-
1
-
-
31544450286
-
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection
-
2006.0008
-
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2:2006.0008. https://doi.org/10.1038/msb4100050.
-
(2006)
Mol Syst Biol
, vol.2
-
-
Baba, T.1
Ara, T.2
Hasegawa, M.3
Takai, Y.4
Okumura, Y.5
Baba, M.6
Datsenko, K.A.7
Tomita, M.8
Wanner, B.L.9
Mori, H.10
-
2
-
-
40549106730
-
Profiling of Escherichia coli Chromosome database
-
Yamazaki Y, Niki H, Kato J. 2008. Profiling of Escherichia coli Chromosome database. Methods Mol Biol 416:385–389. https://doi.org/10.1007/978-1 -59745-321-9_26.
-
(2008)
Methods Mol Biol
, vol.416
, pp. 385-389
-
-
Yamazaki, Y.1
Niki, H.2
Kato, J.3
-
3
-
-
84856372043
-
Virulence determinants in the obligate intracellular pathogen Chlamydia trachomatis revealed by forward genetic approaches
-
Nguyen BD, Valdivia RH. 2012. Virulence determinants in the obligate intracellular pathogen Chlamydia trachomatis revealed by forward genetic approaches. Proc Natl Acad Sci U S A 109:1263–1268. https://doi.org/10.1073/pnas.1117884109.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 1263-1268
-
-
Nguyen, B.D.1
Valdivia, R.H.2
-
4
-
-
73249130761
-
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
-
Langridge GC, Phan MD, Turner DJ, Perkins TT, Parts L, Haase J, Charles I, Maskell DJ, Peters SE, Dougan G, Wain J, Parkhill J, Turner AK. 2009. Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res 19:2308–2316. https://doi.org/10.1101/gr.097097.109.
-
(2009)
Genome Res
, vol.19
, pp. 2308-2316
-
-
Langridge, G.C.1
Phan, M.D.2
Turner, D.J.3
Perkins, T.T.4
Parts, L.5
Haase, J.6
Charles, I.7
Maskell, D.J.8
Peters, S.E.9
Dougan, G.10
Wain, J.11
Parkhill, J.12
Turner, A.K.13
-
5
-
-
70349611730
-
Tn-seq: High-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
-
van Opijnen T, Bodi KL, Camilli A. 2009. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat Methods 6:767–772. https://doi.org/10.1038/nmeth.1377.
-
(2009)
Nat Methods
, vol.6
, pp. 767-772
-
-
van Opijnen, T.1
Bodi, K.L.2
Camilli, A.3
-
6
-
-
70349510646
-
Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung
-
Gawronski JD, Wong SMS, Giannoukos G, Ward DV, Akerley BJ. 2009. Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung. Proc Natl Acad Sci U S A 106:16422–16427. https://doi.org/10.1073/pnas.0906627106.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 16422-16427
-
-
Gawronski, J.D.1
Wong, S.M.S.2
Giannoukos, G.3
Ward, D.V.4
Akerley, B.J.5
-
7
-
-
69949123813
-
Identifying genetic determinants needed to establish a human gut symbiont in its habitat
-
Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI. 2009. Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe 6:279–289. https://doi.org/10.1016/j.chom.2009.08.003.
-
(2009)
Cell Host Microbe
, vol.6
, pp. 279-289
-
-
Goodman, A.L.1
McNulty, N.P.2
Zhao, Y.3
Leip, D.4
Mitra, R.D.5
Lozupone, C.A.6
Knight, R.7
Gordon, J.I.8
-
8
-
-
80052415909
-
The essential genome of a bacterium
-
Christen B, Abeliuk E, Collier JM, Kalogeraki VS, Passarelli B, Coller JA, Fero MJ, McAdams HH, Shapiro L. 2011. The essential genome of a bacterium. Mol Syst Biol 7:528. https://doi.org/10.1038/msb.2011.58.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 528
-
-
Christen, B.1
Abeliuk, E.2
Collier, J.M.3
Kalogeraki, V.S.4
Passarelli, B.5
Coller, J.A.6
Fero, M.J.7
McAdams, H.H.8
Shapiro, L.9
-
9
-
-
84887314032
-
The serum resistome of a globally disseminated multidrug resistant uropathogenic Escherichia coli clone
-
Phan MD, Peters KM, Sarkar S, Lukowski SW, Allsopp LP, Moriel DG, Achard MES, Totsika M, Marshall VM, Upton M, Beatson SA, Schembri MA. 2013. The serum resistome of a globally disseminated multidrug resistant uropathogenic Escherichia coli clone. PLoS Genet 9:e1003834. https://doi.org/10.1371/journal.pgen.1003834.
