Network Biology Lab - User contributions [en]

Web Resources

2011-08-22T00:18:14Z

Beck310: /* Metagenomes */

== Variome ==
*[http://www.mutadatabase.org/ MutaDATABASE] a centralized and standardized DNA variation DB
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap Project] Catalog of human genetic variation
*[http://www.1000genomes.org/ 1000 Genome Project] Deep catalog of human genetic variation
*[http://cancergenome.nih.gov/ TCGA] The Cancer Genome Atlas
*[http://www.icgc.org/home ICGC cancer genome project] International Cancer Genome Consortium Cancer genome project
*[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation of natural population of Arabidopsis

== Transcriptome ==
*[http://www.ncbi.nlm.nih.gov/geo/ GEO]
*[http://www.ebi.ac.uk/arrayexpress/ Arrayexpress]

== Proteome/Localisome ==
*[http://suba.plantenergy.uwa.edu.au/ SUBA] SUBcellular location DB for Arabidopsis proteins

== Phenome/Metabolome ==
*[http://www.ncbi.nlm.nih.gov/omim OMIM] Human disease DB
*[http://www.who.int/classifications/icd/en/ ICD] International Classification of Disease by WHO
*[http://genomernai.de/GenomeRNAi/ GenomeRNAi] A Phenotype DB for large-scale RNAi screens (human, mouse, fly, worm...)
*[http://www.plastid.msu.edu/ cloroplast2010] Phenome/metabolome DB for Arabidopsis clroloplast gene KO lines (by MSU)

== Genotype-to-phenotype map ==
*[http://www.genome.gov/gwastudies/ GWAS catalog]
*[http://distild.jensenlab.org/ DistiLD] Diseases and Traits in Linkage Disequilibrium Blocks
*[http://www.personalgenomes.org/ Personal Genome Project]

== Interactome/Network ==
*[http://code.google.com/p/psicquic/ Protemic Standard Initiative Common QUery InterfaCe (PSICQUIC)]
*[http://www.imexconsortium.org/ International Molecular Exchange Consortium (IMEx)]
*[http://wodaklab.org/iRefWeb/ iRefWeb] a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))
*[http://bond.unleashedinformatics.com/ BIND] the Biomolecular Interaction Network Database
*[http://thebiogrid.org/ BioGRID]
*[http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html CORUM] Comprehensive Resource of Mammalian Protein Complexes
*[http://dip.doe-mbi.ucla.edu/dip/ DIP] Database of Interacting Proteins
*[http://www.ebi.ac.uk/intact/ IntAct]
*[http://www.hprd.org/ HPRD] Human Protein Reference Database
*[http://mint.bio.uniroma2.it/mint/ MINT] Molecular Interaction DB
*[http://mips.helmholtz-muenchen.de/genre/proj/mpact Mpact] Representation of Interaction Data at MIPS
*[http://mips.helmholtz-muenchen.de/proj/ppi/ MPPI] Mammalian PPI DB at MIPS
*[http://string-db.org/ STRING] Known and predicted PPI

== TF/miRNA/Regulaorty network ==
*[http://plntfdb.bio.uni-potsdam.de// PlnTFDB] Plant TF database by University of Potsdam, Germany
*[http://planttfdb.cbi.pku.edu.cn// PlantTFDB] Plant TF database by Peking University, China
*[http://arabidopsis.med.ohio-state.edu/ AGRIS] Arabidopsis Gene Regulatory Information Server (by OSU)
*[http://mirbase.org// miRBase]
*[http://mirgator.kobic.re.kr:8080/MEXWebApp// miRGator]
*[http://www.microrna.org/microrna// microRNA.org]
*[http://www.targetscan.org// TargetScanHuman]
*[http://pictar.mdc-berlin.de// PicTar] An algorithm for miRNA target scan
*[http://jcclab.science.oregonstate.edu// Carrington Lab Resource] Various DBs for plant miRNA
*[http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl// hmChIP] DB for publicly available human and mouse ChIP-seq and ChIP-chip data

== Chemical/Drug/Drug network ==
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem]
*[http://stitch.embl.de/ STITCH] DB for known and predicted chemical-protein interaction

== Ontology/Pathway ==
*[http://www.geneontology.org/ Gene Ontology]
*[http://www.reactome.org/ Reactome] A manually curated and peer-reviewed pathway DB
*[http://biocyc.org/ Biocyc]

== Bacterial genomes ==
*[http://www.pseudomonas.com/ Pseudomonas Genome Database]

== Fungal genomes ==
*[http://www.yeastgenome.org/ Saccharomyces Genome Database]
*[http://www.candidagenome.org/ Candida Genome Database]

== Animal genomes ==
*[http://www.wormbase.org/ WormBase]
*[http://flybase.org/ FlyBase]
*[http://www.informatics.jax.org/ MGI]

== Plant genomes ==
*[http://5e.plantphys.net/index.php Plant Physiology web]
*[http://www.arabidopsis.org/ TAIR]
*[http://www.gramene.org/ Gramene]
*[http://www.maizegdb.org/ MaizeGDB]
*[http://www.agbase.msstate.edu/ AgBase] Curated DB for functional analysis of agriculural animals and plants

== Metagenomes ==
*[http://portal.camera.calit2.net/gridsphere/gridsphere CAMERA 2.0] Curated DB and analysis tool for metagenomes
*[http://www.ncbi.nlm.nih.gov/genomes/lenvs.cgi NCBI Metagenome DB] Categorized with metagenome types, sources and sequencing methods.

