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Genes and Genomes
Peptides and Proteins
Images and Articles
Laboratory Resources
Bioinformatics and Laboratory Tools
More Resources

Genes and Genomes

Alzheimer Disease Mutation Database
Lists of APP, PS1 and PS2 mutations, maintained by Marc Cruts at the University of Antwerp.

DNA From The Beginning
An animated primer on the basics of DNA, genes, and heredity, organized by key concepts. A resource provided by the DNA Learning Center at the Cold Spring Harbor Laboratory.

GenomeWeb
An extensive, searchable collection of genome related web sites from the UK Human Genome Mapping Project Resource Center.

Gene Expression Nervous System Atlas (GENSAT)
The GENSAT database contains a gene expression atlas of the central nervous system of the mouse based on bacterial artificial chromosomes (BACs). A resource provided by the Rockefeller University and is supported by an NINDS grant.

Human Genome Variation Database (HGVbase)
HGVbase is an attempt to summarize all known sequence variations in the human genome, to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes. HGVbase is the product of a European consortium involving the Karolinska Institute (Sweden), the European Bioinformatics Institute (UK), and the European Molecular Biology Laboratory (Germany).

International HapMap Project
The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors.

The Jackson Laboratory Mouse Genome Informatics Page
Provides access to data on the genetics, genomics and biology of the laboratory mouse.

Kyoto Encylopedia of Genes and Genomes (KEGG)
From Kyoto University, an incredible web site, one of the most comprehensive biological information resources on line. The site provides detailed metabolic, regulatory and functional pathways of a huge number of genes/gene products, and a powerful search engine pulls up a compendium of interesting information about specific genes.

Large-Scale Gene Expression Microarray Links and Resources
A collection of web resources on large-scale gene expression studies, especially related to microarray technologies. Maintained by Alan Robinson of the Industry Programme for the European Bioinformatics Institute.

MyMouse
A site hosted by the Neurobiology of Disease Program, Baylor College of Medicine, with the goal of promoting discovery of gene function in the nervous system and the development of novel mouse models of neurological disease. List your mutant, join a bulletin board, find out about new models and learn about where to get your mouse phenotyped.

The National Human Genome Research Institute
Heads the Human Genome Project for NIH. Site contains link to the Human Genome Project, grant information, and an extensive list of genomic and genetic resources.

NCBI Entrez Genomes Page
Entrez Genome provide access to the whole genomes of over 1000 viruses and over 100 microbes. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life - bacteria, archaea, and eukaryota - are represented, as well as many viruses and organelles.

NCBI Human Genome Resources
The NCBI Human Genome Resources sit serves as an integrated, one-stop, genomic information infrastructure for the Human Genome Project and other related projects.

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. The database contains textual information, pictures, and reference information.

PROTEOME Databases
This site, which includes six protein databases, YPD, HumanPSD, WormPD, GPCR-PD, PombePD, and MycopathPD, is the most comprehensive data collection on proteins available. The databases feature quality content based on detailed literature-based curation, comprehensive references, disease information, BioKnowledge transfer, and integrated resources.

RNAi Consortium shRNA Library
The RNAi Consortium is a public-private effort based at the Broad Institute whose mission is to create a shRNA library as well as to validate tools and methods that will enable the scientific community to use RNAi to determine the function of human and mouse genes.

Serial Analysis of Gene Expression (SAGE Genie)
SAGE Genie was produced as part of the Cancer Genome Antamony Project (CGAP) SAGE project by collaborators from Johns Hopkins University, Duke University, the Ludwig Institute for Cancer Research (Sao Paulo Branch), and the National Cancer Institute. SAGE is a method to efficiently count large numbers of mRNA transcripts by sequencing short tags, usually 10 or 17 bp in length. SAGE Genie uses a new analytical method of reliably matching SAGE tags to known genes. Based on this novel tag to gene mapping, the website visualizes human and mouse gene expression analysis in tissues or individual libraries using displays that are highly intuitive.

Single Nucleotide Polymorphisms Database (dbSNP)
Launched in September of 1998, dbSNP accepts submissions from all laboratories and is especially interested in mutations in genes and/or where additional biological information is known. The database has been designed to accept several classes of genetic variation: SNPs, microsatellite repeats, and small insertion/deletion polymorphisms

Trans-NIH Mouse Genomics and Genetics Resources
This site will provide information about funding opportunities; major mouse genomics and genetics resources; policies affecting resources; courses and scientific meetings related to the mouse initiative; and selected reports and publications. When appropriate, items not in response to the initiative, but which are deemed relevant to the initiative, will be posted. Posting decisions are made by a sub-committee of the Trans NIH Genomics Resources Working Group.

Peptides and Proteins

ExPASy Molecular Biology Server
Expert Protein Analysis System of the Swiss Institute of Bioinformatics. The site dedicate to the analysis of protein sequences and structures as well as two-dimensional polyacrylamide gel electrophoresis.

