Genome Biology Program Publications

 


 
 2012

3.

Nucleic Acids Res.

40(1):D115-22

IMG: the integrated microbial genomes database and comparative analysis system.

Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC.

2.

Nucleic Acids Res.

40(1):D571-9

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata.

Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC.

1.

Nucleic Acids Res.

40(1):D123-9

IMG/M: the integrated metagenome data management and comparative analysis system.

Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A, Huntemann M, Liolios K, Pagani I, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC.

 2011

85.

SIGS 5(3):

SOP for pathway inference in Integrated Microbial Genomes (IMG).

Anderson, I.J., Chen, A., Markowitz, V., Kyrpides, N.C. and Ivanova, N.

84.

SIGS

5(3):

Complete genome sequence of Hirschia baltica type strain (IFAM 1418T).

Chertkov, O., Brown, PJB., Kysela, DT., de Pedro, MA., Lucas, S., Copeland, A., Lapidus, A., Glavina Del Rio, T., Tice, H., Bruce, D., Goodwin, L., Pitluck, S., Detter, J.C., Han, C., Larimer, F., Land, M., Hauser, L., Kyrpides, N.C., Ivanova, N., Ovchinnikova, G., Tindall, BJ., Göker, M., Klenk, H-P., Brun, YV.

83.

SIGS

5(3):

Complete genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria.

Grote, J., Altunkaya, A., Bayindirli, C., Bergauer, K., Carpintero de Moraes, P., Chen, H., D’Ambrosio, L., Edwards, B., -Gómez, B-F., Hamisi, M., Logares, R., Nguyen, D., Rii, S., Saeck, E., Schutte, C., Widner, B., Church, M.J., Steward, G.F.,  Karl, D.M., DeLong, E.F., Eppley, J.M., Schuster, S., Kyrpides, N.C., and Rappé, M.S.

82.

SIGS

5(2):243-47

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011.

Gilbert, J.A., Bailey, M., Field, D., Fierer, N., Fuhrman, J., Hu, B., Jansson, J., Knight, R., Kowalchuk, G., Kyrpides, N., Meyer, F., Steven, R.

81.

SIGS

5(2):248-53

ClaMS: A Classifier for Metagenomic Sequences.

Pati A, Heath LS, Kyrpides NC, Ivanova N.

80.

SIGS

5(1):144-53

Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1.

Kallimanis A, Karabika E, Mavromatis K, Lapidus A, Labutti KM, Liolios K, Ivanova N, Goodwin L, Woyke T, Velentzas AD, Perisynakis A, Ouzounis CC, Kyrpides NC, Koukkou AI, Drainas C.

79.

SIGS

5(1):112-20

Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010.

Klenk HP, Lapidus A, Chertkov O, Copeland A, Del Rio TG, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Han C, Bruce D, Goodwin L, Pitluck S, Pati A, Ivanova N, Mavromatis K, Daum C, Chen A, Palaniappan K, Chang YJ, Land M, Hauser L, Jeffries CD, Detter JC, Rohde M, Abt B, Pukall R, Göker M, Bristow J, Markowitz V, Hugenholtz P, Eisen JA.

78.

SIGS

5(1):112-20

Complete genome sequence of Tolumonas auensis type strain (TA 4).

Chertkov O, Copeland A, Lucas S, Lapidus A, Berry KW, Detter JC, Del Rio TG, Hammon N, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin L, Han C, Tapia R, Saunders E, Schmutz J, Brettin T, Larimer F, Land M, Hauser L, Spring S, Rohde M, Kyrpides NC, Ivanova N, Göker M, Beller HR, Klenk HP, Woyke T.

77.

SIGS

5(1):97-111

Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21)

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.

76.

SIGS

5(1):86-96

Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10).

Lapidus A, Chertkov O, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Abt B, Spring S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T.

75.

SIGS

5(1):69-85

Complete genome sequence of "Enterobacter lignolyticus" SCF1

Deangelis KM, D'Haeseleer P, Chivian D, Fortney JL, Khudyakov J, Simmons B, Woo H, Arkin AP, Davenport KW, Goodwin L, Chen A, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, Hazen TC.

74.

SIGS

5(1):50-60

Complete genome sequence of Ferroglobus placidus AEDII12DO

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.

73.

SIGS

5(1):41-9

Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20).

Pati A, Gronow S, Lu M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Mavromatis K, Mikhailova N, Huntemann M, Chen A, Palaniappan K, Land M, Hauser L, Detter JC, Brambilla EM, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N.

72.

SIGS

5(1):30-40

Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113).

Liolios K, Sikorski J, Lu M, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Kotsyurbenko O, Rohde M, Tindall BJ, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.

71.

SIGS

5(1):21-9

Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).

Woyke T, Chertkov O, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Mwirichia R, Sikorski J, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC

70.

SIGS

5(1):12-20

Complete genome sequence of Staphylothermus hellenicus P8.

Anderson I, Wirth R, Lucas S, Copeland A, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Davenport K, Detter JC, Han C, Tapia R, Land M, Hauser L, Pati A, Mikhailova N, Woyke T, Klenk HP, Kyrpides N, Ivanova N.

69.

J. Bacteriology Epub

Genome Sequence of "Candidatus Frankia datiscae" Dg1, the Uncultured Microsymbiont from Nitrogen-Fixing Root Nodules of the Dicot Datisca glomerata.

Persson T, Benson DR, Normand P, Vanden Heuvel B, Pujic P, Chertkov O, Teshima H, Bruce DC, Detter C, Tapia R, Han S, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Ivanova N, Pati A, Land ML, Pawlowski K, Berry AM.

68.

J. Bacteriology 193(24):7001-2

Complete Genome Sequence of the Aerobic Marine Methanotroph Methylomonas methanica MC09.

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.

67.

Appl Environ Microbiol.

Epub

Heterologous expression and characterization of two 1-hydroxy-2naphthoic acid dioxygenases from Arthrobacter phenanthrenivorans

Vandera E, Kavakiotis K, Kallimanis A, Kyrpides NC, Drainas C, Koukkou AI.

66.

ISME J.

Epub

Individual genome assembly from complex community short-read metagenomic datasets.

Luo C, Tsementzi D, Kyrpides NC, Konstantinidis KT.

65.

J. Bacteriology

193(19):5566-7

 

Genome sequence of Kosmotoga olearia strain TBF 19.5.1, a thermophilic bacterium with a wide growth temperature range, isolated from the Troll B oil platform in the North Sea.

Swithers KS, DiPippo JL, Bruce DC, Detter C, Tapia R, Han S, Goodwin LA, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Mikhailova N, Land ML, Nesbř CL, Gogarten JP, Noll KM.

64.

PLoS ONE

6(10):e24222

The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota.

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

63.

Appl Environ Microbiol.

77(22):8052-61

Engineering E. coli for biodiesel production utilizing a bacterial fatty acid methyltransferase.

Nawabi, P., Bauer, S., Kyrpides, N., and Lykidis, A.

62.

J. Bacteriology

193(19):5574-5

Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7.

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.

61.

SIGS

4(3): 393-401

Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2T).

Goker, M., Teshima, H., Lapidus, A., Nolan, M., Lucas, S., Hammon, N.,  Deshpande, S., Cheng, J-F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Huntemann, M., Liolios, K., Ivanova, N., Pagani, I.,  Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Brambilla, E-M., Rohde, M., Spring, S., Detter, J.C., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

60.

SIGS

4(3): 381-392

Complete genome sequence of Pyrolobus fumarii type strain (1AT).

Anderson, I., Göker, M., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J-F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Huntemann, M., Liolios, K., Ivanova, N., Pagani, I., Mavromatis, K., Ovchinikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Brambilla, E-M., Huber, H., Yasawong, M., Rohde, M., Spring, S., Abt, B., Sikorski, J., Wirth, R., Detter, J.C., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Lapidus, A.

59.

SIGS

4(3): 371-380

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT).

Han, C., Mwirichia, R., Chertkov, O., Held, B., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J-F., Tapia, R., Goodwin, L., Pitluck, S., Huntemann, M., Liolios, K., Ivanova, N., Pagani, I., Mavromatis, K., Ovchinikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Brambilla, E-M., Rohde, M., Spring, S., Sikorski, J., Göker, M., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Detter, J.C.

58.

SIGS

4(3): 361-370

Complete genome sequence of Treponema succinifaciens type strain (6091T).

Han, C., Gronow, S., Teshima, H., Lapidus, A., Nolan, N., Lucas, S., Hammon, N., Deshpande, S., Cheng, J-F., Zeytun, A., Tapia, R., Goodwin, L., 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, E-M., Rohde, M., Göker, M., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Detter, J.C.

57.

SIGS

4(3): 352-360

Complete genome sequence of Haliscomenobacter hydrossis type strain (OT).

Daligault, H., Lapidus, A., Zeytun, A., Nolan, M., Lucas, S., Glavina Del Rio, T., Tice, H., Cheng, J-F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Mavromatis, K., Mikhailova, N., Natalia Mikhailova1, Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Brambilla, E-M., Rohde, M., Verbarg, S., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Woyke, T.

56.

SIGS

4(3): 342-351

Complete genome sequence of Tsukamurella paurometabola type strain (no. 33T).

Munk, C., Lapidus, A., Lucas, S., Nolan, M., Tice, H., Cheng, J-F., Glavina Del Rio, T., Goodwin, L., Pitluck, S., Liolios, K., Huntemann, M., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Tapia, R., Han, C., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Brettin, T., Yasawong, M., Brambilla, E-M., Rohde, M., Sikorski, J., Göker, M., Detter, J-C., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C. and Klenk, H-P.

55.

SIGS

4(3): 331-341

Complete genome sequence of Mahella australiensis type strain (50-1 BONT).

