Biomedical Research
Biomedical research resources
Guide Editor: Kristi Holmes
For a more interactive list of the selected Research resources, visit our del.icio.us list at http://del.icio.us/becker.research/. (The del.icio.us list of Research resources is searchable by a variety of different tags and allows subscription by RSS feed.)
Resources:
3-D Structure Tools |
| AGADIR An algorithm to predict the helical content of peptides |
| Cn3D Allows view 3-dimensional structures from NCBI's Entrez retrieval service.Cn3D can simultaneously displays structure, sequence, and alignment, also has powerful annotation and alignment editing features. |
| Conformation Angles DataBase [ CADB-2.0 ] Conformation angles of protein structures, with associated crystallographic data (CADB) |
| PROCHECK Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry |
| PROCHECK-NMR a suite of programs that have been derived from the PROCHECK programs to analyse ensembles of protein structures solved by NMR. |
| Protein Structure Prediction Center |
| RasMol RasMol is a program for molecular graphics visualisation |
| Raster3D Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. |
| RCSB Protein Data Bank The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. |
| SCOP: Structural Classification of Proteins |
| SWISS-Model A fully automated protein structure homology-modeling server, |
| SWISS-MODEL SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide. |
| World Index of Molecular Visualization Resources Comprehensive listing of visualization resources |
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Books |
| Cell biology : a laboratory handbook This four-volume laboratory manual contains comprehensive state-of-the-art protocols essential for research in the life sciences. Techniques are presented in a friendly step-by-step fashion, providing useful tips and potential pitfalls. The important steps and results are illustrated for further ease of use. This collection enables researchers at all stages of their careers to embark on basic biological problems using a variety of technologies and model systems. This thoroughly updated third edition contains 165 new articles in classical as well as rapidly emerging technologies. |
| Protein microarrays Features twenty-four cutting-edge chapters from the leading laboratories in the hot new field of protein microarrays. Dr. Schena, who published the first two papers on DNA microarrays in 1995 and 1996, extends his original vision of parallelism and miniaturization to advance the protein microarray field, which promises important breakthroughs in disease diagnostics and drug discovery, as well as basic research on protein expression, development, the immune system, aging, behavior, and other issues central to medicine. Protein Microarrays is the first comprehensive treatment of protein microarray technology, and includes detailed descriptions of manufacturing methods, surface chemistry, detection strategies, and data analysis for antigen, antibody, and peptide microarray assays. The book also presents numerous biological applications and experimental protocols not available from any other source. |
| A Primer of genome science Bridges the gap between standard genetics textbooks and highly specialized, technical, and advanced treatments of the subdisciplines. It provides up-to-date introduction to the field that is suited to advanced undergraduate or early graduate courses. Bioinformatic principles and experimental strategies are explained side-by-side with the experimental methods, establishing a framework that allows teachers to explore topics and the literature at their own pace. Organized into six chapters, each chapter includes: exercises that can be worked by students using the internet and freely available software for analysis of genomic data; discussion questions; a summary; and suggestions for further reading. An Appendix includes a glossary of terms, with a brief review of key genetic concepts |
| An Introduction to molecular biotechnology : molecular fundmentals, methods and applications in modern biotechnology A very detailed introduction to the fundamentals in molecular and cell biology is followed by an overview of standard techniques applied in molecular biotechnology -- including chromatography and electrophoresis, cloning techniques, gene expression systems, immunological methods, labeling of proteins and in situ-techniques, microscopy and laser systems. The third part then focuses on the key topics of molecular biotechnology, ranging from functional genomics, proteomics and bioinformatics to drug targeting, recombinant antibodies, structural biology, gene therapy and knock mice. The whole is rounded off by a section on biotechnology in industry dealing with patenting issues, company foundation and market opportunities. |
| Bacterial genomes and infectious diseases Presents major findings about bacterial genomes and their impact on strategy and approach for investigating mechanisms of pathogenesis of infectious diseases. This book imparts fundamental knowledge on the structure, organization, and evolution of bacterial genomes. The value and power of comparative genomics and proteomics, bioinformatics, microarrays, and knockout animal models in analyzing genomes, bacteria (host interactions and disease are demonstrated. Also discussed are the genomes of virulent and nonvirulent strains and species, origin and evolution of pathogens, different models of bacteria) host interactions, and diseases mechanisms. |
| Bayesian inference for gene expression and proteomics Discusses the development and application of Bayesian methods in the analysis of high-throughput bioinformatics data, from medical research and molecular and structural biology. The Bayesian approach has the advantage that evidence can be easily and flexibly incorporated into statistical models. A basic overview of the biological and technical principles behind multi-platform high-throughput experimentation is followed by expert reviews of Bayesian methodology, tools, and software for single group inference, group comparisons, classification and clustering, motif discovery and regulatory networks, and Bayesian networks and gene interactions. |
| Biochemistry; Jeremy M. Berg, John L. Tymoczko, Lubert Stryer Popular text presents biochemistry in a completely different manner. Instead of traditionally presenting one topic after the other, it presents each chapter giving a representative molecule or system for explanation and characterization of the material in that chapter . For example, hemoglobin and myoglobin for explaining the three dimensional structure of proteins, lysozyme and chymotrypsin for explaining enzyme action, and a host of others. Each example is critically chosen, considering its role and function in life and metabolism. |
| Bioinformatics : a practical guide to the analysis of genes and proteins This edition provides tools and databases used in bioinformatics, loosely defined as the intersection of molecular and computational biology. With the goal of helping the reader design and implement a successful sequence analysis strategy, topics covered include: using software and Internet resources, submitting DNA sequences to databases, information retrieval from databases, phylogenetic analysis, a database for genome information called ACeDB, and practical aspects of multiple sequence alignment. |
| Bioinformatics : an introduction This introduction is intended to be a complete study companion for the advanced undergraduate or beginning graduate student. It is self-contained in the sense that whatever the starting point may be, the reader will gain insight into bioinformatics. Underlying the work is the belief that bioinformatics is a kind of metaphoric lens through which the entire field of biology can be brought into focus, admittedly as yet imperfect, and understood in a unified way. Reflecting the highly incomplete present state of the field, emphasis is placed on the underlying fundamentals and acquisitions of a broad and comprehensive grasp of the field as a whole. Bioinformatics is interpreted as the application of information science to biology, in which it plays a fundamental and all-pervasive role. This interpretation enables a remarkably unified view of the entire field of biology to be taken and hence offers an excellent entry point into the life sciences for those for whom biology is unfamiliar. |
| Bioinformatics : genes, proteins, and computers Designed for students taking advanced-level courses, including final year undergraduate and taught MSc. Books in this series will also be invaluable to researchers new to a field, and to established researchers as a basic reference text. This book covers both the more traditional approaches to the subject, including gene and protein sequence analysis and structure prediction, and more recent technologies such as datamining of transcriptomic and proteomic data, to provide insights on cellular mechanisms and the causes of disease. |
| Bioinformatics : genomics and post-genomics Provides a clear and concise introduction to the use of bioinformatics to analyse genomic data. It covers basic studies of the genome as well as more advanced post--genomic analysis, and features both biological problems and concepts from informatics. Translated from a successful French edition that was itself based on a course at the well--respected Ecole Polytechnique in Paris |