G Protein-coupled Receptor (GPCR) Database
A major repository of characterization data for G protein-coupled receptors. Provided by the International Union of Basic and Clinical Pharmacology.

PhosphoSite®
An expert-curated knowledge base of information focused on protein phosphorylation mainly in vertebrates. In addition to phosphorylation sites curated from the literature, large numbers of new unpublished sites discovered by MS/MS analyses are being added regularly. Sponsored by Cell Signaling Technology.

Protein Kinase Resource
A web accessible compendium of information on the protein kinase family of enzymes. This resource includes tools for structural and computational analyses as well as links to related information maintained by others. The PKR is a collaborative project of protein kinase researchers and computational biologists working to create a database integrating molecular and cellular information.

RSCB Protein Databank
A database with over 24,000 3-D macromolecular protein structure data determined by X-ray crystallography and NMR. Maintained by the Research Collaboratory for Structural Bioinformatics.

Yeast Protein Interaction Data
A collection of linkage maps that describe the protein-protein interactions found in yeasts. The maps are created by Dr. Stanley Fields and his colleagues at the University of Washington.

Images and Articles

CELLS Alive!
Provides a video library of cells related to microbiology, cell biology, infectious diseases and others. Also provides basic educational materials related to cells.

Internet Brain Volume DB
The goal of IBVD is to provide a Web-based searchable database of brain neuroanatomic volumetric observations. This is designed to access both group volumetric results as well as volume observations in individual cases. A major effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as meta-analysis. Extensions that permit pre-published, non-published, and other representation are planned, again to facilitate comparative analyses.

The Internet Pathology Lab for Medical Education
Includes over 1900 images that demonstrate gross and microscopic pathologic findings associated with human disease conditions. Interesting images could be found under the heading dementias in the CNS Pathology index page.

Mouse Atlas Project (MAP)
The Laboratory of Neuroimaging at UCLA develops MAP which aims to develop a dynamic, probabilistic atlas of the adult and developing C57BL/6J mouse. MAP serves as an imaging framework to house and correlate gene expression with anatomic and molecular information drawn from traditional and novel imaging technologies.

Neuromuscular Disease Center
A superb web site filled with information on hundreds of neuromuscular disorders such as amyotrophic lateral sclerosis, multiple sclerosis and rarer diseases. The site was created by Alan Pestronk, a neurologist at Washington University Medical School, and includes guides to diagnosing, informing patients and treatment.

Neuropathological Examination Research Database
A searchable system providing access to a selection of tissues available through the Tissue Repository at the Institute for Brain Aging and Dementia at University of California, Irvine.

Whole Brain Atlas
Created by a researcher at Harvard Medical School, this excellent, image-based resource includes MRI, functional imaging, clinical descriptions and tours of several Alzheimer's disease cases.

Laboratory Resources

Aging Cell Repository
A collection of cell cultures, collected over the past three decades, available to facilitate research related to the cellular and molecular studies on the mechanisms of aging and related diseases. Maintainted by the Coriell Institute for Medical Research, and sponsored by National Institute of Aging.

Antibody Resources Page
Provides links to antibodies suppliers, including contract and custom preparations of antibodies and immunological services.

Data and tissue available from major study of age-related neurodegenerative diseaeses in Guam.
Considerable data and tissue samples have been obtained during the first two years of this research. Interested and qualified investigators are invited to explore the possibility of sharing some of the information and tissue.

Genentech Research Contracts and Reagents Program
Genentech supports investigators in academic institutions throughout the world by supplying key reagents for their research. To initiate work with Genentech, you can complete the Material Request Form available on their web site to request proteins, antibodies, and cDNAs from Genentech. These requests are granted on the basis of scientific merit and availability of material. This program is not for human protocol or for clinical use.

The Jackson Laboratory
The Jackson Laboratory, a non-profit institution, is the world's largest mammalian genetic research facility. The Laboratory supplies approximately 2 million JAX® Mice to the global research community from more than 2,700 varieties.

Knockout Mouse Database
A resource maintained by the National Institute on Drug Abuse's Genetics Workgroup of gene knockouts in mice that affect nervous system phenotypes and function.

The National Alzheimer's Coordinating Center (NACC)
Provides access to brief descriptions of some 40,000 subjects evaluated at NIA-funded Alzheimer Disease centers, and serves as a gateway for research. ADC and ADRC researchers may also obtain information on the minimum data set for the NACC database.

National Institute on Aging Aged Rodent Tissue Bank and Tissue Arrays
The National Institute on Aging (NIA) has developed under contractual arrangement with BioReliance a repository of tissue collected from the NIA Aged Rodent Colonies. Tissue is available to investigators at academic and nonprofit research institutions who are engaged in funded research on aging. The aged rodent tissue arrays offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community.