Sikorski, J., Teshima, H., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J-F., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Huntemann, M., Mavromatis, K., Ovchinikova, G., Pati, A., Tapia, R., Han, C., Goodwin, L., Chen, A., Palaniappan, K., Land, M., Hauser, L., Ngatchou-Djao, O.D., Rohde, M., Pukall, R., Spring, S., Abt, B., Göker, M., Detter, J.C., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P. and Lapidus, A.

54.

SIGS

4(3): 322-330

Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1T).

Anderson, I., Sikorski, J., Zeytun, A., Nolan, M., Lapidus, A., Lucas, S., Hammon, N., Deshpande, S., Cheng, J-F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Huntemann, M., Mavromatis, M., Ovchinikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Brambilla, E-M., Ngatchou-Djao, O.D., Rohde, M., Tindall, B.J., Göker, M., Detter, J.C., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Klenk, H-P. and Kyrpides, N.C.

53.

SIGS

4(3): 312-321

Complete genome sequence of Halanaerobium praevalens type strain (GSLT).

Ivanova, N., Sikorski, J., Chertkov, O., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J-F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Huntemann, M., Liolios, K., Pagani, I., Mavromatis, K., Ovchinikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Brambilla, E.M., Kannan, K.P., Rohde, M., Tindall, B.J., Göker, M., Detter, J.C., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Lapidus, A.

52.

SIGS

4(3): 303-311

 

Complete genome sequence of Hippea maritima type strain (MH2T)

Huntemann, M., Lu, M., Nolan, M., Lapidus, A., Lucas, S., Hammon, N., Deshpande, S., Cheng, J-F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Ovchinikova, G., Pati, A., Chen, A., Palaniappan, K. Miriam Land, M., Hauser, L., Jeffries, C.D.,  Detter, J.C., Brambilla, E., Rohde, M., Spring, S., Göker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P. and Mavromatis, K.

51.

SIGS

4(3): 293-302

 

Complete genome sequence of Rhodospirillum rubrum type strain (S1T).

Munk, C., Copeland, A., Lucas, S., Lapidus, A., Glavina Del Rio, T., Berry, K., Detter, J.C., Hammon, N., Israni, S., Pitluck, S., Brettin, T., Bruce, D., Han, C., Tapia, R., Gilna, P., Schmutz, J., Larimer, F., Land, M., Kyrpides, N.C., Mavromatis, K., Richardson, P., Rohde, M., Göker, M., Klenk, H-P., Zhang, Y., Roberts, G.P., Reslewic, S., Schwartz, D.C.

50.

J. Bacteriology

193(17):4549-50

Genome sequence of 1,4-dioxane degrading Pseudonocardia dioxanivorans strain CB1190.

Sales CM, Mahendra S, Grostern A, Parales RE, Goodwin L, Woyke T, Nolan M, Lapidus A, Chertkov O, Ovchinnikova G, Szcyrba A, Alvarez-Cohen L.

49.

J. Bacteriology

193(17):4545-6

Complete Genome Sequences of Krokinobacter sp. 4H-3-7-5 and Lacinutrix sp. 5H-3-7-4, polysaccharide-degrading members of the family Flavobacteriaceae.

Klippel B, Lochner A, Bruce DC, Davenport KW, Detter C, Goodwin LA, Han J, Han S, Hauser L, Land ML, Nolan M, Ovchinnikova G, Pennacchio L, Pitluck S, Tapia R, Woyke T, Wiebusch S, Basner A, Abe F, Horikoshi K, Keller M, Antranikian G.

48.

J. Bacteriology

193(22):6418-9

Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96.

Svenning MM, Hestnes AG, Wartiainen I, Stein LY, Klotz MG, Kalyuzhnaya MG, Spang A, Bringel F, Vuilleumier S, Lajus A, Médigue C, Bruce DC, Cheng JF, Goodwin L, Ivanova N, Han J, Han CS, Hauser L, Held B, Land ML, Lapidus A, Lucas S, Nolan M, Pitluck S, Woyke T.

47.

J. Bacteriology

193(18):5049-5

Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype ATCC 29192.

Kouvelis VN, Davenport KW, Brettin TS, Bruce D, Detter C, Han C, Nolan M, Tapia R, Damoulaki A, Kyrpides NC, Typas MA, Pappas KM.

46.

J. Bacteriology

193(18):5051-2

Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype ATCC 10988.

Pappas KM, Kouvelis VN, Saunders E, Brettin TS, Bruce D, Detter C, Balakireva M, Han C, Savvakis G, Kyrpides NC, Typas MA.

45.

J. Bacteriology

193(17):4547-8

Complete genome sequence of the marine, cellulose and xylan degrading bacterium Glaciecola sp. 4H-3-7+YE-5.

Klippel B, Lochner A, Bruce DC, Davenport KW, Detter C, Goodwin LA, Han J, Han S, Land ML, Mikhailova N, Nolan M, Pennacchio L, Pitluck S, Tapia R, Woyke T, Wiebusch S, Basner A, Abe F, Horikoshi K, Keller M, Antranikian G.

44.

BMC Genomics

12(1):334

Complete Genome Sequence of the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aurantiacus.

Tang KH, Barry K, Chertkov O, Dalin E, Han CS, Hauser LJ, Honchak BM, Karbach LE, Land ML, Lapidus A, Larimer FW, Mikhailova N, Pitluck S, Pierson BK, Blankenship RE.

43.

PLoS Biology

9(6):e1001088

The genomic standards consortium.

Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mizrachi I, Klenk HP, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone SA, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J.

42.

SIGS

4(2): 286-92

Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets.

Morrison N, Hancock D, Hirschman L, Dawyndt P, Verslyppe B, Kyrpides N, Kottmann R, Yilmaz P, Glöckner FO, Grethe J, Booth T, Sterk P, Nenadic G, Field D.

41.

SIGS

4(2): 252-56

Meeting report of the RNA Ontology Consortium January 8-9, 2011.

Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, Laederach A.

40.

SIGS

4(2): 233-43

Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139).

Land M, Held B, Gronow S, Abt B, Lucas S, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Hauser L, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A.

39.

SIGS

4(2): 221-32

Complete genome sequence of Cellulophaga lytica type strain (LIM-21).

Pati A, Abt B, Teshima H, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Mavromatis K, Ovchinikova G, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Kannan KP, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N.

38.

SIGS

4(2): 210-20

Complete genome sequence of Oceanithermus profundus type strain (506).

Pati A, Zhang X, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Hauser L, Jeffries CD, Brambilla EM, Röhl A, Mwirichia R, Rohde M, Tindall BJ, Sikorski J, Wirth R, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M.

37.

SIGS

4(2): 200-09

Complete genome sequence of Odoribacter splanchnicus type strain (1651/6).

Göker M, Gronow S, Zeytun A, Nolan M, Lucas S, Lapidus A, Hammon N, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brambilla EM, Rohde M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Eisen JA, Kyrpides NC, Klenk HP.

36.

SIGS

4(2): 191-99

Complete genome sequence of Bacteroides salanitronis type strain (BL78).

Gronow S, Held B, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Eisen JA.

35.

SIGS

4(2): 191-99

Complete genome sequence of Bacteroides salanitronis type strain (BL78).

Gronow S, Held B, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Eisen JA.

34.

SIGS

4(2): 173-82

Complete genome sequence of Desulfurococcus mucosus type strain (O7/1).

Wirth R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ioanna P, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Bilek Y, Hader T, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.

33.

SIGS

4(2): 154-62

Complete genome sequence of Marivirga tractuosa type strain (H-43).

Pagani I, Chertkov O, Lapidus A, Lucas S, Del Rio TG, Tice H, Copeland A, Cheng JF, Nolan M, Saunders E, Pitluck S, Held B, Goodwin L, Liolios K, Ovchinikova G, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Han C, Tapia R, Ngatchou-Djao OD, Rohde M, Göker M, Spring S, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.

32.

SIGS

4(2): 144-53

Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845).

Mavromatis K, Lu M, Misra M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Göker M, Gronow S, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.

31.

SIGS

4(2): 131-43

Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6).

Zeytun A, Sikorski J, Nolan M, Lapidus A, Lucas S, Han J, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Ngatchou-Djao OD, Land M, Hauser L, Jeffries CD, Han C, Detter JC, Ubler S, Rohde M, Tindall BJ, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.

30.

SIGS

4(2): 131-40

Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6).

Zeytun A, Sikorski J, Nolan M, Lapidus A, Lucas S, Han J, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Ngatchou-Djao OD, Land M, Hauser L, Jeffries CD, Han C, Detter JC, Ubler S, Rohde M, Tindall BJ, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.

29.

SIGS

4(2): 123-30

Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3).

Kallimanis A, Labutti KM, Lapidus A, Clum A, Lykidis A, Mavromatis K, Pagani I, Liolios K, Ivanova N, Goodwin L, Pitluck S, Chen A, Palaniappan K, Markowitz V, Bristow J, Velentzas AD, Perisynakis A, Ouzounis CC, Kyrpides NC, Koukkou AI, Drainas C.

28.

J Bacteriology

193(15):3757-64

Genomes of three methylotrophs from a single niche uncover genetic and metabolic divergence of the methylophilaceae.

Lapidus A, Clum A, Labutti K, Kaluzhnaya MG, Lim S, Beck DA, Glavina Del Rio T, Nolan M, Mavromatis K, Huntemann M, Lucas S, Lidstrom ME, Ivanova N, Chistoserdova L.

27.

BMC Genomics

12(1):235

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti.

Galardini M, Mengoni A, Brilli M, Pini F, Fioravanti A, Lucas S, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Land M, Hauser L, Woike T, Mikhailova N, Ivanova N, Daligault H, Bruce D, Detter C, Tapia R, Han C, Teshima H, Mocali S, Bazzicalupo M, Biondi EG.

26.

J Bacteriology

193(15):4023-4

Complete Genome Sequence of the Anaerobic Halophilic Alkalithermophile Natranaerobius thermophilus JW/NM-WN-LFT.

