickers and Stanley T. Crooke -- Antisense Oligonucleotides in the Treatment of Malignant Gliomas / Gerardo Caruso, Mariella Caffo, Giuseppe Raudino, Federica Raudino and Mario Venza, et al. -- Natural Antisense Transcripts Mediate Regulation of Gene Expression / Marco Magistri and Mohammad Ali Faghihi -- Activation and Deactivation of Antisense and RNA Interference Function with Light / Jeane M. Govan and Alexander Deiters -- Ribozymes as Molecular Biology Reagents / Sanchita Bhadra, Arti Pothukuchy and Andrew Ellington -- RNA Technologies for Mitochondrial Genetics / André Dietrich, Katarzyna Rolle, Marta Gabryelska, Eliza Wyszko and Romain Val, et al. -- RNA-Based Therapies for Inherited Metabolic Diseases / Belén Pérez, Magdalena Ugarte and Lourdes R. Desviat -- RNA-Cleaving DNA Enzymes and Their Potential Therapeutic Applications as Antibacterial and Antiviral Agents / P. I. Pradeepkumar and Claudia Höbartner -- Hammerhead Ribozymes Against Virus and Viroid RNAs / Alberto Carbonell, Ricardo Flores and Selma Gago -- Suppression of Hepatitis C Viral Genome Replication with RNA-Cleaving Deoxyribozyme / Dal-Hee Min and Dong-Eun Kim -- Design of Synthetic shRNAs for Targeting Hepatitis C: A New Approach to Antiviral Therapeutics / Brian H. Johnston and Qing Ge -- The Diverse Active Sites in Splicing, Debranching, and MicroRNA Processing Around RNA Phosphodiester Bonds / Sourav Kumar Dey, Eduardo Paredes, Molly Evans and Subha R. Das -- MicroRNAs and Their Antagonists as Novel Therapeutics / Jeppe Vinther, Jakob Lewin Rukov and Noam Shomron -- microRNAs in Human Diseases and Viral Infections / Alessandra Mescalchin and Tobias Restle -- Dysregulation of MicroRNA Expression and Human Diseases? / To-Ha Thai -- Noncoding RNAs: Identification of Cancer-Associated MicroRNAs / Muller Fabbri and George A. Calin -- Targeting Non-coding RNAs for Cancer Therapy / Satya K. Kota and Savithri Balasubramanian -- MicroRNA Pathways in Drosophila / Geetanjali Chawla and Nicholas S. Sokol -- Viroids: The Smallest Known Infectious Agents Cause Accumulation of Viroid-Specific Small RNAs / Jaroslav Matoušek, Detlev Riesner and Gerhard Steger.
- 2014 Springer Protocolsedited by Juan C. Stockert, Jesús Espada, Alfonso Blázquez-Castro.Predictive binding geometry of ligands to DNA minor groove : isohelicity and hydrogen-bonding pattern / Juan C. Stockert -- Using microchip gel electrophoresis to probe DNA-drug binding interactions / Nan Shi and Victor M. Ugaz -- Identifying different types of chromatin using Giemsa staining / Juan C. Stockert, Alfonso Blázquez-Castro, and Richard W. Horobin -- Analysis of DNA damage and repair by comet fluorescence in situ hybridization (comet-FISH) / Michael Glei and Wiebke Schlörmann -- Alkaline nuclear dispersion assays for the determination of DNA damage at the single cell level / Piero Sestili and Carmela Fimognari -- Polarization microscopy of extended chromatin fibers / Maria Luiza S. Mello and Benedicto de Campos Vidal -- DNA labeling in vivo : quantification of epidermal stem cell chromatin content in whole mouse hair follicles using Fiji image processing software / Elisa Carrasco, María I. Calvo, and Jesús Espada -- Historical overview of bromo-substituted DNA and sister chromatid differentiation / Roberto Mezzanotte and Mariella Nieddu -- Image analysis of chromatin remodelling / Benedicto de Campos Vidal, Marina B. Felisbino, and Maria Luiza S. Mello -- FISH methods in cytogenetic studies / Miguel Pita, Juan Orellana, Paloma Martínez-Rodríguez, Ángel Martínez-Ramírez, Begoña Fernández-Calvín, and José L. Bella -- Ultrastructural and immunofluorescent methods for the study of the XY body as a biomarker / Roberta B. Sciurano and Alberto J. Solari -- Atomic force microscopy for analyzing metaphase chromosomes : comparison of AFM images with fluorescence labeling images of banding patterns / Osamu Hoshi and Tatsuo Ushiki -- Selective detection of phagocytic phase of apoptosis in fixed tissue sections / Vladimir V. Didenko -- Selective transport of cationized fluorescent topoisomerase into nuclei of live cells for DNA damage studies / Candace L. Minchew and Vladimir V. Didenko -- Visualization and interpretation of eukaryotic DNA replication intermediates in vivo by electron microscopy / Kai J. Neelsen, Arnab Ray Chaudhuri, Cindy Follonier, Raquel Herrador, and Massimo Lopes -- Combined bidimensional electrophoresis and electron microscopy to study specific plasmid DNA replication intermediates in human cells / Cindy Follonier and Massimo Lopes -- Standard DNA methylation analysis in mouse epidermis : bisulfite sequencing, methylation-specific PCR, and 5-methyl-cytosine (5mC) immunological detection / Jesús Espada, Elisa Carrasco, and María I. Calvo -- Methyl-combing : single-molecule analysis of DNA methylation on stretched DNA fibers / Attila Németh -- Investigating 5-hydroxymethylcytosine (5hmC) : the state of the art / Colm E. Nestor, James P. Reddington, Mikael Benson, and Richard R. Meehan -- Hydroxymethylated DNA immunoprecipitation (hmeDIP) / Colm E. Nestor and Richard R. Meehan -- Microscale thermophoresis for the assessment of nuclear protein-binding affinities / Wei Zhang, Stefan Duhr, Philipp Baaske, and Ernest Laue -- Analysis of histone posttranslational modifications from nucleolus-associated chromatin by mass spectrometry / Stefan Dillinger, Ana Villar Garea, Rainer Deutzmann, and Attila Németh -- Salt-urea, sulfopropyl-sepharose, and covalent chromatography methods for histone isolation and fractionation / Pedro Rodriguez-Collazo -- Chromatin immunoprecipitation / Javier Rodríguez-Ubreva and Esteban Ballestar -- Analysis of chromatin composition of repetitive sequences : the ChIP-Chop assay / Raffaella Santoro -- Purification of specific chromatin domains from single- copy gene loci in Saccharomyces cerevisiae / Stephan Hamperl, Christopher R. Brown, Jorge Perez-Fernandez, Katharina Huber, Manuel Wittner, Virginia Babl, Ulrike Stöckl, Hinrich Boeger, Herbert Tschochner, Philipp Milkereit, and Joachim Griesenbeck -- Deep sequencing of small chromatin-associated RNA : isolation and library preparation / Sarah Daniela Diermeier, Thomas Schubert, and Gernot Längst -- Deep sequencing of small chromatin-associated RNA : bioinformatic analysis / Sarah Daniela Diermeier and Gernot Längst.
- 2012 Springer Protocolsedited by Michael Kaufmann and Claudia Klinger.Prediction of protein tertiary structures using MUFOLD -- Prediction of protein functions -- Genome-wide screens for expressed hypothetical proteins -- Self-custom-made SFP arrays for nonmodel organisms -- Construction and analysis of full-length and normalized cdna libraries from citrus -- Assembling linear DNA templates for in vitro transcription and translation -- Automated computational analysis of genome-wide DNA methylation profiling data from help-tagging assays -- Detection of RNA editing events in human cells using high-throughput sequencing -- Comparative study of differential gene expression in closely related bacterial species by comparative hybridization -- Whole-genome RT-qPCR microRNA expression profiling -- Using quantitative real-time reverse transcriptase polymerase chain reaction to validate gene regulation by pttg -- FRET-based real-time DNA microarrays -- 2-D gel electrophoresis: Constructing 2D-gel proteome reference maps -- The use of antigen microarrays in antibody profiling -- Limited proteolysis in proteomics using protease-immobilized microreactors -- Mass spectrometry for protein quantification in biomarker discovery -- High-throughput microtitre plate-based assay for DNA topoisomerases -- Microscale thermophoresis as a sensitive method to quantify protein: Nucleic acid interactions in solution -- Bioluminescence resonance energy transfer: An emerging tool for the detection of protein-protein interaction in living cells -- LuMPIS: Luciferase-based MBP-pull-down protein interaction screening system -- Yeast two-hybrid screens: Improvement of array-based screening results by N- and C-terminally tagged fusion proteins -- Inducible microRNA-mediated knockdown of the endogenous human lamin A/C gene -- Multiple-gene silencing using antisense RNAs in escherichia coli -- Functional screen of zebrafish deubiquitylating enzymes by morpholino knockdown and in situ hybridization -- Silencing of gene expression by gymnotic delivery of antisense oligonucleotides -- Polycistronic expression of interfering RNAs from RNA polymerase III promoters -- Metabolite analysis of cannabis sativa l. By NMR spectroscopy -- Metabolome analysis of gram-positive bacteria such as staphylococcus aureus by GC-MS and LC-MS -- Metabolic fingerprinting using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry.
- 2006 ScienceDirectedited by S.E. Hemby, S. Bahn.
- 2002 ScienceDirectedited by Brendan Wren and Nick Dorrell.
- 2007 Springeredited by Werner Dubitzky, Martin Granzow, Daniel Berrar.
- 2011 Springer Protocolsedited by Jin-Rong Xu, Burton H. Bluhm.Genome sequencing and assembly / Manfred G. Grabherr, Evan Mauceli, and Li-Jun Ma -- Targeted cloning of fungal telomeres / Mark L. Farman -- Identification and annotation of repetitive sequences in fungal genomes / Braham Dhillon and Stephen B. Goodwin -- Next-generation sequencing and potential applications in fungal genomics / Phillip SanMiguel -- Getting the most out of your fungal microarray data : two cost- and time-effective methods / Sandra M. Mathioni [and others] -- Fusarium graminearum from expression analysis to functional assays / Heather E. Hallen-Adams, Brad L. Cavinder, and Frances Trail -- EST analysis pipeline : use of distributed computing resources / Francisco Javier González and Juan Antonio Vizcaíno -- Application of ChIP-chip analysis in the rice blast pathogen / Soonok Kim and Thomas K. Mitchell -- Proteome studies of filamentous fungi / Scott E. Baker and Ellen A. Panisko -- Bioinformatics pipeline for sequence-based analyses of fungal biodiversity / D. Lee Taylor and Shawn Houston -- Identifying protein complexes by affinity purification and mass spectrometry analysis in the rice blast fungus / Wende Liu [and others] -- Large scale identification of genes involved in plant-fungal interactions using Illumina's sequencing-by-synthesis technology / R.C. Venu [and others] -- High-throughput production of gene replacement mutants in Neurospora crassa / Gyungsoon Park [and others] -- Phenotypic analysis of Neurospora crassa gene deletion strains / Gloria E. Turner -- Efficient approaches for generating GFP fusion and epitope-tagging constructs in filamentous fungi / Xiaoying Zhou, Guotian Li, and Jin-Rong Xu -- Large-scale insertional mutagenesis in Magnaporthe oryzae by Agrobacterium tumefaciens-mediated transformation / Xiao-Lin Chen, Jun Yang, and You-Liang Peng -- Molecular methods for studying the Cryphonectria parasitica -- hypovirus experimental system / Angus L. Dawe [and others] -- Metabolic fingerprinting in Fusarium verticillioides to determine gene function / Jonathon E. Smith and Burton H. Bluhm -- Tapping genomics to unravel ectomycorrhizal symbiosis / Jonathan M. Plett [and others].
- 2013 SpringerDan A. Liebermann, Barbara Hoffman, editors.Emerging evidence indicates that the Gadd45 family of genes play a unique and critical role as sensors of stress, including genotoxic, physiological and oncogenic stress. The stress response Gadd45 family of genes (Gadd45a, Gadd45b & Gadd45g), discovered by Dr. Liebermann and other researchers, encode for small (18 kd) nuclear/cytoplasmic proteins).These genes are rapidly induced by a wide variety of endogenous and exogenous stress stimuli. In spite of marked similarities, Gadd45 genes are regulated differently & exhibit functional diversity. Gadd45 are implicated in cell cycle arrest, DNA demethylation & repair, apoptosis, cell survival, genomic stability, inflammation, & in response to physiological and oncogenic stress. Functions of Gadd45 genes are mediated by protein-protein interactions that modulate structure/function of other cellular proteins implicated in cell cycle regulation and the response of cells to stress; these interactions vary depending upon the biological setting including cell type, developmental stage and stress/stimulus. Protein partners include cdc2/cyclinB1, p21, the p38/JNK stress induced kinase pathways, and PCNA/histones. The purpose of this book is to provide a comprehensive picture of the unique global role Gadd45 genes play as stress sensors & the molecular pathways involved.Also available: Print – 2013
- 2014 SpringerHe-Feng Huang, Jian-Zhong Sheng, editors.The book Gamete and Embryo-fetal Origins of Adult Diseases introduces various diseases resulting from the abnormal gametogenesis and embryo development, which manifests as growth retardation, birth defects, or increased susceptibility to chronic metabolic diseases such as diabetes, cardiovascular disease and cancer in childhood and adult life, even fertility disorders and the risk of transgenerational transmission. Six common kinds of these diseases are discussed in separate chapters. The authors explore the connections between these diseases and epigenetic reprogramming, rapid cell differentiation and organ formation and environmental influences, including assisted reproductive technology and adverse intrauterine environments. With a summary of findings on the causes and progression of adult diseases at the phase of gametogenesis and embryo development, this book provides insights into the pathogenesis of disease and aids in the treatment and prevention of disease, meeting the requirement for improving the quality of the newborn population, and effectively preventing and curing major diseases at an early stage. This book offers new perspectives and will be an enlightening resource for obstetricians, paediatricians, epidemiologists, endocrinologists and sanitarians.
- 2016Siddhartha Mukherjee.The Pulitzer Prize-winning author draws on his scientific knowledge and research to describe the magisterial history of a scientific idea, the quest to decipher the master-code of instructions that makes and defines humans; that governs our form, function, and fate; and that determines the future of our children. The story of the gene begins in earnest in an obscure Augustinian abbey in Moravia in 1856 where Gregor Mendel, a monk working with pea plants, stumbles on the idea of a "unit of heredity." It intersects with Darwin's theory of evolution, and collides with the horrors of Nazi eugenics in the 1940s. The gene transforms postwar biology. It invades discourses concerning race and identity and provides startling answers to some of the most potent questions coursing through our political and cultural realms. It reorganizes our understanding of sexuality, gender identity, sexual orientation, temperament, choice, and free will, thus raising the most urgent questions affecting our personal realms. Above all, the story of the gene is driven by human ingenuity and obsessive minds--from Mendel and Darwin to Francis Crick, James Watson, and Rosalind Franklin to the thousands of scientists working today to understand the code of codes. Woven through the book is the story of Mukherjee's own family and its recurring pattern of schizophrenia, a haunting reminder that the science of genetics is not confined to the laboratory but is vitally relevant to everyday lives. The moral complexity of genetics reverberates even more urgently today as we learn to "read" and "write" the human genome--unleashing the potential to change the fates and identities of our children and our children's children.--Adapted from dust jacket.
- 2007. Kargervolume editor, Jean-Nicolas Volff.Coevolution within and between genes / Galtier, N.; Dutheil, J. -- Evolution of protein-protein interaction network / Makino, T.; Gojobori, T. -- Bacterial flagella and type III secretion: case studies in the evolution of complexity / Pallen, M.J.; Gophna, U. -- Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems / Burroughs, A.M.; Iyer, L.M.; Aravind, L. -- General trends in the evolution of prokaryotic transcriptional regulatory networks / Madan Babu, M.; Balaji, S.; Aravind, L. -- Divergence of regulatory sequences in duplicated fish genes / Van Hellemont, R. ... [et al.] -- Evolution of gene function on the X chromosome versus the autosomes / Singh, N.D.; Petrov, D.A. -- Amino acid repeats and the structure and evolution of proteins / Albà, M.M.; Tompa, P.; Veitia, R.A. -- Origination of chimeric genes through DNA-level recombination / Arguello, J.R. ... [et al.] -- Exaptation of protein coding sequences from transposable elements / Bowen, N.J.; Jordan, I.K. -- Modulation of host genes by mammalian transposable elements / Makalowski, W.; Toda, Y. -- Modern genomes with retro-look: retrotransposed elements, retroposition and the origin of new genes / Volff, J.-N.; Brosius, J.
- 2011 CRCnetBASEWilliam Wu, Helen H. Zhang, Michael J. Welsh, and Peter B. Kaufman."The third edition of this popular reference covers a variety of techniques related to gene manipulation, including DNA isolation, preparation, screening, and analysis. Topics range from very basic methods to current and sophisticated technologies, including methodologies created and tested by the authors. Other topics include approaches to grant funding and SiRNA technology. The authors offer detailed, step-by-step explanations of protocols and helpful troubleshooting guides. This edition features new techniques for every chapter, as well as several new chapters"--Provided by publisher.
- 2014 Springer Protocolsedited by Francesca Storici.RecTEPsy-mediated recombineering in Pseudomonas syringae / Bryan Swingle - Genome manipulations with bacterial recombineering and site-specific integration in Drosophila / Yi Zhang, William Schreiner, and Yikang S. Rong -- Multiple genetic manipulations of DT40 cell line / Akira Motegi and Minoru Takata -- Gene targeting of human pluripotent stem cells by homologous recombination / Sara E. Howden and James A. Thomson -- Methods for the assessment of ssODN-mediated gene correction frequencies in muscle cells / Carmen Bertoni -- Small fragment homologous replacement (SFHR) : sequence-specific modification of genomic DNA in eukaryotic cells by small DNA fragments/ Andrea Luchetti, Arianna Malgieri, and Federica Sangiuolo -- Preparation and application of triple helix forming oligonucleotides and single strand oligonucleotide donors for gene correction / Md. Rowshon Alam ... [et al.] -- Triplex-mediated genome targeting and editing / Faisal Reza and Peter M. Glazer -- Targeting piggyBac transposon integrations in the human genome / Daniel L. Galvan, Claudia S. Kettlun, and Matthew H. Wilson -- Gene targeting in human-induced pluripotent stem cells with adenoviral vectors / Kohnosuke Mitani -- Enhanced gene targeting of adult and pluripotent stem cells using evolved adeno-associated virus / Melissa A. Bartel and David V. Schaffer -- Lentiviral vectors encoding zinc-finger nucleases specific for the model target locus HPRT1 / Laetitia P.L. Pelascini and Manuel A.F.V. Gonçalves -- Designing and testing the activities of TAL effector nucleases / Yanni Lin, Thomas J. Cradick, and Gang Bao -- Bacterial one-hybrid system to isolate homing endonuclease variants with altered DNA target specificities / Rakesh Joshi and Frederick S. Gimble -- Design and analysis of site-specific single-strand nicking endonucleases for gene correction / Michael J. Metzger and Michael T. Certo -- CRISPR-Cas-mediated targeted genome editing in human cells / Luhan Yang ... [et al.] -- RNA-guided genome editing of mammalian cells / Neena K. Pyzocha ... [et al.] -- Nuclease-mediated double-strand break (DSB) enhancement of small fragment homologous recombination (SFHR) gene modification in human- induced pluripotent stem cells (hiPSCs) / R. Geoffrey Sargent, Shingo Suzuki, and Dieter C. Gruenert -- AAV-mediated gene editing via double-strand break repair / Matthew L. Hirsch and R. Jude Samulski -- Genetic modification stimulated by the induction of a site- specific break distant from the locus of correction in haploid and diploid yeast Saccharomyces cerevisiae / Samantha Stuckey and Francesca Storici -- Southern blot protocol to detect chimeric nuclease- mediated gene repair / Céline J. Rocca ... [et al.] -- High-throughput cellular screening of engineered nuclease activity using the single-strand annealing assay and luciferase reporter / Thomas J. Cradick, Christopher J. Antico, and Gang Bao -- Unbiased method for detection of genome-wide off- target effects in cell lines treated with zinc finger nucleases / Cory R. Lindsay and David B. Roth -- Identification of off-target cleavage sites of zinc finger nucleases and TAL effector nucleases using predictive models / Eli J. Fine, Thomas J. Cradick, and Gang Bao -- Method for retinal gene repair in neonatal mouse / Marilyn Dernigoghossian ... [et al.] -- In utero delivery of oligodeoxynucleotides for gene correction / Lingzhi Cai ... [et al.] -- Portal vein delivery of viral vectors for gene therapy for hemophilia / Alexandra Sherman ... [et al.] -- Gene correction of induced pluripotent stem cells derived from a murine model of x-linked chronic granulomatous disorder / Sayandip Mukherjee and Adrian J. Thrasher -- Efficient transduction of hematopoietic stem cells and its potential for gene correction of hematopoietic diseases / Dolly Thomas and Gustavo Mostoslavsky.
