-
1
-
-
83855165105
-
Repetitive DNA and next-generation sequencing: Computational challenges and solutions
-
22124482
-
Repetitive DNA and next-generation sequencing: computational challenges and solutions. Treangen TJ, Salzberg SL, Nat Rev Genet 2011 13 36 46 22124482
-
(2011)
Nat Rev Genet
, vol.13
, pp. 36-46
-
-
Treangen, T.J.1
Salzberg, S.L.2
-
2
-
-
70349866672
-
Genomics. Genome project standards in a new era of sequencing
-
10.1126/science.1180614 19815760
-
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, et al. Science 2009 326 236 237 10.1126/science.1180614 19815760
-
(2009)
Science
, vol.326
, pp. 236-237
-
-
Chain, P.S.1
Grafham, D.V.2
Fulton, R.S.3
Fitzgerald, M.G.4
Hostetler, J.5
Muzny, D.6
Ali, J.7
Birren, B.8
Bruce, D.C.9
Buhay, C.10
Cole, J.R.11
Ding, Y.12
Dugan, S.13
Field, D.14
Garrity, G.M.15
Gibbs, R.16
Graves, T.17
Han, C.S.18
Harrison, S.H.19
Highlander, S.20
Hugenholtz, P.21
Khouri, H.M.22
Kodira, C.D.23
Kolker, E.24
Kyrpides, N.C.25
Lang, D.26
Lapidus, A.27
Malfatti, S.A.28
Markowitz, V.29
Metha, T.30
more..
-
3
-
-
84874194145
-
Sequence assembly demystified
-
10.1038/nrg3367 23358380
-
Sequence assembly demystified. Nagarajan N, Pop M, Nat Rev Genet 2013 14 157 167 10.1038/nrg3367 23358380
-
(2013)
Nat Rev Genet
, vol.14
, pp. 157-167
-
-
Nagarajan, N.1
Pop, M.2
-
4
-
-
84857893016
-
GAGE: A critical evaluation of genome assemblies and assembly algorithms
-
10.1101/gr.131383.111 22147368
-
GAGE: A critical evaluation of genome assemblies and assembly algorithms. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marcais G, Pop M, Yorke JA, Genome Res 2012 22 557 567 10.1101/gr.131383.111 22147368
-
(2012)
Genome Res
, vol.22
, pp. 557-567
-
-
Salzberg, S.L.1
Phillippy, A.M.2
Zimin, A.3
Puiu, D.4
Magoc, T.5
Koren, S.6
Treangen, T.J.7
Schatz, M.C.8
Delcher, A.L.9
Roberts, M.10
Marcais, G.11
Pop, M.12
Yorke, J.A.13
-
5
-
-
84871205244
-
The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation
-
10.1371/journal.pone.0048837 23251337
-
The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, Goodwin L, Woyke T, Lapidus A, Klenk HP, Cottingham RW, Kyrpides NC, PLoS ONE 2012 7 48837 10.1371/journal.pone.0048837 23251337
-
(2012)
PLoS ONE
, vol.7
, pp. 548837
-
-
Mavromatis, K.1
Land, M.L.2
Brettin, T.S.3
Quest, D.J.4
Copeland, A.5
Clum, A.6
Goodwin, L.7
Woyke, T.8
Lapidus, A.9
Klenk, H.P.10
Cottingham, R.W.11
Kyrpides, N.C.12
-
6
-
-
84875483479
-
Genome sequencing of bacteria: Sequencing, de novo assembly and rapid analysis using open source tools
-
10.1186/1471-2164-14-211 23547799
-
Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools. Kisand V, Lettieri T, BMC Genomics 2013 14 211 10.1186/1471-2164-14-211 23547799
-
(2013)
BMC Genomics
, vol.14
, pp. 211
-
-
Kisand, V.1
Lettieri, T.2
-
7
-
-
84880196418
-
GAGE-B: An evaluation of genome assemblers for bacterial organisms
-
10.1093/bioinformatics/btt273 23665771
-
GAGE-B: an evaluation of genome assemblers for bacterial organisms. Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL, Bioinformatics 2013 29 1718 1725 10.1093/bioinformatics/btt273 23665771
-
(2013)
Bioinformatics
, vol.29
, pp. 1718-1725
-
-
Magoc, T.1
Pabinger, S.2
Canzar, S.3
Liu, X.4
Su, Q.5
Puiu, D.6
Tallon, L.J.7
Salzberg, S.L.8
-
8
-
-
43849099955
-
Microbiology in the post-genomic era
-
DOI 10.1038/nrmicro1901, PII NRMICRO1901
-
Microbiology in the post-genomic era. Medini D, Serruto D, Parkhill J, Relman DA, Donati C, Moxon R, Falkow S, Rappuoli R, Nat Rev Micro 2008 6 419 430 (Pubitemid 351696436)
-
(2008)
Nature Reviews Microbiology
, vol.6
, Issue.6
, pp. 419-430
-
-
Medini, D.1
Serruto, D.2
Parkhill, J.3
Relman, D.A.4
Donati, C.5
Moxon, R.6
Falkow, S.7
Rappuoli, R.8
-
9
-
-
84900460571
-
Genome sequence of the mercury-methylating strain Desulfovibrio desulfuricans ND132
-
Genome sequence of the mercury-methylating strain Desulfovibrio desulfuricans ND132. Brown SD, Gilmour CC, Kucken AM, Wall JD, Elias DA, Brandt CC, Podar M, Chertkov O, Held B, Bruce DC, Detter JC, Tapia R, Han CS, Goodwin LA, Cheng J-F, Pitluck S, Woyke T, Mikhailova N, Ivanova NN, Han J, Lucas S, Lapidus AL, Land ML, Hauser LJ, Palumbo AV, J Bacteriol 2078-2079 2011 193
-
J Bacteriol
, vol.2011
, pp. 193
-
-
Brown, S.D.1
Gilmour, C.C.2
Kucken, A.M.3
Wall, J.D.4
Elias, D.A.5
Brandt, C.C.6
Podar, M.7
Chertkov, O.8
Held, B.9
Bruce, D.C.10
Detter, J.C.11
Tapia, R.12
Han, C.S.13
Goodwin, L.A.14
Cheng, J.-F.15
Pitluck, S.16
Woyke, T.17
Mikhailova, N.18
Ivanova, N.N.19
Han, J.20
Lucas, S.21
Lapidus, A.L.22
Land, M.L.23
Hauser, L.J.24
Palumbo, A.V.25
more..
