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    Kyrpides, Nikos

    TitleComputational Biologist Sr SE
    SchoolLawrence Berkeley National Lab
    DepartmentGenomics
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone925/296-5718

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Seshadri R, Reeve WG, Ardley JK, Tennessen K, Woyke T, Kyrpides NC, Ivanova NN. Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria. Sci Rep. 2015; 5:16825.
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      2. Choi DH, Ahn C, Jang GI, Lapidus A, Han J, Reddy TB, Huntemann M, Pati A, Ivanova N, Markowitz V, Rohde M, Tindall B, Göker M, Woyke T, Klenk HP, Kyrpides NC, Cho BC. High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture. Stand Genomic Sci. 2015; 10:98.
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      3. Cadillo-Quiroz H, Browne P, Kyrpides N, Woyke T, Goodwin L, Detter C, Yavitt JB, Zinder SH. Complete Genome Sequence of Methanosphaerula palustris E1-9CT, a Hydrogenotrophic Methanogen Isolated from a Minerotrophic Fen Peatland. Genome Announc. 2015; 3(6).
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      4. Berben T, Sorokin DY, Ivanova N, Pati A, Kyrpides N, Goodwin LA, Woyke T, Muyzer G. Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1(T), a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification. Stand Genomic Sci. 2015; 10:84.
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      5. Berben T, Sorokin DY, Ivanova N, Pati A, Kyrpides N, Goodwin LA, Woyke T, Muyzer G. Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T). Stand Genomic Sci. 2015; 10:85.
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      6. Eshraghi L, De Meyer SE, Tian R, Seshadri R, Ivanova N, Pati A, Markowitz V, Woyke T, Kyrpides NC, Tiwari R, Yates R, Howieson J, Reeve W. High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia. Stand Genomic Sci. 2015; 10:87.
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      7. Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Palaniappan K, Szeto E, Pillay M, Chen IM, Pati A, Nielsen T, Markowitz VM, Kyrpides NC. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). Stand Genomic Sci. 2015; 10:86.
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      8. De Meyer SE, Tian R, Seshadri R, Reddy T, Markowitz V, Ivanova N, Pati A, Woyke T, Kyrpides N, Yates R, Howieson J, Reeve W. High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176. Stand Genomic Sci. 2015; 10:79.
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      9. De Meyer SE, Parker M, Van Berkum P, Tian R, Seshadri R, Reddy TB, Markowitz V, Ivanova N, Pati A, Woyke T, Kyrpides N, Howieson J, Reeve W. High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6. Stand Genomic Sci. 2015; 10:80.
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      10. Markowitz VM, Chen IM, Chu K, Pati A, Ivanova NN, Kyrpides NC. Ten Years of Maintaining and Expanding a Microbial Genome and Metagenome Analysis System. Trends Microbiol. 2015 Nov; 23(11):730-41.
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      11. De Meyer SE, Tian R, Seshadri R, Ivanova N, Pati A, Markowitz V, Woyke T, Yates R, Howieson J, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556(T). Stand Genomic Sci. 2015; 10:64.
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      12. Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO. Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol. 2015 Aug 18; 11(9):625-31.
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      13. Shetty AR, de Gannes V, Obi CC, Lucas S, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Teshima H, Han C, Tapia R, Land M, Hauser LJ, Kyrpides N, Ivanova N, Pagani I, Chain PS, Denef VJ, Woyke T, Hickey WJ. Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4. Stand Genomic Sci. 2015; 10:55.
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      14. Reeve W, Sullivan J, Ronson C, Tian R, Munk C, Han C, Reddy TB, Seshadri R, Woyke T, Pati A, Markowitz V, Ivanova N, Kyrpides N. High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym. Stand Genomic Sci. 2015; 10:54.
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      15. Ntougias S, Lapidus A, Copeland A, Reddy TB, Pati A, Ivanova NN, Markowitz VM, Klenk HP, Woyke T, Fasseas C, Kyrpides NC, Zervakis GI. High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotalea. Stand Genomic Sci. 2015; 10:52.
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      16. Lau SC, Riedel T, Fiebig A, Han J, Huntemann M, Petersen J, Ivanova NN, Markowitz V, Woyke T, Göker M, Kyrpides NC, Klenk HP, Qian PY. Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group. Stand Genomic Sci. 2015; 10:51.
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      17. Tisa LS, Beauchemin N, Cantor MN, Furnholm T, Ghodhbane-Gtari F, Goodwin L, Copeland A, Gtari M, Huntemann M, Ivanova N, Kyrpides N, Markowitz V, Mavrommatis K, Mikhailova N, Nouioui I, Oshone R, Ovchinnikova G, Pagani I, Palaniappan K, Pati A, Sen A, Shapiro N, Szeto E, Wall L, Wishart J, Woyke T. Draft Genome Sequence of Frankia sp. Strain DC12, an Atypical, Noninfective, Ineffective Isolate from Datisca cannabina. Genome Announc. 2015; 3(4).
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      18. Yassin AF, Lapidus A, Han J, Reddy TB, Huntemann M, Pati A, Ivanova N, Markowitz V, Woyke T, Klenk HP, Kyrpides NC. High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395(T) (DSM 45146(T)). Stand Genomic Sci. 2015; 10:50.
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      19. Sakamoto M, Lapidus AL, Han J, Trong S, Haynes M, Reddy TB, Mikhailova N, Huntemann M, Pati A, Ivanova NN, Pukall R, Markowitz VM, Woyke T, Klenk HP, Kyrpides NC, Ohkuma M. High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum. Stand Genomic Sci. 2015; 10:48.
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      20. Hahnke RL, Stackebrandt E, Meier-Kolthoff JP, Tindall BJ, Huang S, Rohde M, Lapidus A, Han J, Trong S, Haynes M, Reddy TB, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Göker M, Kyrpides NC, Klenk HP. High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes. Stand Genomic Sci. 2015; 10:46.
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      21. Tripp HJ, Sutton G, White O, Wortman J, Pati A, Mikhailova N, Ovchinnikova G, Payne SH, Kyrpides NC, Ivanova N. Toward a standard in structural genome annotation for prokaryotes. Stand Genomic Sci. 2015; 10:45.
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      22. Yates R, Howieson J, De Meyer SE, Tian R, Seshadri R, Pati A, Woyke T, Markowitz V, Ivanova N, Kyrpides N, Loi A, Nutt B, Garau G, Sulas L, Reeve W. High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy. Stand Genomic Sci. 2015; 10:44.
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      23. Rooney EA, Rowe KT, Guseva A, Huntemann M, Han JK, Chen A, Kyrpides NC, Mavromatis K, Markowitz VM, Palaniappan K, Ivanova N, Pati A, Liolios K, Nordberg HP, Cantor MN, Hua SX, Shapiro N, Woyke T, Lynd LR, Izquierdo JA. Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a. Genome Announc. 2015; 3(4).
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      24. Gutierrez T, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Pillay M, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TB, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woyke T. Genome Sequence of Halomonas sp. Strain MCTG39a, a Hydrocarbon-Degrading and Exopolymeric Substance-Producing Bacterium. Genome Announc. 2015; 3(4).