Zhao B, Mesbah NM, Dalin E, Goodwin L, Nolan M, Pitluck S, Chertkov O, Brettin TS, Han J, Larimer FW, Land ML, Hauser L, Kyrpides N, Wiegel J.

25.

PLoS ONE

6(5):e20237

Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes.

Anderson I, Scheuner C, Göker M, Mavromatis K, Hooper SD, Porat I, Klenk HP, Ivanova N, Kyrpides N.

24.

PLoS ONE

6(4):e18814

The Complete Genome Sequence of Fibrobacter succinogenes S85 Reveals a Cellulolytic and Metabolic Specialist.

Suen G, Weimer PJ, Stevenson DM, Aylward FO, Boyum J, Deneke J, Drinkwater C, Ivanova NN, Mikhailova N, Chertkov O, Goodwin LA, Currie CR, Mead D, Brumm PJ.

23.

Nature Biotechnology 29(5):415-420

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, Desantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, Gil IS, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spor A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO.

22.

J Bacteriology

193(13):3399-400

Genome sequence of the ethene- and vinyl chloride-oxidizing actinomycete Nocardioides sp. strain JS614.

Coleman NV, Wilson NL, Barry K, Brettin TS, Bruce DC, Copeland A, Dalin E, Detter JC, Glavina Del Rio T, Goodwin LA, Hammon NM, Han S, Hauser LJ, Israni S, Kim E, Kyrpides N, Land ML, Lapidus A, Larimer FW, Lucas S, Pitluck S, Richardson P, Schmutz J, Tapia R, Thompson S, Tice HN, Spain JC, Gossett JG, Mattes TE.

21.

SIGS

4(1): 100-110

Complete genome sequence of Desulfobulbus propionicus type strain (1pr3T).

Pagani I, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Chertkov O, Davenport K, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Kannan KP, Djao OD, Rohde M, Pukall R, Spring S, Göker M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.

20.

SIGS

4(1): 91-99

Complete genome sequence of Truepera radiovictrix type strain (RQ-24).

Ivanova N, Rohde C, Munk C, Nolan M, Lucas S, Del Rio TG, Tice H, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A

19.

SIGS

4(1): 81-90

Complete genome sequence of Weeksella virosa type strain (9751T).

Lang E, Teshima H, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Kopitz M, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC

18.

SIGS

4(1): 72-80

Complete genome sequence of Cellulophaga algicola type strain (IC166T).

Abt B, Lu M, Misra M, Han C, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Tindall BJ, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A.

17.

SIGS

4(1): 63-71

Complete genome sequence of Isosphaera pallida type strain (IS1BT).

Göker M, Cleland D, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Beck B, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.

16.

SIGS

4(1): 54-62

Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1T).

Pitluck S, Sikorski J, Zeytun A, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Djao OD, Rohde M, Spring S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M.

15.

SIGS

4(1): 45-53

Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T).

Pati A, Gronow S, Zeytun A, Lapidus A, Nolan M, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S.

14.

SIGS

4(1): 36-44

Complete genome sequence of Paludibacter propionicigenes type strain (WB4T)

Gronow S, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP

13.

SIGS

4(1): 23-35

Complete genome sequence of Thioalkalivibrio “sulfidophilus” HL-EbGr7.

Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Clum A, Ivanova N, Pati A, d'Haeseleer P, Woyke T, Kyrpides NC.

12.

SIGS

4(1): 13-22

Complete genome sequence of Thermomonospora curvata type strain (B9).

Chertkov O, Sikorski J, Nolan M, Lapidus A, Lucas S, Del Rio TG, Tice H, Cheng JF, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Djao OD, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Han C, Detter JC, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC

11.

SIGS

4(1): 2-12

Complete genome sequence of Leadbetterella byssophila type strain.

Abt B, Teshima H, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC.

10.

SIGS

4(1): 1

Alive and well at 100

Garrity, G.M., Field, D. and Kyrpides, N.C.

9.

J Bacteriology

193(11):2906-7

Complete Genome Sequence of the Cellulolytic Thermophile Clostridium thermocellum DSM1313.

Feinberg L, Foden J, Barrett T, Davenport KW, Bruce D, Detter C, Tapia R, Han C, Lapidus A, Lucas S, Cheng JF, Pitluck S, Woyke T, Ivanova N, Mikhailova N, Land M, Hauser L, Argyros DA, Goodwin L, Hogsett D, Caiazza N.

8.

J Bacteriology

193(11):2880-1

Complete Genome Sequence of the Thermophilic Exiguobacterium sp. AT1b.

Vishnivetskaya TA, Lucas S, Copeland A, Lapidus A, Glavina Del Rio T, Dalin E, Tice H, Bruce DC, Goodwin LA, Pitluck S, Saunders E, Brettin T, Detter C, Han C, Larimer F, Land ML, Hauser LJ, Kyrpides NC, Ovchinnikova G, Kathariou S, Ramaley RF, Rodrigues DF, Hendrix C, Richardson P, Tiedje JM.

7.

J Bacteriology

193(9):2367-8

Genome sequence of the Verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems.

van Passel MW, Kant R, Palva A, Copeland A, Lucas S, Lapidus A, Gavina Del Rio T, Pitluck S, Goltsman E, Clum A, Sun H, Schmutz J, Larimer FW, Land ML, Hauser L, Kyrpides N, Mikhailova N, Richardson PP, Janssen PH, de Vos WM, Smidt H.

6.

J Bacteriology

193(9):2373-4

Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human gastro-intestinal tract.

van Passel MW, Kant R, Palva A, Lucas S, Copeland A, Lapidus A, Glavina Del Rio T, Dalin E, Tice H, Bruce D, Goodwin L, Pitluck S, Davenport KW, Sims D, Brettin TS, Detter JC, Han S, Larimer FW, Land ML, Hauser L, Kyrpides N, Ovchinnikova G, Richardson PP, de Vos WM, Smidt H, Zoetendal EG.

5.

J Bacteriology

193(8):2078-9

Genome Sequence of Mercury-Methylating Desulfovibrio desulfuricans ND132.

Brown SD, Gilmour CC, Kucken AM, Wall JD, Elias DA, Podar M, Chertkov O, Held B, Bruce DC, Detter JC, Tapia R, Han CS, Goodwin LA, Cheng JF, Pitluck S, Woyke T, Mikhailova N, Ivanova NN, Han J, Lucas S, Lapidus AL, Land ML, Hauser LJ, Palumbo AV.

4.

Appl Environ Microbiol.

77(8):2763-71

The genomic potential of Marinobacter aquaeolei - A biogeochemical opportunitroph.

Singer E, Webb EA, Nelson WC, Heidelberg JF, Ivanova N, Pati A, Edwards KJ.

3.

PLoS Genetics

7(2):e1001314

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri.

Frese SA, Benson AK, Tannock GW, Loach DM, Kim J, Zhang M, Oh PL, Heng NC, Patil PB, Juge N, Mackenzie DA, Pearson BM, Lapidus A, Dalin E, Tice H, Goltsman E, Land M, Hauser L, Ivanova N, Kyrpides NC, Walter J.

2.

J. Bacteriology

193(6):1483-4

Complete genome sequences for the anaerobic, extremely thermophilic plant biomass-degrading bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensenis, and Caldicellulosiruptor lactoaceticus.

Blumer-Schuette SE, Ozdemir I, Mistry D, Lucas S, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Land ML, Hauser LJ, Woyke T, Mikhailova N, Pati A, Kyrpides NC, Ivanova N, Detter JC, Walston-Davenport K, Han S, Adams MW, Kelly RM.

1.

ISME J.

5(1):122-30

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium.

Lykidis A, Chen CL, Tringe SG, McHardy AC, Copeland A, Kyrpides NC, Hugenholtz P, Macarie H, Olmos A, Monroy O, Liu WT.

 2010

81.

SIGS

3(3): 337-345

Complete genome sequence of Thermaerobacter marianensis type strain (7p75a).

Han, C., Gu, W., Zhang, X., Lapidus, A., Nolan, M., Copeland, A., Lucas, S., Glavina Del Rio, T., Tice, H., Cheng, J-F., Tapia, R., Goodwin, L., Pitluck, S., Pagani, I., Ivanova,N.,  Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Schneider, S., Rohde, M., Göker, M., Pukall, R., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P.  and Detter, J.C.

80.

SIGS

3(3): 325-336

Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509).

Sun, H., Göker, M., Lapidus, A., Nolan, M., Lucas, S., Glavina Del Rio, T., Tice, H., Cheng, J-F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Pagani, I., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Ngatchou Djao, O.D., Rohde, M., Sikorski, J., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

79.

SIGS

3(3): 315-324

Complete genome sequence of Methanothermus fervidus type strain (V24S).

Anderson, I., Ngatchou Djao, OD., Lucas, S., Lapidus, A., Nolan, M., Glavina Del Rio, T, Tice, H., Cheng, J-F., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Brambilla, E., Chen, A., Palaniappan, K., Land, M., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Sikorski, J., Spring, S., Rohde, M., Eichinger, K., Huber, K., Wirth, R., Göker, M., Detter, J.C., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Klenk, H-P., and Kyrpides, NC.

78.

SIGS

3(3): 304-314

Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1).

Sikorski, J., Lapidus, A., Lucas, S., Glavina Del Rio, T., Tice, H., Cheng, J-F., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Yasawong, M., Rohde, M., Pukall, R., Spring, S., Göker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

77.

SIGS

3(3): 294-303

Complete genome sequence of Intrasporangium calvum type strain (No. 7 KIP)

Glavina Del Rio, T., Chertkov, O., Yasawong, M., Lucas, S., Deshpande, S., Cheng, J-F., Detter, C., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Rohde, M., Pukall, R., Sikorski, J., Göker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P. and Lapidus, A.

