-
1
-
-
84976906486
-
COMBREX-DB: An experiment centered database of protein function: Knowledge, predictions and knowledge gaps
-
Chang, Y.-C. et al. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps. Nucleic Acids Res. 44, D330-D335 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D330-D335
-
-
Chang, Y.-C.1
-
2
-
-
74549221383
-
Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies
-
Schnoes, A. M., Brown, S. D., Dodevski, I. & Babbitt, P. C. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLOS Comput. Biol. 5, e1000605 (2009).
-
(2009)
PLOS Comput. Biol.
, vol.5
, pp. e1000605
-
-
Schnoes, A.M.1
Brown, S.D.2
Dodevski, I.3
Babbitt, P.C.4
-
3
-
-
84907092457
-
Towards an informative mutant phenotype for every bacterial gene
-
Deutschbauer, A. et al. Towards an informative mutant phenotype for every bacterial gene. J. Bacteriol. 196, 3643-3655 (2014).
-
(2014)
J. Bacteriol.
, vol.196
, pp. 3643-3655
-
-
Deutschbauer, A.1
-
4
-
-
81755163097
-
Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions
-
Deutschbauer, A. et al. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet. 7, e1002385 (2011).
-
(2011)
PLoS Genet.
, vol.7
, pp. e1002385
-
-
Deutschbauer, A.1
-
5
-
-
78650475398
-
Phenotypic landscape of a bacterial cell
-
Nichols, R. J. et al. Phenotypic landscape of a bacterial cell. Cell 144, 143-156 (2011).
-
(2011)
Cell
, vol.144
, pp. 143-156
-
-
Nichols, R.J.1
-
6
-
-
84987825028
-
The genetic basis of energy conservation in the sulfatereducing bacterium Desulfovibrio alaskensis G20
-
Price, M. N. et al. The genetic basis of energy conservation in the sulfatereducing bacterium Desulfovibrio alaskensis G20. Front. Microbiol. 5, 577 (2014).
-
(2014)
Front. Microbiol.
, vol.5
, pp. 577
-
-
Price, M.N.1
-
7
-
-
73249130761
-
Simultaneous assay of every Salmonella typhi gene using one million transposon mutants
-
Langridge, G. C. et al. Simultaneous assay of every Salmonella typhi gene using one million transposon mutants. Genome Res. 19, 2308-2316 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 2308-2316
-
-
Langridge, G.C.1
-
8
-
-
70349611730
-
Tn-seq: High-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
-
van Opijnen, T., Bodi, K. L. & Camilli, A. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat. Methods 6, 767-772 (2009).
-
(2009)
Nat. Methods
, vol.6
, pp. 767-772
-
-
Van Opijnen, T.1
Bodi, K.L.2
Camilli, A.3
-
9
-
-
84936929916
-
Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons
-
Wetmore, K. M. et al. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. MBio 6, e00306-e00315 (2015).
-
(2015)
MBio
, vol.6
, pp. e00306-e00315
-
-
Wetmore, K.M.1
-
10
-
-
85041539594
-
Magic pools: Parallel assessment of transposon delivery vectors in bacteria
-
Liu, H. et al. Magic pools: parallel assessment of transposon delivery vectors in bacteria. mSystems 3, e00143-17 (2018).
-
(2018)
MSystems
, vol.3
, pp. e00143-e00217
-
-
Liu, H.1
-
11
-
-
84948658955
-
The essential gene set of a photosynthetic organism
-
Rubin, B. E. et al. The essential gene set of a photosynthetic organism. Proc. Natl Acad. Sci. USA 112, E6634-E6643 (2015).
-
(2015)
Proc. Natl Acad. Sci. USA
, vol.112
, pp. E6634-E6643
-
-
Rubin, B.E.1
-
12
-
-
84936951713
-
Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich peptide and methionine sulfoxide reductase
-
Melnyk, R. A. et al. Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich peptide and methionine sulfoxide reductase. MBio 6, e00233-15 (2015).
