|
2010 |
|
SIGS
2(1):61-70 |
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. |
|
SIGS
2(1): 53-60 |
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. |
|
SIGS
2(1): 41-52 |
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. |
|
SIGS
2(1): 32-40 |
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. |
|
SIGS
2(1): 22-31 |
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. |
|
SIGS
2(1): 9-20 |
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 |
|
SIGS
2(1): 9-20 |
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 |
|
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.
|
|
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. |
|
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. |
|
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.
|
|
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. |
|
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. |
|
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 |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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.
|
|
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. |
|
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.
|
|
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. |
|
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.
|
|
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.
|
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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
|
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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.
|
|
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. |
|
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. |
|
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. |
|
SIGS
1(1): 1-2 |
Standards in Genomic Sciences.
Garrity, G.M., Field, D., and
Kyrpides N.C |
|
Nat
Biotechnol.
27(7):627-32 |
Fifteen years of microbial genomics:
meeting the challenges and fulfilling the dream.
Kyrpides NC. |
|
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. |
|
Environmental Microbiology
11(6):1327-1625 |
Focus: Synergistetes
Hugenholtz, P, Hooper SD, Kyrpides
NC. |
|
PLoS ONE
4(6):e5797 |
Genomic characterization of
methanomicrobiales reveals three classes of methanogens.
Anderson I, Ulrich LE, Lupa B,
Susanti D, Porat I, Hooper SD, Lykidis A, Sieprawska-Lupa M,
Dharmarajan L, Goltsman E, Lapidus A, Saunders E, Han C, Land M,
Lucas S, Mukhopadhyay B, Whitman WB, Woese C, Bristow J,
Kyrpides N. |
|
Genome
Biol.
10(5):R51 |
Genomic and genetic analyses of
diversity and plant interactions of Pseudomonas fluorescens.
Silby MW, Cerdeno-Tarraga AM,
Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon
CD, Gehrig SM, Godfrey SA, Knight CG, Malone JG, Robinson Z,
Spiers AJ, Harris S, Challis GL, Yaxley AM, Harris D, Seeger K,
Murphy L, Rutter S, Squares R, Quail MA, Saunders E, Mavromatis
K, Brettin TS, Bentley SD, Hothersall J, Stephens E, Thomas CM,
Parkhill J, Levy SB, Rainey PB, Thomson NR. |
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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 |
|
Genome
Biology
10(4):R45 |
Microbial co-habitation and lateral
gene transfer: what transposases can tell us
Hooper SD, Mavromatis K, Kyrpides
NC. |
|
Bioinformatics
25(7):977-8 |
OnTheFly: a tool for automated
document-based text annotation, data linking and network
generation.
Pavlopoulos GA,
Pafilis E, Kuhn M, Hooper SD, Schneider R. |
|
BMC
Genomics
10(1):145 |
The complete genome sequence of
Staphylothermus marinus reveals differences in sulfur
metabolism among heterotrophic Crenarchaeota.
Anderson IJ, Dharmarajan L,
Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis
K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin
IB, Whitman WB, Mukhopadhyay B, Woese C, Bristow J, Kyrpides N. |
|
Environ
Microbiol.
11(3):551-3 |
A changing of the guard.
Hugenholtz P, Kyrpides NC. |
|
Nucleic Acids Res.
37(7):2096-104 |
Integration of phenotypic metadata
and protein similarity in Archaea using a spectral
bipartitioning approach.
Hooper SD, Anderson IJ, Pati A,
Dalevi D, Mavromatis K, Kyrpides NC. |
|
PLoS
ONE
4(1):
e4192 |
Genome analysis of the anaerobic
thermohalophilic bacterium Halothermothrix orenii.
Mavromatis K, Ivanova N, Anderson I,
Lykidis A, Hooper SD, Sun H, Kunin V, Lapidus A, Hugenholtz P,
Patel B, Kyrpides NC. |
|
2008 |
|
Microbiol
Mol Biol Rev.