- 2015 Springer Protocolsedited by Xuenong Bo, Joost Verhaagen.Adeno-Associated Viral Vectors for Gene Delivery to the Nervous System -- Lentiviral Vectors for Gene Delivery to the Nervous System -- Gene Therapy for Parkinson's Disease: AAV-5-Mediated Delivery of Glial Cell Line-Derived Neurotrophic Factor (GDNF) -- Gene Delivery and Gene Therapy for Alzheimer's Disease -- Gene Therapy for Huntington's Disease -- Gene Therapy Approaches to Promoting Axonal Regeneration After Spinal Cord Injury -- Gene Delivery to Neurons of the Dorsal Root Ganglia Using Adeno-Associated Viral Vectors -- Targeted Gene Therapy for Ischemic Stroke -- Adeno-Associated Viral Gene Therapy for Retinal Disorders -- Gene Therapy for Epilepsies -- AAV Gene Therapy Strategies for Lysosomal Storage Disorders with Central Nervous System Involvement -- Gene Therapy in Spinal Muscular Atrophy (SMA) Models Using Intracerebroventricular Injection into Neonatal Mice -- Gene Therapy for Chronic Pain: How to Manipulate and Unravel Pain Control Circuits from the Brain? -- Gene Therapy Approaches Using Reproducible and Fully Penetrant Lentivirus-Mediated Endogenous Glioma Models
- 2015 Springer Protocolsedited by Long Jason Lu.Microarray Transposon Tracking for the Mapping of Conditionally Essential Genes in Campylobacter jejuni -- Identifying Essential Streptococcus sanguinis Genes Using Genome-Wide Deletion Mutation -- Defining Essential Genes and Identifying Virulence Factors of Porphyromonas gingivalis by Massively-Parallel Sequencing of Transposon Libraries (Tn-seq) -- Identification of Essential Genes and Synthetic Lethal Gene Combinations in Escherichia coli K-12 -- Identification of Genes Essential for Leptospirosis -- Identifying Essential Genes in Mycobacterium tuberculosis by Global Phenotypic Profiling -- Essential Genes in the Infection Model of Pseudomonas aeruginosa-PCR-Based Signature-Tagged Mutagenesis -- Genome-Wide Synthetic Genetic Screening by Transposon Mutagenesis in Candida albicans -- An Integrated Machine-Learning Model to Predict Prokaryotic Essential Genes -- A Statistical Framework for Improving Genomic Annotations of Transposon Mutagenesis (TM) Assigned Essential Genes -- A Proposed Essential Gene Discovery Pipeline: A Campylobacter jejuni Case Study -- Computational Prediction of Essential Metabolic Genes Using Constraint-Based Approaches -- Three Computational Tools for Predicting Bacterial Essential Genes -- Gene Essentiality Analysis Based on DEG 10, an Updated Database of Essential Genes -- Discovering Essential Domains in Essential Genes.
- 2006 SpringerJun Ma, editor.
- 2011 Springer Protocolsedited by Lorraine O'Driscoll.Real-time PCR and multiplex approaches / Olga L. Gurvich and Mikhail Skoblov -- Reverse-transcriptase polymerase chain reaction to detect extracellular mRNAs / Sweta Rani and Lorraine O'Driscoll -- Microarray analysis of mRNAs : experimental design and data analysis fundamentals / Jai Prakash Mehta -- Software and tools for microarray data analysis / Jai Prakash Mehta and Sweta Rani -- Analysis of gene expression as relevant to cancer cells and circulating tumour cells / Anne M. Friel, John Crown, and Lorraine O'Driscoll -- Gene expression profiling in formalin-fixed, paraffin-embedded tissues using the whole-genome DASL assay / Craig S. April and Jian-Bing Fan -- MicroRNA expression analysis : techniques suitable for studies of intercellular and extracellular MicroRNAs / Erica Hennessy and Lorraine O'Driscoll -- Western blotting analysis as a tool to study receptor tyrosine kinases / Serena Germano and Lorraine O'Driscoll -- 2D gel electrophoresis and mass spectrometry identification and analysis of proteins / Paula Meleady -- Design, construction, and analysis of cell line arrays and tissue microarrays for gene expression analysis / Kathy Gately, Keith Kerr, and Ken O'Byrne -- Immunohistochemical and immunofluorescence procedures for protein analysis / Kishore Reddy Katikireddy and Finbarr O'Sullivan -- Advanced microscopy : laser scanning confocal microscopy / Orla Hanrahan, James Harris, and Chris Egan -- Isolation of exosomes for subsequent mRNA, microRNA, and protein profiling / Sweta Rani [and others] -- Atomic force microscopy and high-content analysis : two innovative technologies for dissecting the relationship between epithelial-mesenchymal transition-related morphological and structural alterations and cell mechanical properties / Stephen T. Buckley, Anthony M. Davies, and Carsten Ehrhardt.
- 2009 CRCnetBASEHinrich Göhlmann, Willem Talloen."Gene expression studies merge three disciplines with different historical backgrounds: molecular biology, bioinformatics, and biostatistics. This book tears down the omnipresent language barriers among researchers of these different backgrounds by explaining the entire process of a gene expression study from conception to interpretation. It covers important technical and statistical pitfalls and problems, helping not only to explain concepts outside the domain of researchers, but to provide additional guidance in their field of expertise. The book also describes technical and statistical methods conceptually with illustrative examples, enabling those inexperienced with gene expression studies to grasp the basic principles"--Provided by publisher.
- 2014 Springer Protocolsedited by Michael F. Ochs, Department of Mathematics & Statistics, the College of New Jersey, Wing, NJ, USA.The Present State and Future Direction of Integrated Gene Function Analysis -- Performing Integrative Functional Genomics Analysis in GeneWeaver.org -- Functional Annotation of Differentially Regulated Gene Set Using WebGestalt: A Gene Set Predictive of Response to Ipilimumab in Tumor Biopsies -- Integrative Data-Mining Tools to Link Gene and Function -- Detection of Driver Protein Complexes in Breast Cancer Metastasis by Large-Scale Transcriptome-Interactome Integration -- Pattern Identification in Time-Course Gene Expression Data with the CoGAPS Matrix Factorization -- Statistical Tools and R Software for Cancer Driver Probabilities -- Predicting the Functional Consequences of Somatic Missense Mutations Found in Tumors -- Determining the Effect of DNA Methylation on Gene Expression in Cancer Cells -- Reverse Engineering Transcriptional Gene Networks -- Integrating In Silico Resources to Map a Signaling Network -- A Method for Inducible Gene Over-Expression and Down-Regulation in Emerging Model Species Using Pogostick -- Construction and Application of Site-Specific Artificial Nucleases for Targeted Gene Editing -- Selection of Recombinant Antibodies from Antibody Gene Libraries -- Construction of Simple and Efficient siRNA Validation Systems for Screening and Identification of Effective RNAi-Targeted Sequences from Mammalian Genes -- Rapid Genetic Modification of Mouse Embryonic Stem Cells by Inducible Cassette Exchange Recombination -- In Ovo Electroporation of miRNA-Based-Plasmids to Investigate Gene Function in the Developing Neural Tube -- Proteomic Strategies: SILAC and 2D-DIGE--Powerful Tool to Investigate Cellular Alterations -- Conditional Gene-Trap Mutagenesis in Zebrafish.
- 2007 Springer Protocolsedited by Michael F. Ochs.Gene function inference from gene expression of deletion mutants / Ghislain Bidaut -- Association analysis for large-scale gene set data / Stefan A. Kirov, Bing Zhang, and Jay R. Snoddy -- Estimating gene function with least squares nonnegative matrix factorization / Guoli Wang and Michael F. Ochs -- From promoter analysis to transcriptional regulatory network prediction using PAINT / Gregory E. Gonye ... [et al.] -- Prediction of intrinsic disorder and its use in functional proteomics / Vladimir N. Uversky ... [et al.] -- Sybil : methods and software for multiple genome comparison and visualization / Jonathan Crabtree ... [et al.] -- Estimating protein function using protein-protein relationships / Shailesh V. Date -- Bioinformatics tools for modeling transcription factor target genes and epigenetic changes / Ramana V. Dvuluri -- Mining biomedical data using MetaMap Transfer (MMTx) and the Unified Medical Language System (UMLS) / John D. Osborne ... [et al.] -- Statistical methods for identifying differentially expressed gene combinations / Yen-Yi Ho ... [et al.] -- Gene function analysis using the chicken B-cell line DT40 / Randolph B. Caldwell ... [et al.] -- Design and application of a shRNA-based gene replacement retrovirus / Rugang Zhang, Peter D. Adams, and Xiaofen Ye -- Construction of simple and efficient DNA vector-based short hairpin RNA expression systems for specific gene silencing in mammalian cells / Tsung-Lin Cheng and Wen-Tsan Chang -- Selection of recombinant antibodies from antibody gene libraries / Michael Hust, Stefan Dübel, and Thomas Schirrmann -- A bacterial/yeast merged two-hybrid system : protocol for yeast screening with single of parallel baits / Nadezhda Y. Tikhmyanova ... [et al.] -- A bacterial/yeast merged two-hybrid system : protocol for bacterial screening / Ilya G. Serebriiskii, Nadia Milech, and Erica A. Golemis -- Engineering Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system / Stacey Thibodeau-Beganny and J. Keith Joung.
- 2009 Springer Protocolsedited by Ralf Kühn, Wolfgang Wurst.Overview on mouse mutagenesis / Ralf Kühn and Wolfgang Wurst -- Construction of gene-targeting vectors by recombineering / Song-Choon Lee, Wei Wang, and Pentao Liu -- Gene-trap vectors and mutagenesis / Silke De-Zolt ... [et al.] -- Chromosome engineering in ES cells / Louise vander Weyden, Charles Shaw-Smith, and Allan Bradley -- Gene modification in embryonic stem cells by single-stranded DNA oligonucleotides / Marieke Aarts ... [et al.] -- Generation of shRNA transgenic mice / Christiane Hitz ... [et al.] -- Mutagenesis of mouse embryonic stem cells with ethylmethanesulfonate / Robert Munroe and John Schimenti -- Gene targeting in mouse embryonic stem cells / Lino Tessarollo ... [et al.] -- Manipulating mouse embryonic stem cells / Eileen Southon and Lino Tessarollo -- ES cell line establishment / Heidrun Kern and Branko Zevnik -- Generation of double-knockout embryonic stem cells / Eva Wielders, Marleen Dekker, and Hein te Riele -- Differentiation analysis of pluripotent mouse embryonic stem (ES) cells in vitro / Insa S. Schroeder ... [et al.] -- Cloning of ES cells and mice by nuclear transfer / Sayaka Wakayama, Satoshi Kishigami, and Teruhiko Wakayama -- Isolation, microinjection, and transfer of mouse blastocysts / Susan W. Reid and Lino Tessarollo -- Aggregation chimeras : combining ES cells, diploid, and tetraploid embryos / Mika Tanaka ... [et al.] -- VelociMouse : fully ES cell-derived F0-generation mice obtained from the injection of ES cells into eight-cell-stage embryos / Thomas M. DeChiara ... [et al.] -- Generation of Cre recombinase-expressing transgenic mice using bacterial artificial chromosomes / Jan Rodriguez Parkitna, David Engblom, and Günther Schütz -- Inducible Cre mice / Susanne Feil, Nadejda Valtcheva, and Robert Feil -- Creation and use of a Cre recombinase transgenic database / Andras Nagy, Lynn Mar, and Graham Watts -- Transposon mutagenesis in mice / David A. Largaespada -- Lentiviral transgenesis / Alexander Pfeifer and Andreas Hofmann -- Sperm cryopreservation and in vitro fertilization / Susan Marschall, Auke Boersma, and Martin Hrabé de Angelis -- Influence of genetic background on genetically engineered mouse phenotypes / Thomas Doetschman -- Pathologic phenotyping of mutant mice / Roderick T. Bronson -- Systemic first-line phenotyping / Valérie Gailus-Durner ... [et al.]
- 2006 Springer Protocolsedited by Minou Bina.Analysis of allele-specific gene expression / Julian C. Knight -- Construction of microRNA-containing vectors for expression in mammalian cells / Yoko Fukuda, Hiroaki Kawasaki, and Kazunari Taira -- Mining microarray data at NCBI's gene expression omnibus (GEO) / Tanya Barrett and Ron Edgar -- The Stanford microarray database: a user's guide / Jeremy Gollub, Catherine A. Ball, and Gavin Sherlock -- Detecting nucleosome ladders on unique DNA sequences in mouse liver nuclei / Tomara J. Fleury, Alfred Cioffi, and Arnold Stein -- DNA methyltransferase probing of DNA-protein interactions / Scott A. Hoose and Michael P. Kladde -- Protein binding microarrays (PBMS) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins / Michael F. Berger and Martha L. Bulyk -- Quantitative profiling of protein-DNA binding on microarrays / Jiannis Ragoussis, Simon Field, and Irina A. Udalova -- Analysis of protein-DNA binding by streptavidin-agarose pulldown / Kenneth K. Wu -- Isolation and mass spectrometry of specific DNA binding proteins / Mariana Yaneva and Paul Tempst -- Isolation of transcription factor complexes by in vivo biotinylation tagging and direct binding to streptavidin beads / Patrick Rodriguez ... [et al.]. Use of genome browsers to locate your favorite genes / Minou Bina -- Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes / Razi Khaja ... [et al.] -- Identification and mapping of paralogous genes on a known genomic DNA sequence / Minou Bina -- Quantitative DNA fiber mapping in genome research and construction of physical maps / Heinz-Ulrich G. Weier and Lisa W. Chu -- PRINS for mapping single copy genes / Avirachan T. Tharapel and Stephen S. Wachtel -- VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes / Inna Dubchak and Dmitriy V. Ryaboy -- Computational prediction of cis-Regulatory modules from multispecies alignments using galaxy, table browser, and GALA / Laura Elnitski, David King, and Ross C. Hardison -- Comparative promoter analysis in vertebrate genomes with the CORG workbench / Christoph Dieterich and Martin Vingron -- cis-Regulatory region analysis using BEARR / Vinsensius Berlian Vega -- A database of 9-Mers from promoter region of human protein-coding genes / Minou Bina, Phillip Wyss, and Syed Rehan Shah -- A program toolkit for the analysis of regulatory regions of genes / Phillip Wyss, Sheryl A. Lazarus, and Minou Bina --
- 2008 CRCnetBASEeditors, Brett A. Lidbury and Suresh Mahalingam.A perspective on the future clinical impact of genetic diagnosis and gene-based drug therapies for patient health / Julian W. Tang -- Virally-encoded microRNA (miRNA): candidates for gene silencing / Ralph A. Tripp ... [et al.] -- Development of gene profile-responsive antisense agents / Sergei A. Kazakov and Brian H. Johnston -- Gene profiles in drug development: applications in target identification, biomarker discovery, and compound characterization / Eric A.G. Blomme and Dimitri Semizarov -- Gene profiles and cancer / Beverly A. Teicher -- RNA viruses and RNA-based drugs: a perfect match for RNA delivery and the identification of candidate therapeutic target inflammatory molecules / Brett A. Lidbury ... [et al.] -- Ethical considerations for a genetic future in diagnosis and drug development / Lexie Brans and Brett A. Lidbury.
- 2013 Springer Protocolsedited by Minou Bina.1. Gene regulation / Minou Bina -- 2. Isolation of nuclei for use in genome-wide DNase hypersensitivity assays to probe chromatin structure / Guoyu Ling and David J. Waxman -- 3. DNase I digestion of isolated nuclei for genome-wide mapping of Denise hypersensitivity sites in chromatin / Guoyu Ling and David J. Waxman -- 4. Isolation and analysis of DNA derived from nucleosome-free regions / Matthew Murtha, Yatong Wang, Claudio Basilico, and Lisa Dailey -- 5. Acquisition of high quality DNA for massive parallel sequencing by in vivo chromatin immunoprecipitation / M. van den Boogaard, L.Y.E. Wong, V.M. Christoffels and P. Barnett -- 6. Luciferase assay to study the activity of a cloned promoter DNA fragment / Nina Solberg and Stefan Krauss -- 7. Promoter deletion analysis using a dual-luciferase reporter system / Yong Zhong Xu, Cynthia Kanagaratham, Sylwia Jancik and Danuta Radzioch -- 8. Application of mRNA display for in vitro selection of DNA-binding transcription factor complexes / Seiji Tateyama and Hiroshi Yanagawa -- 9. Isolation of intracellular protein -- DNA complexes using HaloCHIP an antibody-free alternative to chromatin immunoprecipitation / Danette L. Daniels and Marjeta Urh -- 10. Modified yeast one-hybrid system for genome-wide identification of transcription factor binding sites / Kazuyuki Yanai -- 11. Identifying specific protein-DNA interactions using SILAC-based quantitative proteomics / Cornelia G. Spruijt, H. Irem Baymaz, and Michiel Vermeulen -- 12. Electrophoretic mobility-shift and super-shift assays for studies and characterization of protein-DNA complexes / Elsie I. Pares-Matos -- 13. Combination of native and denaturing PAGE for the detection of protein binding regions in long fragments of genomic DNA / Kristel Kaer and Mart Speek -- 14. Quantitative nanoproteomics approach for protein complex (QNanoPX) using gold nanoparticle-based DNA probe / Shu-Hui Chen and Mei-Yin Lin -- 15. Chromatin assembly and in vitro transcription analyses for evaluation of individual protein activities in multicomponent transcriptional complexes / Takayuki Furumatsu and Hiroshi Asahara -- 16. Using FRET to monitor protein-induced DNA bending : the TBP-TATA complex as a model system / Rebecca H. Blair, James A. Goodrich, and Jennifer F. Kugel -- 17. Promoter independent abortive transcription assays unravel functional interactions between TFIIB and RNA polymerase / Simone C. Wiesler, Finn Werner, and Robert O.J. Weinzierl -- 18. Fluorescence cross-correlation spectroscopy (FCCS) to observe dimerization of transcription factors in living cells / Hisayo Sadamoto and Hideki Muto -- 19. Nuclear recruitment assay as a tool to validate transcription factor interactions in mammalian cells / C.J.J. Boogerd, V.M. Christoffels, and P. Barnett -- 20. Preparation of cell lines for single-cell analysis of transcriptional activation dynamics / Ilona U. Rafalska-Metcalf and Susan M. Janicki -- 21. Peptide microarrays for profiling of serine/threonine kinase activity of recombinant kinases and lysates of cells and tissue samples / Riet Hilhorst, Liesbeth Houkes, Monique Mommersteeg, Joyce Musch, Adriënne van den Berg and Rob Ruijtenbeck -- 22. Immunoaffinity purification of protein complexes from mammalian cells / Chieri Tomomori-Sato, Shigeo Sato, Ronald C. Conaway and Joan W. Conaway -- 23. Simple and efficient identification of chromatin modifying complexes and characterization of complex composition / Jeong-Heon Lee and David Skalnik -- 24. Heavy methyl-SILAC labeling coupled with liquid chromatography and high-resolution mass spectrometry to study the dynamics of site-specific histone methylation / Xing-Jun Cao, Barry M. Zee, and Benjamin A. Garcia -- 25. Analysis of p300 occupancy at the early stage of stem cell differentiation by chromatin immunoprecipitation / Melanie Le May and Qiao Li -- 26. Mammalian two-hybrid assays for studies of interaction of p300 with transcription factors / Daniela B. Mendonnc̦a, Gustavo Mendonc̦a, and Lyndon F. Cooper -- 27. Fluorescence anisotropy microplate assay to investigate the interaction of full-length steroid receptor coactivator-1a with steroid receptors / Chen Zhang, Steven K. Nordeen, and David J. Shapiro -- 28. Use of histone deacetylase inhibitors to examine the roles of bromodomain and histone acetylation in p300-dependent gene expression / Jihong Chen and Qiao Li -- 29. Histone deacetylase inhibitor valproic acid as a small molecule inducer to direct the differentiation of pluripotent stem cells / Jihong Chen, Natascha Lacroix, and Qiao Li -- 30. Sedimentation and immunoprecipitation assays for analyzing complexes that repress transcription / Ping Lu, Bruce S. Hostager, Paul B. Rothman, and John D. Colgan -- 31. Methods for studies of protein interactions with different DNA methyltransferases / Jianchang Yang.
