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Medical Informatics

  • Also available: Print – 2015
    This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conformation searches. This book will be of immense value to researchers and students in the fields of bioinformatics, computational biology and chemistry. Dr. Dongqing Wei is a Professor at the Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China. His research interest is in the general area of structural bioinformatics.
  • Analysis of clinical trials using SAS : a practical guide 2005
    books24x7, SUNet ID login required.
    2005 ProQuest Safari
    Analysis of Stratified Data -- Multiple Comparisons and Multiple Endpoints -- Analysis of Safety and Diagnostic Data -- Interim Data Monitoring -- Analysis of Incomplete Data.
  • "Adding topics useful to medical statisticians, this new edition of a popular intermediate-level reference explores the use of SAS for analyzing medical data. A new chapter on visualizing data includes a detailed account of graphics for investigating data and smoothing techniques. The book also includes new chapters on measurement in medicine, epidemiology/observational studies, meta-analysis, Bayesian methods, and handling missing data. The book maintains its example-based approach, with SAS code and output included throughout and available online"--Provided by publisher.
  • Also available: Print – 2008
    This assessment tool describes in detail how to undertake a first baseline assessment of a national HIS. The assessment process is intended to be both catalytic and synergistic. It should move stakeholders towards a shared and broader vision of a more coherent, integrated, efficient and useful system. The gap between the existing system and this new vision will be an important stimulus for moving to the next stage of planning national HIS reform. Such an assessment process can also be a mechanism for directly engaging stakeholders and for reinforcing broad-based consensus-building.--Publisher's description.
  • Automated data analysis using Excel
    Click LINK above for Print location/circulation status.
    2007 CRCnetBASE
  • Time-frequency analysis : wavelet transforms -- Chaos theory -- Classifier designs -- Electroencephalograms and epilepsy -- Analysis of EEGs in an epileptic patient using wavelet transform -- Wavelet-chaos methodology for analysis of EEGs and EEG sub-bands -- Mixed-band wavelet-chaos neural network methodology -- Principal component analysis-enhanced cosine radial basis function neural network -- Alzheimer's disease and models of computation : imaging, classification, and neural models -- Alzheimer's disease : models of computation and analysis of EEGs -- A spatio-temporal wavelet-chaos methodology for EEG-based diagnosis of Alzheimer's disease -- Spiking neural networks : spiking neurons and learning algorithms -- Improved spiking neural networks with application to EEG classification and epilepsy and seizure detection -- A new supervised learning algorithm for multiple spiking neural networks -- Applications of multiple spiking neural networks : EEG classification and epilepsy and seizure detection.
  • Print Material
  • The book introduces the bioinformatics tools, databases and strategies for the translational research, focuses on the biomarker discovery based on integrative data analysis and systems biological network reconstruction. With the coming of personal genomics era, the biomedical data will be accumulated fast and then it will become reality for the personalized and accurate diagnosis, prognosis and treatment of complex diseases. The book covers both state of the art of bioinformatics methodologies and the examples for the identification of simple or network biomarkers. In addition, bioinformatics software tools and scripts are provided to the practical application in the study of complex diseases. The present state, the future challenges and perspectives were discussed. The book is written for biologists, biomedical informatics scientists and clinicians, etc.
  • Overview of sequencing technology platforms / Samuel Myllykangas, Jason Buenrostro, and Hanlee P. Ji -- Applications of high-throughput sequencing / Rodrigo Goya, Irmtraud M. Meyer, and Marco A. Marra -- Computational infrastructure and basic data analysis for high-throughput sequencing / David Sexton -- Base-calling for bioinformaticians / Mona A. Sheikh and Yaniv Erlich -- De novo short-read assembly / Douglas W. Bryant Jr. and Todd C. Mockler -- Short-read mapping / Paolo Ribeca -- DNA-protein interaction analysis (ChIP-Seq) / Geetu Tuteja -- Generation and analysis of genome-wide DNA methylation maps / Martin Kerick, Axel Fischer, and Michal-Ruth Schweiger -- Differential expression for RNA sequencing (RNA-Seq) data : mapping, summarization, statistical analysis, and experimental design / Matthew D. Young ... [et al.] -- MicroRNA expression profiling and discovery / Michael Hackenberg -- Dissecting splicing regulatory network by integrative analysis of CLIP-Seq data / Michael Q. Zhang -- Analysis of metagenomics data / Elizabeth M. Glass and Folker Meyer -- High-throughput sequencing data analysis software : current state and future developments / Konrad Paszkiewicz and David J. Studholme.
  • [Publisher-supplied data] Presenting an area of research that intersects with and integrates diverse disciplines, including molecular biology, applied informatics, and statistics, among others, Bioinformatics for Omics Data: Methods and Protocols collects contributions from expert researchers in order to provide practical guidelines to this complex study. Divided into three convenient sections, this detailed volume covers central analysis strategies, standardization and data-management guidelines, and fundamental statistics for analyzing Omics profiles, followed by a section on bioinformatics approaches for specific Omics tracks, spanning genome, transcriptome, proteome, and metabolome levels, as well as an assortment of examples of integrated Omics bioinformatics applications, complemented by case studies on biomarker and target identification in the context of human disease. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Bioinformatics for Omics Data: Methods and Protocols serves as an ideal guide to scientists of all backgrounds and aims to convey the appropriate sense of fascination associated with this research field.
  • The emergence of bioinformatics : historical perspective, quick overview and future trends / Christos A. Ouzounis -- The statistical design and interpretation of microarray experiments / Kevin K. Dobbin and Richard M. Simon -- Whole-genome analysis of cancer / Steven A. Enkemann ... [et al.] -- Bioinformatics approaches to the analysis of the transcriptome of animal models of cancer / Mark J. Hoenerhoff ... [et al.] -- Significance of aberrant expression of miRNAs in cancer cells / George A. Calin ... [et al.] -- Proteomic methods in cancer research / Scot Weinberger and Egisto Boschetti -- Comprehensive genomic profiling for biomarker discovery for cancer detection, diagnostics and prognostics / Xiaofeng Zhou ... [et al.] -- Gene expression profiling of the leukemias : oncogenesis, drug responsiveness, and prediction of clinical outcome / Lars Bullinger, Hartmut Dohner, and Jonathon R. Pollack -- Personalized medicine in the clinical management of colorectal cancer / Anthony El-Khoueiry and Heinz Josef Lenz -- PIK3CA gene alterations in human cancers / Sérgia Velho, Carla Oliveira, and Raquel Seruca.
  • "This book is intended to serve both as a textbook for short bioinformatics courses and as a base for a self-teaching endeavor. "--Introduction.
  • Print Material
  • Biomedical Informatics: Computer Applications in Health Care and Biomedicine meets the growing demand of practitioners, researchers, educators, and students for a comprehensive introduction to key topics in the field and the underlying scientific issues that sit at the intersection of biomedical science, patient care, public health, and information technology (IT). This 4th edition reflects the remarkable changes in both computing and health care that continue to occur and the exploding interest in the role that IT must play in care coordination and the melding of genomics with innovations in clinical practice and treatment. New chapters have been introduced on the health information infrastructure, consumer health informatics, telemedicine, translational bioinformatics, clinical research informatics, and health IT policy, while the others have all undergone extensive revisions, in many cases with new authors. The organization and philosophy are unchanged, focusing on the science of information and knowledge management and the role of computers and communications in modern biomedical research, health, and health care. Emphasizing the conceptual basis of the field rather than technical details, it provides an introduction and extensive bibliography so that readers can comprehend, assess, and utilize biomedical informatics and health IT. The volume focuses on easy-to-understand examples, a guide to additional literature, chapter summaries, and a comprehensive glossary with concise definitions of recurring terms for self-study or classroom use.
  • Also available: Print – 2006
  • Biomedical Natural Language Processing" is a comprehensive tour through the classic and current work in the field. It discusses all subjects from both a rule-based and a machine learning approach, and also describes each subject from the perspective of both biological science and clinical medicine. The intended audience is readers who already have a background in natural language processing, but a clear introduction makes it accessible to readers from the fields of bioinformatics and computational biology, as well. The book is suitable as a reference, as well as a text for advanced courses in biomedical natural language processing and text mining.
  • Print Material
  • BYOD for healthcare 2014
    "Where once end users queued up to ask information technology (IT) permission to buy a new computer or new version of software, they are now bypassing IT altogether and buying it on their own. From laptops to smartphones. From iPads to any number of software apps, end users have tasted their freedom and love them. IT is just never going to be the same. Welcome to the brave new world of "bring your own devices" (BYODs). The roots of BYOD can be traced back to the consumerization of all things technology, where technical wizardry is no longer purely the domain of the geek who works for the IT department. Geeks can now be found all over the organization. These workers want to make their own technology choices, whether those choices are on the "approved" list or the company pays for it. Seventy percent of organizations have already adopted BYOD. Gartner predicts this number to increase to 90% by 2014. Most interestingly, a very high percentage of workers think that it is a right rather than a privilege to use their own devices at work. So, it is really not a question of if. It is not even a question of when. It is a question of will you be ready. Of course, the healthcare industry is not the same as most other industries. Hospitals, clinics, and medical offices are not stores, hotels, or assembly lines, although all of these industries are affected by the economy, productivity, regulation, and the need for assessment. hBYOD: Adapting BYOD for the Healthcare Industry provides the guidance necessary for living in this brave new world. You will first learn how to understand these new end users and their demands, as well as the strategic and tactical ramifications of these demands. BYOD will then cover the broad range of technical considerations such as selection, "-- Provided by publisher.