== Others ==
*[http://www.genomesonline.org/ GOLD] Genome Online Database-Genome project statistics and download links
*[http://genomeinterpretation.org/ CAGI] Critical Assessment of Genome Interpretation
*[http://nightscience.org/ nightscience] Collective creativity in scientific discovery games

Web Resources

2011-08-22T00:17:32Z

Beck310: /* Metagenomes */

== Variome ==
*[http://www.mutadatabase.org/ MutaDATABASE] a centralized and standardized DNA variation DB
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap Project] Catalog of human genetic variation
*[http://www.1000genomes.org/ 1000 Genome Project] Deep catalog of human genetic variation
*[http://cancergenome.nih.gov/ TCGA] The Cancer Genome Atlas
*[http://www.icgc.org/home ICGC cancer genome project] International Cancer Genome Consortium Cancer genome project
*[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation of natural population of Arabidopsis

== Transcriptome ==
*[http://www.ncbi.nlm.nih.gov/geo/ GEO]
*[http://www.ebi.ac.uk/arrayexpress/ Arrayexpress]

== Proteome/Localisome ==
*[http://suba.plantenergy.uwa.edu.au/ SUBA] SUBcellular location DB for Arabidopsis proteins

== Phenome/Metabolome ==
*[http://www.ncbi.nlm.nih.gov/omim OMIM] Human disease DB
*[http://www.who.int/classifications/icd/en/ ICD] International Classification of Disease by WHO
*[http://genomernai.de/GenomeRNAi/ GenomeRNAi] A Phenotype DB for large-scale RNAi screens (human, mouse, fly, worm...)
*[http://www.plastid.msu.edu/ cloroplast2010] Phenome/metabolome DB for Arabidopsis clroloplast gene KO lines (by MSU)

== Genotype-to-phenotype map ==
*[http://www.genome.gov/gwastudies/ GWAS catalog]
*[http://distild.jensenlab.org/ DistiLD] Diseases and Traits in Linkage Disequilibrium Blocks
*[http://www.personalgenomes.org/ Personal Genome Project]

== Interactome/Network ==
*[http://code.google.com/p/psicquic/ Protemic Standard Initiative Common QUery InterfaCe (PSICQUIC)]
*[http://www.imexconsortium.org/ International Molecular Exchange Consortium (IMEx)]
*[http://wodaklab.org/iRefWeb/ iRefWeb] a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))
*[http://bond.unleashedinformatics.com/ BIND] the Biomolecular Interaction Network Database
*[http://thebiogrid.org/ BioGRID]
*[http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html CORUM] Comprehensive Resource of Mammalian Protein Complexes
*[http://dip.doe-mbi.ucla.edu/dip/ DIP] Database of Interacting Proteins
*[http://www.ebi.ac.uk/intact/ IntAct]
*[http://www.hprd.org/ HPRD] Human Protein Reference Database
*[http://mint.bio.uniroma2.it/mint/ MINT] Molecular Interaction DB
*[http://mips.helmholtz-muenchen.de/genre/proj/mpact Mpact] Representation of Interaction Data at MIPS
*[http://mips.helmholtz-muenchen.de/proj/ppi/ MPPI] Mammalian PPI DB at MIPS
*[http://string-db.org/ STRING] Known and predicted PPI

== TF/miRNA/Regulaorty network ==
*[http://plntfdb.bio.uni-potsdam.de// PlnTFDB] Plant TF database by University of Potsdam, Germany
*[http://planttfdb.cbi.pku.edu.cn// PlantTFDB] Plant TF database by Peking University, China
*[http://arabidopsis.med.ohio-state.edu/ AGRIS] Arabidopsis Gene Regulatory Information Server (by OSU)
*[http://mirbase.org// miRBase]
*[http://mirgator.kobic.re.kr:8080/MEXWebApp// miRGator]
*[http://www.microrna.org/microrna// microRNA.org]
*[http://www.targetscan.org// TargetScanHuman]
*[http://pictar.mdc-berlin.de// PicTar] An algorithm for miRNA target scan
*[http://jcclab.science.oregonstate.edu// Carrington Lab Resource] Various DBs for plant miRNA
*[http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl// hmChIP] DB for publicly available human and mouse ChIP-seq and ChIP-chip data