| Bioinformatics : sequence and genome analysis Ch. 1. Historical introduction and overview -- Ch. 2. Collecting and storing sequences in the laboratory -- Ch. 3. Alignment of pairs of sequences -- Ch. 4. Multiple sequence alignment -- Ch. 5. Prediction of RNA secondary structure -- Ch. 6. Phylogenetic prediction -- Ch. 7. Database searching of similar sequences -- Ch. 8. Gene prediction -- Ch. 9. Protein classification and structure prediction -- Ch. 10. Genome analysis. |
| Bioinformatics : sequence and genome analysis Provides instruction in computational methods for analyzing DNA, RNA, and protein data, with explanations of the underlying algorithms, the advantages and limitations of each method, and strategies for their application to biological problems. |
| Bioinformatics : the machine learning approach |
| Bioinformatics basics : applications in biological science and medicine Every research in genomics and proteomics now has access to public domain databases containing literally billions of data entries. However, without the right analytical tools and an understanding of the biological significance of the data, cataloging and interpreting the molecular evolutionary processes buried in those databases is difficult, if not impossible. With this new edition, the authors, recognizing the advances in bioinfomatics, have produced a completely revised and updated version of their previous work that includes some fresh approaches to data analysis, while identifying computing techniques that will help manage the massive flow of information. |
| Biomedical informatics Describes the fundamental issues and questions in the field, and reviews the different types of biomedical data resources and open source tools needed to fully utilize biomedical data. Reades are shown how to navigate through the legal, ethical, and technical hazards of biomedical informatics to become self-sufficient and productive, and to finish with an understanding of how to acquire, organize, annotate, and share biomedical data, how to render confidential data harmless through de-identification, and how to use a variety of free and open source utilities to solve common computational tasks. Berman also discusses how the Perl Language is used in biomedical informatics and provides short Perl scripts that can be applied in the biological research and healthcare settings. |
| Cancer : principles & practice of oncology, 7th Edition This completely revised edition reflects the latest breakthroughs in molecular biology, cancer prevention, and multimodality treatment of every cancer type. New chapters examine molecular biologic techniques including proteomics, genomics, targeted therapies, RNA interference, cDNA arrays, and tissue arrays. New sections discuss bioinformatics and societal issues in oncology, including regulatory issues, telemedicine, and international differences in oncology. Coverage also includes new information on functional and metabolic imaging, vaccines, and antiangiogenesis agents. |
| Computational genomics : theory and application Details the application of current computational methods to DNA and protein science. The subjects covered range from the theory and practice of simple database searching and sophisticated multiple sequence manipulation, through structure prediction and proteomic databases, to hardcore data analysis and the latest developments in user interface and conceptualization. Topics are covered in depth but with a practical approach that enables biologists to perform analyses and comparisons of sequence data and to determine functional and structural characteristics of proteins. In particular the book aims to provide an understanding of the ways in which such analyses and comparisons are performed in order to help the scientist to be more effective in performing such tasks and interpreting the results. Topics covered include database searches, sequence analysis and comparison, multiple sequence analysis, large-scale EST analysis, genome browsing, protein structure prediction, microarray data analysis, and proteomics. |
| Computational systems biology Computational systems biology is a field that aims to develop a systems level understanding of biological processes using computational techniques. This book presents a compendium of the state-of-the-art in this new era of biological understanding. The contributors review bioinformation engineering and data integration technologies along with biomedical applications. Different computational approaches to model and simulate biological systems are discussed. Current computational research efforts, comprehensively covered in this volume, are focused on regulatory, signaling and metabolic networks. New concepts for computer representations on multi-scales predicting emergent properties of biological systems are introduced. |
| Database annotation in molecular biology With the recognition of the importance of accurate database annotation and the requirement for individuals with particular constellations of skills to carry it out, annotators are emerging as specialists within the profession of bioinformatics. This book compiles information about annotation - its current status, what is required to improve it, what skills must be brought to bear on database curation and hence what is the proper training for annotators. This book is aimed at people working on biological databases, both biologists and computer scientists. It will be also be of interest to all users of such databases, inclduing molecular biologists, geneticists, protein chemists, clinicians and drug developers. |
| Essential bioinformatics A concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. |
| Essentials of genomics and bioinformatics From amazon.com: Provides an overview of the rapidly evolving field of genomics with coverage of nucleic acid technologies, proteomics and bioinformatics. It includes chapters on applications in human health, agriculture and comparative genomics and also contains two chapters on the legal and ethical issues of genomics, a topic that is becoming increasingly important as genomics moves out of the laboratory into practical applications. |
| Evolving connectionist systems : methods and applications in bioinformatics, brain study and intelligent machines From amazon.com: This book presents generic computational models and techniques that can be used for the development of evolving, adaptive modelling systems. The models and techniques used are connectionist-based (as the evolving brain is a highly suitable paradigm) and, where possible, existing connectionist models have been used and extended. The first part of the book covers methods and techniques, and the second focuses on applications in bioinformatics, brain study, speech, image, and multimodal systems. It also includes an extensive bibliography and an extended glossary. Evolving Connectionist Systems is aimed at anyone who is interested in developing adaptive models and systems to solve challenging real world problems in computing science or engineering. It will also be of interest to researchers and students in life sciences who are interested in finding out how information science and intelligent information processing methods can be applied to their domains. |
| Food allergy Examines the identification and characterization of allergenic proteins within food sources, the underlying mechanisms of action, and treatment options. Particular emphasis is placed on the following topics: clinical aspects of food allergy and advances in diagnosis; cutting edge immunochemical theories and molecular mechanisms; immunotherapy and the role of animal models in advancing food allergy research; the effects of food processing on allergenicity; and methods for preparing hypoallergenic foods. An important feature of the book is its in-depth coverage of bioinformatics tools. Three chapters offer details on how to find and properly implement existing bioinformatics tools, including current websites and sample uses of databases. |
| Gene cloning Designed to give the undergraduate a broad overview of the subject, guiding the student through the basic elements involved and their utility, and further through the interpretation of results and datasets. Having understood the basic processes, the reader is introduced to some of the most common uses of gene cloning, from applications with more research-oriented goals to practical applications in biotechnology in medicine. |
| Genetic analysis of complex diseases Provides a comprehensive introduction to the various strategies, designs, and methods of analysis for the study of human genetic disease. It offers a broad-based understanding of the problems and solutions based on successful applications in the design and execution of gene mapping projects. Chapters present clear and easily referenced overviews of the broad range of considerations involved in genetic analysis of human genetic disease, including design, sampling, data collection, linkage and association studies, and social, legal, and ethical issues. Incorporating all new discussion questions and practical examples within each chapter, the book significantly updates treatment of bioinformatics, multiple comparisons, sample size requirements, parametric linkage analysis, case-control and family based approaches, and genomic screening. It covers new methods for analysis of gene-gene and gene-environmental interactions, and features a complete rewrite of the chapter on determining genetic components of disease. |