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      25. Mazur A, De Meyer SE, Tian R, Wielbo J, Zebracki K, Seshadri R, Reddy T, Markowitz V, Ivanova NN, Pati A, Woyke T, Kyrpides NC, Reeve W. High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland. Stand Genomic Sci. 2015; 10:36.
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      26. Hadjithomas M, Chen IM, Chu K, Ratner A, Palaniappan K, Szeto E, Huang J, Reddy TB, Cimermancic P, Fischbach MA, Ivanova NN, Markowitz VM, Kyrpides NC, Pati A. IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites. MBio. 2015; 6(4).
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      27. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 2015 Aug 18; 43(14):6761-71.
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      28. Mhamdi R, Ardley J, Tian R, Seshadri R, Reddy TB, Pati A, Woyke T, Markowitz V, Ivanova N, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris. Stand Genomic Sci. 2015; 10:34.
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      29. Smalley NE, Taipale S, De Marco P, Doronina NV, Kyrpides N, Shapiro N, Woyke T, Kalyuzhnaya MG. Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of Methyloversatilis discipulorum sp. nov. Int J Syst Evol Microbiol. 2015 Jul; 65(7):2227-33.
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      30. Tschitschko B, Williams TJ, Allen MA, Páez-Espino D, Kyrpides N, Zhong L, Raftery MJ, Cavicchioli R. Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. ISME J. 2015 Sep; 9(9):2094-107.
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      31. Cohen MF, Hu P, Nguyen MV, Kamennaya N, Brown N, Woyke T, Kyrpides N, Holman HY, Torok T. Genome Sequence of the Alkaline-Tolerant Cellulomonas sp. Strain FA1. Genome Announc. 2015; 3(3).
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      32. Gutierrez T, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Pillay M, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TB, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woyke T. Genome Sequence of Porticoccus hydrocarbonoclasticus Strain MCTG13d, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton. Genome Announc. 2015; 3(3).
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      33. Tian R, Parker M, Seshadri R, Reddy T, Markowitz V, Ivanova N, Pati A, Woyke T, Baeshen M, Baeshen N, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Bradyrhizobium sp. Ai1a-2; a microsymbiont of Andira inermis discovered in Costa Rica. Stand Genomic Sci. 2015; 10:33.
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      34. Sharp CE, Smirnova AV, Kalyuzhnaya MG, Bringel F, Hirayama H, Jetten MS, Khmelenina VN, Klotz MG, Knief C, Kyrpides N, Op den Camp HJ, Reshetnikov AS, Sakai Y, Shapiro N, Trotsenko YA, Vuilleumier S, Woyke T, Dunfield PF. Draft Genome Sequence of the Moderately Halophilic Methanotroph Methylohalobius crimeensis Strain 10Ki. Genome Announc. 2015; 3(3).
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      35. De Meyer SE, Fabiano E, Tian R, Van Berkum P, Seshadri R, Reddy T, Markowitz V, Ivanova N, Pati A, Woyke T, Howieson J, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413. Stand Genomic Sci. 2015; 10:31.
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      36. Petit E, Coppi MV, Hayes JC, Tolonen AC, Warnick T, Latouf WG, Amisano D, Biddle A, Mukherjee S, Ivanova N, Lykidis A, Land M, Hauser L, Kyrpides N, Henrissat B, Lau J, Schnell DJ, Church GM, Leschine SB, Blanchard JL. Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PLoS One. 2015; 10(6):e0118285.
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      37. Laviad S, Lapidus A, Han J, Haynes M, Reddy T, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Lang E, Rohde M, Markowitz V, Woyke T, Klenk HP, Kyrpides NC, Halpern M. High quality draft genome sequence of Brachymonas chironomi AIMA4(T) (DSM 19884(T)) isolated from a Chironomus sp. egg mass. Stand Genomic Sci. 2015; 10:29.
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      38. Bräuer S, Cadillo-Quiroz H, Kyrpides N, Woyke T, Goodwin L, Detter C, Podell S, Yavitt JB, Zinder SH. Genome of Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland environments. Microbiology. 2015 Aug; 161(8):1572-81.
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      39. Whitman WB, Woyke T, Klenk HP, Zhou Y, Lilburn TG, Beck BJ, De Vos P, Vandamme P, Eisen JA, Garrity G, Hugenholtz P, Kyrpides NC. Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Stand Genomic Sci. 2015; 10:26.
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      40. Tian R, Parker M, Seshadri R, Reddy T, Markowitz V, Ivanova N, Pati A, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of Panama. Stand Genomic Sci. 2015; 10:27.
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      41. Tian R, Parker M, Seshadri R, Reddy T, Markowitz V, Ivanova N, Pati A, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York. Stand Genomic Sci. 2015; 10:24.
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      42. Lee LL, Izquierdo JA, Blumer-Schuette SE, Zurawski JV, Conway JM, Cottingham RW, Huntemann M, Copeland A, Chen IM, Kyrpides N, Markowitz V, Palaniappan K, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TB, Shapiro N, Nordberg HP, Cantor MN, Hua SX, Woyke T, Kelly RM. Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and "Thermoanaerobacter cellulolyticus". Genome Announc. 2015; 3(3).
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      43. Laviad S, Lapidus A, Copeland A, Reddy T, Huntemann M, Pati A, Ivanova NN, Markowitz VM, Pukall R, Klenk HP, Woyke T, Kyrpides NC, Halpern M. High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass. Stand Genomic Sci. 2015; 10:21.
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      44. De Meyer SE, Fabiano E, Tian R, Van Berkum P, Seshadri R, Reddy T, Markowitz V, Ivanova NN, Pati A, Woyke T, Howieson J, Kyrpides NC, Reeve W. High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512. Stand Genomic Sci. 2015; 10:13.
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      45. Mukherjee S, Huntemann M, Ivanova N, Kyrpides NC, Pati A. Large-scale contamination of microbial isolate genomes by Illumina PhiX control. Stand Genomic Sci. 2015; 10:18.
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      46. Gutierrez T, Thompson HF, Angelova A, Whitman WB, Huntemann M, Copeland A, Chen A, Kyrpides N, Markowitz V, Palaniappan K, Ivanova N, Mikhailova N, Ovchinnikova G, Andersen E, Pati A, Stamatis D, Reddy TB, Ngan CY, Chovatia M, Daum C, Shapiro N, Cantor MN, Woyke T. Genome Sequence of Polycyclovorans algicola Strain TG408, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton. Genome Announc. 2015; 3(2).
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      47. Walworth N, Pfreundt U, Nelson WC, Mincer T, Heidelberg JF, Fu F, Waterbury JB, Glavina Del Rio T, Goodwin L, Kyrpides NC, Land ML, Woyke T, Hutchins DA, Hess WR, Webb EA. Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle. Proc Natl Acad Sci U S A. 2015 Apr 7; 112(14):4251-6.
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      48. Ramsay BD, Hwang C, Woo HL, Carroll SL, Lucas S, Han J, Lapidus AL, Cheng JF, Goodwin LA, Pitluck S, Peters L, Chertkov O, Held B, Detter JC, Han CS, Tapia R, Land ML, Hauser LJ, Kyrpides NC, Ivanova NN, Mikhailova N, Pagani I, Woyke T, Arkin AP, Dehal P, Chivian D, Criddle CS, Wu W, Chakraborty R, Hazen TC, Fields MW. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater. Genome Announc. 2015; 3(2).
