-
1
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
-
10.1126/science.7542800, 7542800
-
Fleischmann R, Adams M, White O, Clayton R, Kirkness E, Kerlavage A, Bult C, Tomb J, Dougherty B, Merrick J, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995, 269:496-512. 10.1126/science.7542800, 7542800.
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.1
Adams, M.2
White, O.3
Clayton, R.4
Kirkness, E.5
Kerlavage, A.6
Bult, C.7
Tomb, J.8
Dougherty, B.9
Merrick, J.10
-
2
-
-
34147132825
-
Identifying bacterial genes and endosymbiont DNA with Glimmer
-
10.1093/bioinformatics/btm009, 2387122, 17237039
-
Delcher A, Bratke K, Powers E, Salzberg S. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23:673-679. 10.1093/bioinformatics/btm009, 2387122, 17237039.
-
(2007)
Bioinformatics
, vol.23
, pp. 673-679
-
-
Delcher, A.1
Bratke, K.2
Powers, E.3
Salzberg, S.4
-
3
-
-
0032518163
-
Microbial gene identification using interpolated Markov models
-
10.1093/nar/26.2.544, 147303, 9421513
-
Salzberg S, Delcher A, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998, 26:544-548. 10.1093/nar/26.2.544, 147303, 9421513.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 544-548
-
-
Salzberg, S.1
Delcher, A.2
Kasif, S.3
White, O.4
-
4
-
-
0033485517
-
Improved microbial gene identification with GLIMMER
-
10.1093/nar/27.23.4636, 148753, 10556321
-
Delcher A, Harmon D, Kasif S, White O, Salzberg S. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27:4636-4641. 10.1093/nar/27.23.4636, 148753, 10556321.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 4636-4641
-
-
Delcher, A.1
Harmon, D.2
Kasif, S.3
White, O.4
Salzberg, S.5
-
5
-
-
0032519353
-
GeneMark.hmm: New solutions for gene finding
-
10.1093/nar/26.4.1107, 147337, 9461475
-
Lukashin A, Borodovsky M. GeneMark.hmm: New solutions for gene finding. Nucleic Acids Res 1998, 26:1107-1115. 10.1093/nar/26.4.1107, 147337, 9461475.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 1107-1115
-
-
Lukashin, A.1
Borodovsky, M.2
-
6
-
-
0035875343
-
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
-
10.1093/nar/29.12.2607, 55746, 11410670
-
Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001, 29:2607-2618. 10.1093/nar/29.12.2607, 55746, 11410670.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2607-2618
-
-
Besemer, J.1
Lomsadze, A.2
Borodovsky, M.3
-
7
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.1
Gish, W.2
Miller, W.3
Myers, E.4
Lipman, D.5
-
8
-
-
0035424711
-
On the total number of genes and their length distribution in complete microbial genomes
-
10.1016/S0168-9525(01)02372-1, 11485798
-
Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A. On the total number of genes and their length distribution in complete microbial genomes. Trends Genet 2001, 17:425-428. 10.1016/S0168-9525(01)02372-1, 11485798.
-
(2001)
Trends Genet
, vol.17
, pp. 425-428
-
-
Skovgaard, M.1
Jensen, L.J.2
Brunak, S.3
Ussery, D.4
Krogh, A.5
-
9
-
-
25444439861
-
GenBank
-
10.1093/nar/gkq1079, 3013681, 21071399
-
Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Sayers E. GenBank. Nucleic Acids Res 2011, 39:D32-D37. 10.1093/nar/gkq1079, 3013681, 21071399.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Benson, D.1
Karsch-Mizrachi, I.2
Lipman, D.3
Ostell, J.4
Sayers, E.5
-
10
-
-
78651305142
-
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes
-
10.1093/nar/gkq1168, 3013729, 21097892
-
Roberts R, Chang Y-C, Hu Z, Rachlin J, Anton B, Pokrzywa R, Choi H-P, Faller L, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick M, Osmani L, Swaminathan R, Tao K, Letovsky S, Vitkup D, Segrè D, Salzberg S, Delisi C, Steffen M, Kasif S. COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res 2011, 39:D11-D14. 10.1093/nar/gkq1168, 3013729, 21097892.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Roberts, R.1
Chang, Y.-C.2
Hu, Z.3
Rachlin, J.4
Anton, B.5
Pokrzywa, R.6
Choi, H.-P.7
Faller, L.8
Guleria, J.9
Housman, G.10
Klitgord, N.11
Mazumdar, V.12
McGettrick, M.13
Osmani, L.14
Swaminathan, R.15
Tao, K.16
Letovsky, S.17
Vitkup, D.18
Segrè, D.19
Salzberg, S.20
Delisi, C.21
Steffen, M.22
Kasif, S.23
more..