-
10
-
-
84856557873
-
Feature-by-feature - Evaluating de novo sequence assembly
-
10.1371/journal.pone.0031002 22319599
-
Feature-by-feature-evaluating de novo sequence assembly. Vezzi F, Narzisi G, Mishra B, PLoS One 2012 7 31002 10.1371/journal.pone.0031002 22319599
-
(2012)
PLoS One
, vol.7
, pp. 531002
-
-
Vezzi, F.1
Narzisi, G.2
Mishra, B.3
-
11
-
-
84878076144
-
REAPR: A universal tool for genome assembly evaluation
-
10.1186/gb-2013-14-5-r47 23710727
-
REAPR: a universal tool for genome assembly evaluation. Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto T, Genome Biol 2013 14 47 10.1186/gb-2013-14-5-r47 23710727
-
(2013)
Genome Biol
, vol.14
, pp. 1847
-
-
Hunt, M.1
Kikuchi, T.2
Sanders, M.3
Newbold, C.4
Berriman, M.5
Otto, T.6
-
12
-
-
84876266928
-
QUAST: Quality assessment tool for genome assemblies
-
10.1093/bioinformatics/btt086 23422339
-
QUAST: quality assessment tool for genome assemblies. Gurevich A, Saveliev V, Vyahhi N, Tesler G, Bioinformatics 2013 29 1072 1075 10.1093/bioinformatics/btt086 23422339
-
(2013)
Bioinformatics
, vol.29
, pp. 1072-1075
-
-
Gurevich, A.1
Saveliev, V.2
Vyahhi, N.3
Tesler, G.4
-
13
-
-
84872968454
-
CGAL: Computing genome assembly likelihoods
-
10.1186/gb-2013-14-1-r8 23360652
-
CGAL: computing genome assembly likelihoods. Rahman A, Pachter L, Genome Biol 2013 14 8 10.1186/gb-2013-14-1-r8 23360652
-
(2013)
Genome Biol
, vol.14
, pp. 188
-
-
Rahman, A.1
Pachter, L.2
-
14
-
-
84883664726
-
Reducing assembly complexity of microbial genomes with single-molecule sequencing
-
10.1186/gb-2013-14-9-r101 24034426
-
Reducing assembly complexity of microbial genomes with single-molecule sequencing. Koren S, Harhay G, Smith T, Bono J, Harhay D, Mcvey S, Radune D, Bergman N, Phillippy A, Genome Biol 2013 14 101 10.1186/gb-2013-14-9-r101 24034426
-
(2013)
Genome Biol
, vol.14
, pp. 18101
-
-
Koren, S.1
Harhay, G.2
Smith, T.3
Bono, J.4
Harhay, D.5
McVey, S.6
Radune, D.7
Bergman, N.8
Phillippy, A.9
-
15
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
10.1126/science.1162986 19023044
-
Real-time DNA sequencing from single polymerase molecules. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Science 2009 323 133 138 10.1126/science.1162986 19023044
-
(2009)
Science
, vol.323
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
Luong, K.4
Lyle, J.5
Otto, G.6
Peluso, P.7
Rank, D.8
Baybayan, P.9
Bettman, B.10
Bibillo, A.11
Bjornson, K.12
Chaudhuri, B.13
Christians, F.14
Cicero, R.15
Clark, S.16
Dalal, R.17
Dewinter, A.18
Dixon, J.19
Foquet, M.20
Gaertner, A.21
Hardenbol, P.22
Heiner, C.23
Hester, K.24
Holden, D.25
Kearns, G.26
Kong, X.27
Kuse, R.28
Lacroix, Y.29
Lin, S.30
more..
-
16
-
-
84865591846
-
A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
-
10.1186/1471-2164-13-341 22827831
-
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. Quail M, Smith M, Coupland P, Otto T, Harris S, Connor T, Bertoni A, Swerdlow H, Gu Y, BMC Genomics 2012 13 341 10.1186/1471-2164-13-341 22827831
-
(2012)
BMC Genomics
, vol.13
, pp. 341
-
-
Quail, M.1
Smith, M.2
Coupland, P.3
Otto, T.4
Harris, S.5
Connor, T.6
Bertoni, A.7
Swerdlow, H.8
Gu, Y.9
-
17
-
-
84863664355
-
A hybrid approach for the automated finishing of bacterial genomes
-
10.1038/nbt.2288 22750883
-
A hybrid approach for the automated finishing of bacterial genomes. Bashir A, Klammer AA, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, Mollova E, Luong K, Lin S, LaMay B, Joshi A, Rowe L, Frace M, Tarr CL, Turnsek M, Davis BM, Kasarskis A, Mekalanos JJ, Waldor MK, Schadt EE, Nat Biotechnol 2012 30 701 707 10.1038/nbt.2288 22750883
-
(2012)
Nat Biotechnol
, vol.30
, pp. 701-707
-
-
Bashir, A.1
Klammer, A.A.2
Robins, W.P.3
Chin, C.S.4
Webster, D.5
Paxinos, E.6
Hsu, D.7
Ashby, M.8
Wang, S.9
Peluso, P.10
Sebra, R.11
Sorenson, J.12
Bullard, J.13
Yen, J.14
Valdovino, M.15
Mollova, E.16
Luong, K.17
Lin, S.18
Lamay, B.19
Joshi, A.20
Rowe, L.21
Frace, M.22
Tarr, C.L.23
Turnsek, M.24
Davis, B.M.25
Kasarskis, A.26
Mekalanos, J.J.27
Waldor, M.K.28
Schadt, E.E.29
more..
-
18
-
-
84869814079
-
Mind the gap: Upgrading genomes with Pacific Biosciences RS long-read sequencing technology
-
10.1371/journal.pone.0047768 23185243
-
Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA, PLoS One 2012 7 47768 10.1371/journal.pone.0047768 23185243
-
(2012)
PLoS One
, vol.7
, pp. 547768
-
-
English, A.C.1
Richards, S.2
Han, Y.3
Wang, M.4
Vee, V.5
Qu, J.6
Qin, X.7
Muzny, D.M.8
Reid, J.G.9
Worley, K.C.10
Gibbs, R.A.11
-
19
-
-
64349087443
-
Genesis, effects and fates of repeats in prokaryotic genomes
-
10.1111/j.1574-6976.2009.00169.x 19396957
-
Genesis, effects and fates of repeats in prokaryotic genomes. Treangen TJ, Abraham A-L, Touchon M, Rocha EPC, FEMS Microbiol Rev 2009 33 539 571 10.1111/j.1574-6976.2009.00169.x 19396957
-
(2009)
FEMS Microbiol Rev
, vol.33
, pp. 539-571
-
-
Treangen, T.J.1
Abraham, A.-L.2
Touchon, M.3
Rocha, E.P.C.4
-
20
-
-
84880798154
-
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
-
10.1038/nmeth.2474 23644548
-
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J, Nat Methods 2013 10 563 569 10.1038/nmeth.2474 23644548
-
(2013)
Nat Methods
, vol.10
, pp. 563-569
-
-
Chin, C.S.1
Alexander, D.H.2
Marks, P.3
Klammer, A.A.4
Drake, J.5
Heiner, C.6
Clum, A.7
Copeland, A.8
Huddleston, J.9
Eichler, E.E.10
Turner, S.W.11
Korlach, J.12
-
21
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
10.1038/nbt.2280 22750884
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads. Koren S, Schatz M, Walenz B, Martin J, Howard J, Ganapathy G, Wang Z, Rasko D, McCombie W, Jarvis E, Phillippy A, Nat Biotechnol 2012 30 693 700 10.1038/nbt.2280 22750884
-
(2012)
Nat Biotechnol
, vol.30
, pp. 693-700
-
-
Koren, S.1
Schatz, M.2
Walenz, B.3
Martin, J.4
Howard, J.5
Ganapathy, G.6
Wang, Z.7
Rasko, D.8
McCombie, W.9
Jarvis, E.10
Phillippy, A.11
-
22
-
-
84883745092
-
The advantages of SMRT sequencing
-
10.1186/gb-2013-14-6-405 23822731
-
The advantages of SMRT sequencing. Roberts R, Carneiro M, Schatz M, Genome Biol 2013 14 405 10.1186/gb-2013-14-6-405 23822731
-
(2013)
Genome Biol
, vol.14
, pp. 405
-
-
Roberts, R.1
Carneiro, M.2
Schatz, M.3
-
23
-
-
84997783038
-
De novo assembly of the Streptomyces sp. Strain Mg1 genome using PacBio single-molecule sequencing
-
De novo assembly of the Streptomyces sp. strain Mg1 genome using PacBio single-molecule sequencing. Hoefler BC, Konganti K, Straight PD, Genome Announc 2013 1 1:e00535 00513
-
(2013)
Genome Announc
, vol.1
-
-
Hoefler, B.C.1
Konganti, K.2
Straight, P.D.3
-
24
-
-
80052150179
-
Origins of the E. Coli strain causing an outbreak of hemolytic-uremic syndrome in Germany
-
10.1056/NEJMoa1106920
-
Origins of the E. Coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin C-S, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Møller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK, N Eng J Med 2011 365 709 717 10.1056/NEJMoa1106920
-
(2011)
N Eng J Med
, vol.365
, pp. 709-717
-
-
Rasko, D.A.1
Webster, D.R.2
Sahl, J.W.3
Bashir, A.4
Boisen, N.5
Scheutz, F.6
Paxinos, E.E.7
Sebra, R.8
Chin, C.-S.9
Iliopoulos, D.10
Klammer, A.11
Peluso, P.12
Lee, L.13
Kislyuk, A.O.14
Bullard, J.15
Kasarskis, A.16
Wang, S.17
Eid, J.18
Rank, D.19
Redman, J.C.20
Steyert, S.R.21
Frimodt-Møller, J.22
Struve, C.23
Petersen, A.M.24
Krogfelt, K.A.25
Nataro, J.P.26
Schadt, E.E.27
Waldor, M.K.28
more..