  • Also available: Print – 2007
  • CDAtm book 2011
    Organization of This Book -- Clinical Documentation -- The HL7 Clinical Document Architecture -- Extensible Markup Language -- Basic Data Types -- Text and Multimedia -- Demographic Data -- Codes and Vocabularies -- Codes -- Dates and Times -- Collections -- HL7 Version 3 Modeling -- Clinical Document Infrastructure -- The CDAtm Header -- The CDAtm Body -- Clinical Statements in the CDAtm -- HL7 Version 2 to CDAtm Release 2 -- Extracting Data from a CDAtm Document -- Templates -- Validating the Content of a CDAtm Document -- Implementation Guides on CDAtm.
  • Chemical library design 2011
    Springer Protocols
    Historical overview of chemical library design / Roland E. Dolle -- Chemoinformatics and library design / Joe Zongxiang Zhou -- Molecular library design using multi-objective optimization methods / Christos A. Nicolaou and Christos C. Kannas -- A scalable approach to combinatorial library design / Puneet Sharma, Srinivasa Salapaka, and Carolyn Beck -- Application of Free-Wilson selectivity analysis for combinatorial library design / Simone Sciabola ... [et al.] -- Application of QSAR and shape pharmacophore modeling approaches for targeted chemical library design / Jerry O. Ebalunode, Weifan Zheng, and Alexander Tropsha -- Combinatorial library design from reagent pharmacophore fingerprints / Hongming Chen, Ola Engkvist, and Niklas Blomberg -- Docking methods for structure-based library design / Claudio N. Cavasotto and Sharangdhar S. Phatak -- Structure-based library design in efficient discovery of novel inhibitors / Shunqi Yan and Robert Selliah -- Structure-based and property-compliant library design of 11[beta]-HSD1 adamantyl amide inhibitors / Genevieve D. Paderes ... [et al.] -- Design of screening collections for successful fragment-based lead discovery / James Na and Qiyue Hu -- Fragment-based drug design / Eric Feyfant ... [et al.] -- LEAP into the Pfizer Global Virtual Library (PGVL) space : creation of readily synthesizable design ideas automatically / Qiyue Hu ... [et al.] -- The design, annotation, and application of a kinase-targeted library / Hualin Xi and Elizabeth A. Lunney -- PGVL hub : an integrated desktop tool for medicinal chemists to streamline design and synthesis of chemical libraries and singleton compounds / Zhengwei Peng ... [et al.] -- Design of targeted libraries against the human Chk1 kinase using PGVL hub / Xengwei Peng and Qiyue Hu -- GLARE : a tool for product-oriented design of combinatorial libraries / Jean-François Truchon -- CLEVER : a general design tool for combinatorial libraries / Tze Hau Lam ... [et al.].
  • Some Trends in Chem(o)informatics / Wendy A. Warr -- Molecular Similarity Measures / Gerald M. Maggiora and Veerabahu Shanmugasundaram -- The Ups and Downs of Structure-Activity Landscapes / Rajarshi Guha -- Computational Analysis of Activity and Selectivity Cliffs / Lisa Peltason and Jurgen Bajorath -- Similarity Searching Using 2D Structural Fingerprints / Peter Willett -- Predicting the Performance of Fingerprint Similarity Searching / Martin Vogt and Jurgen Bajorath -- Bayesian Methods in Virtual Screening and Chemical Biology / Andreas Bender -- Reduced Graphs and Their Applications in Chemoinformatics / Kristian Birchall and Valerie J. Gillet -- Fragment Descriptors in Structure-Property Modeling and Virtual Screening / Alexandre Varnek -- The Scaffold Tree: An Efficient Navigation in the Scaffold Universe / Peter Ertl, Ansgar Schuffenhauer, and Steffen Renner -- Pharmacophore-Based Virtual Screening / Dragos Horvath -- De Novo Drug Design / Markus Hartenfeller and Gisbert Schneider -- Classification of Chemical Reactions and Chemoinformatics Processing of Enzymatic Transformations / Diogo A.R.S. Latino and Joao Aires-de-Sousa -- Informatics Approach to the Rational Design of siRNA Libraries / Jerry O. Ebalunode, Charles Jagun, and Weifan Zheng -- Beyond Rhodopsin: G Protein-Coupled Receptor Structure and Modeling Incorporating the b2-adrenergic and Adenosine A2A Crystal Structures / Andrew J. Tebben and Dora M. Schnur -- Methods for Combinatorial and Parallel Library Design / Dora M. Schnur, Brett R. Beno, Andrew J. Tebben, and Cullen Cavallaro -- The Interweaving of Cheminformatics and HTS / Anne Kummel and Christian N. Parker -- Computational Systems Chemical Biology / Tudor I. Oprea, Elebeoba E. May, Andrei Leitao, and Alexander Tropsha -- Ligand-Based Approaches to In Silico Pharmacology / David Vidal, Ricard Garcia-Serna, and Jordi Mestres -- Molecular Test Systems for Computational Selectivity Studies and Systematic Analysis of Compound Selectivity Profiles / Dagmar Stumpfe, Eugen Lounkine, and Jurgen Bajorath -- Application of Support Vector Machine-Based Ranking Strategies to Search for Target-Selective Compounds / Anne Mai Wassermann, Hanna Geppert, and Jurgen Bajorath -- What Do We Know?: Simple Statistical Techniques that Help / Anthony Nicholls.
  • Clinical bioinformatics 2008
    Springer Protocols
    In silico gene discovery / Bing Yu -- Whole genome-wide association study using Affymetrix SNP chip : a two-stage sequential selection method to identify genes that increase the risk of developing complex diseases / Howard H. Yang ... [et al.] -- Utilizing HapMap and tagging SNPs / Christopher A. Haiman and Daniel O. Stram -- Measuring the effects of genes and environment on complex traits / Jennifer H. Barrett -- Microarrays-planning your experiment / Jean Yee Hwa Yang -- Clinical uses of microarrays in cancer research / Carl Virtanen and James Woodgett -- Microarrays-analysis of signaling pathways / Anassuya Ramachandran ... [et al.] -- Microarrays-identifying molecular portraits for prostate tumors with different Gleason patterns / Alexandre Mendes, Rodney J. Scott, and Pablo Moscato -- Microarrays for the study of viral gene expression during human cytomegalovirus latent infection / Barry Slobedman and Allen K.L. Cheung -- Computer-assisted reading of DNA sequences / Huong Le ... [et al.] -- Evaluating DNA sequence variants of unknown biological significance / Scott A. Grist, Andrew Dubowsky, and Graeme Suthers -- Developing a DNA variant database / David C.Y. Fung -- Protein comparative sequence analysis and computer modeling / Brett D. Hambly, Cecily E. Oakley, and Piotr G. Fajer -- Identification and characterization of microbial proteins using peptide mass fingerprinting strategies / Jonathan W. Arthur -- Statistical analysis of image data provided by two-dimensional gel electrophoresis for discovery proteomics / Ben Crossett ... [et al.] -- Online resources for the molecular contextualization of disease / Chi N.I. Pang and Marc R. Wilkins -- Web-based resources for clinical bioinformatics / Anthony M. Joshua and Paul C. Boutros -- Developing decision support systems in clinical bioinformatics / Vitali Sintchenko and Enrico Coiera -- eConsulting / Siaw-Teng Liaw and Peter Schattner.
  • This book examines the nature of medical knowledge, how it is obtained, and how it can be used for decision support. It provides complete coverage of computational approaches to clinical decision-making. Chapters discuss data integration into healthcare information systems and delivery to point of care for providers, as well as facilitation of direct to consumer access. A case study section highlights critical lessons learned, while another portion of the work examines biostatistical methods including data mining, predictive modelling, and analysis. This book additionally addresses organizational, technical, and business challenges in order to successfully implement a computer-aided decision-making support system in healthcare delivery.