== Chemical/Drug/Drug network ==
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem]
*[http://stitch.embl.de/ STITCH] DB for known and predicted chemical-protein interaction

== Ontology/Pathway ==
*[http://www.geneontology.org/ Gene Ontology]
*[http://www.reactome.org/ Reactome] A manually curated and peer-reviewed pathway DB
*[http://biocyc.org/ Biocyc]

== Bacterial genomes ==
*[http://www.pseudomonas.com/ Pseudomonas Genome Database]

== Fungal genomes ==
*[http://www.yeastgenome.org/ Saccharomyces Genome Database]
*[http://www.candidagenome.org/ Candida Genome Database]

== Animal genomes ==
*[http://www.wormbase.org/ WormBase]
*[http://flybase.org/ FlyBase]
*[http://www.informatics.jax.org/ MGI]

== Plant genomes ==
*[http://5e.plantphys.net/index.php Plant Physiology web]
*[http://www.arabidopsis.org/ TAIR]
*[http://www.gramene.org/ Gramene]
*[http://www.maizegdb.org/ MaizeGDB]
*[http://www.agbase.msstate.edu/ AgBase] Curated DB for functional analysis of agriculural animals and plants

== Metagenomes ==
*[http://portal.camera.calit2.net/gridsphere/gridsphere CAMERA 2.0] Curated DB and analysis tool for metagenomes
*[http://www.ncbi.nlm.nih.gov/genomes/lenvs.cgi] NCBI Metagenome DB. Categorized with metagenome types, sources and sequencing methods.

== Others ==
*[http://www.genomesonline.org/ GOLD] Genome Online Database-Genome project statistics and download links
*[http://genomeinterpretation.org/ CAGI] Critical Assessment of Genome Interpretation
*[http://nightscience.org/ nightscience] Collective creativity in scientific discovery games

Web Resources

2011-08-19T02:31:26Z

Beck310: /* Metagenomes */

== Variome ==
*[http://www.mutadatabase.org/ MutaDATABASE] a centralized and standardized DNA variation DB
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap Project] Catalog of human genetic variation
*[http://www.1000genomes.org/ 1000 Genome Project] Deep catalog of human genetic variation
*[http://cancergenome.nih.gov/ TCGA] The Cancer Genome Atlas
*[http://www.icgc.org/home ICGC cancer genome project] International Cancer Genome Consortium Cancer genome project
*[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation of natural population of Arabidopsis

== Transcriptome ==
*[http://www.ncbi.nlm.nih.gov/geo/ GEO]
*[http://www.ebi.ac.uk/arrayexpress/ Arrayexpress]

== Proteome/Localisome ==
*[http://suba.plantenergy.uwa.edu.au/ SUBA] SUBcellular location DB for Arabidopsis proteins

== Phenome/Metabolome ==
*[http://www.ncbi.nlm.nih.gov/omim OMIM] Human disease DB
*[http://genomernai.de/GenomeRNAi/ GenomeRNAi] A Phenotype DB for large-scale RNAi screens (human, mouse, fly, worm...)
*[http://www.plastid.msu.edu/ cloroplast2010] Phenome/metabolome DB for Arabidopsis clroloplast gene KO lines (by MSU)

== Genotype-to-phenotype map ==
*[http://www.genome.gov/gwastudies/ GWAS catalog]
*[http://www.personalgenomes.org/ Personal Genome Project]

== Interactome/Network ==
*[http://code.google.com/p/psicquic/ Protemic Standard Initiative Common QUery InterfaCe (PSICQUIC)]
*[http://www.imexconsortium.org/ International Molecular Exchange Consortium (IMEx)]
*[http://wodaklab.org/iRefWeb/ iRefWeb] a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))
*[http://bond.unleashedinformatics.com/ BIND] the Biomolecular Interaction Network Database
*[http://thebiogrid.org/ BioGRID]
*[http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html CORUM] Comprehensive Resource of Mammalian Protein Complexes
*[http://dip.doe-mbi.ucla.edu/dip/ DIP] Database of Interacting Proteins
*[http://www.ebi.ac.uk/intact/ IntAct]
*[http://www.hprd.org/ HPRD] Human Protein Reference Database
*[http://mint.bio.uniroma2.it/mint/ MINT] Molecular Interaction DB
*[http://mips.helmholtz-muenchen.de/genre/proj/mpact Mpact] Representation of Interaction Data at MIPS
*[http://mips.helmholtz-muenchen.de/proj/ppi/ MPPI] Mammalian PPI DB at MIPS
*[http://string-db.org/ STRING] Known and predicted PPI