-
11
-
-
84871919091
-
COMBREX Website
-
COMBREX Website. http://combrex.bu.edu/.
-
-
-
-
12
-
-
77949482581
-
Missing genes in the annotation of prokaryotic genomes
-
10.1186/1471-2105-11-131, 3098052, 20230630
-
Warren A, Archuleta J, Feng W, Setubal J. Missing genes in the annotation of prokaryotic genomes. BMC Bioinformatics 2010, 11:131. 10.1186/1471-2105-11-131, 3098052, 20230630.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 131
-
-
Warren, A.1
Archuleta, J.2
Feng, W.3
Setubal, J.4
-
13
-
-
84871920852
-
COMBREX Missed Genes
-
COMBREX Missed Genes. http://combrex.bu.edu/missedGenes.
-
-
-
-
14
-
-
84859436530
-
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
-
10.1093/nar/gkr1079, 3245008, 22121212
-
Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 2012, 40:D130-D135. 10.1093/nar/gkr1079, 3245008, 22121212.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Pruitt, K.D.1
Tatusova, T.2
Brown, G.R.3
Maglott, D.R.4
-
15
-
-
79952267766
-
Using BLAST to teach " E-value-tionary" concepts
-
10.1371/journal.pbio.1001014, 3032543, 21304918
-
Kerfeld CA, Scott KM. Using BLAST to teach " E-value-tionary" concepts. PLoS Biol 2011, 9:e1001014. 10.1371/journal.pbio.1001014, 3032543, 21304918.
-
(2011)
PLoS Biol
, vol.9
-
-
Kerfeld, C.A.1
Scott, K.M.2
-
16
-
-
58149186488
-
The national center for biotechnology information's protein clusters database
-
10.1093/nar/gkn734, 2686591, 18940865
-
Klimke W, Agarwala R, Badretdin A, Chetvernin S, Ciufo S, Fedorov B, Kiryutin B, O'Neill K, Resch W, Resenchuk S, Schafer S, Tolstoy I, Tatusova T. The national center for biotechnology information's protein clusters database. Nucleic Acids Res 2009, 37:D216-D223. 10.1093/nar/gkn734, 2686591, 18940865.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Klimke, W.1
Agarwala, R.2
Badretdin, A.3
Chetvernin, S.4
Ciufo, S.5
Fedorov, B.6
Kiryutin, B.7
O'Neill, K.8
Resch, W.9
Resenchuk, S.10
Schafer, S.11
Tolstoy, I.12
Tatusova, T.13
-
17
-
-
58149183697
-
ARDB-Antibiotic Resistance Genes Database
-
10.1093/nar/gkn656, 2686595, 18832362
-
Liu B, Pop M. ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Res 2009, 37:D443-D447. 10.1093/nar/gkn656, 2686595, 18832362.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Liu, B.1
Pop, M.2
-
18
-
-
77950165418
-
Antibiotic sensitivity profiles determined with an Escherichia coli gene knockout collection: generating an antibiotic bar code
-
10.1128/AAC.00906-09, 2849384, 20065048
-
Liu A, Tran L, Becket E, Lee K, Chinn L, Park E, Tran K, Miller J. Antibiotic sensitivity profiles determined with an Escherichia coli gene knockout collection: generating an antibiotic bar code. Antimicrob Agents Chemother 2010, 54:1393-1403. 10.1128/AAC.00906-09, 2849384, 20065048.
-
(2010)
Antimicrob Agents Chemother
, vol.54
, pp. 1393-1403
-
-
Liu, A.1
Tran, L.2
Becket, E.3
Lee, K.4
Chinn, L.5
Park, E.6
Tran, K.7
Miller, J.8
-
19
-
-
84864030677
-
AntiFam: a tool to help identify spurious ORFs in protein annotation
-
bas003, 10.1093/database/bas003, 3308159, 22434837
-
Eberhardt RY, Haft DH, Punta M, Martin M, O'Donovan C, Bateman A. AntiFam: a tool to help identify spurious ORFs in protein annotation. Database 2012, 2012:bas003. 10.1093/database/bas003, 3308159, 22434837.