  • 2014 ClinicalKey
    Sect. 1: Computer-based clinical decision support: overview, status, and challenges. Ch. 1. Definition, scope and challenges / Robert A. Greenes -- Ch. 2. A brief history of clinical decision support / Robert A. Greenes -- Ch. 3. Features of computer-based clinical decision support / Robert A. Greenes -- Ch. 4. The role of quality measurement and reporting feedback as a driver for care improvement / Floyd Eisenberg -- Sect. 2: Experience with CDS development and adoption : case studies, national initiatives, and lessons learned. Ch. 5. Regenstrief medical informatics / Paul Biondich, [et al.] -- Ch. 6. Patients, doctors, and information technology : clinical decision support at Brigham and Women's Hospital and Partners HealthCare / Adam Wright and David W. Bates -- Ch. 7. Computer-based approaches to improving healthcare quality and safety at LDS Hospital / R. Scott Evans -- Ch. 8. International dimensions of clinical decision support / Hamish Fraser and Jeremy Wyatt -- Ch. 9. Current state of CDS utilization / Robert A. Greenes -- Sect. 3: Sources of knowledge for clinical decision support. Ch. 10. Human-intensive techniques / Vimla L. Patel and Edward H. Shortliffe -- Ch. 11. Generation of knowledge for clinical decision support / Michael E. Matheny and Lucila Ohno-Machado -- Ch. 12. Modernizing evidence synthesis for evidence-based medicine / Byron C. Wallace, [et al.] -- Ch. 13. Big data and population-based decision support / Michael A. Krall, Adi V. Gundlapalli and Matthew H. Samore -- Ch. 14. Clinical decision support for personalized medicine / Brandon M. Welch, [et al.]. Sect. 4: The technology of clinical decision support. Ch. 15. Decision rules and expressions / Robert A. Jenders -- Ch. 16. Guidelines and workflow models / Mor Peleg and Arturo González-Ferrer -- Ch. 17. Ontologies, vocabularies and data models / Stanley M. Huff, [et al.] -- Ch. 18. Grouped knowledge elements / Margarita Sordo and Aziz A. Boxwala -- Ch. 19. Infobuttons and point of care access to knowledge / Guilherme Del Fiol, Hong Yu and James J. Cimino -- Ch. 20. Formal representations and semantice web technologies / Alan Rector and Davide Sottara -- Ch. 21. The role of standards / Kensaku Kawamoto and Robert A. Greenes -- Sect. 5: Adoption of clinical decision support. Ch. 22. Cognitive considerations for health information technology / Amy Franklin and Jiajie Zhang -- Ch. 23. Organizational and cultural change / Joan S. Ash and Timothy H. Hartzog -- Ch. 24. Managing the investment in clinical decision support / John Glaser and Tonya Hongsermeier -- Ch. 25. A clinical decision support implementation guide : practical considerations / Donald Levick and Jerome Osheroff -- Ch. 26. Legal and regulatory issues related to the use of clinical software in health care delivery / Steven H. Brown and Randolph A. Miller -- Ch. 27. Consumers and clinical decision support / Nananda Col and Rosaly Correa-de-Araujo -- Sect. 6: The journey to widespread use of clinical decision support. Ch. 28. A clinical knowledge management program / Roberto A. Rocha, [et al.] -- Ch. 29. Integration of knowledge resources into applications to enable CDS / Kensaku Kawamoto, Emory Fry and Robert Greenes -- Ch. 30. Looking ahead : the road to broad adoption / Robert A. Greenes.
  • Overview of clinical decision support systems / Eta S. Berner and Tonya J. La Londe -- Mathematical foundations of decision support systems / S. Andrew Spooner -- Data mining and clinical decision support systems / J. Michael Hardin and David C. Chhieng -- Design and implementation issues / Jerome H. Carter -- Diagnostic decision support systems / Randolph A. Miller and Antoine Geissbuhler -- Ethical and legal issues in decision support / Kenneth W. Goodman -- Clinical trials of information interventions / E. Andrew Balas and Suzanne Austin Boren -- Clinical decision support at Intermountain Healthcare / Peter J. Haug ... [et al.] -- Clinical decision support within the Regenstrief medical record system / Burke W. Mamlin ... [et al.] -- Decision support during inpatient care provider order entry : the Vanderbilt experience / Randolph A. Miller ... [et al.] -- Decision support for patients / Holly B. Jimison, Paul P. Sher, Jennifer J.B. Jimison.
  • "This book provides foundational coverage of key areas, concepts, constructs, and approaches of medical informatics as it applies to clinical research activities, in both current settings and in light of emerging policies. The field of clinical research is fully characterized (in terms of study design and overarching business processes), and there is emphasis on information management aspects and informatics implications (including needed activities) within various clinical research environments. The purpose of the book is to provide an overview of clinical research (types), activities, and areas where informatics and IT could fit into various activities and business practices. This book introduces and applies informatics concepts only as they have particular relevance to clinical research settings"--Provided by publisher.
  • 1. What are cloud services? -- 2. Benefits and drawbacks of cloud services -- 3. Cloud technologies -- 4. Cloud-based solutions for healthcare IT -- 5. HIPAA and HITECH : cloud perspective -- 6. Adopting cloud services -- 7. Interoperability -- 8. Cloud-based personal health records (PHR) -- 9. Case studies.
  • "Enormous advances in information technology have permeated essentially all facets of life in the past two decades. Formidable challenges remain in fostering tools that enhance productivity but are sensitive to work practices. Cognitive Informatics (CI) is the multidisciplinary study of cognition, information and computational sciences that investigates all facets of human computing including design and computer-mediated intelligent action, thus is strongly grounded in methods and theories from cognitive science. As an applied discipline, it has a close affiliation with human factors and human-computer interaction, and provides a framework for the analysis and modeling of complex human performance in technology-mediated settings and contributes to the design and development of better information systems. In recent years, CI has emerged as a distinct area with special relevance to biomedicine and health care. In addition, it has become a foundation for education and training of health informaticians, the Office of the National Coordinator for Health Information Technology initiating a program including CI as one of its critical elements to support health IT curriculum development. This book represents a first textbook on cognitive informatics and will focus on key examples drawn from the application of methods and theories from CI to challenges pertaining to the practice of critical-care medicine (CCM). Technology is transforming critical care workflows and re-organizing patient care management processes. CCM has proven to be a fertile test bed for theories and methods of cognitive informatics. CI, in turn, has contributed much to our understanding of the factors that result in complexity and patient errors. The topic is strongly interdisciplinary and will be important for individuals from a range of academic and professional backgrounds, including critical care specialists, psychologists, computer scientists, medical informaticians, and anthropologists"--Provided by publisher.
  • Part I. Introduction to simulation -- Part II. Simulation modalities and technologies -- Part III. Simulation for healthcare disciplines -- Part IV. Professional development in simulation -- Part V. Program development in simulation -- Appendices -- Index.
  • Print Material
  • This book introduces the reader to modern computational and statistical tools for translational epigenomics research. Over the last decade, epigenomics has emerged as a key area of molecular biology, epidemiology and genome medicine. Epigenomics not only offers us a deeper understanding of fundamental cellular biology, but also provides us with the basis for an improved understanding and management of complex diseases. From novel biomarkers for risk prediction, early detection, diagnosis and prognosis of common diseases, to novel therapeutic strategies, epigenomics is set to play a key role in the personalized medicine of the future. In this book we introduce the reader to some of the most important computational and statistical methods for analyzing epigenomic data, with a special focus on DNA methylation. Topics include normalization, correction for cellular heterogeneity, batch effects, clustering, supervised analysis and integrative methods for systems epigenomics. This book will be of interest to students and researchers in bioinformatics, biostatistics, biologists and clinicians alike. Dr. Andrew E. Teschendorff is Head of the Computational Systems Genomics Lab at the CAS-MPG Partner Institute for Computational Biology, Shanghai, China, as well as an Honorary Research Fellow at the UCL Cancer Institute, University College London, UK.
  • This greatly expanded 2nd edition provides a practical introduction to - data processing with Linux tools and the programming languages AWK and Perl- data management with the relational database system MySQL, and- data analysis and visualization with the statistical computing environment R for students and practitioners in the life sciences. Although written for beginners, experienced researchers in areas involving bioinformatics and computational biology may benefit from numerous tips and tricks that help to process, filter and format large datasets. Learning by doing is the basic concept of this book. Worked examples illustrate how to employ data processing and analysis techniques, e.g. for - finding proteins potentially causing pathogenicity in bacteria, - supporting the significance of BLAST with homology modeling, or- detecting candidate proteins that may be redox-regulated, on the basis of their structure. All the software tools and datasets used are freely available. One section is devoted to explaining setup and maintenance of Linux as an operating system independent virtual machine. The author's experiences and knowledge gained from working and teaching in both academia and industry constitute the foundation for this practical approach.
  • 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.
  • Bioinformatic Tools for the Search of Disease-Associated Variations / Stefan Coassin, Anita Kloss-Brandstätter and Florian Kronenberg -- Cloud Computing / Bringing Computational Power to Medical Genetics / Lukas Forer, Sebastian Schönherr, Hansi Wei€ensteiner, Günther Specht and Florian Kronenberg, et al. -- High-Throughput Characterization and Comparison of Microbial Communities / Bettina Halwachs, Gregor Gorkiewicz and Gerhard G. Thallinger -- Microarray Meta-Analysis: From Data to Expression to Biological Relationships / Julia Feichtinger, Gerhard G. Thallinger, Ramsay J. McFarlane and Lee D. Larcombe -- Analysis of Labeled Quantitative Mass Spectrometry Proteomics Data / Florian Paul Breitwieser and Jacques Colinge -- Lipidomics, Mass Spectrometry, and Bioinformatics / Jürgen Hartler, Harald C. Köfeler, Christopher J. O. Baker, Ravi Tharakan and Gerhard G. Thallinger -- Protein Sequence-Structure-Function-Network Links Discovered with the ANNOTATOR Software Suite: Application to ELYS/Mel-28 / Georg Schneider, Westley Sherman, Durga Kuchibhatla, Hong Sain Ooi and Fernanda L. Sirota, et al. -- 3D Structure and Drug Design / Kristina Djinović-Carugo and Oliviero Carugo -- Integrating Biomolecular and Clinical Data for Cancer Research: Concepts and Challenges / Pornpimol Charoentong, Hubert Hackl, Bernhard Mlecnik, Gabriela Bindea and Jerome Galon, et al. -- Applied Data Mining: From Biomarker Discovery to Decision Support Systems / M. Osl, M. Netzer, S. Dreiseitl and C. Baumgartner -- Network-Based Methods for Computational Diagnostics by Means of R / Laurin A. J. Mueller, Matthias Dehmer and Frank Emmert-Streib.