-
25
-
-
84884854581
-
Efficient and accurate whole genome assembly and methylome profiling of E. Coli
-
10.1186/1471-2164-14-675 24090403
-
Efficient and accurate whole genome assembly and methylome profiling of E. Coli. Powers JG, Weigman VJ, Shu J, Pufky JM, Cox D, Hurban P, BMC Genomics 2013 14 675 10.1186/1471-2164-14-675 24090403
-
(2013)
BMC Genomics
, vol.14
, pp. 675
-
-
Powers, J.G.1
Weigman, V.J.2
Shu, J.3
Pufky, J.M.4
Cox, D.5
Hurban, P.6
-
26
-
-
84997585139
-
Genome sequence of the autotrophic acetogen Clostridium autoethanogenum JA1-1 strain DSM 10061, a producer of ethanol from carbon monoxide
-
23950130
-
Genome sequence of the autotrophic acetogen Clostridium autoethanogenum JA1-1 strain DSM 10061, a producer of ethanol from carbon monoxide. Bruno-Barcena JM, Chinn MS, Grunden AM, Genome Announc 2013 1 00628 00613 23950130
-
(2013)
Genome Announc
, vol.1
, pp. 500628-600613
-
-
Bruno-Barcena, J.M.1
Chinn, M.S.2
Grunden, A.M.3
-
27
-
-
0028298999
-
Clostridium autoethanogenum, sp. Nov., an anaerobic bacterium that produces ethanol from carbon monoxide
-
DOI 10.1007/s002030050065
-
Clostridium autoethanogenum, sp. nov., an anaerobic bacterium that produces ethanol from carbon monoxide. Abrini J, Naveau H, Nyns EJ, Arch Microbiol 1994 161 345 351 10.1007/BF00303591 (Pubitemid 24133426)
-
(1994)
Archives of Microbiology
, vol.161
, Issue.4
, pp. 345-351
-
-
Abrini, J.1
Naveau, H.2
Nyns, E.-J.3
-
28
-
-
77955610491
-
Clostridium ljungdahlii represents a microbial production platform based on syngas
-
10.1073/pnas.1004716107 20616070
-
Clostridium ljungdahlii represents a microbial production platform based on syngas. Köpke M, Held C, Hujer S, Liesegang H, Wiezer A, Wollherr A, Ehrenreich A, Liebl W, Gottschalk G, Dürre P, Proc Natl Acad Sci USA 2010 107 13087 13092 10.1073/pnas.1004716107 20616070
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 13087-13092
-
-
Köpke, M.1
Held, C.2
Hujer, S.3
Liesegang, H.4
Wiezer, A.5
Wollherr, A.6
Ehrenreich, A.7
Liebl, W.8
Gottschalk, G.9
Dürre, P.10
-
29
-
-
79957995288
-
Fermentative production of ethanol from carbon monoxide
-
10.1016/j.copbio.2011.01.005 21353524
-
Fermentative production of ethanol from carbon monoxide. Köpke M, Mihalcea C, Bromley JC, Simpson SD, Curr Opin Biotechnol 2011 22 320 325 10.1016/j.copbio.2011.01.005 21353524
-
(2011)
Curr Opin Biotechnol
, vol.22
, pp. 320-325
-
-
Köpke, M.1
Mihalcea, C.2
Bromley, J.C.3
Simpson, S.D.4
-
30
-
-
79961098783
-
2,3-butanediol production by acetogenic bacteria, an alternative route to chemical synthesis, using industrial waste gas
-
10.1128/AEM.00355-11 21685168
-
2,3-butanediol production by acetogenic bacteria, an alternative route to chemical synthesis, using industrial waste gas. Köpke M, Mihalcea C, Liew F-M, Tizard JH, Ali MS, Conolly JJ, Al-Sinawi B, Simpson SD, Appl Environ Microbiol 2011 77 5467 5475 10.1128/AEM.00355-11 21685168
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 5467-5475
-
-
Köpke, M.1
Mihalcea, C.2
Liew, F.-M.3
Tizard, J.H.4
Ali, M.S.5
Conolly, J.J.6
Al-Sinawi, B.7
Simpson, S.D.8
-
31
-
-
77951644817
-
Production of biofuels from synthesis gas using microbial catalysts
-
Laskin AI, Sariaslani S, Gadd GM Advances in Applied Microbiology
-
Production of Biofuels from Synthesis Gas Using Microbial Catalysts. Tirado-Acevedo O, Chinn MS, Grunden AM, Production of Biofuels from Synthesis Gas Using Microbial Catalysts, Volume 70, Laskin AI, Sariaslani S, Gadd GM, Advances in Applied Microbiology. 2010 57 92
-
(2010)
Production of Biofuels from Synthesis Gas Using Microbial Catalysts, Volume 70
, pp. 57-92
-
-
Tirado-Acevedo, O.1
Chinn, M.S.2
Grunden, A.M.3
-
32
-
-
81855183336
-
Bioconversion of synthesis gas to second generation biofuels: A review
-
10.1016/j.rser.2011.07.124
-
Bioconversion of synthesis gas to second generation biofuels: A review. Mohammadi M, Najafpour GD, Younesi H, Lahijani P, Uzir MH, Mohamed AR, Renew Sustain Energ Rev 2011 15 4255 4273 10.1016/j.rser.2011.07.124
-
(2011)
Renew Sustain Energ Rev
, vol.15
, pp. 4255-4273
-
-
Mohammadi, M.1
Najafpour, G.D.2
Younesi, H.3
Lahijani, P.4
Uzir, M.H.5
Mohamed, A.R.6
-
33
-
-
77949875923
-