| Genome exploitation : data mining the genome Summarizes the progress in bioinformatics and computational biology in data mining the vasta amount of exciting information emerging from studies of plant and animal genomes, with authoritative analytical reviews apecialized enough to be attractive professional researchers, yet also appealing to the wider audience of scientists in related disciplines. |
| Genomes 3 Genomes, transcriptomes, and proteomes -- Studying DNA -- Mapping genomes -- Sequencing genomes -- Understanding a genome sequence -- Understanding how a genome functions -- Eukaryotic nuclear genomes -- Genomes of prokaryotes and eukaryotic organelles -- Virus genomes and mobile genetic elements -- Accessing the genome -- Assembly of the transcription initiation complex -- Synthesis and processing of RNA -- Synthesis and processing of the proteome -- Regulation of genome activity -- Genome replication -- Mutations and DNA repair -- Recombination -- How genomes evolve -- Molecular phylogenetics. Genomes, transcriptomes, and proteomes -- Studying DNA -- Mapping genomes -- Sequencing genomes -- Understanding a genome sequence -- Understanding how a genome functions -- Eukaryotic nuclear genomes -- Genomes of prokaryotes and eukaryotic organelles -- Virus genomes and mobile genetic elements -- Accessing the genome -- Assembly of the transcription initiation comple -- Synthesis and processing of RNA -- Synthesis and processing of the proteome -- Regulation of genome activity -- Genome replication -- Mutations and DNA repair -- Recombination -- How genomes evolve -- Molecular phylogenetics. |
| Green fluorescent protein : properties, applications, and protocols This new edition places emphasis on the rise of NFPs, including new chapters on NFP properties with detailed protocols, applications of GFPs and NFPs in industry research, and biosensors. This book provides a solid theoretical framework, along with detailed, practical guidance on use of GFPs and NFPs with discussion of potential pitfalls. The expert contributors provide real examples in showing how to tailor GFP/NFP to specific systems, maximize expression, and enhance detection. |
| Harper's illustrated biochemistry Integrates detailed discussions of biochemical diseases, updated clinical information, case studies, and extensive illustrations, this classic can be used as both a text and USMLE review book. Extensively illustrated with 500+ clear, descriptive illustrations and new chapters on amino acids and peptides, structures of protein, and the Human Genome project. |
| In silico' simulation of biological processes |
| Informatics in proteomics This book first addresses the infrastructure needed for public protein databases. It discusses information management systems and user interfaces for storage, retrieval, and visualization of the data as well as issues surrounding data standardization and integration of protein sequences recorded in the last two decades. The authors subsequently examine the application of statistical and bioinformatic tools to data analysis, data presentation, and data mining. They discuss the implementation of algorithms, statistical methods, and computer applications that facilitate pattern recognition and biomarker discovery by integrating data from multiple sources. |
| Introduction to bioinformatics : a theoretical and practical approach From amazon.com: Introduction to Bioinformatics: A Theoretical and Practical Approach was written as an introductory text for the undergraduate, graduate, or professional. This text provides scientists with both a biological framework to understand the questions life scientist confront in the context of the computational issues and tools that are currently available for scientific research It also provides the life scientist with a resource to the various computational tools that are available all supported with their underlying mathematical foundations. The volume also includes a bonus CD-ROM containing valuable software programs including BioDiscovery (for microarray analysis), ClustalX (a sequence alignment program) Ensembl, MicroAnalyser (for microarray analysis on the Macintosh), Staden Sequence Analysis Package, Tree View (for displaying phylogenies) an others. Also included is a complete set of color illustrations from each chapter that will prove invaluable for professors preparing their next bioinformatics course or seminar. |
| Laboratory investigations in molecular biology |
| Mastering Perl for bioinformatics Covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. |
| Molecular biology of the cell |
| Molecular medicine : an introductory text Molecular medicine is the application of gene or DNA based knowledge to the modern practice of medicine. This book provides contemporary insights into how the genetic revolution is influencing medical thinking and practice on a broad front including clinical medicine, innovative therapies and forensic medicine. Extensively revised just after the completion of the Human Genome Project, it provides the latest in molecular medicine developments. |
| Ontologies for bioinformatics The three parts of this book ask, and answer, three pivotal questions: what ontologies are; how ontologies are used; and what ontologies could be (which focuses on how ontologies could be used for reasoning with uncertainty). The authors first introduce the notion of an ontology, from hierarchically organized ontologies to more general network organizations, and survey the best-known ontologies in biology and medicine. They show how to construct and use ontologies, classifying uses into three categories: querying, viewing, and transforming data to serve diverse purposes. Contrasting deductive, or Boolean, logic with inductive reasoning, they describe the goal of a synthesis that supports both styles of reasoning. They discuss Bayesian networks as a way of expressing uncertainty, describe data fusion, and propose that the World Wide Web can be extended to support reasoning with uncertainty. They call this inductive reasoning web the Bayesian web. |
| Pharmacology Designed and edited by top educators, the book helps the student tie together the visual and cognitive elements of learning for superior recognition and recall. More than 500 pictures and diagrams, carefully crafted to complement and amplify the text, are completely integrated with the text. Board-type questions, with detailed explanations of the answers, are included with each chapter. This new Second Edition also includes a series of illustrated case studies. A unique Infolink cross-referencing system between the Pharmacology and Biochemistry volumes of this series enables students to interrelate the two disciplines. |
| Practical bioinformatics Bridges the gap between bioinformaticists and molecular biologists, i.e. the developers and the users of computational methods for biological data analysis and in that it presents examples of practical applications of the bioinformatics tools in the "daily practice" of an experimental research scientist. |
| Principles of gene manipulation and genomics There has been rapid progress in recombinant DNA technology over the last few years, particularly in the area of large-scale biology (genomics and related disciplines). The increasing integration between gene manipulation and genomics is embraced in this book, which brings together for the first time the subjects covered by the best-selling books Principles of Gene Manipulation and Principles of Genome Analysis & Genomics. This new text has been comprehensively revised, updated and rewritten to encompass within one volume, basic and advanced gene manipulation techniques, genome analysis, genomics, transcriptomics, proteomics and metabolomics, as well as the applications of these fascinating new technologies. |
| Protein bioinformatics : an algorithmic approach to sequence and structure analysis Takes the novel approach to cover both the sequence and structure analysis of proteins in one volume and from an algorithmic perspective. It provides a comprehensive introduction to the analysis of protein sequence and structure analysis; takes an algorithmic approach, relying on computational methods rather than theoretical; provides an integrated presentation of theory, examples, exercises and applications; and includes coverage of both protein structure, and sequence, analysis. This book is accessible enough for biologists, yet rigorous enough for computer scientists and mathematicians. |
| Protein structure prediction : concepts and applications While most textbooks on bioinformatics focus on genetic algorithms and treat protein structure prediction only superficially, this course book assumes a novel and unique focus. Adopting a didactic approach, the author explains all the current methods in terms of their reliability, limitations and user-friendliness. She provides practical examples to help first-time users become familiar with the possibilities and pitfalls of computer-based structure prediction. |
| Respiratory genetics Brings together current knowledge in the field of respiratory genetics in a single volume for the first time. The book includes a comprehensive introductory section to provide guidance and aid understanding of key basic concepts in respiratory genetics, including statistical methods, sample collection and storage, bioinformatics, and molecular genetics. This is followed by a series of disease-specific chapters which review epidemiology; natural history; monogenic components and complex traits where relevant; disease management, including genetic counseling issues; and likely future developments. |