76.

SIGS

3(3): 285-293

Complete genome sequence of Aminomonas paucivorans type strain (GLU-3).

Pitluck, S., Yasawong, M., Lapidus, A., Lucas, S., Glavina Del Rio, T., Chen, F., Tice, H., Cheng, J-F., Goodwin, L., Liolios, K., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Pukall, R., Spring, S., Rohde, S., Sikorski, J., Göker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

75.

SIGS

3(3): 276-284

Complete genome sequence of Desulfarculus baarsii type strain (2st14T).

Sun, H., Spring, S., Lapidus, A., Davenport, K., Glavina Del Rio, T., Tice, H., Nolan, M., Copeland, A., Cheng, J-F., Lucas, S., Tapia, R., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Detter, J.C., Han, C., Rohde, M., Brambilla, E., Göker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P. and Land, M.

74.

SIGS

3(3): 267-275

Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1T)

Ngatchou Djao, O.D., Zhang, X., Lucas, S., Lapidus, A., Glavina Del Rio, T., Nolan, M., Tice, H., Cheng, J-F., Han, C., Tapia, R., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Ovchinnikova, G., Pati, A., Brambilla, E., Chen, A., Palaniappan, K., Land, M., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Rohde, M., Sikorski, J., Spring, S., Göker, M., Detter, J.C., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

73.

SIGS

3(3): 249-253

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010

Gilbert, J., Meyer, F., Jansson, J., Gordon, J., Pace, N., Tiedje, J., Ley, R., Fierer, N., Field, D., Kyrpides, N.C., Glöckner, F-O., Klenk, H-P., Wommack, K.E., Glass, E., Docherty, K., Gallery, R., Stevens, R., Knight, R.

72.

SIGS

3(3): 243-248

Meeting Report. The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

Gilbert, J., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C.T., Desai, N., Eisen, J.A., Jansson, J., Knight, R., Knight, J., Kolker, E., Konstantinidis, K., Kostka, J., Kyrpides, N.C., Mackelprang, R., McHardy, A., Quince, C., Raes, J., Sczyrba, A., Shade, A., Stevens, R.

71.

SIGS

3(3): 240-242

Meeting Report: Towards a Critical Assessment of Functional Annotation Experiment (CAFAE) for bacterial genome annotation.

White, O. and Kyrpides, NC.

70.

SIGS

3(3): 235-239

Meeting Report: GSC M5 Roundtable at the 13th International Society for Microbial Ecology Meeting in Seattle, WA, USA.

Gilbert, J.A., Meyer, F., Knight, R., Field, D., Kyrpides, N., Yilmaz, P., Wooley, J.

69.

SIGS

3(3): 225-231

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10.

Glass, E., Meyer, F., Gilbert, J., Field, D., Hunter, S., Kottmann, R., Kyrpides, N., Sansone, S., Schriml, L., Sterk, P., White, O., Wooley, J. 

68.

SIGS

3(3): 216-224

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9.

Davidsen, T., Madupu, R., Sterk, P., Field, D., Garrity, G., Gilbert, J., Glöckner, F.O., Hirschman, L., Kolker, E., Kottmann, R., Kyrpides, N., Meyer, F., Morrison, N., Schriml, L., Tatusova, T., Wooley, J.

67.

Archaea  

2010, 690737

The genome sequence of Methanohalophilus mahii SLPT reveals fundamental differences in the energy metabolism of freshwater-inhabiting and marine members of the Methanosarcinaceae.

Spring, S., Scheuner, C., Lapidus, A., Lucas, S., Glavina Del Rio, T., Tice, H., Copeland, A., Cheng, J-F., Chen, G., Nolan, M., Saunders, E., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Lykidis, A.,  Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Goodwin, L., Detter, J.C., Brettin, T., Rohde, M., Göker, M., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, NC., and Klenk, H-P.

66.

J. Bacteriology

192(24):6494-6  

Sequencing of Multiple Clostridia Genomes Related to Biomass Conversion and Biofuels Production

Hemme, C.L., Mouttaki, H., Lee, Y.J., Goodwin, L., Lucas, S., Copeland, A., Lapidus, A., Glavina del Rio, T., Tice, H., Saunders, E., Brettin, T., Detter, J.C., Han, C.L., Pitluck, S., Land, M., Hauser, L., Kyrpides, N., Mikhailova, N., He, Z., Wu, L., van Nostrand, J.D., Henrissat, B., He,  Q., Lawson, P.A., Tanner, R.S., Lynd, L.R., Wiegel, J., Fields, M.W., Arkin, A.P., Schadt, C.W., Stevenson, B.S., McInerney, M.J., Yang, Y., Dong, H., Huhnke, R.L., Mielenz, J.R., Ding, S-Y.,  Himmel, M.E., Taghavi, S., van der Lelie, D., Rubin, E.M., Zhou, J.

65.

SIGS

3(2): 203-211

Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847T).

Brambilla, E., Djao, O.D.N., Daligault, H., Lapidus, A., Lucas, S., Hammon, N., Nolan, M., Tice, H., Cheng, J-F., Han, C., Tapia, R., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Rohde, M., Spring, S., Sikorski, J., Goker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

64.

SIGS

3(2): 194-202

Complete genome sequence of Sulfurimonas autotrophica  type strain (OK10T).

Sikorski, J., Munk, C., Lapidus, A., Djao, O.D.N., Lucas, S., Glavina Del Rio, T., Nolan, M., Tice, H., Han, C., Cheng, J-F., Tapia, R., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Sims, D., Meinecke, L., Brettin, T., Detter, J.C., Chen, A., Palaniappan, K., Land, M., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Rohde, M., Lang, E., Spring, S., Goker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

63.

SIGS

3(2): 174-182

Complete genome sequence of Ferrimonas balearica type strain (PATT).

Nolan, M., Sikorski, J., Davenport, K., Lucas, S., Glavina Del Rio, T., Tice, H., Cheng, J-F., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Tapia, R., Brettin, T., Detter, J.C., Han, C., Rohde, M., Tindall, B.J., Goker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Lapidus, A.

62.

SIGS

3(2): 153-162

Complete genome sequence of Thermobaculum terrenum type strain (YNP1T).

Kiss, H., Cleland, D., Lapidus, A., Lucas, S., Glavina Del Rio,T., Nolan, M., Tice, H., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Yun- Chang, Y-J., Jeffries, C.D., Lu, M., Brettin, T., Detter, J.C., Goker, M., Tindall, B.J., Beck, B., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Cheng, J-F.

61.

SIGS

3(2): 136-144

Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228T).

Mavromatis, K., Yasawong, M., Chertkov, O., Lapidus, A., Lucas, S., Nolan, M., Glavina Del Rio, T., Tice, H., Cheng, J-F., Pitluck, S., Liolios, K., Ivanova, N., Tapia, R, Han, C., Bruce, D., Goodwin, L., Pati, A.,  Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Detter, J.C., Rohde, M., Brambilla, E., Spring, S., Goker, M., Sikorski, J., Goker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Klenk, H-P., and Kyrpides, NC.

60.

SIGS

3(2): 126-135

Complete genome sequence of Arcanobacterium haemolyticum type strain (11018T).

Yasawong, M., Teshima, H., Lapidus, A., Nolan, M., Lucas, S., Glavina Del Rio, T., Tice, H., Cheng, J-F., Bruce, D., Detter, J.C., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Rohde, M., Sikorski, J., Pukall, R., Goker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

59.

SIGS

3(2): 117-125

Complete genome sequence of Vulcanisaeta distributa type strain (IC-017T)

Mavromatis, K., Sikorski, J., Pabst, E., Teshima, H., Lapidus, A., Lucas, S., Nolan, M., Glavina Del Rio, T., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Rohde, M., Spring, S., Spring, S., Goker, M., Wirth, R., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Klenk, H-P., and Kyrpides, N.C.

58.

SIGS

3(2): 108-116

Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228PT).

Pitluck, S., Yasawong, M., Munk, C., Nolan, M., Lapidus, A., Lucas, S., Glavina Del Rio, T., Tice, H., Cheng, J-F., Bruce, D., Detter, C., Tapia, R., Han, C., Goodwin, L., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Rohde, M., Spring, S., Sikorski, J., Goker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

57.

SIGS

3(1): 93-96

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 8.

Kyrpides, N., Field, D., Sterk, P., Kottmann, R., Glöckner, F-O., Hirschman, L., Garrity, G., Cochrane, G., Wooley, J.

56.

SIGS

3(1): 85-92

Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T).

LaButti, K., Mayilraj, S., Clum, A., Lucas, S., Glavina Del Rio, T., Nolan, M., Tice, H., Cheng, J-F., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Ovchinnikova, G., Pati, A., Goodwin, L., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Rohde, M., Spring, S., Goker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P. and Lapidus, A.

55.

SIGS

3(1): 76-84

Complete genome sequence of Olsenella uli type strain (VPI D76D-27CT).

Goker, M., Held, B., Lucas, S., Nolan, M., Yasawong, M., Glavina Del Rio, T., Tice, H., Cheng, J-F., Bruce, D., Detter, J.C., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Rohde, M., Sikorski, J., Pukall, R., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P. and Lapidus, A.

54.

SIGS

3(1): 66-75

Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1T).

Goker, M., Held, B., Lapidus, A., Nolan, M., Spring, S., Yasawong, M., Lucas, S., Glavina Del Rio, T., Tice, H., Cheng, J-F., Goodwin, L., Tapia, R., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Brettin, T., Detter, J.C., Han, C., Rohde, M., Sikorski, J., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

53.