Biomass-derived syngas fermentation into biofuels: Opportunities and challenges
-
10.1016/j.biortech.2009.12.098
-
Biomass-derived syngas fermentation into biofuels: Opportunities and challenges. Munasinghe PC, Khanal SK, Biores Technol 2010 101 5013 5022 10.1016/j.biortech.2009.12.098
-
(2010)
Biores Technol
, vol.101
, pp. 5013-5022
-
-
Munasinghe, P.C.1
Khanal, S.K.2
-
34
-
-
84860771820
-
SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
-
10.1089/cmb.2012.0021 22506599
-
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko S, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA, J Comput Biol 2012 19 455 477 10.1089/cmb.2012.0021 22506599
-
(2012)
J Comput Biol
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
Kulikov, A.S.6
Lesin, V.M.7
Nikolenko, S.8
Pham, S.9
Prjibelski, A.D.10
Pyshkin, A.V.11
Sirotkin, A.V.12
Vyahhi, N.13
Tesler, G.14
Alekseyev, M.A.15
Pevzner, P.A.16
-
35
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
DOI 10.1101/gr.074492.107
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Zerbino DR, Birney E, Genome Res 2008 18 821 829 10.1101/gr.074492.107 18349386 (Pubitemid 351645072)
-
(2008)
Genome Research
, vol.18
, Issue.5
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
36
-
-
66449136667
-
ABySS: A parallel assembler for short read sequence data
-
10.1101/gr.089532.108 19251739
-
ABySS: A parallel assembler for short read sequence data. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I Genome Res 2009 19 1117 1123 10.1101/gr.089532.108 19251739
-
(2009)
Genome Res
, vol.19
, pp. 1117-1123
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.M.5
Birol, I.6
-
37
-
-
84861205566
-
Draft genome sequence of Rhizobium sp. Strain PDO1-076, a bacterium isolated from Populus deltoides
-
10.1128/JB.00198-12 22493196
-
Draft genome sequence of Rhizobium sp. strain PDO1-076, a bacterium isolated from Populus deltoides. Brown SD, Klingeman DM, Lu TY, Johnson CM, Utturkar SM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, J Bacteriol 2012 194 2383 2384 10.1128/JB.00198-12 22493196
-
(2012)
J Bacteriol
, vol.194
, pp. 2383-2384
-
-
Brown, S.D.1
Klingeman, D.M.2
Lu, T.Y.3
Johnson, C.M.4
Utturkar, S.M.5
Land, M.L.6
Schadt, C.W.7
Doktycz, M.J.8
Pelletier, D.A.9
-
38
-
-
84863992229
-
Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2
-
10.1128/JB.00473-12 22628515
-
Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2. Brown SD, Lamed R, Morag E, Borovok I, Shoham Y, Klingeman DM, Johnson CM, Yang Z, Land ML, Utturkar SM, Keller M, Bayer EA, J Bacteriol 2012 194 3290 3291 10.1128/JB.00473-12 22628515
-
(2012)
J Bacteriol
, vol.194
, pp. 3290-3291
-
-
Brown, S.D.1
Lamed, R.2
Morag, E.3
Borovok, I.4
Shoham, Y.5
Klingeman, D.M.6
Johnson, C.M.7
Yang, Z.8
Land, M.L.9
Utturkar, S.M.10
Keller, M.11
Bayer, E.A.12
-
39
-
-
84866358341
-
Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7
-
10.1128/JB.01174-12 22933770
-
Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7. Brown SD, Podar M, Klingeman DM, Johnson CM, Yang ZK, Utturkar SM, Land ML, Mosher JJ, Hurt RA Jr, Phelps TJ, Palumbo AV, Arkin AP, Hazen TC, Elias DA, J Bacteriol 2012 194 5147 5148 10.1128/JB.01174-12 22933770
-
(2012)
J Bacteriol
, vol.194
, pp. 5147-5148
-
-
Brown, S.D.1
Podar, M.2
Klingeman, D.M.3
Johnson, C.M.4
Yang, Z.K.5
Utturkar, S.M.6
Land, M.L.7
Mosher, J.J.8
-
40
-
-
78049441882
-
Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T
-
10.1128/JB.00950-10 20851897
-
Complete genome sequence of the cellulolytic thermophile Caldicellulosiruptor obsidiansis OB47T. Elkins JG, Lochner A, Hamilton-Brehm SD, Davenport KW, Podar M, Brown SD, Land ML, Hauser LJ, Klingeman DM, Raman B, Goodwin LA, Tapia R, Meincke LJ, Detter JC, Bruce DC, Han CS, Palumbo AV, Cottingham RW, Keller M, Graham DE, J Bacteriol 2010 192 6099 6100 10.1128/JB.00950-10 20851897
-
(2010)
J Bacteriol
, vol.192
, pp. 6099-6100
-
-
Elkins, J.G.1
Lochner, A.2
Hamilton-Brehm, S.D.3
Davenport, K.W.4
Podar, M.5
Brown, S.D.6
Land, M.L.7
Hauser, L.J.8
Klingeman, D.M.9
Raman, B.10
Goodwin, L.A.11
Tapia, R.12
Meincke, L.J.13
Detter, J.C.14
Bruce, D.C.15
Han, C.S.16
Palumbo, A.V.17
Cottingham, R.W.18
Keller, M.19
Graham, D.E.20
more..
