-
1
-
-
0034571446
-
Genomics: what is realistically achievable?
-
Overbeek R, (2000) Genomics: what is realistically achievable? Genome Biol 1: COMMENT2002.
-
(2000)
Genome Biol
, vol.1
-
-
Overbeek, R.1
-
2
-
-
67649159875
-
A flood of microbial genomes-do we need more?
-
Ahmed N, (2009) A flood of microbial genomes-do we need more? PLoS ONE 4: e5831.
-
(2009)
PLoS ONE
, vol.4
-
-
Ahmed, N.1
-
3
-
-
84859165788
-
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
-
Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, et al. (2012) The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 40: D571-579.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Pagani, I.1
Liolios, K.2
Jansson, J.3
Chen, I.M.4
Smirnova, T.5
-
4
-
-
84862179132
-
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
-
Barrett T, Clark K, Gevorgyan R, Gorelenkov V, Gribov E, et al. (2012) BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res 40: D57-63.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Barrett, T.1
Clark, K.2
Gevorgyan, R.3
Gorelenkov, V.4
Gribov, E.5
-
5
-
-
58849113668
-
Beyond the HapMap genotypic data: prospects of deep resequencing projects
-
Zhang W, Dolan ME, (2008) Beyond the HapMap genotypic data: prospects of deep resequencing projects. Curr Bioinform 3: 178.
-
(2008)
Curr Bioinform
, vol.3
, pp. 178
-
-
Zhang, W.1
Dolan, M.E.2
-
6
-
-
34548846699
-
Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition
-
Lefebure T, Stanhope MJ, (2007) Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol 8: R71.
-
(2007)
Genome Biol
, vol.8
-
-
Lefebure, T.1
Stanhope, M.J.2
-
7
-
-
63049138461
-
Sequencing the species pan-genome
-
Bentley S, (2009) Sequencing the species pan-genome. Nat Rev Microbiol 7: 258-259.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 258-259
-
-
Bentley, S.1
-
8
-
-
27444438599
-
The microbial pan-genome
-
Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R, (2005) The microbial pan-genome. Curr Opin Genet Dev 15: 589-594.
-
(2005)
Curr Opin Genet Dev
, vol.15
, pp. 589-594
-
-
Medini, D.1
Donati, C.2
Tettelin, H.3
Masignani, V.4
Rappuoli, R.5
-
9
-
-
77953004087
-
Pathogen microevolution in high resolution
-
Aziz RK, Nizet V, (2010) Pathogen microevolution in high resolution. Sci Transl Med 2: 16ps14.
-
(2010)
Sci Transl Med
, vol.2
-
-
Aziz, R.K.1
Nizet, V.2
-
10
-
-
0038823524
-
The Genome sequence of the SARS-associated coronavirus
-
Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, et al. (2003) The Genome sequence of the SARS-associated coronavirus. Science 300: 1399-1404.
-
(2003)
Science
, vol.300
, pp. 1399-1404
-
-
Marra, M.A.1
Jones, S.J.2
Astell, C.R.3
Holt, R.A.4
Brooks-Wilson, A.5
-
11
-
-
67449110743
-
Emergence of a novel swine-origin influenza A (H1N1) virus in humans
-
Dawood FS, Jain S, Finelli L, Shaw MW, Lindstrom S, et al. (2009) Emergence of a novel swine-origin influenza A (H1N1) virus in humans. N Engl J Med 360: 2605-2615.
-
(2009)
N Engl J Med
, vol.360
, pp. 2605-2615
-
-
Dawood, F.S.1
Jain, S.2
Finelli, L.3
Shaw, M.W.4
Lindstrom, S.5
-
12
-
-
67649538978
-
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
-
Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, et al. (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459: 1122-1125.
-
(2009)
Nature
, vol.459
, pp. 1122-1125
-
-
Smith, G.J.1
Vijaykrishna, D.2
Bahl, J.3
Lycett, S.J.4
Worobey, M.5
-
13
-
-
80052150179
-
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, et al. (2011) Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 365: 709-717.