SIGS

3(1): 57-65

Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288T)

Sikorski, J., Lapidus, A., Chertkov, O., Lucas, S., Copeland, A., Glavina Del Rio, T., Nolan, M., Tice, H., Cheng, J-F., Han, C., Brambilla, E., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Bruce, D., Detter, C.,  Tapia, R., Goodwin, L., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Rohde, M., Göker, M., Spring, S., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

52.

SIGS

3(1):47-56

Complete genome sequence of Planctomyces limnophilus type strain (Mu 290T)

Sikorski, J., Schneider, S., Nolan, M., Lucas, S., Glavina Del Rio, T., Tice, H., Cheng, J-F., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Tindall, B.J., Rohde, M., Göker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P. and Lapidus, A

51.

SIGS

3(1):37-46

Complete genome sequence of Meiothermus silvanus type strain (VI-R2T)

Sikorski, J., Tindall, B.J., Lowry, S., Lucas, S., Nolan, M., Copeland, A., Glavina Del Rio, T., Tice, H., Cheng, J-F., Han, C., Pitluck, S., Liolios, K., Ivanova, N.,  Mavromatis, K., Ovchinnikova, G., Pati, A., Goodwin, L., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Rohde, M., Göker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P. and Lapidus, A.

50.

SIGS

3(1):26-36

Complete genome sequence of Meiothermus ruber type strain (21T)

Tindall, B.J., Sikorski, J., Lucas, S., Goltsman, E., Copeland, A., Glavina Del Rio, T., Nolan, M., Tice, H., Cheng, J-F., Han, C., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Ovchinnikova, G., Pati, A., Fähnrich, R., Goodwin, L., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Rohde, M., Göker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P. and Lapidus, A.

49.

SIGS

3(1):15-25

Complete genome sequence of Cellulomonas flavigena type strain (134T)

Abt, B., Foster, B., Lapidus, A., Clum, A., Sun, H., Pukall, R., Lucas, S., Glavina Del Rio, T., Nolan, M., Tice, H., Cheng, J-F., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, A., Goodwin, L., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Rohde, M., Göker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C. and Klenk, H-P.

48.

SIGS

3(1): 1-14

Complete genome sequence of Acidaminococcus fermentans type strain (VR4T)

Chang, Y-J., Pukall, T., Saunders, E., Lapidus, A., Copeland, A., Nolan, M., Glavina Del Rio, T., Lucas, S., Chen, F., Tice, H., Cheng, J-F., Han, C., Detter, J.C., Bruce, D., Goodwin, L., Pitluck, S., Mikhailova, N., Liolios, K., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Land, M., Hauser, L., Jeffries, C.D., Brettin, T., Rohde, M., Göker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, N.C. and Klenk, H-P.

47.

Environ Microbiol.

12(7) 1803-5

A call for standardized classification of metagenome projects.

Ivanova N, Tringe SG, Liolios K, Liu WT, Morrison N, Hugenholtz P, Kyrpides NC.

46.

SIGS

2(3) 357-360

Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010

Hirschman, L., Sterk, P., Field D., Wooley, J., Cochrane, G., Gilbert, J., Kolker, E., Kyrpides, NC., Meyer, F., Mizrachi, I., Nakamura, Y., Sansone, S., Schriml, L., Tatusova, T., White, O., and Yilmaz, P.

45.

SIGS

2(3) 347-356

Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers.

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., Ovchinnikova, G., Ivanova, N., Mavromatis, K., Markowitz, V., Kyrpides, N.C., Melino, V., Denton, M., Yates, R., and Howieson, J.

44.

SIGS

2(3) 327-346

Complete genome sequence of Archaeoglobus profundus type strain (AV18T)

von Jan, M., Lapidus, A., Glavina Del Rio, T., Copeland, A., Tice, H., Cheng, J-F., 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, Y-J., Jeffries, C.D., Saunders, E., Brettin, T., Detter, J.C., Chain, P., Eichinger, K., Huber, H., Spring, S., Rohde, M., Goker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, NC., and Klenk, H-P.

43.

SIGS

2(3) 318-326

Complete genome sequence of Thermobispora bispora type strain (R51T)

Liolios, K, Sikorski, J., Jando, M., Lapidus, A., Copeland, A., Glavina Del Rio, T., Nolan, M., Lucas, S., Tice, H., Cheng, J-F., Han, C., Woyke, T., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Mikhailova, N., Chertkov, O., Kuske, C., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Detter, J.C., Brettin, T., Rohde, M., Goker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Klenk, H-P., and Kyrpides, N.C.

42.

SIGS

2(3) 300-308

Complete genome sequence of Arcobacter nitrofigilis type strain (CIT)

Pati, A., Gronow, S., Lapidus, A., Copeland, A., Glavina Del Rio, T., Nolan, M., Lucas, S., Tice, H., Cheng, J-F., Han, C., Chertkov, O., Bruce, D., Tapia, R., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, I., Mavromatis, K., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Detter, JC., Rohde, M., Goker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Klenk, H.P., and Kyrpides, NC.

41.

SIGS

2(3) 290-299

Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24 T)

Mavromatis, K., Abt, B., Brambilla, E., Lapidus, A., Copeland, A, Deshpande, S., Nolan, M., Lucas, S., Tice, H., Cheng, J-F., Han, C., Detter, J.C., Bruce, D., 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, Y-J., Jeffries, C.D., Rohde, M., Goker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Klenk, H-P., and Kyrpides, N.C.

40.

SIGS

2(3) 280-289

Complete genome sequence of Aminobacterium colombiense type strain (ALA-1T)

Chertkov, O., Sikorski, J., Brambilla, E., Lapidus, A., Copeland, A., Glavina Del Rio, T., Nolan, M., Lucas, S., Tice, H., Cheng, J-F., Han, C., Detter, JC., Bruce, D., Tapia, R., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, I., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Spring, S., Rohde, M., Goker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P.,  Kyrpides, NC., and Klenk, H.P

39.

SIGS

2(3) 270-279

Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460T)

Kiss, H., Lang, E., Lapidus, A., Copeland, A., Nolan, M., Glavina Del Rio, T., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Pati, A., Ivanova, I., Mavromatis, K., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Spring, S., Rohde, M., Goker, M., Woyke, T., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P.,  Kyrpides, NC., and Klenk, H.P.

38.

SIGS

2(3) 260-269

Complete genome sequence of Brachyspira murdochii type strain (56-150T)

Pati, A., Sikorski, J., Gronow, S., Lapidus, A., Copeland, A., Glavina Del Tio, T, Nolan, M., Lucas, S., Chen, F., Tice, H., Cheng, J-F., Han, C., Detter, J.C., Bruce, D., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, I., Mavromatis, K., Mikhailova, N., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Spring, S., Rohde, M., Goker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P.,  Kyrpides, NC., and Klenk, H.P.

37.

SIGS

2(3) 245-259

Complete genome sequence of Thermosphaera aggregans type strain (M11TLT)

Spring, S., Rachel, R., Lapidus, A., Davenport, K., Tice, H., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, I., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Brettin, T., Detter, J.C., Tapia, R., Han, C., Heimerl, T., Weikl, G., Brambilla, R., Göker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P.,  Kyrpides, NC., and Klenk, H.P.

36.

FEBS

277:2740-53

LmbE proteins from Bacillus cereus are de-N-acetylases with broad substrate specificity and are highly similar to proteins in Bacillus anthracis.

Junier P, Junier T, Podell S, Sims DR, Detter JC, Lykidis A, Han CS, Wigginton NS, Gaasterland T, Bernier-Latmani R.

Deli A, Koutsioulis D, Fadouloglou VE, Spiliotopoulou P, Balomenou S, Arnaouteli S, Tzanodaskalaki M, Mavromatis K, Kokkinidis M, Bouriotis V.

35.

Environ Microbiol.

12(10):2738-54

The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1.

Junier P, Junier T, Podell S, Sims DR, Detter JC, Lykidis A, Han CS, Wigginton NS, Gaasterland T, Bernier-Latmani R.

34.

Environ Microbiol. Epub

The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production.

Sieber JR, Sims DR, Han C, Kim E, Lykidis A, Lapidus AL, McDonnald E, Rohlin L, Culley DE, Gunsalus R, McInerney MJ.

33.

Science

328:994-999

A Catalog of Reference Genomes from the Human Microbiome.

Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, Fitzgerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D.

32.

Nature Method

7(6):455-7

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes

Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC.

31.

PLoS One

5(4):e10314

One bacterial cell, one complete genome.

Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng JF.

30.

PLoS One

5(3):e9729

The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader.

Lykidis A, Pérez-Pantoja D, Ledger T, Mavromatis K, Anderson IJ, Ivanova NN, Hooper SD, Lapidus A, Lucas S, González B, Kyrpides NC.

29.

SIGS

2(2):220-227

Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300T).

Harmon-Smith, M., Celia, L., Chertkov, O., Lapidus, A., Copeland, A., Nolan, M., Lucas, S., Tice, H., Cheng, J-F., Han, C., Detter, J.C., 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, Y-J., Jeffries, C.D., Brettin, T., Göker, M., Beck, B., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P.,  Kyrpides, NC., Klenk, H.P., and Chen, F.

28.

SIGS

2(2):212-219

Complete genome sequence of Conexibacter woesei type strain (ID131577T).

Pukall, R., Lapidus, A., Glavina Del Rio, T., Copeland, A., Tice, H., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Mavromatis, K., Ivanova, N., Mikhailova, N., 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., and Hugenholtz, P.

27.

SIGS

2(2):203-211

Complete genome sequence of Segniliparus rotundus type strain (CDC 1076T).

Sikorski, J., Lapidus, A., Copeland, A., Misra, M., Glavina Del Rio, T., Nolan, M., Lucas, S., Chen, F., Tice, H., Cheng, J-F., Jando, M., Schneider, M., 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, Y-J., Jeffries, C.D., Brettin, T., Detter, JC., Han, C., Rohde, M., Goker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P.,  Kyrpides, NC., and Klenk, HP.