== TF/miRNA/Regulaorty network ==
*[http://plntfdb.bio.uni-potsdam.de// PlnTFDB] Plant TF database by University of Potsdam, Germany
*[http://planttfdb.cbi.pku.edu.cn// PlantTFDB] Plant TF database by Peking University, China
*[http://arabidopsis.med.ohio-state.edu/ AGRIS] Arabidopsis Gene Regulatory Information Server (by OSU)
*[http://mirbase.org// miRBase]
*[http://mirgator.kobic.re.kr:8080/MEXWebApp// miRGator]
*[http://www.microrna.org/microrna// microRNA.org]
*[http://www.targetscan.org// TargetScanHuman]
*[http://pictar.mdc-berlin.de// PicTar] An algorithm for miRNA target scan
*[http://jcclab.science.oregonstate.edu// Carrington Lab Resource] Various DBs for plant miRNA
*[http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl// hmChIP] DB for publicly available human and mouse ChIP-seq and ChIP-chip data

== Chemical/Drug/Drug network ==
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem]
*[http://stitch.embl.de/ STITCH] DB for known and predicted chemical-protein interaction

== Ontology/Pathway ==
*[http://www.geneontology.org/ Gene Ontology]
*[http://www.reactome.org/ Reactome] A manually curated and peer-reviewed pathway DB
*[http://biocyc.org/ Biocyc]

== Bacterial genomes ==
*[http://www.pseudomonas.com/ Pseudomonas Genome Database]

== Fungal genomes ==
*[http://www.yeastgenome.org/ Saccharomyces Genome Database]
*[http://www.candidagenome.org/ Candida Genome Database]

== Animal genomes ==
*[http://www.wormbase.org/ WormBase]
*[http://flybase.org/ FlyBase]
*[http://www.informatics.jax.org/ MGI]

== Plant genomes ==
*[http://5e.plantphys.net/index.php Plant Physiology web]
*[http://www.arabidopsis.org/ TAIR]
*[http://www.gramene.org/ Gramene]
*[http://www.maizegdb.org/ MaizeGDB]
*[http://www.agbase.msstate.edu/ AgBase] Curated DB for functional analysis of agriculural animals and plants

== Metagenomes ==
*[http://portal.camera.calit2.net/gridsphere/gridsphere CAMERA 2.0] Curated DB and analysis tool for metagenomes

== Others ==
*[http://www.genomesonline.org/ GOLD] Genome Online Database-Genome project statistics and download links
*[http://genomeinterpretation.org/ CAGI] Critical Assessment of Genome Interpretation
*[http://nightscience.org/ nightscience] Collective creativity in scientific discovery games

Web Resources

2011-08-19T02:28:29Z

Beck310: /* Metagenomes */

== Variome ==
*[http://www.mutadatabase.org/ MutaDATABASE] a centralized and standardized DNA variation DB
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap Project] Catalog of human genetic variation
*[http://www.1000genomes.org/ 1000 Genome Project] Deep catalog of human genetic variation
*[http://cancergenome.nih.gov/ TCGA] The Cancer Genome Atlas
*[http://www.icgc.org/home ICGC cancer genome project] International Cancer Genome Consortium Cancer genome project
*[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation of natural population of Arabidopsis

== Transcriptome ==
*[http://www.ncbi.nlm.nih.gov/geo/ GEO]
*[http://www.ebi.ac.uk/arrayexpress/ Arrayexpress]

== Proteome/Localisome ==
*[http://suba.plantenergy.uwa.edu.au/ SUBA] SUBcellular location DB for Arabidopsis proteins

== Phenome/Metabolome ==
*[http://www.ncbi.nlm.nih.gov/omim OMIM] Human disease DB
*[http://genomernai.de/GenomeRNAi/ GenomeRNAi] A Phenotype DB for large-scale RNAi screens (human, mouse, fly, worm...)
*[http://www.plastid.msu.edu/ cloroplast2010] Phenome/metabolome DB for Arabidopsis clroloplast gene KO lines (by MSU)

== Genotype-to-phenotype map ==
*[http://www.genome.gov/gwastudies/ GWAS catalog]
*[http://www.personalgenomes.org/ Personal Genome Project]

== Interactome/Network ==
*[http://code.google.com/p/psicquic/ Protemic Standard Initiative Common QUery InterfaCe (PSICQUIC)]
*[http://www.imexconsortium.org/ International Molecular Exchange Consortium (IMEx)]
*[http://wodaklab.org/iRefWeb/ iRefWeb] a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))
*[http://bond.unleashedinformatics.com/ BIND] the Biomolecular Interaction Network Database
*[http://thebiogrid.org/ BioGRID]
*[http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html CORUM] Comprehensive Resource of Mammalian Protein Complexes
*[http://dip.doe-mbi.ucla.edu/dip/ DIP] Database of Interacting Proteins
*[http://www.ebi.ac.uk/intact/ IntAct]
*[http://www.hprd.org/ HPRD] Human Protein Reference Database
*[http://mint.bio.uniroma2.it/mint/ MINT] Molecular Interaction DB
*[http://mips.helmholtz-muenchen.de/genre/proj/mpact Mpact] Representation of Interaction Data at MIPS
*[http://mips.helmholtz-muenchen.de/proj/ppi/ MPPI] Mammalian PPI DB at MIPS
*[http://string-db.org/ STRING] Known and predicted PPI

