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Genetics

  • Prof. Mark Reimers covers the best ways to design and interpret microarray gene expression experiments, including experiment design, pre-processing, exploratory analysis, normalization and statistical testing.
  • 25 years of p53 research 2005, Springer
  • 2D PAGE v. 1-2, 2008., Springer Protocols
    v. 2, 2008 Springer Protocols
    Isolation of mitochondria from plant cell culture / Etienne H. Meyer and A. Harvey Millar -- Isolation and preparation of choroplasts from Arabidopsis thaliana plants / Sybille E. Kubis, Kathryn S. Lilley, and Paul Jarvis -- Isolation of plant cell wall proteins / Elisabeth Jamet ... [et al.] -- Isolation and fractionation of the endoplasmic reticulum from castor bean (Ricinius communis) endosperm for proteomic analyses / William J. Simon, Daniel J. Maltman, and Antoni R. Slabas -- Cell wall fractionation for yeast and fungal proteomics / Aida Pitarch, Césa Nombela, and Concha Gil -- Sample preparation procedure for cellular fungi / Alois Harder -- Isolation and enrichment of secreted proteins from filamentous fungi / Martha L. Medina and Wilson A. Frnacisco -- Isolation and solubilization of cellular membrane proteins from bacteria / Kheir Zuobi-Hasona and L. Jeannine Brady -- Isolation and solubilization of gram-positive bacterial cell wall-associated proteins / Jason N. Cole, Steven P. Djordjevic, and Mark J. Walker -- Cell fractionation of parasitic protozoa / Wanderley de Souza, José Andrés-Morgado-Diaz, and Narcisa L. Cunha-e-SilvaVolume 2. Application of fluorescence dye saturation labeling for differential proteome analysis of 1,000 microdissected cells from pancreatic ductal adenocarcinoma precursoe lesions / Barbara Sitek ... [et al.] -- Albumin and immunoglobulin depletion of human plasma / Rosalind e. Jenkins ... [et al.] -- Multi-component immunoaffinity subtraction and reversed-phase chromatography of human serum / James Martosella and Nina Zolotarjova -- Immunoaffinity fractionation of plasma proteins by chicken IgY antibodies / Lei Huang and Xiangming Fang -- Proteomics of cerebrospinal fluid methods for sample processing / John E. Hale ... [et al.] -- Sample preparation of bronchoalveolar lavage fluid / Baptiste Leroy, Paul Falmagne, and Ruddy Wattiez -- Preparation of nasal secretions for peoteome analysis / Begona Casado, Paolo Iadarola, and Lewis K. Pannell -- Preparation of urine samples for proteomic analysis / Rembert Pieper -- Isolation of cytoplasmatic proteins from cultures cells for two-dimensional gel electrophoresis / Ying Wang, Jen-Fu Chiu, and Qing-Yu He -- Sample preparation of culture medium from Madin-Darby Canine Kidney cells / Daniel Ambort, Daniel Lottaz, and Erwin Sterchi -- Sample preparation for mass spectrometry analysis of formalin-fixed paraffin-embedded tissue proteomic analysis of formalin-fixed tissue / Nicolas A. Stewart and Timothy D. Veenstra -- Metalloproteomics in the molecular study of cell physiology and disease / Hermann-Josef Thierse, Stefanie Helm, and Patrick Pankert -- Protein extraction from green plant tissue / Ragnar Flengsrud -- The terminator a device for high-throughput extraction of plant material / B. M. van den Berg --Volume 1. Mechanical/physical methods of cell disruption and tissue homogenization / Stanley Goldberg -- Bacteria and yeast cell disruption using lytic enzymes / Oriana Salazar -- Sample solublization buffers for two-dimensional electrophoresis / Walter Weiss and Angelika Görg -- Quantitation of protein in samples prepared for 2-D electrophoresis / Tom Berkelman -- Removal of interfering substances in samples prepared for two-dimensional (2-D) electrophoresis / Tom Berkelman -- Protein concentration by hydrophilic interaction chromatography combined with solid phase extraction / Ulrich Schneider -- Difference gel electrophoresis based on lys/cys tagging / Reiner Westermeier and Burghardt Scheibe -- Isotope-coded two-dimensional maps: tagging with deuterated acrylamide and 2-vinylpyridine / Pier Giorgio Righetti, Roberto Sebastiano, and Attilio Citterio.
  • ADAR proteins : structure and catalytic mechanism /Rena A. Goodman, Mark R. Macbeth and Peter A. Beal --ADAR proteins : double-stranded RNA and Z-DNA binding domains /Pierre Barraud and Frédéric H.-T. Allain --Editing of neurotransmitter receptor and ion channel RNAs in the nervous system /Jennifer L. Hood and Ronald B. Emeson --Modulation of microRNA expression and function by ADARs /Bjorn-Erik Wulff and Kazuko Nishikura --Nuclear editing of mRNA 3'-UTRs /Ling-Ling Chen and Gordon G. Carmichael --Control of ADAR1 editing of hepatitis delta virus RNAs /John L. Casey --Bioinformatic approaches for identification of A-to-I editing sites /Eli Eisenberg --ADARs : viruses and innate immunity /Charles E. Samuel --Role of ADARs in mouse development /Carl R. Walkley, Brian Liddicoat and Jochen C. Hartner --Regulation and functions of ADAR in Drosophila /Simona Paro, Xianghua Li, Mary A. O'Connell and Liam P. Keegan.
  • Advanced bacterial genetics 2007, ScienceDirect
    Strain collections and genetic nomenclature / S.R. Maloy ... [et al.] -- Use of antibiotic-resistant transposons for mutagenesis / S.R. Maloy -- In vivo mutagenesis using EZ-Tn5 / J.R. Kirby -- Identification of essential genes in bacteria / D.R. Hillyard ... [et al.] -- Isolation of transposon insertions / S.R. Maloy -- Localized mutagenesis / S.R. Maloy -- Generation of deletions and duplications using transposons as portable regions of homology with emphasis on Mud and Tn10 transposons / K.T. Hughes -- Target-directed proteolysis in vivo / M. Eser ... [et al.] -- Sets of transposon-generated sequence-tagged mutants for structure-function analysis and engineering / B. Traxler ... [et al.] -- Using genomic microarrays to study insertional/transposon mutant libraries / D.N. Baldwin ... [et al.] -- Screening transposon mutant libraries using full-genome oligonucleotide microarrays / K. M. Winterberg ... [et al.] -- Creating recombination-activated genes and sequence-defined mutant libraries using transposons / L. Gallagher ... [et al.] -- Use of operon and gene fusions to study gene regulation in Salmonella / K.T. Hughes ... [et al.] -- Genomic screening for regulatory genes using the T-POP transposon / C. Lee ... [et al.] -- Recombineering: In vivo genetic engineering in E. coli, S. enterica, and beyond / J.A. Sawitzke ... [et al.] -- [lambda]-red genetic engineering in Salmonella enterica serovar Typhimurium / J.E. Karlinsey -- Probing nucleoid structure in bacteria using phage lambda integrase-mediated chromosome rearrangements / N. Garcia-Russell ... [et al.] -- Dissecting nucleic acid-protein interactions using challenge phage / S.R. Maloy ... [et al.] -- Mud-P22 / J.A. Crain ... [et al.] -- Phage metagenomics / V. Casas ... [et al.].
  • Intended as a companion to the Fundamentals of Forensic DNA Typing volume published in 2009, Advanced Topics in Forensic DNA Typing: Methodology contains 18 chapters with 4 appendices providing up-to-date coverage of essential topics in this important field and citation to more than 2800 articles and internet resources. The book builds upon the previous two editions of John Butler's internationally acclaimed Forensic DNA Typing textbook with forensic DNA analysts as its primary audience. This book provides the most detailed information written to-date on DNA databases, low-level DNA, validation, and numerous other topics including a new chapter on legal aspects of DNA testing to prepare scientists for expert witness testimony. Over half of the content is new compared to previous editions. A forthcoming companion volume will cover interpretation issues. Contains the latest information - hot-topics and new technologies Well edited, attractively laid out, and makes productive use of its four-color format Author John Butler is ranked as the number one "high-impact author in legal medicine and forensic science, 2001 to 2011" by ScienceWatch.com.
  • Repair of DNA Interstrand Cross-links Produced by Cancer Chemotherapeutic Drugs /Anderson T. Wang, Peter J. McHugh --DNA-PK, a Pharmacological Target in Cancer Chemotherapy and Radiotherapy? /Bernard Salles D.V.M., Ph.D. --Growth Factor Receptor Signaling, DNA Damage Response, and Cancer Cell Susceptibility to Chemotherapy and Relapses /Moulay Alaoui-Jamali, Amine Saad, Gerald Batist --The Relationship Between DNA-Repair Genes, Cellular Radiosensitivity, and the Response of Tumors and Normal Tissues to Radiotherapy /David Murray, Matthew Parliament --Important Roles of ERCC1 in DNA Repair and Targeted Therapy /Jennifer J. Hu, Joseph de la Garza --The Role of BRCA1 and BRCA2 in Anticancer Drug Therapy /Andrew Y. Shuen, Jorge S. Reis-Filho --DNA-PK in CLL Chemotherapy /L. Amrein, D. Davidson, R. Aloyz, L. Panasci --Poly(ADP) Ribose Polymerase at the Interface of DNA Damage Signaling and DNA Repair /Jana Krietsch, Michele Rouleau, Michel Lebel --Cellular Protection Against the Antitumor Drug Bleomycin /Dindial Ramotar Ph.D., Mustapha Aouida Ph.D. --ATR as a Therapeutic Target /Fiona K. Middleton, Nicola J. Curtin --Telomeres, Telomerase, and DNA Damage Response in Cancer Therapy /Raina A. Tamakawa, Helen B. Fleisig --RAD51 Is a Key Protein of DNA Repair and Homologous Recombination in Humans /Alexander V. Mazin Ph.D., Olga M. Mazina.
  • Microarrays in Gene Expression Studies, p. 1-29 -- Cleaning and Normalization, p. 31-59 -- Some Cluster Analysis Methods, p. 61-97 -- Clustering of Tissue Samples, p. 99-131 -- Screening and Clustering of Genes, p. 133-183 -- Discriminant Analysis, p. 185-220 -- Supervised Classification of Tissue Samples, p. 221-251 -- Linking Microarray Data with Survival Analysis, p. 253-266.
  • Recent studies demonstrated a key role of the androgen receptor in the development of castration-recurrent or -resistant prostate cancer (CRPC), which is deadly and in urgent need of more effective therapies. Understanding the functions of androgen-responsive genes and their regulation and deregulation in prostate cancer progression may lead to new approaches to prevent and treat prostate cancer patients. This book provides an up-to-date review of the overall androgen-responsive gene expression program and the regulation, function, and clinical relevance of both protein coding and non-coding androgen-responsive genes. Experts in the field of androgen action and prostate cancer research discussed the importance of DNA elements, chromatin structure, cellular signaling, and cell-cell interactions in the regulation of androgen-responsive genes in the context of prostate cancer progression, including the development of CRPC. This book is intended for individuals interested in cancer endocrinology and medical and healthcare professionals involved in prostate cancer research.
  • Omics & microarrays revisited -- The commercial microarrays -- Supports & surface chemistries -- The arraying processes -- Gene expression microarray-based applications -- Protein microarray applications -- Multiplex assays.
  • Bacterial artificial chromosomes v. 1-2, 2004., Springer Protocols
    v. 2, 2004 Springer Protocols
    v. 1. Library construction, physical mapping, and sequencing -- v. 2. Functional studies.
  • Bacterial chromatin 2010, Springer
  • Microbial genomes / Voon Loong Chan -- Evolution and origin of virulence isolates / Voon Loong Chan, Philip M. Sherman, and Billy Bourke -- Genomic approach to understanding of infectious disease mechanisms / Voon Loong Chan, Philip M. Sherman, and Billy Bourke -- Knockout and disease models in toll-like receptor-mediated immunity / Huey-Lan Huang and Wen-Chen Yeh -- Campylobacter from glycome to pathogenesis / John Kelly ... [et al.] -- Genomics of helicobacter species / Zhongming Ge and David B. Schauer -- The organization of leptospira at a genomic level / Dieter M. Bulach ... [et al.] -- Listeria monocytogenes / Keith Ireton -- Mycobacterial genomes / David C. Alexander and Jun Liu -- Mycoplasma / Yuko Sasaki -- Genome comparisons of diverse staphylococcus aureus strains / Martin J. McGavin -- Type III secretion, systems in yersinia pestis, and yersinia pseudotuberculosis / James B. Bliska, Michelle B. Ryndak, and Jens P. Grabenstein -- Genomics and the evolution of pathogenic vibrio cholerae / William S. Jermyn ... [et al.] -- Future directions of infectious disease research / Philip M. Sherman, Billy Bourke, and Voon Loong Chan -- Index.