26.

SIGS

2(2):194-202

Complete genome sequence of Thermocrinis albus type strain (HI 11/12T).

Wirth, R., Sikorski, J., Brambilla, E., Misra, M., Lapidus, A., Copeland, A., Nolan, M., Lucas, S., Chen, F., Tice, H., Cheng, J-F., Han, C., Detter, J-C., 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, Y-J., Jeffries, C.D., Tindall, B.J., Rohde, M., Göker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P.,  Kyrpides, NC., and Klenk, HP.

25.

SIGS

2(2):186-193

Complete genome sequence of Kribbella flavida type strain (IFO 14399T).

Pukall, R., Lapidus, A., Glavina Del Rio, T., Copeland, A., Tice, H., Cheng, J-F., 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. and Brettin, T.

24.

SIGS

2(2):176-185

Complete genome sequence of Spirosoma linguale type strain (1T).

Lail, K., Sikorski, J., Saunders, E., Lapidus, A., Glavina Del Rio, A., Copeland, A., Tice, H., Cheng, J-F., 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., and Chen, F.

23.

SIGS

2(2):168-175

Complete genome sequence of Nakamurella multipartita type strain (Y-104T).

Tice, H., Mayilraj, S., Sims, D., Lapidus, A., Nolan, M., Lucas, S., Del Rio, G., Copeland, A., Cheng, J-F., 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. and Chen, F.

22.

SIGS

2(2):158-167

Complete genome sequence of Geodermatophilus obscurus type strain (G-20T).

Ivanova, N., Sikorski, J., Jando, M., Munk,C.,  Lapidus, A., Glavina Del Rio, T., Copeland, A., Tice, H., Cheng, J-F.,  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., and Klenk, HP.

21.

SIGS

2(2):149-157

Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T).

Sikorski, J., Lapidus,A., Copeland, A., Glavina Del Rio, T., Nolan, M., Lucas, S., Chen, F., Tice, H., Cheng, J-F., 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., and Klenk, HP.

20.

Appl.Environ Microbiol

76(7):2304-12

The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium reveals mechanisms for adaptation to low temperature growth.

Ayala-Del-Río HL, Chain PS, Grzymski JJ, Ponder MA, Ivanova N, Bergholz PW, Di Bartolo G, Hauser L, Land M, Bakermans C, Rodrigues D, Klappenbach J, Zarka D, Larimer F, Richardson P, Murray A, Thomashow M, Tiedje JM.

19.

Environ Microbiol

12(5):1205-17

Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge.

He S, Kunin V, Haynes M, Martin HG, Ivanova N, Rohwer F, Hugenholtz P, McMahon KD.

18.

SIGS

2(1):107-116

Complete genome sequence of Haloterrigena turkmenica type strain (4kT).

Saunders, E., Tindall, BJ., Fähnrich, R., Lapidus, A., Copeland, A., Glavina Del Rio, T.,  Lucas, S., Chen, F., Tice, H., Cheng, J-F., Han, C., Detter, CJ., 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., and Kyrpides, NC.

17.

SIGS

2(1):96-106

Complete genome sequence of Haliangium ochraceum type strain (SMP-2T).

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, J-F., 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., and Klenk, HP.

16.

SIGS

2(1):87-95

Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T).

Glavina Del Rio, T., Abt, B., Spring, S., Lapidus, A., Nolan, M., Tice, H., Copeland, A., Cheng, J-F., Chen, F., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Konstantinos 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., and Lucas, S.

15.

SIGS

2(1):77-86

Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419.

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, Y-J., Ivanova, N., Mavromatis, K., Markowitz, V., Kyrpides, N., Gollagher, M., Yates, R., Dilworth, M.,  and Howieson, J.

14.

SIGS

2(1):66-76

Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325

Reeve, W., O’Hara, G., Chain, P., Ardley, J., Bräu, L., Nandesena, K.,  Tiwari, R., Copeland, A., Malfatti, S., Kiss, H., Lapidis, A., Copeland, A., Land, M>, Hauser, L., Chang, Y-J., Ivanova, N, Mavromatis, K., Markowitz, V., Kyrpides, N., Gollagher, M., Yates, R., Dilworth, M., and Howieson, J.

13.

SIGS

2(1):56-65

Complete genome sequence of Veillonella parvula type strain (Te3T).

Gronow, S., Welnitz, S., Lapidus, A., Nolan, M., Ivanova, N., Glavina Del Rio, T., Copeland, A., Chen, F., Tice, H., Pitluck, S., Cheng, J-F., Saunders, E., Brettin, T., Han, C., Detter, JC., Bruce, D., Goodwin, L., Land, M., Hauser, L., Chang, Y-J., 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., and Lucas, S.

12.

SIGS

2(1): 49-56

Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022T).

Pati, A., LaButti, K., Pukall, R., Nolan, M., Glavina Del Rio, T., Tice, H., Cheng, J-F., Lucas, S., Chen, F., Copeland, A., Ivanova, N., Mavrommatis, K., Mikhailova, N., Pitluck, S., Bruce, D., Goodwin, L., Land, M., Hauser, L., Chang, Y-J., Jeffries, C-D., Chen, A., Palaniappan, K., Chain, P., Brettin, T., Rohde, M., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H.P., and Lapidus, A.

11.

SIGS

2(1): 38-48

Complete genome sequence of Desulfohalobium retbaense type strain (HR100T).

Spring, S., Nolan, M., Lapidus, A., Glavina Del Rio, T., Copeland, A., Tice, H., Cheng, J-F., Lucas, S., Land, M., Chen, F., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Pati, A., Mikhailova, N., Chen, A., Palaniappan, K., Hauser, L., Chang, YJ., Jeffries, CD., Munk, C., Kiss2, H., Han, C., Brettin, T., Detter, JC., Schüler, E., P., Rohde, M., Göker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, NC., and Klenk, H-P.

10.

SIGS

2(1): 29-37

Complete genome sequence of Streptosporangium roseum type strain (NI 9100T).

Nolan, M., Sikorski, J., Jando, M., Lucas, S., Lapidus, A., Glavina Del Rio, T., Chen, F., Tice, H., Pitluck, S., Cheng, J-F., 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., , M., Göker, M., Bristow, J., Eisen, JA., Markowitz, V., Hugenholtz, P., Kyrpides, NC., and Klenk, HP.

9.

SIGS

2(1): 19-28

Complete genome sequence of Gordonia bronchialis type strain (3410T).

Ivanova, N., Sikorski, J., Jando, M., Lapidus, A., Nolan, M., Lucas, S., Glavina Del Rio, T., Tice, H., Copeland, A., Cheng, J-F., 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., and Kyrpides, NC.

8.

SIGS

2(1): 9-18

Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT).

Mavromatis, K., Sikorski, J., Lapidus, A., Glavina Del Rio, T., Copeland, A., Tice, H., Cheng, J-F., 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., and Kyrpides, NC

7.

SIGS

2(1): 1-8

Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T).

Foster, B.,  Pukall, R.,  Abt, B., Nolan, M., Glavina Del Rio, T., Chen, F.,  Lucas, S.,  Tice, H., Pitluck, S., Cheng, J-F., 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, H-P., and Lapidus, A.

6.

Bioinformatics

26(3):295-301

Estimating DNA coverage and abundance in metagenomes using a gamma approximation.

Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN, Kyrpides NC.

5.

PLoS One

5(1):e8812

Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community.

Allgaier M, Reddy A, Park JI, Ivanova N, D'haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS, Hugenholtz P.

4.

ISME Journal

4(1):61-77

The complete genome sequence of the algal symbiont Dinoroseobacter shibae - a hitchhiker`s guide to life in the sea.

Wagner-Dobler, I., Baumgart, M., Brinkhoff, T., Buchholz, I., Bunk, B., Cypionka, H., Daniel, R., Drepper, T., Gerdts, G., Hahnke, S., Han, C., Jahn, D., Kalhoefer, D., Kiss, H., Klenk, H-P., Kyrpides, N., Pati, A., Liebl, W., Liesegang, H., Meincke, L., Petersen, J., Piekarski, T., Pommerenke, T., Pradella, S., Pukall, R., Rabus, R., Stackebrandt, E., Thole, S., Thompson, S., Tielen, P., Tomasch, J., von Jan, M., Wanphrut, N., Wichels, A., Zech, H., Simon, M.

3.

J Bacteriology

192(3):841-60

Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium.

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, Mavrommatis K, Mukamolova GV, Oren A, Rokem JS, Smith MC, Young DI, Greenblatt CL.

2.

Nucleic Acids Res.

38:D346-54

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.

Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC.

1.

Nucleic Acids Res.

38:D382-90

The integrated microbial genomes system: an expanding comparative analysis resource.

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

 2009

52.

Nature

462:1056-60

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

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.

51.

PLoS One

4(11):e7979

Gene context analysis in the Integrated Microbial Genomes (IMG) data management system.

Mavromatis K, Chu K, Ivanova N, Hooper SD, Markowitz VM, Kyrpides NC.

50.

SIGS

1(3): 308-316

Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T)

Clum, A., Tindall, BJ., Johannes Sikorski, J., Natalia 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, J.C., 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, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, H-P., and Lapidus, A.

49.

SIGS

1(3): 300-307

Complete genome sequence of Streptobacillus moniliformis type strain (9901T)

Nolan, M., Gronow, S., Lapidus, A., Ivanova, N., Copeland, A., Lucas, S., Glavina Del Rio, T., Chen, F., Tice, H., Pitluck, S., Cheng, J-F., 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, Y-J., Jeffries, CD., Rohde, M., Göker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, H-P., and Chain, P.

48.

SIGS

1(3): 292-299

Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21T).

Munk, C., Lapidus, A., Alex Copeland, A., Marlen Jando, M., Mayilraj, S., Glavina Del Rio, T., Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Han, C., Detter, C.J., 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, Y-J., Jeffries, CD., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, H-P.