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      49. Dedysh SN, Naumoff DG, Vorobev AV, Kyrpides N, Woyke T, Shapiro N, Crombie AT, Murrell JC, Kalyuzhnaya MG, Smirnova AV, Dunfield PF. Draft Genome Sequence of Methyloferula stellata AR4, an Obligate Methanotroph Possessing Only a Soluble Methane Monooxygenase. Genome Announc. 2015; 3(2).
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      50. McIlroy SJ, Lapidus A, Thomsen TR, Han J, Haynes M, Lobos E, Huntemann M, Pati A, Ivanova NN, Markowitz V, Verbarg S, Woyke T, Klenk HP, Kyrpides N, Nielsen PH. High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov. Stand Genomic Sci. 2015; 10:23.
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      51. Mukherjee S, Lapidus A, Shapiro N, Cheng JF, Han J, Reddy T, Huntemann M, Ivanova N, Mikhailova N, Chen A, Palaniappan K, Spring S, Göker M, Markowitz V, Woyke T, Tindall BJ, Klenk HP, Kyrpides NC, Pati A. High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India. Stand Genomic Sci. 2015; 10:8.
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      52. Reeve W, Ardley J, Tian R, Eshragi L, Yoon JW, Ngamwisetkun P, Seshadri R, Ivanova NN, Kyrpides NC. A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey. Stand Genomic Sci. 2015; 10:14.
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      53. Hwang C, Copeland A, Lucas S, Lapidus A, Barry K, Glavina Del Rio T, Dalin E, Tice H, Pitluck S, Sims D, Brettin T, Bruce DC, Detter JC, Han CS, Schmutz J, Larimer FW, Land ML, Hauser LJ, Kyrpides N, Lykidis A, Richardson P, Belieav A, Sanford RA, Löeffler FE, Fields MW. Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment. Genome Announc. 2015; 3(1).
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      54. Gao XY, Zhi XY, Li HW, Zhou Y, Lapidus A, Han J, Haynes M, Lobos E, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Tindall BJ, Markowitz V, Woyke T, Klenk HP, Kyrpides NC, Li WJ. Draft genome sequence of Halomonas lutea strain YIM 91125(T) (DSM 23508(T)) isolated from the alkaline Lake Ebinur in Northwest China. Stand Genomic Sci. 2015; 10:1.
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      55. Scheuner C, Tindall BJ, Lu M, Nolan M, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ivanova N, Pati A, Chen A, Palaniappan K, Jeffries CD, Hauser L, Land M, Mwirichia R, Rohde M, Abt B, Detter JC, Woyke T, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Kyrpides NC, Klenk HP. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Stand Genomic Sci. 2014; 9:10.
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      56. Reeve W, Sullivan J, Ronson C, Tian R, Bräu L, Davenport K, Goodwin L, Chain P, Woyke T, Lobos E, Huntemann M, Pati A, Mavromatis K, Markowitz V, Ivanova N, Kyrpides N. Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B. Stand Genomic Sci. 2014; 9:3.
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      57. Kelly S, Sullivan J, Ronson C, Tian R, Bräu L, Munk C, Goodwin L, Han C, Woyke T, Reddy T, Huntemann M, Pati A, Mavromatis K, Markowitz V, Ivanova N, Kyrpides N, Reeve W. Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A. Stand Genomic Sci. 2014; 9:6.
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      58. Ardley J, Tian R, Howieson J, Yates R, Bräu L, Han J, Lobos E, Huntemann M, Chen A, Mavromatis K, Markowitz V, Ivanova N, Pati A, Goodwin L, Woyke T, Kyrpides N, Reeve W. Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598. Stand Genomic Sci. 2014; 9:5.
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      59. Kelly S, Sullivan J, Ronson C, Tian R, Bräu L, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Munk C, Teshima H, Xu Y, Chain P, Woyke T, Liolios K, Pati A, Mavromatis K, Markowitz V, Ivanova N, Kyrpides N, Reeve W. Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037. Stand Genomic Sci. 2014; 9:7.
        View in: PubMed
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      164. Marx CJ, Bringel F, Chistoserdova L, Moulin L, Farhan Ul Haque M, Fleischman DE, Gruffaz C, Jourand P, Knief C, Lee MC, Muller EE, Nadalig T, Peyraud R, Roselli S, Russ L, Goodwin LA, Ivanova N, Kyrpides N, Lajus A, Land ML, Médigue C, Mikhailova N, Nolan M, Woyke T, Stolyar S, Vorholt JA, Vuilleumier S. Complete genome sequences of six strains of the genus Methylobacterium. J Bacteriol. 2012 Sep; 194(17):4746-8.
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      165. Mead DA, Lucas S, Copeland A, Lapidus A, Cheng JF, Bruce DC, Goodwin LA, Pitluck S, Chertkov O, Zhang X, Detter JC, Han CS, Tapia R, Land M, Hauser LJ, Chang YJ, Kyrpides NC, Ivanova NN, Ovchinnikova G, Woyke T, Brumm C, Hochstein R, Schoenfeld T, Brumm P. Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park. Stand Genomic Sci. 2012 Jul 30; 6(3):381-400.
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      166. Liolios K, Schriml L, Hirschman L, Pagani I, Nosrat B, Sterk P, White O, Rocca-Serra P, Sansone SA, Taylor C, Kyrpides NC, Field D. The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. Stand Genomic Sci. 2012 Jul 30; 6(3):438-47.
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      167. Jiang K, Sanseverino J, Chauhan A, Lucas S, Copeland A, Lapidus A, Del Rio TG, Dalin E, Tice H, Bruce D, Goodwin L, Pitluck S, Sims D, Brettin T, Detter JC, Han C, Chang YJ, Larimer F, Land M, Hauser L, Kyrpides NC, Mikhailova N, Moser S, Jegier P, Close D, Debruyn JM, Wang Y, Layton AC, Allen MS, Sayler GS. Complete genome sequence of Thauera aminoaromatica strain MZ1T. Stand Genomic Sci. 2012 Jul 30; 6(3):325-35.
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      168. Anderson I, Chertkov O, Chen A, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Palaniappan K, Land M, Pan C, Rohde M, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Stand Genomic Sci. 2012 Jul 30; 6(3):1-13.
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      169. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Jacob B, Ratner A, Liolios K, Pagani I, Huntemann M, Mavromatis K, Ivanova NN, Kyrpides NC. IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PLoS One. 2012; 7(7):e40151.
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      170. Wilke A, Harrison T, Wilkening J, Field D, Glass EM, Kyrpides N, Mavrommatis K, Meyer F. The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics. 2012; 13:141.
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      171. Anderson I, Abt B, Lykidis A, Klenk HP, Kyrpides N, Ivanova N. Genomics of aerobic cellulose utilization systems in actinobacteria. PLoS One. 2012; 7(6):e39331.
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      172. Siddaramappa S, Challacombe JF, Delano SF, Green LD, Daligault H, Bruce D, Detter C, Tapia R, Han S, Goodwin L, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Land M, Chang YJ, Kyrpides NC, Ovchinnikova G, Hauser L, Lapidus A, Yan J, Bowman KS, da Costa MS, Rainey FA, Moe WM. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to "Dehalococcoides" strains. Stand Genomic Sci. 2012 May 25; 6(2):251-64.