-
(2012)
Database
, vol.2012
-
-
Eberhardt, R.Y.1
Haft, D.H.2
Punta, M.3
Martin, M.4
O'Donovan, C.5
Bateman, A.6
-
20
-
-
22144474094
-
The microbial rosetta stone database: a compilation of global and emerging infectious microorganisms and bioterrorist threat agents
-
10.1186/1471-2180-5-19, 1127111, 15850481
-
Ecker D, Sampath R, Willett P, Wyatt J, Samant V, Massire C, Hall T, Hari K, McNeil J, Büchen-Osmond C, Budowle B. The microbial rosetta stone database: a compilation of global and emerging infectious microorganisms and bioterrorist threat agents. BMC Microbiol 2005, 5:19. 10.1186/1471-2180-5-19, 1127111, 15850481.
-
(2005)
BMC Microbiol
, vol.5
, pp. 19
-
-
Ecker, D.1
Sampath, R.2
Willett, P.3
Wyatt, J.4
Samant, V.5
Massire, C.6
Hall, T.7
Hari, K.8
McNeil, J.9
Büchen-Osmond, C.10
Budowle, B.11
-
21
-
-
77956556252
-
Complete genome sequence of Lactobacillus fermentum CECT 5716, a probiotic strain isolated from human milk
-
10.1128/JB.00702-10, 2937428, 20639335
-
Jiménez E, Langa S, Martín V, Arroyo R, Martín R, Fernández L, Rodríguez JM. Complete genome sequence of Lactobacillus fermentum CECT 5716, a probiotic strain isolated from human milk. J Bacteriol 2010, 192:4800. 10.1128/JB.00702-10, 2937428, 20639335.
-
(2010)
J Bacteriol
, vol.192
, pp. 4800
-
-
Jiménez, E.1
Langa, S.2
Martín, V.3
Arroyo, R.4
Martín, R.5
Fernández, L.6
Rodríguez, J.M.7
-
22
-
-
84871918524
-
-
Bethesda, Maryland, USA: National Center for Biotechnology Information, GenBank accession no. AE004969
-
Lewis LA, Gillaspy AF, McLaughlin RE, Gipson M, Ducey TF, Ownbey T, Hartman K, Nydick C, Carson MB, Vaughn J, Thomson C, Song L, Lin S, Yuan X, Najar F, Zhan M, Ren Q, Zhu H, Qi S, Kenton SM, Lai H, White JD, Clifton S, Roe BA, Dyer DW. Neisseria gonorrhoeae FA 1090 2010, Bethesda, Maryland, USA: National Center for Biotechnology Information, GenBank accession no. AE004969.
-
(2010)
Neisseria gonorrhoeae FA 1090
-
-
Lewis, L.A.1
Gillaspy, A.F.2
McLaughlin, R.E.3
Gipson, M.4
Ducey, T.F.5
Ownbey, T.6
Hartman, K.7
Nydick, C.8
Carson, M.B.9
Vaughn, J.10
Thomson, C.11
Song, L.12
Lin, S.13
Yuan, X.14
Najar, F.15
Zhan, M.16
Ren, Q.17
Zhu, H.18
Qi, S.19
Kenton, S.M.20
Lai, H.21
White, J.D.22
Clifton, S.23
Roe, B.A.24
Dyer, D.W.25
more..
-
23
-
-
84871922455
-
-
Bethesda, Maryland, USA: National Center for Biotechnology Information, GenBank accession no. FQ312030
-
Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley D, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER, Masignani V. Streptococcus pneumoniae INV104 2011, Bethesda, Maryland, USA: National Center for Biotechnology Information, GenBank accession no. FQ312030.
-
(2011)
Streptococcus pneumoniae INV104
-
-
Donati, C.1
Hiller, N.L.2
Tettelin, H.3
Muzzi, A.4
Croucher, N.J.5
Angiuoli, S.V.6
Oggioni, M.7
Dunning Hotopp, J.C.8
Hu, F.Z.9
Riley, D.10
Covacci, A.11
Mitchell, T.J.12
Bentley, S.D.13
Kilian, M.14
Ehrlich, G.D.15
Rappuoli, R.16
Moxon, E.R.17
Masignani, V.18
-
24
-
-
77954362201
-
Complete genome sequences of Yersinia pestis from natural foci in China
-
10.1128/JB.00340-10, 2897648, 20453098
-
Shen X, Wang Q, Xia L, Zhu X, Zhang Z, Liang Y, Cai H, Zhang E, Wei J, Chen C, Song Z, Zhang H, Yu D, Hai R. Complete genome sequences of Yersinia pestis from natural foci in China. J Bacteriol 2010, 192:3551-3552. 10.1128/JB.00340-10, 2897648, 20453098.