| RNA methodologies : a laboratory guide for isolation and characterization This laboratory guide represents a growing collection of tried, tested and optimized laboratory protocols for the isolation and characterization of eukaryotic RNA, with lesser emphasis on the characterization of prokaryotic transcripts. Collectively the chapters work together to embellish the RNA story, each presenting clear take-home lessons, liberally incorporating flow charts, tables and graphs to facilitate learning and assist in the planning and implementation phases of a project. This edition includes approximately 30% new material, including chapters on the more recent technologies of RNA interference including: RNAi; Microarrays; Bioinformatics. It also includes new sections on: new and improved RT-PCR techniques; innovative 5. and 3. RACE techniques; subtractive PCR methods; methods for improving cDNA synthesis. |
| Statistical methods in bioinformatics : an introduction |
| Statistics for microarrays : design, analysis, and inference Interest in microarrays has increased considerably in the last ten years. This increase in the use of microarray technology has led to the need for good standards of microarray experimental notation, data representation, and the introduction of standard experimental controls, as well as standard data normalization and analysis techniques. This book is the first book that presents a coherent and systematic overview of statistical methods in all stages in the process of analysing microarray data, from getting good data to obtaining meaningful results. Primarily aimed at statistically-minded biologists, bioinformaticians, biostatisticians, and computer scientists working with microarray data, the book is also suitable for postgraduate students of bioinformatics. |
| Structural genomics on membrane proteins Presents a range of structural genomics approaches. It presents examples of studies on whole genomes of specific organisms, types of genes/proteins, and gene protein families and includes sections on such topics as bioinformatics, expression, crystallization, signaling, expression, solubilization, and purification of membrane proteins. It also explores recombinant expression technologies such as nuclear magnetic resonance and electron microscopy techniques. |
| The Elements of statistical learning : data mining, inference, and prediction Describes important statistical ideas in machine learning, data mining, and bioinformatics. Covers a broad range, from supervised learning (prediction), to unsupervised learning, including classification trees, neural networks, and support vector machines. |
| The Mouse in biomedical research Dedicated to the understanding of the mouse and its role in scientific research. This valuable compendium serves as a standard reference source of information for students embarking on scientific careers, specialists in laboratory animal science, technicians in both animal care and research, and the broad scientific community. |
| The Proteomics protocols handbook Hands-on researchers describe in step-by-step detail a wide range of proven laboratory methods and bioinformatics tools essential for analysis of the proteome. These cutting-edge techniques (73 in all) addresses such important tasks as sample preparation, 2D-PAGE, gel staining, protein expression profiling, identifying protein-protein interactions, and protein chip tehcnology, as well as a range of newly developed methodologies for determing the structure and function of a protein, including novel mass spectrometry and LC-MS techniques, protein array technology, and a variety of structural and functional proteomics techniques needed to determine the function of newly discovered protein sequences. |
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Cancer Research |
| Cancer Biomedical Informatics Grid (caBIG) The Cancer Biomedical Informtics Grid (caBIG). this is a bioinformatics network that National Cancer Institute (NCI) created which will connect teams of cancer investigators, their data and their tools of discovery. |
| National Cancer Institute (NCI) |
| National Cancer Institute (NCI) Clinical Trials |
| National Cancer Institute Drug Dictionary The NCI Drug Dictionary contains technical definitions and synonyms for drugs/agents used to treat patients with cancer or conditions related to cancer. Each drug entry includes links to check for clinical trials listed in NCI's PDQ® Cancer Clinical Trials Registry. |
| Research at the Siteman Cancer Center |
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Chemical structure |
| ChemIDplus ChemIDplus provides access to structure and nomenclature information for the identification of chemical substances cited in NLM databases. The database contains over 380,000 chemical records, of which over 263,000 include chemical structures. ChemIDplus Lite is available for Name and RN searching without the need for plugins or applets. |
| DiscoveryGate The databases included in the DiscoveryGate package are: CrossFire Beilstein, CrossFire Gmelin, MDL Available Chemicals Directory, MDL Screening Compounds Directory, MDL Reference Library of Synthetic Methodology, MDL Solid-Phase Organic Reactions, ORGSYN Database, Comprehensive Organic Functional Group Transformations, Comprehensive Asymmetric Catalysis, MDL Comprehensive Medicinal Chemistry, MDL Drug Data Report, MDL Metabolite Database, MDL Toxicity Database, ChemInform Reaction Library, Derwent Journal of Synthetic Methods and the National Cancer Institute Database |
| PubChem PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem includes substance information, compound structures, and bioactivity data in three primary databases, PCSubstance, PCCompound, and PCBioAssay, respectively. The Substance/Compound database, where possible, provides links to bioassay description, literature, references, and assay data points. The BioAssay database also includes links back to the Substance/Compound database. PubChem is integrated with Entrez, NCBI's primary search engine, and also provides compound neighboring, sub/superstructure, similarity structure, bioactivity data, and other searching features. PubChem contains substance and bioassay information from a multitude of depositors. |
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Drug Information |
| DrugBank database The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains nearly 4300 drug entries including >1,000 FDA-approved small molecule drugs, 113 FDA-approved biotech (protein/peptide) drugs, 62 nutraceuticals and >3,000 experimental drugs. Additionally, more than 6,000 protein (i.e. drug target) sequences are linked to these drug entries. Each DrugCard entry contains more than 80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. |
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E-Books |
| Bioinformatics : a practical guide to the analysis of genes and proteins Bioinformatics and the Internet / Andreas D. Baxevanis -- The NCBI data model / James M. Ostell, Sarah J. Wheelan, and Jonathan A. Kans -- The Genbank sequence database / Ilene Karsch-Mizrachi and B.F. Francis Ouellette -- Submitting DNA sequences to the databases / Jonathan A. Kans and B.F. Francis Ouellette -- Structure databases / Christopher W.V. Hogue -- Genomic mapping and mapping databases / Peter S. White and Tara C. Matise -- Information retrieval from biological databases / Andreas D. Baxevanis -- Sequence alignment and database searching / Gregory D. Schuler -- Creation and analysis of protein multiple sequence alignments / Geoffrey J. Barton -- Predictive methods using DNA sequences / Andreas D. Baxevanis -- Predictive methods using protein sequences / Sharmila Banerjee-Basu and Andreas D. Baxevanis -- Expressed sequence tags (ESTs) / Tyra G. Wolfsberg and David Landsman -- Sequence assembly and finishing methods / Rodger Staden, David P. Judge, and James K. Bonfi |
| Bioinformatics : from genomes to drugs |
| Bioinformatics and computational biology solutions using R and Bioconductor This volume's coverage is broad and ranges across most of the key capabilities of the Bioconductor project, including importation and preprocessing of high-through put data from microarray, proteomic, and flow cytometry platforms. |
| Bioinformatics and drug discovery A collection of readily reproducible bioinformatic methods to advance the drug discovery process from gene identification to protein modeling to the identification of specific drug candidates. The authors demonstrate these techniques, including microarray analysis, the analysis of genes as potential drug targets, virtual screening and in silico protein design, and cheminformatics, in a variety of practical situations. Because these technologies are still emergent, each chapter contains an extended introduction that explains the theory and application of the technology and techniques described. |
| Bioinformatics and functional genomics Provides an integrative approach to understanding both the theory and practice of the emerging field of bioinformatics. Broadly encompassing the field of bioinformatics, from sequence analysis, gene expression, microarrays, and proteomics to molecular phylogenics and whole genome studies, this text show how bioinformatics applies to biological questions at different levels, such as gene/protein, disease, and protein structures. The author emphasizes practical skills, such as how to analyze genes and proteins, how to make trees using phylogenic software, how to extract data, and how to identify genes and proteins implicated in disease. |
