NYU School of Medicine Links

• The Center for Health Informatics and Bioinformatics consulting service.
• The Skirball Institute Bioinformatics Web Server
• NYU Bioinformatics Group - Courant Institute of Mathematical Sciences
• NYU Biostatistics - the Division of Biostatistics at NYU School of Medicine is engaged in teaching, statistical and collaborative research, and consultation with researchers in the School of Medicine.

Array Data Management & Analysis Resources

• Affymetrix Software Tools
• BioConductor- A comprehensive collection of bioinformatics data analysis tools developed by a community of open source software developers
• Broad Institute Software Tools RMAExpress - A standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip data using the Robust Multichip Average expression summary.
• The Institute for Genomic Research (TIGR) Microarray Resources - You can explore the TIGR Multiexperiment Viewer (TMEV) for an excellent collection of array analysis tools
• Significance Analysis of Microarrays (SAM) - An Excel add-on that selects significant genes based on differential expression between two or more sets of samples. It uses the false discovery rate and permutation approach for P adjustment.
• Prediction analysis for Microarrays (PAM) - Automated sample classification, as determined from gene expression data. This tool is now available as an Excel add-on or R package.
• GIST Columbia's Web interface for a class prediction tool using Support Vector Machine (SVM)

Gene Annotation Tools

• NETAFFX - gene annotation database for Affymetrix gene sets, updated quarterly.
• SOURCE - at Stanford University, CA, single or batch upload for gene annotation
• DiRE- Cis-REgulatory Module Explorer
• Genomatix Suite- useful tools such as MatInspector

Genomics and Bioinformatics Resources

• MIAME - Minimum Information About Microarray Experiment - publication and data sharing standard
• NCBI Gene Expression Omnibus(GEO) Public array data repository
• Microarray Informatics at the European Bioinformatics Institute (EBI)
• The Microarray Project at the NHGRI
• UCSC Genome Bioinformatics - public genome database
• EnsEMBL Genome Browser - public genome database
• Computational Biology and Informatics Lab (CBIL) at University of Pennsylvania
• MIT Primer3 WWW Interface - an excellent online PCR primer design tool
• Leming Shi's DNA Microarray Page - excellent compilation of links
• Y.F. Leung's Functional Genomics Web Page- another excellent compilation of links
• Gene Ontology (GO) Consortium
• Science Magazine's Functional Genomics Web Page
• Bioinformatics Journal Home Page - sign up for TOC email notification

News

• Press and News - Academic Medicine Development Company (AMDeC) Press Releases