-
(2015)
MBio
, vol.6
, pp. e00233-e00315
-
-
Melnyk, R.A.1
-
13
-
-
70349634435
-
Quantitative phenotyping via deep barcode sequencing
-
Smith, A. M. et al. Quantitative phenotyping via deep barcode sequencing. Genome Res. 19, 1836-1842 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 1836-1842
-
-
Smith, A.M.1
-
14
-
-
0030817267
-
New functions for the three subunits of the CzcCBA cation-proton antiporter
-
Rensing, C., Pribyl, T. & Nies, D. H. New functions for the three subunits of the CzcCBA cation-proton antiporter. J. Bacteriol. 179, 6871-6879 (1997).
-
(1997)
J. Bacteriol.
, vol.179
, pp. 6871-6879
-
-
Rensing, C.1
Pribyl, T.2
Nies, D.H.3
-
15
-
-
84880787194
-
Bacterial adaptation through loss of function
-
Hottes, A. K. et al. Bacterial adaptation through loss of function. PLoS Genet. 9, e1003617 (2013).
-
(2013)
PLoS Genet.
, vol.9
, pp. e1003617
-
-
Hottes, A.K.1
-
16
-
-
84876134492
-
TIGRFAMs and genome properties in 2013
-
Haft, D. H. et al. TIGRFAMs and genome properties in 2013. Nucleic Acids Res. 41, D387-D395 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D387-D395
-
-
Haft, D.H.1
-
17
-
-
84891782659
-
Pfam: The protein families database
-
Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222-D230 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D222-D230
-
-
Finn, R.D.1
-
18
-
-
84855846639
-
Widespread genetic switches and toxicity resistance proteins for fluoride
-
Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233-235 (2012).
-
(2012)
Science
, vol.335
, pp. 233-235
-
-
Baker, J.L.1
-
19
-
-
84876556918
-
EcoCyc: Fusing model organism databases with systems biology
-
Keseler, I. M. et al. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 41, D605-D612 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D605-D612
-
-
Keseler, I.M.1
-
20
-
-
77949425833
-
Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action
-
Hillenmeyer, M. E. et al. Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action. Genome Biol. 11, R30 (2010).
-
(2010)
Genome Biol.
, vol.11
, pp. R30
-
-
Hillenmeyer, M.E.1
-
21
-
-
0033543658
-
Enzyme INtr from Escherichia coli. A novel enzyme of the phosphoenolpyruvate-dependent phosphotransferase system exhibiting strict specificity for its phosphoryl acceptor, NPr
-
Rabus, R., Reizer, J., Paulsen, I. & Saier, M. H. Jr Enzyme INtr from Escherichia coli. A novel enzyme of the phosphoenolpyruvate-dependent phosphotransferase system exhibiting strict specificity for its phosphoryl acceptor, NPr. J. Biol. Chem. 274, 26185-26191 (1999).
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 26185-26191
-
-
Rabus, R.1
Reizer, J.2
Paulsen, I.3
Saier, M.H.4
-
22
-
-
84989894424
-
Strain dependent genetic networks for antibiotic-sensitivity in a bacterial pathogen with a large pan-genome
-
van Opijnen, T., Dedrick, S. & Bento, J. Strain dependent genetic networks for antibiotic-sensitivity in a bacterial pathogen with a large pan-genome. PLoS Pathog. 12, e1005869 (2016).
-
(2016)
PLoS Pathog.
, vol.12
, pp. e1005869
-
-
Van Opijnen, T.1
Dedrick, S.2
Bento, J.3
-
23
-
-
84924035576
-
Escherichia coli radD (yejH) gene: A novel function involved in radiation resistance and double-strand break repair
-
Chen, S. H., Byrne, R. T., Wood, E. A. & Cox, M. M. Escherichia coli radD (yejH) gene: a novel function involved in radiation resistance and double-strand break repair. Mol. Microbiol. 95, 754-768 (2015).
