MSMS 6211, BCOR 5585 Genomics
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Genomics Websites
- A Brief Guide to GenomicsGenomics is the study of all of a person's genes (the genome), including interactions of those genes with each other and with the person's environment.
- Earth MicroBiome ProjectThe Earth Microbiome Project is a proposed massively multidisciplinary effort to analyze microbial communities across the globe. The general premise is to examine microbial communities from their own perspective. Hence we propose to characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe. We will analyze 200,000 samples from these communities using metagenomics, metatranscriptomics and amplicon sequencing to produce a global Gene Atlas describing protein space, environmental metabolic models for each biome, approximately 500,000 reconstructed microbial genomes, a global metabolic model, and a data-analysis portal for visualization of all information.
- GIGA Project“Giga-” is a prefix derived from Greek, meaning “giant.” In modern times, giga- refers to the large datasets and information as the billions of bytes we generate and store on our computers.
- Harte Research InstituteWe seek science-driven solutions for problems facing the Gulf of Mexico to advance its long-term sustainable use and conservation.
- Human ENCODE ProjectThe National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The project started with two components - a pilot phase and a technology development phase.
- Marine Microbiology & Genetics LaboratoryThe thread that now runs through the NSU Oceanographic Center's Microbiology and Genetics Lab ties together marine microbiology, metagenomics and sponge molecular phylogeny.
- Stanford Encyclopedia of Philosophy: Molecular GeneticsThe SEP's page on Molecular Genetics was designed so that each entry is maintained and kept up-to-date by an expert or group of experts in the field. All entries and substantive updates are refereed by the members of a distinguished Editorial Board before they are made public. Consequently, our dynamic reference work maintains academic standards while evolving and adapting in response to new research.
- University of Miami - Marine GenomicsUnderstanding biological importance by evolutionary analyses of genomes, gene expression, and genetic divergence
- Array ExpressArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database.
- Database of Interacting ProteinsThe DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Please, check the reference page to find articles describing the DIP database in greater detail.
- E. coli Genome ProjectThe ASAP database, developed in collaboration with Nicole Perna, is a platform for community sharing of annotation information and data which is made available for downloading by the community.
- GenBankGenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration , which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis.
- Gene Expression OmnibusGEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.
- Marcotte Lab Assorted MS/MS Proteomics DatasetsThis website provides raw/processed data files from (LC/)LC-MS/MS experiments, information on experimental procedures, data collection and post-processing.
- Marcotte Lab MS/MS Shotgun Proteomics Data RepositoryThis website provides raw/processed data files from (LC/)LC-MS/MS experiments, information on experimental procedures, data collection and post-processing.
- MINTWelcome to MINT, the Molecular INTeraction database. MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The full MINT dataset can be freely downloaded.
- Open Proteomics DatabaseThis is the old database that is maintained for historical purposes.
- PlasmoDBPlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.
- Saccharomyces Genome DatabaseThe Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms.
- TetraFGDTetraFGD is a web-accessible functional genomics database of Tetrahymena thermophila. Currently, TetraFGD provides RNA-seq, MICROARRAY, GENE NETWORK and PHOSPHOPROTEOME data for T. thermophila using Gene ID or Gene description searches or Blast Sequences. TetraFGD will be extended to develop/collect other functional genomics data (e.g. proteome) and is intended to be a resource for all members of the scientific research community interested in Tetrahymena. As we develop TetraFGD, we would appreciate input from the community so that we can tailor it to meet your needs. Please feel free to send comments, suggestions, or questions to TetraFGD@ihb.ac.cn
- SEEDWith the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the Fellowship for Interpretation of Genomes (FIG) as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.
- YFGdbAbout the Yeast Functional Genomics Database (YFGdb)
The long term goal of the YFGdb project is to collect, curate, and freely disseminate all available yeast functional genomics data, along with requisite analysis tools. The SGD Lite database is now part of YFGdb.