  • Introducing computational systems biology / Roland Eils, Andres Kriete -- Structural systems biology : modeling interactions and networks for systems studies / Robert B. Russell, Gordana Apic, Olga Kalinina, Leonardo Trabuco, Matthew J. Betts, Qianhao Lu -- Understanding principles of the dynamic biochemical networks of life through systems biology / Hans V. Westerhoff, Fei He, Ettore Murabito, Frederic Cremazy, Matteo Barberis -- Biological foundations of signal transduction, systems biology and aberrations in disease / Ursula Klingmuller, Marcel Schilling, Sofia Depner, Lorenza A. D'Alessandro -- Complexities in quantitative systems analysis of signaling networks / Christina Kiel, Luis Serrano -- Gene networks : estimation, modeling, and simulation / Seiya Imoto, Hiroshi Matsuno, Satoru Miyano -- Reconstruction of metabolic network from genome information and its structural and functional analysis / Hong-Wu Ma, An-Ping Zeng -- Standards, platforms, and applications / Stanley Gu, Herbert Sauro -- Databases, standards, and modeling platforms for systems biology / Juergen Eils, Elena Herzog, Baerbel Felder, Christian Lawerenz, Roland Eils -- Computational models for circadian rhythms : deterministic versus stochastic approaches / Jean-christophe Leloup, Didier Gonze, Albert Goldbeter -- Top-down dynamical modeling of molecular regulatory networks / Reinhard Laubenbacher, Pedro Mendes -- Discrete gene network models for understanding multicellularity and cell reprogramming : from network structure to attractor landscapes landscape / Joseph Xu Zhou, Xiaojie Qiu, Aymeric Fouquier D'Herouel, Sui Huang -- Stochastic simulations of cellular processes : from single cells to colonies / John Cole, Mike J. Hallock, Piyush Labhsetwar, Joseph R. Peterson, John E. Stone, Zaida Luthey-Schulten -- Advances in machine learning for processing and comparison of metagenomic data / Jean-Luc Bouchot, William L. Trimble, Gregory Ditzler, Yemin Lan, Steve Essinger, Gail Rosen -- Systems biology of infectious diseases and vaccines / Helder I. Nakaya -- From cell behavior to tissue deformation : computational modeling and simulation of early animal embryogenesis with the mecagen platform / Julien Delile, Ren Doursat, Nadine Peyriras -- Developing a systems biology of aging / Andres Kriete, Mathieu Cloutier -- Morphometric analysis of tissue heterogeneity in glioblastoma multiforme -- Applications in cancer research : mathematical models of apoptosis / Stefan M. Kallenberger, Stefan Legewie, Roland Eils.
  • Introducing computational systems biology / Andres Kriete and Roland Eils -- Enabling information and integration technologies for systems biology. Databases for systems biology / Jürgen Eils ... [et al.] -- Natural language processing and ontology-enhanced biomedical literature mining for systems biology / Xiaohua Hu -- Integrated imaging informatics / Barham Parvin ... [et al.] -- Simpathica : a computational systems biology tool within the valis bioinformatics environment / Bud mishra ... [et al.] -- Standards, platforms, and applications / Herbert M. Sauro -- Foundations of biochemical network analysis and modeling. Introduction to computational models of biochemical reaction networks / F.J. Bruggeman ... [et al.] -- Biological foundations of signal transduction and the systems biology perspective / Ursula Klingmüller -- Reconstruction of metabolic network from genome information and its structural and functional analysis / Hong-Wu Ma and An-Ping Zeng -- Integrated regulatory and metabolic models / Markus W. Covert -- Computer simulations of dynamic networks. A discrete approach to network modeling / Reinhard Laubenbacher and Pedro Mendes -- Gene networks : estimation, modeling and simulation / Seiya Imoto, Hiroshi Matsuno, and Satoru Miyano -- Computational models for circadian rhythms : deterministic versus stochastic approaches / Jean-Christophe Leloup, Didier Gonze, and Albert Goldbeter -- Multi-scale representations of cells and emerging phenotypes. Multistability and multicellularity : cell fates as high-dimensional attractors of gene regulatory networks / Sui Huang -- Spatio-temporal systems biology / Avijit ghosh ... [et al.] -- Cytomics--from cell states to predictive medicine / Günter Valet ... [et al.] -- The IUPS Physiome Project : progress and plans / Peter Hunter ... [et al.].
  • Functional Genomics and Molecular Networks Gene Expression Regulations in Complex Diseases: Down Syndrome as a Case Study / Marie-Claude Potier and Isabelle Rivals -- Reconstructing Models from Proteomics Data / Lysimachos Zografos, Andrew J. Pocklington and J. Douglas Armstrong -- Using Chemical Kinetics to Model Neuronal Signalling Pathways / Lukas Endler, Melanie I. Stefan, Stuart J. Edelstein and Nicolas Le Novère -- Breakdown of Mass-Action Laws in Biochemical Computation / Fidel Santamaria, Gabriela Antunes and Erik De Schutter -- Spatial Organization and Diffusion in Neuronal Signaling / Sherry-Ann Brown, Raquell M. Holmes and Leslie M. Loew -- The Performance (and Limits) of Simple Neuron Models: Generalizations of the Leaky Integrate-and-Fire Model / Richard Naud and Wulfram Gerstner -- Multi-compartmental Models of Neurons / Upinder S. Bhalla -- Noise in Neurons and Other Constraints / A. Aldo Faisal -- Methodological Issues in Modelling at Multiple Levels of Description / Kevin Gurney and Mark Humphries -- Virtues, Pitfalls, and Methodology of Neuronal Network Modeling and Simulations on Supercomputers / Anders Lansner and Markus Diesmann -- Co-operative Populations of Neurons: Mean Field Models of Mesoscopic Brain Activity / David T. J. Liley, Brett L. Foster and Ingo Bojak -- Cellular Spacing: Analysis and Modelling of Retinal Mosaics / Stephen J. Eglen -- Measuring and Modeling Morphology: How Dendrites Take Shape / Todd A. Gillette and Giorgio A. Ascoli -- Axonal Growth and Targeting / Duncan Mortimer, Hugh D. Simpson and Geoffrey J. Goodhill -- Encoding Neuronal Models in SBML / Sarah M. Keating and Nicolas Le Novère -- NeuroML / Padraig Gleeson, Volker Steuber, R. Angus Silver and Sharon Crook -- XPPAUT / Bard Ermentrout -- NEST by Example: An Introduction to the Neural Simulation Tool NEST / Marc-Oliver Gewaltig, Abigail Morrison and Hans Ekkehard Plesser.
  • Computational Toxicology: Methods and Applications for Risk Assessment is an essential reference on the translation of computational toxicology data into information that can be used for more informed risk assessment decision-making. This book is authored by leading international investigators who have real-world experience in relating computational toxicology methods to risk assessment. Key topics of interest include QSAR modeling, chemical mixtures, applications to metabolomic and metabonomic data sets, toxicogenomic analyses, applications to REACH informational strategies and much more. With a free companion website featuring an image bank from the book and web links for further research and reading, this authoritative reference is your complete guide to computational toxicology methods and applications to risk assessment. Authored by leading international researchers engaged in cutting-edge applications of computational methods for translating complex toxicological data sets into useful risk assessment information. Incorporates real-world examples of how computational toxicological methods have been applied to advance the science of risk assessment Provides the framework necessary for new technologies and fosters common vocabularies and principles upon which the effects of new chemical entities should be compared.
  • Consumer health informatics / Deborah Lewis, Betty L. Chang, Charles P. Friedman -- Empowered consumers / Patricia Flatley Brennan and Charles Safran -- Tailored health communication / Rita Kukafka -- Design and evaluation of consumer health information web sites / Gunther Eysenbach -- Information delivery methods / James H. Harrison, Jr. -- Delivery of online learning for healthcare consumers / Deborah Lewis -- Qualitative evaluation in consumer health informatics / Bonnie Kaplan -- Patient-to-patient communication: support groups and virtual communities / Gunther Eysenbach -- Electronic patient-centered communication: e-mail and other e-ways to communicate clinically / Daniel Z. Sands -- Consumer health vocabulary / Catherine Arnott Smith and P. Zoë Stavri -- Disability informatics / Richard Appleyard -- Ethical issues in consumer health informatics / Holly B. Jimison -- Social informatics and consumer health / Steve Sawyer -- Security of healthcare information systems / Roy Schoenberg -- The National Library of Medicine reaches out to consumers / Joyce E.B. Backus and Eve-Marie Lacroix -- Baby CareLink: collaborative tools to support families / Charles Safran and Denise Goldsmith -- CHOICEs: patients as participants in shared care planning at the point of care / Cornelia M. Ruland -- MedCERTAIN/MedCIRCLE: using semantic web technologies for quality management of health information on the web / Gunther Eysenbach -- The MI-HEART Project / Rita Kukafka, Yves A. Lussier, and James J. Cimino -- CHESS: 10 years of research and development in consumer health informatics for broad populations, including the underserved / David H. Gustafson ... [et al.].
