Describing our tools

  1. RAST The RAST Server: Rapid annotations using subsystems technology. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. BMC Genomics. 2008 Feb 8;9:75. PubMedID 18261238
  2. nmpdr The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53. [Epub 2006 Dec 1] PubMedID 17145713
  3. NIAID National Institute of Allergy and Infectious Diseases bioinformatics resource centers: New assets for pathogen informatics. Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, Sobral B, Stevens R, White O, Di Francesco V. Infect Immun. 2007 Jul;75(7):3212-9. [Epub 2007 Apr 9] PubMedID 17420237
  4. CHEMREV Annotation of bacterial and archaeal genomes: Improving accuracy and consistency. Overbeek R, Bartels D, Vonstein V, Meyer F. Chem Rev. 2007 Aug;107(8):3431-47. [Epub 2007 Jul 21] PubMedID 17658903
  5. FIG The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. PubMedID 16214803

Using our tools

  1. Mutations in ampG and lytic transglycosylase genes affect the net release of peptidoglycan monomers from Vibrio fischeri. FIG Adin DM, Engle JT, Goldman WE, McFall-Ngai MJ, Stabb EV. J Bacteriol. 2009 Apr;191(7):2012-22. [Epub 2008 Dec 12] PubMedID 19074387
  2. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. RAST Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. PLoS Genet. 2009 Feb;5(2):e1000362. [Epub 2009 Feb 6] PubMedID 19197347
    • The RAST server was used as one tool to develop a comprehensive annotation of the features in this genome.
  3. Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis. nmpdr FIG Sorci L, Martynowski D, Rodionov DA, Eyobo Y, Zogaj X, Klose KE, Nikolaev EV, Magni G, Zhang H, Osterman AL. Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3083-8. [Epub 2009 Feb 9] PubMedID 19204287
    • Analysis of the NAD and NADP cofactor biosynthesis global subsystem predicted a route of NAD synthesis in Francisella tularensis in which the amidation of NaMN to nicotinamide mononucleotide (NMN) is catalyzed by NMN synthetase, followed by adenylylation performed by an NMN adenylyltransferase of the NadM family. This alternative route is in reverse order and does not employ NaMN adenylyltransferase (nadD), which is indispensable and conserved in nearly all bacterial pathogens except F. tularensis .
  4. Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. FIG Pinchuk GE, Rodionov DA, Yang C, Li X, Osterman AL, Dervyn E, Geydebrekht OV, Reed SB, Romine MF, Collart FR, Scott JH, Fredrickson JK, Beliaev AS. Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2874-9. [Epub 2009 Feb 5] PubMedID 19196979
    • Metabolic reconstruction and comparative genomic analyses were combined with genetic and biochemical techniques for the detailed analysis of the Lactate Utilization subsystem. This subsystem enabled the discovery of a gene cluster encoding novel enzymes required for oxidation of d- and l-lactate to pyruvate in a large number of diverse bacteria, which were experimentally verified.
  5. Biogenesis and Homeostasis of Nicotinamide Adenine Dinucleotide Cofactor. FIG Osterman A. "Module" Posted February 13, 2009 in A. Böck, R. Curtiss III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, T. Nyström, J. M. Slauch, and C. L. Squires, and D. Ussery (ed.), EcoSal— Escherichia coli and Salmonella: Cellular and molecular biology. ASM Press, Washington, DC.