-
(2015)
Mol. Microbiol.
, vol.95
, pp. 754-768
-
-
Chen, S.H.1
Byrne, R.T.2
Wood, E.A.3
Cox, M.M.4
-
24
-
-
84936747255
-
Functional characterization of two SOS-regulated genes involved in mitomycin C resistance in Caulobacter crescentus
-
Lopes-Kulishev, C. O. et al. Functional characterization of two SOS-regulated genes involved in mitomycin C resistance in Caulobacter crescentus. DNA Repair (Amst.) 33, 78-89 (2015).
-
(2015)
DNA Repair (Amst.)
, vol.33
, pp. 78-89
-
-
Lopes-Kulishev, C.O.1
-
25
-
-
84908101886
-
Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: Basis of interstrand cross-link repair by FAN1
-
Gwon, G. H. et al. Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: basis of interstrand cross-link repair by FAN1. Genes Dev. 28, 2276-2290 (2014).
-
(2014)
Genes Dev.
, vol.28
, pp. 2276-2290
-
-
Gwon, G.H.1
-
26
-
-
38349050376
-
Morphological plasticity as a bacterial survival strategy
-
Justice, S. S., Hunstad, D. A., Cegelski, L. & Hultgren, S. J. Morphological plasticity as a bacterial survival strategy. Nat. Rev. Microbiol. 6, 162-168 (2008).
-
(2008)
Nat. Rev. Microbiol.
, vol.6
, pp. 162-168
-
-
Justice, S.S.1
Hunstad, D.A.2
Cegelski, L.3
Hultgren, S.J.4
-
27
-
-
38949166091
-
Characterization of the SOS regulon of Caulobacter crescentus
-
da Rocha, R. P., Paquola, A. C. de M., Marques Mdo, V., Menck, C. F. M. & Galhardo, R. S. Characterization of the SOS regulon of Caulobacter crescentus. J. Bacteriol. 190, 1209-1218 (2008).
-
(2008)
J. Bacteriol.
, vol.190
, pp. 1209-1218
-
-
Da Rocha, R.P.1
Paquola, A.C.D.M.2
Marques Mdo, V.3
Menck, C.F.M.4
Galhardo, R.S.5
-
28
-
-
37449019352
-
Cohabitation of two different lexA regulons in Pseudomonas putida
-
Abella, M., Campoy, S., Erill, I., Rojo, F. & Barbé, J. Cohabitation of two different lexA regulons in Pseudomonas putida. J. Bacteriol. 189, 8855-8862 (2007).
-
(2007)
J. Bacteriol.
, vol.189
, pp. 8855-8862
-
-
Abella, M.1
Campoy, S.2
Erill, I.3
Rojo, F.4
Barbé, J.5
-
29
-
-
33749585217
-
Defining the Pseudomonas aeruginosa SOS response and its role in the global response to the antibiotic ciprofloxacin
-
Cirz, R. T., O'Neill, B. M., Hammond, J. A., Head, S. R. & Romesberg, F. E. Defining the Pseudomonas aeruginosa SOS response and its role in the global response to the antibiotic ciprofloxacin. J. Bacteriol. 188, 7101-7110 (2006).
-
(2006)
J. Bacteriol.
, vol.188
, pp. 7101-7110
-
-
Cirz, R.T.1
O'Neill, B.M.2
Hammond, J.A.3
Head, S.R.4
Romesberg, F.E.5
-
30
-
-
84904895656
-
Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, a member of the marine roseobacter clade
-
Wiegmann, K. et al. Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, a member of the marine roseobacter clade. Appl. Environ. Microbiol. 80, 4725-4737 (2014).
-
(2014)
Appl. Environ. Microbiol.
, vol.80
, pp. 4725-4737
-
-
Wiegmann, K.1
-
31
-
-
33748754005
-
Identification of the missing links in prokaryotic pentose oxidation pathways: Evidence for enzyme recruitment
-
Brouns, S. J. J. et al. Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment. J. Biol. Chem. 281, 27378-27388 (2006).