  • Chapter 1. Estimation and Testing in Time-Course Microarray Experiments -- Chapter 2. Classification for Differential Gene Expression Using Bayesian Hierarchical Models -- Chapter 3. Applications of MOSS for Discrete Multi-Way Data -- Chapter 4. Nonparametric Bayesian Bioinformatics -- Chapter 5. Measurement Error and Survival Model for cDNA Microarrays -- Chapter 6. Bayesian Robust Inference for Differential Gene Expression -- Chapter 7. Bayesian Hidden Markov Modeling of Array CGH Data -- Chapter 8. Bayesian Approaches to Phylogenetic Analysis -- Chapter 9. Gene Selection for the Identification of Biomarkers in High-Throughput Data -- Chapter 10. Sparsity Priors for Protein - Protein Interaction Predictions -- Chapter 11. Learning Bayesian Networks for Gene Expression Data -- Chapter 12. In-Vitro to In-Vivo Factor Profiling in Expression Genomics -- Chapter 13. In-Vitro to In-Vivo Factor Profiling in Expression Genomics Machines -- Chapter 14. A Bayesian Mixture Model for Protein Biomarker Discovery -- Chapter 15. Bayesian Methods for Detecting Differentially Expressed Genes -- Chapter 16. Bayes and Empirical Bayes Methods for Spotted Microarray Data Analysis -- Chapter 17. Bayesian Classification Method for QTL Mapping.
  • Behavioral neurogenetics 2012, Springer
  • The regulation of gene expression -- The regulation of enzyme activity -- Structure and function of signal pathways -- Signaling by nuclear receptors -- G protein-coupled signal transmission pathways -- Intracellular messenger substance : second messengers -- Ser/Thr-specific protein kinases and protein phosphates -- Signal transmission via transmembrane receptors with tyrosine-specific protein kinase activity -- Signal transmission via ras proteins -- Intracellular signal transduction : the protein cascades of the MAP kinase pathways -- Membrane receptors with associated tyrosine kinase activity -- Other receptor classes -- Regulation of the cell cycle -- Malfunction of signaling pathways and tumorigenesis : oncogenes and tumor suppressor genes -- Apoptosis.
  • Similarity searching using BLAST / Kit J. Menlove, Mark Clement, and Keith A. Crandall -- Gene orthology assessment with OrthologID / Mary Egan ... [et al.] -- Multiple alignment of DNA sequences with MAFFT / Kazutaka Katoh, George Asimenos, and Hiroyuki Toh -- SeqVis : a tool for detecting compositional heterogeneity among aligned nucleotide sequences / Lars Sommer Jermiin ... [et al.] -- Selection of models of DNA evolution with jModelTest / David Posada -- Estimating maximum likelihood phylogenies with PhyML / Stéphane Guindon ... [et al.] -- Trees from trees : construction of phylogenetic supertrees using clann / Christopher J. Creevey and James O. McInerney -- Detecting signatures of selection from DNA sequences using datamonkey / Art F.Y. Poon, Simon D.W. Frost, and Sergei L. Kosakovsky Pond -- Recombination detection and analysis using RDP3 / Darren P. Martin -- CodonExplorer : an interactive online database for the analysis of codon usage and sequence composition / Jesse Zaneveld ... [et al.] -- Genetic code prediction for metazoan mitochondria with GenDecoder / Federico Abascal, Rafael Zardoya, and David Posada -- Computational gene annotation in new genome assemblies using GeneID / Enrique Blanco and Josep F. Abril -- Promoter analysis : gene regulatory motif identification with A-GLAM / Leonardo Mariño-Ramírez ... [et al.] -- Analysis of genomic DNA with the UCSC Genome Browser / Jonathan Pevsner -- Mining for SNPs and SSRs using SNPServer, dbSNP and SSR taxonomy tree / Jacqueline Batley and David Edwards -- Analysis of transposable element sequences using CENSOR and RepeatMasker / Ahsan Huda and I. King Jordan -- DNA sequence polymorphism analysis using DnaSP / Julio Rozas.
  • Preface xi -- Acknowledgments xiii -- 1 Introduction I -- 1.1 Hybridization 1 -- 1.2 Affymetrix GeneChip Technology 3 -- 1.3 Spotted Arrays 6 -- 1.4 Serial Analysis of Gene Expression (SAGE) 8 -- 1.5 Example: Affymetrix vs. Spotted Arrays 9 -- 1.6 Summary 11 -- 1.7 Further Reading 13 -- 2 Overview of Data Analysis 15 -- 3 Basic Data Analysis 17 -- 3.1 Absolute Measurements 17 -- 3.2 Scaling 18 -- 3.2.1 Example: Linear and Nonlinear Scaling 20 -- 3.3 Detection of Outliers 20 -- 3.4 Fold Change 21 -- 3.5 Significance 22 -- 3.5.1 Nonparametric Tests 24 -- 3.5.2 Correction for Multiple Testing 24 -- 3.5.3 Example I: t-Test and ANOVA 25 -- 3.5.4 Example II: Number of Replicates 26 -- 3.6 Summary 28 -- 3.7 Further Reading 29 -- 4 Visualization by Reduction of Dimensionality 33 -- 4.1 Principal Component Analysis 33 -- 4.2 Example 1: PCA on Small Data Matrix 35 -- 4.3 Example 2: PCA on Real Data 37 -- 4.4 Summary 37 -- 4.5 Further Reading 39 -- 5 Cluster Analysis 41 -- 5.1 Hierarchical Clustering 41 -- 5.2 K-means Clustering 43 -- 5.3 Self-Organizing Maps 44 -- 5.4 Distance Measures 45 -- 5.4.1 Example: Comparison of Distance Measures 47 -- 5.5 Normalization 49 -- 5.6 Visualization of Clusters 50 -- 5.6.1 Example: Visualization of Gene Clusters in -- Bladder Cancer 50 -- 5.7 Summary 50 -- 5.8 Further Reading 52 -- 6 Beyond Cluster Analysis 55 -- 6.1 Function Prediction 55 -- 6.2 Discovery of Regulatory Elements in Promoter -- Regions 56 -- 6.2.1 Example 1: Discovery of Proteasomal Element 57 -- 6.2.2 Example 2: Rediscovery of Mlu Cell Cycle -- Box (MCB) 57 -- 6.3 Integration of data 58 -- 6.4 Summary 59 -- 6.5 Further Reading 59 -- 7 Reverse Engineering of Regulatory Networks 63 -- 7.1 The Time-Series Approach 63 -- 7.2 The Steady-State Approach 64 -- 7.3 Limitations of Network Modeling 65 -- 7.4 Example 1: Steady-State Model 65 -- 7.5 Example 2: Steady-State Model on Real Data 66 -- 7.6 Example 3: Steady-State Model on Real Data 68 -- 7.7 Example 4: Linear Time-Series Model 68 -- 7.8 Further Reading 71 -- 8 Molecular Classifiers 75 -- 8.1 Classification Schemes 76 -- 8.1.1 Nearest Neighbor 76 -- 8.1.2 Neural Networks 76 -- 8.1.3 Support Vector Machine 76 -- 8.2 Example I: Classification of Cancer Subtypes 77 -- 8.3 Example II: Classification of Cancer Subtypes 78 -- 8.4 Summary 79 -- 8.5 Further Reading 79 -- 9 Selection of Genes for Spotting on Arrays 81 -- 9.1 Gene Finding 82 -- 9.2 Selection of Regions Within Genes 82 -- 9.3 Selection of Primers for PCR 83 -- 9.4 Selection of Unique Oligomer Probes 83 -- 9.4.1 Example: Finding PCR Primers for Gene -- AF105374 83 -- 9.5 Experimental Design 84 -- 9.6 Further Reading 84 -- 10 Limitations of Expression Analysis 87 -- 10.1 Relative VersusAbsoluteRNA Quantification 88 -- 10.2 Further Reading 88 -- 11 Genotyping Chips 91 -- 11.1 Example: NeuralNetworksfor GeneChipprediction 91 -- 11.2 Further Reading 93 -- 12 Software Issues and Data Formats 95 -- 12.1 Standardization Efforts 96 -- 12.2 Standard File Format 97 -- 12.2.1 Example: Small Scripts in Awk 97 -- 12.3 Software for Clustering 98 -- 12.3.1 Example: Clustering with ClustArray 99 -- 12.4 Software for Statistical Analysis 99 -- 12.4.1 Example: StatisticalAnalysis with R 99 -- 12.4.2 The affyR Software Package 103 -- 12.4.3 Commercial Statistics Packages 103 -- 12.5 Summary 103 -- 12.6 Further Reading 104 -- 13 Commercial Software Packages 105 -- 14 Bibliography 109 -- Index 123.
  • When quantum mechanics was first proposed a century ago, nobody could have anticipated how deeply it would affect our lives. Today, we are connected and powered through devices whose existence is predicated on the basic principles of this strange physics. Not even the biological sciences have escaped its reach. As scientists query the deepest mysteries of the living world, the physical scales probed and the types of questions asked are increasingly blurring the lines between biology and physics. The hybrid field of biophysics represents the new frontier of the 21st century. The ribosome has been at the heart of three Nobel Prizes. Understanding its essential nature and how it interacts with other proteins and nucleic acids to control protein synthesis has been one of the central foundations in our understanding of the biology at the molecular level. With the advent of atomic scale structures, methods to visualize and separate individual molecules, and the computational power to model the complex interactions of over a million atoms at once, our understanding of how gene expression is controlled at the level of protein translation is now deeply ensconced in the biophysical realm. This book provides a premier resource to a wide audience, whether it be the general reader seeking a broad view of the field, a clinician interested in the role of protein translation in human disease, the bench researcher looking for state-of-the-art technologies, or computational scientists involved in cutting edge molecular modeling.
  • "Genes and environment. Biology and behavior. Nature and nurture. The terminology may be clear-cut, but the processes themselves are far from simple: unlike the direct cause-and-effect dichotomies of past frameworks, researchers now recognize these family-based connections as multifaceted, transactional, and emergent. [This book] aims at illuminating a multiplicity of approaches and methodologies for studying family dynamics, to match the complex interplay of physiological factors, environmental challenges, and behavioral adaptations that characterize family life and development. Chapters illustrate physical and social influences on parenting, childhood, adolescence, fertility, and family formation, providing analytical frameworks for understanding key areas such as family behavior, health, development, and adaptation to contextual stressors."--Book jacket.
  • Identification of fungal pathogenicity genes by Agrobacterium tumefaciens-mediated transformation / Karunakaran Maruthachalam ... [et al.] -- The genetics and molecular biology of carotenoid biosynthesis in mucorales / Catalina Sanz, Mahdi Shahriari, and Arturo P. Eslava -- Induction and repression of carbohydrate degrading enzymes in fungi with special reference to their coding genes / Pauline Walsh, Alan Hernon, and Anthonia O'Donovan -- Involvement of ADH1, IPT1, and PMT genes in Candida albicans pathogenesis / Mahmoud Rouabhia and Mahmoud Ghannoum -- Enhanced resistance to fungal pathogens in plants through selective utilization of useful fungal genes / B.K. Sarma ... [et al.] -- Genes encoding penicillin and cephalosporin biosinthesis in Acremonium chrysogenum : two separate clusters are required for cephalosporin production / Juan-Francisco Martøn, Carlos Garcia-Estrada, and Ricardo V. Ullon -- A review of the fungal B-galactosidase gene and its biotechnological applications / Anne G. Lydon -- Trichoderma genes involved in interactions with fungi and plants / Mala Mukherjee -- Use of luciferases as a tool to analyze fungal physiology in association with gene transcription / David M. Arana and Jess Pla --Fungal genes and their respective enzymes in industrial food, bio-based, and pharma applications / Marco van den Berg ... [et al.] -- Fungal metacaspases : an overview / Anthonia O'Donovan, Finola E. Cliffe, and Mary C. Shier -- Signaling molecules in the Arbuscular mycorrhizal fungi / Mohammad Miransari -- Role of pathogenic genes of Fusarium oxysporum, coding cell wall degrading enzymes during wilt infection in plants / Vijai Kumar Gupta, Maria Tuohy, and A. Manimaran -- Engineering fungal expression systems : recombinant expression of two class I alpha-1, 2-mannosidases from the filamentous fungus Aspergillus nidulans / C. Joshua Eades and William E. Hintz -- PCR-diagnostic of Septoria nodorum berk : aggresivenes in wheat tissue / I.V. Maksimov and A.Sh. Valeev -- Detection of toxigeneic and pathogenic fungi targeting metabolic pathway genes / Venkataramana Mudili ... [et al.] -- Pathogenicity genes in entomopathogenic fungia used as biopesticides / K. Uma Devi ... [et al.].