  6. NAD biosynthesis evolution in bacteria: Lateral gene transfer of kynurenine pathway in Xanthomonadales and Flavobacteriales. FIG Lima WC, Varani AM, Menck CF. Mol Biol Evol. 2009 Feb;26(2):399-406. [Epub 2008 Nov 12] PubMedID 19005186
  7. Characterization of the LacI-type transcriptional repressor RbsR controlling ribose transport in Corynebacterium glutamicum ATCC 13032. FIG Nentwich SS, Brinkrolf K, Gaigalat L, Hüser AT, Rey DA, Mohrbach T, Marin K, Pühler A, Tauch A, Kalinowski J. Microbiology. 2009 Jan;155(1):150-64. PubMedID 19118356
  8. Gene order phylogeny of the genus Prochlorococcus. FIG Luo H, Shi J, Arndt W, Tang J, Friedman R. PLoS ONE. 2008;3(12):e3837. [Epub 2008 Dec 3] PubMedID 19050756
  9. A novel class of modular transporters for vitamins in prokaryotes. FIG Rodionov DA, Hebbeln P, Eudes A, ter Beek J, Rodionova IA, Erkens GB, Slotboom DJ, Gelfand MS, Osterman AL, Hanson AD, Eitinger T. J Bacteriol. 2009 Jan;191(1):42-51. [Epub 2008 Oct 17] PubMedID 18931129
  10. Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: A new role for GTP cyclohydrolase I. FIG Phillips G, El Yacoubi B, Lyons B, Alvarez S, Iwata-Reuyl D, de Crécy-Lagard V. J Bacteriol. 2008 Dec;190(24):7876-84. [Epub 2008 Oct 17] PubMedID 18931107
  11. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. FIG Kazakov AE, Rodionov DA, Alm E, Arkin AP, Dubchak I, Gelfand MS. J Bacteriol. J Bacteriol. 2009 Jan;191(1):52-64. [Epub 2008 Sep 26] PubMedID 18820024
  12. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. FIG Ivars-Martinez E, Martin-Cuadrado AB, D'Auria G, Mira A, Ferriera S, Johnson J, Friedman R, Rodriguez-Valera F. ISME J. 2008 Dec;2(12):1194-212. [ Epub 2008 Jul 31] PubMedID 18670397
  13. Identification of genes encoding the folate- and thiamine-binding membrane proteins in firmicutes. FIG Eudes A, Erkens GB, Slotboom DJ, Rodionov DA, Naponelli V, Hanson AD. J Bacteriol. 2008 Nov;190(22):7591-4. [Epub 2008 Sep 5] PubMedID 18776013
  14. The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon in response to the availability of sulphide acceptor molecules. FIG Rückert C, Milse J, Albersmeier A, Koch DJ, Pühler A, Kalinowski J. BMC Genomics. 2008 Oct 14;9:483. PubMedID 18854009
    • Despite a lack of functional clustering, Cg0156 was shown to activate transcription of the genes in the pathway for assimilatory reduction of sulphate, fpr2 cysIXHDNYZ, in the Cysteine Biosynthesis subsystem.
  15. RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes. nmpdr FIG Grosjean H, Marck C, Gaspin C, Decatur WA, de Crecy-Lagard V. BMC Genomics. 2008 Oct 9;9(1):470. PubMedID 18844986
  16. Identification and characterization of genes underlying chitinolysis in Collimonas fungivorans Ter331. FIG Fritsche K, de Boer W, Gerards S, van den Berg M, van Veen JA, Leveau JH. FEMS Microbiol Ecol. 2008 Oct;66(1):123-35. [Epub 2008 Jul 30] PubMedID 18671744
  17. Rise and persistence of global M1T1 clone of Streptococcus pyogenes. FIG Aziz RK, Kotb M. Emerg Infect Dis. 2008 Oct;14(10):1511-7. PubMedID 18826812
  18. Vibrio cholerae VciB promotes iron uptake via ferrous iron transporters. nmpdr Mey AR, Wyckoff EE, Hoover LA, Fisher CR, Payne SM. J Bacteriol. 2008 Sep;190(17):5953-62. [Epub 2008 Jun 27] PubMedID 18586940
  19. Genome sequence of a Lancefield group C Streptococcus zooepidemicus strain causing epidemic nephritis: New information about an old disease. FIG Beres SB, Sesso R, Pinto SW, Hoe NP, Porcella SF, Deleo FR, Musser JM. PLoS ONE. 2008 Aug 21;3(8):e3026. PubMedID 18716664
    • The RAST server was used as one tool to develop a comprehensive annotation of the features in this genome.
