Favorite Links

The following is a list of our favorite links related to genomics and microarray.

University of Kansas Genomics-Related Research Facilities

• Applied Bioinformatics Laboratory
• Bioinformatics Core Facility
• DNA Sequencing Laboratory
• High Throughput Screening Laboratory
• Kansas Center for Advanced Scientific Computing
• Microscopy and Analytical Imaging Laboratory
• Molecular Structures Group
• Transgenic Mouse Facility
• Tissue Culture and Hybridoma Laboratory
• Bioinformatics Facility (Medical Center)
• Microarray Facility (Medical Center)
• Transgenic and Gene-targeting Institutional Facility (Medical Center)

University of Kansas Genomics-Related Departments and Centers

• Center for Bioinformatics
• Chemistry, Department of
• Electrical Engineering and Computer Science, Department of
• Higuchi Biosciences Center (HBC)
• Information and Telecommunication Technology Center (ITTC)
• Kansas Mental Retardation and Developmental Disability Research Center (MRDDRC)
• Medicinal Chemistry, Department of
• Molecular Biosciences, Department of
• Pharmaceutical Chemistry, Department of
• Pharmacology and Toxicology, Department of

Comprehensive Genomics & Bioinformatics Portals

• BMC Bioinformatics & Genomics Gateway: latest open access research from over 140 journals; new evaluation listings from Faculty of 1000 Biology; news from The Scientist
• BMC Microarrays Gateway
• BMC Systems Biology Gateway

Databases

Genomics-related databases

Due to the explosively large number of biological databases becoming now available, it is hard to keep track of them for most investigators. To meet this challenge, Nucleic Acids Research (NAR) keeps an annually updated list of major databases in the field.

Database list by categories (NAR )

Microarray databases

• Gene Expression Omnibus (GEO): an NCBI database for high-throughput gene expression data, including microarray data. Integrated with other NCBI databases.
• Stanford Microarray Database
• ArrayExpress: microarray data public repository maintained by European Bioinformatics Institute.
• Gene Expression Database (GXD): a database of Mouse Genome Informatics at the Jackson laboratory.
• Human Gene Expression Index (HuGE Index): aims to provide a comprehensive database to understand the expression of human genes in normal human tissues.
• Oncomine: curates public cancer microarray studies and provides data-mining tools so that genes and datasets of interest may be queried efficiently and groups of studies meta-analyzed.
• READ (RIKEN cDNA Expression Array Database): A database maintained by RIKEN (The institute of Physical and Chemical Research), Japan.
• Saccharomyces Genome Database (SGD) - Expression Connection: search gene expression data in the Saccharomyces genome database at Stanford University.
• Yale Microarray Database

Genomics Data Analysis Tools

Gene Ontology Analysis

• A comprehensive list of Gene Ontology analysis tools: hosted by The Gene Ontology Project site

Biological Pathway Analysis

• ArrayXpath
• BioMiner
• GenMAPP: a good tool for both pathway and gene ontology analysis
• PathFinder
• PathMAPA: for Arabidopsis
• PathwayExplorer: pathway resources include KEGG, BioCarta and GenMAPP.
• Pathway Express
• Pathway Miner
• Major pathway databases: KEGG, BioCarta, CMAP, GeneAssist Pathway Atlas

Genomics_Related Discussion Groups

• nodalpoint.org - A bioinformatics weblog
• Microarray group @ Yahoo! Groups
• Real-time qPCR group @ Yahoo! Groups
• SAM (Significance Analysis of Microarrays) group @ Yahoo! Groups
• GeneSpring users group @ Yahoo! Groups
• GenMAPP google group
• The Bioconductor project mailing list

Journals

• Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
• Bioinformatics
• BMC Bioinformatics
• BMC Genomics
• Briefings in Bioinformatics
• Briefings in Functional Genomics & Proteomics
• Comparative and Functional Genomics
• Current Genomics
• Functional & Integrative Genomics
• Genome
• Genome Biology
• Genome Research
• Genomics
• Genomics & Human Genetics - Annual Reviews
• Genomics, Proteomics & Bioinformatics
• Journal of Biomedical Informatics
• Journal of Structural and Functional Genomics
• Molecular Systems Biology
• Nature
• Nature Genetics
• Nucleic Acids Research
• OMICS: A Journal of Integrative Biology
• Online Journal of Bioinformatics (OJB)
• Physiological Genomics
• PLoS Biology
• PLoS Computational Biology
• PNAS
• Science

Organizations

• Genome.gov
• International Society for Computational Biology
• Microarray Gene Expression Data (MGED) Society