  • Executive summary -- Report of the working-group meeting / Christos Louis and Bart G.J. Knols -- Review of previous applications of genetics to vector control / Chris F. Curtis -- Genomics and expected benefits for vector entomology / Christos Louis -- Genetic approaches for malaria control / Marcelo Jacobs-Lorena -- Current thoughts about the integration of field and laboratory sciences in genetic control of disease vectors / Thomas W. Scott -- Genetic approaches in Aedes aegypti for control of dengue: an overview / Kenneth Olson .... [et al.] -- Malaria and dengue vector biology and control in West and Central Africa / Didier Fontenille and Pierre Carnevale -- Malaria and dengue vector biology and control in Southern and Eastern Africa / Maureen Coetzee -- Malaria and dengue vector biology and control in Southeast Asia / Pattamaporn Kittayapong -- Malaria and dengue vector biology and control in Latin America / Mario H. Rodriguez -- Transition from the laboratory to the field and effective interplay / Christos Louis -- Evaluation of drive mechanisms (including transgenes and drivers) in different environmental conditions and genetic backgrounds / Anthony A. James ... [et al.] -- Tools for monitoring the genetic structure and stability of mosquito populations / Gregory C. Lanzaro, Sergey Nuzhdin and Frederic Tripet -- What are relevant assays for refractoriness / George K. Christophides ... [et al.] -- Fitness studies: developing a consensus methodology / Thomas W. Scott ... [et al.] --Mosquito mating behaviour / Willem Takken ... [et al.] -- Pathogen evolution issues in genetically modified mosquito vector strategies / Mario H. Rodriquez -- Models to investigate some issues regarding the feasibility of driving refractoriness genes into mosquito vector populations / Chris F. Curtis -- Identification and characterization of field sites for genetic control of disease vectors / Bart G.J. Knols and Hervé Bossin -- Application of genetically modified mosquitoes in national vector control programmes: thoughts on integrated control / Abraham Mnzava ... [et al.] -- Entomological correlates of epidemiological impacts: how do we know it is working? / Andrew Githeko -- Ethical, legal and social issues in the use of genetically modified vectors for disease control / Yeya T. Touré and Lucien Manga.
  • Brutes or angels 2013, ebrary
    A guide to the rapidly progressing Age of Biotechnology, Brutes or Angels provides basic information on a wide array of new technologies in the life sciences, along with the ethical issues raised by each. With stem cell research, Dolly the cloned sheep, in vitro fertilization, age retardation, and pharmaceutical mind enhancement, humankind is now faced with decisions that it has never before had to consider. The thoughtfulness, or lack of it, that we bring to those decisions will largely determine the future character of the living world.
  • C. elegans 2006, Springer Protocols
    An overview of C. elegans biology / Kevin Strange -- Comparative genomics in C. elegans, C. briggsae, and other Caenorhabditis species / Avril Coghlan, Jason E. Stajich, and Todd W. Harris -- WormBase: methods for data mining and coparative genomics / Todd W. Harris and Lincoln D. Stein -- C. elegans deletion mutant screening / Robert J. Barstead and Donald G. Moerman -- Insertional mutagenesis in C. elegans using the drosophila transposon Mos1: a method for the rapid identification of mutated genes / Jean-Louis Bessereau -- Single nucleotide polymorphism mapping / M. Wayne Davis and Marc Hammarlund -- Creation of transgenic lines using microparticle bombardment methods / Vida Praitis -- Construction of plasmids for RNA interference and in vitro transcription of double-stranded RNA / Lisa Timmons -- Delivery methods for RNA interference in C. elegans / Lisa Timmons -- Functional genomic approaches in C. elegans / Todd Lamitina -- Assays for toxicity studies in C. elegans with Bt crystal proteins / Larry J. Bischof, Danielle L. Huffman, and Raffi V. Aroian -- Fluorescent reporter methods / Harald Hutter -- Electrophysiological analysis of neuronal and muscle function in C. elegans / Michael M. Francis and Andres Villu Maricq -- Sperm and oocyte isolation methods for biochemical and proteomic analysis / Michael A. Miller -- Preservation of C. elegans tissue via high-pressure freezing and freeze-substitution for ultrastructural analysis and immunocytochemistry / Robby M. Weimer -- Intracellular pH measurements in vivo using green fluorescent protein variants / Keith Nehrke -- Automated imaging of C. elegans behavior / Christopher J. Cronin, Zhaoyang Feng, and William R. Schafer -- Intracellular Ca2+ imaging in C. elegans / Rex A. Kerr and William R. Schafer -- In vitro culture of C. elegans somatic cells / Kevin Strange and Rebecca Morrison -- Techniques for analysis, sorting, and dispensing of C. elegans on the COPAS flow-sorting system / Rock Pulak.
  • Caenorhabditis elegans. 2nd ed. 2011, ScienceDirect
    Pt.I Genetics and functional genomics :Mapping mutations in C. elegans /Eric J. Lambie --Specialized chromosomes and their uses in caenorhabditis elegans /Martin R. Jones,Zoe Lohn,Ann M. Rose --Genome engineering by transgene-instructed gene conversion in C. elegans /Valérie J.P. Robert,Jean-Louis Bessereau --RNAi methods and screening : RNAi based high-throughput genetic interaction screening /Patricia G. Cipriani,Fabio Piano --Dissection of genetic pathways in C. elegans /Zheng Wang,David R. Sherwood --Pt.II Molecular biology and biochemistry :Transgenesis in C. elegans /Vida Praitis,Morris F. Maduro --RNA processing in C. elegans /J. Jason Morton,Thomas Blumenthal --Analysis of microRNA expression and function /Priscilla M. Van Wynsberghe,Shih-Peng Chan,Frank J. Slack,Amy E. Pasquinelli --In situ hybridization of embryos with antisense RNA probes /Gina Broitman-Maduro,Morris F. Maduro --Gene-centered regulatory network mapping /Albertha J.M. Walhout --Affinity purification of protein complexes in C. elegans /Esther Zanin,Julien Dumont,RetoGassmann,Iain Cheeseman,Paul Maddox,Shirin Bahmanyar,Ana Carvalho,Sherry Niessen,John R. Yates III,Karen Oegema,Arshad Desai --Pt.III Development :Cell indentification and cell lineage analysis /Claudiu A. Giurumescu,Andrew D. Chisholm --Thegenetics and cell biology of fertilization /Brian D. Geldziler,Mathew R. Marcello,Diane C. Shakes,Andrew Singson --Imaging embryonic morphogenesis in C. elegans /Jeff Hardin --Molecular and genetic approaches for the analysis of C. elegans neuronal development /Dong Yan,Yishi Jin --Methods for evaluating the caenorhabditis elegans dauer state : standard dauer-formation assay using synthetic daumones and proteomic analysis of O-GIcNAc modifications /Jeeyong Lee,Kwang-Youl Kim,Kyoe-Jin Joo,Keekyeong Kim,Pan-Young Jeong,Young-Ki Paik.
  • Cancer genomics 2013, Springer
    Genomic Pathology of Lung Cancer /Kenneth J. Craddock, Shirley Tam, Chang-Qi Zhu, Ming-Sound Tsao --Understanding Melanoma Progression by Gene Expression Signatures /J. Tímár, T. Barbai, B. Győrffy, E. Rásó --Prognostic Testing in Uveal Melanoma /Michael Zeschnigk, Dietmar R. Lohmann --Capturing and Deciphering the Molecular Signatures of Head and Neck Cancer /Thomas J. Belbin, Roberto A. Lleras, Richard V. Smith --Predictive and Prognostic Biomarkers for Colorectal Cancer /Lara Lipton, Michael Christie, Oliver Sieber --Expression Profiling of Hepatocellular Carcinoma /Rosina Maria Critelli, Elisabetta Cariani, Erica Villa --Kidney Cancer Genomics: Paving the Road to a New Paradigm of Personalized Medicine /George M. Yousef, Nicole M. A. White, Andrew H. Girgis --Pancreatic Cancer Genomics /Vincenzo Corbo, Andrea Mafficini, Eliana Amato, Aldo Scarpa --Breast Cancer Genomics: From Portraits to Landscapes /Ulrich Pfeffer, Valentina Mirisola, Alessia Isabella Esposito --Genomic Landscape of Ovarian Cancer /Delia Mezzanzanica, Loris De Cecco, Marina Bagnoli, Patrizia Pinciroli --Genetics of Endometrial Carcinoma /M. Angeles López-García, Begoña Vieites, M. Angeles Castilla --Usefulness of Molecular Biology in Follicular-Derived Thyroid Tumors: From Translational Research to Clinical Practice /Alexandre Bozec, Marius Ilie, Paul Hofman --Sarcomas Genetics: From Point Mutation to Complex Karyotype, from Diagnosis to Therapies /Frédéric Chibon, Alain Aurias, Jean-Michel Coindre --Novel Molecular Acquisitions in Leukemias /Sabina Chiaretti, Robin Foà --Where Do We Stand in the Genomics of Lymphomas? /Francesco Bertoni, Zhi-Ming Li, Emanuele Zucca --The Genomics of Multiple Myeloma and Its Relevance in the Molecular Classification and Risk Stratification of the Disease /Antonino Neri, Luca Agnelli --Genome-Wide Analysis and Gene Expression Profiling of Neuroblastoma: What Contribution Did They Give to the Tumor Treatment? /Gian Paolo Tonini.
  • Cancer genomics 2014, ScienceDirect
    Cancer Genomics addresses how recent technological advances in genomics are shaping how we diagnose and treat cancer. Built on the historical context of cancer genetics over the past 30 years, the book provides a snapshot of the current issues and state-of-the-art technologies used in cancer genomics. Subsequent chapters highlight how these approaches have informed our understanding of hereditary cancer syndromes and the diagnosis, treatment and outcome in a variety of adult and pediatric solid tumors and hematologic malignancies. The dramatic increase in cancer genomics research and ever-increasing availability of genomic testing are not without significant ethical issues, which are addressed in the context of the return of research results and the legal considerations underlying the commercialization of genomic discoveries. Finally, the book concludes with "Future Directions", examining the next great challenges to face the field of cancer genomics, namely the contribution of non-coding RNAs to disease pathogenesis and the interaction of the human genome with the environment. Tools such as sidebars, key concept summaries, a glossary, and acronym and abbreviation definitions make this book highly accessible to researchers from several fields associated with cancer genomics.Contributions from thought leaders provide valuable historical perspective to relate the advances in the field to current technologies and literature.