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 27378-27388
-
-
Brouns, S.J.J.1
-
32
-
-
70350443043
-
D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii
-
Johnsen, U. et al. d-xylose degradation pathway in the halophilic archaeon Haloferax volcanii. J. Biol. Chem. 284, 27290-27303 (2009).
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 27290-27303
-
-
Johnsen, U.1
-
33
-
-
33947372119
-
Genetic analysis of a novel pathway for d-xylose metabolism in Caulobacter crescentus
-
Stephens, C. et al. Genetic analysis of a novel pathway for d-xylose metabolism in Caulobacter crescentus. J. Bacteriol. 189, 2181-2185 (2007).
-
(2007)
J. Bacteriol.
, vol.189
, pp. 2181-2185
-
-
Stephens, C.1
-
34
-
-
84976907502
-
KEGG as a reference resource for gene and protein annotation
-
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D457-D462
-
-
Kanehisa, M.1
Sato, Y.2
Kawashima, M.3
Furumichi, M.4
Tanabe, M.5
-
35
-
-
84891804612
-
The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST)
-
Overbeek, R. et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42, D206-D214 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D206-D214
-
-
Overbeek, R.1
-
36
-
-
0026085431
-
Direct evidence of the entner-doudoroff pathway operating in the metabolism of d-glucosamine in bacteria
-
Iwamoto, R. & Imanaga, Y. Direct evidence of the Entner-Doudoroff pathway operating in the metabolism of d-glucosamine in bacteria. J. Biochem. 109, 66-69 (1991).
-
(1991)
J. Biochem.
, vol.109
, pp. 66-69
-
-
Iwamoto, R.1
Imanaga, Y.2
-
37
-
-
0028872628
-
The Escherichia coli glycine transport system and its role in the regulation of the glycine cleavage enzyme system
-
Ghrist, A. C. & Stauffer, G. V. The Escherichia coli glycine transport system and its role in the regulation of the glycine cleavage enzyme system. Microbiology 141, 133-140 (1995).
-
(1995)
Microbiology
, vol.141
, pp. 133-140
-
-
Ghrist, A.C.1
Stauffer, G.V.2
-
38
-
-
84949255688
-
Adaptation to sustained nitrogen starvation by Escherichia coli requires the eukaryote-like serine/threonine kinase Yea G
-
Figueira, R. et al. Adaptation to sustained nitrogen starvation by Escherichia coli requires the eukaryote-like serine/threonine kinase Yea G. Sci. Rep. 5, 17524 (2015).
-
(2015)
Sci. Rep.
, vol.5
, pp. 17524
-
-
Figueira, R.1
-
39
-
-
40949113533
-
Cloning, expression, purification and characterization of the stress kinase YeaG from Escherichia coli
-
Tagourti, J., Landoulsi, A. & Richarme, G. Cloning, expression, purification and characterization of the stress kinase YeaG from Escherichia coli. Protein Expr. Purif. 59, 79-85 (2008).
-
(2008)
Protein Expr. Purif.
, vol.59
, pp. 79-85
-
-
Tagourti, J.1
Landoulsi, A.2
Richarme, G.3
-
40
-
-
84936977074
-
Molybdenum availability is key to nitrate removal in contaminated groundwater environments
-
Thorgersen, M. P. et al. Molybdenum availability is key to nitrate removal in contaminated groundwater environments. Appl. Environ. Microbiol. 81, 4976-4983 (2015).
-
(2015)
Appl. Environ. Microbiol.
, vol.81
, pp. 4976-4983
-
-
Thorgersen, M.P.1
-
41
-
-
85008486121
-
Complete genome sequence of Cupriavidus basilensis 4G11, isolated from the oak ridge field research center site
-
Ray, J. et al. Complete genome sequence of Cupriavidus basilensis 4G11, isolated from the Oak Ridge Field Research Center site. Genome Announc. 3, e00322-15 (2015).