72(4):
557-78 |
A bioinformatician's guide to
metagenomics.
Kunin V, Copeland A, Lapidus A,
Mavromatis K, Hugenholtz P. |
|
BMC
Genomics
9(1):547 |
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. |
|
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. |
|
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. |
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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. |
|
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. |
|
PLoS
ONE. 3(7):e2607 |
A molecular study of microbe
transfer between distant environments.
Hooper SD, Raes J, Foerstner KU,
Harrington ED, Dalevi D, Bork P. |
|
OMICS
12(2):157-60 |
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
OMICS
12(2):137-41 |
Toward an Online Repository of Standard
Operating Procedures (SOPs) for (Meta)genomic Annotation.
Angiuoli , S.V., Gussman, G.,
Klimke, W., Cochrane, G., Field, D., Garrity, G., Kodira, C.D.,
Kyrpides, N.C., Madupu, R., Markowitz, V., Tatusova, T.,
Thomson, N., White, O. |
|
OMICS
12(2):129-36 |
Habitat-Lite: A GSC Case Study Based on Free
Text Terms for Environmental Metadata.
Hirschman, L., Clark, C., Bretonnel
Cohen, K., Mardis, S., Luciano, J., Kottmann, R., Cole, J.,
Markowitz, V., Kyrpides, N., Field. D. |
|
Genome Res.
18(2):293-7 |
A bacterial metapopulation adapts locally to
phage predation despite global dispersal.
Kunin V, He S, Warnecke F, Peterson
SB, Garcia Martin H, Haynes M, Ivanova N, Blackall LL, Breitbart
M, Rohwer F, McMahon KD, Hugenholtz P. |
|
J Bacteriology 190(8), 2957-65 |
Genome sequence of Thermofilum pendens
reveals an exceptional loss of biosynthetic pathways without
genome reduction.
Anderson, I., Rodriguez, J.,
Susanti, D., Porat, I., Recih, C., Ulrich, E., Elkins, JG.,
Mavromatis, K., Lykidis, A., Kim, E., Thompson, LS., Nolan, M.,
Land, M., Copeland, A., Lapidus, A., Lucas, S., Detter, C.,
Zhulin, IB., Olsen, G., Whitman, W., Mukhopadhyay, B., Bristow,
J. and Kyrpides, N.C. |
|
Nucleic Acids Res.
36, D534-8 |
IMG/M: a data management and analysis system
for metagenomes.
Markowitz VM, Ivanova NN, Szeto E,
Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I,
Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC. |
|
Nucleic Acids Res.
36, D528-33 |
The integrated microbial genomes (IMG) system in 2007: data
content and analysis tool extensions.
Markowitz VM, Szeto E, Palaniappan
K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A,
Mavromatis K, Ivanova NN, Kyrpides NC. |
|
Nucleic Acids Res.
36, D475-9 |
The Genomes On Line Database (GOLD) in 2007: status of
genomic and metagenomic projects and their associated metadata.
Liolios K, Mavromatis K,
Tavernarakis N, Kyrpides NC. |
|
2007 |
|
Nature
450(7169):560-5 |
Metagenomic and functional analysis of hindgut microbiota of
a wood-feeding higher termite.
Warnecke F, Luginbühl P, Ivanova N,
Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC,
Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin
HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E,
Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG,
Ottesen EA, Zhang X, Hernández M, Murillo C, Acosta LG,
Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ,
Robertson DE, Hugenholtz P, Leadbetter JR. |
|
Methods Mol Biol.
395:35-56 |
Comparative Genome Analysis in the Integrated Microbial
Genomes (IMG) System.
Markowitz, VM., Kyrpides NC. |
|
PLoS ONE
2(9):e955 |
Deinococcus geothermalis: The Pool of Extreme
Radiation Resistance Genes Shrinks
Makarova KS, Omelchenko MV,
Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Lapidus A,
Copeland A, Kim E, Land M, Mavromatis K, Pitluck S, Richardson
PM, Detter C, Brettin T, Saunders E, Lai B, Ravel B, Kemner KM,
Wolf YI, Sorokin A, Gerasimova AV, Gelfand MS, Fredrickson JK,
Koonin EV, Daly MJ. |
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Febs Lett.