  • Cancer genomics and proteomics 2007, Springer Protocols
    Reciprocal subtraction differential RNA display (RSDD) : an efficient technology for cloning differentially expressed genes / Devanand Sarkar, Dong-chul Kang, and Paul B. Fisher -- Cloning differentially expressed genes using rapid subtraction hybridization (RaSH) / Habib Boukerche ... [et al.] -- The application of differential display as a gene profiling tool / Ken Chien-Neng Chang ... [et al.] -- Serial analysis of gene expression (SAGE) / Fred van Ruissen and Frank Baas -- Gene expression profile analysis of tumors / Katia Basso and Riccardo Dalla-Favera -- cDNA microarray and bioinformatic analysis of nuclear factor [kappa]B related genes in squamous cell carcinoma / Zhong Chen ... [et al.] -- Gene profiling uncovers retinoid target genes / Yan Ma ... [et al.] -- Complete open reading frame (C-ORF) technique : rapid and efficient method for obtaining complete protein coding sequences / Dong-chul Kang and Paul B. Fisher -- Chromatin immunoprecipitation assays : molecular analysis of chromatin modification and gene regulation / Piyali Dasgupta and Srikumar P. Chellappan -- Manipulating genes and gene copy number by bacterial artificial chromosome transfection / Stephanie F. Phelps, Sharon Illenye, and Nicholas H. Heintz -- Molecular cytogenetic applications in analysis of the cancer genome / Pulivarthi H. Rao, Subhadra V. Nandula, and Vundavalli V. Murty -- Monitoring methylation and gene expression in cancer / Hetty Carraway and James Herman -- The use of phage display peptide libraries for basic and translational research / Renee Brissette and Neil I. Goldstein -- Yeast and mammalian two-hybrid systems for studying protein-protein interactions / Shu-ichi Matsuzawa and John C. Reed -- Ribonomic and short hairpin RNA gene silencing methods to explore functional gene programs associated with tumor growth arrest / Timothy E. Baroni ... [et al.] -- Surface-epitope masking (SEM) : an immunological subtraction approach for developing monoclonal antibodies targeting surface-expressed molecules / Neil I. Goldstein and Paul B. Fisher -- Approaches for monitoring signal transduction changes in normal and cancer cells / Paul Dent ... [et al.] -- PKR in innate immunity, cancer, and viral oncolysis / Siddharth Balachandran and Glen N. Barber -- Analysis of transformation and tumorigenicity using mouse embryonic fibroblast cells / Hong Sun and Reshma Taneja -- Analysis of growth properties and cell cycle regulation using mouse embryonic fibroblast cells / Hong Sun, Neriman Tuba Gulbagci, and Reshma Taneja -- Reverse phase protein microarrays for monitoring biological responses / Virginia Espina ... [et al.] -- Protein crystallization / Champion Deivanayagam, William J. Cook, and Mark R. Walter.
  • The ouput of eukaryotic genomes is much more complex than expected. Genes produce different variants of RNAs from multiple promoters. One of the ultimate targets of biological analysis is to establish a relationship between the messenger RNAs that are transcribed from the genome and the genomic regions that control their expression - the promoters - in order to decipher the networks that regulate gene expression and the transcription factors that act as master regulators of transcriptional control. Novel technologies have recently appeared that allow deciphering of transcriptional network, based on the identification of the starting site of gene transcription, with the simultaneous measurement of expression level and identification of the promoter elements. These tagging technologies (including cap-analysis gene expression - CAGE - and others) are further boosted from the development of the novel generation of sequencing instruments, which allow transcriptional profiling by sequencing at the cost of microarray experiments. This book is a guide for users of new technologies, as it includes accurately proven protocols, allowing readers to prepare their samples for experiments. Additionally, it provides a guide for the bioinformatics tools that are available for the analysis of the obtained tags, including the design of the software, the sources and web information where they can be downloaded. Finally, the book provides examples of the application of these technologies to identify promoters, annotate genomes, identify new RNAs and reconstruct models of transcriptional control. Although examples mainly regard mammalians, the discussion expands to other groups of eukaryotes, where these approaches are complementing genome sequencing.
  • 1. A Recent Breakthrough in the CCN Field: Functional Interactions Between CCN2 and CCN3 are Uncovered / Bernard Perbal -- 2. Report on the Fifth International Workshop on the CCN Family of Genes / A. E. Irvine, B. Perbal, and H. Yeger -- 3. Asking the Right Questions: What Can the Structure of the CCN Protein Domains Tell Us? / Kenneth P. Holbourn, Bernard Perbal, and K. Ravi Acharya -- 4. Nucleophosmin/B23: A Multifunctional Regulator that Determines the Fate of CCN2 mRNA / Satoshi Kubota, Yoshiki Mukudai, Harumi Kawaki, Seiji Kondo, Takanori Eguchi, Kumi Sumiyoshi, Toshihiro Ohgawara, Tsuyoshi Shimo, and Masaharu Takigawa -- 5. The CCN Genes as the “Master” Regulators of Angiogenesis, Vasculogenesis, Fibrogenesis and Cell Differentiation/Fate Specification in Mechanical Force-Driven Developmental Processes and Pathological Events / Mary Hanna and Brahim Chaqour -- 6. A Monoclonal Antibody Approach to CCN5 Domain Analysis / Lan Wei, Frank McKeon, Joshua W. Russo, Joan Lemire, and John Castellot -- 7. Matricellular Protein CCN2 Produced by Tubular Epithelial Cells Plays a Pivotal Role in Renal Fibrogenesis / Hirokazu Okada, Tsutomu Inoue, and Hiromichi Suzuki -- 8. Cooperative Regulation of Cell Proliferation and Differentiation by CCN2 and CCN3 / Masaharu Takigawa, Harumi Kawaki, Satoshi Kubota, Karen M. Lyons, and Bernard Perbal -- 9. The Role of CCN3 in Mesenchymal Stem Cells / Ken-Ichi Katsube -- 10. Role of Connective Tissue Growth Factor in Cardiac Fibrosis / Daiji Kawanami, Saptarsi M. Haldar, and Mukesh K. Jain -- 11. Gene Expression of CCN Family Members in Young and Aged Human Skin In Vivo / Taihao Quan, Sharon Shin, Zhaoping Qin, and Gary J. Fisher -- 12. Global Expression Profiling Reveals a Role for CTGF/CCN2 in Lactogenic Differentiation of Mouse Mammary Epithelial Cells / Weihan Wang, Cynthia Jose, Nicholas Kenney, Bethanie Morrison, and Mary Lou Cutler -- 13. CCN3 (NOV): A Negative Regulator of CCN2 (CTGF) Activity and an Endogenous Inhibitor of Fibrosis in Experimental Diabetic Nephropathy / Bruce. L. Riser, Feridoon Najmabadi, Bernard Perbal, Jo Ann Rambow, Melisa L. Riser, Ernest Sukowski, Herman Yeger, Sarah C. Riser, and Darryl R. Peterson -- 14. Inhibitors of Connective Tissue Growth Factor (CCN2)-Mediated Fibrogenesis: Underlying Mechanisms and Prospects for Anti-fibrotic Therapy / David R. Brigstock -- 15. CCN3 Promotes Melanoma Progression by Regulating Integrin Expression, Adhesion and Apoptosis Induced by Cytotoxic Drugs / Viviana Vallacchi, Maria Daniotti, Annamaria De Filippo, Licia Rivoltini, Bernard Perbal, and Monica Rodolfo -- 16. CCN3: A NOVel Growth Factor in Leukaemia / Lynn McCallum and Alexandra E Irvine -- 17. Prognostic Relevance of CCN3 in Bone Sarcomas / Bernard Perbal, Noureddine Lazar, Diana Zambelli, Monia Zuntini, Massimo Serra, Jose Antonio Lopez-Guerrero, Antonio Llombart-Bosch, Piero Picci, and Katia Scotlandi -- 18. CCN6 Regulates Breast Cancer Growth and Invasion Through Modulation of IGF Signaling and Epithelial to Mesenchymal Transition / Anupama Pal, Wei Huang, and Celina G. Kleer -- 19. Novel Transcriptional Regulation of CCN2/CTGF by Nuclear Translocation of MMP3 / Takanori Eguchi, Satoshi Kubota, Kazumi Kawata, Yoshiki Mukudai, Junji Uehara, Toshihiro Ohgawara, Soichiro Ibaragi, Akira Sasaki, Takuo Kuboki, and Masaharu Takigawa -- Fifth International Workshop on the CCN Family of Genes: Abstracts and Posters October 18-22, 2008.
  • Cell line development 2009, Springer
    Mammalian cell lines command an effective monopoly for the production of therapeutic proteins that require post-translational modifications. This book deals with the methodology involved in the development of cell lines and the cell engineering approach that can be employed to enhance productivity and improve cell function.
  • Cell-based microarrays 2011, Springer Protocols
    Cell-Based Microarrays: Overview / Ella Palmer -- Cell-Based Co-transfection Microarrays for Use with HEK293T Cells on a Poly d-Lysine-Coated Polystyrene Microplate / Meenal Soni, Fang Lai -- Large-Scale Cell-Based Microarrays and Their Use with HEK293T Cells and Downstream Apoptotic Assays / Ella Palmer, Tom C. Freeman -- A Novel Fluorescent Transcriptional Reporter for Cell-Based Microarray Assays / Tanya M. Redmond, Michael D. Uhler -- High-Throughput Subcellular Protein Localization Using Transfected-Cell Arrays: Subcellular Protein Localization Using Cell Arrays / Yuhui Hu, Michal Janitz -- Cell Arrays for the Measurement of Organelle Dynamics in Living Cells / Holger Erfle, Tautvydas Lisauskas, Christoph Claas, Jürgen Reymann, Vytaute Starkuviene -- High-Throughput Immunofluorescence Microscopy Using Yeast Spheroplast Cell-Based Microarrays / Wei Niu, G. Traver Hart, Edward M. Marcotte -- Cell-Based Microarrays of Infectious Adenovirus Encoding Short Hairpin RNA (shRNA) / Hansjürgen Volkmer, Frank Weise -- Reverse Transfected Cell Microarrays in Infectious Disease Research / Andreas Konrad, Ramona Jochmann, Elisabeth Kuhn, Elisabeth Naschberger, Priya Chudasama, Michael Stürzl -- Transfected Cell Microarrays for the Expression of Membrane-Displayed Single-Chain Antibodies / Baochuan Lin, James B. Delehanty -- Blood Cell Capture on Antibody Microarrays and Monitoring of the Cell Capture Using Surface Plasmon Resonance Imaging / Yoann Roupioz, Sarah Milgram, André Roget, Thierry Livache -- Immobilized Culture and Transfection Microarray of Non-adherent Cells / Satoshi Yamaguchi, Erika Matsunuma, Teruyuki Nagamune -- Plasma Polymer and PEG-Based Coatings for DNA, Protein and Cell Microarrays / Andrew L. Hook, Nicolas H. Voelcker, Helmut Thissen -- Polymer Microarrays for Cellular High-Content Screening / Salvatore Pernagallo, Juan J. Diaz-Mochon -- High-Throughput Analyses of Gene Functions on a Cell Chip by Electroporation / Koichi Kato, Hiroo Iwata -- Microfluidic Image Cytometry / Ken-ichiro Kamei, Jing Sun, Hsian-Rong Tseng, Robert Damoiseaux.
  • Chemical genomics 2006, Springer
  • Chemical genomics 2005, Springer Protocols
  • Ch. 1. Utilizing small molecules in chemical genomics : toward high-throughput (HT) approaches / György Dormán and Ferenc Darvas -- ch. 2. Development and application of novel analytical methods in lipidomics / Yuqin Wang ... [et al.] -- ch. 3. From chemical genomics to chemical proteomics : the power of microarray technology / Sándor Spisák and András Guttman -- ch. 4. Genomic and proteomic biomarkers in the drug R&D process / László Takács, Anna Debreceni, and István Kurucz -- ch. 5. Quo vadis biomedical sciences in the omics era : toward computational biology and medicine / András Falus ... [et al.] -- ch. 6. Novel chemogenomic approaches to drug design / Didier Rognan.
  • Chromosomal mutagenesis 2008, Springer Protocols
    Biallelic gene knockouts in Chinese hamster ovary cells / Naoko Yamane-Ohnuki, Kazuya Yamano, and Mitsuo Satoh -- Highly proficient gene targeting by homologous recombination in the human pre-B cell line Nalm-6 / Noritaka Adachi, Aya Kurosawa, and Hideki Koyama -- Robust cell line development using meganucleases / Jean-Pierre Cabaniols and Frédéric Pâques -- Design and testing of zinc finger nucleases for use in mammalian cells / Matthew Porteus -- Gene targeting in Drosophila and Caenorhabditis elegans with zinc-finger nucleases / Dana Carroll ... [et al.] -- Orpheus recombination : a comprehensive bacteriophage system for murine targeting vector construction by transplacement / Knut Woltjen ... [et al.] -- Transposition -mediated mutagenesis in somatic cells : identification of transposon-genomic DNA junctions / David A. Largaespada and Lara S. Collier -- Insertional mutagenesis of the mouse germline with sleeping beauty transposition / Junji Takeda, Zsuzsanna Izsvák, and Zoltán Ivics -- Conditional gene trapping using the FLEx system / Thomas Floss and Frank Schnütgen -- Steps toward targeted insertional mutagenesis with class II transposable elements / Sareina Chiung-Yuan wu ... [et al.] -- Targeting integration of the Saccharomyces Ty5 retrotransposon / Troy L. Brady, Clarice L. Schmidt, and Daniel F. Voytas -- Site-specific chromosomal integration mediated by [phi]C31 integrase / Annahita Keravala and Michele P. Calos-- Triplex-mediated gene modification / Erica B. Schleifman, Joanna Y.Chin, and Peter M. Glazer -- Allelic exchange of unmarked mutations in Mycobacterium tuberculosis / Martin S. Pavelka, Jr. -- Mycobacterial recombineering Julia C. van Kessel and Graham F. Hatfull -- Chromosomal engineering of Clostridium perfringens using group II introns / Phalguni Gupta and Yue Chen.