-
(2011)
N Engl 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
-
14
-
-
82355173436
-
Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC)
-
Brzuszkiewicz E, Thurmer A, Schuldes J, Leimbach A, Liesegang H, et al. (2011) Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC). Arch Microbiol 193: 883-891.
-
(2011)
Arch Microbiol
, vol.193
, pp. 883-891
-
-
Brzuszkiewicz, E.1
Thurmer, A.2
Schuldes, J.3
Leimbach, A.4
Liesegang, H.5
-
15
-
-
11844306574
-
The SEED: a peer-to-peer environment for genome annotation
-
Overbeek R, Disz T, Stevens R, (2004) The SEED: a peer-to-peer environment for genome annotation. Commun ACM 47: 46-51.
-
(2004)
Commun ACM
, vol.47
, pp. 46-51
-
-
Overbeek, R.1
Disz, T.2
Stevens, R.3
-
16
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691-5702.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
-
17
-
-
34548329975
-
Annotation of bacterial and archaeal genomes: improving accuracy and consistency
-
Overbeek R, Bartels D, Vonstein V, Meyer F, (2007) Annotation of bacterial and archaeal genomes: improving accuracy and consistency. Chem Rev 107: 3431-3447.
-
(2007)
Chem Rev
, vol.107
, pp. 3431-3447
-
-
Overbeek, R.1
Bartels, D.2
Vonstein, V.3
Meyer, F.4
-
18
-
-
34248632008
-
Toward the automated generation of genome-scale metabolic networks in the SEED
-
DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, et al. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 8: 139.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 139
-
-
DeJongh, M.1
Formsma, K.2
Boillot, P.3
Gould, J.4
Rycenga, M.5
-
19
-
-
67650573077
-
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations
-
Henry CS, Zinner JF, Cohoon MP, Stevens RL, (2009) iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol 10: R69.
-
(2009)
Genome Biol
, vol.10
-
-
Henry, C.S.1
Zinner, J.F.2
Cohoon, M.P.3
Stevens, R.L.4
-
20
-
-
77956696072
-
High-throughput generation, optimization and analysis of genome-scale metabolic models
-
Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, et al. (2010) High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 28: 977-982.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 977-982
-
-
Henry, C.S.1
DeJongh, M.2
Best, A.A.3
Frybarger, P.M.4
Linsay, B.5
-
21
-
-
77953347739
-
Accessing the SEED genome databases via Web services API: tools for programmers
-
Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, et al. (2010) Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics 11: 319.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 319
-
-
Disz, T.1
Akhter, S.2
Cuevas, D.3
Olson, R.4
Overbeek, R.5
-
23
-
-
40549120596
-
The RAST Server: rapid annotations using subsystems technology
-
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
DeJongh, M.4
Disz, T.5
-
24
-
-
0036081062
-
The KEGG databases at GenomeNet
-
Kanehisa M, Goto S, Kawashima S, Nakaya A, (2002) The KEGG databases at GenomeNet. Nucleic Acids Res 30: 42-46.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 42-46
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Nakaya, A.4
-
25
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M, (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32: D277-280.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
26
-
-
48449090785
-
KEGG Atlas mapping for global analysis of metabolic pathways
-
Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, et al. (2008) KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 36: W423-426.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Okuda, S.1
Yamada, T.2
Hamajima, M.3
Itoh, M.4
Katayama, T.5
-
27
-
-
51049107514
-
Group contribution method for thermodynamic analysis of complex metabolic networks
-
Jankowski MD, Henry CS, Broadbelt LJ, Hatzimanikatis V, (2008) Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J 95: 1487-1499.
-
(2008)
Biophys J
, vol.95
, pp. 1487-1499
-
-
Jankowski, M.D.1
Henry, C.S.2
Broadbelt, L.J.3
Hatzimanikatis, V.4
-
28
-
-
0036330798
-
Genome-scale metabolic model of Helicobacter pylori 26695
-
Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, et al. (2002) Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol 184: 4582-4593.