- 2012 Springer Protocolsedited by Bart Deplancke, Nele Gheldof.pt. I. Regulatory state components. 1. How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome / Juan M. Vaquerizas, Sarah A. Teichmann, and Nicholas M. Luscombe. 2. Expression pattern analysis of regulatory transcription factors in Caenorhabditis elegans / Huiyun Feng, Hannah L. Craig, and Ian A. Hope. 3. High-throughput SELEX determination of DNA sequences bound by transcription factors in vitro / Nobuo Ogawa and Mark D. Biggin. 4. Convenient determination of protein-binding DNA sequences using quadruple 9-mer-based microarray and DsRed-monomer fusion protein / Min-Jeong Kim, Pil Joong Chung, Tae-Ho Lee, Tae-Hoon Kim, Baek Hie Nahm, and Yeon-Ki Kim. 5. Analysis of specific protein-DNA interactions by bacterial one-hybrid assay / Marcus B. Noyes. 6. MITOMI : a microfluidic platform for in vitro characterization of transcription factor-DNA interaction / Sylvie Rockel, Marcel Geertz, and Sebastian J. Maerkl. 7. Detecting protein-protein interactions with the split-ubiquitin sensor / Alexander Dünkler, Judith Müller, and Nils Johnsson. 8. Genome-wide dissection of posttranscriptional and posttranslational interactions / Mukesh Bansal and Andrea Califano. 9. Linking cellular signalling to gene expression using EXT-encoded reporter libraries / Anna Botvinik and Moritz J. Rossner. 10. Sample preparation for small RNA massive parallel sequencing / Willemijn M. Gommans and Eugene Berezikov -- pt. II. Genomic components. 11. CAGE (cap analysis of gene expression) : a protocol for the detection of promoter and transcriptional networks / Hazuki Takahashi, Sachi Kato, Mitsuyoshi Murata, and Piero Carninci. 12. Detecting DNaseI-hypersensitivity sites with MLPA / Thomas Ohnesorg, Stefanie Eggers, and Stefan J. White. 13. Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method / Nele Gheldof, Marion Leleu, Daan Noordermeer, Jacques Rougemont, and Alexandre Reymond -- pt. III. Mapping protein-DNA interactions. 14. Analyzing transcription factor occupancy during embryo development using ChIP-seq / Yad Ghavi-Helm and Eileen E.M. Furlong. 15. Genome-wide profiling of DNA-binding proteins using barcode-based multiplex solexa sequencing / Sunil Kumar Raghav and Bart Deplancke. 16. Computational analysis of protein-DNA interactions from ChIP-seq data / Jacques Rougemont and Felix Naef. 17. Using a yeast inverse one-hybrid system to identify functional binding sites of transcription factors / Jizhou Yan and Shawn M. Burgess. 18. Using cisTargetX to predict transcriptional targets and networks in Drosophila / Delphine Potier, Zeynep Kalender Atak, Marina Naval Sanchez, Carl Herrmann, and Stein Aerts. 19. Proteomic methodologies to study transcription factor function / Harry W. Jarrett. 20. High-throughput gateway-compatible yeast one-hybrid screen to detect protein-DNA interactions / Korneel Hens, Jean-Daniel Feuz, and Bart Deplancke -- pt. IV. Visualization GRNs. 21. BioTapestry : a tool to visualize the dynamic properties of gene regulatory networks / William J.R. Longabaugh -- pt. V. Modeling of GRNs. 22. Implicit methods for qualitative modeling of gene regulatory networks / Abhishek Garg, Kartik Mohanram, Giovanni De Micheli, and Ioannis Xenarios.
- 2012 Springer Protocolsedited by Jean Peccoud.Part I. Assembly of oligonucleotides in synthons. Building block synthesis using the polymerase chain assembly method / Julie A. Marchand and Jean Peccoud. Oligonucleotide assembly in yeast to produce synthetic DNA fragments / Daniel G. Gibson. Topdown real-time gene synthesis / Mo Chao Huang [and others] De novo DNA synthesis using single-molecule PCR / Tuval Ben Yehezekel, Gregory Linshiz, and Ehud Shapiro -- Part II. Synthon assembly. SLIC : a method for sequence- and ligation-independent cloning / Mamie Z. Li and Stephen J. Elledge. Assembly of standardized DNA parts using bioBrick ends in E. coli / Olivia Ho-Shing [and others] Assembling DNA fragments by USER fusion / Narayana Annaluru [and others] Fusion PCR via novel overlap sequences / Kamonchai Cha-aim [and others] Using recombineering to generate point mutations : the oligonucleotide-based "Hit and Fix" method / Suhwan Chang, Stacey Stauffer, and Shyam K. Sharan. Using recombineering to generate point mutations : galK-based positive-negative selection method / Kajal Biswas, Stacey Stauffer, and Shyam K. Sharan. Assembling large DNA segments in yeast / Héloïse Muller [and others] Recursive construction of perfect DNA molecules and libraries from imperfect oligonucleotides / Gregory Linshiz, Tuval Ben Yehezkel, and Ehud Shapiro. Cloning whole bacterial genomes in yeast / Gwynedd A. Benders. Production of infectious poliovirus from synthetic viral genomes / Jeronimo Cello and Steffen Muller -- Part III. Software for gene synthesis. In silico design of functional DNA constructs / Alan Villalobos, Mark Welch, and Jeremy Minshull. Using DNAworks in designing oligonucleotides for PCR-based gene synthesis / David Hoover. De novo gene synthesis design using TmPrime software / Mo-Huang Li [and others] Design-a-gene with GeneDesign / Sarah M. Richardson [and others] -- Part IV. Education and security. Leading a successful iGEM team / Wayne Materi. The Build-a-Genome course / Eric M. Cooper [and others] DNA synthesis security / Ali Nouri and Christopher F. Chyba.
- 2010 SpringerMauro Giacca.
- 2015 ScienceDirectPatrick Arbuthnot, Wits and South African Medical Research Council, Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, South Africa.Essentials of viruses and their suitability for treatment ssing gene therapy -- Harnessing RNAi to silence viral gene expression -- Engineering sequence-specific DNA binding proteins for antiviral gene editing -- Viral vectors for delivery of antiviral sequences -- Delivery of antiviral nucleic acids with nonviral vectors -- Gene therapy for chronic hepatitis B virus infection -- Gene therapy for hepatitis C virus infection -- Gene therapy for HIV-1 infection -- Gene therapy for respiratory viral infections -- Gene therapy for infection with hemorrhagic fever viruses -- Gene transfer for prophylaxis and therapy of viral infections -- Antiviral gene therapy : summary and perspectives.
- Gene therapy of cancer : translational approaches from preclinical studies to clinical implementation. Third edition [3rd ed.]2013 ClinicalKeyedited by Edmund Lattime, Stanton Gerson.Ex Vivo Gene Therapy: Utilization of Genetic Vectors for the Generation of Genetically Modified Cell Products for Therapy -- Targeting Tumor Vasculature Using Adeno-Associated Virus Phage Vectors Coding Tumor Necrosis Factor-a -- Viral Insertion Site Detection and Analysis in Cancer Gene Therapy -- Targeted Systemic Delivery of Therapeutic siRNA -- Bacterial Delivery of RNAi Effectors -- Gene-Directed Enzyme Prodrug Cancer Therapy -- Electroporation Gene Therapy -- Toxin-Based Cancer Gene Therapy: Under the Control of Oncofetal H19 Regulatory Sequences -- Gene Therapy in Radiotherapy of Cancer -- Advances in Oncolytic Virotherapy for Brain Tumors -- Oncolytic Adenoviruses in the Treatment of Cancer in Humans -- Selectively Replicating Oncolytic Adenoviruses Combined with Chemotherapy, Radiotherapy, or Molecular Targeted Therapy for Treatment of Human Cancers -- Reoviral Therapy for Cancer: Strategies for Improving Antitumor Efficacy Using Radio- and Chemotherapy -- Selectively Replicating Herpes Simplex Viral Vectors -- Modified Oncolytic Herpesviruses for Gene Therapy of Cancer -- The Lister Strain of Vaccinia Virus as an Anticancer Therapeutic Agent -- Poxvirus-Based Strategies for Combined Vaccine and Tumor Microenvironment Manipulation -- Genetically Engineered (T Cell Receptor) T Cells for AdoptiveTherapy -- Genetically Modified Dendritic Cell Vaccines for Solid Tumors -- Dendritic Cell Vaccination -- Chemokine Gene-Modified Dendritic Cells for Cancer Therapy -- The Use of T Cell Costimulation to Enhance the Immunogenicity of Tumors -- Clinical Application of Plasmid-Based Cancer Vaccines -- Lentivector Vaccines -- Therapeutic Efficacy and Systemic Antitumor T Cell Immunity Induced by RheoSwitch-Regulated IL-12 Expression after Intratumoral Injection of Adenovirus Vector or Vector-Transduced Dendritic Cells -- Clinical Trials Using LV-P140K-MGMT for Gliomas -- RNA Interference Therapeutics for Tumor Therapy: Promising Work in Progress -- MGMT Stem Cell Selection and Protection: Preclinical Large Animal and Clinical Studies -- Cytidine Deaminase in Myeloprotective Gene Therapy -- Genetically Engineered Salmonella typhimurium for Targeted Cancer Therapy -- Imaging of Oncolytic Virus Gene Expression -- Lentiviral-Encoded Sodium Iodide Symporter-Mediated Cancer Gene Therapy -- Bacteriophage: From Bacteria to a Successful Targeted Systemic Gene Delivery for Cancer -- Issues in Moving Gene Therapy Approaches to Early Clinical Trials -- The FDA Review Process for Cancer Gene Therapy -- Ethics in Translational Gene Transfer Research.
- 2015 Springer Protocolsedited by Wolfgang Walther and Ulrike Stein.Aptamer targeting the ERBB2 receptor tyrosine kinase for applications in tumor therapy / Georg Mahlknecht, Michael Sela, and Yosef Yarden -- Gene gun her2/neu DNA vaccination : evaluation of vaccine efficacy in a syngeneic her2/neu mouse tumor model / Tam Nguyen-Hoai, Antonio Pezzutto, and Jörg Westermann -- MIDGE technology for the production of a fourfold gene-modified, allogenic cell-based vaccine for cancer therapy / Manuel Schmidt, Barbara Volz, Patrick Grossmann, Kerstin Heinrich, and Burghardt Wittig -- Evaluation of bystander cell killing effects in suicide gene therapy of cancer : engineered thymidylate kinase (TMPK)/AZT enzyme-prodrug axis / Takeya Sato, Anton Neschadim, Ryo Nakagawa, Teruyuki Yanagisawa, and Jeffrey A. Medin -- Oncoleaking : use of the pore-forming Clostridium perfringens enterotoxin (CPE) for suicide gene therapy / Jessica Pahle, Jutta Aumann, Dennis Kobelt, and Wolfgang Walther -- iCaspase 9 suicide gene system / Xiaoou Zhou, Antonio Di Stasi, and Malcolm K. Brenner -- p53-encoding pDNA purification by affinity chromatography for cancer therapy / Ângela Sousa, João A. Queiroz, and Fani Sousa -- Phase 2, open-label, randomized study of pexa-vec (JX-594) administered by intratumoral injection in patients with unresectable primary hepatocellular carcinoma / Caroline J. Breitbach, Anne Moon, James Burke, Tae-Ho Hwang, and David H. Kirn -- Antiangiogenic metargidin peptide (AMEP) tene therapy in disseminated melanoma / Iben Spanggaard and Julie Gehl -- Clinical evaluation of ErbB-targeted CAR T-cells, rollowing intracavity delivery in patients with ErbB-expressing solid tumors / Sophie Papa, May van Schalkwyk, and John Maher.
- v. 1-, 2008- Springer Protocolsedited by Joseph Ledoux.v. 1. Production and in vivo applications of gene transfer vectors. Preparation and quantification of pseudotyped retroviral vector / Hong Yu and Young Jik Kwon. Production of retroviral vectors for clinical use / Kenneth Cornetta, Lilith Reeves, and Scott Cross. Methods for the production of helper-dependent adenoviral vectors / Donna J. Palmer and Philip Ng. Methods for the production of first generation adenoviral vectors / Donna J. Palmer and Philip Ng. Large-scale production of recombinant adeno-associated viral vectors / Alejandro Negrete and Robert M. Kotin. Construction and production of recombinant herpes simplex virus vectors / William F. Goins ... [et al.] Plasmid-based gene transfer in mouse skeletal muscle by electroporation / Jonathan D. Schertzer and Goron S. Lynch. Chitosan nanoparticle-mediated gene transfer / Dongwon Lee and Shyam S. Mohapatra. PEG-PEI copolymers for oligonucleotide delivery to cells and tissues / Gordon J. Lutz, Shashank R. Sirsi, and Jason H. Williams. Non-viral gene delivery with cationic liposome-DNA complexes / Kai K. Ewert ... [et al.] Applications of lentiviral vectors in noninvasive molecular imaging / Abhijit De ... [et al.] Retroviral modification of mesenchymal stem cells for gene therapy of hemophilia A / Christopher B. Doering. Transduction of murine hematopoietic stem cells and in vivo selection of gene-modified cells / Lucienne M. Ide, Elisabeth Javazon, and H. Trent Spencer. Assessment of CFTR function after gene transfer in vitro and in vivo / Uta Griesenbach ... [et al.] Oncolytic adenoviruses for cancer gene therapy / Ta-Chiang Liu, Stephen H. Thorne, and David H. Kirn. Design of trans-splicing adeno-associated viral vectors for Duchenne muscular dystrophy gene therapy / Yi Lai ... [et al.] Prevention of type 1 diabetes in NOD mice by genetic engineering of hematopoietic stem cells / Jessamyn Bagley, Charoui Tian, and John Iacomini. Lentiviral vector delivery of siRNA and shRNA encoding genes into cultured and primary hematopoietic cells / Mingjie Li and John J. Rossi. Nanoparticle-mediated gene delivery to the lung / Rajagopal Ramesh. Retroviral-mediated gene therapy for the differentiation of primary cells into a mineralizing osteoblastic phenotype / Jennifer E. Phillips and Andrés J. García. In vivo siRNA delivery to the mouse hypothalamus shows a role of the co-chaperone XAP2 in regulating TRH transcription / Stéphanie Decherf, Zahra Hassani, and Barbara A. Demeneix. Efficient retroviral gene transfer to epidermal stem cells / Pedro Lei and Stelios T. Andreadis.
- 2003 ScienceDirecteditor, Savvas C. Makrides.Also available: Print – 2003
- developed at the University of Washington.
- 2011 SpringerBohuslav Ostadal, Makoto Nagano, Naranjan S. Dhalla, editors.pt. 1. Genes and the heart -- pt. 2. Development and gender -- pt. 3. Mitochondrial diseases -- pt. 4. Ischemic heart disease -- pt. 5. Hypertension and arrhythmias -- pt. 6. Hypertrophy and failure.
- 2007 Springeredited with commentary by Howard D. Lipshitz.
- 2010 SpringerHoyle Leigh.Genes and mental illness -- How does stress work? the role of memes in epigenesis -- Culture and mental illness -- Genetic-memetic model of mental illness-migration and natural disasters as illustrations -- What do we inherit from our parents and ancestors? -- Genes -- Evolution -- Learning, imitation, and memes -- Storage and evolution of memes in the brain -- External storage of memes: culture, media, cyberspace -- Culture and the individual -- What is mental health -- What is mental illness? -- Psychiatric diagnosis: toward a memetic-epigenetic multiaxial model -- Memetic diagnosis, memetic assessment and biopsychosocial epigenetic formulation -- Principles of memetic therapy -- Broad-spectrum memetic therapy -- Specific memetic therapies -- Genetic-memetic prevention -- Overview of specific syndromes -- Attention-cognition spectrum syndromes: delirium, dementia, impulse control syndromes, ADHD, antisocial personality, obsessive-compulsive personality traits, obsessive-compulsive syndrome -- Anxiety-mood spectrum syndromes: anxiety, panic, phobias, ASD, PTSD, borderline syndrome, dependent and avoidant personalities, social phobia, bipolarity and mania, depression-neurotic and syndromic, adjustment disorders -- Reality perception spectrum syndromes (imagination, dissociation, conversion, somatoform, misattribution somatization, psychosis) -- Pleasure spectrum syndromes (substance use/abuse, additions to substances and beliefs, fanaticism) -- Primary memetic syndromes: eating disorders, factitious disorders, malingering, meme-directed destructive behaviors -- Challenges for the future.
- 2013 SpringerSuzanne Lentzsch, editor.This state-of-the-art book is written by a group of international experts to provide insight into the newest breakthroughs from basic pathogenesis to clinical aspects of multiple myeloma. The book provides a comprehensive overview of the genetic and molecular epidemiology of multiple myeloma in order to get a more refined and conclusive understanding of this disease. Areas, which are covered include the characterization of different myeloma entities by genomics and proteomics, notch signaling and targeting protein translation as a new treatment for multiple myeloma, cell cycle control of plasma cell differentiation, the role of bone disease in the pathogenesis of multiple myeloma as well as the molecular interaction of multiple myeloma with a microenvironment. Genetic and Molecular Epidemiology of Multiple Myeloma is a valuable resource for cancer researchers, medical, surgical, and radiation oncologists.
- 2013 Cambridge[edited by] Paul Shaw, Medhi Tafti, Michael Thorpy."The Genetic Basis of Sleep and Sleep Disorders covers detailed reviews of the general principles of genetics and genetic techniques in the study of sleep and sleep disorders. The book contains sections on the genetics of circadian rhythms, of normal sleep and wake states and of sleep homeostasis. There are also sections discussing the role of genetics in the understanding of insomnias, hypersomnias including narcolepsy, parasomnias and sleep-related movement disorders. The final chapter highlights the use of gene therapy in sleep disorders. Written by genetic experts and sleep specialists from around the world, the book is up to date and geared specifically to the needs of both researchers and clinicians with an interest in sleep medicine."--Provided by publisher.
- 2007 SpringerGundela Meyer.
- 2014 Oxford Medicine OnlineIan M. MacFarlane, Patricia McCarthy Veach, Bonnie S. LeRoy.Developing research questions -- Finding sources -- Writing a review of literature -- Ethics in research -- Choosing a paradigm -- Designing a quantitative study -- Quantitative data analysis : I've got data, how do I get answers? -- Conducting qualitative genetic counseling research -- Preparing a manuscript for publication -- Guidelines for directing research.
- 2008 Springeredited by Veikko Launis, Juha Räikkä.Introduction : the scope and importance of genetic democracy / Veikko Launis -- The prerequisites for genetic democracy / Helena Siipi -- Ethical expertise in democratic societies / Eerik Lagerspetz -- Towards global bioethics : the UNESCO universal declaration on bioethics and human rights / Henk ten Have -- Autonomy and genetic privacy / Juha Räikkä -- Values, rights and GMO : against radicalism -- The precautionary principle and the risks of modern agri-biotechnology / Marko Ahteensuu -- Population databanks and democracy in light of the Icelandic experience / Vilhjálmur Árnason and Stefán Hjörleifsson -- Equality and community in public deliberation : genetic democracy in Taiwan / Terence Hua Tai and Wen-Tsong Chiou -- Genetic resources, genetic democracy and genetic equity / Keekok Lee -- Moral constraints on permissible genetic design / Thomas Pogge.
- 2010 SpringerAhmad S. Teebi, editor.
- v. 27-28, 2006-2007. Springerv. 28, 2007 SpringerHollaender, Alexander; Setlow, Jane K.Also available: Print – v. 1-28, 1979-2007.
- 2006 Springeredited by Jan A. Nolta.Also available: Print – 2006
- 2009 Springer Protocolsedited by M. Dawn Teare.Molecular Genetics and Genetic Variation / Mohammed-Elfatih Twfieg, M. Dawn Teare -- Terminology, Concepts, and Models in Genetic Epidemiology / M. Dawn Teare, Mauro F. Koref -- An Introduction to Epidemiology / Cother Hajat -- Genetic Distance and Markers Used in Linkage Mapping / Kristina Allen-Brady, Nicola J. Camp -- Approaches to Genetic Linkage Analysis / M. Dawn Teare -- Fine-Scale Structure of the Genome and Markers Used in Association Mapping / Karen Curtin, Nicola J. Camp -- Genome-Wide Association Studies / Mark M. Iles -- Candidate Gene Association Studies / M. Dawn Teare -- Family-Based Association Studies / Frank Dudbridge -- Genome Variation: A Review of Web Resources / Andrew Collins, William J. Tapper -- Advanced Methods in Twin Studies / Jaakko Kaprio, Karri Silventoinen -- Mendelian Randomisation: A Tool for Assessing Causality in Observational Epidemiology / Nuala A. Sheehan, Sha Meng, Vanessa Didelez -- Copy Number Variation / Louise V. Wain, Martin D. Tobin -- Epigenetic Variation / Kevin Walters -- Modeling the Effect of Susceptibility Factors (HLA and PTPN22) in Rheumatoid Arthritis / Hervé Perdry, Françoise Clerget-Darpoux -- Coronary Artery Disease: An Example Case Study / Jennifer H. Barrett -- The Genetic Epidemiology of Obesity: A Case Study / Laura M. Johnson.
- 2016 SpringerJanusz K. Rybakowski, Alessandro Serretti, editors.
- 2004 NCBI Bookshelf[Laura Dean, Johanna McEntyre].