-
41
-
-
84997834642
-
Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals
-
23792749
-
Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals. Utturkar SM, Bollmann A, Brzoska RM, Klingeman DM, Epstein SE, Palumbo AV, Brown SD, Genome Announc 2013 1 00322 00313 23792749
-
(2013)
Genome Announc
, vol.1
, pp. 500322-600313
-
-
Utturkar, S.M.1
Bollmann, A.2
Brzoska, R.M.3
Klingeman, D.M.4
Epstein, S.E.5
Palumbo, A.V.6
Brown, S.D.7
-
42
-
-
84997605221
-
Draft Genome Sequence for Ralstonia sp. Strain OR214, a Bacterium with Potential for Bioremediation
-
23792748
-
Draft Genome Sequence for Ralstonia sp. Strain OR214, a Bacterium with Potential for Bioremediation. Utturkar SM, Bollmann A, Brzoska RM, Klingeman DM, Epstein SE, Palumbo AV, Brown SD, Genome Announc 2013 1 00321 00313 23792748
-
(2013)
Genome Announc
, vol.1
, pp. 500321-600313
-
-
Utturkar, S.M.1
Bollmann, A.2
Brzoska, R.M.3
Klingeman, D.M.4
Epstein, S.E.5
Palumbo, A.V.6
Brown, S.D.7
-
43
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
10.1186/1471-2105-11-119 20211023
-
Prodigal: prokaryotic gene recognition and translation initiation site identification. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ, BMC Bioinformatics 2010 11 119 10.1186/1471-2105-11-119 20211023
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
Chen, G.L.2
Locascio, P.F.3
Land, M.L.4
Larimer, F.W.5
Hauser, L.J.6
-
44
-
-
61349123255
-
Influence of process parameters on growth of Clostridium ljungdahlii and Clostridium autoethanogenum on synthesis gas
-
10.1016/j.enzmictec.2008.11.002
-
Influence of process parameters on growth of Clostridium ljungdahlii and Clostridium autoethanogenum on synthesis gas. Cotter JL, Chinn MS, Grunden AM, Enzym Microb Tech 2009 44 281 288 10.1016/j.enzmictec.2008.11.002
-
(2009)
Enzym Microb Tech
, vol.44
, pp. 281-288
-
-
Cotter, J.L.1
Chinn, M.S.2
Grunden, A.M.3
-
45
-
-
62949105310
-
Ethanol and acetate production by Clostridium ljungdahlii and Clostridium autoethanogenum using resting cells
-
10.1007/s00449-008-0256-y
-
Ethanol and acetate production by Clostridium ljungdahlii and Clostridium autoethanogenum using resting cells. Cotter JL, Chinn MS, Grunden AM, Bioproc Biosyst Eng 2009 32 369 380 10.1007/s00449-008-0256-y
-
(2009)
Bioproc Biosyst Eng
, vol.32
, pp. 369-380
-
-
Cotter, J.L.1
Chinn, M.S.2
Grunden, A.M.3
-
46
-
-
84892649883
-
Influence of carbon source preadaptation on Clostridium ljungdahlii growth and product formation
-
Influence of carbon source preadaptation on Clostridium ljungdahlii growth and product formation. Tirado-Acevedo O, Cotter JL, Chinn MS, Grunden AM, J Bioprocess Biotechniq 2011 S2 001
-
(2011)
J Bioprocess Biotechniq
, vol.2
, pp. 001
-
-
Tirado-Acevedo, O.1
Cotter, J.L.2
Chinn, M.S.3
Grunden, A.M.4
-
47
-
-
0027460190
-
Clostridium ljungdahlii sp. Nov., an acetogenic species in clostridial rRNA homology group I
-
Clostridium ljungdahlii sp. nov., an acetogenic species in Clostridial rRNA homology group I. Tanner RS, Miller LM, Yang D, Int J Syst Bacteriol 1993 43 232 236 10.1099/00207713-43-2-232 7684239 (Pubitemid 23118460)
-
(1993)
International Journal of Systematic Bacteriology
, vol.43
, Issue.2
, pp. 232-236
-
-
Tanner, R.S.1
Miller, L.M.2
Yang, D.3
-
48
-
-
0032781650
-
Phylogenetic basis for a taxonomic dissection of the genus Clostridium
-
DOI 10.1016/S0928-8244(99)00039-5, PII S0928824499000395
-
Phylogenetic basis for a taxonomic dissection of the genus Clostridium. Stackebrandt E, Kramer I, Swiderski J, Hippe H, FEMS Immunol Med Microbiol 1999 24 253 258 10.1111/j.1574-695X.1999.tb01291.x 10397308 (Pubitemid 29332600)
-
(1999)
FEMS Immunology and Medical Microbiology
, vol.24
, Issue.3
, pp. 253-258
-
-
Stackebrandt, E.1
Kramer, I.2
Swiderski, J.3
Hippe, H.4
-
49
-
-
33644787447
-
OrthoMCL-DB: Querying a comprehensive multi-species collection of ortholog groups
-
10.1093/nar/gkj123 16381887
-
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Chen F, Mackey AJ, Stoeckert CJ Jr, Roos DS, Nucleic Acids Res 2006 34 363 D368 10.1093/nar/gkj123 16381887
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Chen, F.1
Mackey, A.J.2
Stoeckert Jr., J.C.3
Roos, D.S.4
-
50
-
-
0026112556
-
2 as a source of carbon and energy
-
2 as a source of carbon and energy. Wood HG, FASEB J 1991 5 156 163 1900793 (Pubitemid 21892874)
-
(1991)
FASEB Journal
, vol.5
, Issue.2
, pp. 156-163
-
-
Wood, H.G.1
-
51
-
-
84876573682
-
Clostridium difficile is an autotrophic bacterial pathogen
-
10.1371/journal.pone.0062157 23626782
-
Clostridium difficile is an autotrophic bacterial pathogen. Köpke M, Straub M, Dürre P, PLoS One 2013 8 62157 10.1371/journal.pone.0062157 23626782
-
(2013)
PLoS One
, vol.8
, pp. 562157
-
-
Köpke, M.1
Straub, M.2
Dürre, P.3
-
52
-
-
84884198848
-
NADP-specific electron-bifurcating [FeFe]-hydrogenase in a functional complex with formate dehydrogenase in Clostridium autoethanogenum grown on CO
-
10.1128/JB.00678-13 23893107
-
NADP-specific electron-bifurcating [FeFe]-hydrogenase in a functional complex with formate dehydrogenase in Clostridium autoethanogenum grown on CO. Wang S, Huang H, Kahnt J, Mueller AP, Köpke M, Thauer RK, J Bacteriol 2013 195 4373 4386 10.1128/JB.00678-13 23893107