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      173. Klenk HP, Lu M, Lucas S, Lapidus A, Copeland A, Pitluck S, Goodwin LA, Han C, Tapia R, Brambilla EM, Pötter G, Land M, Ivanova N, Rohde M, Göker M, Detter JC, Li WJ, Kyrpides NC, Woyke T. Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T)). Stand Genomic Sci. 2012 May 25; 6(2):265-75.
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      174. Klenk HP, Held B, Lucas S, Lapidus A, Copeland A, Hammon N, Pitluck S, Goodwin LA, Han C, Tapia R, Brambilla EM, Pötter G, Land M, Ivanova N, Rohde M, Göker M, Detter JC, Kyrpides NC, Woyke T. Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128(T)). Stand Genomic Sci. 2012 May 25; 6(2):220-9.
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      175. Copeland A, Zhang X, Misra M, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Djao OD, Göker M, Sikorski J, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Stand Genomic Sci. 2012 May 25; 6(2):145-54.
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      176. Anderson I, Saunders E, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Chang YJ, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). Stand Genomic Sci. 2012 May 25; 6(2):155-64.
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      177. Anderson I, Held B, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)). Stand Genomic Sci. 2012 May 25; 6(2):174-84.
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      178. Huntemann M, Teshima H, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). Stand Genomic Sci. 2012 May 25; 6(2):185-93.
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      179. Abt B, Han C, Scheuner C, Lu M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Gronow S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand Genomic Sci. 2012 May 25; 6(2):194-209.
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      180. Mavromatis K, Chertkov O, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Bruce D, Goodwin LA, Pitluck S, Huntemann M, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1). Stand Genomic Sci. 2012 May 25; 6(2):210-9.
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      182. Siddaramappa S, Challacombe JF, Decastro RE, Pfeiffer F, Sastre DE, Giménez MI, Paggi RA, Detter JC, Davenport KW, Goodwin LA, Kyrpides N, Tapia R, Pitluck S, Lucas S, Woyke T, Maupin-Furlow JA. A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. BMC Genomics. 2012; 13:165.
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      183. Neupane S, Finlay RD, Alström S, Goodwin L, Kyrpides NC, Lucas S, Lapidus A, Bruce D, Pitluck S, Peters L, Ovchinnikova G, Chertkov O, Han J, Han C, Tapia R, Detter JC, Land M, Hauser L, Cheng JF, Ivanova N, Pagani I, Klenk HP, Woyke T, Högberg N. Complete genome sequence of Serratia plymuthica strain AS12. Stand Genomic Sci. 2012 May 25; 6(2):165-73.
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      187. Lucas-Elío P, Goodwin L, Woyke T, Pitluck S, Nolan M, Kyrpides NC, Detter JC, Copeland A, Teshima H, Bruce D, Detter C, Tapia R, Han S, Land ML, Ivanova N, Mikhailova N, Johnston AW, Sanchez-Amat A. Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1(T)). Stand Genomic Sci. 2012 Mar 19; 6(1):63-73.
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      189. Anderson I, Tindall BJ, Rohde M, Lucas S, Han J, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Peters L, Pati A, Mikhailova N, Pagani I, Teshima H, Han C, Tapia R, Land M, Woyke T, Klenk HP, Kyrpides N, Ivanova N. Complete genome sequence of Halopiger xanaduensis type strain (SH-6(T)). Stand Genomic Sci. 2012 Mar 19; 6(1):31-42.
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      190. Han C, Kotsyurbenko O, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)). Stand Genomic Sci. 2012 Mar 19; 6(1):94-103.
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      191. Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One. 2012; 7(2):e30087.
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      195. Göker M, Daligault H, Mwirichia R, Lapidus A, Lucas S, Deshpande S, Pagani I, Tapia R, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Han C, Land M, Hauser L, Pan C, Brambilla EM, Rohde M, Spring S, Sikorski J, Wirth R, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea hydrothermal vent. Stand Genomic Sci. 2011 Dec 31; 5(3):407-15.
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      196. Grote J, Bayindirli C, Bergauer K, Carpintero de Moraes P, Chen H, D'Ambrosio L, Edwards B, Fernández-Gómez B, Hamisi M, Logares R, Nguyen D, Rii YM, Saeck E, Schutte C, Widner B, Church MJ, Steward GF, Karl DM, Delong EF, Eppley JM, Schuster SC, Kyrpides NC, Rappé MS. Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. Stand Genomic Sci. 2011 Dec 31; 5(3):269-78.
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      197. Chertkov O, Brown PJ, Kysela DT, de Pedro MA, Lucas S, Copeland A, Lapidus A, Del Rio TG, Tice H, Bruce D, Goodwin L, Pitluck S, Detter JC, Han C, Larimer F, Chang YJ, Jeffries CD, Land M, Hauser L, Kyrpides NC, Ivanova N, Ovchinnikova G, Tindall BJ, Göker M, Klenk HP, Brun YV. Complete genome sequence of Hirschia baltica type strain (IFAM 1418(T)). Stand Genomic Sci. 2011 Dec 31; 5(3):287-97.
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      198. Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Foster B, Sun H, Ivanova N, Pati A, D'haeseleer P, Woyke T, Kyrpides NC. Complete genome sequence of Thioalkalivibrio sp. K90mix. Stand Genomic Sci. 2011 Dec 31; 5(3):341-55.
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      199. Kiss H, Nett M, Domin N, Martin K, Maresca JA, Copeland A, Lapidus A, Lucas S, Berry KW, Glavina Del Rio T, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin L, Han C, Detter JC, Schmutz J, Brettin T, Land M, Hauser L, Kyrpides NC, Ivanova N, Göker M, Woyke T, Klenk HP, Bryant DA. Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95(T)). Stand Genomic Sci. 2011 Dec 31; 5(3):356-70.
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      200. Anderson I, Chen A, Markowitz V, Kyrpides N, Ivanova N. SOP for pathway inference in Integrated Microbial Genomes (IMG). Stand Genomic Sci. 2011 Dec 31; 5(3):420-3.
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      201. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2012 Jan; 40(Database issue):D571-9.
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      202. Boden R, Cunliffe M, Scanlan J, Moussard H, Kits KD, Klotz MG, Jetten MS, Vuilleumier S, Han J, Peters L, Mikhailova N, Teshima H, Tapia R, Kyrpides N, Ivanova N, Pagani I, Cheng JF, Goodwin L, Han C, Hauser L, Land ML, Lapidus A, Lucas S, Pitluck S, Woyke T, Stein L, Murrell JC. Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J Bacteriol. 2011 Dec; 193(24):7001-2.
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      203. Pati A, Heath LS, Kyrpides NC, Ivanova N. ClaMS: A Classifier for Metagenomic Sequences. Stand Genomic Sci. 2011 Nov 30; 5(2):248-53.
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      204. Vandera E, Kavakiotis K, Kallimanis A, Kyrpides NC, Drainas C, Koukkou AI. Heterologous expression and characterization of two 1-hydroxy-2-naphthoic acid dioxygenases from Arthrobacter phenanthrenivorans. Appl Environ Microbiol. 2012 Feb; 78(3):621-7.
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      206. Luo C, Tsementzi D, Kyrpides NC, Konstantinidis KT. Individual genome assembly from complex community short-read metagenomic datasets. ISME J. 2012 Apr; 6(4):898-901.