== TF/miRNA/Regulaorty network ==
*[http://plntfdb.bio.uni-potsdam.de// PlnTFDB] Plant TF database by University of Potsdam, Germany
*[http://planttfdb.cbi.pku.edu.cn// PlantTFDB] Plant TF database by Peking University, China
*[http://arabidopsis.med.ohio-state.edu/ AGRIS] Arabidopsis Gene Regulatory Information Server (by OSU)
*[http://mirbase.org// miRBase]
*[http://mirgator.kobic.re.kr:8080/MEXWebApp// miRGator]
*[http://www.microrna.org/microrna// microRNA.org]
*[http://www.targetscan.org// TargetScanHuman]
*[http://pictar.mdc-berlin.de// PicTar] An algorithm for miRNA target scan
*[http://jcclab.science.oregonstate.edu// Carrington Lab Resource] Various DBs for plant miRNA
*[http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl// hmChIP] DB for publicly available human and mouse ChIP-seq and ChIP-chip data

== Chemical/Drug/Drug network ==
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem]
*[http://stitch.embl.de/ STITCH] DB for known and predicted chemical-protein interaction

== Ontology/Pathway ==
*[http://www.geneontology.org/ Gene Ontology]
*[http://www.reactome.org/ Reactome] A manually curated and peer-reviewed pathway DB
*[http://biocyc.org/ Biocyc]

== Bacterial genomes ==
*[http://www.pseudomonas.com/ Pseudomonas Genome Database]

== Fungal genomes ==
*[http://www.yeastgenome.org/ Saccharomyces Genome Database]
*[http://www.candidagenome.org/ Candida Genome Database]

== Animal genomes ==
*[http://www.wormbase.org/ WormBase]
*[http://flybase.org/ FlyBase]
*[http://www.informatics.jax.org/ MGI]

== Plant genomes ==
*[http://5e.plantphys.net/index.php Plant Physiology web]
*[http://www.arabidopsis.org/ TAIR]
*[http://www.gramene.org/ Gramene]
*[http://www.maizegdb.org/ MaizeGDB]
*[http://www.agbase.msstate.edu/ AgBase] Curated DB for functional analysis of agriculural animals and plants

== Metagenomes ==
*[http://portal.camera.calit2.net/gridsphere/gridsphere CAMERA 2.0] Community Cyberinfrastructure for Advanced Microbial Ecology Research & Analysis

== Others ==
*[http://www.genomesonline.org/ GOLD] Genome Online Database-Genome project statistics and download links
*[http://genomeinterpretation.org/ CAGI] Critical Assessment of Genome Interpretation
*[http://nightscience.org/ nightscience] Collective creativity in scientific discovery games

Web Resources

2011-08-19T02:27:22Z

Beck310: /* Metagenomes */

== Variome ==
*[http://www.mutadatabase.org/ MutaDATABASE] a centralized and standardized DNA variation DB
*[http://hapmap.ncbi.nlm.nih.gov/ HapMap Project] Catalog of human genetic variation
*[http://www.1000genomes.org/ 1000 Genome Project] Deep catalog of human genetic variation
*[http://cancergenome.nih.gov/ TCGA] The Cancer Genome Atlas
*[http://www.icgc.org/home ICGC cancer genome project] International Cancer Genome Consortium Cancer genome project
*[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation of natural population of Arabidopsis

== Transcriptome ==
*[http://www.ncbi.nlm.nih.gov/geo/ GEO]
*[http://www.ebi.ac.uk/arrayexpress/ Arrayexpress]

== Proteome/Localisome ==
*[http://suba.plantenergy.uwa.edu.au/ SUBA] SUBcellular location DB for Arabidopsis proteins

== Phenome/Metabolome ==
*[http://www.ncbi.nlm.nih.gov/omim OMIM] Human disease DB
*[http://genomernai.de/GenomeRNAi/ GenomeRNAi] A Phenotype DB for large-scale RNAi screens (human, mouse, fly, worm...)
*[http://www.plastid.msu.edu/ cloroplast2010] Phenome/metabolome DB for Arabidopsis clroloplast gene KO lines (by MSU)

== Genotype-to-phenotype map ==
*[http://www.genome.gov/gwastudies/ GWAS catalog]
*[http://www.personalgenomes.org/ Personal Genome Project]

