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Publications

Describing our tools

  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. icon PMID: 18803844
  3. 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. icon PMID: 18261238
  4. 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] icon PMID: 17145713
  5. 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] icon PMID: 17420237
  6. 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] icon PMID: 17658903
  7. 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. icon PMID: 16214803

Using our tools

  1. 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] icon PMID: 18931107
  2. 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] icon PMID: 18776013
  3. 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. icon PMID: 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.
  4. 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. icon PMID: 18844986
  5. 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] icon PMID: 18671744
  6. Rise and persistence of global M1T1 clone of Streptococcus pyogenes. Aziz RK, Kotb M. Emerg Infect Dis. 2008 Oct;14(10):1511-7. icon PMID: 18826812
  7. 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] icon PMID: 18586940
  8. 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. icon PMID: 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.
  9. 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. icon PMID: 18716664
    • The RAST server was used as one tool to develop a comprehensive annotation of the features in this genome.
  10. 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] icon PMID: 18641144
  11. 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. icon PMID: 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.
  12. 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] icon PMID: 18604222
  13. 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. icon PMID: 18665241
  14. 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] icon PMID: 18487409
  15. 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] icon PMID: 18452587
  16. 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. icon PMID: 18575584
    • MG-RAST and our subsystems were used to reconstruct and compare the taxonomy and metabolism of a soil community from metatranscriptomic data.
  17. 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] icon PMID: 18310350
  18. 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] icon PMID: 18296538
    • A phylogenetically representative set of full-length bacterial SSU rRNA sequences was extracted from The SEED.
  19. 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] icon PMID: 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
  20. 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] icon PMID: 18276643
  21. 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] icon PMID: 18276644
  22. 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. icon PMID: 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.
  23. 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. icon PMID: 18337718
    • MG-RAST and our subsystems were used to reconstruct and compare the metabolism of different microbial environments.
  24. ComPath: Comparative enzyme analysis and annotation in pathway/subsystem contexts. Choi K, Kim S. BMC Bioinformatics. 2008 Mar 6;9:145. icon PMID: 18325116
    • ComPath provides a total of 327 model pathways combining 205 pathways from KEGG database and 122 subsystems from The SEED and NMPDR.
  25. 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] icon PMID: 18156253
  26. 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. icon PMID: 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.
  27. 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] icon PMID: 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.
  28. 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] icon PMID: 18223640
    • MG-RAST and our subsystems were used to directly measure niche breadth for bacterial functional assemblages.
  29. 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] icon PMID: 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.
  30. 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. icon PMID: 18275811
  31. 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] icon PMID: 17986616
  32. 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. icon PMID: 17852564
  33. The biological role of death and lysis in biofilm development. Bayles KW. Nat Rev Microbiol. 2007 Sep;5(9):721-6. icon PMID: 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.
  34. 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] icon PMID: 17690205
    • Subsystems were used to identify and categorize the functions of expressed proteins detected in the proteome of Shewanella oneidensis MR-1.
  35. Identification of genes encoding tRNA modification enzymes by comparative genomics. de Crécy-Lagard V. Methods Enzymol. 2007;425:153-83. icon PMID: 17673083
  36. 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. icon PMID: 17645794
    • Subsystem construction tools in the SEED and the SignatureGenesTool 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.
  37. 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
  38. 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] icon PMID: 17362878
  39. 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. icon PMID: 17462086
    • Subsystems were used to guide the automated generation of substantially complete metabolic networks from a collection of modular components called "scenarios."
  40. 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] icon PMID: 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.
  41. 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] iconPMID: 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.
  42. 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] iconPMID: 17323930
  43. 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] iconPMID: 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.
  44. 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] iconPMID: 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.
  45. 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] iconPMID: 17173478
  46. 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] iconPMID: 17032654
  47. 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] icon PMID: 17012394
    • EssentialGenes of E. coli were analyzed in terms of metabolic subsystems across multiple genomes.
  48. 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] icon PMID: 16926157
    • The domains that are fused in this Neisseria protein were identified as separate but clustered peptides using the Find Clusters function.
  49. 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] icon PMID: 16978855
    • The genomic scale screens for essential genes that are displayed on the EssentialGenes page are reviewed and discussed in the context of comparative analysis of subsystems. icon Supplemental data tables
  50. 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] icon PMID: 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.
  51. 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 icon PMID: 16980476
    • NMPDR team members used bioinformatics to produce supplemental file 1, "Table S8, Characterization of small stable RNA molecules identified in this study."
  52. 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] icon PMID: 16964242
  53. 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. icon PMID: 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.
  54. 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. icon PMID: 16901339
  55. 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. icon PMID: 16856937
  56. 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. icon PMID: 16585762
  57. 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] icon PMID: 16595627
  58. 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. icon PMID: 16549033
    • Subsystems were used to characterize two distinctly different microbial communities from short pyrosequence reads during the development of the MG-RAST server.
  59. An application of statistics to comparative metagenomics. Rodriguez-Brito B, Rohwer F, Edwards RA. BMC Bioinformatics. 2006 Mar 20;7:162. icon PMID: 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.
  60. 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. icon PMID: 16439655
  61. 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. icon PMID: 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.
  62. 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. icon PMID: 16159395
    • The conservation of this cluster among the Actinomycetales was explored using Compare Regions.
  63. 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. icon PMID: 15995210

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Citing our work

  1. Genomic-scale prioritization of drug targets: The TDR Targets database. Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC, Verlinde CL. Nat Rev Drug Discov. 2008 Nov;7(11):900-7. [Epub 2008 Oct 17] icon PMID: 18927591
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  3. Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform 'Open Genome Resource' (OGeR). Klein J, Münch R, Biegler I, Haddad I, Retter I, Jahn D. Nucleic Acids Res. 2008 Oct 14. [Epub ahead of print] icon PMID: 18854354
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Topic revision: r12 - 19 Dec 2008 - 19:30:12 - LeslieMcNeil
 
NMPDR is 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.