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Comparative genome analysis in the integrated microbial genomes (IMG) system.
Markowitz VM, Kyrpides NC. Markowitz VM, et al. Among authors: kyrpides nc. Methods Mol Biol. 2007;395:35-56. doi: 10.1007/978-1-59745-514-5_3. Methods Mol Biol. 2007. PMID: 17993666
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction.
Overbeek R, Larsen N, Pusch GD, D'Souza M, Selkov E Jr, Kyrpides N, Fonstein M, Maltsev N, Selkov E. Overbeek R, et al. Among authors: kyrpides n. Nucleic Acids Res. 2000 Jan 1;28(1):123-5. doi: 10.1093/nar/28.1.123. Nucleic Acids Res. 2000. PMID: 10592199 Free PMC article.
The ERGO genome analysis and discovery system.
Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E Jr, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P, Kapatral V, Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N. Overbeek R, et al. Among authors: kyrpides n. Nucleic Acids Res. 2003 Jan 1;31(1):164-71. doi: 10.1093/nar/gkg148. Nucleic Acids Res. 2003. PMID: 12519973 Free PMC article.
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide.
Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC. Liolios K, et al. Among authors: kyrpides nc. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D332-4. doi: 10.1093/nar/gkj145. Nucleic Acids Res. 2006. PMID: 16381880 Free PMC article.
The integrated microbial genomes (IMG) system.
Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A, Zhao X, Dubchak I, Hugenholtz P, Anderson I, Lykidis A, Mavromatis K, Ivanova N, Kyrpides NC. Markowitz VM, et al. Among authors: kyrpides nc. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D344-8. doi: 10.1093/nar/gkj024. Nucleic Acids Res. 2006. PMID: 16381883 Free PMC article.
An experimental metagenome data management and analysis system.
Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Lykidis A, Anderson I, Mavromatis K, Kunin V, Garcia Martin H, Dubchak I, Hugenholtz P, Kyrpides NC. Markowitz VM, et al. Among authors: kyrpides nc. Bioinformatics. 2006 Jul 15;22(14):e359-67. doi: 10.1093/bioinformatics/btl217. Bioinformatics. 2006. PMID: 16873494
IMG/M: a data management and analysis system for metagenomes.
Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC. Markowitz VM, et al. Among authors: kyrpides nc. Nucleic Acids Res. 2008 Jan;36(Database issue):D534-8. doi: 10.1093/nar/gkm869. Epub 2007 Oct 11. Nucleic Acids Res. 2008. PMID: 17932063 Free PMC article.
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.
Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC. Markowitz VM, et al. Among authors: kyrpides nc. Nucleic Acids Res. 2008 Jan;36(Database issue):D528-33. doi: 10.1093/nar/gkm846. Epub 2007 Oct 12. Nucleic Acids Res. 2008. PMID: 17933782 Free PMC article.
Annotation of metagenome short reads using proxygenes.
Dalevi D, Ivanova NN, Mavromatis K, Hooper SD, Szeto E, Hugenholtz P, Kyrpides NC, Markowitz VM. Dalevi D, et al. Among authors: kyrpides nc. Bioinformatics. 2008 Aug 15;24(16):i7-13. doi: 10.1093/bioinformatics/btn276. Bioinformatics. 2008. PMID: 18689842
IMG ER: a system for microbial genome annotation expert review and curation.
Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. Markowitz VM, et al. Among authors: kyrpides nc. Bioinformatics. 2009 Sep 1;25(17):2271-8. doi: 10.1093/bioinformatics/btp393. Epub 2009 Jun 27. Bioinformatics. 2009. PMID: 19561336
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