-
(2013)
Plos Genet
, vol.9
-
-
Phan, M.D.1
Peters, K.M.2
Sarkar, S.3
Lukowski, S.W.4
Allsopp, L.P.5
Moriel, D.G.6
Achard, M.E.S.7
Totsika, M.8
Marshall, V.M.9
Upton, M.10
Beatson, S.A.11
Schembri, M.A.12
-
10
-
-
84994420285
-
Fluorescence-based flow sorting in parallel with transposon insertion site sequencing identifies multidrug efflux systems in Acinetobacter baumannii
-
Hassan KA, Cain AK, Huang T, Liu Q, Elbourne LDH, Boinett CJ, Brzoska AJ, Li L, Ostrowski M, Nhu NTK, Nhu TDH, Baker S, Parkhill J, Paulsen IT. 2016. Fluorescence-based flow sorting in parallel with transposon insertion site sequencing identifies multidrug efflux systems in Acinetobacter baumannii. mBio 7:e01200-16. https://doi.org/10.1128/mBio.01200-16.
-
(2016)
Mbio
, vol.7
-
-
Hassan, K.A.1
Cain, A.K.2
Huang, T.3
Liu, Q.4
Elbourne, L.D.H.5
Boinett, C.J.6
Brzoska, A.J.7
Li, L.8
Ostrowski, M.9
Nhu, N.T.K.10
Nhu, T.D.H.11
Baker, S.12
Parkhill, J.13
Paulsen, I.T.14
-
11
-
-
85043521336
-
Physical enrichment of transposon mutants from saturation mutant libraries using the TraDISort approach
-
Paulsen IT, Cain AK, Hassan KA. 2017. Physical enrichment of transposon mutants from saturation mutant libraries using the TraDISort approach. Mob Genet Elements 7:1–7. https://doi.org/10.1080/2159256X.2017.1313805.
-
(2017)
Mob Genet Elements
, vol.7
, pp. 1-7
-
-
Paulsen, I.T.1
Cain, A.K.2
Hassan, K.A.3
-
12
-
-
0347473810
-
Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways
-
Parsons AB, Brost RL, Ding H, Li Z, Zhang C, Sheikh B, Brown GW, Kane PM, Hughes TR, Boone C. 2004. Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol 22:62–69. https://doi.org/10.1038/nbt919.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 62-69
-
-
Parsons, A.B.1
Brost, R.L.2
Ding, H.3
Li, Z.4
Zhang, C.5
Sheikh, B.6
Brown, G.W.7
Kane, P.M.8
Hughes, T.R.9
Boone, C.10
-
13
-
-
84962811927
-
-/- phox mice
-
-/- phox mice. Infect Immun 84:989–997. https://doi.org/10.1128/IAI.01423-15.
-
(2016)
Infect Immun
, vol.84
, pp. 989-997
-
-
Grant, A.J.1
Oshota, O.2
Chaudhuri, R.R.3
Mayho, M.4
Peters, S.E.5
Clare, S.6
Maskell, D.J.7
Mastroeni, P.8
-
14
-
-
84985993195
-
Global Tn-seq analysis of carbohydrate utilization and vertebrate infectivity of Borrelia burgdorferi
-
Troy EB, Lin T, Gao L, Lazinski DW, Lundt M, Camilli A, Norris SJ, Hu LT. 2016. Global Tn-seq analysis of carbohydrate utilization and vertebrate infectivity of Borrelia burgdorferi. Mol Microbiol 101:1003–1023. https://doi.org/10.1111/mmi.13437.
-
(2016)
Mol Microbiol
, vol.101
, pp. 1003-1023
-
-
Troy, E.B.1
Lin, T.2
Gao, L.3
Lazinski, D.W.4
Lundt, M.5
Camilli, A.6
Norris, S.J.7
Hu, L.T.8
-
15
-
-
84864590175
-
Control of virulence by small RNAs in Streptococcus pneumoniae
-
Mann B, van Opijnen T, Wang J, Obert C, Wang Y-D, Carter R, McGoldrick DJ, Ridout G, Camilli A, Tuomanen EI, Rosch JW. 2012. Control of virulence by small RNAs in Streptococcus pneumoniae. PLoS Pathog 8:e1002788. https://doi.org/10.1371/journal.ppat.1002788.
-
(2012)
Plos Pathog
, vol.8
-
-
Mann, B.1
van Opijnen, T.2
Wang, J.3
Obert, C.4
Wang, Y.-D.5
Carter, R.6
McGoldrick, D.J.7
Ridout, G.8
Camilli, A.9
Tuomanen, E.I.10
Rosch, J.W.11
-
16
-
-
40549105704
-
Modeling competitive outgrowth of mutant populations: Why do essentiality screens yield divergent results?
-
Grenov AI, Gerdes SY. 2008. Modeling competitive outgrowth of mutant populations: why do essentiality screens yield divergent results? Methods Mol Biol 416:361–367. https://doi.org/10.1007/978-1 -59745-321-9_24.