581(24):4639-4644 |
Localization and regulation of
mouse pantothenate kinase 2.
Leonardi R, Zhang YM, Lykidis A,
Rock CO, Jackowski S. |
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Proc Natl Acad Sci USA
104(29):11889-94. |
Dissecting biological "dark matter"
with single-cell genetic analysis of rare and uncultivated TM7
microbes from the human mouth.
Marcy Y, Ouverney C, Bik EM,
Losekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz,
P Relman DA, Quake SR. |
|
BMC Bioinformatics
8(1): 209 |
CRISPR Recognition Tool (CRT): a
tool for automatic detection of clustered regularly interspaced
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Prog Lipid Res.
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Comparative genomics and evolution of eukaryotic phospholipid
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Nature Methods
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Use of simulated data sets to evaluate the
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Microbial Ecology
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The Positive Role of the Ecological Community in the Genomic
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Bioinformatics
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TreeQ-VISTA: An Interactive Tree
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Gu S, Anderson I, Kunin V, Cipriano
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J Bacteriology
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Genome Sequence and Analysis of
the Soil Cellulolytic Actinomycete Thermobifida fusca YX.
Lykidis, A,
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2006 |
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J Bacteriology
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The Methanosarcina barkeri
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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,
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Nature
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Symbiosis insights through
metagenomic analysis of a microbial consortium.
Woyke T, Teeling H,
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Nature Biotechnology.
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Metagenomic analysis of two
enhanced biological phosphorus removal (EBPR) sludge
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Martin HG, Ivanova N, Kunin V,
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Bioinformatics
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An experimental metagenome data
management and analysis system.
Markowitz VM, Ivanova N, Palaniappan
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J Bacteriology
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The Genome of the Obligately
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Mavromatis K, Doyle CK, Lykidis A,
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J Bacteriology
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Disruption of the operon encoding
Ehb hydrogenase limits anabolic CO2 assimilation in the archaeon
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Nucleic Acids Res. 34: D344-8 |
The Integrated Microbial Genomes
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Markowitz V, Korzeniewski F,
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Nucleic Acids Res. 34:D332-4 |
The Genomes On Line Database
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FEMS Microbiol Letters
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Comparative genome analysis of
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Anderson I, Sorokin A, Kapatral V,
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Kaznadzey D, Walunas T, Markd'souza, Larsen N, Pusch G, Liolios
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Proc Natl Acad Sci U S A
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Comparison of the complete genome
sequences of Pseudomonas syringae pv. syringae B728a and
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Feil H, Feil WS, Chain P, Larimer
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Goltsman E, Thiel J, Malfatti S, Loper JE, Lapidus A, Detter JC,
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PLoS Biology
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The Wolbachia genome of Brugia malayi:
endosymbiont evolution within a human pathogenic nematode.
Foster J, Ganatra M, Kamal I, Ware
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Posfai J, Vincze T, Ingram J, Moran L, Lapidus A, Omelchenko M,
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J Biol Chemistry 280(35):30856-63. |
Peptidoglycan N-Acetylglucosamine
Deacetylases from Bacillus cereus, Highly Conserved Proteins in
Bacillus anthracis.
Psylinakis E, Boneca IG,
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The Integrated Microbial Genomes (IMG)
System, A Case Study in Biological Data Management.
Markowitz, VM, Korzeniewski, F,
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Nature Biotechnology 22(12):1554-8 |
Complete sequence and comparative
genome analysis of the dairy bacterium Streptococcus
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Bolotin A, Quinquis B, Renault P,
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Mazur M, Pusch GD, Fonstein M, Overbeek R, Kyprides N, Purnelle
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