47.

SIGS

1(3): 283-291

Complete genome sequence of Rhodothermus marinus type strain (R-10T)

Nolan, M., Tindall, BJ., Pomrenke, H., Lapidus, A., Copeland, A., Glavina Del Rio, T., Lucas, S., Chen, F., Tice, Cheng, J-F., 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, Y-J., Jeffries, CD., Brettin, T., Göker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, H-P., and Detter, JC.

46.

SIGS

1(3): 270-277

Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T).

Tindall, B.J., Lapidus, A., Copeland, A., Glavina Del Rio, T., Nolan, M., Lucas, S., Chen, F., Tice, H., Cheng, J-F., Saunders, E., Bruce, D., Goodwin, L., Pitluck, S., Mikhailova, N., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Chain, P., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Brettin, T., Han, C., Rohde, M., Göker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Klenk, H-P., Kyrpides, NC., and Detter, JC.

45.

SIGS

1(3): 262-269

Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134T).

Pukall, R., Gehrich-Schröter, G., Lapidus, A., Nolan, M., Glavina Del Rio, T., Lucas, S., Chen, F., Tice, H., Pitluck, S., Jan-Fang Cheng, J-F., Copeland, A., Saunders, E., Brettin, T., Detter, JC., Bruce, D., Goodwin, L., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Chain, P., Göker, M., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, H-P., and Han, C.

44.

SIGS

1(3): 254-261

Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T).

Chovatia, M., Sikorski, J., Schröder, M., Lapidus, A., Matt Nolan1, Hope Tice1, Glavina Del Rio, T., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Chain, P., Saunders, E., Detter, JC., Brettin, T., Rohde, M., Göker, M., Spring, S., Bristow, J., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, HP., and Eisen, JA.

43.

SIGS

1(3): 242-253

Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T).

Spring, S., Lapidus, A., Schröder, M., Gleim, D., Sims, D., Meincke, L., Glavina Del Rio, T., Tice, H., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jeffries, CD., Chain, P., Saunders, E., Brettin, T., Detter, J.C., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, NC., Klenk, HP., and Han, C.

42.

SIGS

1(3): 234-241

Complete genome sequence of Slackia heliotrinireducens type strain (RSH 1T).

Pukall, R., Lapidus, A., Nolan, M., Copeland, A., Glavina Del Rio, T., Lucas, S., Chen, F., Tice, H., Cheng, J-F., Chertkov, O., Bruce, D., Goodwin, L., Kuske, C., Brettin, T., Detter, JC., Han, C., Pitluck, S., Pati, A., Mavromatis, K., Ivanova, N., Ovchinnikova, G., Chen, A., Palaniappan, K., Schneider, S., Rohde, M., Chain, P., D'haeseleer, P., Göker, M., Bristow, J., Eisen, J., Markowitz, V, Kyrpides, NC., Klenk, HP., and Hugenholtz, P.

41.

SIGS

1(3): 226-233

Complete genome sequence of Kangiella koreensis type strain (SW-125T).

Anderson, I., Tindall, B.J., Göker, M., Lapidus, A., Nolan, M., Copeland, A., Glavina Del Rio, T., Chen, F., Tice, H., Cheng, J-F., Lucas, S., Chertkov, O., Bruce, D., Brettin, T., Detter, J.C., Han, C., Goodwin, L., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Pitluck, S., Pati, A., Mavromatis, K., Ivanova, N., Ovchinnikova, G., Chen, A., Palaniappan, K., Chain, P., Rohde, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C. and Klenk, H-P.

40.

SIGS

1(3): 218-225

Complete genome sequence of Halorhabdus utahensis type strain (AX-2T).

Anderson, I., Tindall, B.J., Göker, M., Lapidus, A., Nolan, M., Copeland, A., Glavina Del Rio, T., Chen, F., Tice, H., Cheng, J-F., Lucas, S., Chertkov, O., Bruce, D., Brettin, T., Detter, J.C., Han, C., Goodwin, L., Land, M., Hauser, L., Chang, Y-J., Jeffries, C.D., Pitluck, S., Pati, A., Mavromatis, K., Ivanova, N., Ovchinnikova, G., Chen, A., Palaniappan, K., Chain, P., Rohde, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C. and Klenk, H-P.

39.

SIGS

1(2): 197-203

Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1.

Anderson, IJ., Sun, H., Lapidus, A., Copeland, A., Glavina Del Rio, T., Tice, H., Dalin, E., Lucas, S., Barry, K., Land, M., Richardson, P., Huber, H., and Kyrpides, N.C.

38.

SIGS

1(2): 189-196

Complete genome sequence of Methanocorpusculum labreanum Zhao et al. 1989 type strain Z.

Anderson, IJ., Sieprawska-Lupa, M., Goltsman, E., Lapidus, A., Copeland, A., Glavina Del Rio, T., Tice, H., Dalin, E., Barry, K., Pitluck, S., Hauser, L., Land, M., Lucas, S., Richardson, P., Whitman, WB., and Kyrpides, N.C.

37.

SIGS

1(2): 183-188

Complete genome sequence of Methanoculleus marisnigri type strain JR1.

Anderson, I.J., Sieprawska-Lupa, M., Lapidus, A., Nolan, M., Copeland, A., Glavina Del Rio, T., Tice, H., Dalin, E., Barry, K., Saunders, E., Han, C., Brettin, T., Detter, J.C., Bruce, D., Mikhailova, N., Pitluck, S., Hauser, L., Land, M., Lucas, S., Richardson, P., Whitman, W.B., and Kyrpides, N.C.

36.

SIGS

1(2): 174-182

Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255T).

Saunders, E., Pukall, R., Abt, B., Lapidus, A., Glavina Del Rio, T., Copeland, A., Tice, H., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis, K., Ovchinnikova, G., Pati, G., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-C., Jeffries, C.D., Chain, P., Meincke, L., Sims, D., Brettin, T., Detter, J.C., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Han, C.

35.

SIGS

1(2): 166-173

Complete genome sequence of Atopobium parvulum type strain (IPP 1246T).

Copeland, A., Sikorski, J., Lapidus, A., Nolan, M., Glavina Del Rio, T., Lucas, S., Chen, F., Tice, H., Pitluck, S., Cheng, J-F., Pukall, R., Chertkov, O., Brettin, T., Han, C., Kuske, C., Bruce, D., Goodwin, L., Ivanova, N., Mavromatis, K., Mikhailova, N., Chen, A., Palaniappan, K., Chain, P., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Detter, C.J.

34.

SIGS

1(2): 159-165

Complete genome sequence of Anaerococcus prevotii type strain (PC1T).

LaButti, K., Pukall, R., Steenblock, K., Glavina Del Rio, T., Tice, H., Copeland, A., Cheng, J-F., 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, Y-J., Jeffries, C.D., Chain, P., Saunders, E., Brettin, T., Detter, J.C., Han, C., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Lapidus, A.

33.

SIGS

1(2): 150-158

Complete genome sequence of Halogeometricum borinquense type strain (PR3T).

Malfatti, S., Tindall, B.J., Lapidus, A., LaButtii, K., Copeland, A., Glavina Del Rio, T., Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S.,  Anderson, I., Pati, A., Ivanova, N., Mavromatis, K.,  Chen, A., Palaniappan, K., D'haeseleer, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P.,  Kyrpides, N.C., Klenk, H-P., and Chain, P.

32.

SIGS

1(2): 141-149

Complete genome sequence of Saccharomonospora viridis type strain (P101T).

Pati, A., Sikorski, J., Nolan, M., Lapidus, A., Copeland, A., Glavina Del Rio, Lucas, S., Chen, F., Tice, H., Pitluck, S., Cheng, J-F., Chertkov, O., Brettin, T., Han, C., Detter, J.C., Kuske, C., Bruce, D., Goodwin, L., Chain, P., D'haeseleer, P., Chen, A., Palaniappan, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Rohde, M., Tindall, B.J., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and Klenk, H-P.

31.

SIGS

1(2): 133-140

Complete genome sequence of Dyadobacter fermentans type strain (NS114T).

Lang, E., Lapidus, A., Chertkov, O., Brettin, T., Detter, J.C., Han, C., Copeland, A., Glavina Del Rio, Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Land, M., Hauser, L., Chang, Y.Y., Jeffries, C.D., Bruce, D., Goodwin, L., Pitluck, S., Ovchinnikova, G., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Chain, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Göker, M., Rohde, M., Kyrpides, N.C., and Klenk, H-P.

30.

SIGS

1(2): 126-132

Complete genome sequence of Leptotrichia buccalis type strain (C-1013-bT).

Ivanova, N., Gronow, S., Lapidus, A., Copeland, A., Glavina Del Rio, Nolan, M., Lucas, S., Chen, F., Tice, T., Cheng, J-F., Saunders, L., Bruce, D., Goodwin, L., Brettin, T., Detter, J.C., Han, C., Pitluck, S., Mikhailova, N., Pati, A., Mavromatis, K., Chen, A., Palaniappan, K., Land, M., Hauser, L. Chang, Y.Y., Jeffries, C.D., Chain, P., Rohde, C., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, Kyrpides, N.C., and  Klenk, H-P.

29.

SIGS

1(2): 119-125

Complete genome sequence of Catenulispora acidiphila type strain (ID 139908T).

Copeland, A., Lapidus, A., Glavina Del Rio, Nolan, M., Lucas, S., Chen, F., Tice, T., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Mikhailova, N., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Chain, P., Land, M., Hauser, L. Chang, Y.Y., Jeffries, C.D., Chertkov, O., Brettin, T., Detter, J.C., Han, C., Ali, Z., Tindall, B.J., Göker, M., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., and  Klenk, H-P.

28.