-
(2008)
Methods Mol Biol
, vol.416
, pp. 361-367
-
-
Grenov, A.I.1
Gerdes, S.Y.2
-
17
-
-
34748820665
-
Microarray analysis of Mu transposition in Salmonella enterica, serovar Typhimurium: Transposon exclusion by high-density DNA binding proteins
-
Manna D, Porwollik S, McClelland M, Tan R, Higgins NP. 2007. Microarray analysis of Mu transposition in Salmonella enterica, serovar Typhimurium: transposon exclusion by high-density DNA binding proteins. Mol Microbiol 66:315–328. https://doi.org/10.1111/j.1365-2958.2007.05915.x.
-
(2007)
Mol Microbiol
, vol.66
, pp. 315-328
-
-
Manna, D.1
Porwollik, S.2
McClelland, M.3
Tan, R.4
Higgins, N.P.5
-
18
-
-
84925883643
-
Identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems
-
Curtis PD, Brun YV. 2014. Identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems. Mol Microbiol 93:713–735. https://doi.org/10.1111/mmi.12686.
-
(2014)
Mol Microbiol
, vol.93
, pp. 713-735
-
-
Curtis, P.D.1
Brun, Y.V.2
-
19
-
-
84929224505
-
Tn-seq explorer: A tool for analysis of high-throughput sequencing data of transposon mutant libraries
-
Solaimanpour S, Sarmiento F, Mrázek J. 2015. Tn-seq explorer: a tool for analysis of high-throughput sequencing data of transposon mutant libraries. PLoS One 10:e0126070. https://doi.org/10.1371/journal.pone.0126070.
-
(2015)
Plos One
, vol.10
-
-
Solaimanpour, S.1
Sarmiento, F.2
Mrázek, J.3
-
20
-
-
0031902183
-
FtsK is a bifunctional protein involved in cell division and chromosome localization in Escherichia coli
-
Liu G, Draper GC, Donachie WD. 1998. FtsK is a bifunctional protein involved in cell division and chromosome localization in Escherichia coli. Mol Microbiol 29:893–903. https://doi.org/10.1046/j.1365-2958.1998.00986.x.
-
(1998)
Mol Microbiol
, vol.29
, pp. 893-903
-
-
Liu, G.1
Draper, G.C.2
Donachie, W.D.3
-
21
-
-
78649592020
-
Multiple regions along the Escherichia coli FtsK protein are implicated in cell division
-
Dubarry N, Possoz C, Barre F-X. 2010. Multiple regions along the Escherichia coli FtsK protein are implicated in cell division. Mol Microbiol 78:1088–1100. https://doi.org/10.1111/j.1365-2958.2010.07412.x.
-
(2010)
Mol Microbiol
, vol.78
, pp. 1088-1100
-
-
Dubarry, N.1
Possoz, C.2
Barre, F.-X.3
-
22
-
-
0031720923
-
Only the N-terminal domain of FtsK functions in cell division
-
Draper GC, McLennan N, Begg K, Masters M, Donachie WD. 1998. Only the N-terminal domain of FtsK functions in cell division. J Bacteriol 180:4621–4627.
-
(1998)
J Bacteriol
, vol.180
, pp. 4621-4627
-
-
Draper, G.C.1
McLennan, N.2
Begg, K.3
Masters, M.4
Donachie, W.D.5
-
23
-
-
0031933996
-
Localization of cell division protein FtsK to the Escherichia coli septum and identification of a potential N-terminal targeting domain
-
Yu XC, Tran AH, Sun Q, Margolin W. 1998. Localization of cell division protein FtsK to the Escherichia coli septum and identification of a potential N-terminal targeting domain. J Bacteriol 180:1296–1304.
-
(1998)
J Bacteriol
, vol.180
, pp. 1296-1304
-
-
Yu, X.C.1
Tran, A.H.2
Sun, Q.3
Margolin, W.4
-
24
-
-
0034725994
-
Membrane topology of the N-terminus of the Escherichia coli FtsK division protein
-
Dorazi R, Dewar SJ. 2000. Membrane topology of the N-terminus of the Escherichia coli FtsK division protein. FEBS Lett 478:13–18. https://doi.org/10.1016/S0014-5793(00)01820-2.
-
(2000)
FEBS Lett
, vol.478
, pp. 13-18
-
-
Dorazi, R.1
Dewar, S.J.2
-
25
-
-
0031949032
-
FtsK is an essential cell division protein that is localized to the septum and induced as part of the SOS response
-
Wang L, Lutkenhaus J. 1998. FtsK is an essential cell division protein that is localized to the septum and induced as part of the SOS response. Mol Microbiol 29:731–740. https://doi.org/10.1046/j.1365-2958.1998.00958.x.