  • Mechanical approaches to elucidate mechanisms of chromosome condensation at the nano- and microlevels / Kazushige Kawabata ... [et al.] -- Development of novel AFM probes for chromosome manipulation / Masato Saito, Gen Hashiguchi and Eiichi Tamiya -- Microchamber array-based sequence-specific DNA detection from a single chromosome via trace volume PCR / Masato Saito and Eiichi Tamiya -- On-chip chromosome sorter using electric and magnetic fields / Takahito Inoue ... [et al.] -- Fluorescence microscopy for analysis of chromosome dynamics / Sachihiro Matsunaga -- Fluorescence in situ hybridization (FISH) as a tool for comparative genomics: application of FISH to studies of chromosome evolution in vertebrates / Yoichi Matsuda ... [et al.] -- Immunocytochemistry for analyzing chromosomes / Osamu Hoshi ... [et al.] --Proteome analysis of human metaphase chromosomes / Kiichi Fukui and Susumu Uchiyama -- Antipeptide antibodies for examining the conformation and molecular assembly of an intracellular protein / Masatoshi Nakagawa ... [et al.] -- Structure and interactions of the imitation SWI-type chromatin-remodeling complex, ATP-dependent chromatin-assembly facter / Tadayasu Ohkubo ... [et al.] -- Dynamic and functional analysis of chromosomal proteins / Nobuko Ohmido ... [et al.] -- Development of a sustainable chromosome imaging database / Kenji Taniguchi ... [et al.] -- Image database and image analysis of chromosome information / Shin-ichi Toyabe ... [et al.].Transmission and scanning electron microscopy of mammalian metaphase chromosomes / Sumire Inaga, Keiichi Tanaka and Tatsuo Ushiki -- Atomic force microscopy of human chromosomes in relation to their higher-order structure / Osamu Hoshi, Daisuke Fukushi and Tatsuo Ushiki -- Mechanism of higher-order chromatin folding revealed by AFM observation of in vitro reconstituted chromatin / Kohji Hizume ... [et al.] -- Scanning near-field optical/atomic force microscopy as a tool for simultaneous specification of chromosome topography and particular gene location on the nanometer scale / Motoharu Shichiri ... [et al.] -- Isolation of human and plant chromosomes as nanomaterials / Susumu Uchiyama, Tomoyuki Doi and Kiichi Fukui --
  • Circadian rhythms are such an innate part of our lives that we rarely pause to speculate why they even exist. Perhaps this is the reason why in the medical practice the circadian variability of hormones, metabolites, physiological behaviors or the relevance of time in the presence or absence of different pathologies, have been practically ignored in the past. Some studies have suggested that the disruption of the circadian system may be cause for obesity and manifestations of Metabolic Syndrome (MetS). Shift-work, sleep-deprivation and bright-light-exposure at night are related to increased adiposity (obesity) and prevalence of MetS. Chronobiology and Obesity examines recent advances that have led to researchers to find the relevant link which exists between chronobiology and obesity, but, as it is emphasized throughout the book, there is much more that needs to be explored between the connection.
  • Clinical applications of PCR. 2nd ed. 2006, Springer Protocols
    Clinical applications of plasma Epstein-Barr virus DNA analysis and protocols for the quantitative analysis of the size of circulating Epstein-Barr virus DNA / K.C. Allen Chan and Y.M. Dennis Lo -- Molecular analysis of circulating RNA in plasma / Nancy B.Y. Tsui, Enders K.O. Ng, and Y.M. Dennis Lo -- Molecular analysis of mitochondrial DNA point mutations by polymerase chain reaction / Lee-Jun C. Wong, Bryan R. Cobb, and Tian-Jian Chen -- Novel applications of polymerase chain reaction to urinary nucleic acid analysis / Anatoly V. Lichtenstein ... [et al.] -- Detection and quantitation of circulating plasmodium falciparum DNA by polymerase chain reaction / Shira Gal and James S. Wainscoat -- Molecular diagnosis of severe acute respiratory syndrome / Enders K.O. Ng and Y.M. Dennis Lo -- Genomic sequencing of the severe acute respiratory syndrome-coronavirus / Stephen S.C. Chim, Rossa W.K. Chiu, and Y.M. Dennis Lo.Introduction to the polymerase chain reaction / Y.M. Dennis Lo and K.C. Allen Chan -- Setting up a polymerase chain reaction laboratory / Y.M. Dennis Lo and K.C. Allen Chan -- Real-time polymerase chain reaction and melting curve analysis / Robert J. Pryor and Carl T. Wittwer -- Qualitative and quantitative polymerase chain reaction-based methods for DNA methylation analyses / Ivy H.N. Wong -- In-cell polymerase chain reaction: strategy and diagnostic applications / T. Vauvert Hviid -- Qualitative and quantitative DNA and RNA analysis by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry / Chunming Ding -- Analysis of polymerase chain reaction products by denaturing high-performance liquid chromatography / Ching-Wan Lam -- Use of real-time polymerase chain reaction for the detection of fetal aneuploidies / Bernhard Zimmermann ... [et al.] -- Noninvasive prenatal diagnosis by analysis of fetal DNA in maternal plasma / Rossa W. K. Chiu and Y. M. Dennis Lo --
  • Codes of life 2008, Springer
    Codes of biosequences / Edward N. Trifonov -- The mechanisms of evolution : natural selection and natural conventions / Marcello Barbieri -- Catalytic propensity of amino acids and the origins of the genetic code and proteins / Ádám Kun ... [et al.] -- Why the genetic code originated : implications for the origin of protein synthesis / Massimo Di Giulio -- Self-referential formation of the genetic system / Romeu Cardoso Guimarães, Carlos Henrique Costa Moreira, and Sávio Torres de Farias -- The mathematical structure of the genetic code / Diego L. Gonzalez -- The arithmetical origin of the genetic code / Vladimir shCherbak -- Protein linguistics and the modular code of the cytoskeleton / Mario Gimona -- A lipid-based code in nuclear signaling / Nadir M. Maraldi -- Biological information transfer beyond the genetic code : the sugar code / Hans-Joachim Gabius -- The immune self code : from correspondence to complexity / Yair Neuman -- Signal transduction codes and cell fate / Marcella Faria -- Towards an understanding of language origins / Eörs Szathmáry -- The codes of language : turtles all the way up? / Stephen J. Cowley -- Code and context in gene expression, cognition, and consciousness / Seán Ó Nualláin -- Neural coding in the neuroheuristic perspective / Alessandro E.P. Villa -- Error detection and correction codes / Diego L. Gonzalez -- The musical code between nature and nurture : ecosemiotic and neurobiological claims / Mark Reybrouck.
  • Introduction -- Chronology -- Fundamentals -- Prologue -- Molecular basis of genetics -- Analysis of DNA -- Variability of DNA -- Processing of DNA -- Eukaryotic cells -- Formal genetics -- Chromosomes -- Regulation of gene function -- Epigenetic modifications -- Genetic signal pathways -- Genes in embryonic development -- Genomics -- Genetics and medicine -- Imbalanced homeostasis -- Metabolic disorders -- Immune system -- Origins of cancer -- Impaired cell and tissue structure -- Hemoglobin disorders -- Sex determination and differentiation -- Atypical patternns of genetic transmission -- Sensory perception -- Karyotype-phenotype relationnship -- A grief guide to genetic diagnosis -- Morbid anatomy of the human genome - chromosomal locations - alphabetic list -- Appendix -- Supplementary data.
  • Comparative genomics 2006, Springer
  • Comparative genomics v. 1-2, 2007, Springer Protocols
    v. 2, 2007 Springer Protocols
    v. 1. Genome visualization and annotation ; Sequence alignments ; Identification of conserved sequences and biases in codon usage ; Identification and structural characterization of noncoding RNAs -- v. 2. Comparative analysis of domain and protein families ; Orthologs, synteny, and genome evolution ; Experimental analysis of whole genomes : analysis of copy number and sequence polymorphisms.
  • Comparative genomics 2008, CRCnetBASE
    Introduction : the broad horizons of comparative genomics / James R. Brown -- Advances in next-generation DNA sequencing technologies / Michael L. Metzker -- Large scale phylogenetic reconstruction / Bernard M.E. Moret -- Comparative genomics of viruses using bioinformatics tools / Chris Upton and Elliot J. Lefkowitz -- Archaebacteria and the prokaryote-to-eukaryote transition (and the role of mitochondria therein) / William Martin, Tal Dagan, and Katrin Henze -- Comparative genomics of invertebrates / Takeshi Kawashima ... [et al.] -- Comparative vertebrate genomics / James W. Thomas -- Gaining insight into human population-specific selection pressure / Michael R. Barnes -- Comparative genomics in drug discovery / James R. Brown -- Comparative genomics and the development of novel antimicrobials / Diarmaid Hughes -- Comparative genomics and the development of antimalarial and antiparasitic therapeutics / Emilio F. Merino, Steven A. Sullivan, and Jane M. Carlton -- Comparative genomics in AIDS research / Philippe Lemey, Koen Deforche, and Anne-Mieke Vandamme -- Detailed comparisons of cancer genomes / Timon P.H. Buys ... [et al.] -- Comparative cancer epigenomics / Alice N.C. Kuo ... [et al.] -- G protein-coupled receptors and comparative genomics / Steven M. Foord -- Comparative toxicogenomics in mechanistic and predictive toxicology / Joshua C. Kwekel, Lyle D. Burgoon, and Tim R. Zacharewski -- Comparative genomics and crop improvement / Michael Francki and Rudi Appels -- Domestic animals : a treasure trove for comparative genomics / Leif Andersson.
  • Comparative genomics 2013, Springer
    This book provides an evolutionary conceptual framework for comparative genomics, with the ultimate objective of understanding the loss and gain of genes during evolution, the interactions among gene products, and the relationship between genotype, phenotype and the environment. The many examples in the book have been carefully chosen from primary research literature based on two criteria: their biological insight and their pedagogical merit. The phylogeny-based comparative methods, involving both continuous and discrete variables, often represent a stumbling block for many students entering the field of comparative genomics. They are numerically illustrated and explained in great detail. The book is intended for researchers new to the field, i.e., advanced undergraduate students, postgraduates and postdoctoral fellows, although professional researchers who are not in the area of comparative genomics will also find the book informative.
  • Computational chemogenomics 2013, CRCnetBASE
    This book focuses on applications of compound library design and virtual screening to expand the bioactive chemical space, to target hopping of chemotypes to identify synergies within related drug discovery projects or to repurpose known drugs, to propose mechanism of action of compounds, or to identify off-target effects by cross-reactivity analysis. Both ligand-based and structure-based in silico approaches, as reviewed in this book, play important roles for all these applications. Computational chemogenomics is expected to increase the quality and productivity of drug discovery and lead.
  • Computational biology: are we there yet? / Gary Peltz -- Statistical theory in QTL mapping / Benjamin Yakir, Anne PisanteÃÅ, and Ariel Darvasi -- Haplotype-based computational genetic analysis in mice / Jianmei Wang and Gary Peltz -- Haplotype structure of the mouse genome / Jianmei Wang ... [et al.] -- SNP discovery and genotyping: methods and applications / Jun Wang ... [et al.] -- Genetic and genomic approaches to complex lung disease using mouse models / Michael J. Holtzman, Edy Y. Kim, and Jeffrey D. Morton -- Murine models of osteoporosis / Robert F. Klein -- Murine models of substance and alcohol dependence: unraveling genetic complexities / Kim Cronise and John C. Crabbe -- Murine models of alcoholism: from QTL to gene / Chris Downing, Beth Bennett, and Thomas E. Johnson -- HLA polymorphism and disease susceptibility / -- Henry A. Erlich -- Asthma genetics: a case study / William Cookson.
