PLoS ONE

4(6):e5797

Genomic characterization of methanomicrobiales reveals three classes of methanogens.

Anderson I, Ulrich LE, Lupa B, Susanti D, Porat I, Hooper SD, Lykidis A, Sieprawska-Lupa M, Dharmarajan L, Goltsman E, Lapidus A, Saunders E, Han C, Land M, Lucas S, Mukhopadhyay B, Whitman WB, Woese C, Bristow J, Kyrpides N.

Genome Biol.

10(5):R51

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens.

Silby MW, Cerdeno-Tarraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey SA, Knight CG, Malone JG, Robinson Z, Spiers AJ, Harris S, Challis GL, Yaxley AM, Harris D, Seeger K, Murphy L, Rutter S, Squares R, Quail MA, Saunders E, Mavromatis K, Brettin TS, Bentley SD, Hothersall J, Stephens E, Thomas CM, Parkhill J, Levy SB, Rainey PB, Thomson NR.

ISME J.

2009 Apr 30

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation.

Allen MA, Lauro FM, Williams TJ, Burg D, Siddiqui KS, De Francisci D, Chong KW, Pilak O, Chew HH, De Maere MZ, Ting L, Katrib M, Ng C, Sowers KR, Galperin MY, Anderson IJ, Ivanova N, Dalin E, Martinez M, Lapidus A, Hauser L, Land M, Thomas T, Cavicchioli R

Genome Biology

10(4):R45

Microbial co-habitation and lateral gene transfer: what transposases can tell us

Hooper SD, Mavromatis K, Kyrpides NC.

Bioinformatics

25(7):977-8

OnTheFly: a tool for automated document-based text annotation, data linking and network generation.

Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R.

BMC Genomics

10(1):145

The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota.

Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin IB, Whitman WB, Mukhopadhyay B, Woese C, Bristow J, Kyrpides N.

Environ Microbiol.

11(3):551-3

A changing of the guard.

Hugenholtz P, Kyrpides NC.

Nucleic Acids Res. 37(7):2096-104

Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach.

Hooper SD, Anderson IJ, Pati A, Dalevi D, Mavromatis K, Kyrpides NC.

 PLoS ONE 4(1): e4192

Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii.

Mavromatis K, Ivanova N, Anderson I, Lykidis A, Hooper SD, Sun H, Kunin V, Lapidus A, Hugenholtz P, Patel B, Kyrpides NC.

 Microbiol Mol Biol Rev. 72(4): 557-78

A bioinformatician's guide to metagenomics.

Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P.

BMC Genomics

9(1):547

Rodrigues DF, Ivanova N, He Z, Huebner M, Zhou J, Tiedje JM.

Genome Biol. 9(11):R158

Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall M, Lykidis A, Mavrommatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH Jr, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO.

Res Microbiol. 159(9-10):609-27

Tsiamis G, Katsaveli K, Ntougias S, Kyrpides N, Andersen G, Piceno Y, Bourtzis K.

Nat Biotechnol.

26(9):1029-34

Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E, Salamov A, Grigoriev IV, Suciu D, Levine SR, Markowitz VM, Rigoutsos I, Tringe SG, Bruce DC, Richardson PM, Lidstrom ME, Chistoserdova L.

Bioinformatics

24(16):i7-13

Dalevi D, Ivanova NN, Mavromatis K, Hooper SD, Szeto E, Hugenholtz P, Kyrpides NC, Markowitz VM.

PLoS ONE. 3(7):e2607

A molecular study of microbe transfer between distant environments.

Hooper SD, Raes J, Foerstner KU, Harrington ED, Dalevi D, Bork P.

OMICS

12(2):157-60

Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O.

OMICS

12(2):109-13

Field D, Garrity GM, Sansone SA, Sterk P, Gray T, Kyrpides N, Hirschman L, Glöckner FO, Kottmann R, Angiuoli S, White O, Dawyndt P, Thomson N, Gil IS, Morrison N, Tatusova T, Mizrachi I, Vaughan R, Cochrane G, Kagan L, Murphy S, Schriml L; and the Genomic Standards Consortium.

OMICS

12(2):101-8

Field D, Glöckner FO, Garrity GM, Gray T, Sterk P, Cochrane G, Vaughan R, Kolker E, Kottmann R, Kyrpides N, Angiuoli S, Dawyndt P, Guralnick R, Goldstein P, Hall N, Hirschman L, Kravitz S, Lister AL, Markowitz V, Thomson N, Whetzel T.

PNAS

105(23):8102-7

Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter KO.

Mol Syst Biol.

 4:198

Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P.

OMICS

12(2):123-7

Brabant, BV., Gray, T., Verslyppe, Β., Kyrpides, N.C., Dietrich, K., Glockner, F.O., Cole, J., Farris, R., Schriml, L., De Vos, P., De Baets, B., Field, T., and Dawyndt, P.

Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Allen, M.J., Angiuolii, SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C et al.

OMICS

12(2):137-41

Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation.

Angiuoli , S.V., Gussman, G., Klimke, W., Cochrane, G., Field, D., Garrity, G., Kodira, C.D., Kyrpides, N.C., Madupu, R., Markowitz, V., Tatusova, T., Thomson, N., White, O.

OMICS

12(2):129-36

Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata.

Hirschman, L., Clark, C., Bretonnel Cohen, K., Mardis, S., Luciano, J., Kottmann, R., Cole, J., Markowitz, V., Kyrpides, N., Field. D.

Genome Res.

18(2):293-7

A bacterial metapopulation adapts locally to phage predation despite global dispersal.

Kunin V, He S, Warnecke F, Peterson SB, Garcia Martin H, Haynes M, Ivanova N, Blackall LL, Breitbart M, Rohwer F, McMahon KD, Hugenholtz P.