  • Part I. Introducing the Domain and Levels of Service -- 1. Character of domain and organization of book -- 2. Economy 1: immanent mismatch between demand and supply of health care workforce -- 3. Level 0: searching-finding-trusting-acting-risking one's life? -- 4. Level 1: enhancing the provider- client relation through IT -- 5. Level 2: services without in-person contact between provider and client -- 6. Level 3: patient power on the web: the multifaceted role of personal health wisdom -- 7. Distinctive features of services conveyed through mobile apps -- Part II. Building Safety Nets Around the Active Client -- 8. Dimensions of patient risks and requirements for patient safety -- 9. Services for all stages of the metabolic syndrome and its consequences -- 10. Basic services reach out towards under-served populations -- 11. Smart homes: empowering the patient till the end -- 12. Partial solutions for patient safety -- Part III. Additional Methodology -- 13. Privacy and data protection: mission impossible? -- 14. The patient-centered electronic health record and patient portals -- 15. Scrutinized proof of effectiveness or cost effectiveness regarding patient reported outcomes -- 16. Economy 2: economic subsistence of services when research funding ends -- 17. Towards future consumer health informatics adapted health care legislation -- Trademarks -- Nomenclature -- General index -- Index of services.
  • "Mobile technology has transformed our lives, and personal genomics is revolutionizing biology. But despite the availability of technologies that can provide wireless, personalized health care at lower cost, the medical community has resisted change. In The Creative Destruction of Medicine, Eric Topol--one of the nation's top physicians--calls for consumer activism to demand innovation and the democratization of medical care." -- [Publisher-provided data]
  • Section I. Innovation and process considerations in the role of IS/IT in e-health. -- 1. Improving e-performance management in healthcare using intelligent IT solutions / Fatemeh Hoda Moghimi and Nilmini Wickramasinghe -- 2. An intelligence e-risk detection model to improve decision efficiency in the context of the orthopaedic operating room / Fatemeh Hoda Mogihim, Hossein Zadeh, and Nilmini Wickramasinghe -- 3. Healthcare information systems design : using a strategic improvisation model / Say Yen Teoh and Nilmini Wickramasinghe -- 4. Assimilation of healthcare information systems (HIS) : an analysis and critique / Hidayah Sulaiman and Nilmini Wichramasinghe -- 5. e-health in China : an evaluation / Yu Yun ... [et al.] -- 6. Improving the process of healthcare delivery in an outpatient environment : the case of a urology department / Chris Gonzalez and Nilmini Wickramasinghe -- 7. Adaptations for e-kiosk systems in Germany to develop barrier-free terminals for handicapped persons / Manuel Zwicker, Juergen Seitz, and Nilmini Wichramasinghe -- Section II. Design and organisation designing supportive and collaborative electronic health environments. -- 8. Collaborative approach for sustainable citizen-centered health care / Pirkko Nykänen and Antto Seppäla ̈-- 9. Strategies and solutions in e-health : a literature review / Marco De Marco, Francesca Ricciardi, and Jan vom Brocke -- 10. Online discussion forum as a means of peer support / R. Halonen -- 11. Designing persuasive health behavior change interventions / Tuomas Lehto -- 12. Accessiblility in the web for disabled people / Irene Krebs, Arnim Nethe, and Reetta Raitoharju -- Section III. The importance of people in e-health : lest we forget. -- 13. Knowledge management : often neglected but crucial to ehealth / Juerg P. Bleuer ... [et al.] -- 14. Patient Empowerment : a two way road / Lodewijk Bos -- 15. Citizen empowerment / Amir Hannan -- 16. E-health : focusing on people-centric dimensions / Rajeev K. Bali ... [et al.] -- 17. A model of estimating the direct benefits of implementing electronic data exchange of EMRs and state immunization information systems / Michael L. Popovich and Xiaohui Zhang -- Section IV. Innovation in e-health. -- 18. Business models for electronic healthcare services in Germany / S. Duennebeil, J. Leimeister, and H. Krcmar -- 19. Smart objects in healthcare : impact on clinical logistics / Martin Sedlmayr and Ulli Münch -- 20. Agency theory in e-healthcare and telemedicine : a literature study / Joerg Leukel ... [et al.] -- 21. Cost accounting and decision support for healthcare institutions / L. Waehlert, A. Wagner, and H. Czap -- 22. A comprehensive approach to the IT : clinial practice interface / David Zakim and Mark Dominik Alscher
  • Part I. Machine Learning Tools and Techniques: -- 1. What's it all about? -- 2. Input: concepts, instances, and attributes -- 3. Output: knowledge representation -- 4. Algorithms: the basic methods -- 5. Credibility: evaluating what's been learned -- Part II. Advanced Data Mining: -- 6. Implementations: real machine learning schemes -- 7. Data transformation -- 8. Ensemble learning -- 9. Moving on: applications and beyond -- Part III. The Weka Data Mining Workbench: -- 10. Introduction to Weka -- 11. The explorer -- 12. The knowledge flow interface -- 13. The experimenter -- 14 The command-line interface -- 15. Embedded machine learning -- 16. Writing new learning schemes -- 17. Tutorial exercises for the Weka explorer.
  • Deep sequencing data analysis 2013
    Springer Protocols
    Introduction to high-throughput sequencing experiments : design and bioinformatics analysis / Rachelly Normand and Itai Yanai -- Compressing resequencing data with GReEn / Armando J. Pinho, Diogo Pratas, and Sara P. Garcia -- On the accuracy of short read mapping / Peter Menzel ... [et al.] -- Statistical modeling of coverage in high-throughput data / David Golan and Saharon Rosset -- Assembly algorithms for deep sequencing data : basics and pitfalls / Nitzan Kol and Noam Shomron -- Short read mapping for exome sequencing / Xueya Zhou ... [et al.] -- Profiling short tandem repeats from short reads / Melissa Gymrek and Yaniv Erlich -- Exome sequencing analysis : a guide to disease variant detection / Ofer Isakov, Marie Perrone, and Noam Shomron -- Identifying RNA editing sites in miRNAs by deep sequencing / Shahar Alon and Eli Eisenberg -- Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS / Juw Won Park ... [et al.] -- Optimizing detection of transcription factor-binding sites in ChIP-seq experiments / Aleksi Kallio and Laura L. Elo -- Statistical analysis of ChIP-seq data with MOSAiCS / Guannan Sun ... [et al.] -- Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing / Lukasz J. Kielpinski ... [et al.].
  • "In the United States, approximately 14 million people have had cancer and more than 1.6 million new cases are diagnosed each year. However, more than a decade after the Institute of Medicine (IOM) first studied the quality of cancer care, the barriers to achieving excellent care for all cancer patients remain daunting. Care often is not patient-centered, many patients do not receive palliative care to manage their symptoms and side effects from treatment, and decisions about care often are not based on the latest scientific evidence. The cost of cancer care also is rising faster than many sectors of medicine--having increased to 125 billion in 2010 from 72 billion in 2004--and is projected to reach 173 billion by 2020. Rising costs are making cancer care less affordable for patients and their families and are creating disparities in patients' access to high-quality cancer care. There also are growing shortages of health professionals skilled in providing cancer care, and the number of adults age 65 and older--the group most susceptible to cancer--is expected to double by 2030, contributing to a 45 percent increase in the number of people developing cancer. The current care delivery system is poorly prepared to address the care needs of this population, which are complex due to altered physiology, functional and cognitive impairment, multiple coexisting diseases, increased side effects from treatment, and greater need for social support. Delivering High-Quality Cancer Care: Charting a New Course for a System in Crisis presents a conceptual framework for improving the quality of cancer care. This study proposes improvements to six interconnected components of care: (1) engaged patients; (2) an adequately staffed, trained, and coordinated workforce; (3) evidence-based care; (4) learning health care information technology (IT); (5) translation of evidence into clinical practice, quality measurement and performance improvement; and (6) accessible and affordable care. This report recommends changes across the board in these areas to improve the quality of care. Delivering High-Quality Cancer Care: Charting a New Course for a System in Crisis provides information for cancer care teams, patients and their families, researchers, quality metrics developers, and payers, as well as HHS, other federal agencies, and industry to reevaluate their current roles and responsibilities in cancer care and work together to develop a higher quality care delivery system. By working toward this shared goal, the cancer care community can improve the quality of life and outcomes for people facing a cancer diagnosis."--Publisher's description.
  • Part I Designing the User Study -- Overview -- Variables -- Design equation and statistics -- Between-subjects design -- Within-subject designs -- Advanced designs -- Part II Practical Tips -- Understanding main and interaction effects -- Conducting multiple comparisons -- Gold standard and user evaluations -- Recruiting and motivating study participants -- Institutional review board (IRB) approval -- Resources -- Part III Common Mistakes to Avoid -- Avoid bias -- Avoid missing the effect -- Avoid missing variables or conditions -- Other errors to avoid -- Appendix: cookbook for designing user studies in informatics.