-
(2013)
J Bacteriol
, vol.195
, pp. 4373-4386
-
-
Wang, S.1
Huang, H.2
Kahnt, J.3
Mueller, A.P.4
Köpke, M.5
Thauer, R.K.6
-
53
-
-
80755187812
-
CRISPR-Cas systems in Bacteria and Archaea: Versatile small RNAs for adaptive defense and regulation
-
10.1146/annurev-genet-110410-132430 22060043
-
CRISPR-Cas systems in Bacteria and Archaea: Versatile small RNAs for adaptive defense and regulation. Bhaya D, Davison M, Barrangou R, Ann Rev Genet 2011 45 273 297 10.1146/annurev-genet-110410-132430 22060043
-
(2011)
Ann Rev Genet
, vol.45
, pp. 273-297
-
-
Bhaya, D.1
Davison, M.2
Barrangou, R.3
-
54
-
-
39149142575
-
CRISPR - A widespread system that provides acquired resistance against phages in bacteria and archaea
-
DOI 10.1038/nrmicro1793, PII NRMICRO1793
-
CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea. Sorek R, Kunin V, Hugenholtz P, Nat Rev Microbiol 2008 6 181 186 10.1038/nrmicro1793 18157154 (Pubitemid 351256313)
-
(2008)
Nature Reviews Microbiology
, vol.6
, Issue.3
, pp. 181-186
-
-
Sorek, R.1
Kunin, V.2
Hugenholtz, P.3
-
55
-
-
34248400310
-
A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
-
A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. Haft DH, Selengut J, Mongodin EF, Nelson KE, PloS Comp Biol 2005 1 474 483
-
(2005)
PloS Comp Biol
, vol.1
, pp. 474-483
-
-
Haft, D.H.1
Selengut, J.2
Mongodin, E.F.3
Nelson, K.E.4
-
56
-
-
79956157571
-
Evolution and classification of the CRISPR-Cas systems
-
10.1038/nrmicro2577 21552286
-
Evolution and classification of the CRISPR-Cas systems. Makarova KS, Haft DH, Barrangou R, Brouns SJJ, Charpentier E, Horvath P, Moineau S, Mojica FJM, Wolf YI, Yakunin AF, van der Oost J, Koonin EV, Nat Rev Microbiol 2011 9 467 477 10.1038/nrmicro2577 21552286
-
(2011)
Nat Rev Microbiol
, vol.9
, pp. 467-477
-
-
Makarova, K.S.1
Haft, D.H.2
Barrangou, R.3
Brouns, S.J.J.4
Charpentier, E.5
Horvath, P.6
Moineau, S.7
Mojica, F.J.M.8
Wolf, Y.I.9
Yakunin, A.F.10
Van Der Oost, J.11
Koonin, E.V.12
-
57
-
-
64449088715
-
Comparative analysis of CRISPR loci in lactic acid bacteria genomes
-
10.1016/j.ijfoodmicro.2008.05.030 18635282
-
Comparative analysis of CRISPR loci in lactic acid bacteria genomes. Horvath P, Coute-Monvoisin AC, Romero DA, Boyaval P, Fremaux C, Barrangou R, Int J Food Microbiol 2009 131 62 70 10.1016/j.ijfoodmicro.2008.05.030 18635282
-
(2009)
Int J Food Microbiol
, vol.131
, pp. 62-70
-
-
Horvath, P.1
Coute-Monvoisin, A.C.2
Romero, D.A.3
Boyaval, P.4
Fremaux, C.5
Barrangou, R.6
-
58
-
-
33748096466
-
A putative viral defence mechanism in archaeal cells
-
A putative viral defence mechanism in archaeal cells. Lillestøl RK, Redder P, Garrett RA, Brügger K, Archaea 2006 2 59 72 10.1155/2006/542818 16877322 (Pubitemid 44377988)
-
(2006)
Archaea
, vol.2
, Issue.1
, pp. 59-72
-
-
Lillestol, R.K.1
Redder, P.2
Garrett, R.A.3
Brugger, K.4
-
59
-
-
77956628107
-
Transcription, processing and function of CRISPR cassettes in Escherichia coli
-
10.1111/j.1365-2958.2010.07265.x 20624226
-
Transcription, processing and function of CRISPR cassettes in Escherichia coli. Pougach K, Semenova E, Bogdanova E, Datsenko KA, Djordjevic M, Wanner BL, Severinov K, Mol Microbiol 2010 77 1367 1379 10.1111/j.1365-2958.2010.07265.x 20624226
-
(2010)
Mol Microbiol
, vol.77
, pp. 1367-1379
-
-
Pougach, K.1
Semenova, E.2
Bogdanova, E.3
Datsenko, K.A.4
Djordjevic, M.5
Wanner, B.L.6
Severinov, K.7
-
60
-
-
0034902930
-
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum
-
DOI 10.1128/JB.183.16.4823-4838.2001
-
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. Nölling J, Breton G, Omelchenko MV, Makarova KS, Zeng Q, Gibson R, Lee HM, Dubois J, Qiu D, Hitti J, Wolf YI, Tatusov RL, Sabathe F, Doucette-Stamm L, Soucaille P, Daly MJ, Bennett GN, Koonin EV, Smith DR, GTC Sequencing Center Production Finishing Bioinformatics Teams, J Bacteriol 2001 183 4823 4838 10.1128/JB.183.16.4823-4838.2001 11466286 (Pubitemid 32708967)
-
(2001)
Journal of Bacteriology
, vol.183
, Issue.16
, pp. 4823-4838
-
-
Nolling, J.1
Breton, G.2
Omelchenko, M.V.3
Makarova, K.S.4
Zeng, Q.5
Gibson, G.6
Hong Mei Lee7
Dubois, J.8
Qiu, D.9
Hitti, J.10
Aldredge, T.11
Ayers, M.12
Bashirzadeh, R.13
Bochner, H.14
Boivin, M.15
Bross, S.16
Bush, D.17
Butler, C.18
Caron, A.19
Caruso, A.20
Cook, R.21
Daggett, P.22
Deloughery, C.23
Egan, J.24
Ellston, D.25
Engelstein, M.26
Ezedi, J.27
Gilbert, K.28
Goyal, A.29
Guerin, J.30
Ho, T.31
Holtham, K.32
Joseph, P.33
Keagle, P.34
Kozlovsky, J.35
LaPlante, M.36
LeBlanc, G.37
Lumm, W.38
Majeski, A.39
McDougall, S.40
Mank, P.41
Mao, J.-I.42
Nocco, D.43
Patwell, D.44
Phillips, J.45
Pothier, B.46
Prabhakar, S.47
Richterich, P.48
Rice, P.49
Rosetti, D.50
Rossetti, M.51
Rubenfield, M.52
Sachdeva, M.53
Snell, P.54
Spadafora, R.55
Spitzer, L.56
Shimer, G.57
Thomann, H.-U.58
Vicaire, R.59
Wall, K.60
Wang, Y.61
Weinstock, K.62
Lai Peng Wong63
Wonsey, A.64
Xu, Q.65
Zhang, L.66
Wolf, Y.I.67
Tatusov, R.L.68
Sabathe, F.69
Doucette-Stamm, L.70
Soucaille, P.71
Daly, M.J.72
Bennett, G.N.73
Koonin, E.V.74
Smith, D.R.75
more..