- 2016 Springer Protocolsedited by Jeffrey L. Bose.Understanding staphylococcal nomenclature / Christina N. Krute and Jeffrey L. Bose -- Restriction-modification systems as a barrier for genetic manipulation of Staphylococcus aureus / Marat R. Sadykov -- Complementation plasmids, inducible gene-expression systems, and reporters for Staphylococci / Ralph Bertram -- De novo assembly of plasmids using yeast recombinational cloning / Ameya A. Mashruwala and Jeffrey M. Boyd -- Splicing by overlap extension PCR to obtain hybrid DNA products / Justin A. Thornton -- Method for preparation and electroporation of S. aureus and S. epidermidis / Melinda R. Grosser and Anthony R. Richardson -- Rapid isolation of DNA from staphylococcus / Kelsey L. Krausz and Jeffrey L. Bose -- Bacteriophage transduction in Staphylococcus aureus : broth-based method / Kelsey L. Krausz and Jeffrey L. Bose -- Bacteriophage transduction in Staphylococcus aureus / Michael E. Olson -- Batch transduction of transposon mutant libraries for rapid phenotype screening in staphylococcus / Katherine L. Maliszewski -- Conjugative transfer in Staphylococcus aureus / Cortney R. Halsey and Paul D. Fey -- Allelic exchange / McKenzie K. Lehman, Jeffrey L. Bose, and Kenneth W. Bayles -- Creation of staphylococcal mutant libraries using transposon Tn917 / Kelly C. Rice -- Generation of a transposon mutant library in Staphylococcus aureus and staphylococcus epidermidis using bursa aurealis / Vijaya Kumar Yajjala ... [et al.] -- Chemical and UV mutagenesis / Jeffrey L. Bose -- Pulse field gel electrophoresis / Batu K. Sharma-Kuinkel, Thomas H. Rude, and Vance G. Fowler Jr. -- RNA-sequencing of Staphylococcus aureus messenger RNA / Ronan K. Carroll, Andy Weiss, and Lindsey N. Shaw -- Quantitative real-time PCR (qPCR) workflow for analyzing Staphylococcus aureus gene expression / April M. Lewis and Kelly C. Rice -- Electrophoretic mobility shiftaAssays / Sarah E. Rowe and James P. O'Gara -- Rapid amplification of cDNA ends for RNA transcript sequencing in staphylococcus / Eric Miller.
- 2012 Cambridgeedited by Audrey R. Chapman."The manner in which genetic research associated with addiction is conducted, interpreted and translated into clinical practice and policy initiatives raises important social, ethical and legal issues. Genetic Research on Addiction fulfils two key aims; the first is to identify the ethical issues and requirements arising when carrying out genetically-based addiction research, and the second is to explore the ethical, legal and public policy implications of interpreting, translating and applying this research. The book describes research guidelines on human protection issues such as improving the informed consent process, protecting privacy, responsibilities to minors and determining whether to accept industry funding. The broader public health policy implications of the research are explored and guidelines offered for developing effective social interventions. Highly relevant for clinicians, researchers, academics and policy-makers in the fields of addiction, mental health and public policy"--Provided by publisher.
- Genetic studies of endocrine function and metabolic regulation by the corpora cardiaca cells in Drosophila melanogaster2011Erika L. Bustamante.In humans, the hormones insulin and glucagon are the principal regulators of blood sugar homeostasis. In the fruit fly, Drosophila melanogaster, the regulation of circulating sugar levels is similarly controlled by insulin-like and glucagon-like factors. Insulin signaling in Drosophila has been studied intensively; by contrast, relatively little is known about the genetic regulation of Drosophila Adipokinetic hormone (Akh), the polypeptide with glucagon-like functions, and the corpora cardiaca (CC) cells that produce Akh. Here I describe the use of an enhancer trap screen that led to the identification of a novel regulator of CC function, the homeodomain transcription factor unplugged (unpg). Knocking down unpg in the CC cells results in decreased Akh transcript levels and reduced circulating glucose and trehalose. I also describe the identification of a number of enhancer traps that are capable of driving GFP expression in the CC cells, suggesting a role for the associated genes in CC cell function. As in human diabetes, insulin deficiency in the fruit fly elevates circulating glucose levels and impairs triglyceride regulation. Reduced insulin signaling in Drosophila also increases expression of the adipokine Akh, a phenotype reminiscent of the excessive glucagon signaling that accompanies human diabetes. Thus, it remains unclear if insulin deficiency or adipokine excess is the primary basis for diabetic phenotypes in flies lacking insulin-producing cells. Here I show that simultaneous targeted ablation of cells producing Drosophila insulin and adipokinetic hormone results in hypoglycemia. Mutation of the gene encoding the Akh receptor (Akhr) reduces circulating glucose levels in adult Drosophila lacking insulin, arguing that excessive Akh signaling is the basis for hyperglycemia in insulin-deficient flies. Simultaneous attenuation of insulin and Akh synthesis also produced hypoglycemic flies. Similar approaches revealed triglyceride imbalance from insulin deficiency requires Akh. Thus adipokines like Akh, not insulin, may be the principal hormonal regulators of glucose and lipid balance in some non-mammalian animal classes and states of insulin deficiency.
- 2013 SpringerKevin Morgan, Minerva M. Carrasquillo, editors.Since 2009, a revolution has been witnessed in Alzheimer's Disease genetics. New genetic links are being discovered at an unprecedented pace and our understanding of the molecular mechanisms of neurodegeneration have taken a quantum leap forward. This book provides a thorough description of the genes that have been implicated in the aetiology of late-onset Alzheimer's disease (LOAD) based on evidence of genetic association. These "AD susceptibility genes" are described both in their genomic and cellular context, as well as with respect to their known or suspected molecular functions. Although these genes are not sufficient to explain all of the genetic contributions to LOAD, they represent the best replicated set of genes to date. Undoubtedly the list will grow as more advanced genomic approaches towards the identification of novel LOAD genes progresses.
- 2012 Springer Protocolsedited by Jean-Rene Martin.In vivo functional brain imaging using a genetically encoded Ca2+-scensitive bioluminescence reporter, GFP-Aequorin / Jean-Rene Martin -- Ca2+ imaging in brain slices using bioluminescent reporters / Ludovic Tricoire, Estelle Drobac, and Bertrand Lambolez -- Calcium imaging of neural activity in the olfactory system of drosophila / Antonia Strutz [and others] -- Functional imaging of antennal lobe neurons in drosophila with synapto-pHluorin / Dinghui Yu and Ronald L. Davis -- Performing electrophysiology and two-photon calcium imaging in the adult drosophila central brain during walking behavior / M. Eugenia Chiappe and Vivek Jayaraman -- In Vivo optical recording of brain interneuron activities from a drosophila male on a treadmill / Soh Kohatsu, Masayuki Koganezawa, and Daisuke Yamamoto -- Two-photon imaging of population activity with genetically encoded calcium indicators in living flies / Robert A.A. Campbell [and others] -- Engineering and application of genetically encoded calcium indicators / Jasper Akerboom [and others] -- Imaging cAMP dynamics in the drosophila brain with the genetically encoded sensor Epac1-Camps / Katherine R. Lelito and Orie T. Shafer.
- 2006 Wileyedited by Knut J. Heller.Part I. Application and Perspectives -- ch. 1. Transgenic modification of production traits in farm animals / Gottfried Brem, Mathias Müller -- ch. 2. Genetically modified plants / Susanne Stirn, Horst Lörz -- ch. 3. Fermentation of food by means of genetically modified yeast and filamentous fungi / Rena Leisegang, Elke Nevoigt, Anja Spielvogel, Georg Kristan, Anke Niederhaus, Ulf Stahl -- ch. 4. Production of food additives using filamentous fungi / Carsten M. Hjort -- ch. 5. Genetic engineering of bacteria used in food fermentation / Arnold Geis -- Part II. Legislation in Europe -- ch. 6. The Legal situation for genetically engineered food in Europe / Rudolf Streinz, Jan Kalbheim -- Part III. Methods of Detection -- ch. 7. Detection of genetic modifications : some basic considerations / Knut J. Heller -- ch. 8. DNA-based methods for detection of genetic modifications / Ralf Einspanier -- ch. 9. Genetic engineering of fish, and methods of detection / Hartmut Rehbein -- ch. 10. Detection methods for genetically modified crops / Rolf Meyer -- ch. 11. Methods for detection of genetically modified organisms in composite and processed foods / Karl-Heinz Engel, Francisco Moreano, Alexandra Ehlert -- ch. 12. Mutations in Lactococcus lactis and their detection / Jan Kok, Bertus van den Burg -- ch. 13. Methods for detection of genetically modified microorganisms used in food fermentation processes / Walter P. Hammes, Christian Hertel, Torsten Bauer.
- 2012 Kargervolume editors, Pascale Piguet, Philippe Poindron.Genetically modified organisms : concepts and methods -- Restriction enzymes : from their discovery to their applications -- Transforming growth factor-beta superfamily : animal models for development and disease -- Transfection of human neuroblastoma cells with Alzheimer's Disease brain hallmarks as a promising strategy to investigate the role of neurosteroidogenesis in neuroprotection -- Investigating therapeutic strategies for Fragile X syndrome in mice -- Innovative therapeutic perspectives in neuromuscular diseases -- Gene therapy for cancer treatment : state of the art -- Manipulating the mitochondrial genetic system.
- 2009Daniel L. Hartl and Elizabeth W. Jones.Genes, genomes, and genetic analysis -- DNA structure and genetic variation -- Transmission genetics : the principle of segregation -- Chromosomes and sex-chromosome inheritance -- Genetic linkage and chromosome mapping -- Molecular biology of DNA replication and recombination -- Molecular organization of chromosomes -- Human karyotypes and chromosome behavior -- Genetics of bacteria and their viruses -- Molecular biology of gene expression -- Molecular mechanisms of gene regulation -- Genomics, proteomics, and transgenics -- Genetic control of development -- Molecular mechanisms of mutation and DNA repair -- Molecular genetics of the cell cycle and cancer -- Mitochondrial DNA and extranuclear inheritance -- Molecular evolution and population genetics -- The genetic basis of complex traits.
- 2008Leland H. Hartwell ... [et al.].Genetics: the study of biological information -- Mendel's breakthrough: patterns, particles, and principles of heredity -- Extensions to mendel: complexities in relating genotype to phenotype -- The chromosome theory of inheritance -- Linkage, recombination, and the the mapping of genes on chromosomes -- DNA: how the molecule of heredity carries, replicates, and recombines information -- Anatomy and function of a gene: dissection through mutation -- Gene expression: the flow of genetic information from DNA to RNA to protein -- Deconstructing the genome: DNA at high resolution -- Reconstructing the genome through genetic and molecular analysis -- The direct detection of genotype distinguishes individual genomes -- Systems biology and proteomics -- The eukaryotic chromosome: an organelle for packaging and managing DNA -- Chromosomal rearrangements and changes in chromosome number reshape eukaryotic genomes -- The prokaryotic chromosome: genetic analysis in bacteria -- The chromosomes of organelles outside the nucleus exhibit non-mendelian patterns of inheritance -- Gene regulation in prokaryotes -- Gene regulation in eukaryotes -- Cell-cycle regulation and the genetics of cancer -- Using genetics to study development -- The genetic analysis of populations and how they evolve -- Evolution at the molecular level.
- 2010 CRCnetBASEAnatoly Ruvinsky.Limits and uncertainty in nature and logic -- Quantum fluctuations, mutations, and "fixation" of uncertainty -- Recombination and randomness -- Uncertainty of development -- Organized randomness -- Random genetic drift and "deterministic" selection -- Life : making uncertainty certain.
- 2016 Kargervolume editors Michael Posthumus, Malcolm Collins.Core concepts in human genetics : understanding the complex phenotype of sport performance and susceptibility to sport injury / Gibson, W.T -- Nature versus nurture in determining athletic ability / Yan, X., Papadimitriou, I., Lidor, R., Eynon, N -- Recent research in the genetics of exercise training adaptation / Venezia, A.C., Roth, S.M -- Genes and athletic performance : an update / Ahmetov, I.I., Egorova, E.S., Gabdrakhmanova, L.J., Fedotovskaya, O.N -- The future of genomic research in athletic performance and adaptation to training / Wang, G., Tanaka, M., Eynon, N., North, K.N., Williams, A.G., Collins, M., Moran, C.N., Britton, S.L., Fuku, N., Ashley, E.A., Klissouras, V., Lucia, A., Ahmetov, I.I., de Geus, E., Alsayrafi, M., Pitsiladis, Y.P -- Genetics of musculoskeletal exercise-related phenotypes / Collins, M., O'Connell, K., Posthumus, M -- Genes and musculoskeletal soft-tissue injuries / Rahim, M., Collins, M., September, A -- Genetic testing for sports performance, responses to training and injury risk : practical and ethical considerations / Williams, A.G., Wackerhage, H., Day, S.H.
- 2009 Kargervolume editor, Malcolm Collins.Key concepts in human genetics : understanding the complex phenotype / W.T. Gibson -- Nature versus nurture in determining athletic ability / T.D. Brutsaert, E.J. Parra -- Genetics and sports : an overview of the pre-molecular biology era / M.W. Peeters ... [et al.] -- Genes, athlete status, and training : an overview / I.I. Ahmetov, V.A. Rogozkin -- Angiotensin : converting enzyme, renin-angiotensin system and human performance / D. Woods -- Actinin-3 and performance / N. yang, F. Garton, K. North -- East African runners : their genetics, lifestyle, and athletic prowess / V.O. Onywera -- Gene-lifestyle interactions and their consequences on human health / J. Pomeroy, A.M. Söderberg, P.W. Franks -- Genetic risk factors for musculoskeletal soft tissue injuries / M. Collins, S.M. Raleigh -- Innovative strategies for treatment of soft tissue injuries in human and animal athletes / A. Hoffmann, G. Gross -- Gene doping : possibilities and practicalities / D.J. Wells -- Genetic testing of athletes / A.G. Williams, H. Wackerhage -- The future of genetic research in exercise science and sports medicine / R.J. Trent, B. Yu.
- 2013 SpringerSheela Srivastava.Described as the earliest, simplest life forms, with unlimited metabolic versatility, bacteria are ideally suited to answer some very fundamental questions on life and its processes. They have been employed in almost all fields of biological studies, including Genetics. The whole edifice of science of Genetics centers around three processes: the generation, expression, and transmission of biological variation, and bacteria offer immediate advantages in studying all the three aspects of heredity. Being haploid and structurally simple, it becomes easy to isolate mutations of various kinds and relate them to a function. The availability of such mutants and their detailed genetic and biochemical analyses lead to a gamut of information on gene expression and its regulation. While studying the transmission of biological variation, it is clear that unlike their eukaryotic counterpart, a more genetic approach needs to be employed. Transmission of genetic information in most eukaryotic organisms rests on sexual reproduction that allows the generation of genetically variable offspring through the process of gene recombination. Even though bacteria show an apparent preference for asexual reproduction, they too have evolved mechanisms to trade their genetic material. In fact, bacteria not only could acquire many genes from close relatives, but also from entirely distant members through the process of horizontal gene transfer. Their success story of long evolutionary existence will stand testimony to these mechanisms. While teaching a course on Microbial Genetics to the post-graduate students at Delhi University, it was realized that a book devoted to bacterial genetics may be very handy to the students, researchers, and teachers alike. A strong foundation in genetics also helps in comprehending more modern concepts of molecular biology and recombinant DNA technology, always a favorite with the students and researchers. Planning the format of the book, emphasis has been laid on the generation and transmission of biological variability. The omission of expression part is indeed intentional because lots of information is available on this aspect in any modern biology book. The contents are spread over seven chapters and the text is supported with figures/tables wherever possible. The endeavor has been to induce the readers to appreciate the strength of bacterial genetics and realize the contribution of these tiny organisms to the growth of biological sciences as a whole and genetics in particular.
- 2013edited by Rajesh V. Thakker [and others].This book identifies and analyzes the genetic basis of bone disorders in humans and demonstrates the utility of mouse models in furthering the knowledge of mechanisms and evaluations of treatments. The book is aimed at all students of bone biology and genetics, and with this in mind, it includes general introductory chapters on genetics and bone biology and more specific disease-orientated chapters, which comprehensively summarize the clinical, genetic, molecular genetic, animal model, functional and molecular pathology, diagnostic, counselling and treatment aspects of each disorder. Saves academic, medical, and pharma researchers time in quickly accessing the very latest details on a broad range of genetic bone issues, as opposed to searching through thousands of journal articles. Provides a common language for bone biologists and geneticists to discuss the development of bone cells and genetics and their interactions in the development of disease. Researchers in all areas bone biology and genetics will gain insight into how clinical observations and practices can feed back into the research cycle and will, therefore, be able to develop more targeted genomic and proteomic assays. For those clinical researchers who are also MDs, correct diagnosis (and therefore correct treatment) of bone diseases depends on a strong understanding of the molecular basis for the disease.
- 2009 SpringerJohn D. Potter, Noralane M. Lindor, editors.
- 2016 Kargervolume editors, Barbara Vona, Thomas Haaf.Genetics and deafness : a view from the inside / Blankmeyer Burke, T. Snoddon, K., Wilkinson, E. -- Hearing loss in older age and its effect on the individuals, their families, and the community / McMahon, C.M -- Audiological assessment and management in the era of precision medicine / Munro, K.J., Newton, V.E., Moore, D.R -- Next-generation newborn hearing screening / Shen, J., Morton, C.C -- Clinical challenges in diagnosing the genetic etiology of hearing loss / Birkeland, A.C., Lesperance, M.M. -- Genetic elucidation of nonsyndromic hearing loss in the high-throughput sequencing era / Vona, B., Hofrichter, M.A.H., Chioza, B.A., Crosby, A.H., Nanda, I., Haaf, T. -- Genetic modifiers of hearing loss / Yousaf, R., Friedman, T.B., Riazuddin, S. -- Genetics of age-related hearing loss / Dawes, P., Payton, A. -- Genetic modifiers of hearing loss in mice : the case of phenotypic modification in homozygous cdh23ahl age-related hearing loss / Kikkawa, Y., Miyasaka, Y. -- Using zebrafish to study human deafness and hearing regeneration / Varshney, G.K., Pei, W., Burgess, S.M. -- Current understanding and potential of gene therapy for hearing restoration in humans / Akil, O., Lustig, L.
- 2014 SpringerStruan F.A. Grant, editor.In the past four years, many genetic loci have been implicated for BMI from the outcomes of genome-wide association studies (GWAS), primarily in adults. Insulin-induced gene 2 (INSIG2) was the first locus to be reported by this method to have a role in obesity, but replication attempts have yielded inconsistent outcomes. The identification of the second locus, the fat mass- and obesity-associated gene (FTO), has been more robustly observed by others. Studies from both FTO knock out and FTO over expression mouse model support the fact that FTO is directly involved in the regulation of energy intake and metabolism in mice, where the lack of FTO expression leads to leanness while enhanced expression of FTO leads to obesity. Along with numerous other studies, a number of genetic variants have been established robustly in the context of obesity, giving us fresh insights into the pathogenesis of the disease. This book provides a comprehensive overview of efforts aimed at uncovering genetic variants associated with obesity, which have been particularly successful in the past 5 years with the advent of genome-wide association studies (GWAS). The Genetics of Obesity covers this state of the art technology and its application to obesity in great detail. Topics include genetics of childhood obesity, genetics of syndromic obesity, copy number variants and extreme obesity, co-morbidities of obesity genetics, and functional follow-up of genetic variants.
- 2007G.I. Hickey, H.L. Fletcher, and P. Winter.