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      207. Siebers B, Zaparty M, Raddatz G, Tjaden B, Albers SV, Bell SD, Blombach F, Kletzin A, Kyrpides N, Lanz C, Plagens A, Rampp M, Rosinus A, von Jan M, Makarova KS, Klenk HP, Schuster SC, Hensel R. The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota. PLoS One. 2011; 6(10):e24222.
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      208. Chang YJ, Land M, Hauser L, Chertkov O, Del Rio TG, Nolan M, Copeland A, Tice H, Cheng JF, Lucas S, Han C, Goodwin L, Pitluck S, Ivanova N, Ovchinikova G, Pati A, Chen A, Palaniappan K, Mavromatis K, Liolios K, Brettin T, Fiebig A, Rohde M, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). Stand Genomic Sci. 2011 Oct 15; 5(1):97-111.
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      209. Suen G, Stevenson DM, Bruce DC, Chertkov O, Copeland A, Cheng JF, Detter C, Detter JC, Goodwin LA, Han CS, Hauser LJ, Ivanova NN, Kyrpides NC, Land ML, Lapidus A, Lucas S, Ovchinnikova G, Pitluck S, Tapia R, Woyke T, Boyum J, Mead D, Weimer PJ. Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7. J Bacteriol. 2011 Oct; 193(19):5574-5.
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      210. Anderson I, Risso C, Holmes D, Lucas S, Copeland A, Lapidus A, Cheng JF, Bruce D, Goodwin L, Pitluck S, Saunders E, Brettin T, Detter JC, Han C, Tapia R, Larimer F, Land M, Hauser L, Woyke T, Lovley D, Kyrpides N, Ivanova N. Complete genome sequence of Ferroglobus placidus AEDII12DO. Stand Genomic Sci. 2011 Oct 15; 5(1):50-60.
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      265. Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci. 2010; 3(3):243-8.
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      272. Davidsen T, Madupu R, Sterk P, Field D, Garrity G, Gilbert J, Glöckner FO, Hirschman L, Kolker E, Kottmann R, Kyrpides N, Meyer F, Morrison N, Schriml L, Tatusova T, Wooley J. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9. Stand Genomic Sci. 2010; 3(3):216-24.
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      298. Tindall BJ, Sikorski J, Lucas S, Goltsman E, Copeland A, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Han C, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Fähnrich R, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Meiothermus ruber type strain (21). Stand Genomic Sci. 2010; 3(1):26-36.
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      299. Ivanova N, Tringe SG, Liolios K, Liu WT, Morrison N, Hugenholtz P, Kyrpides NC. A call for standardized classification of metagenome projects. Environ Microbiol. 2010 Jul; 12(7):1803-5.
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      300. Pati A, Sikorski J, Gronow S, Munk C, Lapidus A, Copeland A, Glavina Del Tio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Spring S, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Brachyspira murdochii type strain (56-150). Stand Genomic Sci. 2010; 2(3):260-9.
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      301. Mavromatis K, Abt B, Brambilla E, Lapidus A, Copeland A, Deshpande S, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Woyke T, Goodwin L, Pitluck S, Held B, Brettin T, Tapia R, Ivanova N, Mikhailova N, Pati A, Liolios K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24). Stand Genomic Sci. 2010; 2(3):290-9.
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      302. Pati A, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Chertkov O, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Arcobacter nitrofigilis type strain (CI). Stand Genomic Sci. 2010; 2(3):300-8.
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      303. von Jan M, Lapidus A, Del Rio TG, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Goodwin L, Han C, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Chertkov O, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Saunders E, Brettin T, Detter JC, Chain P, Eichinger K, Huber H, Spring S, Rohde M, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Archaeoglobus profundus type strain (AV18). Stand Genomic Sci. 2010; 2(3):327-46.
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      304. Reeve W, O'Hara G, Chain P, Ardley J, Bräu L, Nandesena K, Tiwari R, Copeland A, Nolan M, Han C, Brettin T, Land M, Ovchinikova G, Ivanova N, Mavromatis K, Markowitz V, Kyrpides N, Melino V, Denton M, Yates R, Howieson J. Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers. Stand Genomic Sci. 2010; 2(3):347-56.
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      305. Hirschman L, Sterk P, Field D, Wooley J, Cochrane G, Gilbert J, Kolker E, Kyrpides N, Meyer F, Mizrachi I, Nakamura Y, Sansone SA, Schriml L, Tatusova T, White O, Yilmaz P. Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010. Stand Genomic Sci. 2010; 2(3):357-60.
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      306. Spring S, Rachel R, Lapidus A, Davenport K, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Brettin T, Detter JC, Tapia R, Han C, Heimerl T, Weikl F, Brambilla E, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Thermosphaera aggregans type strain (M11TL). Stand Genomic Sci. 2010; 2(3):245-59.
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      307. Kiss H, Lang E, Lapidus A, Copeland A, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Cheng JF, Han C, Goodwin L, Pitluck S, Liolios K, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Spring S, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460). Stand Genomic Sci. 2010; 2(3):270-9.
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      308. Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Spring S, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). Stand Genomic Sci. 2010; 2(3):280-9.
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      309. Liolios K, Sikorski J, Jando M, Lapidus A, Copeland A, Glavina T. Complete genome sequence of Thermobispora bispora type strain (R51). Stand Genomic Sci. 2010; 2(3):318-26.
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      310. Copeland A, Sikorski J, Lapidus A, Nolan M, Glavina T. Erratum to: Complete genome sequence of Atopobium parvulum type strain (IPP 1246). Stand Genomic Sci. 2010; 2(3):361-2.
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      311. A catalog of reference genomes from the human microbiome. Science. 2010 May 21; 328(5981):994-9.
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      312. Clum A, Tindall BJ, Sikorski J, Ivanova N, Mavromatis K, Lucas S, Glavina Del Rio T, Nolan M, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Kuske C, Bruce D, Goodwin L, Ovchinikova G, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Stand Genomic Sci. 2010; 2(2):228-88.
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      313. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 2010 Jun; 7(6):455-7.
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      314. Tice H, Mayilraj S, Sims D, Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Copeland A, Cheng JF, Meincke L, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chen F. Complete genome sequence of Nakamurella multipartita type strain (Y-104). Stand Genomic Sci. 2010; 2(2):168-75.
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      315. Lail K, Sikorski J, Saunders E, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Brettin T, Detter JC, Schütze A, Rohde M, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chen F. Complete genome sequence of Spirosoma linguale type strain (1). Stand Genomic Sci. 2010; 2(2):176-85.
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      316. Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Labutti K, Pati A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Brettin T. Complete genome sequence of Kribbella flavida type strain (IFO 14399). Stand Genomic Sci. 2010; 2(2):186-93.
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      317. Wirth R, Sikorski J, Brambilla E, Misra M, Lapidus A, Copeland A, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Tapia R, Bruce D, Goodwin L, Pitluck S, Pati A, Anderson I, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Bilek Y, Hader T, Land M, Hauser L, Chang YJ, Jeffries CD, Tindall BJ, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Thermocrinis albus type strain (HI 11/12). Stand Genomic Sci. 2010; 2(2):194-202.