National Institutes of Health (NIH) Stem Cell Information
The NIH Stem Cell Information website includes the NIH Human Embryonic Stem Cell Registry listing stem cell lines that meet the eligibility criteria for Federally funded research that are currently available for shipping. Also available through the website are resources such stem cell material transfer agreements; reports and general information such as stem cell basics; adminstration statements and recent congressional testimony.

The Nun Study
The Nun Study is a longitudinal study of aging and Alzheimer Disease sponsored by NIA and housed in the Sanders-Brown Center on Aging in University of Kentucky. Started in 1986, the study currently involved 678 American members of the School Sisters of Notre Dame religious congregation who were 75-103 years of age. The web site also provide data from the study to researchers.

Primate Info Net
Developed by the Wisconsin Primate Research Center at the University of Wisconsin-Madison, the Primate Info Net lists resources in primatology, federally funded primate research, an international directory of primatology organizations, a world directory of primatologists, as well as products and services for primates.

Primate Resources
Directory of regional research centers, academic facilities, commercial sources and other information on aged non-human primates.

Transmissible Spongiform Encephalopathy (TSE) Resource Centre
Provides various reagents, including anti-recPrP monoclonal antibodies to the TSE research community. Maintained by two researchers from the Crompton Laboratory of the Institute of Animal Health in UK.

The Whole Mouse Catalog
A compendium of web sites with useful information for scientists using mice in research.

Bioinformatics and Laboratory Tools

Arrowsmith
Developed by University of Chicago researchers Neil Smalheiser and Don Swanson, this novel information retrieval system searches the biomedical literature for implicit connections, for example between one biological process and a seemingly unrelated one. This demonstration site is free for anyone to use. The creators welcome feedback from users.

Bioinformatics Organization, Inc. (Bioinformatics.org)
Founded in 1998 by J.W. Bizzaro, Bioinformatics.Org aims to facilitate world-wide communications and collaborations between practicing and neophyte bioinformatic scientists and technicians. The Organization provides these individuals, as well as the public at large, free and open access to methods and materials for and from scientific research, software development, and education.

Caret (Computerized Anatomical Reconstruction and Editing Toolkit)
A software package developed by the Van Essen Laboratory for visualizing, editing, analyzing, and flattening cortical surface reconstructions. Also available through the site are data sets for the human, macaque, and mouse brain atlases. Each atlas includes surface reconstructions of the left and right cerebral hemispheres plus the cerebellum, along with high-resolution structural MRI volumes. The associated experimental data sets include cortical areas delineated by multiple partitioning schemes for the human and macaque, plus exemplar fMRI data sets for human cortex and anatomical connectivity data for the macaque.

Computational Neuroscience/Neuroinformatics
The Computational Neuroscience/Neuroinformatics web site aims to unravel the complex structure-function relationships of the brain at all levels from molecule to behavior in an integrative effort of many scientific disciplines and intends to foster the development of the field and the growth of an active community with a focus on Europe.

Cytoscape
Cytoscape is an open-source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Cytoscape is under continuous development by scientists at Institute of Systems Biology, UC San Diego, Whitehead Institute and The Memorial Sloan-Kettering Cancer Center. Other scientists and software developers can download the source code at no cost.

Gene Chips (DNA Microarrays)
A basic how-to site on gene chip technology, run by computational chemist Leming Shi. Includes extensive directories of links to other sites with microarray information.

iProtocol
A superb, searchable, free site maintained by M.I.T.-affiliated researchers and software engineers, providing detailed information on hundreds of research protocols used in bioscience.

NIH Image
Free, public-domain software for image capturing, processing and analysis.

SenseLab
The SenseLab Project at the Yale University School of Medicine is a long term effort to build integrated, multidisciplinary models of neurons and neural systems. Databases from this project includes three neuronal databases: Cellular Properties Database (CellPropDB); NeuronDB; and ModelDB, and three olfactory databases.

Telemakus System
Developed at the University of Washington, the goal of the Telemakus System is to enhance the knowledge discovery process by developing retrieval, visual and interaction tools to mine and map research findings from the research literature. The Caloric Restriction & Nutritional Aspects in Aging database covers the majority of original research articles in English with data tables in that field since 1935. The Biomarkers in Alzheimer's Disease (bioAD KB) database covers studies on the biomarkers apolipoprotein E, amyloidβ, tau and isoprostanes, among others, in Alzheimer’s disease.

Webcutter
Popular free software developed by Max Heiman to map restriction sites.

More Resources

The Molecular Biology Database Collection: 2005 Updates
The Nucleic Acids Research Molecular Biology Database Collection is a public online resource that lists publicly accessible databases that are of value to biologists. The 2005 version contains 719 databases from around the world.

Neurosciences on the Internet
A searchable and browsable index of neuroscience resources on the Internet.

Wikipedia
Review the current entry for Alzheimer disease and add your expertise.