-
(1998)
Mol Microbiol
, vol.29
, pp. 731-740
-
-
Wang, L.1
Lutkenhaus, J.2
-
26
-
-
4344668509
-
Translation arrest of SecM is essential for the basal and regulated expression of SecA
-
Murakami A, Nakatogawa H, Ito K. 2004. Translation arrest of SecM is essential for the basal and regulated expression of SecA. Proc Natl Acad Sci U S A 101:12330–12335. https://doi.org/10.1073/pnas.0404907101.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 12330-12335
-
-
Murakami, A.1
Nakatogawa, H.2
Ito, K.3
-
27
-
-
84885009677
-
A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data
-
DeJesus MA, Ioerger TR. 2013. A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data. BMC Bioinformatics 14:303. https://doi.org/10.1186/1471-2105-14-303.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 303
-
-
Dejesus, M.A.1
Ioerger, T.R.2
-
28
-
-
84984986357
-
Combining Shigella Tn-seq data with gold-standard E. Coli gene deletion data suggests rare transitions between essential and non-essential gene functionality
-
Freed NE, Bumann D, Silander OK. 2016. Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality. BMC Microbiol 16:203. https://doi.org/10.1186/s12866-016-0818-0.
-
(2016)
BMC Microbiol
, vol.16
, Issue.203
-
-
Freed, N.E.1
Bumann, D.2
Silander, O.K.3
-
29
-
-
84864974258
-
ESSENTIALS: Software for rapid analysis of high throughput transposon insertion sequencing data
-
Zomer A, Burghout P, Bootsma HJ, Hermans PWM, van Hijum SAFT. 2012. ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. PLoS One 7:e43012. https://doi.org/10.1371/journal.pone.0043012.
-
(2012)
Plos One
, vol.7
-
-
Zomer, A.1
Burghout, P.2
Bootsma, H.J.3
Hermans, P.W.M.4
van Hijum, S.A.F.T.5
-
30
-
-
84875251958
-
Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Metha-nococcus maripaludis
-
Sarmiento F, Mrázek J, Whitman WB. 2013. Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Metha-nococcus maripaludis. Proc Natl Acad Sci U S A 110:4726–4731. https://doi.org/10.1073/pnas.1220225110.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 4726-4731
-
-
Sarmiento, F.1
Mrázek, J.2
Whitman, W.B.3
-
31
-
-
84866887386
-
Global assessment of genomic regions required for growth in Mycobacterium tuberculosis
-
Zhang YJ, Ioerger TR, Huttenhower C, Long JE, Sassetti CM, Sacchettini JC, Rubin EJ. 2012. Global assessment of genomic regions required for growth in Mycobacterium tuberculosis. PLoS Pathog 8:e1002946. https://doi.org/10.1371/journal.ppat.1002946.
-
(2012)
Plos Pathog
, vol.8
-
-
Zhang, Y.J.1
Ioerger, T.R.2
Huttenhower, C.3
Long, J.E.4
Sassetti, C.M.5
Sacchettini, J.C.6
Rubin, E.J.7
-
32
-
-
0027120805
-
Broad host range plasmids carrying the Escherichia coli lactose and galactose operons
-
Lodge J, Fear J, Busby S, Gunasekaran P, Kamini NR. 1992. Broad host range plasmids carrying the Escherichia coli lactose and galactose operons. FEMS Microbiol Lett 74:271–276. https://doi.org/10.1111/j.1574 -6968.1992.tb05378.x.
-
(1992)
FEMS Microbiol Lett
, vol.74
, pp. 271-276
-
-
Lodge, J.1
Fear, J.2
Busby, S.3
Gunasekaran, P.4
Kamini, N.R.5
-
33
-
-
84055223612
-
Translation of a minigene in the 5’ leader sequence of the enterohaemorrhagic Escherichia coli LEE1 transcription unit affects expression of the neighbouring downstream gene
-
Islam MS, Shaw RK, Frankel G, Pallen MJ, Busby SJW. 2012. Translation of a minigene in the 5’ leader sequence of the enterohaemorrhagic Escherichia coli LEE1 transcription unit affects expression of the neighbouring downstream gene. Biochem J 441:247–253. https://doi.org/10.1042/BJ20110912.
-
(2012)
Biochem J
, vol.441
, pp. 247-253
-
-
Islam, M.S.1
Shaw, R.K.2
Frankel, G.3
Pallen, M.J.4
Busby, S.J.W.5
-
34
-
-
73849087355
-
Update on the Keio collection of Escherichia coli single-gene deletion mutants
-
Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H. 2009. Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol Syst Biol 5:335. https://doi.org/10.1038/msb.2009.92.
-
(2009)
Mol Syst Biol
, vol.5
, Issue.335
-
-
Yamamoto, N.1
Nakahigashi, K.2
Nakamichi, T.3
Yoshino, M.4
Takai, Y.5
Touda, Y.6
Furubayashi, A.7
Kinjyo, S.8
Dose, H.9
Hasegawa, M.10
Datsenko, K.A.11
Nakayashiki, T.12
Tomita, M.13
Wanner, B.L.14
Mori, H.15
-
35
-
-
0025754277
-
Analysis of the altered mRNA stability (Ams) gene from Escherichia coli. Nucleotide sequence, transcriptional analysis, and homology of its product to MRP3, a mitochondrial ribosomal protein from Neurospora crassa
-
Claverie-Martin F, Diaz-Torres MR, Yancey SD, Kushner SR. 1991. Analysis of the altered mRNA stability (ams) gene from Escherichia coli. Nucleotide sequence, transcriptional analysis, and homology of its product to MRP3, a mitochondrial ribosomal protein from Neurospora crassa. J Biol Chem 266:2843–2851.