== Interactome/Network ==
*[http://code.google.com/p/psicquic/ Protemic Standard Initiative Common QUery InterfaCe (PSICQUIC)]
*[http://www.imexconsortium.org/ International Molecular Exchange Consortium (IMEx)]
*[http://wodaklab.org/iRefWeb/ iRefWeb] a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))
*[http://bond.unleashedinformatics.com/ BIND] the Biomolecular Interaction Network Database
*[http://thebiogrid.org/ BioGRID]
*[http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html CORUM] Comprehensive Resource of Mammalian Protein Complexes
*[http://dip.doe-mbi.ucla.edu/dip/ DIP] Database of Interacting Proteins
*[http://www.ebi.ac.uk/intact/ IntAct]
*[http://www.hprd.org/ HPRD] Human Protein Reference Database
*[http://mint.bio.uniroma2.it/mint/ MINT] Molecular Interaction DB
*[http://mips.helmholtz-muenchen.de/genre/proj/mpact Mpact] Representation of Interaction Data at MIPS
*[http://mips.helmholtz-muenchen.de/proj/ppi/ MPPI] Mammalian PPI DB at MIPS
*[http://string-db.org/ STRING] Known and predicted PPI

== TF/miRNA/Regulaorty network ==
*[http://plntfdb.bio.uni-potsdam.de// PlnTFDB] Plant TF database by University of Potsdam, Germany
*[http://planttfdb.cbi.pku.edu.cn// PlantTFDB] Plant TF database by Peking University, China
*[http://arabidopsis.med.ohio-state.edu/ AGRIS] Arabidopsis Gene Regulatory Information Server (by OSU)
*[http://mirbase.org// miRBase]
*[http://mirgator.kobic.re.kr:8080/MEXWebApp// miRGator]
*[http://www.microrna.org/microrna// microRNA.org]
*[http://www.targetscan.org// TargetScanHuman]
*[http://pictar.mdc-berlin.de// PicTar] An algorithm for miRNA target scan
*[http://jcclab.science.oregonstate.edu// Carrington Lab Resource] Various DBs for plant miRNA
*[http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl// hmChIP] DB for publicly available human and mouse ChIP-seq and ChIP-chip data

== Chemical/Drug/Drug network ==
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem]
*[http://stitch.embl.de/ STITCH] DB for known and predicted chemical-protein interaction

== Ontology/Pathway ==
*[http://www.geneontology.org/ Gene Ontology]
*[http://www.reactome.org/ Reactome] A manually curated and peer-reviewed pathway DB
*[http://biocyc.org/ Biocyc]

== Bacterial genomes ==
*[http://www.pseudomonas.com/ Pseudomonas Genome Database]

== Fungal genomes ==
*[http://www.yeastgenome.org/ Saccharomyces Genome Database]
*[http://www.candidagenome.org/ Candida Genome Database]

== Animal genomes ==
*[http://www.wormbase.org/ WormBase]
*[http://flybase.org/ FlyBase]
*[http://www.informatics.jax.org/ MGI]

== Plant genomes ==
*[http://5e.plantphys.net/index.php Plant Physiology web]
*[http://www.arabidopsis.org/ TAIR]
*[http://www.gramene.org/ Gramene]
*[http://www.maizegdb.org/ MaizeGDB]
*[http://www.agbase.msstate.edu/ AgBase] Curated DB for functional analysis of agriculural animals and plants

== Metagenomes ==
*[https://portal.camera.calit2.net/gridsphere/gridsphere CAMERA 2.0] Community Cyberinfrastructure for Advanced Microbial Ecology Research & Analysis

== Others ==
*[http://www.genomesonline.org/ GOLD] Genome Online Database-Genome project statistics and download links
*[http://genomeinterpretation.org/ CAGI] Critical Assessment of Genome Interpretation
*[http://nightscience.org/ nightscience] Collective creativity in scientific discovery games

People:S Beck

2011-04-06T09:36:36Z

Beck310:

[[Image:548640570_n_0_240x240.jpg|165px|thumb|left]]
==Educational background==
*'''Post Doctoral research.''', ''Yonsei University Seoul, Korea'', Department of Biotechnology (Supervisor: Professor Insuk Lee) (04/2011-Present) 
*'''Ph.D.''', ''Seoul National University'', School of Agricultural Bitechnology (Supervisor: Professor Yun-jaie Choi) (03/2004 - 02/2011) 
Thesis Title: Development of Intelligent Drug Delivery System Targeting Brain Cancer Stem Cell Using Phage Display Technology 
*'''B.Sc.''', ''Seoul National University'', Department of Animal Biotechnology (03/1999 - 02/2004). 
 