| Bioinformatics for geneticists |
| Bioinformatics methods and protocols |
| Complexity in biological information processing "Symposium on Complexity in Biological Information Processing, held at the Kaiserin-Freidrich-Haus, Berlin, Germany, 4-6 July 2000"--P. v. Includes bibliographical references and indexes. |
| Computational genome analysis : an introduction Presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. This book features: topics organized around biological problems, such as sequence alignment and assembly, DNA signals, analysis of gene expression, and human genetic variation; presentation of fundamentals of probability, statistics, and algorithms Implementation of computational methods with numerous examples based upon the R statistics package; extensive descriptions and explanations to complement the analytical development More than 100 illustrations and diagrams (some in color) to reinforce concepts and present key results from the primary literature |
| Current protocols in bioinformatics |
| Developmental hematopoiesis : methods and protocols Genetic approaches -- Analysis of cell fate outcomes in transplantation models -- Animal models -- Bioinformatics and functional genomics. |
| Essentials of medical genomics Deciphering the Human Genome Project -- Genomic technology -- Bioinformatics tools -- Genome databases -- Human genetic variation -- Genetic testing for the practitioner / Harry Ostrer -- Gene therapy / John G. Hay -- Microarrays -- Pharmacogenomics and toxicogenomics -- Proteomics -- The ethics of medical genomics. |
| Gene expression profiling : methods and protocols The transcription of messenger RNA from a DNA template is a key process in a wide variety of biological systems. In this book, leaders in gene expression methodology and bioinformatics data analysis share their best methods for measuring RNA levels in cells and tissues. Each proven protocol is described in step-by-step detail and contains an introduction outlining the principle behind the technique, lists of equipment and reagents, and tips on troubleshooting and avoiding known pitfalls. |
| Genes VIII Genes VIII ; Benjamin Lewin. Login and password are required. Call the Reference Desk at 362-7085 for more information. Click on Sign In. Click on Molecular Biology Full Edition, under Web Modules, Books. |
| Immunoinformatics : bioinformatic strategies for better understanding of immune function Encompasses key developments in immunoinformatics, including immunological databases, sequence analysis, structure modelling, mathematical modelling of the immune system, simulation of laboratory experiments, statistical support for immunilogical experimentation and immuogenomics. |
| Java for bioinformatics and biomedical applications The science and practice of medicine has undergone a fundamental change as a result of large-scale genome projects that led to the sequencing of a number of important microbial, plant and animal genomes in the last 5 years. This book aims to combine industry standard software engineering and design principles, genomics and bioinformatics and cancer research. It focuses on creating and integrating practical, useful tools for the scientific community in the context of real-life, real-value biomedical problems that researchers face on a routine basis, rather than being just a didactic exercise in learning a programming platform. The book leverages technologies for molecular biology, genomics and bioinformatics and cancer research developed by the NIH, NCI-Center for Bioinformatics (NCICB), the National Center for Biotechnology Information (NCBI, a division of the National Library of Medicine (NLM) at the NIH) and Stanford University. |
| Medical informatics : knowledge management and data mining in biomedicine Medical Informatics and biomedical computing have grown in quantum measure over the past decade. An abundance of advances have come to the foreground in this field with the vast amounts of biomedical and genomic data, the Internet, and the wide application of computer use in all aspects of medical, biological, and health care research and practice. This volume covers the basic foundations of the area while extending the foundational material to include the recent leading-edge research in the field. The newer concepts, techniques, and practices of biomedical knowledge management and data mining are introduced and examined in detail. It is the research and applications in these areas that are raising the technical horizons and expanding the utility of informatics to an increasing number of biomedical professionals and researchers. |
| Molecular and cellular signaling Malfunction in the control layer is responsible for a host of human disorders ranging from neurological disorders to cancers. Most drugs target components in the control layer, and difficulties in drug design are intimately related to the architecture of the control layer. This book will be useful to students and individuals in medicine and pharmacology interested in broadening their understanding of how the control layer works. To further that goal, there are chapters on cancers and apoptosis, and on bacteria and viruses. In those chapters not specifically devoted to pathogens, connections between diseases, drugs and signaling are made. The audience for this book includes students in chemistry, physics and computer science who intend to work in biological and medical physics, and bioinformatics and systems biology. |
| PCR mutation detection protocols |
| Steroid receptor methods protocols and assays Bioinformatics -- Purification protocols -- Steroid hormone-binding assays -- Protein interaction assays -- Cancer research and drug discovery. |
| Stroke genomics : methods and reviews Introduction to stroke genomics / Simon J. Read and Frank C. Barone -- Choice, methodology, and characterization of ischemic stroke models : the search for clinical relevance / David Virley -- Mutant animal models of stroke and gene expression : the stroke prone spontaneously hypertensive rat / Hilary V.O. Carswell ... [et al.] -- Gene therapy in neurological disease / Midori A. Yenari and Robert M. Sapolsky -- Stem cell transplantation after middle cerebral artery occlusion / Paul Stroemer and Helen Hodges -- Endogenous brain protection : models, gene expression, and mechanisms / Frank C. Barone -- Production of transgenic and mutant mouse models / Alex Harper -- 3-nitropropionic acid model of metabolic stress : assessment by magnetic resonance imaging / Toby John Roberts -- Practicalities of genetic studies in human stroke / Ahamad Hassan and Hugh S. Markus -- Evaluation of the interactions of common genetic mutations in stroke / Zoltán Szolnoki -- Technologies of disease-related gene discovery using preclinical models of stroke / Xinkang Wang -- Quantitative analysis of gene transcription in stroke models using real-time RT-PCR / David C. Harrison and Brian C. Bond -- Effective analysis of genomic data / Paul R. Nelson, Andrew B. Goulter, and Richard J. Davis -- Bioinformatic approaches to assigning protein function from novel sequence data / David Michalovich and Richard Fagan -- Pragmatic target discovery from novel gene to functionally defined drug target : the interleukin-1 story / Stuart McRae Allen. |
| Structural bioinformatics |
| The RNA world Recent studies on the activities of RNA in the cell have revolutionized our understanding of the many roles played by this molecule. The first two editions of The RNA World (1993, 1999) shed light on the pre-biotic era dominated by this versatile molecule, and provided an overview of the state of RNA research at the time. The new third edition of The RNA World updates this perspective, describing the vast array of newly discovered roles for RNA in the modern world. The updated original chapters are supplemented with new chapters on RNA-protein complexes, snRNPs and snoRNPs, telomerase RNA, RNAi, microRNAs, noncoding RNA, and many other subjects. |
| YAC protocols This completely revised and updated edition takes advantage of the many new advances in biology since the publication of the first edition, including the sequencing of the human genome, the genomes of a wide variety of other organisms, and the increased use of transgenic animals for understanding the molecular basis of human and animal disease. It also provides a much-needed update on the new techniques currently employed and to help redefine and illustrate the important roles still to be palyed by yeast artificial chromosome (YAC) technologies in the postgenomic age. |
|
Enzymes |
| Catalytic Site Atlas (CSA) The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. |
| Enzyme Structures Database This database contains the known enzyme structures that have been deposited in the Protein Data Bank (PDB). |
| fireDB fireDB is a fully automated search system for structures in the Protein Data Bank, that contain annotations of residues participating in a functional site. The Database can be accessed by PDB codes or UniProt accession numbers. |
| IntEnz (Integrated relational Enzyme database) A freely available resource focused on enzyme nomenclature |