  • Recent advances in development of sequencing technology has resulted in a deluge of genomic data. In order to make sense of this data, there is an urgent need for algorithms for data processing and quantitative reasoning. An emerging in silico approach, called computational genomic signatures, addresses this need by representing global species-specific features of genomes using simple mathematical models. This text introduces the general concept of computational genomic signatures, and it reviews some of the DNA sequence models which can be used as computational genomic signatures. The text takes the position that a practical computational genomic signature consists of both a model and a measure for computing the distance or similarity between models. Therefore, a discussion of sequence similarity/distance measurement in the context of computational genomic signatures is presented. The remainder of the text covers various applications of computational genomic signatures in the areas of metagenomics, phylogenetics and the detection of horizontal gene transfer.
  • Conditional mutagenesis 2007, Springer
    Conditional somatic mutagenesis in the mouse using site-specific recombinases -- Cre/loxP-mediated chromosome engineering of the mouse genome -- Tetracycline-controlled genetic switches -- Novel gene switches -- Improved embryonic stem cell technologies -- Gene trap mutagenesis -- RNA interference in mice -- Viral vectors: a wide range of choices and high levels of service -- Conditional mutagenesis by cell-permeable proteins: potential, limitations and prospects -- Analysis of mouse development with conditional mutagenesis -- Conditional mouse models of cancer -- Conditional mutagenesis reveals immunological functions of widely expressed genes: activation thresholds, homeostatic mechanisms and disease models -- Conditional transgenesis and recombination to study the molecular mechanisms of brain plasticity and memory -- A novel conditional knockout strategy applied to serotonin receptors -- Conditional mouse models for Friedreich Ataxia, a neurodegenerative disorder associating cardiomyopathy -- Animal models in cardiovascular diseases: new insights from conditional models -- Conditional animal models for the study of lipid metabolism and lipid disorders -- Conditional mouse models to study developmental and pathophysiological gene function in muscle -- Analysis of calcuim channels by conditional mutagenesis -- Conditional mutagenesis of G-protein coupled receptors and G-proteins -- Contribution of targeted conditional somatic mutagenesis to deciphering retinoid X receptor functions and to generating mouse models of human diseases.
  • CRISPR-Cas systems 2013, Springer
    CRISPR-Cas is a recently discovered defense system which protects bacteria and archaea against invasion by mobile genetic elements such as viruses and plasmids. A wide spectrum of distinct CRISPR-Cas immune systems has been identified in at least half of the available prokaryotic genomes. On-going biochemical and functional analyses have resulted in substantial insight into the functions and possible applications of these fascinating systems, although many secrets remain to be uncovered. In this book, experts summarize the state of the art of this exciting field.
  • ch. 1. Genetic Mapping -- ch. 2. Genotyping -- ch. 3. Somatic Cell Hybrids -- ch. 4. Cytogenetics -- ch. 5. Strategies for Large-Insert Cloning and Analysis -- ch. 6. Identifying Candidate Genes in Genomic DNA -- ch. 7. Searching Candidate Genes for Mutations -- ch. 8. Clinical Cytogenetics -- ch. 9. Clinical Molecular Genetics -- ch. 10. Cancer Genetics -- ch. 11. Transcriptional Profiling -- ch. 12. Vectors for Gene Therapy -- ch. 13. Delivery Systems for Gene Therapy -- ch. 14. Forensic Genetics -- ch. 15. Model Systems for the Analysis of Human Disease -- ch. 16. Automation and Robotics in Genetic Analysis -- ch. 17. Biochemical Genetics --ch. 18. High-Throughput Sequencing -- ch. 19. Mitochondrial Genetics -- ch. 20. Epigenetics -- Appendix 1. Abbreviations and Useful Data -- Appendix 2. Laboratory Guidelines, Equipment, and Stock Solutions -- Appendix 3. Commonly Used Techniques -- Appendix 4. Chromosome Karyotyping and Idiograms -- Appendix 5. Genetic Linkage Reference Maps: Access to Internet-Based Resources -- Appendix 6. Human-Mouse Comparative Maps -- Appendix. Suppliers.
  • Data mining in proteomics 2011, Springer Protocols
    Instruments and methods in proteomics -- In-depth protein characterization by mass spectrometry -- Analysis of phosphoproteomics data -- The origin and early reception of sequence databases -- Laboratory data and sample management for proteomics -- PRIDE and "Database on demand" As valuable tools for computational proteomics -- Analysing proteomics identifications in the context of functional and structural protein annotation: Integrating annotation using PICR, DAS, and BioMart -- Tranche distributed repository and proteomecommons.Org -- Data standardization by the HUPO-PSI: How has the community benefitted? -- mzIdentML: An open community-built standard format for the results of proteomics spectrum identification algorithms -- Spectra, chromatograms, metadata: mzML-the standard data format for mass spectrometer output -- imzML: Imaging mass spectrometry markup language: A common data format for mass spectrometry imaging -- Tandem mass spectrometry spectral libraries and library searching -- Inter-lab proteomics: Data mining in collaborative projects on the basis of the HUPO brain proteome project's pilot studies -- Data management and data integration in the HUPO plasma proteome project -- Statistics in experimental design, preprocessing, and analysis of proteomics data -- The evolution of protein interaction networks -- Cytoscape: Software for visualization and analysis of biological networks -- Text mining for systems modeling -- Identification of alternatively spliced transcripts using a proteomic informatics approach -- Distributions of ion series in ETD and CID spectra: Making a comparison -- Evaluation of peak-picking algorithms for protein mass spectrometry -- OpenMS and TOPP: Open source software for LC-MS data analysis -- LC/MS data processing for label-free quantitative analysis -- Spectral properties of correlation matrices - towards enhanced spectral clustering -- Standards, databases, and modeling tools in systems biology -- Modeling of cellular processes: Methods, data, and requirements.
  • Dictyostelium discoideum protocols 2006, Springer Protocols
  • Global analysis of gene expression by differential display : a mathematical model / Shitao Yang and Peng Liang -- Automation of fluorescent differential display with digital readout / Jonathan D. Meade ... [et al.] -- Ordered differential display / Mikhail V. Matz and Ella A. Meleshkevitch -- GeneCalling : transcript profiling coupled to a gene database query / Richard A. Shimkets -- High-density sampling differential display of prokaryotic mRNAs with RAP-PCR / Dana M. Walters and Pierre E. Rouviere -- Vertical arrays : microarrays of complex mixtures of nucleic acids / Rosana Risques ... [et al.] -- Automated pattern ranking in differential display data analysis / Tero Aittokallio ... [et al.] -- Linking cDNA-AFLP-based gene expression patterns and ESTs / Ling Qin, Pjotr Prins, and Johannes Helder -- Differentially expressed genes associated with hepatitis B virus HBx and MHBs protein function in hepatocellular carcinoma / Dae-Ghon Kim -- Identification of disease markers by differential display : prion disease / Michael Clinton ... [et al.] -- Saturation screening for p53 target genes by digital fluorescent differential display / Yong-Jig Cho ... [et al.] -- Identification of p53-regulated genes by the method of differential display / Yunping Lin, Roger P. Leng, and Samuel Benchimol --Identification by differential display of IL-24 autocrine loop activated by ras oncogenes / Zhongjia Tan, Mai Wang, and Peng Liang -- Comprehensive analysis of ovarian gene expression during ovulation using differential display / Lawrence L. Espey -- Functional analysis of nocturnin : a circadian clock-regulated gene identified by differential display / Julie E. Baggs and Carla B. Green -- Isolation and characterization of anthocyanin 5-0-glucosyltransferase in perilla frutescens var. crispa by differential display / Mami Yamasaki and Kazuki Saito -- Identification of target genes of a yeast transcriptional repressor / Bernard Mai and Linda L. Breeden -- Detection of an mRNA polymorphism by differential display / Shan Liang ... [et al.] -- Silencing in yeast : identification of CLr4 targets / Sergey V. Ivanov and Alla V. Ivanova -- Identification of mRNA bound to RNA binding proteins by differential display / Anne Carr-Schmid, Xinfu Jiao, and Megerditch Kiledjian.
  • ch. 1. Introduction, p. 1-3 / Kai Johnsson and Susanne Brakmann, p. 1-3 -- ch. 2. Evolutionary Biotechnology - From Ideas and Concepts to Experiments and Computer Simulations / Peter Schuster, p. 5-28 -- ch. 3. Using Evolutionary Strategies to Investigate the Structure and Function of Chorismate Mutases / Donald Hilvert, Sean V. Taylor and Peter Kast, p. 29-62 -- ch. 4. Construction of Environmental Libraries for Functional Screening of Enzyme Activity / Rolf Daniel, p. 63-78 -- ch. 5. Investigation of Phage Display for the Directed Evolution of Enzymes / Patrice Soumillion and Jacques Fastrez, p. 79-110 -- ch. 6. Directed Evolution of Binding Proteins by Cell Surface Display: Analysis of the Screening Process / K. Dane Wittrup, p. 111-126 -- ch. 7. Yeast n-Hybrid Systems for Molecular Evolution / Brian T. Carter, Hening Lin and Virginia W. Cornish, p. 127-158 -- ch. 8. Advanced Screening Strategies for Biocatalyst Discovery / Andreas Schwienhorst, p. 159-175 -- ch. 9. Engineering Protein Evolution / Stefan Lutz and Stephen J. Benkovic, p. 177-213 -- ch. 10. Exploring the Diversity of Heme Enzymes through Directed Evolution / Patrick C. Cirino and Frances H. Arnold, p. 215-243 -- ch. 11. Directed Evolution as a Means to Create Enantioselective Enzymes for Use in Organic Chemistry / Manfred T. Reetz and Karl-Erich Jaeger, p. 245-279 -- ch. 12. Applied Molecular Evolution of Enzymes Involved in Synthesis and Repair of DNA / John F. Davidson, Jon Anderson, Haiwei Guo, Daniel Landis and Lawrence A. Loeb, p. 281-307 -- ch. 13. Evolutionary Generation Versus Rational Design of Restriction Endonucleases with Novel Specificity / Thomas Lanio, Albert Jeltsch and Alfred Pingoud, p. 309-327 -- ch. 14. Evolutionary Generation of Enzymes with Novel Substrate Specificities / Uwe T. Bornscheuer, p. 329-341.
  • Lynch syndrome (LS) is the most common cause of inherited colorectal cancer, a disease with a high mortality rate. An estimated 37,000 of diagnosed colorectal cancer cases worldwide are attributed to Lynch syndrome each year. Intensive cancer screening, with early initiation and frequent follow-up, can reduce colorectal cancer incidence and mortality in LS patients. This book provides an up-to-date overview on the genetic and epigenetic basis of Lynch syndrome. It evaluates clinical features of the disease and critically comments on molecular tools available for identifying mutations responsible for Lynch syndrome; in addition the importance of functional assays that can help clarify the clinical nature of identified mutations is also discussed. The book also focuses on challenges in genetic counselling of at-risk individuals and discusses related ethical issues. The purpose of the book is to give a concise knowledge base for the broader scientific and medical community, including genetic counselors, in order to improve awareness on the potential impact that the diagnosis of LS has on treatment, management and surveillance of LS patients.