-
61
-
-
79251640164
-
Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018
-
10.1186/1471-2164-12-93 21284892
-
Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018. Hu S, Zheng H, Gu Y, Zhao J, Zhang W, Yang Y, Wang S, Zhao G, Yang S, Jiang W, BMC Genomics 2011 12 93 10.1186/1471-2164- 12-93 21284892
-
(2011)
BMC Genomics
, vol.12
, pp. 93
-
-
Hu, S.1
Zheng, H.2
Gu, Y.3
Zhao, J.4
Zhang, W.5
Yang, Y.6
Wang, S.7
Zhao, G.8
Yang, S.9
Jiang, W.10
-
62
-
-
80052516578
-
Complete genome sequence of Clostridium acetobutylicum DSM 1731, a solvent-producing strain with multireplicon genome architecture
-
10.1128/JB.05596-11 21742891
-
Complete genome sequence of Clostridium acetobutylicum DSM 1731, a solvent-producing strain with multireplicon genome architecture. Bao G, Wang R, Zhu Y, Dong H, Mao S, Zhang Y, Chen Z, Li Y, Ma Y, J Bacteriol 2011 193 5007 5008 10.1128/JB.05596-11 21742891
-
(2011)
J Bacteriol
, vol.193
, pp. 5007-5008
-
-
Bao, G.1
Wang, R.2
Zhu, Y.3
Dong, H.4
Mao, S.5
Zhang, Y.6
Chen, Z.7
Li, Y.8
Ma, Y.9
-
63
-
-
84999837798
-
Complete genome sequence of the solvent producer Clostridium saccharobutylicum NCP262 (DSM 13864)
-
10.1128/genomeA.00997-13 24285650
-
Complete genome sequence of the solvent producer Clostridium saccharobutylicum NCP262 (DSM 13864). Poehlein A, Hartwich K, Krabben P, Ehrenreich A, Liebl W, Dürre P, Gottschalk G, Daniel R, Genome Announc 2013 1 00997-13 6 10.1128/genomeA.00997-13 24285650
-
(2013)
Genome Announc
, vol.1
, Issue.6
-
-
Poehlein, A.1
Hartwich, K.2
Krabben, P.3
Ehrenreich, A.4
Liebl, W.5
Dürre, P.6
Gottschalk, G.7
Daniel, R.8
-
64
-
-
84886053131
-
Genome sequence of the butanol hyperproducer Clostridium saccharoperbutylacetonicum N1-4
-
23516201
-
Genome sequence of the butanol hyperproducer Clostridium saccharoperbutylacetonicum N1-4. del Cerro C, Felpeto-Santero C, Rojas A, Tortajada M, Ramón D, García JL, Genome Announc 2013 1 0007013 23516201
-
(2013)
Genome Announc
, vol.1
, pp. 50007013
-
-
Del Cerro, C.1
Felpeto-Santero, C.2
Rojas, A.3
Tortajada, M.4
Ramón, D.5
García, J.L.6
-
65
-
-
75149115227
-
Genome sequence of the cellulosome-producing mesophilic organism Clostridium cellulovorans 743B
-
10.1128/JB.01450-09 19948806
-
Genome sequence of the cellulosome-producing mesophilic organism Clostridium cellulovorans 743B. Tamaru Y, Miyake H, Kuroda K, Nakanishi A, Kawade Y, Yamamoto K, Uemura M, Fujita Y, Doi RH, Ueda M, J Bacteriol 2010 192 901 902 10.1128/JB.01450-09 19948806
-
(2010)
J Bacteriol
, vol.192
, pp. 901-902
-
-
Tamaru, Y.1
Miyake, H.2
Kuroda, K.3
Nakanishi, A.4
Kawade, Y.5
Yamamoto, K.6
Uemura, M.7
Fujita, Y.8
Doi, R.H.9
Ueda, M.10
-
66
-
-
84888616602
-
Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass
-
10.1186/1754-6834-6-179 24295562
-
Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass. Wilson CM, Rodriguez M, Johnson CM, Martin SL, Chu T-M, Wolfinger RD, Hauser LJ, Land ML, Klingeman DM, Syed M, Ragauskas AJ, Tschaplinski TJ, Mielenz JR, Brown SD, Biotechnol Biofuels 2013 6 179 10.1186/1754-6834-6-179 24295562
-
(2013)
Biotechnol Biofuels
, vol.6
, pp. 179
-
-
Wilson, C.M.1
Rodriguez, M.2
Johnson, C.M.3
Martin, S.L.4
Chu, T.-M.5
Wolfinger, R.D.6
Hauser, L.J.7
Land, M.L.8
Klingeman, D.M.9
Syed, M.10
Ragauskas, A.J.11
Tschaplinski, T.J.12
Mielenz, J.R.13
Brown, S.D.14
-
67
-
-
79958084551
-
Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313
-
10.1128/JB.00322-11 21460082
-
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 J-F, Pitluck S, Woyke T, Ivanova N, Mikhailova N, Land M, Hauser L, Argyros DA, Goodwin L, Hogsett D, Caiazza N, J Bacteriol 2011 193 2906 2907 10.1128/JB.00322-11 21460082
-
(2011)
J Bacteriol
, vol.193
, pp. 2906-2907
-
-
Feinberg, L.1
Foden, J.2
Barrett, T.3
Davenport, K.W.4
Bruce, D.5
Detter, C.6
Tapia, R.7
Han, C.8
Lapidus, A.9
Lucas, S.10
Cheng, J.-F.11
Pitluck, S.12
Woyke, T.13
Ivanova, N.14
Mikhailova, N.15
Land, M.16
Hauser, L.17
Argyros, D.A.18
Goodwin, L.19
Hogsett, D.20
Caiazza, N.21
more..
-
68
-
-
77957851639
-
T
-
10.1128/JB.00877-10 20729368
-
T. Paul D, Austin FW, Arick T, Bridges SM, Burgess SC, Dandass YS, Lawrence ML, J Bacteriol 2010 192 5554 5555 10.1128/JB.00877-10 20729368
-
(2010)
J Bacteriol
, vol.192
, pp. 5554-5555
-
-
Paul, D.1
Austin, F.W.2
Arick, T.3
Bridges, S.M.4
Burgess, S.C.5
Dandass, Y.S.6
Lawrence, M.L.7
-
69
-
-
84868111481
-
Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis
-
10.1093/nar/gks737 22879377
-
Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis. Richter H, Zoephel J, Schermuly J, Maticzka D, Backofen R, Randau L, Nucleic Acids Res 2012 40 9887 9896 10.1093/nar/gks737 22879377
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 9887-9896
-
-
Richter, H.1
Zoephel, J.2
Schermuly, J.3
Maticzka, D.4
Backofen, R.5
Randau, L.6
-
70
-
-
49649114086
-
Small CRISPR RNAs guide antiviral defense in prokaryotes
-
10.1126/science.1159689 18703739
-
Small CRISPR RNAs guide antiviral defense in prokaryotes. Brouns SJJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJH, Snijders APL, Dickman MJ, Makarova KS, Koonin EV, van der Oost J, Science 2008 321 960 964 10.1126/science.1159689 18703739
-
(2008)
Science
, vol.321
, pp. 960-964
-
-
Brouns, S.J.J.1
Jore, M.M.2
Lundgren, M.3
Westra, E.R.4
Slijkhuis, R.J.H.5
Snijders, A.P.L.6
Dickman, M.J.7
Makarova, K.S.8
Koonin, E.V.9
Van Der Oost, J.10
-
71
-
-
58049191229
-
Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes
-
10.1101/gad.1742908 19141480
-
Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Carte J, Wang RY, Li H, Terns RM, Terns MP, Genes Dev 2008 22 3489 3496 10.1101/gad.1742908 19141480
-
(2008)
Genes Dev
, vol.22
, pp. 3489-3496
-
-
Carte, J.1
Wang, R.Y.2
Li, H.3
Terns, R.M.4
Terns, M.P.5
-
72
-
-
62949197925
-
CRISPR families of the crenarchaeal genus Sulfolobus: Bidirectional transcription and dynamic properties
-
10.1111/j.1365-2958.2009.06641.x 19239620
-
CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Lillestol RK, Shah SA, Brugger K, Redder P, Phan H, Christiansen J, Garrett RA, Mol Microbiol 2009 72 259 272 10.1111/j.1365-2958.2009.06641.x 19239620
-
(2009)
Mol Microbiol
, vol.72
, pp. 259-272
-
-
Lillestol, R.K.1
Shah, S.A.2
Brugger, K.3
Redder, P.4
Phan, H.5
Christiansen, J.6
Garrett, R.A.7
-
73
-
-
84856792673
-
Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs
-
10.1016/j.molcel.2011.10.023 22227116
-
Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Hale CR, Majumdar S, Elmore J, Pfister N, Compton M, Olson S, Resch AM, Glover CVC, Graveley BR, Terns RM, Terns MP, Mol Cell 2012 45 292 302 10.1016/j.molcel.2011.10.023 22227116
-
(2012)
Mol Cell
, vol.45
, pp. 292-302
-
-
Hale, C.R.1
Majumdar, S.2
Elmore, J.3
Pfister, N.4
Compton, M.5
Olson, S.6
Resch, A.M.7
Glover, C.V.C.8
Graveley, B.R.9
Terns, R.M.10
Terns, M.P.11
-
74
-
-
0033998365
-
Bacteriophage infections in the industrial acetone butanol (AB) fermentation process
-
Bacteriophage infections in the industrial acetone butanol (AB) fermentation process. Jones DT, Shirley M, Wu XY, Keis S, J Mol Microbiol Biotechnol 2000 2 21 26 10937483 (Pubitemid 30125156)
-
(2000)
Journal of Molecular Microbiology and Biotechnology
, vol.2
, Issue.1
, pp. 21-26
-
-
Jones, D.T.1
Shirley, M.2
Wu, X.3
Keis, S.4
-
75
-
-
33846975418
-
PILER-CR: Fast and accurate identification of CRISPR repeats
-
10.1186/1471-2105-8-18 17239253
-
PILER-CR: Fast and accurate identification of CRISPR repeats. Edgar R, BMC Bioinformatics 2007 8 18 10.1186/1471-2105-8-18 17239253
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 18
-
-
Edgar, R.1
-
76
-
-
34250662138
-
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
-
DOI 10.1186/1471-2105-8-172
-
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. Grissa I, Vergnaud G, Pourcel C, BMC Bioinformatics 2007 8 172 10.1186/1471-2105-8-172 17521438 (Pubitemid 46930568)
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 172
-
-
Grissa, I.1
Vergnaud, G.2
Pourcel, C.3
-
77
-
-
79955795335
-
CRISPR Inhibition of Prophage Acquisition in Streptococcus pyogenes
-
10.1371/journal.pone.0019543 21573110
-
CRISPR Inhibition of Prophage Acquisition in Streptococcus pyogenes. Nozawa T, Furukawa N, Aikawa C, Watanabe T, Haobam B, Kurokawa K, Maruyama F, Nakagawa I, PLoS One 2011 6 5 19543 10.1371/journal.pone.0019543 21573110
-
(2011)
PLoS One
, vol.6
, Issue.5
, pp. 519543
-
-
Nozawa, T.1
Furukawa, N.2
Aikawa, C.3
Watanabe, T.4
Haobam, B.5
Kurokawa, K.6
Maruyama, F.7
Nakagawa, I.8
-
78
-
-
84900455329
-
CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA
-
CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA. Marraffini LA, Sontheimer EJ, Science 1843-1845 2008 322
-
(1843)
Science
, vol.2008
, pp. 322
-
-
Marraffini, L.A.1
Sontheimer, E.J.2
-
79
-
-
84862010951
-
Clostridia: The importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications
-
10.1016/j.copbio.2011.10.008 22079352
-
Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. Tracy BP, Jones SW, Fast AG, Indurthi DC, Papoutsakis ET, Curr Opin Biotechnol 2012 23 364 381 10.1016/j.copbio.2011.10.008 22079352
-
(2012)
Curr Opin Biotechnol
, vol.23
, pp. 364-381
-
-
Tracy, B.P.1
Jones, S.W.2
Fast, A.G.3
Indurthi, D.C.4
Papoutsakis, E.T.5
-
80
-
-
52949096084
-
Next-Generation DNA sequencing methods
-
10.1146/annurev.genom.9.081307.164359 18576944
-
Next-Generation DNA sequencing methods. Mardis ER, Annu Rev Genomics Hum Genet 2008 9 387 402 10.1146/annurev.genom.9.081307.164359 18576944
-
(2008)
Annu Rev Genomics Hum Genet
, vol.9
, pp. 387-402
-
-
Mardis, E.R.1
-
81
-
-
84997719788
-
Draft genome sequences for three mercury-methylating, sulfate-reducing bacteria
-
23950126
-
Draft genome sequences for three mercury-methylating, sulfate-reducing bacteria. Brown SD, Hurt RA, Gilmour CC, Elias DA, Genome Announc 2013 1 00618 00613 23950126
-
(2013)
Genome Announc
, vol.1
, pp. 500618-600613
-
-
Brown, S.D.1
Hurt, R.A.2
Gilmour, C.C.3
Elias, D.A.4
-
82
-
-
80051980539
-
Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum
-
10.1073/pnas.1102444108 21825121
-
Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Brown SD, Guss A, Karpinets T, Parks J, Smolin N, Yang S, Land ML, Klingeman DM, Bhandiwad A, Rodriguez JM, Raman B, Shao X, Mielenz JR, Smith JC MK, Lynd LR, Proc Natl Acad Sci USA 2011 108 13752 13757 10.1073/pnas.1102444108 21825121
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 13752-13757
-
-
Brown, S.D.1
Guss, A.2
Karpinets, T.3
Parks, J.4
Smolin, N.5
Yang, S.6
Land, M.L.7
Klingeman, D.M.8
Bhandiwad, A.9
Rodriguez, J.M.10
Raman, B.11
Shao, X.12
Mielenz, J.R.13
Smith Jc, M.K.14
Lynd, L.R.15
-
83
-
-
69649109364
-
Circos: An information aesthetic for comparative genomics
-
10.1101/gr.092759.109 19541911
-
Circos: An information aesthetic for comparative genomics. Krzywinski M, Schein J, Birol I Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA, Genome Res 2009 19 1639 1645 10.1101/gr.092759.109 19541911
-
(2009)
Genome Res
, vol.19
, pp. 1639-1645
-
-
Krzywinski, M.1
Schein, J.2
Birol, I.3
Connors, J.4
Gascoyne, R.5
Horsman, D.6
Jones, S.J.7
Marra, M.A.8
-
84
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
10.1186/gb-2004-5-2-r12 14759262
-
Versatile and open software for comparing large genomes. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL, Genome Biol 2004 5 12 10.1186/gb-2004-5-2-r12 14759262
-
(2004)
Genome Biol
, vol.5
, pp. 1812
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
Salzberg, S.L.7
-
85
-
-
77956193448
-
Progressive Mauve: Multiple genome alignment with gene gain, loss and rearrangement
-
10.1371/journal.pone.0011147 20593022
-
Progressive Mauve: multiple genome alignment with gene gain, loss and rearrangement. Darling AE, Mau B, Perna NT, PLoS One 2010 5 11147 10.1371/journal.pone.0011147 20593022
-
(2010)
PLoS One
, vol.5
, pp. 511147
-
-
Darling, A.E.1
Mau, B.2
Perna, N.T.3
-
86
-
-
79959979274
-
PHAST: A fast phage search tool
-
10.1093/nar/gkr485 21672955
-
PHAST: a fast phage search tool. Zhou Y, Liang YJ, Lynch KH, Dennis JJ, Wishart DS, Nucleic Acids Res 2011 39 347 W352 10.1093/nar/gkr485 21672955
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Zhou, Y.1
Liang, Y.J.2
Lynch, K.H.3
Dennis, J.J.4
Wishart, D.S.5
-
87
-
-
33845613147
-
Phage-Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences
-
DOI 10.1093/nar/gkl732
-
Phage-Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences. Fouts DE, Nucleic Acids Res 2006 34 5839 5851 10.1093/nar/gkl732 17062630 (Pubitemid 44941163)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.20
, pp. 5839-5851
-
-
Fouts, D.E.1
|