*'''Contact''': beck310(at)gmail

==Research Interests==
*Tumor Development, Cancer Genomics, Systems Biology

==Publications==
* '''Beck S''', Jin X, Sohn YW, Kim JK, Kim SH, Yin J, Pian X, Kim SC, Nam DH, Choi YJ, Kim H. Telomerase activity-independent function of TERT allows glioma cells to attain cancer stem cell characteristics by inducing EGFR expression. Mol Cells. 2010 Dec 24.
* Jin X*, '''Beck S'''*, Sohn YW, Kim JK, Kim SH, Yin J, Pian X, Kim SC, Choi YJ, Kim H. (*Equal contribution) Human telomerase catalytic subunit (hTERT) suppresses p53-mediated anti-apoptotic response via induction of basic fibroblast growth factor. Exp Mol Med. 2010 Aug 31;42(8):574-82.
* Jin X, Jeon HY, Joo KM, Kim JK, Jin J, Kim SH, Kang BG, '''Beck S''', Lee SJ, Kim JK, Park AK, Park WY, Choi YJ, Nam DH, Kim H. Frizzled 4 regulates stemness and invasiveness of migrating glioma cells established by serial intracranial transplantation. Cancer Res. 2011 Mar 1. [Epub ahead of print]
* Yin J, Jin X, '''Beck S''', Kang DH, Hong Z, Li Z, Jin Y, Zhang Q, Choi YJ, Kim SC, Kim H. In vitro myogenic and adipogenic differentiation model of genetically engineered bovine embryonic fibroblast cell lines. Biotechnol Lett. 2010 Feb;32(2):195-202.
* Jin X, Kim JG, Oh MJ, Oh HY, Sohn YW, Pian X, Yin JL, '''Beck S''', Lee N, Son J, Kim H, Yan C, Wang JH, Choi YJ, Whang KY.Opposite roles of MRF4 and MyoD in cell proliferation and myogenic differentiation. Biochem Biophys Res Commun. 2007 Dec 21;364(3):476-82.
* Jeon HM, Sohn YW, Oh SY, Kim SH, '''Beck S''', Kim S, Kim H. Inhibitor of differentiation 4 imparts chemoresistance and cancer stemness to glioma cells by derepressing miR-9*-mediated suppression of SOX2. Cancer Res. 2011 In press

People:S Beck

2011-04-06T09:20:55Z

Beck310:

People:S Beck

2011-04-06T09:18:03Z

Beck310: Created page with "==Educational background== *'''Post Doctoral research.''', ''Yonsei University Seoul, Korea'', Department of Biotechnology (Supervisor: Professor Insuk Lee) (04/2011-Present) <br..."

==Educational background==
*'''Post Doctoral research.''', ''Yonsei University Seoul, Korea'', Department of Biotechnology (Supervisor: Professor Insuk Lee) (04/2011-Present) 
*'''Ph.D.''', ''Seoul National University'', School of Agricultural Bitechnology (Supervisor: Professor Yun-jaie Choi) (03/2004 - 02/2011) 
Thesis Title: Development of Intelligent Drug Delivery System Targeting Brain Cancer Stem Cell Using Phage Display Technology 
*'''B.Sc.''', ''Seoul National University'', Department of Animal Biotechnology (03/1999 - 02/2004).

People

2011-04-06T09:04:29Z

Beck310: /* Postdoctoral fellows */

__NOTOC__
==Principal Investigator==
{|border="0" width="600"
|align="left"|[[File:People_ISLee_01.jpg|77px|link=people:IS_Lee]]
|
|
|-
|align="left"|[[people:IS_Lee|InSuk Lee]]
|
|
|-
|}
==Postdoctoral fellows==
{|border="0" width="400"
|align="left"|[[File:People_TYOh_cut.png|70px|link=people:TY_Oh]]
|align="left"|[[File:People_JE_Shim.JPG|70px|link=people:JE_Shim]]
|align="left"|[[File:People_SYHwang.JPG|70px|link=people:SH_Hwang]]
|align="left"|[[File:People_JWSong.jpg|70px|link=people:JW_Song]]
|align="left"|[[File:548640570_n_0_240x240.jpg|70px|link=people:S_Beck]]

|-
|align="left"|[[people:TY_Oh|Taeyun Oh]]
|align="left"|[[people:JE_Shim|Jung Eun Shim]]
|align="left"|[[people:SH_Hwang|SoHyun Hwang]]
|align="left"|[[people:JW_Song|Jawon Song]]
|align="left"|[[people:S_Beck|Samuel Beck]]
|}

==Graduate Students==
{|border="0" width="600"
|align="center"|[[File:People_Junha_Shin_cut.gif|70px|link=people:JH_Shin]]
|align="center"|[[File:People_HHKim_cut.jpg|70px|link=people:HH_Kim]]
|align="center"|[[File:People_SGJi_cut.jpeg|70px|link=people:SG_Ji]]
|align="center"|[[File:People_ARCho_cut.png|70px|link=people:AR_Cho]]
|align="center" cell-width="200"|[[File:Banmyungham.JPG|70px|link=people:ER_Kim]]
|align="center"|[[File:tak_sajin.jpg|70px|link=people:T_Lee]]
|-
|align="center"|[[people:JH_Shin|JunHa Shin]]
|align="center"|[[people:HH_Kim|HanHae Kim]]
|align="center"|[[people:SG_Ji|Sun-Gou Ji]]
|align="center"|[[people:AR_Cho|ARa Cho]]
|align="center"|[[people:ER_Kim|Eiru Kim]]
|align="center"|[[people:T_Lee|Tak Lee]]
|}