| Restriction Enzyme Database (REBASE) The Restriction Enzyme Database (REBASE) is a collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. |
|
Gene Expression Resources |
| ArrayExpress ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with MGED recommendations. The ArrayExpress Data Warehouse stores gene-indexed expression profiles from a curated subset of experiments in the repository. |
| BodyMap BodyMap is a data bank of expression information of human and mouse genes, novel or known, in various cells or tissue types and various timings. |
| Center for Information Biology Gene Expression (CIBEX) Database CIBEX is a gene expression database system in compliance with MIAME, which is a standard that the MGED Society has developed for comparing and data produced in microarray experiments at different laboratories worldwide. |
| Gene Expression Database (GXD) The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. |
| Gene Expression Omnibus (GEO) Gene expression/molecular abundance repository supporting MIAME compliant data submissions, and a curated, online resource for gene expression data browsing, query and retrieval. |
| Microarray Resources |
| RAD (RNA Abundance Database) RAD is a resource for gene expression studies, which stores highly curated MIAME-compliant studies (i.e. experiments) employing a variety of technologies such as filter arrays, 2-channel microarrays, Affymetrix chips, SAGE, MPSS and RT-PCR. Data are available for querying and downloading based on the MGED ontology, publications or genes. Both public and private studies (the latter viewable only by users having appropriate logins and permissions) are available from this website |
| Riken cDNA Expression Array Database (READ) Includes gene expression data for 49 mouse embryonic and adult tissues using cDNA microarrays |
| Stanford Microarray Database Raw and normalized data from array experiments |
| Stanford Microarray Database Microarray Resources |
|
Gene Prediction Tools |
| GeneBuilder An integrated computing system for protein-coding gene prediction. |
| GeneComber GeneComber is a graphical interface to the output of several gene prediction algorithms. |
| geneid geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. |
| GeneMark A family of gene prediction programs developed at GIT |
| GeneMark The GeneMark program is accessing the coding potential of DNA sequences by using Markov models of coding and non-coding regions within a sliding window. This local approach is sensitive to local variations of coding potential and is able to show details of the coding potential distribution along with gene identification. |
| GeneZilla GeneZilla is a state-of-the-art program for computational prediction of protein-coding genes in eukaryotic DNA, and is based on the Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN and GENIE. |
| GenomeScan Predicts the locations and exon-intron structures of genes in genomic sequences from a variety of organisms. It incorporates protein homology information when predicting genes. |
| GenScan Predicts the locations and exon-intron structures of genes in genomic sequences from a variety of organisms. It incorporates protein homology information when predicting genes. |
| GENVIEW An integrated computing system for protein-coding prediction. Splice sites prediction, potential coding regions, protein homology search, TATA box prediction, Poly-A site prediction, etc. |
| Glimmer Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. |
| GlimmerM A gene finder derived from Glimmer, but developed specifically for eukaryotes. |
| GrailEXP GrailEXP is a software package that predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements within DNA sequence. |
| HomoloGene HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. |
| Manatee Manatee is a web-based gene evaluation and genome annotation tool that can view, modify, and store annotation for prokaryotic and eukaryotic genomes. |
| ORF Finder A graphical analysis tool can find all reading frames of a selectable minimum size in a user's sequence or a sequence from the database. |
| Softberry |
| TwinScan TWINSCAN is a gene prediction system that has been developed at Washington University to model both gene structure and evolutionary conservation.It can work on the following organisms: Any mammalian genome Arabidopsis thaliana C. elegans and C. brig |
| WebGene Tools for prediction and analysis of protein-coding gene structure |
| Wise2 The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. |
|
General Information |
| BioTech's Life Science Dictionary BioTech's life science dictionary contains over 8,300 terms. |
| BioWiki BioWiki is an effort to build a community for life sciences researchers which everyone can edit, a unique interface between the researchers creating the tools, databases, protocols and the researchers who are using them. We hope your contributions will help grow this archive of freely available, high-quality, well-maintained material which supports education, research and self-learning. |
| CRISP (Computer Retrieval of Information on Scientific Projects) CRISP (Computer Retrieval of Information on Scientific Projects) is a searchable database of federally funded biomedical research projects conducted at universities, hospitals, and other research institutions. |
| DDBJ DNA Data Bank of Japan |
| Dictionary of Algorithms and Data Structures This is a dictionary of algorithms, algorithmic techniques, data structures, archetypal problems, and related definitions. Algorithms include common functions, such as Ackermann's function. Problems include traveling salesman and Byzantine generals. Some entries have links to implementations and more information. Index pages list entries by area and by type. |
| EMBOSS (European Molecular Biology Open Software Suite) EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages. Within EMBOSS you will find hundreds of applications covering areas such as: sequence alignment, rapid database searching with sequence patterns, protein motif identification, including domain analysis, nucleotide sequence pattern analysis---for example to identify CpG islands or repeats, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, presentation tools for publication, and much more. |
| Ensembl Genome Browser The Ensembl project is a collaborative effort between the Sanger Institute and the European Bioinformatics Institute (EBI) to develop a software system which produces automatic annotation on eukaryotic genomes. Ensembl offers sequence data and the best possible automatic annotation for eukaryotic genomes. Documentation related to the project is available. |
| European Bioinformatics Institute/EMBL |
| Gene Expression Omnibus (GEO) The National Center for Biotechnology Information within the National Library of Medicine of the U.S. National Institutes of Health offers the Gene Expression Omnibus (GEO), a database of gene expression data. Information about types of gene expression data from any artificial source or organism is retrievable. The entity fields of the GEO include submitter, platform, sample, and series. |
| Gene Ontology Consortium |
| General Molecular Biology Data NEB site which includes the following topics: The Genetic Code, Amino Acid Structures, DNA Base Pairs, Nucleic Acid Data, Isotope Data, Acids & Bases, Protein Data, Common Plasmid Gene Products, Nucleotide Physical Properties, Agarose Gel Resolution, pH vs Temp for Tris Buffer, Avoiding Ribonuclease Contamination |
| Genomics Glossaries Site maintained by Mary Chitty of Cambridge Healthtech Institute. In addition to a number of different glossaries and general topics in genomics, this site also features resources on topics such as: drug discovery and development, informatics, genomics and proteomics, lab techniques and others. |
| Human Genome Project (HGP) |
| International Nucleotide Sequence Database Collaboration The International Nucleotide Sequence Databases (INSD) have been developed and maintained collaboratively between DDBJ , EMBL , and GenBank for almost 20 years. |
| Molecular Biology Net The largest biosciences database, with links to bioinformatics tools, database, books. |
| NCBI The most comprehensive free public bioinformatics resources. |
| NHGRI policy and legislation database This database contains Federal and State laws/statutes; Federal legislative materials; and Federal administrative and executive materials, including regulations, institutional policies, and executive orders. The database currently focuses on the following subject areas: privacy of genetic information/confidentiality; informed consent; insurance and employment discrimination; genetic testing and counseling; and commercialization and patenting. |
| Nucleic Acids Research Annual Database Issue The NAR online Molecular Biology Database Collection is a public resource that contains links to the databases described in this issue of Nucleic Acids Research, previous NAR database issues, as well as a selection of other molecular biology databases that are freely available on the web and might be useful to the molecular biologist. The 2007 update includes 968 databases, 110 more than the previous one. Many databases that have been described in earlier issues of NAR come with updated summaries, which reflect recent progress and, in some instances, an expanded scope of these databases. Galperin, MY. Nucleic Acids Res. 2007 Jan;35(Database issue):D3-4. |