-
(1991)
J Biol Chem
, vol.266
, pp. 2843-2851
-
-
Claverie-Martin, F.1
Diaz-Torres, M.R.2
Yancey, S.D.3
Kushner, S.R.4
-
36
-
-
0036197752
-
RNase E levels in Escherichia coli are controlled by a complex regulatory system that involves transcription of the rne gene from three promoters
-
Ow MC, Liu Q, Mohanty BK, Andrew ME, Maples VF, Kushner SR. 2002. RNase E levels in Escherichia coli are controlled by a complex regulatory system that involves transcription of the rne gene from three promoters. Mol Microbiol 43:159–171. https://doi.org/10.1046/j.1365 -2958.2002.02726.x.
-
(2002)
Mol Microbiol
, vol.43
, pp. 159-171
-
-
Ow, M.C.1
Liu, Q.2
Mohanty, B.K.3
Andrew, M.E.4
Maples, V.F.5
Kushner, S.R.6
-
37
-
-
0033568606
-
E-dependent extracytoplasmic stress response is controlled by the regulated proteolysis of an anti-sigma factor
-
E-dependent extracytoplasmic stress response is controlled by the regulated proteolysis of an anti-sigma factor. Genes Dev 13:2449–2461. https://doi.org/10.1101/gad.13.18.2449.
-
(1999)
Genes Dev
, vol.13
, pp. 2449-2461
-
-
Ades, S.E.1
Connolly, L.E.2
Alba, B.M.3
Gross, C.A.4
-
39
-
-
0029670766
-
Multicopy suppressors of prc mutant Escherichia coli include two HtrA (DegP) protease homologs (HhoAB), DksA, and a truncated R1pA
-
Bass S, Gu Q, Christen A. 1996. Multicopy suppressors of prc mutant Escherichia coli include two HtrA (DegP) protease homologs (HhoAB), DksA, and a truncated R1pA. J Bacteriol 178:1154–1161. https://doi.org/10.1128/jb.178.4.1154-1161.1996.
-
(1996)
J Bacteriol
, vol.178
, pp. 1154-1161
-
-
Bass, S.1
Gu, Q.2
Christen, A.3
-
40
-
-
0030066650
-
Characterization of degQ and degS, Escherichia coli genes encoding homologs of the DegP protease
-
Waller PR, Sauer RT. 1996. Characterization of degQ and degS, Escherichia coli genes encoding homologs of the DegP protease. J Bacteriol 178:1146–1153. https://doi.org/10.1128/jb.178.4.1146-1153.1996.
-
(1996)
J Bacteriol
, vol.178
, pp. 1146-1153
-
-
Waller, P.R.1
Sauer, R.T.2
-
41
-
-
66049121818
-
An ABC transport system that maintains lipid asymmetry in the Gram-negative outer membrane
-
Malinverni JC, Silhavy TJ. 2009. An ABC transport system that maintains lipid asymmetry in the Gram-negative outer membrane. Proc Natl Acad Sci U S A 106:8009–8014. https://doi.org/10.1073/pnas.0903229106.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 8009-8014
-
-
Malinverni, J.C.1
Silhavy, T.J.2
-
42
-
-
84987704895
-
Defining key roles for auxiliary proteins in an ABC transporter that maintains bacterial outer membrane lipid asymmetry
-
Thong S, Ercan B, Torta F, Fong ZY, Wong HYA, Wenk MR, Chng S-S. 2016. Defining key roles for auxiliary proteins in an ABC transporter that maintains bacterial outer membrane lipid asymmetry. Elife 5:e19042. https://doi.org/10.7554/eLife.19042.
-
(2016)
Elife
, vol.5
-
-
Thong, S.1
Ercan, B.2
Torta, F.3
Fong, Z.Y.4
Wong, H.Y.A.5
Wenk, M.R.6
Chng, S.-S.7
-
43
-
-
0035422651
-
Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli
-
Kato J, Katayama T. 2001. Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli. EMBO J 20:4253–4262. https://doi.org/10.1093/emboj/20.15.4253.
-
(2001)
EMBO J
, vol.20
, pp. 4253-4262
-
-
Kato, J.1
Katayama, T.2
-
44
-
-
33746604804
-
Hda-mediated inactivation of the DnaA protein and dnaA gene autoregulation act in concert to ensure homeostatic maintenance of the Escherichia coli chromosome
-
Riber L, Olsson JA, Jensen RB, Skovgaard O, Dasgupta S, Marinus MG, Løbner-Olesen A. 2006. Hda-mediated inactivation of the DnaA protein and dnaA gene autoregulation act in concert to ensure homeostatic maintenance of the Escherichia coli chromosome. Genes Dev 20: 2121–2134. https://doi.org/10.1101/gad.379506.