- v. 1-, 2007- Springer
- 2016 SpringerToni Cathomen, Matthew Hirsch, Matthew Porteus, editors.Gene editing 20 years later -- The development and use of zinc-finger nucleases -- The use and development of TAL effector nucleases -- Genome editing for neuromuscular diseases -- Phage integrases for genome editing -- Precise genome modification using triplex forming oligonucleotides and peptide nucleic acids -- Genome editing by Aptamer-Guided Gene Targeting (AGT) -- Stimulation of AAV gene editing via DSB repair -- Engineered nucleases and trinucleotide repeat diseases -- Using engineered nucleases to create HIV-resistant cells -- Strategies to determine off-target effects of engineered nucleases -- Cellular engineering and disease modeling with gene-editing nucleases -- Index.Also available: Print – 2016
- 2005 Springeredited by Erich A. Nigg.Also available: Print – 2005
- 2011Penka Vassileva Markova-Raina.Recent advances in technology have unleashed a breathtaking amount of genome sequence data. My doctoral research builds on the resulting opportunities of whole genome sequence data and analysis in a quest for gaining new insights into molecular evolution, and in particular molecular evolution and adaptation of proteins. Chapter One of my dissertation is focused on methodology, specifically the impact that the choice of multiple sequence alignment procedure has on the inference of positive selection. I find that selection inference is highly dependent on the choice of alignment procedure. Furthermore, in the case of the 12 Drosophila genomes proteins and commonly used alignment programs, most of the inferences are false positives, caused by misaligned codons. These results put into question the reliability of some of the previously reported conclusions on adaptation in these proteins, as well as in similar studies of other species. The second chapter relates these alignment errors to specific regions in the proteins, the so-called intrinsically disordered protein regions. Disordered protein regions do not have a stable fold in native physiological conditions, and therefore do not fit the standard assumptions made in codon-based evolutionary analyses about structure and folding constraints. My findings indicate that in the case of the false-positively inferred positively selected sites, as well as in general throughout the alignments, most alignment errors and ambiguities originate in disordered regions. Indels in the alignments also appear predominantly in those regions. Examination of widely used alignment benchmarks indicates that disordered regions have mostly been excluded from the benchmarks. I discuss implications of these findings for both evolutionary research and development of alignment software. The last chapter of my dissertation characterizes the evolution of disordered regions in Drosophila. I survey protein substitution and polymorphism patterns in D. melanogaster and D. simulans, and find that relative to structured regions, disordered ones have multiple-fold higher rates of replacement polymorphisms and substitutions, as well as fewer rare polymorphisms. Structured regions appear to be significantly more impacted by both positive and purifying selection, contrary to indications from previous reports where within-species data was not incorporated in the analysis.
- 2009 SpringerVishvanath Nene, Chittaranjan Kole, editors.
- 2008 SpringerWayne Hunter, Chittaranjan Kole (editors).Honeybee / D. Schlipalius, P.R. Ebert, G.J. Hunt -- Bumblebee / L. Wilfert, P. Schmid-Hempel, J. Gadau -- The jewel wasp - Nasonia / J. Gadau ... [et al.] -- Silkworm / Y. Yasukochi, H. Fujii, M.R. Goldsmith -- Pea aphid / J.A. Brisson, G.K. Davis -- Mosquito / D.W. Severson -- Hessian fly / J.J. Stuart, M.-S. Chen, M.O. Harris -- Tick / A.J. Ullmann, J.J. Stuart, C.A. Hill.
- 2008 SpringerThomas D. Kocher, Chittaranjan Kole (editors).
- 2012 SpringerPaul Denny, Chittaranjan Kole, editors.Genomics in the sea urchin : new perspectives on a perennial model system / Katherine M. Buckley amd Jonathan P. Rast -- Genome mapping and genomics of Caenorhabditis elegans / Jonathan Hodgkin, Michael Paulini, and mary Ann Tuli -- Genome mapping and genomics in Drosophila / Boris Adryan and Steven Russell -- Genome structure, functional genomics, and proteomics in ascidians / Yasunori Sasakura, Nicolas Sierro, Kenta Nakai, Kazuo Inaba, and takehiro G. Kusakabe -- Punching above their weight : the compact genomes of pufferfishes / Brian Cusack and Hugues Roest Crollius -- Medaka genomics and the methods and resources for decoding genomic functions / Tetsuaki Kimura, Yasuhiro Kamei, Yusuke Takehana, Takao Sasado, and Kiyoshi Naruse -- Xenopus genomics and genetics : progress and prospects / Amy K. Sater and Michael J. Gilchrist -- Mouse genome mapping and genomics / Paul Denny -- Rat genome mapping and genetics / Claude Szpirer and Göran Levan.
- 2013 SpringerVijaykumar Yogesh Muley, Vishal Acharya.Introduction -- From genomes to protein functions -- Co-evolutionary signals within genome sequences reflect functional dependence of proteins -- Chromosomal proximity of genes as an indicator of functional linkage -- Analyses of complex genome-scale biological networks -- Application of protein interaction networks.
- 2012Yue Wan.RNA plays an important role in regulating cellular gene expression. Its ability to fold into secondary and tertiary structures underlies the RNA's ability to function and be processed in every step of its life cycle, including transcription, splicing, cellular localization, translation and turnover of the RNA. However, structural information for most RNAs in the cells, such as mRNAs, is missing due to the low throughput nature of RNA structure probing and the traditional difficulty of probing long RNAs, making it difficult to assess the full impact of RNA structure in biology. To fulfill the need to understand the roles of RNA structure on a global scale, we developed for the first time a novel strategy termed Parallel Analysis of RNA Structure (PARS), which couples structure-specific probing to high throughput sequencing to simultaneously generate secondary structures for thousands of RNA species at single nucleotide resolution. Applying PARS to the yeast transcriptome identified distinct structural organization of mRNAs, including a three nucleotide periodicity in the coding region and increased accessibility near the start codon for translation. Furthermore, we demonstrated that PARS can be used to study dynamics by probing the yeast transcriptome across a temperature gradient to identify functional structural regions that have differential propensity to melt. PARS can be readily applied to different organisms and conditions, to identify structural determinants that regulate gene expression changes across organisms in different cellular states. This expansion of RNA structural data will likely enhance our understanding of how RNA structure translates into RNA function in cellular systems, as well as open doors to potentially targeting these structural elements to regulate cellular behavior in diseases.
- Genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genomic stability2010Renee Darlene Paulsen.Genome instability has long been known to be a hallmark of cancerous cells, but the cellular causes and consequences of such instability are still not fully understood. Mutations, translocations, DNA rearrangements, as well as chromosomal loss can all result in the loss of genomic integrity. To prevent the disruption of cellular homeostasis due to DNA damage accumulation, cells contain pathways to sense and respond to DNA damage including cell cycle checkpoints and numerous DNA repair processes, collectively known as the DNA damage response (DDR). Mutations in many of the genes involved in the DDR are linked to several diseases, including premature aging, neurodegeneration and cancer. These signaling pathways are especially critical during DNA replication when the DNA is unwound and vulnerable to processing. Here, the cell relies on the S-phase checkpoint to sense DNA damage at the sites of replication forks and to facilitate a number of downstream pathways to maintain genomic stability. These processes include blocking further origin firing, facilitating DNA repair, preventing cell cycle progression, and stabilizing stalled replication forks. Here, two genome-wide siRNA screens were employed to identify additional genes involved in genome stabilization by monitoring phosphorylation of the histone variant H2AX, an early mark of DNA damage. The first screen looked at H2AX phosphorylation that occurred simply by individual protein depletion, and the second screen used a low level of a replication inhibitor, aphidicolin, to specifically identify genes that were needed to prevent DNA damage during S-phase, potentially due to the loss of replication fork stabilization mechanisms. While the results from the second screen are still undergoing further characterization, we did discover hundreds of genes whose down-regulation led to elevated levels of H2AX phosphorylation in the absence of any external stress. From this gene set, we identified many gene networks that were significantly enriched amongst our screening hits as well as several intriguing individual genes that were chosen for follow up study. These included genes involved in mRNA processing, the pathology of Charcot-Marie-Tooth syndrome, and the histone methyl transferase protein, Set8.
- 2012Daniel Jeffrey Kvitek.Adaptive evolution by natural selection is largely responsible for the variety of forms and functions observable in the natural world. Identifying the genetic changes underlying adaptive evolution of organisms to their environment is of fundamental importance in understanding the history of life, as well as predicting how organisms will evolve to novel environments in the future. Experimental evolution of microbes in the laboratory provides a precisely controlled environment for investigations into the genetic basis of adaptation, while also allowing for large population sizes and experimental replication, benefits that are often not available in natural populations. Recent technologies have enabled the identification of the genetic changes responsible for adaptive evolution genome-wide, giving us a genomic view of adaptation during evolution experiments. Here, I have added to our understanding of the genomic basis of adaptation by investigating how Saccharomyces cerevisiae adapts to limiting glucose environments during experimental evolution. Throughout this work, I utilize next- generation, whole-genome sequencing to identify the mutations responsible for adaptation. In Chapter 1, I investigate how genetic interactions define the fitness landscape, and find that very strong negative epistasis between two beneficial mutations creates a fitness valley, so each mutation effectively determines the evolutionary trajectory of adaptation. In Chapter 2, I take a step back and look more broadly at adaptation while asking the question: is there a general functional theme for the genomic basis of adaptation to limiting glucose? To facilitate answering this question in an unbiased manner, I develop a whole-population, whole-genome sequencing technique, and find that the theme of adaptation in the constant and predictable environment of the glucose-limited chemostat is for the yeast to lose function of signaling networks responsible for sensing environmental stimulus, effectively decoupling environmental sensing from response. In Chapter 3, in a collaborative project, we seek to understand the extent that genotypic convergence underlies phenotypic convergence by evolving genetically distinct yeast under different conditions. We find a single gene is recurrently mutated across most genetic backgrounds, suggesting that genotypic convergence plays a large role in adaptive evolution.
- 2008 Springeredited by Jon F. Wilkins.DNA methylation reprogramming in the germ line / Diane J. Lees-Murdock and Colum P. Walsh -- Control of imprinting at the GNAS cluster / Jo Peters and Christine M. Williamson -- The GNAS locus and pseudohypoparathyroidism / Murat Bastepe -- Imprinted genes, postnatal adaptations, and enduring effects on energy homeostasis / Margalida Frontera ... [et al.] -- What are imprinted genes doing in the brain? / William Davies ... [et al.] -- Genomic imprinting and human psychology : cognition, behavior, and pathology / Lisa M. Goos and Gillian Ragsdale -- Genomic imprinting in plants / Olivier Garnier, Sylvia Laouiellé-Duprat, and Charles Spillane -- Imprinted genes and human disease : an evolutionary perspective / Francisco Úbeda and Jon F. Wilkins -- Evolutionary theories of imprinting ; enough already! / Tom Moore and Walter Mills.Also available: Print – 2008
- 2012 Springer Protocolsedited by Nora Engel.Uniparental embryos in the study of genomic imprinting / Yong Cheng, Dasari Amarnath, and Keith E. Latham -- Derivation of induced pluripotent stem cells by retroviral gene transduction in mammalian species / Masanori Imamura [and others] -- Generation of trophoblast stem cells / Michael C. Golding -- Immunomagnetic purification of murine primordial germ cells / Emily Y. Smith and James L. Resnick -- Whole genome methylation profiling by immunoprecipitation of methylated DNA / Andrew J. Sharp -- Identification of imprinted loci by transcriptome sequencing / Tomas Babak -- Data mining as a discovery tool for imprinted genes / Chelsea Brideau and Paul Soloway -- Engineering of large deletions and duplications in vivo / Louis Lefebvre -- Methylated DNA immunoprecipitation (MeDIP) from low amounts of cells / Julie Borgel, Sylvain Guibert, and Michael Weber -- Chromatin immunoprecipitation to characterize the epigenetic profiles of imprinted domains / Purnima Singh and Piroska E. Szabo -- Quantitative chromosome conformation capture / Raffaella Nativio, Yoko Ito, and Adele Murrell -- Genome-wide analysis of DNA methylation in low cell numbers by reduced representation bisulfite sequencing / Sebastien A. Smallwood and Gavin Kelsey -- Isolation of RNA and DNA from single preimplantation embryos and a small number of mammalian oocytes for Imprinting Studies / Sarah Rose Huffman, Md Almamun, and Rocio Melissa Rivera -- Generation of cDNA libraries from RNP-derived regulatory noncoding RNAs / Mathieu Rederstorff -- Co-immunoprecipitation of long noncoding RNAs / Victoria A. Moran, Courtney N. Niland, and Ahmad M. Khalil -- Specialized technologies for epigenetics in plants / Wenyan Xiao -- Computational studies of imprinted genes / Martina Paulsen -- Insights on imprinting from beyond mice and men / Andrew Pask -- Nonmammalian parent-of-origin effects / Elena de la Casa-Esperon.
- 2012 Springer Protocolsedited by Lars Feuk.What have studies of genomic disorders taught us about our genome / Alexandra D. Simmons, Claudia M.B. Carvalho, and James R. Lupski -- Microdeletion and microduplication syndromes / Lisenka E.L.M. Vissers and Paweł Stankiewicz -- Structural genomic variation in intellectual disability / Rolph Pfundt and Joris A. Veltman -- Copy number variation and psychiatric disease risk / Rebecca J. Levy [and others] -- Detection and characterization of copy number variation in autism spectrum disorder / Christian R. Marshall and Stephen W. Scherer -- Structural variation in subtelomeres / M. Katharine Rudd -- Array-based approaches in prenatal diagnosis / Paul D. Brady [and others] -- Structural variation and its effect on expression / Louise Harewood, Evelyne Chaignat, and Alexandre Reymond -- Challenges of studying complex and dynamic regions of the human genome / Edward J. Hollox -- Population genetic nature of copy number variation / Per Sjodin and Mattias Jakobsson -- Detection and interpretation of genomic structural variation in mammals / Ira M. Hall and Aaron R. Quinlan -- Structural genetic variation in the context of somatic mosaicism / Jan P. Dumanski and Arkadiusz Piotrowski -- Online resources for genomic structural variation / Tam P. Sneddon and Deanna M. Church -- Algorithm implementation for CNV discovery using affymetrix and illumina SNP array data / Laura Winchester and Jiannis Ragoussis -- Targeted screening and validation of copy number variations / Shana Ceulemans, Karlijn van der Ven, and Jurgen Del-Favero -- High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues / Hendrik F. van Essen and Bauke Ylstra -- Characterizing and interpreting genetic variation from personal genome sequencing / Anna C.V. Johansson and Lars Feuk -- Massively parallel sequencing approaches for characterization of structural variation / Daniel C. Koboldt [and others].
- 2014 SpringerGyörgy Marko-Varga, editor.This book offers a valuable resource that allows students, researchers, educators and the general public to learn about proteomics and genomics. Chromosomes form the basis for our genetic heritage and are the code for protein synthesis. The Human Genome Map was presented in 2002, and the Proteome Sequence Map is currently being created by a global consortia initiative. Proteome and genome building blocks already form the basis of scientific research areas and shape major areas of the pharmaceutical and biomedical industries. The book provides background information on and our current understanding of these gene and protein areas, and explains in detail how cutting-edge science is using these resources to develop new medicines and new diagnostics for patient treatment and care. The book will benefit all students and researchers who need a good understanding of genomics and proteomics within the clinical field. Its content is also suitable for a broad readership, including those not specialized in this field. Dr. Marko-Varga is head of Div. Clinical Protein Science & Imaging at the Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University. He's also Professor at the 1st Department of Surgery, Tokyo Medical University, Tokyo, Japan.
- 2012Eric Lyman Van Nostrand.Although the development of high-throughput techniques to quantify gene expression have enabled us to characterize genes that change in various conditions, identifying the regulators that drive these changes remains a challenging problem. Recent efforts to identify direct transcription factor targets provide a foothold to addressing the identification of regulators, by allowing inference of critical factors based on the expression patterns of their targets. However, success in this approach requires an improved ability to infer factor-responsive targets (those regulated by the transcription factor) from direct targets (those bound by the factor). By identifying factor-specific binding sites (i.e., those regions bound by the factor of interest but not by many additional random transcription factors), we found that the link between direct and functional targets was significantly improved -- e.g., although only 26% of significant HLH-1 binding sites correlated with altered expression when HLH-1 was over-expressed, over 40% of factor-specific significant binding sites did so. In the course of this work, we identified HOT (Highly Occupied Target) regions that were bound by more than 65% of factors assayed. Surprisingly, our analysis indicated that these regions were not artifacts of the target identification methodology. Rather, they instead indicate a potentially novel regulatory mechanism for expression of housekeeping genes, as genes associated with HOT regions were highly and ubiquitously expressed and essential for development. Next, we applied this approach to the study of aging. Although genome-wide microarray experiments in C. elegans have identified over a thousand genes with age-dependent expression, only a handful of transcriptional regulators are known to link altered lifespan with modulation of genes that change during wild-type aging. We describe an approach to infer potential regulators of aging and longevity by interrogating direct transcription factor targets generated by the modENCODE project. We identify nine factors with targets significantly enriched for altered expression with age, including three previously shown to modulate lifespan. We further show that for two additional factors, NHR-28 and NHR-76, strains in which these factors are over-expressed show increased lifespan, suggesting that these factors may represent additional links between age-dependent gene expression changes with longevity. This approach identified HOX co-factor unc-62 (Homothorax) as a developmental regulator that binds age-regulated transcripts and modulates lifespan. In the intestine (in which UNC-62 knockdown increases lifespan) we identify multiple activities: UNC-62 binds to and activates both intestine-expressed yolk protein genes that decline with age as well as neuronal-enriched genes that increase in intestinal expression with age. An alternatively spliced, tissue-specific isoform of unc-62 is expressed exclusively in the intestine and declines with age, providing a potential mechanism for distinct activities of UNC-62 between tissues and stages. Thus, UNC-62 provides a proof of principle for uncovering unexplored transcription factors effecting aging and longevity through integrated analysis of developmental regulatory targets.
- 2013 SpringerAnton G. Kutikhin, Arsenij E. Yuzhalin.The Biology of Toll-like Receptors and NOD-like Receptors: Toggles of Inflammation -- Pattern Recognition Receptors, Gene Polymorphisms, and Cancer: A Double-Edged Sword -- Structural Genomic Variation in Toll-Like Receptor 4 and Cancer -- Structural Genomic Variation in Other Toll-like Receptors and Cancer -- Structural Genomic Variation in Toll-Like Receptor Signaling Pathway and Cancer -- Structural Genomic Variation in Toll-like Receptor Pathway and Prostate Cancer -- Structural Genomic Variation in NOD-Like Receptors and Cancer -- Structural Genomic Variation in Pattern Recognition Receptors and Cardiovascular Diseases -- Hot Spots In the Field: Where Should We Go.
- 2008 Springer Protocolsedited by Mike Starkey, Ramnath Elaswarapu.Protein profiling based on two-dimensional difference gel electrophoresis / Gert Van den Bergh and Lutgarde Arckens -- Quantitative protein profiling by mass spectrometry using isotope-coded affinity tags / Arsalan S. Haqqani, John F. Kelly, and Danica B. Stanimirovic -- Quantitative protein profiling by mass spectrometry using label-free proteomics / Arsala S. Haqqani, John F. Kelly, and Danica B. Stanimirovic -- Using 2D-LC-MS/MS to identify Francisella tularensis peptides in extracts from an infected mouse macrophage cell line / John F. Kelly and Wen Ding -- Baculovirus expression vector system : an emerging host for high-throughput eukaryotic protein expression / Binesh Shrestha, Carol Smee, and Opher Gileadi -- Coimmunoprecipitation and proteomic analyses / S. Fabio Falsone, Bernd Gesslbauer, and Andreas J. Kungl -- Tandem affinity purification combined with mass spectrometry to identify components of protein complexes / Peter Kaiser ... [et al.] -- Mammalian two-hybrid assay for detecting protein-protein interactioins in vivo / Runtao He and Xuguang Li -- Detection of protein-protein interactions in live cells and animals with split firefly luciferase protein fragment complementation / Victor Villalobos, Snehal Naik, and David Piwnica-Worms -- Subcellular localization of intracellular human proteins by construction of tagged fusion proteins and transient expression in COS-7 cells / John E. Collins -- GeneFAS : a tool for the prediction of gene function using multiple sources of data / Trupti Joshi ... [et al.] --Comparative genomics-based prediction of protein function / Toni Gabaldón -- Design, manufacture, and assay of the efficacy of siRNAs for gene silencing / Louise A. Dawson and Badar A. Usmani. Whole genome amplification with Phi29 DNA polymerase to enable genetic or genomic analysis of samples of low DNA yield / Kaisa Silander and Janna Saarela -- Scanning for DNA variants by denaturant capillary electrophoresis / Per O. Ekstrøm -- Identification of SNPs, or mutations in sequence chromatograms / Nicole Draper -- BeadArray-based genotyping / Helen Butler and Jiannis Ragoussis -- Microsattelite-based candidate gene linkage analysis studies / Cathryn Mellersh -- Full complexity genomic hybridization on 60-mer oligonucleotide microarrays for array comparative genomic hybridization (aCGH) / Alexei Protopopov, Bin Feng, and Lynda Chin -- Detection of copy number changes at multiple loci in DNA prepared from formalin-fixed, paraffin-embedded tissue by multiplex ligation -dependent probe amplification / Minoru Takata -- Application of microarrays for DNA methylation profiling / Axel Schumacher, Andreas Weinhäusl, and Arturas Petronis -- Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray / Byung-Kwan Cho, Eric M. Knight, and Bernhard Ø. Palsson -- Transcriptional profiling of small samples in the central nervous system / Stephen D. Ginsberg -- Quantitative expression profiling of RNA from formalin-fixed, paraffin-embedded tissues using randomly assembled bead arrays / Marina Bibikova ... [et al.] -- Expression profiling of microRNAs in cancer cells : technical considerations / Mouldy Sioud and Lina Cekaite -- Identification of disease biomarkers by profiling of serum proteins using SELDI-TOF mass spectrometry / Sigrun Langbein -- The applicability of a cluster of differentiation monoclonal antibody microarray to the diagnosis of human disease / Peter Ellmark ... [et al.] --
- 2014 Springer Protocolsedited by L. María Sierra, Isabel Gaivão.Genotoxicity and DNA Repair: A Practical Approach provides a key reference for determining how to analyze the genotoxic activity of molecules or materials and, at the same time, serves as a useful tool for researchers in the Environmental Mutagenesis and DNA Repair fields. Focused on genotoxicity assays recommended by the "OECD guidelines for the testing of chemicals", this volume also covers other useful assays, such as some gene mutation assays, the comet assay in different species and applications, and the SMART assays of Drosophila. For all the assays, the book presents brief theoretical introductions to the topics and updated standard and modified step-by-step protocols to perform them. Special emphasis is placed on the analysis of nanoparticles, including an integrative approach analysis. The DNA Repair section includes several assays that provide information on repair activity in vitro and in vivo, as well as recent applications to study DNA repair in humans, cell cultures, and animal models. As a volume in the Methods in Pharmacology and Toxicology series, the chapters contain the kind of detail and key implementation advice that ensures reproducible results in the lab.