  20. The type III pantothenate kinase encoded by coaX is essential for growth of Bacillus anthracis. FIG Paige C, Reid SD, Hanna PC, Claiborne A. J Bacteriol. 2008 Sep;190(18):6271-5. [Epub 2008 Jul 18] PubMedID 18641144
  21. Towards environmental systems biology of Shewanella. FIG Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM. Nat Rev Microbiol. 2008 Aug;6(8):592-603. [Epub 2008 Jul 7] PubMedID 18604222
  22. Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions FIG Martin-Cuadrado AB, Rodriguez-Valera F, Moreira D, Alba JC, Ivars-Martínez E, Henn MR, Talla E, López-García P. ISME J. 2008 Aug;2(8):865-86. [Epub 2008 May 8] PubMedID 18463691
  23. Streptococcus iniae M-Like protein contributes to virulence in fish and is a target for live attenuated vaccine development. nmpdr FIG Locke JB, Aziz RK, Vicknair MR, Nizet V, Buchanan JT. PLoS ONE. 2008 3(7): e2824. doi:10.1371/journal.pone.0002824. PubMedID 18665241
  24. Identification of a cellobiose utilization gene cluster with cryptic beta-galactosidase activity in Vibrio fischeri. FIG Adin DM, Visick KL, Stabb EV. Appl Environ Microbiol. 2008 Jul;74(13):4059-69. [Epub 2008 May 16] PubMedID 18487409
  25. Large-scale transposon mutagenesis of Mycoplasma pulmonis. nmpdr French CT, Lao P, Loraine AE, Matthews BT, Yu H, Dybvig K. Mol Microbiol. 2008 Jul;69(1):67-76. [Epub 2008 Apr 28] PubMedID 18452587
  26. Biochemical and phylogenetic characterization of a novel diaminopimelate biosynthesis pathway in prokaryotes identifies a diverged form of LL-diaminopimelate aminotransferase. FIG Hudson AO, Gilvarg C, Leustek T. J Bacteriol. 2008 May;190(9):3256-63. [Epub 2008 Feb 29] PubMedID 18310350
  27. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. FIG Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ. Appl Environ Microbiol. 2008 Apr;74(8):2461-70. [Epub 2008 Feb 22] PubMedID 18296538
    • A phylogenetically representative set of full-length bacterial SSU rRNA sequences was extracted from The SEED.
  28. Phylogenomic and functional analysis of pterin-4a-carbinolamine dehydratase family (COG2154) proteins in plants and microorganisms. FIG Naponelli V, Noiriel A, Ziemak MJ, Beverley SM, Lye LF, Plume AM, Botella JR, Loizeau K, Ravanel S, Rébeillé F, de Crécy-Lagard V, Hanson AD. Plant Physiol. 2008 Apr;146(4):1515-27. [Epub 2008 Feb 1] PubMedID 18245455
    • The COG2154 family of proteins was discovered to have members in genomes with or without aromatic amino acid hydroxylases (AAHs), which generate oxidized pterin cofactors recycled by Pterin-4a-carbinolamine dehydratases (PCDs). Partnerless PCDs are hypothesized to support the function of presently unrecognized pterin-dependent enzymes. A signature motif for PCD activity, which may be used as a query term in protSCAN (available from our Sequence Search page), was discovered to be: any(EDKH) 3...3 H any(HN) any(PCS) 5...6 any(YWF) 9...9 any(HW) 8...15 D
  29. Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators. FIG Rodionov DA, De Ingeniis J, Mancini C, Cimadamore F, Zhang H, Osterman AL, Raffaelli N. Nucleic Acids Res. 2008 Apr;36(6):2047-59. [Epub 2008 Feb 14] PubMedID 18276643
  30. Transcriptional regulation of NAD metabolism in bacteria: Genomic reconstruction of NiaR (YrxA) regulon. FIG Rodionov DA, Li X, Rodionova IA, Yang C, Sorci L, Dervyn E, Martynowski D, Zhang H, Gelfand MS, Osterman AL. Nucleic Acids Res. 2008 Apr;36(6):2032-46. [Epub 2008 Feb 14] PubMedID 18276644
  31. Cohesion Group Approach for Evolutionary Analysis of TyrA, a Protein Family with Wide-Ranging Substrate Specificities. FIG Bonner CA, Disz T, Hwang K, Song J, Vonstein V, Overbeek R, Jensen RA. Microbiol Mol Biol Rev. 2008 Mar;72(1):13-53. PubMedID 18322033
    • The TyrA dehydrogenases are used as a prototype example of how a credible picture of evolutionary events can be deduced within the vertical trace of inheritance in combination with intervening events of lateral gene transfer (LGT). Figures and tables supplemental to the paper are found on the TyrA page.