-
(2006)
Genes Dev
, vol.20
, pp. 2121-2134
-
-
Riber, L.1
Olsson, J.A.2
Jensen, R.B.3
Skovgaard, O.4
Dasgupta, S.5
Marinus, M.G.6
Løbner-Olesen, A.7
-
45
-
-
0037628613
-
Controlled initiation of chromosomal replication in Escherichia coli requires functional Hda protein
-
Camara JE, Skarstad K, Crooke E. 2003. Controlled initiation of chromosomal replication in Escherichia coli requires functional Hda protein. J Bacteriol 185:3244–3248. https://doi.org/10.1128/JB.185.10.3244-3248.2003.
-
(2003)
J Bacteriol
, vol.185
, pp. 3244-3248
-
-
Camara, J.E.1
Skarstad, K.2
Crooke, E.3
-
46
-
-
0037099742
-
TadA, an essential tRNA-specific adenosine deaminase from Escherichia coli
-
Wolf J, Gerber AP, Keller W. 2002. tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli. EMBO J 21:3841–3851. https://doi.org/10.1093/emboj/cdf362.
-
(2002)
EMBO J
, vol.21
, pp. 3841-3851
-
-
Wolf, J.1
Gerber, A.P.2
Keller, W.3
-
47
-
-
34147099429
-
Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli
-
Bubunenko M, Baker T, Court DL. 2007. Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J Bacteriol 189:2844–2853. https://doi.org/10.1128/JB.01713-06.
-
(2007)
J Bacteriol
, vol.189
, pp. 2844-2853
-
-
Bubunenko, M.1
Baker, T.2
Court, D.L.3
-
48
-
-
84977589257
-
Mutations affecting potassium import restore the viability of the Escherichia coli DNA polymerase III holD mutant
-
Durand A, Sinha AK, Dard-Dascot C, Michel B. 2016. Mutations affecting potassium import restore the viability of the Escherichia coli DNA polymerase III holD mutant. PLOS Genet 12:e1006114. https://doi.org/10.1371/journal.pgen.1006114.
-
(2016)
PLOS Genet
, vol.12
-
-
Durand, A.1
Sinha, A.K.2
Dard-Dascot, C.3
Michel, B.4
-
49
-
-
0141707650
-
Lethality of bypass polymerases in Escherichia coli cells with a defective clamp loader complex of DNA polymerase III
-
Viguera E, Petranovic M, Zahradka D, Germain K, Ehrlich DS, Michel B. 2003. Lethality of bypass polymerases in Escherichia coli cells with a defective clamp loader complex of DNA polymerase III. Mol Microbiol 50:193–204. https://doi.org/10.1046/j.1365-2958.2003.03658.x.
-
(2003)
Mol Microbiol
, vol.50
, pp. 193-204
-
-
Viguera, E.1
Petranovic, M.2
Zahradka, D.3
Germain, K.4
Ehrlich, D.S.5
Michel, B.6
-
50
-
-
84908336141
-
Ssb gene duplication restores the viability of ΔholC and ΔholD Escherichia coli mutants
-
Duigou S, Silvain M, Viguera E, Michel B. 2014. ssb gene duplication restores the viability of ΔholC and ΔholD Escherichia coli mutants. PLoS Genet 10:e1004719. https://doi.org/10.1371/journal.pgen.1004719.
-
(2014)
Plos Genet
, vol.10
-
-
Duigou, S.1
Silvain, M.2
Viguera, E.3
Michel, B.4
-
51
-
-
31544443526
-
Escherichia coli K-12: A cooperatively developed annotation snapshot— 2005
-
Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL. 2006. Escherichia coli K-12: a cooperatively developed annotation snapshot— 2005. Nucleic Acids Res 34:1–9. https://doi.org/10.1093/nar/gkj405.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 1-9
-
-
Riley, M.1
Abe, T.2
Arnaud, M.B.3
Berlyn, M.K.4
Blattner, F.R.5
Chaudhuri, R.R.6
Glasner, J.D.7
Horiuchi, T.8
Keseler, I.M.9
Kosuge, T.10
Mori, H.11
Perna, N.T.12
Plunkett, G.13
Rudd, K.E.14
Serres, M.H.15
Thomas, G.H.16
Thomson, N.R.17
Wishart, D.18
Wanner, B.L.19
-
52
-
-
56749151013
-
Small membrane proteins found by comparative genomics and ribosome binding site models
-
Hemm MR, Paul BJ, Schneider TD, Storz G, Rudd KE. 2008. Small membrane proteins found by comparative genomics and ribosome binding site models. Mol Microbiol 70:1487–1501. https://doi.org/10.1111/j.1365 -2958.2008.06495.x.
-
(2008)
Mol Microbiol
, vol.70
, pp. 1487-1501
-
-
Hemm, M.R.1
Paul, B.J.2
Schneider, T.D.3
Storz, G.4
Rudd, K.E.5
-
53
-
-
0029785522
-
Stringent and growth-rate-dependent control of the gua operon of Escherichia coli K-12
-
Davies IJ, Drabble WT. 1996. Stringent and growth-rate-dependent control of the gua operon of Escherichia coli K-12. Microbiology 142: 2429–2437. https://doi.org/10.1099/00221287-142-9-2429.