- 2013 Springer Protocolsedited by Alok Dhawan, Mahima Bajpayee.Genetic toxicology is recognized by geneticists and researchers concerned with the genetic impact of man-made chemicals.In Genotoxicity Assessment: Methods and Protocols, expert researchers in the field provide comprehensive genetictoxicology protocols. These include in vitro and in vivo protocols on mutation assays, cytogenetic techniques, and primary DNA damage, assays in alternate to animal models, and updated ICH guidelines. Written in the highly successfulMethods in Molecular Biology series format, the chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, as well as key tips ontroubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Genotoxicity Assessment: Methods and Protocols seeks to aid research students and scientists working in regulatory toxicology as well as biomedical, biochemical and pharmaceutical sciences.
- 2013 SpringerTim Schedl, editor.Also available: Print – 2013
- 2010 ScienceDirectedited by Paul M. Wassarman and Philippe M. Soriano.Also available: Print – 2010
- Handbook for DNA-encoded chemistry : theory and applications for exploring chemical space and drug discovery2014 Wileyedited by Robert A. Goodnow, Jr.Just enough knowledge? -- A brief history of the development of combinatorial chemistry and the emerging need for DNA-encoded chemistry -- A history of DNA-encoding -- DNA-compatible chemistry -- Foundations of a DNA-encoded library (DEL) -- Practices for synthesizing DNA-encoded libraries -- Chemical gene design for DNA-encoded libraries -- Analytical challenges for DNA-encoded library systems -- Information technology: functionality and architectures for DNA-encoding -- Theoretical considerations of the application of DNA-encoded libraries to drug discovery -- Begin with the end in mind : the hit-to-lead process -- Enumeration and visualization of large combinatorial chemical libraries -- Screening large compound collections -- Reported applications of DNA-encoded library chemistry -- Dual-pharmacophore DNA-encoded chemical libraries -- Hit identification and hit follow-up -- Using DNA to program chemical synthesis, discover new reactions, and detect ligand binding -- An outlook and the changing feasibility and economics of chemical diversity exploration with DNA-encoded combinatorial approaches -- Keeping the promise? an outlook on dna chemical library technology.
- 2009 SpringerYong-Kyu Kim, editor.
- v. 1-5, 1974-75.Robert C. King, editor.v. 1. Bacteria, bacteriophages and fungi.--v. 2. Plants, plant viruses, and protists.--v. 3.Invertebrates of genetic interest.--v. 4. Vertebrates of genetic interest.--v. 5. Molecular genetics.
- 2010 Springeredited by Kenneth P. Tercyak.
- 2009 ScienceDirectedited by Richard D. Cummings and J. Michael Pierce.
- 2016 SpringerRicardo H Alvarez ... [and more].1. Introduction and background biology -- 2. HER2 testing -- 3. HER2-positive breast cancer, neoadjuvant and adjuvant therapy -- 4. HER2-positive metastatic breast cancer, first-line treatment -- 5. HER2-positive metastatic breast cancer, second-line treatment -- 6. Emerging targeted agents for HER2-positive breast cancer.
- 2005 Wileyedited by Roland K. Hartmann ... [et al.].Part I. RNA Synthesis - Enzymatic RNA Synthesis, Ligation and Modification -- Chapter 1. Enzymatic RNA Synthesis using Bacteriophage T7 RNA Polymerase / Heike Gruegelsiepe, Astrid Schön, Leif A. Kirsebom and Roland K. Hartmann, p. 3-21 -- Chapter 2. Production of RNAs with Homogeneous 5' and 3' Ends / Mario Mörl, Esther Lizano, Dagmar K. Willkomm and Roland K. Hartmann, p. 22-35 -- Chapter 3. RNA Ligation using T4 DNA Ligase / Mikko J. Frilander and Janne J. Turunen, p. 36-52 -- Chapter 4. T4 RNA Ligase / Tina Persson, Dagmar K. Willkomm and Roland K. Hartmann, p. 53-74 -- Chapter 5. Co- and Post-Transcriptional Incorporation of Specific Modifications Including Photoreactive Groups into RNA Molecules / Nathan H. Zahler and Michael E. Harris, p. 75-85 -- Chapter 6. 3'-Terminal Attachment of Fluorescent Dyes and Biotin / Dagmar K. Willkomm and Roland K. Hartmann, p. 86-94 -- Part I. RNA Synthesis - Chemical RNA Synthesis -- Chapter 7. Chemical RNA Synthesis, Purification and Analysis / Brian S. Sproat, p. 95-111 -- Chapter 8. Modified RNAs as Tools in RNA Biochemistry / Thomas E. Edwards and Snorri T. H. Sigurdsson, p. 112-129 -- Part II. Structure Determination - Molecular Biology Methods -- Chapter 9. Direct Determination of RNA Sequence and Modification by Radiolabeling Methods / Olaf Gimple and Astrid Schön, p. 132-150 -- Chapter 10. Probing RNA Structures with Enzymes and Chemicals In Vitro and In Vivo / Eric Huntzinger, Maria Possedko, Flore Winter, Hervé Moine, Chantal Ehresmann and Pascale Romby, p. 151-171 -- Chapter 11. Study of RNA-Protein Interactions and RNA Structure in Ribonucleoprotein Particles / Virginie Marchand, Annie Mougin, Agnès Méreau and Christiane Branlant, p. 172-204 -- Chapter 12. Terbium(III) Footprinting as a Probe of RNA Structure and Metal-binding Sites / Dinari A. Harris and Nils G. Walter, p. 205-213 -- Chapter 13. Pb2+-induced Cleavage of RNA / Leif A. Kirsebom and Jerzy Ciesiolka, p. 214-228 -- Chapter 14. In Vivo Determination of RNA Structure by Dimethylsulfate / Christina Waldsich and Renée Schroeder, p. 229-237 -- Chapter 15. Probing Structure and Binding Sites on RNA by Fenton Cleavage / Gesine Bauer and Christian Berens, p. 238-249 -- Chapter 16. Measuring the Stoichiometry of Magnesium Ions Bound to RNA / A. J. Andrews and Carol Fierke, p. 250-258 -- Chapter 17. Nucleotide Analog Interference Mapping and Suppression: Specific Applications in Studies of RNA Tertiary Structure, Dynamic Helicase Mechanism and RNA-Protein Interactions, p. 259-293 / Olga Fedorova, Marc Boudvillain, Jane Kawaoka and Anna Marie Pyle -- Chapter 18. Nucleotide Analog Interference Mapping: Application to the RNase P System / Simona Cuzic and Roland K. Hartmann, p. 294-318 -- Chapter 19. Identification and Characterization of Metal Ion Binding by Thiophilic Metal Ion Rescue / Eric L. Christian, p. 319-344 -- Chapter 20. Identification of Divalent Metal Ion Binding Sites in RNA/DNA-metabolizing Enzymes by Fe(II)-mediated Hydroxyl Radical Cleavage / Yan-Guo Ren, Niklas Henriksson and Anders Virtanen, p. 345-353 -- Chapter 21. Protein-RNA Crosslinking in Native Ribonucleoprotein Particles / Henning Urlaub, Klaus Hartmuth and Reinhard Lührmann, p. 354-373 -- Chapter 22. Probing RNA Structure by Photoaffinity Crosslinking with 4-Thiouridine and 6-Thioguanosine / Michael E. Harris and Eric L. Christian, p. 374-384 -- Part II. Structure Determination - Biophysical Methods -- Chapter 23. Structural Analysis of RNA and RNA-Protein Complexes by Small-angle X-ray Scattering / Tao Pan and Tobin R. Sosnick, p. 385-397 -- Chapter 24. Temperature-Gradient Gel Electrophoresis of RNA / Detlev Riesner and Gerhard Steger, p. 398-414 -- Chapter 25. UV Melting, Native Gels and RNA Conformation / Andreas Werner, p. 415-427 -- Chapter 26. Sedimentation Analysis of Ribonucleoprotein Complexes / Jan Medenbach, Andrey Damianov, Silke Schreiner and Albrecht Bindereif, p. 428-437 -- Chapter 27. Preparation and Handling of RNA Crystals / Boris François, Aurélie Lescoute-Phillips, Andreas Werner and Benoît Masquida, p. 438-452 -- Part II. Structure Determination - Fluorescence and Single Molecule Studies -- Chapter 28. Fluorescence Labeling of RNA for Single Molecule Studies / Filipp Oesterhelt, Enno Schweinberger and Claus Seidel, p. 453-474 -- Chapter 29. Scanning Force Microscopy and Scanning Force Spectroscopy of RNA / Wolfgang Nellen, p. 475-487 -- Part III. RNA Genomics and Bioinformatics - Fluorescence and Single Molecule Studies -- Chapter 30. Comparative Analysis of RNA Secondary Structure: 6S RNA / James W. Brow and J. Christopher Ellis, p. 490-512 -- Chapter 31. Secondary Structure Prediction / Gerhard Steger, p. 513-535 -- Chapter 32. Modeling the Architecture of Structured RNAs within a Modular and Hierarchical Framework, p. 536-545 / Benoît Masquida and Eric Westhof -- Chapter 33. Modeling Large RNA Assemblies using a Reduced Representation, p. 546-559 / Jason A. Mears, Scott M. Stagg and Stephen C. Harvey -- Chapter 34. Molecular Dynamics Simulations of RNA Systems / Pascal Auffinger and Andrea C. Vaiana, p. 560-576 -- Chapter 35. Seeking RNA Motifs in Genomic Sequences / Matthieu Legendre and Daniel Gautheret, p. 577-594 -- Chapter 36. Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: RNA Mining / Jörg Vogel, E. Gerhart and H. Wagner, p. 595-613 -- Chapter 37. Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: Functional Analysis of Identified Non-mRNAs / E. Gerhart, H. Wagner and Jörg Vogel, p. 614-642 -- Chapter 38. Experimental RNomics: A Global Approach to Identify Non-coding RNAs in Model Organisms / Alexander Hüttenhofer, p. 643-654 -- Chapter 39. Large-scale Analysis of mRNA Splice Variants by Microarray / Young-Soo Kwon, Hai-Ri Li and Xiang-Dong Fu, p. 655-663 -- Part IV. Analysis of RNA Function 665 - RNA-Protein Interactions in vitro -- Chapter 40. RNA-Protein Interactions in vitro / Steffen Schiffer, Sylvia Rösch, Bettina Späth, Markus Englert, Hildburg Beier and Anita Marchfelder, p. 666-675 -- Chapter 41. Biotin-based Affinity Purification of RNA-Protein Complexes / Zsofia Palfi, Jingyi Hui and Albrecht Bindereif, p. 676-693 -- Chapter 42. Immunoaffinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein Complexes / Cindy L. Will, Evgeny M. Makarov, Olga V. Makarova and Reinhard Lührmann, p. 694-709 -- Chapter 43. Northwestern Techniques for the Identification of RNA-binding Proteins from cDNA Expression Libraries and the Analysis of RNA-Protein Interactions / Ángel Emilio Martínez De Alba, Michela Alessandra Denti and Martin Tabler, p. 710-728 -- Part IV. Analysis of RNA Function 665 - RNA-Protein Interactions in vivo -- Chapter 44. Fluorescent Detection of Nascent Transcripts and RNA-binding Proteins in Cell Nuclei, p. 729-736 / Jennifer A. Geiger and Karla M. Neugebauer -- Chapter 45. Identification and Characterization of RNA-binding Proteins through Three-hybrid Analysis / Felicia Scott and David R. Engelke, p. 737-754 -- Chapter 46. Analysis of Alternative Splicing In Vivo using Minigenes / Yesheng Tang, Tatyana Novoyatleva, Natalya Benderska, Shivendra Kishore, Alphonse Thanaraj and Stefan Stamm, p. 755-782 -- Part IV. Analysis of RNA Function 665 - SELEX -- Chapter 47. Artificial Selection: Finding Function amongst Randomized Sequences / Ico de Zwart, Catherine Lozupone, Rob Knight, Amanda Birmingham, Mali Illangasekare, Vasant Jadhav, Michal Legiewicz, Irene Majerfeld, Jeremy Widmann and Michael Yarus, p. 783-806 -- Chapter 48. Aptamer Selection against Biological Macromolecules: Proteins and Carbohydrates / C. Stefan Vörtler and Maria Milovnikova, p. 807-839 -- Chapter 49. In Vivo SELEX Strategies / Thomas A. Cooper, p. 840-852 -- Chapter 50. In Vitro Selection against Small Targets / Dirk Eulberg, Christian Maasch, Werner G. Purschke and Sven Klussmann, p. 853-877 -- Chapter 51. SELEX Strategies to Identify Antisense and Protein Target Sites in RNA or Heterogeneous Nuclear Ribonucleoprotein Complexes / Martin Lützelberger, Martin R. Jakobsen and Jørgen Kjems, p. 878-894 -- Chapter 52. Gene Silencing Methods for Mammalian Cells: Application of Synthetic Short Interfering RNAs / Matthias John, Anke Geick, Philipp Hadwiger, Hans-Peter Vomlocher and Olaf Heidenreich, p. 896-909 -- Appendix. UV Spectroscopy for the Quantitation of RNA, p. 910-913.
- v. 1-2, 2007 Wileyeditors, D.J. Balding, M. Bishop, C. Cannings.Also available: Print – v. 1-2., 2007
- v.1-4=, 2014 Wileyedited by Stefan Dubel and Janice M. Reichert.Volume 1. Defining the Right Antibody Composition -- Volume 2. Clinical Development of Antibodies -- Volume 3. Approved Therapeutic Antibodies -- Volume 4. Approved Therapeutic Antibodies and in vivo Diagnostics.
- 2007 CRCnetBASEedited by Sankar Ghosh.
- 2010 SpringerShili Lin, Hongyu Zhao, editors.
- 2015 Springer Protocolsedited by Natalia A. Riobo.Luciferase reporter assays to study transcriptional activity of hedgehog signaling in normal and cancer cells / Silvia Pandolfi and Barbara Stecca -- Measuring expression levels of endogenous gli genes by immunoblotting and real-time PCR / Pawel Niewiadomski and Rajat Rohatgi -- Quantitative immunoblotting of endogenous hedgehog pathway components / Shohreh F. Farzan and David J. Robbins -- Measuring Gli2 phosphorylation by selected reaction monitoring mass spectrometry / Robert Ahrends, Pawel Niewiadomski, Mary N. Teruel, and Rajat Rohatgi -- Rapid screening of Gli2/3 mutants using the Flp-In system / Pawel Niewiadomski and Rajat Rohatgi -- Insights into gli factors ubiquitylation methods / Paola Infante, Romina Alfonsi, and Lucia Di Marcotullio -- Determination of acetylation of the gli transcription factors / Sonia Coni, Laura Di Magno, and Gianluca Canettieri -- Efficient detection of indian hedgehog during endochondral ossification by whole-mount immunofluorescence / João Francisco Botelho, Daniel Smith-Paredes, and Veronica Palma A. -- Methods for detection of Ptc1-driven LacZ expression in adult mouse skin / Donna M. Brennan-Crispi, My G. Mahoney, and Natalia A. Riobo -- Determination and analysis of cellular metabolic changes by noncanonical hedgehog signaling / Raffaele Teperino and John Andrew Pospisilik.
- 2007 Springer Protocolsedited by Jamila I. Horabin.Purifying the hedgehog protein and its variants / Darren P. Baker, Frederick R. Taylor, and R. Blake Pepinsky -- Application of sonic hedgehog to the developing chick limb / Eva Tieck and Cheryll Tickle -- Manipulation of hedgehog signaling in Xenopus by means of embryo microinjection and application of chemical inhibitors / Thomas Hollemann .. [et al.] -- Isolation of rat telencephalic neural explants to assay Shh GABAergic interneuron differentiation-inducing activity / Rina Mady and Jhumku D. Kohtz -- Genetic analysis of the vertebrate hedgehog-signaling pathway using muscle cell fate specification in the zebrafish embryo / Sudipto Roy -- Efficient manipulation of hedgehog/GLI signaling using retroviral expression systems / Maria Kasper ... [et al.] -- Cell surface marker and cell cycle analysis, hedgehog signaling, and flow cytometry / Krsting Detmer and Ronald E. Garner -- Detecting tagged hedgehog with intracellular and extracellular immunocytochemistry for functional analysis / Ainhoa Callejo, Luis Quijada, and Isabel Guerrero -- Confocal analysis of hedgehog morphogenetic gradient coupled with fluorescent in situ hybridization of hedgehog target genes / Armel Gallet and Pascal P. Thérond -- RNA in the hedgehog signaling pathway : pFRiPE, a vector for temporally and spatially controlled RNAi in Drosophila / Eric Marois and Suzanne Eaton -- Germline clone analysis for maternally acting Drosophila hedgehog components / Erica M. Selva and Beth E. Stronach -- Clone analysis of hedgehog signaling in Drosophila somatic tissues / Christing M. Bankers and Joan E. Hooper -- GAL4/UAS targeted gene expression for studying Drosophila hedgehog signaling / Denise Bussona nd Anne-Marie Pret -- Biochemical fractionation of Drosophila cells / Melanie Stegman and David Robbins -- Using immunoprecipitation to study protein-protein interactions in the hedgehog-signaling pathway / Chao Ton and Jin Jiang -- Sequence analyses to study the evolutionary history and cis-regulatory elements of hedgehog genes / Ferenc Müller and Anne-Gaelle Borycki.
- 2010 SpringerMiguel A. Rodriguez-Bigas, Raul Cutait, Patrick M. Lynch, Ian Tomlinson, Hans F.A. Vasen, editors.Colorectal cancer is the third most commonly diagnosed cancer in the US and the third most recently linked to cancer deaths. The national annual incidence rate of colorectal cancer is approximately 148,000+, striking slightly more females than males. The lifetime risk of colorectal cancer is 5-6percent, however patients with a familial risk (with two or more first or second degree relatives) make up 20percent of the patients. Persons who carry genetic mutations linked to hereditary colorectal cancer are the most likely to develop the disease.
- 2013Sarah Elizabeth Pierce.The Saccharomyces cerevisiae deletion collection has revolutionized yeast genetics by allowing genome-wide deletion screens to be performed in pooled cultures. The inclusion of unique, 20-bp DNA sequences known as "tags" or "barcodes" in each strain allows all ~6000 yeast deletion mutants to be analyzed in a single culture by using a microarray to detect changes in tag abundance. Here we discuss improvements and extensions made to the pooled-yeast-deletion assay. This includes a redesign of the barcode array that is used for detecting the tags included in the deletion collection. Our analysis of this barcode array examines whether it is better to use available microarray surface area on a single feature for each probe, or to instead include multiple smaller features. It also covers aspects of data analysis such as the correction of hybridization defects and array saturation, tag-sequence repairs, and estimation of background hybridization. In addition to these microarray changes, we also examine the impact of experimental design on the quality of pooled growth data. Each step in both the experimental protocol and the data-analysis pipeline is examined for possible improvement. Finally, we discuss preliminary experiments testing the application of pooled fitness profiling to the study of epistasis. Data are shown that demonstrate the feasibility of a pooled-double-mutant fitness assay that is compatible with existing barcode array technology. This assay has the potential to become a valuable functional-genomics tool that may provide an improved understanding of pathway relationships in yeast.
- 2011 Springer Protocolsedited by Young Min Kwon, Steven C. Ricke.[Publisher-supplied data] Due to their novel concepts and extraordinary high-throughput sequencing capacity, the next generation sequencing methods allow scientists to grasp system-wide landscapes of the complex molecular events taking place in various biological systems, including microorganisms and microbial communities. These methods are now being recognized as essential tools for a more comprehensive and deeper understanding of the mechanisms underlying many biological processes. In High-Throughput Next Generation Sequencing: Methods and Applications, experts in the field explore the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities; however, the methods described in this book will also offer general applications relevant to the study of any living organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, High-Throughput Next Generation Sequencing: Methods and Applications is an excellent collection of chapters to aid all scientists who wish to apply these innovative research tools to enhance their own pursuits in microbiology and also biology in general.