  32. ComPath: Comparative enzyme analysis and annotation in pathway/subsystem contexts. FIG Choi K, Kim S. BMC Bioinformatics. 2008 Mar 6;9:145. PubMedID 18325116
    • ComPath provides a total of 327 model pathways combining 205 pathways from KEGG database and 122 subsystems from The SEED and NMPDR.
  33. Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways. FIG Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. J Bacteriol. 2008 Mar;190(5):1773-82. [Epub 2007 Dec 21] PubMedID 18156253
  34. Sialic acid mutarotation is catalyzed by the Escherichia coli beta-propeller protein YjhT. FIG Severi E, Müller A, Potts JR, Leech A, Williamson D, Wilson KS, Thomas GH. J Biol Chem. 2008 Feb 22;283(8):4841-9. [Epub 2007 Dec 5] PubMedID 18063573
    • A previously uncharacterized protein present in many sialic acid-utilizing pathogens, YjhT, was proven to accelerate the equilibration of the alpha- and beta-anomers of N-acetylneuraminic acid, thus describing a novel sialic acid mutarotase activity. The conservation of its genomic position near sialometabolic and sialic acid-inducible genes was explored using Compare Regions.
  35. Structural basis for substrate binding and the catalytic mechanism of type III pantothenate kinase. FIG Yang K, Strauss E, Huerta C, Zhang H. Biochemistry. 2008 Feb 5;47(5):1369-80. [Epub 2008 Jan 11] PubMedID 18186650
    • A comprehensive analysis of the PanK-encoding genes in the Coenzyme A Biosynthesis subsystem revealed that PanK-III enzymes have a much wider phylogenetic distribution than the better known PanK-I, being present in 12 of the 13 major bacterial groups, and in many pathogens.
  36. Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: Structure and function in bacterial NAD metabolism. FIG Huang N, Sorci L, Zhang X, Brautigam CA, Li X, Raffaelli N, Magni G, Grishin NV, Osterman AL, Zhang H. Structure. 2008 Feb;16(2):196-209. PubMedID 18275811
  37. An in vivo expression technology screen for Vibrio cholerae genes expressed in human volunteers. nmpdr Lombardo MJ, Michalski J, Martinez-Wilson H, Morin C, Hilton T, Osorio CG, Nataro JP, Tacket CO, Camilli A, Kaper JB. Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):18229-34. [Epub 2007 Nov 6] PubMedID 17986616
  38. Comparative RNomics and modomics in Mollicutes: Prediction of gene function and evolutionary implications. nmpdr FIG de Crécy-Lagard V, Marck C, Brochier-Armanet C, Grosjean H. IUBMB Life. 2007 Oct;59(10):634-58. PubMedID 17852564
  39. The biological role of death and lysis in biofilm development. Bayles KW. Nat Rev Microbiol. 2007 Sep;5(9):721-6. PubMedID 17694072
    • The functional roles, phylogenetic distribution, and biological importance of the Murein Hydrolase Regulation and Cell Death subsystem, which was developed in conjunction with an NMPDR curator, are described.