| OMIM Online Mendelian inheritance in man This database is a catalog of human genes and genetic disorders, authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. It contains textual information, pictures, and reference information. It also contains copious links to NCBI's Entrez database of MEDLINE articles and sequence information. |
| SGD Glossary Glossary of terms from the Saccharomyces Genome Database |
| The International HapMap Project The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals. |
|
Genome Browsers |
| Ensembl Genome Browser |
| NCBI Map Viewer |
| UCSC Genome Browser |
|
Motif Discovery Tools |
| BioProspector Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes |
| DiLiMoT - Discovery of Linear Motifs |
| MD scan A Fast and Accurate Motif Finding Algorithm With Applications To Chromatin Immunoprecipitation Microarray Experiments |
| MEME |
| MOTIF search Searching Protein and Nucleic Acid Sequence Motifs |
| PRINTS iteratively scan the SWISS-PROT/TrEMBL composite to find the conserved motifs |
|
NCBI Bookshelf |
| NCBI Bookshelf Homepage In collaboration with authors and publishers, the National Center for Biotechnology Information (NCBI) is adapting biomedical books for the web. |
|
Nucleic Acids |
| DHPLC Melt Program |
| EMBOSS (European Molecular Biology Open Software Suite) EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages. Within EMBOSS you will find hundreds of applications covering areas such as: sequence alignment, rapid database searching with sequence patterns, protein motif identification, including domain analysis, nucleotide sequence pattern analysis---for example to identify CpG islands or repeats, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, presentation tools for publication, and much more. |
| International Nucleotide Sequence Database Collaboration The International Nucleotide Sequence Databases (INSD) have been developed and maintained collaboratively between DDBJ , EMBL , and GenBank for almost 20 years. |
| Mutability Mutability will check a DNA sequence to determine how many single point mutations would result in nonsense mutations, missense mutations, and neutral mutations. It will also print the sequence with potential STOP codons highlighted, print the sequence with potential Missense codons highlighted, print the sequence with potential Neutral codons highlighted, count the number of CpG sites in the sequence, print the sequence with CpG sites highlighted. |
| Nucleic Acid Database a repository of three-dimensional structural information about nucleic acids |
| Riboapt DB Riboapt DB is the comprehensive database of Ribozymes and Aptamer sequences. Ribozymes are RNAs which have catalytic property and Aptamers are either RNA or DNA oligonucleotides which can bind tightly to the target molecules like nucleic acids, proteins, lipids and ligands like organic, inorganic molecules. |
| WEB-THERMODYN Web-based program that analyzes DNA sequences and computes the DNA helical stability, i.e. the free energy required to unwind the two strands of the double helix. |
|
Open Course Ware (OCW) |
| Biochemistry OCW |
| Bioinformatics OCW |
| Biotechnology OCW |
| Cell biology OCW |
| Chemistry OCW |
| Genetics OCW |
| Google OCW |
| Immunology OCW |
| Microbiology OCW |
| MIT's OpenCourseWare |
| Molecular biology OCW |
| OCW Consortium |
| OCW Finder |
| OpenContentOnline.com |
| Proteomics OCW |
| RNAi OCW |
| Wikipedia: OpenCourseWare OpenCourseWare (OCW) is university material that is available for all to see and use, analogous to open source software. |
|
Pathways |
| Ingenuity Pathways Analysis (IPA) IPA is a software application that enables biologists and bioinformaticians to identify the biological mechanisms, pathways, and functions most relevant to their experimental datasets or genes of interest. It allows researchers to graphically view, analyze, and query data in a comprehensive and seamless manner to understand molecular interactions, biological functions and disease on multiple levels. Access to IPA during the 2007 fiscal year is free for the entire medical school community. Access is unrestricted through May 2007, after which only two concurrent users will be allowed at a time. To request access to IPA, please send an email to Pat Gunn at gunnp@wustl.edu with the following information: Name, Department, Phone Number, and your Campus Box. After registration, Ingenuity Systems will send each registrant, via e-mail, their individual password and login instructions. Please note, the first time you login to your IPA account, it may take a few minutes to load the application. Additionally, please disable all pop-up blockers prior to signing in as they may prevent the application from loading. For technical questions, please email askbioinfo@msnotes.wustl.edu. For supplemental information from the recent IPA training event on campus, please see http://becker.wustl.edu/resources/bioinfo/suppl-IPA.html. |
| KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG is a "biological systems" database integrating both molecular building block information and higher-level systemic information. Molecular building blocks are distinguished between genetic building blocks (KEGG GENES) and chemical building blocks (KEGG LIGAND), while the systemic information is represented as molecular wiring diagrams (KEGG PATHWAY) and hierarchies and relationships among biological objects (KEGG BRITE). |
| Pathway Interaction Database The Pathway Interaction Database is a highly structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG). |
| Protein Lounge Protein Lounge is a leader in the field of system biology. We have developed many interactive web-based databases and software to help the life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene/protein data. Protein Lounge has met this concern by organizing all necessary data about genes/proteins into one portal. |
| Reactome The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. The information in this database is authored by biological researchers with expertise in their fields, maintained by the Reactome editorial staff, and cross-referenced with the sequence databases at NCBI, Ensembl and UniProt, the UCSC Genome Browser, HapMap, KEGG (Gene and Compound ), ChEBI, PubMed and GO. In addition to curated human events, inferred orthologous events in 22 non-human species including mouse, rat, chicken, zebra fish, worm, fly, yeast, two plants and E.coli are also available. Reactome is a free on-line resource, and Reactome software is open-source. |
|
Pharmacogenomics |
| PharmGKB PharmGKB is a publicly available Internet research tool developed by Stanford University with funding from the National Institutes of Health (NIH) and is part of the NIH Pharmacogenetics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. The contributers tab contains the links to all of the projects submitting data to the PharmGKB. |
|
Promoter Scanning Tools |
| Berkeley Drosophila Genome Project (BDGP) Our training and test sets of human and Drosophila melanogaster promoter sequences are available to the community for testing transcription start site predictors. These sites also contain our representative, standardized data sets of human and Drosophila melanogaster genes. |
| Dragon GC+ Start Finder |
| Dragon Gene Start Finder |
| Improbizer A tool that searches motifs in DNA or RNA sequence that occour with improbable frequency using a variation of the expectation maximization (EM) algorithm. |
| PROMOSER Human, rat and mouse promoter extraction service |
| Promoter 2.0 |
| Promoter Finder |
| Promoter Scan This tool can predict the promoter region by comparing the scoring homology with putative eukaryotic pol II promoter sequence. |
| Regulatory Sequence Analysis Tools (RSAT) This site provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences. |
| TRANSFAC TRANSFAC - a database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. The public version is free for non-commercial users, and the professional version is license based. |
| VISTA Enhancer Browser The VISTA Enhancer Browser is a central resource for experimentally validated human noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation with other vertebrates. The results of this enhancer screen are provided through this publicly available website. |
|
Protein Databases |
| AGADIR An algorithm to predict the helical content of peptides |
| BOBASE proteome databases |
| Conformation Angles DataBase [ CADB-2.0 ] Conformation angles of protein structures, with associated crystallographic data (CADB) |
| Entrez Protein The protein entries in the Entrez search and retrieval system have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq. |
| EXProt (database for EXPerimentally verified Protein functions) EXProt (database for EXPerimentally verified Protein functions) is a non-redundant database containing protein sequences for which the function has been experimentally verified. |
| Human Mitochodrial Protein Database The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. |
| Organelle DB Organelle DB compiles protein localization data from organisms spanning the eukaryotic kingdom and presents an organized catalog of the known protein constituents of more than 50 organelles, subcellular structures, and protein complexes. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. |
| OWL OWL is a non-redundant composite of 4 publicly-available primary sources: SWISS-PROT, PIR (1-3), GenBank (translation) and NRL-3D. |