  • Understanding human brain function is one of the most important endeavors in modern science. There is growing evidence that cognitive functions are executed by large-scale networks, comprising multiple interacting anatomically-connected brain areas. Although considerable progress has been made in understanding which specific brain areas are involved in particular cognitive functions, very little is known about the integrative functioning of large-scale brain networks. This is due in part to the lack of methods to pursue this line of research. This dissertation describes computational methods for detecting and characterizing large-scale human brain networks, combining data from task-free functional magnetic resonance imaging (fMRI) and structural diffusion tensor imaging (DTI), two complementary brain imaging modalities. Application of our methods to task-free fMRI and DTI data obtained from a wide range of subject populations provided new insights into how large-scale human brain networks develop, mature, and get disrupted in psychiatric and neurological disorders. More generally, this work demonstrates the power of our multimodal network-analytic approach to obtain a system-level understanding of brain function across the human lifespan.
  • Autoimmune diseases are painful and debilitating conditions which affect millions of people in the United States and all over the world. At present such conditions are often difficult to diagnose and many have no satisfactory treatment. Given the wealth and availability of genomic data such as genetic variation and gene expression, computational integrative methods provide a powerful opportunity to improve human health by refining the current knowledge about diagnostics, therapeutics and disease mechanism. For instance numerous genome-wide association studies (GWAS) performed across autoimmune diseases, provide a great opportunity to study disease relationships based on genetic variation. Comparing such profiles allows us to quantify allele-specific pair-wise relationships between these diseases to find two broad clusters of autoimmune disease. We furthermore find that certain polymorphisms, toggle SNPs, predispose individuals to one class of autoimmune disease but are protective against the other class. While studying allelic differences between diseases may point to key novel disease-specific genes and pathways, studying similarities across diseases might lead to discovery of common therapeutic options as well as common disease mechanisms. In particular we integrate genetic variation data across several studies to discover the role of a complement factor in Rheumatoid Arthritis and Multiple Sclerosis. Gene expression microarrays are also often used to study human diseases as well as the perturbation of biological systems by drug compounds providing an opportunity to discover novel relationships between diseases and drugs. We present a systematic computational method to predict novel therapeutic indications based on gene expression. We tested our top prediction for Crohn's disease (CD) using the rat model of inflammatory bowel disease (IBD), and successfully demonstrated the predicted efficacy of an anti-seizure drug in treating disease. In this work, we have showed that integrative computational tools can be used to improve diagnostics, learn more about disease mechanism and discover novel therapeutics for autoimmune disease.
  • Print Material
    For the past few decades, technology has been touted as the cure for all of healthcare's ills, yet medicine stubbornly resisted computerization-- until now. Thanks largely to billions of dollars in federal incentives, healthcare has finally gone digital. Wachter examines healthcare at the dawn of its computer age, and shows how technology is changing care at the bedside. He questions whether government intervention has been useful or destructive-- and does so with clarity, insight, humor, and compassion.
  • Making a good diagnostic image is only the beginning; keeping it good and diagnostically sound is a much more difficult proposition, one that is often neglected or forgotten by clinical practitioners. With anything digital, the assumption of persistent original quality opens a Pandora's box of medical fiascos. Poorly selected image interpolation, thoughtlessly used compression, confused image enhancement options and the like can transform a good original into a useless clutter of pixels. This book is dedicated to learning better options.
  • Part I. Introduction to DICOM -- 1. What Is DICOM? -- 2. How does DICOM work? 3. Where do you get DICOM from? -- Part II. DICOM and clinical data -- 4. A brief history of DICOM -- 5. Parlez-vous DICOM? 6. Medical images in DICOM -- Part III. DICOM comunications -- 7. DICOM SOPs: Basic 8. DICOM SOPs: Beyond basic -- 9. DICOM associations -- Part IV: DICOM media and security -- 10. DICOM media: files, folders, and DICOMDIRs -- 11. DICOM security -- 12. Incompatibility of compatible -- Part V. Advanced topics -- 13. DICOM and teleradiology -- 14. Standards and system integration in digital medicine -- 15. Disaster PACS planning and management -- 16. DICOM applications: usual and not -- 17. DICOM software development -- 18. DICOM implementation plans -- 19. DICOM FAQs.
  • The current unprecedented rate of digitization of longitudinal health data --- continuous device monitoring data, laboratory measurements, medication orders, treatment reports, reports of physician assessments --- allows visibility into patient health at increasing levels of detail. A clearer lens into this data could help improve decision making both for individual physicians on the front lines of care, and for policy makers setting national direction. However, this type of data is high-dimensional (an infant with no prior clinical history can have more than 1000 different measurements in the ICU), highly unstructured (the measurements occur irregularly, and different numbers and types of measurements are taken for different patients) and heterogeneous (from ultrasound assessments to lab tests to continuous monitor data). Furthermore, the data is often sparse, systematically not present, and the underlying system is non-stationary. Extracting the full value of the existing data requires novel approaches. In this thesis, we develop novel methods to show how longitudinal health data contained in Electronic Health Records (EHRs) can be harnessed for making novel clinical discoveries. For this, one requires access to patient outcome data --- which patient has which complications. We present a method for automated extraction of patient outcomes from EHR data; our method shows how natural languages cues from the physicians notes can be combined with clinical events that occur during a patient's length of stay in the hospital to extract significantly higher quality annotations than previous state-of-the-art systems. We develop novel methods for exploratory analysis and structure discovery in bedside monitor data. This data forms the bulk of the data collected on any patient yet, it is not utilized in any substantive way post collection. We present methods to discover recurring shape and dynamic signatures in this data. While we primarily focus on clinical time series, our methods also generalize to other continuous-valued time series data. Our analysis of the bedside monitor data led us to a novel use of this data for risk prediction in infants. Using features automatically extracted from physiologic signals collected in the first 3 hours of life, we develop Physiscore, a tool that predicts infants at risk for major complications downstream. Physiscore is both fully automated and significantly more accurate than the current standard of care. It can be used for resource optimization within a NICU, managing infant transport to a higher level of care and parental counseling. Overall, this thesis illustrates how the use of machine learning for analyzing these large scale digital patient data repositories can yield new clinical discoveries and potentially useful tools for improving patient care.
  • The debate over eHealth is alive as never before. Supporters suggest that it will result in dramatic innovations in healthcare, including a giant leap towards patient-centered care, new opportunities to improve effectiveness, and enhanced wellness and quality of life. In addition, the growing market value of investments in health IT suggests that eHealth can offer at least a partial cure for the current economic stagnation. Detractors counter these arguments by claiming that eHealth has already failed: the UK Department of Health has shut down the NHS National Program for IT, Google has discontinued its Health flagship, and doubts have arisen over privacy safeguards for both patients and medical professionals. This book briefly explains why caregivers, professionals, technicians, patients, politicians, and others should all consider themselves stakeholders in eHealth. It offers myth-busting responses to some ill-considered arguments from both sides of the trench, in the process allowing a fresh look at eHealth. In addition, it describes how the technical failures of previous eHealth systems can be avoided, examines the legal basis of eHealth, and discusses associated ethical issues.
  • An overview of healthcare disparities -- Provider factors in healthcare disparities -- Patient factors in healthcare disparities -- Healthcare system factors in healthcare disparities -- The social "nonmedical" determinants of health -- The role of the Internet in American life -- The iHealth revolution -- Digital disparities -- The role of eHealth in patient engagement and quality improvement -- Medical informatics -- Public health informatics -- Beyond traditional paradigms in disparities research -- Health information technology policy perspectives and healthcare disparities -- Disparities and eHealth: achieving the promise and the potential.
  • Part 1. Introduction -- part 2. Identifying and preventing EHR safety concerns -- part 3. EHR users and usability -- part 4. Clinical decision support -- part 5. Referrals -- part 6. Laboratory test result management -- part 7. Bar coded medication administration -- part 8. Computer-based provider order entry.
  • Introduction to e-Healthcare Information Security / Charles A. Shoniregun, Kudakwashe Dube and Fredrick Mtenzi -- Securing e-Healthcare Information / Charles A. Shoniregun, Kudakwashe Dube and Fredrick Mtenzi -- Laws and Standards for Secure e-Healthcare Information / Charles A. Shoniregun, Kudakwashe Dube and Fredrick Mtenzi -- Secure e-Healthcare Information Systems / Charles A. Shoniregun, Kudakwashe Dube and Fredrick Mtenzi -- Towards a Comprehensive Framework for Secure e-Healthcare Information / Charles A. Shoniregun, Kudakwashe Dube and Fredrick Mtenzi -- Towards a Unified Security Evaluation Framework for e-Healthcare Information Systems / Charles A. Shoniregun, Kudakwashe Dube and Fredrick Mtenzi -- Discussions / Charles A. Shoniregun, Kudakwashe Dube and Fredrick Mtenzi.
  • v. 1. A-L -- v. 2. M-Z.
  • Common diseases arise out of combination of both genetic and environmental influences. Advances in genomic technology have enabled investigators to create hypotheses regarding the contribution of genetic factors at a breathtaking pace. However, the assessment of multiple and specific environmental factors--and their interactions with the genome-- has not. We lack high-throughput analytic methodologies to comprehensively and systematically associate multiple physical and specific environmental factors, or the "envirome", to disease and human health. We claim that the creation of hypotheses regarding the environmental contribution to disease is practicable through high-throughput analytic methods that have been well established in genomics. In the following dissertation, we develop and apply methods to systematically and comprehensively associate specific factors of the envirome with disease states, prioritizing factors for in-depth future study. The current disciplines of studying the environmental determinants of health include toxicology and epidemiology, which operate on molecular and population scales, respectively. This dissertation proposes approaches in both of these disciplines. For example, we have developed a framework to conduct the first "Environment-wide Association Study" (EWAS), systematically associating environmental factors to disease on a population scale. We have applied this framework to investigate type 2 diabetes and heart disease on cohorts that are representative United States population, finding novel and robust associations in diverse and independent cohorts. Given the lack of explained risk resulting from current day genome-wide studies, the time is ripe to usher in a more comprehensive study of the environment, or "enviromics", toward better understanding of multifactorial diseases and their prevention.
