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Publications

Describing our tools

1. 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. 18261238
2. 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] 17145713
3. 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] 17420237
4. 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] 17658903
5. 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. 16214803

Using our tools

1. Mutations in ampG and lytic transglycosylase genes affect the net release of peptidoglycan monomers from Vibrio fischeri. Adin DM, Engle JT, Goldman WE, McFall-Ngai MJ, Stabb EV. J Bacteriol. 2009 Apr;191(7):2012-22. [Epub 2008 Dec 12] 19074387
2. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. 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] 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. 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] 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. 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] 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. Osterman A. "Module 3.6.3.10" 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. http://www.ecosal.org. ASM Press, Washington, DC.
6. NAD biosynthesis evolution in bacteria: Lateral gene transfer of kynurenine pathway in Xanthomonadales and Flavobacteriales. Lima WC, Varani AM, Menck CF. Mol Biol Evol. 2009 Feb;26(2):399-406. [Epub 2008 Nov 12] 19005186
7. Characterization of the LacI-type transcriptional repressor RbsR controlling ribose transport in Corynebacterium glutamicum ATCC 13032. 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. 19118356
8. Gene order phylogeny of the genus Prochlorococcus. Luo H, Shi J, Arndt W, Tang J, Friedman R. PLoS ONE. 2008;3(12):e3837. [Epub 2008 Dec 3] 19050756
9. A novel class of modular transporters for vitamins in prokaryotes. 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] 18931129
10. Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: A new role for GTP cyclohydrolase I. 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] 18931107
11. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. 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] 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. 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] 18670397
13. Identification of genes encoding the folate- and thiamine-binding membrane proteins in firmicutes. Eudes A, Erkens GB, Slotboom DJ, Rodionov DA, Naponelli V, Hanson AD. J Bacteriol. 2008 Nov;190(22):7591-4. [Epub 2008 Sep 5] 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. Rückert C, Milse J, Albersmeier A, Koch DJ, Pühler A, Kalinowski J. BMC Genomics. 2008 Oct 14;9:483. 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. Grosjean H, Marck C, Gaspin C, Decatur WA, de Crecy-Lagard V. BMC Genomics. 2008 Oct 9;9(1):470. 18844986
16. Identification and characterization of genes underlying chitinolysis in Collimonas fungivorans Ter331. 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] 18671744
17. Rise and persistence of global M1T1 clone of Streptococcus pyogenes. Aziz RK, Kotb M. Emerg Infect Dis. 2008 Oct;14(10):1511-7. 18826812
18. Vibrio cholerae VciB promotes iron uptake via ferrous iron transporters. Mey AR, Wyckoff EE, Hoover LA, Fisher CR, Payne SM. J Bacteriol. 2008 Sep;190(17):5953-62. [Epub 2008 Jun 27] 18586940
19. Genome sequence of a Lancefield group C Streptococcus zooepidemicus strain causing epidemic nephritis: New information about an old disease. Beres SB, Sesso R, Pinto SW, Hoe NP, Porcella SF, Deleo FR, Musser JM. PLoS ONE. 2008 Aug 21;3(8):e3026. 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. Paige C, Reid SD, Hanna PC, Claiborne A. J Bacteriol. 2008 Sep;190(18):6271-5. [Epub 2008 Jul 18] 18641144
21. Towards environmental systems biology of Shewanella. 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] 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 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] 18463691
23. Streptococcus iniae M-Like protein contributes to virulence in fish and is a target for live attenuated vaccine development. Locke JB, Aziz RK, Vicknair MR, Nizet V, Buchanan JT. PLoS ONE. 2008 3(7): e2824. doi:10.1371/journal.pone.0002824. 18665241
24. Identification of a cellobiose utilization gene cluster with cryptic beta-galactosidase activity in Vibrio fischeri. Adin DM, Visick KL, Stabb EV. Appl Environ Microbiol. 2008 Jul;74(13):4059-69. [Epub 2008 May 16] 18487409
25. Large-scale transposon mutagenesis of Mycoplasma pulmonis. French CT, Lao P, Loraine AE, Matthews BT, Yu H, Dybvig K. Mol Microbiol. 2008 Jul;69(1):67-76. [Epub 2008 Apr 28] 18452587
26. Biochemical and phylogenetic characterization of a novel diaminopimelate biosynthesis pathway in prokaryotes identifies a diverged form of LL-diaminopimelate aminotransferase. Hudson AO, Gilvarg C, Leustek T. J Bacteriol. 2008 May;190(9):3256-63. [Epub 2008 Feb 29] 18310350
27. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. 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] 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. 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] 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. 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] 18276643
30. Transcriptional regulation of NAD metabolism in bacteria: Genomic reconstruction of NiaR (YrxA) regulon. 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] 18276644