J Bacteriology 190(8), 2957-65

Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction.

Anderson, I., Rodriguez, J., Susanti, D., Porat, I., Recih, C., Ulrich, E., 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, G., Whitman, W., Mukhopadhyay, B., Bristow, J. and Kyrpides, N.C.

Nucleic Acids Res.

36, D534-8

IMG/M: a data management and analysis system for metagenomes.

Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC.

Nucleic Acids Res.

36, D528-33

The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.

Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC.

Nucleic Acids Res.

36, D475-9

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.

Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC.

Nature

450(7169):560-5

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.

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.

Methods Mol Biol.

395:35-56

Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System.

Markowitz, VM., Kyrpides NC.

PLoS ONE

2(9):e955

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Lapidus A, Copeland A, Kim E, Land M, Mavromatis K, Pitluck S, Richardson PM, Detter C, Brettin T, Saunders E, Lai B, Ravel B, Kemner KM, Wolf YI, Sorokin A, Gerasimova AV, Gelfand MS, Fredrickson JK, Koonin EV, Daly MJ.

Febs Lett.

581(24):4639-4644

Localization and regulation of mouse pantothenate kinase 2.

Leonardi R, Zhang YM, Lykidis A, Rock CO, Jackowski S.

Proc Natl Acad Sci USA

104(29):11889-94.

Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth.

Marcy Y, Ouverney C, Bik EM, Losekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz, P Relman DA, Quake SR.

BMC Bioinformatics

8(1): 209

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.

Bland, C, Sabree, F., Ramsey, T.L., Lowe, M., Brown, K. Kyrpides, N.C., Hugenholtz, P.

Prog Lipid Res.

46(304): 171-99

Comparative genomics and evolution of eukaryotic phospholipid biosynthesis.

Lykidis, A.

Nature Methods

 4(6):495-500

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.

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, and Kyrpides, NC

Microbial Ecology

 53(3):507-11

The Positive Role of the Ecological Community in the Genomic Revolution.

Field, D and Kyrpides N

Bioinformatics

 23(6):764-6

TreeQ-VISTA: An Interactive Tree Visualization Tool with Functional Annotation Query Capabilities.

Gu S, Anderson I, Kunin V, Cipriano M, Minovitsky S, Weber G, Amenta N, Hamann B, and Dubchak I

J Bacteriology

 189(6):2477-86

Genome Sequence and Analysis of the Soil Cellulolytic Actinomycete Thermobifida fusca YX.

Lykidis, A, Mavrommatis, K, Ivanova, N, Anderson IJ, Land, M, DiBartolo, G, Martinez, M, Lapidus, A., Lucas, S, Copeland, A, Richardson, P, Wilson, DB and Kyrpides, NC

J Bacteriology

188(22):7922-31.

The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes.

Maeder DL, Anderson I, Brettin TS, Bruce DC, Gilna P, Han CS, Lapidus A, Metcalf WW, Saunders E, Tapia R, Sowers KR.

Nature

443(7114):950-5

Symbiosis insights through metagenomic analysis of a microbial consortium.

Woyke T, Teeling H, Ivanova NN, Hunteman 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.

Nature Biotechnology.

24(10):1263-9

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities.

Martin HG, 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

Bioinformatics

 22(14):e359-67.

An experimental metagenome data management and analysis system.

Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Lykidis A, Anderson I, Mavrommatis K, Kunin V, Garcia Martin H, Dubchak I, Hugenholtz P, Kyrpides NC.

J Bacteriology

 188(11):4015-23.

The Genome of the Obligately Intracellular Bacterium Ehrlichia canis Reveals Themes of Complex Membrane Structure and Immune Evasion Strategies.

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

J Bacteriology

 188(4):1373-80

Disruption of the operon encoding Ehb hydrogenase limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis.

Porat I, Kim W, Hendrickson EL, Xia Q, Zhang Y, Wang T, Taub F, Moore BC, Anderson IJ, Hackett M, Leigh JA, Whitman WB.

Nucleic Acids Res.  34: D344-8

The Integrated Microbial Genomes (IMG) System.

Markowitz V, 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.

Nucleic Acids Res. 34:D332-4

The Genomes On Line Database (GOLD) v.2: a monitor of Genome Projects world-wide.

Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC.

FEMS Microbiol Letters

250(2):175-84.

Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis.

Anderson I, Sorokin A, Kapatral V, Reznik G, Bhattacharya A, Mikhailova N, Burd H, Joukov V, Kaznadzey D, Walunas T, Markd'souza, Larsen N, Pusch G, Liolios K, Grechkin Y, Lapidus A, Goltsman E, Chu L, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N, Ivanova N.

Proc Natl Acad Sci U S A

102(31):11064-9.

Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000.

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.

PLoS Biology

 3(4):e121.

The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode.

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.

J Biol Chemistry 280(35):30856-63.

Peptidoglycan N-Acetylglucosamine Deacetylases from Bacillus cereus, Highly Conserved Proteins in Bacillus anthracis.

Psylinakis E, Boneca IG, Mavromatis K, Deli A, Hayhurst E, Foster SJ, Varum KM, Bouriotis V.

Proceedings of the 31st International Conference on Very Large Data Bases

The Integrated Microbial Genomes (IMG) System, A Case Study in Biological Data Management.

Markowitz, VM, Korzeniewski, F, Palaniappan, K, Szeto, E, Ivanova, N, and Kyrpides, N

Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus.

Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch GD, Fonstein M, Overbeek R, Kyprides N, Purnelle B, Prozzi D, Ngui K, Masuy D, Hancy F, Burteau S, Boutry M, Delcour J, Goffeau A, Hols P.