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      318. Ivanova N, Sikorski J, Jando M, Munk C, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Meincke L, Brettin T, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Geodermatophilus obscurus type strain (G-20). Stand Genomic Sci. 2010; 2(2):158-67.
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      319. Sikorski J, Lapidus A, Copeland A, Misra M, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Jando M, Schneider S, Bruce D, Goodwin L, Pitluck S, Liolios K, Mikhailova N, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Chertkov O, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Segniliparus rotundus type strain (CDC 1076). Stand Genomic Sci. 2010; 2(2):203-11.
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      320. Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Ivanova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Meincke L, Sims D, Brettin T, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz P. Complete genome sequence of Conexibacter woesei type strain (ID131577). Stand Genomic Sci. 2010; 2(2):212-9.
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      321. Harmon-Smith M, Celia L, Chertkov O, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Goodwin L, Pitluck S, Pati A, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Göker M, Beck B, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chen F. Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300). Stand Genomic Sci. 2010; 2(2):220-7.
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      322. Sikorski J, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Chain P, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Lang E, Spring S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Sulfurospirillum deleyianum type strain (5175). Stand Genomic Sci. 2010; 2(2):149-57.
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      323. Lykidis A, Pérez-Pantoja D, Ledger T, Mavromatis K, Anderson IJ, Ivanova NN, Hooper SD, Lapidus A, Lucas S, González B, Kyrpides NC. The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. PLoS One. 2010; 5(3):e9729.
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      324. Reeve W, O'Hara G, Chain P, Ardley J, Bräu L, Nandesena K, Tiwari R, Malfatti S, Kiss H, Lapidus A, Copeland A, Nolan M, Land M, Ivanova N, Mavromatis K, Markowitz V, Kyrpides N, Melino V, Denton M, Yates R, Howieson J. Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum. Stand Genomic Sci. 2010; 2(1):66-76.
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      325. Glavina Del Rio T, Abt B, Spring S, Lapidus A, Nolan M, Tice H, Copeland A, Cheng JF, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand Genomic Sci. 2010; 2(1):87-95.
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      326. Saunders E, Tindall BJ, Fähnrich R, Lapidus A, Copeland A, Del Rio TG, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Goodwin L, Chain P, Pitluck S, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Haloterrigena turkmenica type strain (4k). Stand Genomic Sci. 2010; 2(1):107-16.
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      327. Ivanova N, Daum C, Lang E, Abt B, Kopitz M, Saunders E, Lapidus A, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Copeland A, Cheng JF, Chen F, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Markowitz V, Eisen JA, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Haliangium ochraceum type strain (SMP-2). Stand Genomic Sci. 2010; 2(1):96-106.
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      328. Foster B, Pukall R, Abt B, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Bruce D, Goodwin L, Ivanova N, Mavromatis K, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07). Stand Genomic Sci. 2010; 2(1):1-8.
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      329. Nolan M, Sikorski J, Jando M, Lucas S, Lapidus A, Glavina Del Rio T, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Sims D, Meincke L, Brettin T, Han C, Detter JC, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Ivanova N, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Streptosporangium roseum type strain (NI 9100). Stand Genomic Sci. 2010; 2(1):29-37.
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      330. Pati A, Labutti K, Pukall R, Nolan M, Glavina Del Rio T, Tice H, Cheng JF, Lucas S, Chen F, Copeland A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Chen A, Palaniappan K, Chain P, Brettin T, Sikorski J, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Stand Genomic Sci. 2010; 2(1):49-56.
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      331. Reeve W, Chain P, O'Hara G, Ardley J, Nandesena K, Bräu L, Tiwari R, Malfatti S, Kiss H, Lapidus A, Copeland A, Nolan M, Land M, Hauser L, Chang YJ, Ivanova N, Mavromatis K, Markowitz V, Kyrpides N, Gollagher M, Yates R, Dilworth M, Howieson J. Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419. Stand Genomic Sci. 2010; 2(1):77-86.
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      332. Mavromatis K, Sikorski J, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Meincke L, Sims D, Chertkov O, Han C, Brettin T, Detter JC, Wahrenburg C, Rohde M, Pukall R, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA). Stand Genomic Sci. 2010; 2(1):9-18.
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      333. Ivanova N, Sikorski J, Jando M, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Copeland A, Cheng JF, Chen F, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Han C, Detter JC, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Gordonia bronchialis type strain (3410). Stand Genomic Sci. 2010; 2(1):19-28.
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      334. Spring S, Nolan M, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Land M, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Munk C, Kiss H, Chain P, Han C, Brettin T, Detter JC, Schüler E, Göker M, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)). Stand Genomic Sci. 2010; 2(1):38-48.
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      335. Gronow S, Welnitz S, Lapidus A, Nolan M, Ivanova N, Glavina Del Rio T, Copeland A, Chen F, Tice H, Pitluck S, Cheng JF, Saunders E, Brettin T, Han C, Detter JC, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Pati A, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Chain P, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S. Complete genome sequence of Veillonella parvula type strain (Te3). Stand Genomic Sci. 2010; 2(1):57-65.
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      336. Munk C, Lapidus A, Copeland A, Jando M, Mayilraj S, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Goodwin L, Chain P, Pitluck S, Göker M, Ovchinikova G, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21). Stand Genomic Sci. 2009; 1(3):234-41.
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      337. Nolan M, Gronow S, Lapidus A, Ivanova N, Copeland A, Lucas S, Del Rio TG, Chen F, Tice H, Pitluck S, Cheng JF, Sims D, Meincke L, Bruce D, Goodwin L, Brettin T, Han C, Detter JC, Ovchinikova G, Pati A, Mavromatis K, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spröer C, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chain P. Complete genome sequence of Streptobacillus moniliformis type strain (9901). Stand Genomic Sci. 2009; 1(3):300-7.
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      338. Clum A, Tindall BJ, Sikorski J, Ivanova N, Mavrommatis K, Lucas S, Glavina T. Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Stand Genomic Sci. 2009; 1(3):308-16.
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      339. Nolan M, Tindall BJ, Pomrenke H, Lapidus A, Copeland A, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, Han C, Bruce D, Goodwin L, Chain P, Pitluck S, Ovchinikova G, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Rhodothermus marinus type strain (R-10). Stand Genomic Sci. 2009; 1(3):283-90.
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      340. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009 Dec 24; 462(7276):1056-60.
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      341. Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN, Kyrpides NC. Estimating DNA coverage and abundance in metagenomes using a gamma approximation. Bioinformatics. 2010 Feb 1; 26(3):295-301.
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      342. Young M, Artsatbanov V, Beller HR, Chandra G, Chater KF, Dover LG, Goh EB, Kahan T, Kaprelyants AS, Kyrpides N, Lapidus A, Lowry SR, Lykidis A, Mahillon J, Markowitz V, Mavromatis K, Mukamolova GV, Oren A, Rokem JS, Smith MC, Young DI, Greenblatt CL. Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium. J Bacteriol. 2010 Feb; 192(3):841-60.
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      398. 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. Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers. OMICS. 2008 Jun; 12(2):123-7.
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      399. 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. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008 May; 26(5):541-7.
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      400. Anderson I, Rodriguez J, Susanti D, Porat I, Reich C, Ulrich LE, Elkins JG, Mavromatis K, Lykidis A, Kim E, Thompson LS, Nolan M, Land M, Copeland A, Lapidus A, Lucas S, Detter C, Zhulin IB, Olsen GJ, Whitman W, Mukhopadhyay B, Bristow J, Kyrpides N. Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J Bacteriol. 2008 Apr; 190(8):2957-65.