==Undergrad Research Assistant==
{|border="0" width="400"
|align="center"|[[File:People_ESKim2.jpg|70px|link=people:ES_Kim]]
|align="center"|[[File:People_MHLee.jpg|70px|link=people:MH_Lee]]
|align="center"|[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]
|align="center"|[[File:APBC2011_01.jpg|70px|link=people:HJ_Han]]
|-
|align="center"|[[people:ES_Kim|Eul Soo Kim]]
|align="center"|[[people:MH_Lee|Moon Hee Lee]]
|align="center"|[[people:KS_Kim|Kyung Soo Kim]]
|align="center"|[[people:HJ_Han|Heon Jong Han]]
|}
==Research Programmers==
{|border="0" width="200"
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]
|align="center"|[[File:Peolpe_HYHwang_s.JPG‎|70px|link=people:HY_Hwang]]
|-
|align="center"|[[people:SM_Yang|Soon Mo Yang]]
|align="center"|[[people:HY_Hwang|Hee Yeon Hwang]]
|}

People

2011-04-06T09:03:52Z

Beck310: /* Postdoctoral fellows */

__NOTOC__
==Principal Investigator==
{|border="0" width="600"
|align="left"|[[File:People_ISLee_01.jpg|77px|link=people:IS_Lee]]
|
|
|-
|align="left"|[[people:IS_Lee|InSuk Lee]]
|
|
|-
|}
==Postdoctoral fellows==
{|border="0" width="400"
|align="left"|[[File:People_TYOh_cut.png|70px|link=people:TY_Oh]]
|align="left"|[[File:People_JE_Shim.JPG|70px|link=people:JE_Shim]]
|align="left"|[[File:People_SYHwang.JPG|70px|link=people:SH_Hwang]]
|align="left"|[[File:People_JWSong.jpg|70px|link=people:JW_Song]]
|align="left"|[[File:People_548640570_n_0_240x240.jpg|70px|link=people:S_Beck]]

|-
|align="left"|[[people:TY_Oh|Taeyun Oh]]
|align="left"|[[people:JE_Shim|Jung Eun Shim]]
|align="left"|[[people:SH_Hwang|SoHyun Hwang]]
|align="left"|[[people:JW_Song|Jawon Song]]
|align="left"|[[people:S_Beck|Samuel Beck]]
|}

==Graduate Students==
{|border="0" width="600"
|align="center"|[[File:People_Junha_Shin_cut.gif|70px|link=people:JH_Shin]]
|align="center"|[[File:People_HHKim_cut.jpg|70px|link=people:HH_Kim]]
|align="center"|[[File:People_SGJi_cut.jpeg|70px|link=people:SG_Ji]]
|align="center"|[[File:People_ARCho_cut.png|70px|link=people:AR_Cho]]
|align="center" cell-width="200"|[[File:Banmyungham.JPG|70px|link=people:ER_Kim]]
|align="center"|[[File:tak_sajin.jpg|70px|link=people:T_Lee]]
|-
|align="center"|[[people:JH_Shin|JunHa Shin]]
|align="center"|[[people:HH_Kim|HanHae Kim]]
|align="center"|[[people:SG_Ji|Sun-Gou Ji]]
|align="center"|[[people:AR_Cho|ARa Cho]]
|align="center"|[[people:ER_Kim|Eiru Kim]]
|align="center"|[[people:T_Lee|Tak Lee]]
|}

==Undergrad Research Assistant==
{|border="0" width="400"
|align="center"|[[File:People_ESKim2.jpg|70px|link=people:ES_Kim]]
|align="center"|[[File:People_MHLee.jpg|70px|link=people:MH_Lee]]
|align="center"|[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]
|align="center"|[[File:APBC2011_01.jpg|70px|link=people:HJ_Han]]
|-
|align="center"|[[people:ES_Kim|Eul Soo Kim]]
|align="center"|[[people:MH_Lee|Moon Hee Lee]]
|align="center"|[[people:KS_Kim|Kyung Soo Kim]]
|align="center"|[[people:HJ_Han|Heon Jong Han]]
|}
==Research Programmers==
{|border="0" width="200"
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]
|align="center"|[[File:Peolpe_HYHwang_s.JPG‎|70px|link=people:HY_Hwang]]
|-
|align="center"|[[people:SM_Yang|Soon Mo Yang]]
|align="center"|[[people:HY_Hwang|Hee Yeon Hwang]]
|}

File:548640570 n 0 240x240.jpg

2011-04-06T09:02:33Z

Beck310: S Beck

S Beck