  • Overview: theoretical perspectives and methodologies for the evaluation of healthcare information systems -- Qualitative research methods for evaluating computer information systems -- Multiple perspectives: evaluating healthcare information systems in collaborative environments -- Survey methods for assessing social impacts of computers in healthcare organizations -- Using the Internet for surveys and research -- Cognitive approaches to the evaluation of healthcare information systems -- Work-sampling: a statistical approach to evaluation of the effect of computers on work patterns in health care -- Evaluation of health informatics: social network analysis -- Evaluation in health informatics: computer simulation -- Computers in the consulting room: a case study of clinician and patient perspectives -- Introducing physician order entry at a major academic medical center, A: Impact on organizational culture and behavior, B: Impact on medical education -- Evaluating the capability of information technology to prevent adverse drug events: a computer simulation approach -- Implementing computers in ambulatory care: implications of physician practice patterns for system design -- Nursing documentation time during implementation of an electronic medical record -- Computer charting: an evaluation of a respiratory care computer system -- Research and evaluation: future directions.
  • Also available: Print – 2006
    Challenges of Evaluation in Biomedical Informatics, p. 1-20 -- Evaluation as a Field, p. 21-47 -- Determining What to Study, p. 48-84 -- The Structure of Objectivist Studies, p. 85-112 -- Measurement Fundamentals, p. 113-144 -- Developing and Improving Measurement Methods, p. 145-187 -- The Design of Demonstration Studies, p. 188-223 -- Analyzing the Results of Demonstration Studies, p. 224-247 -- Subjectivist Approaches to Evaluation, p. 248-266 -- Performing Subjectivist Studies in the Qualitative Traditions Responsive to Users / Joan Ash, Allen Smith and P. Starvi, p. 267-300 -- Economic Aspects of Evaluation / Mark Roberts, p. 301-337 -- Proposing and Communicating the Results of Evaluation Studies: Ethical, Legal, and Regulatory Issues, p. 338-361.
  • Also available: Print – 2006
  • One of the American Medical Association's core strategic objectives is to advance health care delivery and payment models that enable high-quality, affordable care and restore and preserve physician satisfaction. Such changes could yield a more sustainable and effective health care system with highly motivated physicians. To that end, the AMA asked RAND Health to characterize the factors that lead to physician satisfaction. RAND sought to identify high-priority determinants of professional satisfaction that can be targeted within a variety of practice types, especially as smaller and independent practices are purchased by or become affiliated with hospitals and larger delivery systems. Researchers gathered data from 30 physician practices in six states, using a combination of surveys and semistructured interviews. This report presents the results of the subsequent analysis, addressing such areas as physicians' perceptions of the quality of care, use of electronic health records, autonomy, practice leadership, and work quantity and pace. Among other things, the researchers found that physicians who perceived themselves or their practices as providing high-quality care reported better professional satisfaction. Physicians, especially those in primary care, were frustrated when demands for greater quantity of care limited the time they could spend with each patient, detracting from the quality of care in some cases. Electronic health records were a source of both promise and frustration, with major concerns about interoperability between systems and with the amount of physician time involved in data entry.
  • Intelligent automation / James M. Dixon -- Neurally inspired algorithms as computational tools / Mark Flynn and Garrett T. Kenyon -- Using pharmacodynamic biomarkers to accelerate early clinical drug development / Ole Vesterqvist -- Opportunities in CNS drug discovery and development / Albert Pinhasov ... [et al.] -- Clinical success of antibody therapeutics in oncology / Bernard J. Scallon ... [et al.] -- Relating target sequence to biological function / Greg M. Arndt -- Use of protein microarrays for molecular network analysis and signal-pathway profiling / Katherine R. Calvo, Lance A. Liotta, and Emanuel F. Petricoin -- Laser-microdissection-based transcriptomics using microarrays / Fredrik Kamme ... [et al.].
  • Print Material
    Computers and medical information elective at Texas A&M University / Gale G. Hannigan -- Instructional outreach and liaison to a veterinary medicine program at Washington State University / Sarah K. McCord, Vicki F. Croft -- Researching the evidence in physical therapy at the University of Missouri-Columbia / Rebecca S. Graves, Evan Prost, Yvette Silvey -- The librarian as partner in the development of the health care informatics curriculum at James Madison University / Jennifer McCabe -- Educating users of the health sciences library system at the University of Pittsburgh / Linda M. Hartman -- Hardin Library for the Health Sciences : experiencing change / Denise H. Britigan, Anne K. Gehringer -- Medical informatics intervention : teaching the teaching residents at Christiana Care Health System / Sharon Easterby-Gannett, Ellen Justice -- The librarian's role as information technology educator at the University of South Alabama / Justin Robertson -- Using computer-based case studies for developing information searching skills and implementing evidence-based medicine at Jefferson Medical College / Anthony J. Frisby, Daniel Kipnis -- Education and e-learning at the William H. Welch Medical Library / Cynthia Sheffield, Jayne Campbell, Dongming Zhang -- An informatics course for first-year pharmacy students at the University of California, San Francisco / David J. Owen, Gail L. Persily, Patricia Babbitt -- Building an effective user education program : the medical librarian as coeducator at the University of the West Indies / Ernesta Greenidge, Meerabai Gosine-Boodoo -- Educational programs at the New York University College of Dentistry / Luis J. Gonzalez, Van B. Afes, Christopher Evjy -- Education services at the Health Sciences Library at the University of North Carolina at Chapel Hill / Julia Shaw-Kokot -- A month-long daily instruction curriculum for residents at the University of Pittsburgh : can intensive training make a difference? / Nancy Tannery ... [et al.] -- Health care informatics education at Stony Brook University : evolution of end-user education and mission redefinition for the academic health sciences library / Guillaume Van Moorsel -- Integrating medical informatics into the school of medicine curriculum at the University of California, San Francisco / Keir Reavie, Gail L. Persily, Kevin H. Souza -- Thinkpads, medical education, and the library at Wake Forest University / David C. Stewart.
  • Also available: Print – 2006
  • "Foreword Personal health information comprises the most sensitive and intimate details of one's life, such as those relating to one's physical or mental health, and the health history of one's family. Intuitively, we understand the importance of protecting health information in order to ensure the confidentiality of such personal data and the privacy of the individual to whom it relates. Personal health information must also be accurate, complete, and accessible to health care practitioners in order to provide individuals with necessary health care. At a broader level, for secondary uses that go beyond the treatment of the individual, health-related data are needed for the benefit of society as a whole. These vitally important secondary uses include activities to improve the quality of care, health research, and the management of publicly funded health care systems. As the information and privacy commissioner of Ontario, Canada, my role includes the oversight of health privacy legislation governing the collection, use, and disclosure of personal health information by organizations and individuals involved in the delivery of health care services. Ontario's Personal Health Information Protection Act (PHIPA) aims to respect an individual's right to privacy in relationship to his or her own personal health information while accommodating the legitimate need to access health information for well-defined purposes. PHIPA does this in part by establishing clear rules for the use and disclosure of personal health information for secondary purposes. The object of these rules is to maximize the benefits of both respecting personal privacy and making health information accessible for purposes that serve society as a whole"--Provided by publisher.
  • Handbook of bioinspired algorithms and applications
    Click LINK above for Print location/circulation status.
    2006 CRCnetBASE
  • Chapter 1. Representing Two-Dimensional (2D) Chemical Structures with Molecular Graphs / Ovidiu Ivanciuc -- Chapter 2. Algorithms to Store and Retrieve Two-Dimensional (2D) Chemical Structures / Milind Misra, Jean-Loup Faulon -- Chapter 3. Three-Dimensional (3D) Molecular Representations / Egon L. Willighagen -- Chapter 4. Molecular Descriptors / Nikolas Fechner, Georg Hinselmann, Jor̈g Kurt Wegner -- Chapter 5. Ligand- and Structure-Based Virtual Screening / Robert D. Clark, Diana C. Roe -- Chapter 6. Predictive Quantitative Structure-Activity Relationships Modeling: Data Preparation and the General Modeling Workflow / Alexander Tropsha, Alexander Golbraikh -- Chapter 7. Predictive Quantitative Structure-Activity Relationships Modeling: Development and Validation of QSAR Models / Alexander Tropsha, Alexander Golbraikh -- Chapter 8. Structure Enumeration and Sampling / Markus Meringer -- Chapter 9. Computer-Aided Molecular Design / Donald P. "Visco, Jr." -- Chapter 10. Computer-Aided Molecular Design / Diana C. Roe -- Chapter 11. Reaction Network Generation / Jean-Loup Faulon, Pablo Carbonell -- Chapter 12. Open Source Chemoinformatics Software and Database Technologies / Rajarshi Guha -- Chapter 13. Sequence Alignment Algorithms / Tatsuya Akutsu -- Chapter 14. Machine Learning-Based Bioinformatics Algorithms / Shawn Martin -- Chapter 15. Using Systems Biology Techniques to Determine Metabolic Fluxes and Metabolite Pool Sizes / Fangping Mu, Amy L. Bauer, James R. Faeder, William S. Hlavacek.