  40. Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation. FIG Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Genome Res. 2007 Sep;17(9):1362-77. [Epub 2007 Aug 9] PubMedID 17690205
    • Subsystems were used to identify and categorize the functions of expressed proteins detected in the proteome of Shewanella oneidensis MR-1.
  41. Identification of genes encoding tRNA modification enzymes by comparative genomics. nmpdr FIG de Crécy-Lagard V. Methods Enzymol. 2007;425:153-83. PubMedID 17673083
  42. Comparative genomics of bacterial and plant folate synthesis and salvage: Predictions and validations. FIG de Crécy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. BMC Genomics. 2007 Jul 23;8:245. PubMedID 17645794
    • Subsystem construction tools in the SEED and the Signature Genes Tool at NMPDR were used to predict the pathways and to identify cases of missing genes for almost every step of the Folate Biosynthesis subsystem. Candidates for such missing genes in bacteria and plants were then predicted using our compare regions view, and representative candidates were verified experimentally.
  43. Free methionine-(R)-sulfoxide reductase from Escherichia coli reveals a new GAF domain function. FIG Lin Z, Johnson LC, Weissbach H, Brot N, Lively MO, Lowther WT. Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9597-602. [Epub 2007 May 29]
    • The yebR gene of E.coli was proven to function as a free methionine-(R)-sulfoxide reductase, and the conservation of its genomic position adjacent to ProQ was explored using Compare Regions
  44. Characterization of a TIR-like protein from Paracoccus denitrificans. nmpdr Low LY, Mukasa T, Reed JC, Pascual J. Biochem Biophys Res Commun. 2007 May 4;356(2):481-6. [Epub 2007 Mar 7] PubMedID 17362878
  45. Toward the automated generation of genome-scale metabolic networks in the SEED. FIG DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A.BMC Bioinformatics. 2007 Apr 26;8:139. PubMedID 17462086
    • Subsystems were used to guide the automated generation of substantially complete metabolic networks from a collection of modular components called "scenarios."
  46. The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum. FIG Brune I, Jochmann N, Brinkrolf K, Huser AT, Gerstmeir R, Eikmanns BJ, Kalinowski J, Puhler A, Tauch A. J Bacteriol. 2007 Apr;189(7):2720-33. [Epub 2007 Jan 26] PubMedID 17259312
    • The Cg1486 gene was proven to function as a repressor of genes in the leucine and tryptophan biosynthetic pathways, and the conservation of its genomic position upstream of leuCD was explored using Compare Regions.
  47. Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. FIG Rodionov DA, Kurnasov OV, Stec B, Wang Y, Roberts MF, Osterman AL. Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4279-84. [Epub 2007 Mar 2] PubMedID 17360515
    • Comparative genomic analyses predicted two genes that were previously missing, which were included in a new subsystem that accurately describes the Di-Inositol-Phosphate biosynthesis pathway.
  48. Structure of the type III pantothenate kinase from Bacillus anthracis at 2.0 A resolution: Implications for coenzyme A-dependent redox biology. FIG Nicely NI, Parsonage D, Paige C, Newton GL, Fahey RC, Leonardi R, Jackowski S, Mallett TC, Claiborne A. Biochemistry. 2007 Mar 20;46(11):3234-45.[ Epub 2007 Feb 27] PubMedID 17323930
  49. Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module. FIG Hebbeln P, Rodionov DA, Alfandega A, Eitinger T. Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2909-14. [Epub 2007 Feb 14] PubMedID 17301237
    • The ECF class transporters subsystem describes a group of bacterial and archaeal transporters containing typical ABC proteins that seem to be independent of solute-binding proteins.