-
(1996)
Microbiology
, vol.142
, pp. 2429-2437
-
-
Davies, I.J.1
Drabble, W.T.2
-
54
-
-
45149111446
-
Genetic interaction between the Escherichia coli AcpT phosphopantetheinyl transferase and the YejM inner membrane protein
-
De Lay NR, Cronan JE. 2008. Genetic interaction between the Escherichia coli AcpT phosphopantetheinyl transferase and the YejM inner membrane protein. Genetics 178:1327–1337. https://doi.org/10.1534/genetics.107.081836.
-
(2008)
Genetics
, vol.178
, pp. 1327-1337
-
-
de Lay, N.R.1
Cronan, J.E.2
-
55
-
-
19744376674
-
Global topology analysis of the Escherichia coli inner membrane proteome
-
Daley DO, Rapp M, Granseth E, Melén K, Drew D, von Heijne G. 2005. Global topology analysis of the Escherichia coli inner membrane proteome. Science 308:1321–1323.
-
(2005)
Science
, vol.308
, pp. 1321-1323
-
-
Daley, D.O.1
Rapp, M.2
Granseth, E.3
Melén, K.4
Drew, D.5
von Heijne, G.6
-
56
-
-
84926637728
-
Delivery of cardiolipins to the Salmonella outer membrane is necessary for survival within host tissues and virulence
-
Dalebroux ZD, Edrozo MB, Pfuetzner RA, Ressl S, Kulasekara BR, Blanc M-P, Miller SI. 2015. Delivery of cardiolipins to the Salmonella outer membrane is necessary for survival within host tissues and virulence. Cell Host Microbe 17:441–451. https://doi.org/10.1016/j.chom.2015.03.003.
-
(2015)
Cell Host Microbe
, vol.17
, pp. 441-451
-
-
Dalebroux, Z.D.1
Edrozo, M.B.2
Pfuetzner, R.A.3
Ressl, S.4
Kulasekara, B.R.5
Blanc, M.-P.6
Miller, S.I.7
-
57
-
-
12244261594
-
Regulation of capsule synthesis and cell motility in Salmonella enterica by the essential gene igaA
-
Cano DA, Domínguez-Bernal G, Tierrez A, Garcia-Del Portillo F, Casa-desús J. 2002. Regulation of capsule synthesis and cell motility in Salmonella enterica by the essential gene igaA. Genetics 162:1513–1523.
-
(2002)
Genetics
, vol.162
, pp. 1513-1523
-
-
Cano, D.A.1
Domínguez-Bernal, G.2
Tierrez, A.3
Garcia-Del Portillo, F.4
Casa-Desús, J.5
-
58
-
-
84919922342
-
Detecting envelope stress by monitoring β-barrel assembly
-
Cho S-H, Szewczyk J, Pesavento C, Zietek M, Banzhaf M, Roszczenko P, Asmar A, Laloux G, Hov A-K, Leverrier P, Van der Henst C, Vertommen D, Typas A, Collet J-F. 2014. Detecting envelope stress by monitoring β-barrel assembly. Cell 159:1652–1664. https://doi.org/10.1016/j.cell.2014.11.045.
-
(2014)
Cell
, vol.159
, pp. 1652-1664
-
-
Cho, S.-H.1
Szewczyk, J.2
Pesavento, C.3
Zietek, M.4
Banzhaf, M.5
Roszczenko, P.6
Asmar, A.7
Laloux, G.8
Hov, A.-K.9
Leverrier, P.10
van Der Henst, C.11
Vertommen, D.12
Typas, A.13
Collet, J.-F.14
-
59
-
-
0030936995
-
Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK
-
Harrison CJ, Hayer-Hartl M, Di Liberto M, Hartl F, Kuriyan J. 1997. Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK. Science 276:431–435. https://doi.org/10.1126/science.276.5311.431.
-
(1997)
Science
, vol.276
, pp. 431-435
-
-
Harrison, C.J.1
Hayer-Hartl, M.2
Di Liberto, M.3
Hartl, F.4
Kuriyan, J.5
-
60
-
-
0024406857
-
A novel genetic system to detect protein-protein interactions
-
Fields S, Song O. 1989. A novel genetic system to detect protein-protein interactions. Nature 340:245–246. https://doi.org/10.1038/340245a0.
-
(1989)
Nature
, vol.340
, pp. 245-246
-
-
Fields, S.1
Song, O.2
-
61
-
-
0032510783
-
A bacterial two-hybrid system based on a reconstituted signal transduction pathway
-
Karimova G, Pidoux J, Ullmann A, Ladant D. 1998. A bacterial two-hybrid system based on a reconstituted signal transduction pathway. Proc Natl Acad Sci U S A 95:5752–5756.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, pp. 5752-5756
-
-
Karimova, G.1
Pidoux, J.2
Ullmann, A.3
Ladant, D.4
-
62
-
-
33749005086
-
In vivo and in vitro protein solubility assays using split GFP
-
Cabantous S, Waldo GS. 2006. In vivo and in vitro protein solubility assays using split GFP. Nat Methods 3:845–854. https://doi.org/10.1038/nmeth932.
