SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models
暂无分享,去创建一个
Fangfang Xia | Rick L. Stevens | Robert A. Edwards | Gordon D. Pusch | Veronika Vonstein | Christopher S. Henry | Terrence Disz | Ross Overbeek | Ramy K. Aziz | Gary J. Olsen | Scott Devoid | Bruce Parrello | R. Overbeek | G. Pusch | G. Olsen | C. Henry | R. Stevens | R. Edwards | R. Olson | Fangfang Xia | V. Vonstein | B. Parrello | R. Aziz | T. Disz | Scott Devoid | Robert Olson
[1] N. Ahmed. A Flood of Microbial Genomes–Do We Need More? , 2009, PloS one.
[2] O. White,et al. Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.
[3] Rachael P. Huntley,et al. The UniProt-GO Annotation database in 2011 , 2011, Nucleic Acids Res..
[4] Obi L. Griffith,et al. The Genome Sequence of the SARS-Associated Coronavirus , 2003, Science.
[5] Robert Olson,et al. Real Time Metagenomics: Using k-mers to annotate metagenomes , 2012, Bioinform..
[6] R. Overbeek,et al. The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[7] Susumu Goto,et al. The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..
[8] Ross Overbeek,et al. Genomics: what is realistically achievable? , 2000, Genome Biology.
[9] Robert Olson,et al. Accessing the SEED Genome Databases via Web Services API: Tools for Programmers , 2010, BMC Bioinformatics.
[10] Daniela Bartels,et al. Annotation of bacterial and archaeal genomes: improving accuracy and consistency. , 2007, Chemical reviews.
[11] L. Finelli,et al. Emergence of a novel swine-origin influenza A (H1N1) virus in humans. , 2009, The New England journal of medicine.
[12] John Gould,et al. Toward the automated generation of genome-scale metabolic networks in the SEED , 2007, BMC Bioinformatics.
[13] R. Overbeek,et al. FIGfams: yet another set of protein families , 2009, Nucleic acids research.
[14] Rick L. Stevens,et al. The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.
[15] Tatiana A. Tatusova,et al. BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata , 2011, Nucleic Acids Res..
[16] Matthew D. Jankowski,et al. Group contribution method for thermodynamic analysis of complex metabolic networks. , 2008, Biophysical journal.
[17] E. Brzuszkiewicz,et al. Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC) , 2011, Archives of Microbiology.
[18] R. Mahadevan,et al. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. , 2003, Metabolic engineering.
[19] James H. Bullard,et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. , 2011, The New England journal of medicine.
[20] M. Stanhope,et al. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition , 2007, Genome Biology.
[21] Rick L Stevens,et al. iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations , 2009, Genome Biology.
[22] Rick L. Stevens,et al. High-throughput generation, optimization and analysis of genome-scale metabolic models , 2010, Nature Biotechnology.
[23] Cathy H. Wu,et al. UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..
[24] Robert A. Edwards,et al. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies , 2012, Nucleic acids research.
[25] S. Bentley,et al. Sequencing the species pan-genome , 2009, Nature Reviews Microbiology.
[26] Naryttza N. Diaz,et al. The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.
[27] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[28] M. Dolan,et al. Beyond the HapMap Genotypic Data: Prospects of Deep Resequencing Projects. , 2008, Current bioinformatics.
[29] E. Koonin,et al. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. , 2001, Genome research.
[30] G. Church,et al. Genome-Scale Metabolic Model of Helicobacter pylori 26695 , 2002, Journal of bacteriology.
[31] V. Nizet,et al. Pathogen Microevolution in High Resolution , 2010, Science Translational Medicine.
[32] I-Min A. Chen,et al. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..
[33] Susumu Goto,et al. The KEGG databases at GenomeNet , 2002, Nucleic Acids Res..
[34] H. Tettelin,et al. The microbial pan-genome. , 2005, Current opinion in genetics & development.
[35] I-Min A. Chen,et al. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata , 2011, Nucleic Acids Res..
[36] Mark D'Souza,et al. Use of contiguity on the chromosome to predict functional coupling , 1998, Silico Biol..
[37] Gavin J. D. Smith,et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic , 2009, Nature.
[38] B. Snel,et al. Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.
[39] Rick L. Stevens,et al. The SEED: a peer-to-peer environment for genome annotation , 2004, CACM.
[40] G. Moreno-Hagelsieb,et al. The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons , 2010, Nucleic acids research.
[41] Rick L. Stevens,et al. Connecting genotype to phenotype in the era of high-throughput sequencing. , 2011, Biochimica et biophysica acta.
[42] S. Daefler,et al. Biolog phenotype microarrays. , 2012, Methods in molecular biology.
[43] Peer Bork,et al. KEGG Atlas mapping for global analysis of metabolic pathways , 2008, Nucleic Acids Res..