  • DNA and RNA profiling in human blood 2009, Springer Protocols
    PCR-ELISA for high-throughput blood group genotyping / Maryse St-Louis -- Single base extension in multiplex blood group genotyping / Gregory A. Denomme -- Real-time PCR assays for high-throughput blood group genotyping / Fernando Araujo -- Real-time PCR assays for high-throughput human platelet antigen typing / Simon E. McBride -- Multiplex ABO genotyping by minisequencing / Gianmarco Ferri and Susi Pelotti -- Multiplex genotyping for thrombophilia-associated SNPs by universal bead arrays / Susan Bortolin -- Pyrosequencing of toll-like receptor polymorphisms of functional relevance / Parviz Ahmad-Nejad -- Multiplex HLA-typing by pyrosequencing / Ying Lu ... [et al.] -- High-throughput multiplex HLA-typing by ligase detection reaction (LDR) and universal array (UA) approach / Clarissa Consolandi -- Medium- to high-throughput SNP genotyping using VeraCode microbeads / Charles H. Lin ... [et al.] -- The use of maternal plasma for prenatal RhD blood group genotyping / Kirstin Finning, Pete Martin, and Geoff Daniels -- Nanoliter high-throughput PCR for DNA and RNA profiling / Colin J.H. Brenan, Douglas Roberts, and James Hurley -- RNA stabilization of peripheral blood and profiling by bead chip analysis / Svenja Debey-Pascher, Daniela Eggle, and Joachim L. Schultze -- RNA profiling in peripheral blood cells by fluorescent differential display PCR / Martin Steinau and Mangalathu S. Rajeevan -- cDNA amplification by SMART-PCR and suppression subtractive hybridization (SSH)-PCR / Andrew Hillmann, Eimear Dunne, and Dermot Kenny -- Transcript profiling of human platelets using microarray and serial analysis of gene expression (SAGE) / Dmitri V. Gnatenko ... [et al.] -- Genome-wide platelet RNA profiling in clinical samples / Angelika Schedel and Nina Rolf -- PCR-based amplification of platelet mRNA sequences obtained from small-scale platelet samples / Jutta M. Rox, Jens Müller, and Bernd Pötzsch -- MicroRNA profiling of megakaryocytes / Ramiro Garzon -- Serial analysis of gene expression adapted for downsized extracts / SAGE/SADE) analysis in reticulocytes / Béatrice Bonafoux and Thérèse Commes -- Real-time PCR analysis for blood cell lineage specific markers / Louise Edvardsson and Tor Olofsson -- Monitoring the immune response using real-time PCR / Patrick Stordeur.
  • DNA arrays 2002, CRCnetBASE
  • DNA: alternative conformations and biology / Vladimir N. Potaman and Richard R. Sinden -- Sequence-dependent variability of B-DNA: an update on bending and curvature / Victor B. Zhurkin ... [et al.] -- Curved DNA and prokaryotic promoters: a mechanism for activation of transcription / Munehiko Asayama and Takashi Ohyama -- Repression of transcription by curved DNA and nucleoid protein H-NS: a mode of bacterial gene regulation / Cynthia L. Pon, Stefano Stella and Claudio O. Gualerzi -- Curved DNA and transcription in eukaryotes / Takashi Ohyama -- Putative roles of kin17, a mammalian protein binding -- Curved DNA, in transcription / Jaime F. Angulo ... [et al.] -- Roles for Z- and double-stranded RNA in transcription: encoding genetic information by shape rather than by sequence / Alan Herbert -- Do DNA triple helices or quadruplexes have a role in transcription? / Michael W. Van Dyke -- Nucleic acid structures and the transcription defects in fragile X syndrome and Friedreich's ataxia / Karen Usdin -- Possible roles of DNA supercoiling in transcription / Susumu Hirose and Kuniharu Matsumoto -- Gene regulation by HMGA and HMGB chromosomal proteins and related architectural DNA-binding proteins / Andrew A. Travers -- Molecular mechanisms of male sex determination: the enigma of SRY / Michael A. Weiss -- The role of unusual DNA structures in chromatin organization for transcription / Takashi Ohyama -- DNA bendability and nucleosome positioning in transcriptional regulation / Mensur Dlaki, David W. Ussery and Sren Brunak.
  • In situ detection of apoptosis by the TUNEL assay: An overview of techniques -- Combination of TUNEL assay with immunohistochemistry for simultaneous detection of DNA fragmentation and oxidative cell damage -- EM-ISEL: A useful tool to visualize DNA damage at the ultrastructural level -- In situ labeling of DNA breaks and apoptosis by T7 DNA polymerase -- In situ ligation: A decade and a half of experience -- In situ ligation simplified: Using PCR fragments for detection of double-strand DNA breaks in tissue sections -- 5'OH DNA breaks in apoptosis and their labeling by topoisomerase-based approach -- Detection of DNA strand breaks in apoptotic cells by flow- and image-cytometry -- Fluorochrome-labeled inhibitors of caspases: Convenient in vitro and in vivo markers of apoptotic cells for cytometric analysis -- Combining fluorescent in situ hybridization with the comet assay for targeted examination of DNA damage and repair -- Simultaneous labeling of single- and double-strand DNA breaks by DNA breakage detection-FISH (DBD-FISH) -- Co-localization of DNA repair proteins with UV-induced DNA damage in locally irradiated cells -- Ultrasound imaging of apoptosis: Spectroscopic detection of DNA-damage effects at high and low frequencies -- Quantifying etheno-DNA adducts in human tissues, white blood cells, and urine by ultrasensitive (32)P-postlabeling and immunohistochemistry -- ELISpot assay as a tool to study oxidative stress in peripheral blood mononuclear cells -- Cytokinesis-block micronucleus cytome assay in lymphocytes -- Buccal micronucleus cytome assay -- [Gamma]-H2AX detection in peripheral blood lymphocytes, splenocytes, bone marrow, xenografts, and skin -- Immunologic detection of benzo(a)pyrene-DNA adducts -- Non-invasive assessment of oxidatively damaged DNA: Liquid chromatography-tandem mass spectrometry analysis of urinary 8-oxo-7,8-dihydro-2'-deoxyguanosine -- Assessing sperm DNA fragmentation with the sperm chromatin dispersion test.
  • DNA damage recognition 2005, CRCnetBASE
  • DNA methylation : three decades in search of function / Aharon Razin -- Epigenetic mechanisms of gene regulation : relationships between DNA methylation, histone modification, and chromatin structure / Keith D. Robertson -- DNA hypo- vs. hypermethylation in cancer : tumor specificity, tumor progression, and therapeutic implications / Melanie Ehrlich and Guanchao Jiang -- DNA methylation in urological cancers / Wolfgang A. Schulz and Hans-Helge Seifert -- DNA methylation in colorectal cancer / Jeremy R. Jass ... [et al.] -- CpG island hypermethylation of tumor suppressor genes in human cancer : concepts, methodologies and uses / Michel Herranz and Manel Esteller -- The loss of methyl groups in DNA of tumor cells and tissues : the immunochemical approach / Alain Niveleau ... [et al.] -- Identifying clinicopathological association of DNA hypermethylation in cancers using CpG island microarrays / Susan H. Wei ... [et al.] -- Methylation analysis in cancer : (epi)genomic fast track from discovery to clinical routine / Carolina Haefliger, Sabine Maier and Alexander Olek --Regulation of DNA methyltransferases in cancer / Nancy Detich and Moshe Szyf -- Inhibition of poly(ADP-ribosyl)ation allows DNA hypermethylation / Anna Reale ... [et al.] -- The role of active demethylation in cancer and its therapeutic potential / Moshe Szyf ... [et al.] -- Purine analogues and their role in methylation and cancer chemotherapy / Katherine L. Seley and Sylvester L. Mosley -- DNA methyltransferase inhibitors : paving the way for epigenetic cancer therapeutics / Gregory K. Reid and A. Robert MacLeod -- Preclinical and clinical studies on 5-aza-2'-deoxycytidine, a potent inhibitor of DNA methylation, in cancer therapy / Richard L. Momparler -- Anticancer gene therapy by in vivo DNA electrotransfer of MBD2 antisense / Pascal Bigey and Daniel Scherman.
  • DNA methylation microarrays 2008, CRCnetBASE
  • Regulation of chromatin and DNA-methylation patterns in blood cell development / C. Bonifer, P. Lefevre, and H. Tagoh -- Methylation dynamics in the early mammalian embryo : implications of genome reprogramming defects for development / T. Haaf -- Epigenetic regulation in drosophila / F. Lyko ... [et.al.] -- Epimutations in human disease / B. Horsthemke -- Epigenotypes of latent herpesvirus genomes / J. Minarovits -- Epigenetics of complex diseases : from general theory to laboratory experiments / A. Schumacher and A. Petronis -- MSL proteins and the regulation of gene expression / S. Rea and A. Akhtar -- DNA methylation profiles of female steroid hormone-driven human malignancies / M. Campan, D.J. Weisenberger, and P.W. Laird -- Genome-wide analysis of DNA methylation changes in human malignancies / C. Plass and D.J. Smiraglia -- Decreased fidelity in replicating DNA methylation patterns in cancer cells leads to dense methylation of a CpG island / N. Watanabe ... [et.al.] -- Methylation of endogenous human retroelements in health and disease / W. A. Schulz, C. Steinhoff, and A.R. Florl -- Cancer-linked DNA hypomethylation and its relationship to hypermethylation / M. Ehrlich.
  • DNA microarrays. Part A-B pt. A-B, 2006., ScienceDirect
    pt. B, 2006 ScienceDirect
    Pt. A. Array platforms and wet-bench protocols -- pt. B. Databases and statistics.
  • Biochemical assays for the characterization of DNA helicases / Robert M. Brosh Jr. and Sudha Sharma -- Repair synthesis assay for nucleotide excision repair activity using fractionated cell extracts and UV-damaged plasmid DNA / Maureen Biggerstaff and Richard D. Wood -- Assaying for the dual incisions of nucleotide excision repair using DNA with a lesion at a specific site / Mahmud K.K. Shivji ... [et al.] -- Analysis of proliferating cell nuclear antigen (PCNA) associated with DNA excision repair sites in mammalian cells / A. Ivana Scovassi and Ennio Prosperi -- Analysis of DNA repair and chromatin assembly in vitro using immobilized damaged DNA substrates / Jill A. Mello, Jonathan G. Moggs, and Geneviève Almouzni.Cytometric assessment of histone H2AX phosphorylation: a reporter of DNA damage / Xuan Huang and Zbigniew Darzynkiewicz -- Detection of DNA strand breaks by flow and laser scanning cytometry in studies of apoptosis and cell proliferation (DNA replication) / Zbigniew Darzynkiewicz, Xuan Huang, and Masaki Okafuji -- In vitro rejoining of double-strand breaks in genomic DNA / George Iliakis and Nge Cheong -- Detection of DNA double-strand breaks and chromosome translocations using ligation-mediated PCR and inverse PCR / Michael J. Villalobos, Christopher J. Betti, and Andrew T.M. Vaughan -- Plasmid-based assays for DNA end-joining in vitro / George Iliakis ... [et al.] -- Use of gene targeting to study recombination in mammalian cell DNA repair mutants / Rodney S. Nairn and Gerald M. Adair --Gene-specific and mitochondrial repair of oxidative DNA damage / R. Michael Anson, Penelope A. Mason, and Vilhelm A. Bohr -- Quantitative PCR-based measurement of nuclear and mitochondrial DNA damage and repair in mammalian cells / Janine H. Santos ... [et al.] -- Measuring the formation and repair of DNA damage by ligation-mediated PCR / Gerd P. Pfeifer -- Immunochemical detection of UV-induced DNA damage and repair / Marcus S. Cooke and Alistair Robson -- A dot-blot immunoassay for measuring repair of ultraviolet photoproducts / Shirley McCready -- Quantification of photoproducts in mammalian cell DNA using radioimmunoassay / David L. Mitchell -- DNA damage quantitation by alkaline gel electrophoresis / Betsy M. Sutherland, Paula V. Bennett, and John C. Sutherland --Isolation of mutagen-sensitive Chinese hamster cell lines by replica plating / Malgorzata Z. Zdzienicka -- Complementation assays adapted for DNA repair-deficient keratinocytes / Mathilde Fréchet ... [et al.] -- Cytogenetic challenge assays for assessment of DNA repair capacities / William W. Au and Salama A. Salama -- Evaluating the delayed effects of cellular exposure to ionizing radiation / Shruti Nagar, James J. Corcoran, and William F. Morgan -- Inhibition of DNA synthesis by ionizing radiation: a marker for an S-phase checkpoint / Nicolaas G.J. Jaspers and Malgorzata Z. Zdzienicka -- Analysis of inhibition of DNA replication in irradiated cells using the SV40-based in vitro assay of DNA replication / George Iliakis, Ya Wang, and Hong Yan Wang --The comet assay: a sensitive genotoxicity test for the detection of DNA damage and repair / Günter Speit and Andreas Hartmann -- Fast micromethod DNA single-strand-break assay / Heinz C. Schröder ... [et al.] -- ³²P-postlabeling DNA-damage assays: PAGE, TLC, and HPLC / Shinya Shibutani, Sung Yeon Kim, and Naomi Suzuki -- Electrophoretic mobility shift assays to study protein binding to damaged DNA / Vaughn Smider, Byung Joon Hwang, and Gilbert Chu -- Construction of MMR plasmid substrates and analysis of MMR error correction and excision / Huixian Wang and John B. Hays -- Characterization of enzymes that initiate base excision repair at abasic sites / Walter A. Deutsch and Vijay Hegde -- Base excision repair in mammalian cells / Yoshihiro Matsumoto -- In vitro base excision repair assay using mammalian cell extracts / Guido Frosina ... [et al.] --
  • DNA repair. Part A-B pt. A-B, 2006., ScienceDirect
    pt. B, 2006 ScienceDirect
  • Drosophila cytogenetics protocols 2004, Springer Protocols
  • dsRNA genetic elements 2002, CRCnetBASE
  • E. coli gene expression protocols 2002, Springer Protocols
  • Ecological genomics : 2014, Springer
    "Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. Ecological genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation"-- Publisher's description.