-
(2002)
J Bacteriol
, vol.184
, pp. 4582-4593
-
-
Schilling, C.H.1
Covert, M.W.2
Famili, I.3
Church, G.M.4
Edwards, J.S.5
-
29
-
-
80052054573
-
Connecting genotype to phenotype in the era of high-throughput sequencing
-
Henry CS, Overbeek R, Xia F, Best AA, Glass E, et al. (2011) Connecting genotype to phenotype in the era of high-throughput sequencing. Biochim Biophys Acta 1810: 967-977.
-
(2011)
Biochim Biophys Acta
, vol.1810
, pp. 967-977
-
-
Henry, C.S.1
Overbeek, R.2
Xia, F.3
Best, A.A.4
Glass, E.5
-
30
-
-
84866465018
-
Biolog phenotype microarrays
-
Shea A, Wolcott M, Daefler S, Rozak DA, (2012) Biolog phenotype microarrays. Methods Mol Biol 881: 331-373.
-
(2012)
Methods Mol Biol
, vol.881
, pp. 331-373
-
-
Shea, A.1
Wolcott, M.2
Daefler, S.3
Rozak, D.A.4
-
31
-
-
1642457253
-
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
-
Mahadevan R, Schilling CH, (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 5: 264-276.
-
(2003)
Metab Eng
, vol.5
, pp. 264-276
-
-
Mahadevan, R.1
Schilling, C.H.2
-
32
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
-
33
-
-
0032169271
-
Conservation of gene order: a fingerprint of proteins that physically interact
-
Dandekar T, Snel B, Huynen M, Bork P, (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23: 324-328.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
34
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N, (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 96: 2896-2901.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
35
-
-
0033301555
-
Use of contiguity on the chromosome to predict functional coupling
-
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N, (1999) Use of contiguity on the chromosome to predict functional coupling. In Silico Biol 1: 93-108.
-
(1999)
In Silico Biol
, vol.1
, pp. 93-108
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
36
-
-
0035085816
-
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
-
Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV, (2001) Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res 11: 356-372.
-
(2001)
Genome Res
, vol.11
, pp. 356-372
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Kondrashov, A.S.3
Koonin, E.V.4
-
37
-
-
84934444303
-
Inferring functional relationships from conservation of gene order
-
Moreno-Hagelsieb G, (2008) Inferring functional relationships from conservation of gene order. Methods Mol Biol 453: 181-199.
-
(2008)
Methods Mol Biol
, vol.453
, pp. 181-199
-
-
Moreno-Hagelsieb, G.1
-
38
-
-
79953160460
-
The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons
-
Muro EM, Mah N, Moreno-Hagelsieb G, Andrade-Navarro MA, (2010) The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons. Nucleic Acids Res 39: 1732-1738.
-
(2010)
Nucleic Acids Res
, vol.39
, pp. 1732-1738
-
-
Muro, E.M.1
Mah, N.2
Moreno-Hagelsieb, G.3
Andrade-Navarro, M.A.4
-
39
-
-
84876310365
-
Real Time Metagenomics: Using k-mers to annotate metagenomes
-
Edwards RA, Olson R, Disz T, Pusch GD, Vonstein V,et al. Real Time Metagenomics: Using k-mers to annotate metagenomes. Bioinformatics In Press.
-
Bioinformatics
-
-
Edwards, R.A.1
Olson, R.2
Disz, T.3
Pusch, G.D.4
Vonstein, V.5
-
40
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
-
41
-
-
9144232912
-
UniProt: the Universal Protein knowledgebase
-
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, et al. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 32: D115-119.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Apweiler, R.1
Bairoch, A.2
Wu, C.H.3
Barker, W.C.4
Boeckmann, B.5
-
42
-
-
84862192725
-
The UniProt-GO Annotation database in 2011
-
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, et al. (2012) The UniProt-GO Annotation database in 2011. Nucleic Acids Res 40: D565-570.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Dimmer, E.C.1
Huntley, R.P.2
Alam-Faruque, Y.3
Sawford, T.4
O'Donovan, C.5
-
43
-
-
84868099390
-
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies
-
Akhter S, Aziz RK, Edwards RA, (2012) PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res 40: e126.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Akhter, S.1
Aziz, R.K.2
Edwards, R.A.3
|