- History of the Avon Longitudinal Study of Parents and Children (ALSPAC), c. 1980-2000 : the transcript of a Witness Seminar held by the History of Modern Biomedicine Research Group, Queen Mary, University of London, on 24 May 20112012 Wellcome Trustedited by C. Overy, L.A. Reynolds and E.M. Tansey.
- 2014 Springer Protocolsedited by David R. Edgell.Homing endonucleases : from genetic anomalies to programmable genomic clippers / Marlene Belfort and Richard P. Bonocora -- Bioinformatic identification of homing endonucleases and their target sites / Eyal Privman -- PCR-based bioprospecting for homing endonucleases in fungal mitochondrial rRNA genes / Mohamed Hafez [and four others.] -- Mapping homing endonuclease cleavage sites using in vitro generated protein / Richard P. Bonocora and Marlene Belfort -- Mapping free-standing homing endonuclease promoters using 5'RLM-RACE / Ewan A. Gibb -- PCR analysis of chloroplast double-strand break (DSB) repair products induced by I-CreII in chlamydomonas and arabidopsis / Taegun Kwon [and three others ] -- A two-plasmid bacterial selection system for characterization and engineering of homing endonucleases / Ning Sun and Huimin Zhao -- Rapid screening of endonuclease target site preference using a modified bacterial two-plasmid selection / Jason M. Wolfs, Benjamin P. Kleinstiver, and David R. Edgell -- A yeast-based recombination assay for homing endonuclease activity / Jean-Charles Epinat -- Rapid determination of homing endonuclease DNA binding specificity profile / Lei Zhao and Barry L. Stoddard -- Quantifying the information content of homing endonuclease target sites by single base pair profiling / Joshua I. Friedman, Hui Li, and Raymond J. Monnat, Jr. -- Homing endonuclease target site specificity defined by sequential enrichment and next-generation sequencing of highly complex target site libraries/ Hui Li and Raymond J. Monnat Jr. -- Homing endonuclease target determination Using SELEX adapted for yeast surface display / Kyle Jacoby and Andrew M. Scharenberg -- Engineering and flow-cytometric analysis of chimeric LAGLIDADG homing endonucleases from homologous I-OnuI-family enzymes / Sarah K. Baxter, Andrew M. Scharenberg, and Abigail R. Lambert -- Bioinformatics identification of coevolving residues / Russell J. Dickson and Gregory B. Gloor -- Identification and analysis of genomic homing endonuclease target sites / Stefan Pellenz and Raymond J. Monnat Jr. -- Redesigning the specificity of protein-DNA interactions with Rosetta / Summer Thyme and David Baker.
- 2009 Springer Protocolsedited by Maria Boekels Gogarten, Johann Peter Gogarten, and Lorraine Olendzenski.Gene transfer: who benefits? / L. Olendzenski and J.P. Gogarten -- Defining the mobilome / J.L. Siefert -- The interplay of homologous recombination and horizontal gene transfer in bacterial speciation / J.G. Lawrence and A.C. Retchless -- Epistemological impacts of horizontal gene transfer on classification in microbiology / E. Bapteste and Y. Boucher -- Persistence mechanisms of conjugative plasmids / M.I. Bahl, L.H. Hansen and S.J. Sorensen -- The integron/gene cassette system: an active player in bacterial adaptation / M. Labbate, R.J. Case and H.W. Stokes -- Ancient gene transfer as a tool in phylogenetic reconstruction / J. Huang and J.P. Gogarten -- The tree of life viewed through the contents of genomes / C.H. House -- Horizontal gene transfer and the evolution of methanogenic pathways / G. Fournier -- Genome acquisition in horizontal gene transfer: symbiogenesis and macromolecular sequence analysis / L. Margulis -- Detection and quantitative assessment of horizontal gene transfer / O. Zhaxybayeva -- Composition-based methods to identify horizontal gene transfer / D. Cortez ... [et al.] -- Testing phylogenetic methods to identify horizontal gene transfer / M. Poptsova -- Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction / R.G. Beiko and M.A. Ragan -- Construction and use of flow cytometry optimized plasmid-sensor strains / M.I. Bahl ... [et al.] -- Experimental evolution of an essential Bacillus gene in an E. coli host / M. Larios-Sanz and M. Travisano -- Mass action models describing extant horizontal transfer of plasmids: inferences and parameter sensitivities / B.F. Smets and L. Lardon -- Interdomain transfers of sugar transporters overcome barriers to gene expression / K.M. Noll and K. Thirangoon -- The role of horizontal gene transfer in photosynthesis, oxygen production, and oxygen tolerance / J. Raymond -- Horizontal gene transfer in cyanobacterial signature genes / S. Yerrapragada, J.L. Siefert and G.E. Fox -- Population genomics and the bacterial species concept / M.A. Riley and M. Lizotte-Waniewski -- A critique of prokaryotic species concepts / R.T. Papke -- What antimicrobial resistance has taught us about horizontal gene transfer / M. Barlow -- Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface / J.M. Coombs -- Horizontal gene transfer and mobile genetic elements in marine systems / P.A. Sobecky and T.H. Hazen -- Horizontal gene transfer in metal and radionuclide contaminated soils / P.A. Sobecky and J.M. Coombs -- Horizontal gene transfer between microbial eukaryotes / J.O. Andersson -- Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis / U.C. Alsmark ... [et al.] -- Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids / P.J. Keeling -- Role of horizontal gene transfer in the evolution of plant parasitism among nematodes / M. Mitreva, G. Smant and J. Helder.
- 2002 ScienceDirectedited by Michael Syvanen and Clarence I. Kado.
- 2007 SpringerSpyros Papageorgiou [ed.].
- 2014 Springer Protocolsedited by Yacine Graba, René Rezsohazy.Discovery and classification of homeobox genes in animal genomes / Ferdinand Marlétaz, Jordi Paps, Ignacio Maeso, and Peter W. H. Holland -- How to study hox gene expression and function in mammalian oocytes and early embryos / Delphine Paul, Caroline Sauvegarde, René Rezsohazy, and Isabelle Donnay -- Genetic lineage tracing analysis of anterior hox expressing cells / Brigitte Laforest, Nicolas Bertrand, and Stéphane Zaffran -- A genetic strategy to obtain P-Gal4 elements in the Drosophila hox genes / Luis de Navas, David Foronda, Delia del Saz, and Ernesto Sánchez-Herrero -- Hox complex analysis through BAC recombineering / Mark Parrish, Youngwook Ahn, Christof Nolte, Bony De Kumar and Robb Krumlauf -- The genetics of murine Hox loci : TAMERE, STRING, and PANTHERE to engineer chromosome variants / Patrick Tschopp and Denis Duboule -- Topological organization of Drosophila hox genes using DNA fluorescent in situ hybridization / Frédéric Bantignies and Giacomo Cavalli -- Mining the Cis-regulatory elements of hox clusters / Navneet Kaur Matharu and Rakesh K. Mishra -- Functional analysis of hox genes in Zebrafish / Franck Ladam and Charles G. Sagerström -- Transgenesis in non-model organisms : the case of Parhyale / Zacharias Kontarakis and Anastasios Pavlopoulos -- Tissue specific RNA isolation in Drosophila embryos : a strategy to analyze context dependent transcriptome landscapes using FACS / Arnaud Defaye and Laurent Perrin -- Hox transcriptomics in Drosophila embryos / Maria Polychronidou and Ingrid Lohmann -- Measuring hox-DNA binding by electrophoretic mobility / Kelly Churion [and four others] -- Chromatin immunoprecipitation and chromatin immunoprecipitation with massively parallel sequencing on mouse embryonic tissue / Shilu Amin and Nicoletta Bobola -- chIP for hox proteins from Drosophila imaginal discs / Pavan Agrawal and L. S. Shashidhara -- SELEX-seq : a method for characterizing the compete repertoire of binding site preferences for transcription factor complexes / Todd R. Riley [and six others] -- DamID as an approach to studyinhg long-distance chromatin iteractions / Fabienne Cléard, François Karch, and oRbert K. Maeda -- cgCHIP : a cell type- and gene-specific method for chromatin analysis / Marios Agelopoulos, Daniel J. McKay, and Ricahrd S. Mann -- Bimolecular fluorescence complementation (biFC) in live Drosophila embryos / Marilyne Duffraisse, Bruno Hudry, and Samir Merabet -- Rational drug repurposing using sscMap analysis in a HOX-TALE model of leukemia / Laura M. Kettyle, Fabio G. Liberante, and Alexander Thompson.
- 2012 Springeredited by Jean S. Deutsch.Regulation of hox activity : insights from protein motifs / Samir Merabet ... [et al.] -- Cis-regulation in the drosophila : bithorax complex / Robert K. Maeda and François Karch -- Maintenance of hox gene expression patterns / Samantha Beck ... [et al.] -- Control of vertebrate hox clusters by remote and global cis-acting regulatory sequences / François Spitz -- The early evolution of hox genes : a battle of belief? / Bernd Schierwater and Kai Kamm -- Evolution of hox complexes / David E.K. Ferrier -- The nematode story : hox gene loss and rapid evolution / Aziz Aboobaker and Mark Blaxter -- Are the deuterostome posterior hox genes a fast-evolving class? / Robert Lanfear -- Hox genes and the body plans of chelicerates and pycnogonids / Wim G.M. Damen -- Hox3/zen and the evolution of extraembryonic epithelia in insects / Urs Schmidt-Ott, Ab. Matteen Rafiqi and Steffen Lemke -- Hox genes and brain development in drosophila / Heinrich Reichert and Bruno Bello -- Homeosis and beyond : what is the function of the hox genes? / Jean S. Deutsch.Also available: Print – 2010
- 2012 SpringerHerman E. Wyandt, Vijay S. Tonk.pt. 1. Human chromosome methods and nomenclature -- pt. 2. Chromosome heteromorphism (summaries) -- pt. 3. Fragile sites -- pt. 4. Copy number vairiants.
- 2012 ScienceDirectLeon E. Rosenberg and Diane Drobnis Rosenberg.In the nearly 60 years since Watson and Crick proposed the double helical structure of DNA, the molecule of heredity, waves of discoveries have made genetics the most thrilling field in the sciences. The study of genes and genomics today explores all aspects of the life with relevance in the lab, in the doctor's office, in the courtroom and even in social relationships. In this helpful guidebook, one of the most respected and accomplished human geneticists of our time communicates the importance of genes and genomics studies in all aspects of life. With the use of core concepts and the integration of extensive references, this book provides students and professionals alike with the most in-depth view of the current state of the science and its relevance across disciplines. Bridges the gap between basic human genetic understanding and one of the most promising avenues for advances in the diagnosis, prevention and treatment of human disease. Includes the latest information on diagnostic testing, population screening, predicting disease susceptibility, pharmacogenomics and moreExplores ethical, legal, regulatory and economic aspects of genomics in medicine. Integrates historical (classical) genetics approach with the latest discoveries in structural and functional genomics.
- 2011 ScienceDirectRichards, Julia E.; Hawley, R. Scott.As genetic issues play a growing role in health practice and public policy, new knowledge in this field will continue to have significant implications for individuals and society. Written to communicate sound and modern science in an accessible way for professionals and students with various levels of scientific background, this thoroughly revised edition of The Human Genome contributes to creating a genetically literate research and clinical population. With case studies and introductory vignettes which illustrate a wide range of perspectives on complex topics in genetics and updated material on the latest research on disease-specific topics, this book serves as a valuable resource for students and working professionals alike. Full-color illustrations enhance and reinforce key concepts and themes * Chapters include interest boxes that focus on human health and disease, chapter-opening case studies, and concept statements to engage non-specialist readers.
- 2013 SpringerYuri B. Yurov, Svetlana G. Vorsanova, Ivan Y. Iourov, editors.
- 2006 SpringerHans-Juergen Bandelt, Vincent Macaulay, Martin Richards, (eds).
- 2011Daniel Patrick Riordan.The unique post-transcriptional behavior of each mRNA is thought to be largely determined by features present in its molecular sequence, representing a type of RNA regulatory code. However, the details by which distinct regulatory outcomes are programmed into the sequences of different transcripts are mostly unknown. We set out to identify features of yeast mRNAs that influence their post-transcriptional fates. Using bioinformatic and in vitro selection approaches, we characterized several RNA recognition elements involved in mediating specific interactions with individual yeast RNA-binding proteins (RBPs). Most of the RNA elements we uncovered were associated with significant mRNA expression changes and were phylogenetically conserved in related yeasts, providing insights into the function and evolution of the corresponding interactions. We also analyzed RNA-protein interaction sites for the yeast Puf3 RBP by high-throughput sequencing under different growth conditions. These results provided high-resolution experimental evidence for Puf3 binding at consensus RNA elements in the transcriptome, and enabled detailed comparisons of individual interaction sites. Finally, we developed complementary methods for transcriptome-wide mapping of potential sites of RNA 2'-O-methylation. Application of these methods to the yeast transcriptome successfully recovered known sites of RNA modification and suggested that ribose methylation of functionally-related transcripts may occur and influence the regulation of endogenous yeast mRNAs. Overall, these results contribute to understanding of how RNA sequence features help to specify global differences in gene expression characteristics.
- 2013 Springer Protocolsedited by Yaron Shav-Tal.As imaging technologies and approaches have evolved, the scope of certain imaging techniques has moved far beyond the production of purely illustrative images or appealing time-lapse movies to providing the scientist with a rich range of ways to measure and quantify the biological process and outcome of gene expression. In Imaging Gene Expression: Methods and Protocols, expert authors offer up-to-date approaches and protocols that scientists in the field have developed, which would benefit the broader scientific community. Divided in three convenient parts, this detailed book covers the output of a gene, namely the RNA molecules that are transcribed from the gene and the way by which these molecules can be tracked or quantified in fixed or living cells, protocols that focus on the gene, DNA, or chromatin, as well as a variety of ways by which nuclear processes intertwined with gene expression can be followed and quantified in living cells as well as approaches for studying several sub-nuclear structures found in eukaryotic cells. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective subjects, lists of materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Imaging Gene Expression: Methods and Protocols will serve researchers working toward imaging in the context of complete organisms.
- Immediate early genes and inducible transcription factors in mapping of the central nervous system function and dysfunction2002 ScienceDirecteditors, L. Kaczmarek, H.A. Robertson.
- 2006 Springeredited by Raphael Pinaud and Liisa A. Tremere.Also available: Print – 2006
- 2012 Springer Protocolsedited by Frank T. Christiansen, Brian D. Tait.Major histocompatibility complex : a paradigm for studies of the human genome / Richard J.N. Allcock -- HLA typing by SSO and SSP methods / Heather Dunckley -- Methods for diagnostic HLA typing in disease association and drug hypersensitivity / Michael D. Varney [and others] -- HLA typing using bead-based methods / Daniel Trajanoski and Samantha J. Fidler -- HLA Typing by Direct DNA Sequencing / Linda K. Smith -- Data analysis of HLA sequencing using assign-SBT v3.6+ from conexio / Carla Wirtz and David Sayer -- Simple methods for the detection of HLA-G variants in coding and non-coding regions / Holger Nuckel [and others] -- Molecular typing of HLA-E / Nina Lauterbach [and others] -- Molecular analysis of complement component C4 gene copy number / Alison S.L. Castley and O. Patricia Martinez -- Genotyping of single nucleotide polymorphisms by 5' nuclease allelic discrimination / Mari Malkki and Effie W. Petersdorf -- High resolution MICA genotyping by sequence-based typing (SBT) / Yizhou Zou and Peter Stastny -- Standard methods for the management of immunogenetic data / Pierre-Antoine Gourraud [and others] -- Analytical methods for immunogenetic population data / Steven J. Mack [and others] -- Analytical methods for disease association studies with immunogenetic data / Jill A. Hollenbach [and others] -- Impact of HLA matching and HLA antibodies in organ transplantation : a collaborative transplant study view / Caner Susal and Gerhard Opelz -- Screening for antibodies against MICA by luminex flow cytometry / Yizhou Zou and Peter Stastny -- HLA antibody detection and characterization by solid phase immunoassays : methods and pitfalls / Andrea A. Zachary [and others] -- Detection and characterisation of alloreactive T cells / Mandvi Bharadwaj, Nicole A. Mifsud, and James McCluskey -- Detection of allo-HLA cross-reactivity by virus-specific memory T-cell clones using single HLA-transfected K562 cells / Lloyd J. D'Orsogna [and others] -- Separation and cryopreservation of lymphocytes from spleen and lymph node / Gabriella Tassone and Samantha J. Fidler -- Crossmatching by Complement-Dependent Lymphocytotoxicity / Samantha J. Fidler -- Lymphocyte crossmatch by flow cytometry for Kidney Transplantation / Jonathan Downing -- Overview of the killer cell immunoglobulin-like receptor system / Raja Rajalingam -- KIR typing by non-sequencing methods : polymerase-chain reaction with sequence-specific primers / David Ordonez [and others] -- Killer cell immunoglobulin-like receptors (KIR) typing by DNA sequencing / Lihua Hou [and others] -- Overview of methods required to evaluate donor NK cell alloreactivity for haploidentical haemopoietic stem cell transplantation / Andrea Velardi -- Detection of NK cell alloreactivity by flow cytometric CD107a assay / Dianne De Santis [and others] -- Clinical production and therapeutic applications of alloreactive natural killer cells / David H. McKenna [and others] -- Minor histocompatibility antigen typing by DNA sequencing for clinical practice in hematopoietic stem-cell transplantation / Eric Spierings and Els Goulmy -- Donor registries and search strategies / Carolyn K. Hurley, Machteld Oudshoorn, and Michelle Setterholm -- Cytokine gene polymorphisms : methods of detection and biological significance / Gurvinder Kaur and Narinder Mehra -- IMGT® tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations : IMGT/V-QUEST and IMGT/HighV-QUEST for NGS / Eltaf Alamyar -- IMGT/DomainGapAlign : the IMGT® tool for the analysis of IG, TR, MH, IgSF, and MhSF domain amino acid polymorphism / Francois Ehrenmann and Marie-Paule Lefranc -- Human Gm, Km, and Am allotypes and their molecular characterization : a remarkable demonstration of polymorphism / Marie-Paule Lefranc and Gerard Lefranc.
- v. 2-, 2009- Springer
- 2014 CRCnetBASEedited by Bharat B. Aggarwal, David Heber.Chapter 1. Evolution of innate and adaptive immunity / David Heber and Bharat B. Aggarwal -- chapter 2. Cellular mechanisms of cytokine activation / David Heber and Bharat B. Aggarwal -- chapter 3. Cellular lipids and inflammation / David Heber and Susanne Henning -- chapter 4. Biomarkers of inflammation and the Western diet / David Heber and Susanne Henning -- chapter 5. Phytochemicals and immune function / David Heber -- chapter 6. Genetic and environmental modifiers of immune function / David Heber -- chapter 7. Cancer and inflammation / David Heber -- chapter 8. Abdominal obesity : pathophysiology and related metabolic complications / Ana F.T.A. Junqueria and Caroline M. Apovian -- chapter 9. Type 2 diabetes and inflammation / Zhaoping Li and David Heber -- chapter 10. Heart disease and inflammation / Kaveh Daniel Navab -- chapter 11. Chronic kidney disease and inflammation / Karl J. Neff and Carel Le Roux -- chapter 12. Alzheimer's disease and inflammation / Stephen T. Chen and Gary W. Small -- chapter 13. Nutrition in autoimmunity : a focus on systemic lupus erythematosus and rheumatoid arthritis / Maureen McMahon -- chapter 14. Asthma and inflammation / Andre Nel and David Heber -- chapter 15. Muscle and immune function / Anthony Thomas and David Heber -- chapter 16. Approaches to reducing abdominal obesity / Zhaoping Li and David Heber -- chapter 17. Barriers to fruit and vegetable consumption and practical strategies for increasing fruit and vegetable intake / Susan Bowerman -- chapter 18. Healthy fats and oils : balancing omega-3 and omega-6 acids in tissues / Bill Lands -- chapter 19. Spices and dietary supplements with anti-inflammatory activity / Bharat B. Aggarwal and David Heber.
