Eugene Yaschenko

Publications (14)154.75 Total impact

• Source

  Available from: Anna R Panchenko

  Article: Database resources of the National Center for Biotechnology Information.

  Eric W Sayers, Tanya Barrett, Dennis A Benson, Evan Bolton, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael Dicuccio, Scott Federhen, [......], Karl Sirotkin, Douglas Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A Tatusova, Lukas Wagner, Yanli Wang, W John Wilbur, Eugene Yaschenko, Jian Ye
  [show abstract] [hide abstract]
  ABSTRACT: In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
  Nucleic Acids Research 12/2011; 40(Database issue):D13-25. · 8.03 Impact Factor
• Source

  Available from: Ilene Karsch-Mizrachi

  Article: BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.

  Tanya Barrett, Karen Clark, Robert Gevorgyan, Vyacheslav Gorelenkov, Eugene Gribov, Ilene Karsch-Mizrachi, Michael Kimelman, Kim D Pruitt, Sergei Resenchuk, Tatiana Tatusova, Eugene Yaschenko, James Ostell
  [show abstract] [hide abstract]
  ABSTRACT: As the volume and complexity of data sets archived at NCBI grow rapidly, so does the need to gather and organize the associated metadata. Although metadata has been collected for some archival databases, previously, there was no centralized approach at NCBI for collecting this information and using it across databases. The BioProject database was recently established to facilitate organization and classification of project data submitted to NCBI, EBI and DDBJ databases. It captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. Concomitantly, the BioSample database is being developed to capture descriptive information about the biological samples investigated in projects. BioProject and BioSample records link to corresponding data stored in archival repositories. Submissions are supported by a web-based Submission Portal that guides users through a series of forms for input of rich metadata describing their projects and samples. Together, these databases offer improved ways for users to query, locate, integrate and interpret the masses of data held in NCBI's archival repositories. The BioProject and BioSample databases are available at http://www.ncbi.nlm.nih.gov/bioproject and http://www.ncbi.nlm.nih.gov/biosample, respectively.
  Nucleic Acids Research 12/2011; 40(Database issue):D57-63. · 8.03 Impact Factor
• Article: Database resources of the National Center for Biotechnology Information.

  Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, [......], Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye
  Nucleic Acids Research. 01/2011; 39:38-51.
• Source

  Available from: Anna R Panchenko

  Article: Database resources of the National Center for Biotechnology Information.

  Eric W Sayers, Tanya Barrett, Dennis A Benson, Evan Bolton, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael DiCuccio, Scott Federhen, [......], Karl Sirotkin, Douglas Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A Tatusova, Lukas Wagner, Yanli Wang, W John Wilbur, Eugene Yaschenko, Jian Ye
  [show abstract] [hide abstract]
  ABSTRACT: In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
  Nucleic Acids Research 01/2011; 39(Database issue):D38-51. · 8.03 Impact Factor
• Article: Public data archives for genomic structural variation.

  Deanna M Church, Ilkka Lappalainen, Tam P Sneddon, Jonathan Hinton, Michael Maguire, John Lopez, John Garner, Justin Paschall, Michael DiCuccio, Eugene Yaschenko, Stephen W Scherer, Lars Feuk, Paul Flicek
  Nature Genetics 10/2010; 42(10):813-4. · 35.53 Impact Factor
• Article: Database resources of the National Center for Biotechnology Information.

  Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, [......], Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye
  Nucleic Acids Research. 01/2010; 38:5-16.
• Source

  Available from: Anna R Panchenko

  Article: Database resources of the National Center for Biotechnology Information.

  Eric W Sayers, Tanya Barrett, Dennis A Benson, Evan Bolton, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael Dicuccio, Scott Federhen, [......], Karl Sirotkin, Douglas Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A Tatusova, Lukas Wagner, Yanli Wang, W John Wilbur, Eugene Yaschenko, Jian Ye
  [show abstract] [hide abstract]
  ABSTRACT: In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, Reference Sequence, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Peptidome, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
  Nucleic Acids Research 11/2009; 38(Database issue):D5-16. · 8.03 Impact Factor
• Source

  Available from: Michael Feolo

  Article: Database resources of the National Center for Biotechnology Information.

  Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, [......], Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko, Jian Ye
  [show abstract] [hide abstract]
  ABSTRACT: In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
  Nucleic Acids Research 01/2009; 37:5-15. · 8.03 Impact Factor
• Source

  Available from: Michael Feolo

  Article: Database resources of the National Center for Biotechnology Information.

  David L Wheeler, Tanya Barrett, Dennis A Benson, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael Dicuccio, Ron Edgar, Scott Federhen, [......], Martin Shumway, Edwin Sequeira, Steven T Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L Tatusov, Tatiana A Tatusova, Lukas Wagner, Eugene Yaschenko
  [show abstract] [hide abstract]
  ABSTRACT: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
  Nucleic Acids Research 02/2008; 36(Database issue):D13-21. · 8.03 Impact Factor
• Source

  Available from: Michael Feolo

  Article: The NCBI dbGaP database of genotypes and phenotypes.

  Matthew D Mailman, Michael Feolo, Yumi Jin, Masato Kimura, Kimberly Tryka, Rinat Bagoutdinov, Luning Hao, Anne Kiang, Justin Paschall, Lon Phan, [......], Michael Kholodov, Kerry Zbicz, Jeffrey Beck, Michael Kimelman, Sergey Shevelev, Don Preuss, Eugene Yaschenko, Alan Graeff, James Ostell, Stephen T Sherry
  [show abstract] [hide abstract]
  ABSTRACT: The National Center for Biotechnology Information has created the dbGaP public repository for individual-level phenotype, exposure, genotype and sequence data and the associations between them. dbGaP assigns stable, unique identifiers to studies and subsets of information from those studies, including documents, individual phenotypic variables, tables of trait data, sets of genotype data, computed phenotype-genotype associations, and groups of study subjects who have given similar consents for use of their data.
  Nature Genetics 11/2007; 39(10):1181-6. · 35.53 Impact Factor
• Source

  Available from: Kim D Pruitt

  Article: Database resources of the National Center for Biotechnology Information.

  David L Wheeler, Tanya Barrett, Dennis A Benson, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael DiCuccio, Ron Edgar, Scott Federhen, [......], Gregory D Schuler, Edwin Sequeira, Steven T Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L Tatusov, Tatiana A Tatusova, Lukas Wagner, Eugene Yaschenko
  [show abstract] [hide abstract]
  ABSTRACT: In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
  Nucleic Acids Research 02/2007; 35(Database issue):D5-12. · 8.03 Impact Factor
• Source

  Available from: Kim D Pruitt

  Article: Database resources of the National Center for Biotechnology Information.

  David L Wheeler, Tanya Barrett, Dennis A Benson, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael DiCuccio, Ron Edgar, Scott Federhen, [......], Edwin Sequeira, Stephen T Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tugba O Suzek, Roman Tatusov, Tatiana A Tatusova, Lukas Wagner, Eugene Yaschenko
  [show abstract] [hide abstract]
  ABSTRACT: In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.
  Nucleic Acids Research 02/2006; 34(Database issue):D173-80. · 8.03 Impact Factor
• Source

  Available from: Joan U Pontius

  Article: Database resources of the National Center for Biotechnology Information.

  David L Wheeler, Tanya Barrett, Dennis A Benson, Stephen H Bryant, Kathi Canese, Deanna M Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Wolfgang Helmberg, [......], Lynn M Schriml, Edwin Sequeira, Steven T Sherry, Karl Sirotkin, Grigory Starchenko, Tugba O Suzek, Roman Tatusov, Tatiana A Tatusova, Lukas Wagner, Eugene Yaschenko
  [show abstract] [hide abstract]
  ABSTRACT: In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data retrieval systems and computational resources for the analysis of data in GenBank and other biological data made available through NCBI's website. NCBI resources include Entrez, Entrez Programming Utilities, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.
  Nucleic Acids Research 02/2005; 33(Database issue):D39-45. · 8.03 Impact Factor
• Source

  Available from: PubMed Central

  Article: The genome Assembly Archive: a new public resource.

  Steven L Salzberg, Deanna Church, Michael DiCuccio, Eugene Yaschenko, James Ostell
  PLoS Biology 10/2004; 2(9):E285. · 11.45 Impact Factor