| Promoter 2.0 Prediction Server Promoter2.0 predicts transcription start sites of vertebrate PolII promoters in DNA sequences. It has been developed as an evolution of simulated transcription factors that interact with sequences in promoter regions. It builds on principles that are common to neural networks and genetic algorithms. |
| Protein Folding Database (PFD) Searchable repository of freely available experimental protein folding data; aims to assist folders with standardised reference data and fitting tools, an importantly to provide a common source for sharing and publication of folding data, including 'raw' experimental data and references. |
| Protein Information Resource The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. |
| Protein Information Resource (PIR) The Protein Information Resource (PIR), located at Georgetown University Medical Center, is an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. PIR, directed by Dr. Cathy Wu, maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283,000 sequences covering the entire taxonomic range. PSD grew out of the Atlas of protein sequence and structure edited by Margaret Dayhoff. It also provides access to various databases that reference sequence data from Swiss-Prot, TrEMBL and others. |
| RCSB Protein Data Bank The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. |
| Secreted Protein Database |
| The C. Elegance Protein Database Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project, which is carried out jointly by the Sanger Institute in Cambridge, UK and the Genome Sequencing Center in St. Louis, USA. |
| UniProt UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. |
| UniProtKB/Swiss-Prot/TrEMBL protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases |
|
Protein Resources |
| CUTTER a tool to generate and analyze proteolytic fragments |
| CYSREDOX Predicting the redox state of cysteins in proteins from multiple sequence alignments |
| MassSearch Searching SwissProt or EMBL by protein mass after digestion |
| PeptideMass PeptideMass cleaves a protein sequence from the UniProt Knowledgebase (Swiss-Prot and TrEMBL) or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the protein of interest. If desired, PeptideMass can return the mass of peptides known to carry post-translational modifications, and can highlight peptides whose masses may be affected by database conflicts, isoforms or splice variants. |
| PredictProtein PredictProtein is a service for sequence analysis, structure and function prediction. When you submit any protein sequence PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure and function |
| PROCHECK Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry |
| PROCHECK-NMR a suite of programs that have been derived from the PROCHECK programs to analyse ensembles of protein structures solved by NMR. |
| Protein Calculator Estimates molecular weight, absorbance, solvent content, isoelectric point, mass, ultra-violent absorption, and charge at any pH. |
| Protein lounge Protein Lounge is a leader in the field of system biology. We have developed many interactive web-based databases and software to help the life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene/protein data. Protein Lounge has met this concern by organizing all necessary data about genes/proteins into one portal. |
| Protein Prospector Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments. |
| Protein Search Tools |
| Proteome BioKnowledge library Proteome BioKnowledge library contains six database volumes providing information about proteins in mammals, yeasts, nematodes, and fungi. Each volume focuses on a different organism important in pharmaceutical research. Incyte scientists manually collect and curate the information in each BioKnowledge Library volume from current scientific literature. The information in each volume represents thousands of independent research results. The BioKnowledge Library currently contains information about more than 60,000 scientific references on more than 80,000 proteins, including data on protein classification and function. The six databases are: GPCR-PD (a G Protein-coupled Receptors database for human, mouse and rat proteins, their ligands and downstream signaling molecules); HumanPSD (a Proteome Survey Database for information on human, mouse, and rat proteins); YPD (Saccharomyces cerevisiae); PombePD (Schizosaccaharomyces pombe); WormPD (Caenorhabditis elegans); and MycoPathPD. Access is restricted to the Medical School faculty, staff, and students. Access to the databases is by personal username and password. Each first-time user must establish a personal account by clicking on Register, and creating a personal username and password. |
| ProTherm ProTherm is a collection of numerical data of thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature etc. for wild type and mutant proteins, that are important for understanding the structure and stability of proteins. It also contains information about secondary structure and accessibility of wild type residues, experimental conditions (pH, temperature, buffer, ion and protein concentration), measurements and methods used for each data, and activity information (Km and Kcat ). |
| ProtParam ProtParam is a tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY) |
| Qgrid Provides cluster tree diagrams for proteins based on the charges on the atoms or hydrophobicity of a residue. Euclidean distances between charged atoms (or CA atoms of hydrophobic residues) are calculated and cluster tree diagrams are generated using hierarchical clustering method. These diagrams can be used to visually inspect hydrophobic and charged regions in proteins quickly. |
| SAPS Statistical Analysis of Protein Sequences SAPS evaluates by statistical criteria a wide variety of protein sequence properties. Properties considered include compositional biases, clusters and runs of charge and other amino acid types, different kinds and extents of repetitive structures, locally periodic motifs, and anomalous spacings between identical residue types. The statistics are computed for any single (or appropriately concatenated) protein sequence input. |
| STORM (Systematic Tailored Orf-data Retrieval & Management) STORM combines protein analyses of BLAST, FASTA, Pfam and ProtParam on a batch-file of protein sequences. It subsequently summarizes and organizes the output in an Access database format. |
| TagIdent TagIdent is a tool which allows the generation of a list of proteins close to a given pI and Mw, the identification of proteins by matching a short sequence tag of up to 6 amino acids against proteins in the UniProt Knowledgebase (Swiss-Prot and TrEMBL) databases close to a given pI and Mw, and the identification of proteins by their mass, if this mass has been determined by mass spectrometric techniques |
| Virtual Ribosome The Virtual Ribosome is a comprehensive tool for translating DNA sequences to the corresponding peptide sequences. Besides being a strong translation tool in it's own right (with an integrated ORF finder, support for all translation tables defined by the NCBI taxonomy group, and a number of options regarding START and STOP codons), the Virtual Ribosome can work directly on files containing annotation of gene structure. This makes it easy to map various aspect of Intron/Exon structure onto the translated sequence. |
|
Protocols |
| Arabidopsis protocols |
| Breast cancer research protocols A collection of both well-established and cutting-edge methods for investigating breast cancer biology not only in the laboratory, but also in clinical settings. These readily reproducible techniques solve a variety of problems, ranging from how to collect, store, and prepare human breast tumor samples for analysis, to analyzing cells in vivo and in vitro. Additional chapters address the technology of handling biopsies, new methods for analyzing genes and gene expression, markers of clinical outcome and progress, analysis of tumor-derived proteins and antigens, validating targets, and investigating the biology of newly discovered genes. |
| Calcium signaling protocols |
| Cancer cell signaling methods and protocols |
| Cell imaging techniques : methods and protocols |
| Cell imaging techniques : methods and protocols This book presents state-of-the-art chapters on a wide variety of microscopy-based imaging techniques. It covers a wide range of complimentary techniques, including methods such as fluorescence microscopy, electron microscopy, atomic force microscopy, and laser scanning cytometry, to name a few. Cell imaging techniques are now used in a variety of disciplines, including cell biology, pathology, physiology, pharmacology, molecular biology, neurobiology, biophysics and genetics. This book will prompt researchers to consider using a variety of complimentary imaging techniques to address their specific research questions, as opposed to the previously limited selection available. |
| Cell-cell interactions methods and protocols |
| Clinical applications of PCR Text offering a collection of core PCR techniques for the study and diagnosis of human diseases. Techniques heavily utilize nonisotopic, solution phase, and in situ amplification methods. |
| Current protocols in Bioinformatics |
| Current Protocols in Cell Biology |
| Current Protocols in Cytometry |
| Current protocols in human genetics |
| Current Protocols in Immunology |
| Current Protocols in Magnetic Resonance Imaging |