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      401. Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang X, Hernández M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholtz P, Leadbetter JR. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature. 2007 Nov 22; 450(7169):560-5.
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      402. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2008 Jan; 36(Database issue):D475-9.
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      403. Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 2008 Jan; 36(Database issue):D528-33.
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      404. Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 2008 Jan; 36(Database issue):D534-8.
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      405. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007; 8:209.
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      406. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 2007 Jun; 4(6):495-500.
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      407. Field D, Kyrpides N. The positive role of the ecological community in the genomic revolution. Microb Ecol. 2007 Apr; 53(3):507-11.
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      408. Lykidis A, Mavromatis K, Ivanova N, Anderson I, Land M, DiBartolo G, Martinez M, Lapidus A, Lucas S, Copeland A, Richardson P, Wilson DB, Kyrpides N. Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. J Bacteriol. 2007 Mar; 189(6):2477-86.
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      409. Markowitz VM, Kyrpides NC. Comparative genome analysis in the integrated microbial genomes (IMG) system. Methods Mol Biol. 2007; 395:35-56.
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      410. García Martín H, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol. 2006 Oct; 24(10):1263-9.
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      411. Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO, Boffelli D, Anderson IJ, Barry KW, Shapiro HJ, Szeto E, Kyrpides NC, Mussmann M, Amann R, Bergin C, Ruehland C, Rubin EM, Dubilier N. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature. 2006 Oct 26; 443(7114):950-5.
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      412. Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Lykidis A, Anderson I, Mavromatis K, Mavrommatis K, Kunin V, Garcia Martin H, Dubchak I, Hugenholtz P, Kyrpides NC. An experimental metagenome data management and analysis system. Bioinformatics. 2006 Jul 15; 22(14):e359-67.
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      413. Mavromatis K, Doyle CK, Lykidis A, Ivanova N, Francino MP, Chain P, Shin M, Malfatti S, Larimer F, Copeland A, Detter JC, Land M, Richardson PM, Yu XJ, Walker DH, McBride JW, Kyrpides NC. The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies. J Bacteriol. 2006 Jun; 188(11):4015-23.
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      414. Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D332-4.
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      415. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A, Zhao X, Dubchak I, Hugenholtz P, Anderson I, Lykidis A, Mavromatis K, Ivanova N, Kyrpides NC. The integrated microbial genomes (IMG) system. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D344-8.
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      416. Anderson I, Sorokin A, Kapatral V, Reznik G, Bhattacharya A, Mikhailova N, Burd H, Joukov V, Kaznadzey D, Walunas T. Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis. FEMS Microbiol Lett. 2005 Sep 15; 250(2):175-84.
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      417. Feil H, Feil WS, Chain P, Larimer F, DiBartolo G, Copeland A, Lykidis A, Trong S, Nolan M, Goltsman E, Thiel J, Malfatti S, Loper JE, Lapidus A, Detter JC, Land M, Richardson PM, Kyrpides NC, Ivanova N, Lindow SE. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci U S A. 2005 Aug 2; 102(31):11064-9.
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      418. Foster J, Ganatra M, Kamal I, Ware J, Makarova K, Ivanova N, Bhattacharyya A, Kapatral V, Kumar S, Posfai J, Vincze T, Ingram J, Moran L, Lapidus A, Omelchenko M, Kyrpides N, Ghedin E, Wang S, Goltsman E, Joukov V, Ostrovskaya O, Tsukerman K, Mazur M, Comb D, Koonin E, Slatko B. The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol. 2005 Apr; 3(4):e121.
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      419. Gerdes SY, Scholle MD, Campbell JW, Balázsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabási AL, Oltvai ZN, Osterman AL. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol. 2003 Oct; 185(19):5673-84.
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      420. Kapatral V, Ivanova N, Anderson I, Reznik G, Bhattacharyya A, Gardner WL, Mikhailova N, Lapidus A, Larsen N, D'Souza M, Walunas T, Haselkorn R, Overbeek R, Kyrpides N. Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586. Genome Res. 2003 Jun; 13(6A):1180-9.
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      421. Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E, Larsen N, D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature. 2003 May 1; 423(6935):87-91.
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      422. Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P, Kapatral V, Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N. The ERGO genome analysis and discovery system. Nucleic Acids Res. 2003 Jan 1; 31(1):164-71.
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      423. Bhattacharyya A, Stilwagen S, Reznik G, Feil H, Feil WS, Anderson I, Bernal A, D'Souza M, Ivanova N, Kapatral V, Larsen N, Los T, Lykidis A, Selkov E, Walunas TL, Purcell A, Edwards RA, Hawkins T, Haselkorn R, Overbeek R, Kyrpides NC, Predki PF. Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights. Genome Res. 2002 Oct; 12(10):1556-63.
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      424. Bhattacharyya A, Stilwagen S, Ivanova N, D'Souza M, Bernal A, Lykidis A, Kapatral V, Anderson I, Larsen N, Los T, Reznik G, Selkov E, Walunas TL, Feil H, Feil WS, Purcell A, Lassez JL, Hawkins TL, Haselkorn R, Overbeek R, Predki PF, Kyrpides NC. Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains. Proc Natl Acad Sci U S A. 2002 Sep 17; 99(19):12403-8.
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      425. Kapatral V, Anderson I, Ivanova N, Reznik G, Los T, Lykidis A, Bhattacharyya A, Bartman A, Gardner W, Grechkin G, Zhu L, Vasieva O, Chu L, Kogan Y, Chaga O, Goltsman E, Bernal A, Larsen N, D'Souza M, Walunas T, Pusch G, Haselkorn R, Fonstein M, Kyrpides N, Overbeek R. Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J Bacteriol. 2002 Apr; 184(7):2005-18.
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      426. DelVecchio VG, Kapatral V, Redkar RJ, Patra G, Mujer C, Los T, Ivanova N, Anderson I, Bhattacharyya A, Lykidis A, Reznik G, Jablonski L, Larsen N, D'Souza M, Bernal A, Mazur M, Goltsman E, Selkov E, Elzer PH, Hagius S, O'Callaghan D, Letesson JJ, Haselkorn R, Kyrpides N, Overbeek R. The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc Natl Acad Sci U S A. 2002 Jan 8; 99(1):443-8.
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      427. Tavernarakis N, Everett JK, Kyrpides NC, Driscoll M. Structural and functional features of the intracellular amino terminus of DEG/ENaC ion channels. Curr Biol. 2001 Mar 20; 11(6):R205-8.
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      428. Sianidis G, Karamanou S, Vrontou E, Boulias K, Repanas K, Kyrpides N, Politou AS, Economou A. Cross-talk between catalytic and regulatory elements in a DEAD motor domain is essential for SecA function. EMBO J. 2001 Mar 1; 20(5):961-70.
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      429. Bernal A, Ear U, Kyrpides N. Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res. 2001 Jan 1; 29(1):126-7.
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      430. Graham DE, Kyrpides N, Anderson IJ, Overbeek R, Whitman WB. Genome of Methanocaldococcus (Methanococcus) jannaschii. Methods Enzymol. 2001; 330:40-123.