-
(2015)
Genome Announc.
, vol.3
, pp. e00322-e00415
-
-
Ray, J.1
-
42
-
-
84987914616
-
Novel metal cation resistance systems from mutant fitness analysis of denitrifying Pseudomonas stutzeri
-
Vaccaro, B. J. et al. Novel metal cation resistance systems from mutant fitness analysis of denitrifying Pseudomonas stutzeri. Appl. Environ. Microbiol. 82, 6046-6056 (2016).
-
(2016)
Appl. Environ. Microbiol.
, vol.82
, pp. 6046-6056
-
-
Vaccaro, B.J.1
-
43
-
-
0028793123
-
Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes
-
Kovach, M. E. et al. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166, 175-176 (1995).
-
(1995)
Gene
, vol.166
, pp. 175-176
-
-
Kovach, M.E.1
-
44
-
-
31544450286
-
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection
-
2006.0008
-
Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).
-
(2006)
Mol. Syst. Biol.
, vol.2
-
-
Baba, T.1
-
45
-
-
84903975403
-
Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20
-
Kuehl, J. V. et al. Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. MBio 5, e01041-14 (2014).
-
(2014)
MBio
, vol.5
, pp. e01041-e01114
-
-
Kuehl, J.V.1
-
46
-
-
77955964940
-
Effect of the deletion of qmoABC and the promoter-distal gene encoding a hypothetical protein on sulfate reduction in Desulfovibrio vulgaris Hildenborough
-
Zane, G. M., Yen, H. C. & Wall, J. D. Effect of the deletion of qmoABC and the promoter-distal gene encoding a hypothetical protein on sulfate reduction in Desulfovibrio vulgaris Hildenborough. Appl. Environ. Microbiol. 76, 5500-5509 (2010).
-
(2010)
Appl. Environ. Microbiol.
, vol.76
, pp. 5500-5509
-
-
Zane, G.M.1
Yen, H.C.2
Wall, J.D.3
-
47
-
-
77953169216
-
Grofit: Fitting biological growth curves with R
-
Kahm, M., Hasenbrink, G., Lichtenberg-Frate, H., Ludwig, J. & Kschischo, M. grofit: fitting biological growth curves with R. J. Stat. Softw. 33, 1-21 (2010).
-
(2010)
J. Stat. Softw.
, vol.33
, pp. 1-21
-
-
Kahm, M.1
Hasenbrink, G.2
Lichtenberg-Frate, H.3
Ludwig, J.4
Kschischo, M.5
-
48
-
-
84860771820
-
SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477 (2012).
-
(2012)
J. Comput. Biol.
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
-
49
-
-
84863664355
-
A hybrid approach for the automated finishing of bacterial genomes
-
Bashir, A. et al. A hybrid approach for the automated finishing of bacterial genomes. Nat. Biotechnol. 30, 701-707 (2012).
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 701-707
-
-
Bashir, A.1
-
50
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
51
-
-
84914689868
-
Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement
-
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9, e112963 (2014).
-
(2014)
PLoS One
, vol.9
, pp. e112963
-
-
Walker, B.J.1
-
52
-
-
84866391549
-
An integrated pipeline for de novo assembly of microbial genomes
-
Tritt, A., Eisen, J. A., Facciotti, M. T. & Darling, A. E. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 7, e42304 (2012).
-
(2012)
PLoS One
, vol.7
, pp. e42304
-
-
Tritt, A.1
Eisen, J.A.2
Facciotti, M.T.3
Darling, A.E.4
-
53
-
-
84951969455
-
Circlator: Automated circularization of genome assemblies using long sequencing reads
-
Hunt, M. et al. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 16, 294 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 294
-
-
Hunt, M.1
-
54
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy, S. R. Accelerated profile HMM searches. PLOS Comput. Biol. 7, e1002195 (2011).
-
(2011)
PLOS Comput. Biol.