  50. GISMO--gene identification using a support vector machine for ORF classification. FIG Krause L, McHardy AC, Nattkemper TW, Pühler A, Stoye J, Meyer F. Nucleic Acids Res. 2007 January; 35(2): 540–549. [Epub 2006 Dec 14] PubMedID 17175534
    • ThiS in the Thiamin Biosynthesis subsystem was given as one example of how our subsystems were used to validate the automatic identification of very small genes.
  51. Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria. FIG Rodionov DA, Gelfand MS, Todd JD, Curson AR, Johnston AW. PLoS Comput Biol. 2006 Dec 15;2(12):e163. [Epub 2006 Oct 18] PubMedID 17173478
  52. Discovery of a new prokaryotic type I GTP cyclohydrolase family. FIG El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crecy-Lagard V. J Biol Chem. 2006 Dec 8;281(49):37586-93. [Epub 2006 Oct 10] PubMedID 17032654
  53. Experimental and computational assessment of conditionally essential genes in Escherichia coli. FIG Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S. J Bacteriol. 2006 Dec;188(23):8259-71. [Epub 2006 Sep 29] PubMedID 17012394
    • Essential Genes of E. coli were analyzed in terms of metabolic subsystems across multiple genomes.
  54. The thioredoxin domain of Neisseria gonorrhoeae PilB can use electrons from DsbD to reduce downstream methionine sulfoxide reductases. FIG Brot N, Collet JF, Johnson LC, Jonsson TJ, Weissbach H, Lowther WT. J Biol Chem. 2006 Oct 27;281(43):32668-75. [Epub 2006 Aug 22] PubMedID 16926157
    • The domains that are fused in this Neisseria protein were identified as separate but clustered peptides using the Find Clusters function.
  55. Essential genes on metabolic maps. FIG Gerdes S, Edwards R, Kubal M, Fonstein M, Stevens R, Osterman A. Curr Opin Biotechnol. 2006 Oct;17(5):448-56. [Epub 2006 Sep 15] PubMedID 16978855
    • The genomic scale screens for essential genes that are displayed on the Essential Genes page are reviewed and discussed in the context of comparative analysis of subsystems. icon Supplemental data tables
  56. Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. FIG Yang C, Rodionov DA, Li X, Laikova ON, Gelfand MS, Zagnitko OP, Romine MF, Obraztsova AY, Nealson KH, Osterman AL. J Biol Chem. 2006 Oct 6;281(40):29872-85. [Epub 2006 Jul 20] PubMedID 16857666
    • A novel variant of the classical three-step biochemical conversion of GlcNAc to fructose 6-phosphate was described in the Chitin and N-acetylglucosamine Utilization subsystem. The functional roles GlcN-6-P deaminase and GlcNAc kinase were assigned to two genes of previously unknown function based on Compare Regions and experimental verification.
  57. Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover. Anderson KL, Roberts C, Disz T, Vonstein V, Hwang K, Overbeek R, Olson PD, Projan SJ, Dunman PM. J Bacteriol. 2006 Oct;188(19):6739-56 PubMedID 16980476
    • NMPDR team members used bioinformatics to produce supplemental file 1, "Table S8, Characterization of small stable RNA molecules identified in this study."
  58. Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16. FIG Pohlmann A, Fricke WF, Reinecke F, Kusian B, Liesegang H, Cramm R, Eitinger T, Ewering C, Pötter M, Schwartz E, Strittmatter A, Voss I, Gottschalk G, Steinbüchel A, Friedrich B, Bowien B. Nat Biotechnol. 2006 Oct;24(10):1257-62. [Epub 2006 Sep 10] PubMedID 16964242
  59. Crystal structure of a type III pantothenate kinase: insight into the mechanism of an essential coenzyme A biosynthetic enzyme universally distributed in bacteria. FIG Yang K, Eyobo Y, Brand LA, Martynowski D, Tomchick D, Strauss E, Zhang H. J Bacteriol. 2006 Aug;188(15):5532-40. PubMedID 16855243
    • A comprehensive survey of the phylogenetic distribution of type I, II and III PanKs in more than 300 complete or nearly complete genomes from the Archaea, Eukarya, and 13 major groups of Bacteria was performed.