SIGS

1(2): 110-118

Complete genome sequence of Sanguibacter keddieii type strain (ST-74T).

Ivanova, N., Sikorski, J., Sims, D., Brettin, T., Detter, J.C., Han, C., Lapidus, A., Copeland, A., Glavina Del Rio, Nolan, M., Lucas, S., Chen, F., Tice, T., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Pati, A., Mavromatis, K., Chen, A., Palaniappan, K., D'haeseleer, P., Chain, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, Göker, M., Pukall, R., Klenk, H-P., and Kyrpides, N.C

27.

SIGS

1(2): 101-109

Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T).

Mavromatis, K., Gronow, S., Saunders, E.,  Land, M., Lapidus, A., Copeland, A., Glavina Del Rio, T., Nolan, M., Lucas, S., Tice, H., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S.,  Pati, A., Ivanova, N., Chen, A., Palaniappan, K., Chain, P., Hauser, L. Chang, Y.Y., Jeffries, C.D., Brettin, T., Detter, J.C., Han, C., Bristow, J.,  Göker, M., Rohde, M., Eisen, J.A., Markowitz, V., Kyrpides, N.C., Klenk, H-P., and Hugenholtz, P.

26.

SIGS

1(2): 93-100

Complete genome sequence of Cryptobacterium curtum type strain (12-3T).

Mavromatis, K., Pukall, R., Rohde, C., Sims, D., Brettin, T., Kuske, C., Detter, J., Han, C., Lapidus, A., Copeland, A., Glavina Del Rio, T., Nolan, M., Lucas, S., Tice, H., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Ovchinnikova, G., Pati, A., Ivanova, N., Chen, A., Palaniappan, K., Chain, P., D'haeseleer, P., Bristow, J., Eisen, J.A, Markowitz, V., Hugenholtz, P., Rohde, M., Klenk, H-P., and Kyrpides, N.C.

25.

Science

326, 236-7

Genomics. Genome project standards in a new era of sequencing.

Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A; Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter JC.

24.

PNAS

106, 15527-33

The genomic basis of trophic stragegy in marine bacteria,

Lauro, F., McDougald, D., Thomas, T., Williams, T., Egan, S., Rice, S., DeMaere, M., Ting, L., Ertan, H., Johnson, J., Ferriera, S., Lapidus, A., Anderson, I., Kyrpides, N., Munk, C., Detter, C., Han, C., Brown, M., Robb, F., Kjelleberg, S., Cavicchioli, R.

23.

Nature

461, 68-70

Prepublication data sharing.

Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J.

22.

SIGS

1(1): 68-71

Meeting Reports from the Genomic Standards Consortium (GSC) Workshops 6 and 7.

Field, D., Sterk, P., Kyrpides, N., Glockner, F-O., Kottman, R., Hirschman, L., Garrity, G.M., Wooley, J., and Gilna, P.

21.

SIGS

1(1): 63-67

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial genomes.

Mavromatis, K., Ivanova, N., Chen, A., Szeto, E., Markowitz, V.M., and Kyrpides, N.C.

20.

SIGS

1(1): 54-62

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T)

Han, C., Spring, S., Lapidus, A., Glavina Del Rio, T., Tice, H., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N, Mavromatis, K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y-J., Jefferies, C.C., Saunders, L., Chertkov, O., Brettin, T., Goker, M., Rohde, M., Bristow, J., J., Eisen, J.A., Markowitz, V., Hugenholtz, P.,  Kyrpides, N.C., Klenk, H-P. and Detter, J.C.

19.

SIGS

1(1): 46-53

Complete genome sequence of Actinosynnema mirum type strain (101T)

Land, M., Lapidus, A., Mayilraj, S., Chen, F., Copeland, A., Glavina Del Rio, T., Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Chertkov, O., Bruce, D., Goodwin, L., Pitluck, S., Rohde, M., Göker, M., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Hauser, L., Chang, Y.Y., Jeffries, C.D.,  Brettin, T., Detter, C.J., Han, C., Chain, P., Tindall, B.J., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P.,  Kyrpides, N.C., and Klenk, H-P.

18.

SIGS

1(1): 38-45

Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT).

Clum, A., Nolan, M., Lang, E., Glavina Del Rio, T., Tice, H., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis , K., Mikhailova, N., Pati, A., Chen, A., Palaniappan, K., Goker, M., Spring, S., Land, M., Hauser, L. Chang, Y.Y., Jeffries, C.D., Chain, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, Kyrpides, N.C., Klenk, H-P., and Lapidus, A.

17.

SIGS

1(1): 29-37

Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

Copeland, A., Spring, S., Goker, M., Schneider, S., Lapidus, A., Glavina Del Rio, T., Tice, H., Cheng, J-F., 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, Y.Y., Jeffries, C.D., Meincke ,L., Sims, D., Brettin, T., Detter, J.C., Han, C., Chain, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, Kyrpides, N.C., Klenk, H-P., and Lucas, S.

16.

SIGS

1(1): 21-28

Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122T)

Land, M., Pukall, R., Abt, B., Rohde, M., Glavina Del Rio, T., Tice, T., Copeland, A., Cheng, J-F., Lucas, S., Chen, F., Nolan, M., Bruce, D., Goodwin, L., Pitluck, S., Ivanova, N., Mavromatis ,K., Ovchinnikova, G., Pati, A., Chen, A., Hauser, L., Chang, Y-Y., Jeffries, C.D., Saunders, L.,  Brettin, T., Detter, J.C., Han, C., Chain, P., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H-P., and Lapidus, A.

15.

SIGS

1(1): 12-20

Complete genome sequence of Kytococcus sedentarius type strain (strain 541T)

Sims, D., Brettin, T., Detter, JC., Han, C., Lapidus, A., Copeland, A., Glavina Del Rio, T., Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Ovchinnikova, G., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., D'haeseleer, P., Chain, P., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Schneider , S., Goker, M., Pukall, R., Kyrpides, N.C. and Klenk, H-P.

14.

SIGS

1(1): 3-11

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10T)

Lapidus, A., Pukall, R., LaButtii, K., Copeland, A., Glavina Del Rio, T., Nolan, M., Chen, F., Lucas, S., Tice, H., Cheng, J-F., Bruce, D., Goodwin, L., Pitluck, S., Rohde, M., Goker, M., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., D'haeseleer, P., Chain, P., Bristow, J., Eisen, J., Markowitz, V., Hugenholtz, P., Kyrpides, N. and Klenk, H-P.

13.

SIGS

1(1): 1-2

Standards in Genomic Sciences.

Garrity, G.M., Field, D., and Kyrpides N.C

12.

Nat Biotechnol.

27(7):627-32

Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream.

Kyrpides NC.

11.

Bioinformatics

25(17):2271-8

IMG ER: A System for Microbial Genome Annotation Expert Review and Curation.

Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC.

10.

Environmental Microbiology

11(6):1327-1625

Focus: Synergistetes

Hugenholtz, P, Hooper SD, Kyrpides NC.

9.

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.

8.

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.

7.

ISME J.

3(9):1012-35

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

6.

Genome Biology

10(4):R45

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

Hooper SD, Mavromatis K, Kyrpides NC.

5.

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.

4.

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.

3.

Environ Microbiol.

11(3):551-3

A changing of the guard.

Hugenholtz P, Kyrpides NC.

2.

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.

1.

 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.

 2008

21.

 Microbiol Mol Biol Rev.

72(4): 557-78

A bioinformatician's guide to metagenomics.

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

20.

BMC Genomics

9(1):547

Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach.

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

19.

Genome Biol.

9(11):R158

A genomic analysis of the archaeal system Ignicoccus hospitalis: Nanoarchaeum equitans.

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.

18.

Res Microbiol.

159(9-10):609-27

Prokaryotic community profiles at different operational stages of a Greek solar saltern.

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

17.

Nat Biotechnol.

26(9):1029-34

High-resolution metagenomics targets specific functional types in complex microbial communities.

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.

16.

Bioinformatics

24(16):i7-13

Annotation of metagenome short reads using proxygenes.

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

15.

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.

14.

OMICS

12(2):157-60

Toward a standards-compliant genomic and metagenomic publication record.

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.

13.

OMICS

12(2):109-13

Meeting Report: The Fifth Genomic Standards Consortium (GSC) Workshop.

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.

12.

OMICS

12(2):101-8

Meeting Report: The Fourth Genomic Standards Consortium (GSC) Workshop.

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.

11.

PNAS

105(23):8102-7

A korarchaeal genome reveals insights into the evolution of the Archaea.

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.

10.

Mol Syst Biol.

 4:198

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.

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

9.

OMICS

12(2):123-7

Laying the Foundation for a Genomic Rosetta Stone: Creating Information Hubs through the Use of Consensus Identifiers.

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.

8.

Nat Biotechnol.

26(5):541-7

The minimum information about a genome sequence (MIGS) specification.

Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Allen, 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.

7.

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.

6.

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.

5.

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.

4.

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.

3.

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.

2.

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.

1.

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.

 2007

11.

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.

10.

Methods Mol Biol.

395:35-56

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

Markowitz, VM., Kyrpides NC.

9.

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.

8.

Febs Lett.

581(24):4639-4644

Localization and regulation of mouse pantothenate kinase 2.

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

7.

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.

6.

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.

5.

Prog Lipid Res.

46(304): 171-99

Comparative genomics and evolution of eukaryotic phospholipid biosynthesis.

Lykidis, A.

4.

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

3.

Microbial Ecology

 53(3):507-11

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

Field, D and Kyrpides N

2.

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

1.

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

2006

8.

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.

7.

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.

6.

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

5.

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.

4.

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

3.

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.

2.

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.

1.

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.

2005

5.

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.

4.

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.

3.

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.

2.

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.

1.

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

2004

1.

Nature Biotechnology 22(12):1554-8

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.

  



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