  • v. 1. Genetics -- v. 2. Genetics -- v. 3. Genomics -- v. 4. Genomics -- v. 5. Proteomics -- v. 6. Proteomics -- v. 7. Bioinformatics -- v. 8. Bioinformatics.
  • v. 1. A-L -- v. 2. M-Z.
  • Multiple endocrine neoplasia type 1 / Agarwal, S.K. -- Multiple endocrine neoplasia type 2 / Lodish, M. -- Von Hippel-Lindau syndrome / Chou, A. ... [et al.] -- Carney complex -- Espiard, S., Bertherat, J. -- Multiple endocrine neoplasia type 4 / Lee, M., Pellegata, N.S. -- Novel hereditary forms of pheochromocytomas and paragangliomas / Dahia, P.L.M. -- Carney triad / Carney, J.A. -- Genetics of pituitary adenomas / Gadelha, M.R. ... [et al.] -- Clinical behavior and genetics of nonsyndromic, familial nonmedullary thyroid cancer / Bauer, A.J. -- Genetic defects associated with familial and sporadic hyperparathyroidism / Hendy, G.N., Cole, D.E.C. -- Endocrine tumors associated with neurofibromatosis type 1, Peutz-Jeghers syndrome, and other familial neoplasia syndromes / Kalkan, E., Waguespack, S.G.
  • The capacity of the epigenome to interpret both internal and external stimuli and alter expression programs is a critical component in normal development, aging, and disease pathogenesis. In the past decade, we have witnessed an explosion of unprecedented research on and support for epigenetics, epigenomics, and their interface with human health and disease. In this volume, Environmental Epigenomics in Health and Disease - Epigenetics and Complex Diseases, a number of leading investigators in the field of epigenetics discuss patterns of epigenomic modifications in normal cells, and how environmentally-induced changes in them are associated with disease pathogenesis. The authors comprehensively review the epigenetic adaptations that occur in human embryonic stem cells, as well as in differentiating cells and organs such as the brain when exposed to environmental factors, and discuss the legal and ethical implications of such alterations. The overall purpose of this volume and its companion, Environmental Epigenomics in Health and Disease - Epigenetics and Disease Origins, is to give readers an overview of how environmental exposures during early development can influence disease formation by disrupting epigenetic programming.
  • Exposure to environmental toxicants is associated with changes in DNA methylation and gene expression profiles that together can contribute to increased disease susceptibility. The chapters in this volume, Environmental Epigenomics in Health and Disease - Epigenetics and Disease Origins, address a wide range of environmental exposures, such as airborne particulates, cocaine, radiation, tobacco smoke, and xenoestrogens. Particular emphasis is placed on the consequences of environmental exposures during development on epigenetic reprogramming that influences adult disease pathogenesis. Health outcomes associated with these exposures include autoimmune disorders, neurodevelopmental disorders, and cancer. Importantly, dietary supplements and drugs can modify the epigenetic effects induced by these agents, thereby reducing their toxicological impact. The overall purpose of this volume and its companion, Environmental Epigenomics in Health and Disease - Epigenetics and Complex Diseases, is to give readers an overview of how environmental exposures during early development can influence disease formation by disrupting epigenetic processes and developmental programming.
  • Environmental genomics 2007, Springer Protocols
    Preface --Contributors --Pt. 1.Gene expression profiling --1.High-throughput whole mount in situ hybridization of zebrafish embryos for analysis of tissue-specific gene expression changes after environmental perturbation /Louise E. Coverdale, Lindsay E. Burton, and C. Cristofre Martin --2.Fluorescent RNA arbitrarily primed polymerase chain reaction /Doug Crump ... [et al.] --3.Isolation of O₃-response genes from Arabidopsis thaliana using cDNA macroarray /Masanori Tamaoki --4.Use of cDNA macroarrays and gene profiling for detection of effects of environmental toxicants /Jason L. Blum ... [et al.] --5.Constructing and screening a cDNA library /Kevin Larade and Kenneth B. Storey --6.Comparative molecular physiological genomics /Sean F. Eddy and Kenneth B. Storey --7.Proteomic analysis of neuroendocrine peptidergic system disruption using the AtT20 pituitary cell line as a model /Fumin Dong ... [et al.] --8.Proteomics-based method for risk assessment of peroxisome proliferating pollutants in the marine environment /Susana Cristobal --9.Environmental metabolomics using ¹H-NMR spectroscopy /Mark R. Viant --Pt. 2.Detection of whole genome mutation --10.Restriction landmark genome scanning for the detection of mutations /Jun-ichi Asakawa --11.Use of the comet assay in environmental toxicology /Loren D. Knopper and James P. McNamee --12.The micronucleus assay determination of chromosomal level DNA damage /Michael Fenech --13.Fluorescence in situ hybridization for the detection of chromosome aberrations and aneuploidy induced by environmental toxicants /Francesca Pacchierotti and Antonella Sgura --14.Laboratory methods for the detection of chromosomal structural aberrations in human and mouse sperm by fluorescence in situ hybridization /Francesco Marchetti, Debby Cabreros, and Andrew J. Wyrobek --Pt. 3.Determination of species diversity --15.Assembling DNA barcodes /Jeremy R. deWaard ... [et al.] --16.Application of suppressive subtractive hybridization to uncover the metagenomic diversity of environmental samples /Elizabeth A. Galbraith, Dionysios A. Antonopoulos, and Bryan A. White --17.16S rRNA targeted DGGE fingerprinting of microbial communities /Vesela A. Tzeneva ... [et al.] --18.An emulsion polymerase chain reaction-based method for molecular haplotyping /James G. Wetmur and Jia Chen --Index.
  • Introduction --Immune System and Atopic Disorders --Epigenetics --Epigenetics, Environment, and Allergic Diseases --Conclusions and Future Perspectives.
  • Behavioral Epigenetics is the study of how environmental factors affect alterations in behavior, addressing the fundamental mechanisms that shape development and individual vulnerability/resilience to adverse behavioral outcome. With an understanding of the molecular mechanisms involved in epigenetic modulation, researchers believe it will be possible to develop targeted therapies for those individuals in whom it malfunctions. This volume will address current understanding of the roles of epigenetic processes at the molecular/cellular level, their impact on neural development and behavior.
  • Epigenetic risks of cloning 2006, CRCnetBASE
  • Epigenetics 2004, Cold Spring Harb Lab Press
    Epigenetic reprogramming and genomic imprinting -- Chromosome inactivation -- DNA methylation -- Histone modification and nucleosome structure -- Chromatin structure and dynamics -- Polycomb and related silencing mechanisms -- Nuclear organization and dynamics -- Heterochromatin and transposon silencing -- RNA interference and related mechanisms -- Epigenetic regulation of phenotypes.
  • Epigenetics and cancer 2013, Springer
    Systems and Network Biology to Investigate Epigenetic De-regulatory Mechanisms of MicroRNAs in Pancreatic Cancer /Irfana Muqbil, Fazlul H. Sarkar, Ramzi M. Mohammad --Role of MicroRNAs in Cancer Epigenetics /Kishore B. Challagundla, Petra Wise, Muller Fabbri --Epigenetic Regulation of EZH2 and Its Targeted MicroRNAs /Sandy Leung-Kuen Au, Irene Oi-Lin Ng, Chun-Ming Wong --Epigenetics and MicroRNAs in Renal Cancer /Shahana Majid ... [et al.] --Epigenetic Regulation of MicroRNA in Colon Cancer /Qiong Zhang, Mukesh Verma, Sharad Khare --Epigenetic Regulation of miRNAs in Breast Cancer Formation and Progression /Zhiqian Zhang ... [et al.] --Epigenetic Variations of Stem Cell Markers in Cancer /Sripathi M. Sureban, Dongfeng Qu, Courtney W. Houchen --Recent Updates on Epigenetic Biomarkers for Prostate Cancer /Karen Chiam, Tanya Kate Day, Tina Bianco-Miotto --Epigenetics and Racial Disparities in Prostate Cancer /Benjamin A. Rybicki --Epigenetic Signatures of Breast Cancer Genes /Shrikant Anant, Animesh Dhar, Satish Ramalingam --Exploiting Epigenetic Modifiers to Circumvent Melanoma Dual Resistance to TCR-Engineered Immunotherapy- and BRAF V⁶⁰⁰E-Kinase Inhibitor /Ali R. Jazirehi CLS, --The Role of Epigenetics in Radiation Therapy and the DNA Damage Response /Steven P. Zielske --Plant Polyphenols as Epigenetic Modulators of Glutathione S-Transferase P1 Activity /Vijay S. Thakur, Sanjay Gupta --Epigenetic Regulations of mRNAs and miRNAs by Nutraceuticals /Yiwei Li ... [et al.] --Towards Curative Cancer Therapy with Maspin: A Unique Window of Opportunity to Target Cancer Dormancy /Alexander Kaplun, M. Margarida Bernardo, Sijana Dzinic.
  • Chromatin remodeling factors and DNA replication -- Epigenetic inheritance of chromatin states mediated by polycomb and trithorax group proteins in drosophila -- How to pack the genome for a safe trip -- Chromatin modifications on the inactive x chromosome -- Chromatin mechanisms in drosophila dosage compensation -- DNA methylation in epigenetic control of gene expression -- The epigenetic breakdown of cancer cells: from DNA methylation to histone modifications -- Developmental regulation of the beta-globin gene locus -- Epigenetic regulation of mammalian imprinted genes: from primary to functional imprints -- Seed development and genomic imprinting in plants.
  • Epigenetics and disease 2011, Springer
  • Epigenetics and cancer: DNA methylation / Santiago Ropero and Manel Esteller -- Epigenetics and cancer: histone modifications / Mario F. Fraga and Manel Esteller -- Epigenetic drugs: DNA demethylating agents / Ehab Atallah, Guillermo Garcia-Manero -- Epigenetic drugs: histone deacetylase inhibitors / Melissa Peart, Ricky W. Johnstone -- Sirtuins in biology and disease / Alejandro Vaquero, Danny Reinberg -- MicroRNAs in cell biology and disease / Muller Fabbri, Carlo M. Croce, George A. Calin -- Chromatin modifications by polycomb complexes / Miguel Vidal -- Epigenetics and its genetic syndromes / Richard J. Gibbons -- Epigenetics and immunity / Esteban Ballestar and Bruce C. Richardson -- Aetiology of major psychosis: why do we need epigenetics? / Gabriel Oh and Arturas Petronis -- Epigenetics and cardiovascular disease / Gertrund Lund and Silvio Zaina -- Epigenetics and plant biology / Luis Valledor ... [et al.] -- Epigenetics, environment, and evolution / Douglas M. Ruden, Parsa Rasouli, Xiangyi Lu -- Epigenetics and epigenomics / Jose Ignacio Martin-Subero, Reiner Siebert.
  • Epigenetics of aging 2010, Springer

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There are 120 high level MeSH Subject Headings under which all MeSH terms fall. Choose a subject heading to see the journals Lane offers in that subject area.

 

[print] 2014

New Book

Authored by
Stanford Alumni - Jeremy M. Berg
and
Michelle L. Kienholz

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