  • SU Catalog (SearchWorks) Click LINK above for Print location/circulation status.
  • Conceptual apparatus -- Types of user assessments of IT-based solutions -- Choosing or constructing methods -- Overview of assessment methods -- Descriptions of methods and techniques -- Other useful information -- Methodological and methodical perils and pitfalls at assessment, background information -- Approach to identification of pitfalls and perils -- Framework for meta-assessment of assessment studies.
  • Also available: Print – 2005
  • "A hands-on, analytics road map for health industry leadersThe industry-wide transformation taking place across the health and life sciences ecosystem is mandating that organizations adopt new decision-making capabilities, based on science and real-world information. Analytics will be a required competency for the modern health enterprise; this book is about how to "cross the chasm." The ultimate analytics guide for the health industry leader, this essential book equips business leaders with little-to-no experience in analytics to understand how to incorporate analytics as a cornerstone of their 21st century competitive business strategy. Paints the picture for a new health enterprise, one focused on the patient Explores the financial components of this new operating model, using analytics to optimize the tradeoffs between cost and value Deals with the rising role of the consumer, using analytics to create a completely new health engagement model with individual recipients of care Looks at how analytics can drive innovations in care practice, patient-experienced medical outcomes, and analytically driven novel therapies optimized for the individual patient Presents a variety of text, tables, and graphics illustrating the various concepts being described Within each section and chapter, Health Analytics assesses the current landscape, proposing a new model/concept, sharing real-world stories of how the old and new world come together, and framing a "how-to" for the reader in terms of growing that particular set of capabilities in their own enterprises"-- Provided by publisher.
  • "The revised third edition of Health Care Information Systems is a comprehensive text that offers an understanding of health care information systems that helps readers work effectively with and support information systems design, as well as the development and implementation. It covers current and developing information systems of interest to managers in health services organizations; health care information systems architecture; security and privacy issues; uses of health care information for clinical and strategic analysis and decision support; techniques for developing and evaluating an information system request for proposal; and information on the future"--Provided by publisher.
  • Print Material
    Electronic health records : how they work, what they document and how they advance patient care / Don Quackenbush -- Electronic health records : selecting the EHR solution and negotiating the licensing agreement / Lee Kim -- Regional extension centers : "boots on the ground" support of EHR technology in small physician practices / Nathan Gibson, Nicholas P. Heesters, Jr., and Adam Kehler -- Personal health records and patient portals : leveraging technology to empower and engage patients / Stephen A. Snyder -- Health information exchange : a critical foundation to improve health care value / Kate Berry and Jon Dimsdale -- Telemedicine : an expanding frontier in patient care / Mary P. Maiberger -- Electronic health and mobile health medical technology : platforms of innovation / Afia K. Asamoah [and 3 others] -- Medical devices in the digital age / David J. Sykeman [and 3 others] -- The role of social media in health care : the trend toward health care consumerism / Kathryn R. Coburn -- 9/11 : a personal experience / Linda V. Tiano -- Contingency planning for health plans and providers : lessons from 9/11 / Linda V. Tiano and Daly D.E. Temchine -- The evolution of HIPAA : protecting the privacy of individuals in their physician's office, in the hospital, at the lab, as a subject of research, and throughout the world / Arthur E. Peabody, Jr. -- Electronic health records : technology standards and incentives for meaningful use / Arthur E. Peabody, Jr. -- The federal data breach notification law for breaches of protected health information / Arthur E. Peabody, Jr. and Lucy J. Thomson -- Safety risks associated with EHRs : how real? / Arthur E. Peabody, Jr. -- Health care data breaches and information security : addressing threats and risks to patient data / Lucy L. Thomson -- Data encryption : essential to afford security and privacy in health care / Eric A. Hibbard -- Enforcement under HIPAA and HITECH : why you need to worry again about HIPAA / Sarah E. Swank -- Enforcing HIPAA in the age of electronic health records : the view of the Office of Civil Rights from its director / Leon Rodriguez.
  • Print Material
    Health information on the Internet -- The structures of knowledge related to health information on the Internet -- Accessing health information on the Internet -- Quality -- Physicians and other health professionals' use of the Internet -- Consumer health information on the Internet -- Telemedicine and online medical services -- Future trends and challenges.
  • Theoretical underpinnings : comparing the PPACA and HITECH acts -- Impact of E-government on electronic health literacy -- Financial, social, and environmental impact of government HITadoption policies -- Self-management technologies and type 2 diabetes -- Individualized prevention solutions to childhood obesity -- Health IT in community health centers -- Case study of physicians as entrepreneurs -- The micro, meso, and macro perspectives of HIT adoption -- Geographic disparities in healthcare -- International comparisons: differences in U.K. and U.S. preventive health.
  • An introduction to the US health care industry, information technology, and informatics / by Stephan Kudyba, Richard Temple -- "Quality time" in healthcare : strategies for achieving national goals for meaningful use of health information technology / by Michael H. Zaroukian, Peter Basch -- A project management framework for healthcare informatics initiatives / by Christi Rushnell, Mary Beattie -- Nursing roles in the implementation of clinical information systems / by Terry Moore -- Architecting computerized physician order entry (CPOE) for optimal utilization / by James F. Keel III, D. Arlo Jennings -- Knowledge translation and informatics in healthcare / by Ann McKibbon -- Self service technology in healthcare / by Tomas Gregorio -- The world of health analytics / by Jason Burke -- Enhancing data resources and business intelligence in healthcare / by Stephan Kudyba, Mark Rader -- Application of healthcare informatics to improving patient safety and outcomes : learning from the experiences of Trinity Health / by Rajiv Kohli ... [et al.] -- Data mining in health care / by Wullianallur Raghupathi -- Using data mining to build alerting systems for decision support in healthcare / by Billie Anderson, Cali M. Davis, J. Michael Hardin -- Data mining techniques to enhance health care cost savings through the identification of abusive billing practices and the optimization of care enhancement services / by Theodore L. Perry ... [et al.].
  • The Evolution of Healthcare Infrastructure -- History of Health Determinants -- Public Health Success When Simple -- Public Health Failure When Complex -- Medicine Success When Simple -- Medicine Failure When Complex -- Medical Records for Health Systems -- Health Determinants for Individuals and Populations -- Measurement of Individual Activity (Explicit Text) -- Sensors for Individual Ability (Implicit Data) -- Genomes for Individual Ability (Features) -- Networks for Population Function (Persons) -- Mobile Monitors for Health Systems -- The Future of Healthcare Infrastructure.
  • Also available: Print – 2014
    This volume highlights the most interesting biomedical and clinical applications of high-dimensional flow and mass cytometry. It reviews current practical approaches used to perform high-dimensional experiments and addresses key bioinformatic techniques for the analysis of data sets involving dozens of parameters in millions of single cells. Topics include single cell cancer biology; studies of the human immunome; exploration of immunological cell types such as CD8+ T cells; decipherment of signaling processes of cancer; mass-tag cellular barcoding; analysis of protein interactions by proximity ligation assays; Cytobank, a platform for the analysis of cytometry data; computational analysis of high-dimensional flow cytometric data; computational deconvolution approaches for the description of intracellular signaling dynamics; and hyperspectral cytometry. All 10 chapters of this book have been written by respected experts in their fields. It is an invaluable reference book for both basic and clinical researchers.

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A repository of medical knowledge from internal medicine, cardiology, genetics, pharmacy, diagnosis and management, basic sciences, patient care, and more. Continuously expanding, all databases in the repository contain the latest editions of selected medical titles.MicroMedex: Premier pharmaceutical information source containing multiple databases and drug reference tools. Of particular value is DRUGDEX Evaluations, one of the most comprehensive drug sources available.DynaMed is a clinical information resource used by physicians to answer clinical questions quickly and easily at the point of care. Topics are updated daily as new evidence becomes available. 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Large number of high quality software and database programming titles from O'Reilly. Other software titles are also available from Sams and Prentice Hall. Limited to 7 concurrent users.Vast collection of software and database programming titles from multiple publishers, including Microsoft Press.Largest provider of engineering-related eBooks; includes titles in computer science and biomedical engineering.Over 4,000 full-text e-books covering scientific and technical information from CRC Press and others. Many handbooks and single volume reference sources.Includes peer-reviewed life science and biomedical research protocols compiled from Methods in Molecular Biology, Methods in Molecular Medicine, Methods in Biotechnology, Methods in Pharmacology and Toxicology, Neuromethods, the Biomethods Handbook, the Proteomics Handbook, and Springer Laboratory Manuals.Contains full text access to selected biomedical and nursing books.Provides online, full-text access to Springer's journal titles as well as journals from other publishers. Subjects include: life sciences, chemical sciences, environmental sciences, geosciences, computer science, mathematics, medicine, physics and astronomy, engineering and economics. Also includes eBooks.Collection of over 8 thousand fulltext titles in engineering, math, and basic and applied biomedical research. Coverage is from 1967 to the present.A library of ebooks on a wide array of topics, digitized and made available online in conjunction with the original publishers.