31. Cohesion Group Approach for Evolutionary Analysis of TyrA, a Protein Family with Wide-Ranging Substrate Specificities. Bonner CA, Disz T, Hwang K, Song J, Vonstein V, Overbeek R, Jensen RA. Microbiol Mol Biol Rev. 2008 Mar;72(1):13-53. 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. Choi K, Kim S. BMC Bioinformatics. 2008 Mar 6;9:145. 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. Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. J Bacteriol. 2008 Mar;190(5):1773-82. [Epub 2007 Dec 21] 18156253
34. Sialic acid mutarotation is catalyzed by the Escherichia coli beta-propeller protein YjhT. 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] 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. Yang K, Strauss E, Huerta C, Zhang H. Biochemistry. 2008 Feb 5;47(5):1369-80. [Epub 2008 Jan 11] 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. 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. 18275811
37. An in vivo expression technology screen for Vibrio cholerae genes expressed in human volunteers. 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] 17986616
38. Comparative RNomics and modomics in Mollicutes: Prediction of gene function and evolutionary implications. de Crécy-Lagard V, Marck C, Brochier-Armanet C, Grosjean H. IUBMB Life. 2007 Oct;59(10):634-58. 17852564
39. The biological role of death and lysis in biofilm development. Bayles KW. Nat Rev Microbiol. 2007 Sep;5(9):721-6. 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. 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] 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. de Crécy-Lagard V. Methods Enzymol. 2007;425:153-83. 17673083
42. Comparative genomics of bacterial and plant folate synthesis and salvage: Predictions and validations. de Crécy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. BMC Genomics. 2007 Jul 23;8:245. 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. 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. Low LY, Mukasa T, Reed JC, Pascual J. Biochem Biophys Res Commun. 2007 May 4;356(2):481-6. [Epub 2007 Mar 7] 17362878
45. Toward the automated generation of genome-scale metabolic networks in the SEED. DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A.BMC Bioinformatics. 2007 Apr 26;8:139. 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. 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] 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. 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] 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. 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] 17323930
49. Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module. 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] 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. 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] 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. Rodionov DA, Gelfand MS, Todd JD, Curson AR, Johnston AW. PLoS Comput Biol. 2006 Dec 15;2(12):e163. [Epub 2006 Oct 18] 17173478
52. Discovery of a new prokaryotic type I GTP cyclohydrolase family. 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] 17032654
    • The Signature Genes Tool was used in conjunction with Compare Regions and the Folate Biosynthesis subsystem to discover the function of COG1469 family proteins.
53. Experimental and computational assessment of conditionally essential genes in Escherichia coli. 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] 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. 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] 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. 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] 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. Supplemental data tables
56. Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. 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] 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 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. 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] 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. Yang K, Eyobo Y, Brand LA, Martynowski D, Tomchick D, Strauss E, Zhang H. J Bacteriol. 2006 Aug;188(15):5532-40. 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. Mormann S, Lömker A, Rückert C, Gaigalat L, Tauch A, Pühler A, Kalinowski J. BMC Genomics. 2006 Aug 10;7:205. 16901339
61. Study of an alternate glyoxylate cycle for acetate assimilation by Rhodobacter sphaeroides. Alber BE, Spanheimer R, Ebenau-Jehle C, Fuchs G. Mol Microbiol. 2006 Jul;61(2):297-309. 16856937
62. Comparative genomics of NAD biosynthesis in cyanobacteria. Gerdes SY, Kurnasov OV, Shatalin K, Polanuyer B, Sloutsky R, Vonstein V, Overbeek R, Osterman AL. J Bacteriol. 2006 Apr;188(8):3012-23. 16585762
63. A hidden metabolic pathway exposed. Osterman A. Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5637-8. [Epub 2006 Apr 4] 16595627
64. Community genomics among stratified microbial assemblages in the ocean's interior. 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. 16439655
65. Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: Evidence for a novel group of ATP-binding cassette transporters. Rodionov DA, Hebbeln P, Gelfand MS, Eitinger T. J Bacteriol. 2006 Jan;188(1):317-27. 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. 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. 15995210