-
(2010)
J Bacteriol
, vol.192
, pp. 3551-3552
-
-
Shen, X.1
Wang, Q.2
Xia, L.3
Zhu, X.4
Zhang, Z.5
Liang, Y.6
Cai, H.7
Zhang, E.8
Wei, J.9
Chen, C.10
Song, Z.11
Zhang, H.12
Yu, D.13
Hai, R.14
-
25
-
-
32044474423
-
Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host
-
1361709, 16365377
-
Toh H, Weiss B, Perkin S, Yamashita A, Oshima K, Hattori M, Aksoy S. Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. Genome Res 2006, 16:149-156. 1361709, 16365377.
-
(2006)
Genome Res
, vol.16
, pp. 149-156
-
-
Toh, H.1
Weiss, B.2
Perkin, S.3
Yamashita, A.4
Oshima, K.5
Hattori, M.6
Aksoy, S.7
-
26
-
-
0037418012
-
The genome sequence of Clostridium tetani, the causative agent of tetanus disease
-
10.1073/pnas.0335853100, 298770, 12552129
-
Bruggemann H, Baumer S, Fricke WF, Wiezer A, Liesegang H, Decker I, Herzberg C, Martinez-Arias R, Merkl R, Henne A, Gottschalk G. The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc Natl Acad Sci USA 2003, 100:1316-1321. 10.1073/pnas.0335853100, 298770, 12552129.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 1316-1321
-
-
Bruggemann, H.1
Baumer, S.2
Fricke, W.F.3
Wiezer, A.4
Liesegang, H.5
Decker, I.6
Herzberg, C.7
Martinez-Arias, R.8
Merkl, R.9
Henne, A.10
Gottschalk, G.11
-
27
-
-
34247648202
-
The complete genome sequence of Bacillus thuringiensis Al Hakam
-
10.1128/JB.00241-07, 1855882, 17337577
-
Challacombe J, Altherr M, Xie G, Bhotika S, Brown N, Bruce D, Campbell C, Campbell M, Chen J, Chertkov O, Cleland C, Dimitrijevic M, Doggett N, Fawcett J, Glavina T, Goodwin L, Green L, Han C, Hill K, Hitchcock P, Jackson P, Keim P, Ramesh A, Longmire J, Lucas S, Malfatti S, Martinez D, McMurry K, Meincke L, Misra M, et al. The complete genome sequence of Bacillus thuringiensis Al Hakam. J Bacteriol 2007, 189:3680-3681. 10.1128/JB.00241-07, 1855882, 17337577.
-
(2007)
J Bacteriol
, vol.189
, pp. 3680-3681
-
-
Challacombe, J.1
Altherr, M.2
Xie, G.3
Bhotika, S.4
Brown, N.5
Bruce, D.6
Campbell, C.7
Campbell, M.8
Chen, J.9
Chertkov, O.10
Cleland, C.11
Dimitrijevic, M.12
Doggett, N.13
Fawcett, J.14
Glavina, T.15
Goodwin, L.16
Green, L.17
Han, C.18
Hill, K.19
Hitchcock, P.20
Jackson, P.21
Keim, P.22
Ramesh, A.23
Longmire, J.24
Lucas, S.25
Malfatti, S.26
Martinez, D.27
McMurry, K.28
Meincke, L.29
Misra, M.30
more..
-
28
-
-
0034150045
-
An automated system for genome analysis to support microbial whole-genome shotgun sequencing
-
10.1271/bbb.64.670, 10803979
-
Sakiyama T, Takami H, Ogasawara N, Kuhara S, Kozuki T, Doga K, Ohyama A, Horikoshi K. An automated system for genome analysis to support microbial whole-genome shotgun sequencing. Biosci Biotechnol Biochem 2000, 64:670-673. 10.1271/bbb.64.670, 10803979.
-
(2000)
Biosci Biotechnol Biochem
, vol.64
, pp. 670-673
-
-
Sakiyama, T.1
Takami, H.2
Ogasawara, N.3
Kuhara, S.4
Kozuki, T.5
Doga, K.6
Ohyama, A.7
Horikoshi, K.8
-
29
-
-
34247846229
-
The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes
-
10.1128/JB.01726-06, 1855855, 17293413
-
Johnson T, Kariyawasam S, Wannemuehler Y, Mangiamele P, Johnson S, Doetkott C, Skyberg J, Lynne A, Johnson J, Nolan L. The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes. J Bacteriol 2007, 189:3228-3236. 10.1128/JB.01726-06, 1855855, 17293413.
-
(2007)
J Bacteriol
, vol.189
, pp. 3228-3236
-
-
Johnson, T.1
Kariyawasam, S.2
Wannemuehler, Y.3
Mangiamele, P.4
Johnson, S.5
Doetkott, C.6
Skyberg, J.7
Lynne, A.8
Johnson, J.9
Nolan, L.10
|