, vol.7
, pp. e1002195
-
-
Eddy, S.R.1
-
55
-
-
84859242353
-
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
-
Wu, M. & Scott, A. J. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28, 1033-1034 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 1033-1034
-
-
Wu, M.1
Scott, A.J.2
-
56
-
-
77949718257
-
FastTree 2-approximately maximumlikelihood trees for large alignments
-
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2-approximately maximumlikelihood trees for large alignments. PLoS One 5, e9490 (2010).
-
(2010)
PLoS One
, vol.5
, pp. e9490
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
57
-
-
85019872465
-
Validating regulatory predictions from diverse bacteria with mutant fitness data
-
Sagawa, S., Price, M. N., Deutschbauer, A. M. & Arkin, A. P. Validating regulatory predictions from diverse bacteria with mutant fitness data. PLoS One 12, e0178258 (2017).
-
(2017)
PLoS One
, vol.12
, pp. e0178258
-
-
Sagawa, S.1
Price, M.N.2
Deutschbauer, A.M.3
Arkin, A.P.4
-
58
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D. & Maltsev, N. The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA 96, 2896-2901 (1999).
-
(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
-
59
-
-
40549120596
-
The RAST Server: Rapid annotations using subsystems technology
-
Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75 (2008).
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
-
60
-
-
84976877782
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
-
Caspi, R. et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 44, D471-D480 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D471-D480
-
-
Caspi, R.1
-
61
-
-
85041536616
-
PaperBLAST: Text mining papers for information about homologs
-
Price, M. N. & Arkin, A. P. PaperBLAST: text mining papers for information about homologs. mSystems 2, e00039-17 (2017).
-
(2017)
MSystems
, vol.2
, pp. e00039-e00117
-
-
Price, M.N.1
Arkin, A.P.2
-
62
-
-
84941042486
-
CDD: NCBI's conserved domain database
-
Marchler-Bauer, A. et al. CDD: NCBI's conserved domain database. Nucleic Acids Res. 43, D222-D226 (2015).
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D222-D226
-
-
Marchler-Bauer, A.1
-
63
-
-
0036226603
-
BLAT - The BLAST-like alignment tool
-
Kent, W. J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
64
-
-
0042525860
-
DNA binding and cleavage by the periplasmic nuclease Vvn: A novel structure with a known active site
-
Li, C.-L. et al. DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site. EMBO J. 22, 4014-4025 (2003).
-
(2003)
EMBO J.
, vol.22
, pp. 4014-4025
-
-
Li, C.-L.1
-
65
-
-
0017710949
-
The release of endonuclease I from Escherichia coli by a new cold shock procedure
-
Ananthaswamy, H. N. The release of endonuclease I from Escherichia coli by a new cold shock procedure. Biochem. Biophys. Res. Commun. 76, 289-298 (1977).
-
(1977)
Biochem. Biophys. Res. Commun.
, vol.76
, pp. 289-298
-
-
Ananthaswamy, H.N.1
-
66
-
-
0015289151
-
Leakage of periplasmic enzymes by mutants of Escherichia coli and Salmonella typhimurium: Isolation of 'periplasmic leaky' mutants
-
Lopes, J., Gottfried, S. & Rothfield, L. Leakage of periplasmic enzymes by mutants of Escherichia coli and Salmonella typhimurium: isolation of 'periplasmic leaky' mutants. J. Bacteriol. 109, 520-525 (1972).
-
(1972)
J. Bacteriol.
, vol.109
, pp. 520-525
-
-
Lopes, J.1
Gottfried, S.2
Rothfield, L.3
-
67
-
-
0014010845
-
The release of enzymes by osmotic shock from Escherichia coli in exponential phase
-
Nossal, N. G. & Heppel, L. A. The release of enzymes by osmotic shock from Escherichia coli in exponential phase. J. Biol. Chem. 241, 3055-3062 (1966).
-
(1966)
J. Biol. Chem.
, vol.241
, pp. 3055-3062
-
-
Nossal, N.G.1
Heppel, L.A.2
|