|
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 |
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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
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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. |
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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. |
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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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