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      431. Kyrpides NC, Ouzounis CA, Iliopoulos I, Vonstein V, Overbeek R. Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools. Nucleic Acids Res. 2000 Nov 15; 28(22):4573-6.
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      432. Overbeek R, Larsen N, Pusch GD, D'Souza M, Selkov E, Kyrpides N, Fonstein M, Maltsev N, Selkov E. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 2000 Jan 1; 28(1):123-5.
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      433. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. Protein interaction maps for complete genomes based on gene fusion events. Nature. 1999 Nov 4; 402(6757):86-90.
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      434. Tavernarakis N, Driscoll M, Kyrpides NC. The SPFH domain: implicated in regulating targeted protein turnover in stomatins and other membrane-associated proteins. Trends Biochem Sci. 1999 Nov; 24(11):425-7.
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      435. Kyrpides N, Overbeek R, Ouzounis C. Universal protein families and the functional content of the last universal common ancestor. J Mol Evol. 1999 Oct; 49(4):413-23.
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      436. Kyrpides NC. Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. Bioinformatics. 1999 Sep; 15(9):773-4.
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      437. Kyrpides NC, Olsen GJ. Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry? Trends Genet. 1999 Aug; 15(8):298-9.
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      438. Kyrpides NC, Ouzounis CA. Transcription in archaea. Proc Natl Acad Sci U S A. 1999 Jul 20; 96(15):8545-50.
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      439. Kyrpides NC, Ouzounis CA. Whole-genome sequence annotation: 'Going wrong with confidence'. Mol Microbiol. 1999 May; 32(4):886-7.
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      440. Stravopodis DJ, Kyrpides NC. Identification of protein-tyrosine phosphatases in Archaea. J Mol Evol. 1999 May; 48(5):625-7.
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      441. Kyrpides NC, Ouzounis CA. Errors in genome reviews. Science. 1998 Sep 4; 281(5382):1457.
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      442. Kyrpides NC, Woese CR. Tetratrico-peptide-repeat proteins in the archaeon Methanococcus jannaschii. Trends Biochem Sci. 1998 Jul; 23(7):245-7.
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      443. Rodriguez-Monge L, Ouzounis CA, Kyrpides NC. A ferredoxin-like domain in RNA polymerase 30/40-kDa subunits. Trends Biochem Sci. 1998 May; 23(5):169-70.
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      444. Kyrpides NC, Woese CR. Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families. Proc Natl Acad Sci U S A. 1998 Mar 31; 95(7):3726-30.
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      445. Kyrpides NC, Woese CR. Universally conserved translation initiation factors. Proc Natl Acad Sci U S A. 1998 Jan 6; 95(1):224-8.
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      446. Kyrpides NC, Ouzounis CA. Bacterial sigma 70 transcription factor DNA-binding domains in the archaeon Methanococcus jannaschii. J Mol Evol. 1997 Dec; 45(6):706-7.
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      447. Ouzounis CA, Kyrpides NC. ThiD-TenA: a gene pair fusion in eukaryotes. J Mol Evol. 1997 Dec; 45(6):708-11.
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      448. Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidman JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, Venter JC. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 1997 Nov 27; 390(6658):364-70.
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      449. Ouzounis CA, Kyrpides NC. The core histone fold: limits to functional versatility. J Mol Evol. 1996 Dec; 43(6):541-2.
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      450. Kyrpides NC, Woese CR, Ouzounis CA. KOW: a novel motif linking a bacterial transcription factor with ribosomal proteins. Trends Biochem Sci. 1996 Nov; 21(11):425-6.
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      451. Ouzounis C, Kyrpides N. The emergence of major cellular processes in evolution. FEBS Lett. 1996 Jul 22; 390(2):119-23.
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      452. Ouzounis CA, Kyrpides NC. Parallel origins of the nucleosome core and eukaryotic transcription from Archaea. J Mol Evol. 1996 Feb; 42(2):234-9.
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      453. Kyrpides NC, Olsen GJ, Klenk HP, White O, Woese CR. Methanococcus jannaschii genome: revisited. Microb Comp Genomics. 1996; 1(4):329-38.
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      454. Kyrpides N, Tavernarakis N, Papamatheakis J, Thireos G. A transient GCN4 mRNA destabilization follows GCN4 translational derepression. J Biol Chem. 1995 Jul 21; 270(29):17317-20.
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      455. Kyrpides NC, Ouzounis CA. Nucleic acid-binding metabolic enzymes: living fossils of stereochemical interactions? J Mol Evol. 1995 Jun; 40(6):564-9.
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      456. Kyrpides NC, Ouzounis CA. The eubacterial transcriptional activator Lrp is present in the archaeon Pyrococcus furiosus. Trends Biochem Sci. 1995 Apr; 20(4):140-1.
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      457. Ouzonis C, Kyrpides N, Sander C. Novel protein families in archaean genomes. Nucleic Acids Res. 1995 Feb 25; 23(4):565-70.
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      458. Ouzounis CA, Kyrpides NC. On the evolution of arginases and related enzymes. J Mol Evol. 1994 Jul; 39(1):101-4.
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      459. Ouzounis CA, Kyrpides NC. Reverse interpretation: a hypothetical selection mechanism for adaptive mutagenesis based on autoregulated mRNA stability. J Theor Biol. 1994 Apr 21; 167(4):373-9.
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      460. Kyrpides NC, Ouzounis CA. Mechanisms of specificity in mRNA degradation: autoregulation and cognate interactions. J Theor Biol. 1993 Aug 7; 163(3):373-92.
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      461. Vassiliadis S, Stravopodis D, Kyrpides N, Grigoriou M, Papamatheakis J. One and two-level regulation patterns affecting NF-kappa B mRNA and nuclear NF-kappa B activity after treatment with TNF-alpha, IFN-gamma and IL-4. Eur Cytokine Netw. 1993 Jan-Feb; 4(1):25-30.
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      462. Vassiliadis S, Kyrpides N, Stravopodis D, Grigoriou M, Athanassakis I, Papamatheakis J. Investigation of intracellular signals generated by gamma-interferon and IL-4 leading to the induction of class II antigen expression. Mediators Inflamm. 1993; 2(5):343-8.
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      463. Vassiliadis S, Kyrpides N, Papamatheakis J. The role of IL-4 in human myeloid leukemia: stimulation of RNA synthesis and transduction of differentiation signals through an IL-4 receptor leads to functional and HLA positive HL-60 cells. Leuk Lymphoma. 1992 Jun; 7(3):235-42.
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      464. Vassiliadis S, Guilbert L, Kyrpides N, Papamatheakis J. Different molecular mechanisms lead to same endpoints with different function: TNF-alpha induces non-functional CSF-1 receptors on HL-60 cells in contrast to interferon-gamma. J Recept Res. 1992; 12(1):59-70.
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      465. Scouras ZG, Kyrpides N, Mavragani-Tsipidou P. The prominent role of ectopic pairing in the toroidal conformation of Drosophila polytene chromosome bands. Cytobios. 1992; 69(276):47-54.
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      466. Mavragani-Tsipidou P, Kyrpides N, Scouras ZG. Evolutionary implications of duplications and Balbiani rings in Drosophila. A study of Drosophila serrata. Genome. 1990 Aug; 33(4):478-85.
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