- 2011 Springer Protocolsedited by Bing Yu, Marcus Hinchcliffe.Accessing and selecting genetic markers from available resources / Christopher G. Bell -- Linkage analysis / Jennifer H. Barrett and M. Dawn Teare -- Association mapping / Jodie N. Painter, Dale R. Nyholt, and Grant W. Montgomery -- The ForeSee (4C) approach for integrative analysis in gene discovery / Yike Guo, Robin E.J. Munro, Dimitrios Kalaitzopoulos, and Anita Grigoriadis -- R statistical tools for gene discovery / Andrea S. Foulkes and Kinman Au -- In silico PCR analysis / Bing Yu and Changbin Zhang -- In silico analysis of the exome for gene discovery / Marcus Hinchcliffe and Paul Webster -- In silico knowledge and content tracking / Herman van Haagen and Barend Mons -- Application of gene ontology to gene identification / Hugo P. Bastos . [and others] -- Phenotype mining for functional genomics and gene discovery / Philip Groth, Ulf Leser, and Bertram Weiss -- Conceptual thinking for in silico prioritization of candidate disease genes / Nicki Tiffin -- Web tools for the prioritization of candidate disease genes / Martin Oti, Sara Ballouz, and Merridee A. Wouters -- Comparative view of in silico DNA sequencing analysis tools / Sissades Tongsima [and others] -- Mutation surveyor : an in Silico tool for sequencing analysis / Chongmei Dong and Bing Yu -- In silico searching for disease -- associated functional DNA variants / Rao Sethumadhavan, C. George Priya Doss, and R. Rajasekaran -- In silico prediction of transcriptional factor-binding sites / Dmitry Y. Oshchepkov and Victor G. Levitsky -- In silico prediction of splice-affecting nucleotide variants / Claude Houdayer -- In silico tools for qPCR assay design and data analysis / Stephen Bustin, Anders Bergkvist, and Tania Nolan -- RNA structure prediction / Stephan H. Bernhart -- In silico prediction of post-translational modifications / Chunmei Liu and Hui Li -- In silico protein motif discovery and structural analysis / Catherine Mooney [and others].
- In the right place at the right time : understanding basic microRNA biology through the control of developmental timing by lin-4 and let-7 in Caenorhabditis elegans2012Huibin Zhang.MicroRNAs are an important class of short RNA molecules that regulate gene expression in diverse organisms. Despite their short history, extensive research on microRNAs has revealed how microRNAs are made, their regulatory mechanisms and functions in different biological processes. In addition, novel experimental techniques and computational algorithms have been developed to study microRNAs. Our knowledge of microRNAs is constantly evolving as newer studies turn up exceptions to canonical models established by early studies. This highlights how our understanding of microRNAs is far from complete and much work is still needed to investigate unexplored aspects of the microRNA world. The founding microRNAs, C. elegans lin-4 and let-7, have well-characterized heterochronic defects in mutant animals and their target genes have been genetically validated. Combined with powerful experimental tools available in C. elegans, the microRNA function of lin-4 and let-7 in developmental timing of C. elegans is an ideal in vivo model system for testing microRNA-related hypotheses. Using functional assays to evaluate lin-4 and let-7 rescue activities in transgenic animals, we have investigated several poorly understood aspects of microRNAs, from biogenesis to functional mechanism. In this work, we first demonstrated the cell autonomous nature of lin-4 in C. elegans temporal development. Through tissue/cell-specific expression of lin-4 and the use of tissue/cell-specific reporters and microRNA sponges, we have shown that lin-4 rescue activities were limited to sites of lin-4 expression, despite its broad endogenous expression and function in many tissues. Next, we showed that intron-containing microRNAs ("inc-miRs") are functional in C. elegans, raising the possibility that mature microRNAs need not be encoded as contiguous units in the genome. This result also highlights a blindspot in our current novel microRNA discovery methods that assume inc-miRs do not exist. Lastly, we investigated the partnership between microRNA "seed" and "non-seed" sequences in providing microRNA function during C. elegans temporal development. By assessing microRNA function in transgenic mutant animals expressing lin-4 or let-7 mutant microRNA, we found contrasting results between lin-4 and let-7. While the results suggest a functional requirement for lin-4 seed sequence, mutations in either let-7 seed or non-seed sequences provided similar levels of functional activities. Using C. elegans lin-4 and let-7 as an experimental model, this work has furthered our understanding on microRNA autonomy, microRNA biogenesis and functional partnership between microRNA seed and non-seed sequence.
- 2010 Springer Protocolsedited by Jeff Braman.Mutagenesis protocols in Saccharomyces cerevisiae by in vivo overlap extension / Mibuel Alcalde -- In vitro mutagenesis of Brucella species / Thomas A. Ficht, Jianwu Pei, and Melissa Kahl-McDonagh -- Random mutagenesis strategies for Campylobacter and Helicobacter species / Duncan J.H. Gaskin and Arnoud H.M. van Vliet -- Mutagenesis of the repeat regions of herpesviruses cloned as bacterial artificial chromosomes / Yuguang Zhao and Venugopal Nair -- An efficient protocol for VZV BAC-based mutagenesis / Zhen Zhang, Ying Huang, and Hua Zhu -- A method for rapid genetic integration into Plasmodium falciparum utilizing mycobacteriophage Bxb1 integrase / Sophie H. Adjalley, Marcus C.S. Lee, and David A. Fidock -- Random mutagenesis by error-prone PCR / Elizabeth O. McCullum ... [et al.] -- A rapid and versatile PCR-based site-directed mutagenesis protocol for generation of mutations along the entire length of a cloned cDNA / Vincent Dammai -- Rapid sequence scanning mutagenesis using in silico oligo design and the megaprimer PCR of whole plasmid method (MegaWhop) / Urich Krauss, Karl-Erich Jaeger, and Thorsten Eggert -- Insertion and deletion mutagenesis by overlap extension PCR / Jehan Lee ... [et al.] -- Targeted amplification of mutant strands for efficient site-directed mutagenesis and mutant screening / Lei Young and Qihan Dong -- A modified inverse PCR procedure for insertion, deletion, or replacement of a DNA fragment in a target sequence and its application in the ligand interaction scan method for generation of ligand-regulated proteins / Oran Erster and Moti Liscovitch -- Amplification of orthologous genes using degererate primers / Samya Chakravorty and jim O. Vigoreaux -- Computational evaluation of protein stability change upon mutations / Shuangye Yin, Feng Ding, and Nikolay V. Dokholyan -- Approaches for using animal models to identify loci that genetically interact with human disease-causing point mutations / Josef D. Franke -- Using peptide loop insertion mutagenesis for the evolution of proteins / Christian Heinis and Kai Johnsson -- Massive mutagenesis : high-throughput combinatorial site-directed mutagenesis / Julien Sylvestre -- Directed in vitro evolution of reporter genes based on semi-rational design and high-throughput screening / Ai-Sheng Xiong ... [et al.] -- Ribosome display for rapid protein evolution by consecutive rounds of mutation and selection / Hayato Yanagida, Tomoaki Matsuura, and Tetsuya Yomo -- Fine-tuning enzyme activity through saturation mutagenesis / Holly H. Hogrefe -- Characterization of structural determinants of type 1 corticotropin releasing hormone (CRH) receptor signalling properties / Danijela Markovic and Dimitris K. Grammatopoulos -- Site-directed mutagenesis for improving biophysical properties of Vh domains / Mehdi Arbabi-Ghahroudi, Roger MacKenzie, and Jamshid Tanha -- Phenotype based functional gene screening using retrovirus-mediated gene trapping in quasi-haploid RAW 264.7 cells / Sung Ouk Kim and Soon-Duck Ha -- Site-directed disulfide cross-linking to probe conformational changes of a transporter during its functional cycle : Escherichia coli AcrB multidrug exporter as an example / Yumiko Takatsuka and Hiroshi Nikaido -- Site-specific incorporation of extra components into RNA by transcription using unnatural base pair systems / Michiko Kimoto and Ichiro Hirao -- Mutagen : a random mutagenesis method providing a complementary diversity generated by human error-prone DNA polymerases / Philippe Mondon ... [et al.] -- Random-scanning mutagenesis / Robert A. Smith -- Easy two-step method for randomizing and cloning gene fragments / Vivan Q. Zhang and Holly H. Hogrefe -- Random mutagenesis using a mutator strain / Ghazala Muteeb and Ranjan Sen -- En passant mutagenesis : a two step markerless red recombination system / B. Karsten Tischer, Gregory A. Smith, and Nikolaus Osterrieder.
- 2007 Springer Protocolsedited by Guido Grandi.Energy systems for ATP regeneration in cell-free protein synthesis reactions / Kara A. Calhoun and James R. Swartz -- Continuous-exchange protein-synthesizing systems / Vladimir A. Shirokov ... [et al.] -- Cell-free production of integral membrane proteins on a preparative scale / Christian Klammt ... [et al.] -- SIMPLEX : a novel method for high-throughput construction and screening of protein libraries / Suang Rungpragayphan, Tsuneo Yamane, and Hideo Nakano -- Methods for high-throughput materialization of genetic information based on the wheat germ cell-free expression system / Tatsuya Sawasaki ... [et al.] -- Exogenous protein expression in Xenopus oocytes : basic procedures / Elena Bossi ... [et al.] -- In vitro translation to study HIV protease activity / Zene Matsuda ... [et al.] -- The protein truncation test in mutation detection and molecular diagnosis / Oliver Hauss and Oliver Muller -- Creation of novel enantioselective lipases by SIMPLEX / Yuichi Koga, Tsuneo Yamane, and Hideo Nakano -- In vitro transcription and translation coupled with two-dimensional electrophoresis for bacterial proteome analysis / Nathalie Norais ... [et al.] -- In vitro screen of bioinformatically selected Bacillus anthracis vaccine candidates by coupled transcription, translation, and immunoprecipitation analysis / Orit Gat, Haim Grosfeld, and Avigdor Shafferman -- Functional expression of Type 1 rat GABA transporter in microinjected Xenopus laevis oocytes / Stefano Giovannardi ... [et al.] -- Production of protein for nuclear magnetic resonance study using the wheat germ cell-free system / Toshiyuki Kohno and Yaeta Endo.
- In vivo characterization of chromatin state and its relationship to the expression of foreign, non-integrating transgenic DNA in mouse liver2012Lia Eun Hee Gracey.The pursuit of gene therapy to treat a wide-spectrum of diseases holds great promise, but its application in the clinic is still blocked by several barriers. Gene therapy approaches that rely on a virus to carry genetic material are plagued by problems with a host immune response and difficulty reaching therapeutic doses. Nonviral approaches have the advantage that delivering naked DNA does not illicit the same significant immune response and therapeutic levels are often initially easily attained. But, one prominent barrier to nonviral gene therapy is the lack of in vivo sustained expression from a foreign transgene. In the early stages after delivery, robust expression can be achieved from transgenic DNA, but this expression is very quickly and efficiently silenced, with loss of the desired effect of gene replacement. Our work took a two-step approach to further our understanding of how to create a better expression vector, both for gene therapy purposes as well as basic scientific goals of sustaining expression from delivered transgenic DNA. First, we studied whether we could manipulate and control the chromatin structure that a delivered gene adopts in vivo via nucleosome positioning signals on plasmid DNA in mouse liver. We developed a selective hybridization assay that allowed us to use a high-throughput sequencing approach to more rapidly screen the nucleosome occupancy and positioning of numerous constructs with varied DNA elements. We were able to transiently control the initial chromatin structure, but other forces in the cell soon overcame the thermodynamic preferences of nucleosome formation. We now believe that the use of nucleosome eviction elements may be a more promising approach: it will likely be more feasible to exclude nucleosome formation using rigid DNA sequences instead of permanently positioning a nucleosome using DNA sequence alone. Secondly, we gained a more fundamental understanding of the mechanism(s) responsible for the silencing of episomal (non-integrating) DNA constructs in mouse liver. We studied the differences between plasmid DNA and minicircle DNA, which was derived from a parental plasmid but lacked bacterial backbone sequences. At 6 weeks after delivery, plasmid DNA was effectively silenced but there was still active expression from the minicircle. We used high-throughput sequencing approaches to quantitate the levels of transcription and the enrichment of various histone modifications and RNA polymerase II (Pol II) on plasmid and minicircle. We found that Pol II appeared to stall at the transcription start site on the plasmid but was present at the 5' and 3' ends of the gene on the minicircle. This observation may explain the 28-fold higher level of transcript produced by the minicircle versus the plasmid. Though we saw enrichment of activating and silencing histone modifications on both plasmid and minicircle (likely due to our analysis of a population of cells which at any given point could have a construct that is actively expressed or silenced) we observed a striking abundance of a well-characterized histone modification associated with silencing on the plasmid and not on the minicircle. These results represent a contribution to the fields of gene therapy and chromatin biology that will help us move in the direction of achieving safe, therapeutic, and sustained expression of transgenic DNA.
- Incorporating the dynamic nature of molecules improves performance of structure-based function prediction methods2010Dariya S. Glazer.Structural Genomics consortia aim to determine the structure of proteins with novel folds. In order to interpret their biological significance, it is critical to annotate the functions of these structures. Most structures are solved by X-ray crystallography experiments and represent static snapshots of the molecules. Structure-based function prediction methods do not perform well when the snapshots fail to display the relevant functional conformations. We show that coupling structure-based function prediction methods to molecular dynamics simulations considerably improves their performance in locating calcium binding sites. Our approach can be easily extended to other functions of interest. In particular, we generated short- to medium- scale molecular simulation trajectories (1ns -- 10ns) using GROMACS, a software suite developed for creating molecular dynamics simulations. Gromos 43a5, Gromos 53a6, AMBER '96, AMBER '99SB, AMBER '03, and OPLS-AA force fields were used to generate trajectories for 11 pairs of PDB structures, HOLO and APO form for the presence of calcium ions in the structures (22 structrures in total). Extracting structures at various time points over the course of the simulations we created structural ensembles which inform about the dynamic nature of each of the simulation systems. Using FEATURE, a machine learning algorithm that evaluates the presence of enriched physico-chemical properties around a site of interest, we analyzed the structural ensembles for the presence of calcium binding sites. We devised a clustering algorithm which allowed for definitive determination of the similarity of the local environments around the points identified by FEATURE as potential calcium binding site centers in different structural ensembles for each of the 22 PDB structures. Our results indicate that short scale simulations with 2 or 3 different force fields generate sufficient structural diversity to allow for improved identification of calcium binding sites. Furthermore, inclusion of calcium ions in the simulation systems does not significantly improve the performance of FEATURE. This result highlights the need for improved force fields, such that the dynamic nature of calcium binding sites can be accurately reproduced.
- 2007 Springeredited by Anne Fagot-Largeault, Shahid Rahman and Juan Manuel Torres.Pt. 1. Genetics and the life sciences -- Pt. 2. Genetics and philosophy of science: the reductionism debate and beyond -- Pt. 3. Genetics and the ethical, legal and sociological debate.
- 2014 SpringerBernard Puech, Jean-Jacques De Laey, Graham E. Holder, editors.Introduction to Molecular Genetics and Genetic Testing for Retinal Dystrophies -- Electrophysiological Testing -- Dark Adaptation -- Fluorescein Angiography -- Indocyanine Green Angiography -- Fundus Autofluorescence Imaging in Retinal Dystrophies -- Spectral-Domain Optical Coherence Tomography in Hereditary Retinal Dystrophies -- Inherited Stationary Disorders of the Retina -- Retinitis Pigmentosa and Allied Disorders -- Leber Congenital Amaurosis and Early-Onset Retinal Dystrophy -- Retinitis Punctata Albescens -- Usher Syndromes -- Cone and Cone-Rod Dystrophies -- Enhanced S-Cone Syndrome -- Chorioretinopathies: Choroideraemia and Gyrate Atrophy -- Late-Onset Retinal Dystrophy (LORD) -- Stargardt Disease -- The Bestrophinopathies -- Retinal Dystrophies Associated with the PRPH2 Gene -- Alström Syndrome -- Bardet-Biedl Syndrome -- Cohen Syndrome -- Juvenile Neuronal Ceroid Lipofuscinoses (JNCL) -- Adult Refsum Disease (ARD) -- Abetalipoproteinemia -- LCHAD Deficiency -- Jalili Syndrome -- Spinocerebellar Ataxia 7 -- Dominant Cystoid Macular Dystrophy -- Autosomal Dominant Stargardt-Like Macular Dystrophy (ELOVL4) -- Spastic Paraplegia and Retinal Degeneration: Kjellin Syndrome -- Autosomal Dominant Drusen -- Cuticular Drusen -- Extensive Macular Atrophy with Pseudodrusen-Like Appearance -- Congenital Hypotrichosis with Juvenile Macular Dystrophy -- Mitochondrial Retinopathies -- Sorsby Fundus Dystrophy -- Bietti Crystalline Corneoretinal Dystrophy -- Cystinosis -- Primary Oxalosis -- Alport Syndrome -- X-Linked Retinoschisis -- Paramacular Choriocapillaris Atrophy -- Exudative Vitreoretinopathy -- Stickler Syndrome -- Wagner Syndrome -- Incontinentia Pigmenti Type II (IP2) -- Ganglion Cell Diseases -- Pseudoxanthoma Elasticum -- Aicardi Syndrome -- Microcephaly and Chorioretinopathy With or Without Mental Retardation and Lymphedema -- Alagille Syndrome -- Future Therapies for Retinitis Pigmentosa.
- 2014 Springer Protocolsedited by Hans-Joachim Anders, Adriana Migliorini.Detection of RNA modifications by HPLC analysis and competitive ELISA / Gernot Nees, Andreas Kaufmann, and Stefan Bauer -- Enzymatic synthesis and purification of a defined RIG-I ligand / Marion Goldeck ... [et al.] -- Crystallization of mouse RIG-I ATPase domain : in situ proteolysis / Filiz Civril and Karl-Peter Hopfner -- Isolation of RIG-I-associated RNAs from virus-infected cells / Andreas Schmidt ... [et al.] -- Structure modeling of Toll-Like Receptors / Jing Gong and Tiandi Wei -- Nucleic acid recognition in dendritic cells / Alexander Heiseke, Katharina Eisenächer, and Anne Krug -- Viral nucleic acid recognition in human nonimmune cells : in vitro systems / Andrea Ribeiro and Markus Wörnle -- Analysis of nucleic acid-induced nonimmune cell death in vitro / Simone Romoli and Adriana Migliorini -- In vitro analysis of nucleic acid recognition in B lymphocytes / Saskia Ziegler and Isabelle Bekeredjian-Ding -- Mapping of optimal CD8 T cell epitopes / Julia Roider, Thomas Vollbrecht, and Rika Draenert -- Modular approach to suppression assays : TLR ligands, conditioned medium, and viral infection / Viktor H. Koelzer and David Anz -- MicroRNA methodology : advances in miRNA technologies/ Theresa Kaeuferle ... [et al.] -- Expression profiling by real-time quantitative polymerase chain reaction (RT-qPCR) / Maciej Lech and Hans-Joachim Anders -- Evaluating the role of nucleic acid antigens in murine models of systemic lupus erythematosus / Amanda A. Watkins, Ramon G. B. Bonegio, and Ian R. Rifkin -- Induction and analysis of nephrotoxic serum nephritis in mice / John M. Hoppe and Volker Vielhauer -- Isolation of intratumoral leukocytes of TLR-stimulated tumor-bearing mice / Moritz Rapp, David Anz, and Max Schnurr -- Bifunctional siRNAs for tumor therapy / Fanny Matheis and Robert Besch.
- 2013Yun Pei Sharon Goh.It has been proposed that allergic immune responses, like those mediated by type 2 immunity, evolved to protect the host from damage caused by environmental challenges, including toxins, xenobiotics, and helminth infections (1, 2). Despite some support for this hypothesis (3, 4), the underlying mechanisms by which type 2 innate responses orchestrate the regeneration of injured tissues remain largely unknown. Here, we demonstrate a requirement for type 2 innate immunity in regeneration of liver after partial hepatectomy and toxin-mediated injury. Injury to liver results in rapid recruitment of eosinophils, which secrete IL-4 to promote the proliferation of quiescent hepatocytes. Surprisingly, signaling via the IL-4R[alpha] in macrophages, which have been implicated in tissue repair (3-5), is dispensable for hepatocyte proliferation and liver regrowth after injury. Instead, IL-4 exerts its mitogenic actions by directly activating IL-4R[alpha] in hepatocytes. Our findings have thus uncovered an unexpected mechanism by which allergic type 2 innate immunity stimulates hepatocyte proliferation to promote liver regeneration.
- 2006 SpringerBernhard Haubold, Thomas Wiehe.
- 2007 CRCnetBASEAniruddha Datta, Edward R. Dougherty.Review of organic chemistry -- Energy considerations in biochemical reactions -- Proteins -- DNA -- Transcription and translation -- Chromosomes and gene regulation -- Genetic variation -- DNA technology -- Cell division -- Cell cycle control, cell death, and cancer -- Expression microarrays -- Classification -- Clustering -- Genetic regulatory networks -- Intervention -- External intervention based on optimal control theory.
- Accurate methods for ancestry and relatedness inference — Epigenetics protocols. 2nd ed. (153)
- Epigenetics, the environment, and children's health across lifespans — Introduction to genomic signal processing with control (153)
- Investigations in yeast functional genomics and molecular biology — Protein engineering protocols (153)
- Proteins and proteomics of Leishmania and Trypanosoma — Zebrafish-- genetics, genomics, and transcriptomics. Fourth edition. [4th ed.] (152)
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