  60. Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway. FIG Mormann S, Lömker A, Rückert C, Gaigalat L, Tauch A, Pühler A, Kalinowski J. BMC Genomics. 2006 Aug 10;7:205. PubMedID 16901339
  61. Study of an alternate glyoxylate cycle for acetate assimilation by Rhodobacter sphaeroides. FIG Alber BE, Spanheimer R, Ebenau-Jehle C, Fuchs G. Mol Microbiol. 2006 Jul;61(2):297-309. PubMedID 16856937
  62. Comparative genomics of NAD biosynthesis in cyanobacteria. FIG Gerdes SY, Kurnasov OV, Shatalin K, Polanuyer B, Sloutsky R, Vonstein V, Overbeek R, Osterman AL. J Bacteriol. 2006 Apr;188(8):3012-23. PubMedID 16585762
  63. A hidden metabolic pathway exposed. FIG Osterman A. Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5637-8. [Epub 2006 Apr 4] PubMedID 16595627
  64. Community genomics among stratified microbial assemblages in the ocean's interior. FIG DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM. Science. 2006 Jan 27;311(5760):496-503. PubMedID 16439655
  65. Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: Evidence for a novel group of ATP-binding cassette transporters. FIG Rodionov DA, Hebbeln P, Gelfand MS, Eitinger T. J Bacteriol. 2006 Jan;188(1):317-27. PubMedID 16352848
    • Positional gene clustering of identified candidate nickel/cobalt transporters with known Ni- and Co-containing enzymes was analyzed with Compare Regions and captured in the Transport of Nickel and Cobalt subsystem.
  66. Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cysIXHDNYZ gene cluster involved in assimilatory sulphate reduction. Ruckert C, Koch DJ, Rey DA, Albersmeier A, Mormann S, Puhler A, Kalinowski J. BMC Genomics. 2005 Sep 13;6:121. PubMedID 16159395
    • The conservation of this cluster among the Actinomycetales was explored using Compare Regions.
  67. Low-molecular-weight protein tyrosine phosphatases of Bacillus subtilis. Musumeci L, Bongiorni C, Tautz L, Edwards RA, Osterman A, Perego M, Mustelin T, Bottini N. J Bacteriol. 2005 Jul;187(14):4945-56. PubMedID 15995210


Citing our work

  1. SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes. FIG Lemoine F, Labedan B, Lespinet O. BMC Bioinformatics. 2008 Dec 16;9:536. PubMedID 19087285
  2. Harnessing genomics for evolutionary insights. RAST Rokas A, Abbot P. Trends Ecol Evol. 2009 Apr;24(4):192-200. [Epub 2009 Feb 7] PubMedID 19201503
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metagenomics related papers and citations

  1. icon The smallest cells pose the biggest problems: High-performance computing and the analysis of metagenome sequence data. Edwards RA. J. Phys. Conf. Ser. 2008 125:012050 DOI:10.1088/1742-6596/125/1/012050
  2. MG-RAST The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA. BMC Bioinformatics. 2008 Sep 19;9:386. PubMedID 18803844

  1. Molecular Diversity of a North Carolina Wastewater Treatment Plant As Revealed by Pyrosequencing. FIG RAST Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM. Environ Microbiol. Appl Environ Microbiol. 2009 March; 75(6):1688-1696. [Epub 2008 Dec 29] PubMedID 19114525
    • MG-RAST and our subsystems were used to characterize the functional gene content of microbial communities from activated sludge.