-
(2006)
Nat Methods
, vol.3
, pp. 845-854
-
-
Cabantous, S.1
Waldo, G.S.2
-
63
-
-
79957852570
-
Complex transcrip- tional organization regulates an Escherichia coli locus implicated in lipopolysaccharide biogenesis
-
Martorana AM, Sperandeo P, Polissi A, Dehò G. 2011. Complex transcrip- tional organization regulates an Escherichia coli locus implicated in lipopolysaccharide biogenesis. Res Microbiol 162:470–482. https://doi.org/10.1016/j.resmic.2011.03.007.
-
(2011)
Res Microbiol
, vol.162
, pp. 470-482
-
-
Martorana, A.M.1
Sperandeo, P.2
Polissi, A.3
Dehò, G.4
-
64
-
-
33745974919
-
Non-essential KDO biosynthesis and new essential cell envelope biogenesis genes in the Escherichia coli yrbG–yhbG locus
-
Sperandeo P, Pozzi C, Dehò G, Polissi A. 2006. Non-essential KDO biosynthesis and new essential cell envelope biogenesis genes in the Escherichia coli yrbG–yhbG locus. Res Microbiol 157:547–558. https://doi.org/10.1016/j.resmic.2005.11.014.
-
(2006)
Res Microbiol
, vol.157
, pp. 547-558
-
-
Sperandeo, P.1
Pozzi, C.2
Dehò, G.3
Polissi, A.4
-
65
-
-
0034612342
-
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
-
Datsenko KA, Wanner BL. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640–6645. https://doi.org/10.1073/pnas.120163297.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 6640-6645
-
-
Datsenko, K.A.1
Wanner, B.L.2
-
66
-
-
0017807890
-
Construction and characterization of ampli-fiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid
-
Chang AC, Cohen SN. 1978. Construction and characterization of ampli-fiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol 134:1141–1156.
-
(1978)
J Bacteriol
, vol.134
, pp. 1141-1156
-
-
Chang, A.C.1
Cohen, S.N.2
-
67
-
-
0031573415
-
Comparison of DNA sequences with protein sequences
-
Pearson WR, Wood T, Zhang Z, Miller W. 1997. Comparison of DNA sequences with protein sequences. Genomics 46:24–36. https://doi.org/10.1006/geno.1997.4995.
-
(1997)
Genomics
, vol.46
, pp. 24-36
-
-
Pearson, W.R.1
Wood, T.2
Zhang, Z.3
Miller, W.4
-
68
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170.
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
69
-
-
84891822155
-
RefSeq microbial genomes database: New representation and annotation strategy
-
Tatusova T, Ciufo S, Fedorov B, O’Neill K, Tolstoy I. 2014. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res 42:D553–D559. https://doi.org/10.1093/nar/gkt1274.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D553-D559
-
-
Tatusova, T.1
Ciufo, S.2
Fedorov, B.3
O’Neill, K.4
Tolstoy, I.5
-
70
-
-
31544450286
-
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection
-
2006.0008
-
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2:2006.0008. https://doi.org/10.1038/msb4100050.
-
(2006)
Mol Syst Biol
, vol.2
-
-
Baba, T.1
Ara, T.2
Hasegawa, M.3
Takai, Y.4
Okumura, Y.5
Baba, M.6
Datsenko, K.A.7
Tomita, M.8
Wanner, B.L.9
Mori, H.10
-
71
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. https://doi.org/10.1093/bioinformatics/btq033.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
72
-
-
0033635022
-
Artemis: Sequence visualization and annotation
-
Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944–945. https://doi.org/10.1093/bioinformatics/16.10.944.
-
(2000)
Bioinformatics
, vol.16
, pp. 944-945
-
-
Rutherford, K.1
Parkhill, J.2
Crook, J.3
Horsnell, T.4
Rice, P.5
Rajandream, M.A.6
Barrell, B.7
-
73
-
-
84875904855
-
EcoGene 3.0
-
Zhou J, Rudd KE. 2013. EcoGene 3.0. Nucleic Acids Res 41:D613–D624. https://doi.org/10.1093/nar/gks1235.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D613-D624
-
-
Zhou, J.1
Rudd, K.E.2
-
74
-
-
56449107474
-
BioVenn—a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
-
Hulsen T, de Vlieg J, Alkema W. 2008. BioVenn—a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics 9:488. https://doi.org/10.1186/1471-2164-9-488.
-
(2008)
BMC Genomics
, vol.9
, pp. 488
-
-
Hulsen, T.1
de Vlieg, J.2
Alkema, W.3
-
75
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
|