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Citing our work

1. SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes. Lemoine F, Labedan B, Lespinet O. BMC Bioinformatics. 2008 Dec 16;9:536. 19087285
2. Harnessing genomics for evolutionary insights. Rokas A, Abbot P. Trends Ecol Evol. 2009 Apr;24(4):192-200. [Epub 2009 Feb 7] 19201503
3. DIYA: A bacterial annotation pipeline for any genomics lab. Stewart AC, Osborne B, Read TD. Bioinformatics. 2009 Apr 1;25(7):962-3. [Epub 2009 Mar 2] 19254921
4. Role and regulation of fatty acid biosynthesis in the response of Shewanella piezotolerans WP3 to different temperatures and pressures. Wang F, Xiao X, Ou HY, Gai Y, Wang F. J Bacteriol. 2009 Apr;191(8):2574-84. [Epub 2009 Feb 6] 19201790
5. TACOA: Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. Diaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW. BMC Bioinformatics. 2009 Feb 11;10:56. 19210774
6. The Genome Reverse Compiler: An explorative annotation tool. Warren AS, Setubal JC. BMC Bioinformatics. 2009 Jan 27;10:35. 19173744
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18. Annotation of metagenome short reads using proxygenes. Dalevi D, Ivanova NN, Mavromatis K, Hooper SD, Szeto E, Hugenholtz P, Kyrpides NC, Markowitz VM. Bioinformatics. 2008 Aug 15;24(16):i7-i13. 18689842
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22. Laying the foundation for a Genomic Rosetta Stone: Creating information hubs through the use of consensus identifiers. Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glöckner FO, Cole J, Farris R, Schriml LM, De Vos P, De Baets B, Field D, Dawyndt P; Genomic Standards Consortium. OMICS. 2008 Jun;12(2):123-7. 18479205
23. An instant cell recognition system using a microfabricated coordinate standard chip useful for combinable cell observation with multiple microscopic apparatuses. Yamada Y, Yamaguchi N, Ozaki M, Shinozaki Y, Saito M, Matsuoka H. Microsc Microanal. 2008 Jun;14(3):236-42. [Epub 2008 Mar 3] 18312725
24. The minimum information about a genome sequence (MIGS) specification. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A. Nat Biotechnol. 2008 May;26(5):541-7. 18464787
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metagenomics related papers and citations

1. 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. 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. 18803844

1. Molecular Diversity of a North Carolina Wastewater Treatment Plant As Revealed by Pyrosequencing. 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] 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. 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] 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. Demanèche S, David MM, Navarro E, Simonet P, Vogel TM. J Microbiol Methods. 2009 Jan;76(1):105-7. [Epub 2008 Sep 17] 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. 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] 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. Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. PLoS ONE. 2008 Aug 22;3(8):e3042. 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. 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. 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. 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. 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. 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. 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. Mou X, Sun S, Edwards RA, Hodson RE, Moran MA. Nature. 2008 Feb 7;451(7179):708-11.[ Epub 2008 Jan 27] 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. 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. 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.