  2. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. FIG Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA. Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1948-53. [Epub 2009 Jan 30] PubMedID 19181843
    • MG-RAST and our subsystems were used to characterize and compare three fiber-adherent microbiomes and one liquid sample pooled from bovine rumens.
  3. Evaluation of functional gene enrichment in a soil metagenomic clone library. FIG Demanèche S, David MM, Navarro E, Simonet P, Vogel TM. J Microbiol Methods. 2009 Jan;76(1):105-7. [Epub 2008 Sep 17] PubMedID 18922230
    • MG-RAST and our subsystems were used to characterize sequence reads from selected clones and total bacterial DNA.
  4. Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico. FIG Breitbart M, Hoare A, Nitti A, Siefert J, Haynes M, Dinsdale E, Edwards R, Souza V, Rohwer F, Hollander D. Environ Microbiol. 2009 Jan;11(1):16-34. [ Epub 2008 Sep 1] PubMedID 18764874
    • MG-RAST and our subsystems were used to characterize the functional gene content of microbial communities from living microbialites.
  5. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. FIG Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. PLoS ONE. 2008 Aug 22;3(8):e3042. PubMedID 18725995
    • MG-RAST and our subsystems were used to reconstruct and compare the taxonomy and metabolism of metagenomic and metatranscriptomic data sets collected in replicate from two communities at two time points.
  6. Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. FIG Qu A, Brulc JM, Wilson MK, Law BF, Theoret JR, Joens LA, Konkel ME, Angly F, Dinsdale EA, Edwards RA, Nelson KE, White BA. PLoS ONE. 2008 Aug 13;3(8):e2945. PubMedID 18698407
    • MG-RAST and our subsystems were used to characterize the microbial community structure and functional gene content of the chicken cecal microbiome from a pathogen-free chicken and one that had been challenged with Campylobacter jejuni.
  7. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC. PLoS ONE. 2008 Jun 25;3(6):e2527. PubMedID 18575584
    • MG-RAST and our subsystems were used to reconstruct and compare the taxonomy and metabolism of a soil community from metatranscriptomic data.
  8. Functional metagenomic profiling of nine biomes. FIG Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, Mc Daniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F. Nature 2008 Mar 12. PubMedID 18337718
    • MG-RAST and our subsystems were used to reconstruct and compare the metabolism of different microbial environments.
  9. Microbial ecology of four coral atolls in the Northern Line Islands. Dinsdale EA, Pantos O, Smriga S, Edwards RA, Angly F, Wegley L, Hatay M, Hall D, Brown E, Haynes M, Krause L, Sala E, Sandin SA, Thurber RV, Willis BL, Azam F, Knowlton N, Rohwer F. PLoS ONE. 2008 Feb 27;3(2):e1584. PubMedID 18301735
    • MG-RAST and our subsystems were used to characterize differences in microbial communities across atolls that could reflect natural environmental variation or human impacts.
  10. Bacterial carbon processing by generalist species in the coastal ocean. FIG Mou X, Sun S, Edwards RA, Hodson RE, Moran MA. Nature. 2008 Feb 7;451(7179):708-11.[ Epub 2008 Jan 27] PubMedID 18223640
    • MG-RAST and our subsystems were used to directly measure niche breadth for bacterial functional assemblages.
  11. Using pyrosequencing to shed light on deep mine microbial ecology. Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC Jr, Rohwer F. BMC Genomics. 2006 Mar 20;7:57. PubMedID 16549033
    • Subsystems were used to characterize two distinctly different microbial communities from short pyrosequence reads during the development of the MG-RAST server.
  12. An application of statistics to comparative metagenomics. Rodriguez-Brito B, Rohwer F, Edwards RA. BMC Bioinformatics. 2006 Mar 20;7:162. PubMedID 16549025
    • Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenomes when compared to non-redundant databases were identified using statistical methods later incorporated into the MG-RAST server.
Topic revision: r58 - 29 Jun 2009 - 20:29:32 - TWiki Guest
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (, a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.