OnLine resources
NAR - database summary papers
UCSC Genome Browser - genome browser
Ensembl - genome browser
NCBI - GenBank
EBI - EMBL, UniProt, InterPro
KEGG - Kyoto Encyclopedia of Genes and Genome
PhyloFacts - phylogenomic encyclopedias across the Tree of Life
Cytoscape - visualizing and integrating molecular interaction networks
GenMAPP - Gene map annotator and pathway profiler (from wikipathways)
Protege - ontology editor and knowledge-base framework.
Genepattern - scientific workflow platform with more than 90 genomic analysis tools.
Galaxy - multiple alignemnts, compare genomic annotations, profile metagenomic samples, etc

Pathogens
PATHPORT - lists services (for pathogens)
BRC Central - the pathogen data repository.

Metagenomic
NAST - Nearest Alignment Space Termination
GreenGenes - searching 16S rRNA genes
DOTUR - assigns operation taxonomic units (OTUs)
MUSCLE - multiple sequence comparison by log-expectation
DNA Dist - compute distance matrix (part of phylip)

Organism Databases
Flybase - a database for drosophila genetics and molecular biology.
Wormbase - database on the genetics of C elegans and related nematodes.
SGD - genetic and molecular biological information about Saccharomyces cerevisiae. EcoCYC - Encyclopedia of Escherichia coli K-12 Genes and Metabolism
TAIR - The Arabidopsis Information Resource
DictyBase - social amoeba Dictyostelium discoideum.
RGD - rat genome database
Gramene - comparative grass genomics
PlantGDB - plant species-specific EST and GSS databases

Genome sequencing projects
GOLD - Genomes OnLine Databases
TIGR/JCVI - sequenced archaea/virus/bacteria
JGI - microbial genomes (GO, KEGG, KOG)
NIH - Microbial Sequencing Centers
Sanger Center - sequencing genome projects
GSC - sequencing genome projects
BCM - sequencing genome projects
BROAD - sequencing genome projects

Genomic Literature/Journals
Nature
Science
PNAS
Plant Physiology
Plant Pathology
The Plant Journal
Genome Research
Genes and Development
Genetics
Genomics
Nature Genetics
Molercular Biology and Evolution
Trends
  Trends in Plant Science
  Trends in Biotechnology
Oxford Journals
  Briefing in Bioinformatics
  Bioinformatics
  Nucleic Acids Research
BMC BioMed Centreal
  BMC Bioinformatics
  BMC Genomics
Mary Ann Liebert, Inc
  OMICS: A Journal of Integrative Biology
International Journal of Computing Intelligence and System Biology (IJCIBSB)

Bioinformatics Programs
University of British Columbia - graduate program