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Bibliography (54 total) : Review Only   Up

• 2013


• Nakayashiki T, Saito N, Takeuchi R, Kadokura H, Nakahigashi K, Wanner BL, Mori H (2013) The tRNA thiolation pathway modulates the intracellular redox state in Escherichia coli. J Bacteriol 195:2039-49



• Baisa G, Stabo NJ, Welch RA (2013) Characterization of Escherichia coli D-Cycloserine Transport and Resistant Mutants. J Bacteriol 195:1389-99



• Nakayashiki T, Mori H (2013) Genome-wide screening with hydroxyurea reveals a link between nonessential ribosomal proteins and reactive oxygen species production. J Bacteriol 195:1226-35



• Baran R, Bowen BP, Price MN, Arkin AP, Deutschbauer AM, Northen TR (2013) Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. ACS Chem Biol 8:189-99



• Woodruff LB, Pandhal J, Ow SY, Karimpour-Fard A, Weiss SJ, Wright PC, Gill RT (2013) Genome-scale identification and characterization of ethanol tolerance genes in Escherichia coli. Metab Eng 15:124-33



• 2012


• Ojima Y, Hakamada K, Nishinoue Y, Nguyen MH, Miyake J, Taya M (2012) Motility behavior of rpoS-deficient Escherichia coli analyzed by individual cell tracking. J Biosci Bioeng 114:652-6



• Matsuda A, Kurono N, Kawano C, Shirota K, Hirabayashi A, Horino M, Etchuya R, Sobue R, Sasaki Y, Miyaue S, Sekoguchi A, Sugiura C, Shibata Y, Ito M, Ando T, Maeda S (2012) Genome-wide screen for Escherichia coli genes involved in repressing cell-to-cell transfer of non-conjugative plasmids. Biochem Biophys Res Commun 428:445-50



• Reyes VC, Li M, Hoek EM, Mahendra S, Damoiseaux R (2012) Genome-wide assessment in Escherichia coli reveals time-dependent nanotoxicity paradigms. ACS Nano 6:9402-15



• Prigent-Combaret C, Sanguin H, Champier L, Bertrand C, Monnez C, Colinon C, Blaha D, Ghigo JM, Cournoyer B (2012) The bacterial thiopurine methyltransferase tellurite resistance process is highly dependent upon aggregation properties and oxidative stress response. Environ Microbiol 14:2645-60



• Yao Z, Davis RM, Kishony R, Kahne D, Ruiz N (2012) Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli. Proc Natl Acad Sci U S A 109:E2561-8



• Du H, Lo TM, Sitompul J, Chang MW (2012) Systems-level analysis of Escherichia coli response to silver nanoparticles: The roles of anaerobic respiration in microbial resistance. Biochem Biophys Res Commun 424:657-62



• Gagarinova A, Emili A (2012) Genome-scale genetic manipulation methods for exploring bacterial molecular biology. Mol Biosyst 8:1626-38 Review



• Kurono N, Matsuda A, Etchuya R, Sobue R, Sasaki Y, Ito M, Ando T, Maeda S (2012) Genome-wide screening of Escherichia coli genes involved in execution and promotion of cell-to-cell transfer of non-conjugative plasmids: rodZ (yfgA) is essential for plasmid acceptance in recipient cells. Biochem Biophys Res Commun 421:119-23



• Orchard SS, Rostron JE, Segall AM (2012) Escherichia coli enterobactin synthesis and uptake mutants are hypersensitive to an antimicrobial peptide that limits the availability of iron in addition to blocking Holliday junction resolution. Microbiology 158:547-59



• Gagarinova A, Babu M, Greenblatt J, Emili A (2012) Mapping bacterial functional networks and pathways in Escherichia Coli using synthetic genetic arrays. J Vis Exp :



• 2011


• Tran L, van Baarsel JA, Washburn RS, Gottesman ME, Miller JH (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J Bacteriol 193:2229-35



• Donath MJ, Dominguez MA, Withers ST (2011) Development of an automated platform for high-throughput P1-phage transduction of Escherichia coli. J Lab Autom 16:141-7



• Haverkorn van Rijsewijk BR, Nanchen A, Nallet S, Kleijn RJ, Sauer U (2011) Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli. Mol Syst Biol 7:477



• Rooney JP, Patil A, Joseph F, Endres L, Begley U, Zappala MR, Cunningham RP, Begley TJ (2011) Cross-species Functionome analysis identifies proteins associated with DNA repair, translation and aerobic respiration as conserved modulators of UV-toxicity. Genomics 97:133-47



• Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA (2011) Phenotypic landscape of a bacterial cell. Cell 144:143-56



• Babu M, Gagarinova A, Emili A (2011) Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli. Methods Mol Biol 781:99-126



• Moore SD (2011) Assembling new Escherichia coli strains by transduction using phage P1. Methods Mol Biol 765:155-69



• Babu M, Gagarinova A, Greenblatt J, Emili A (2011) Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli. Methods Mol Biol 765:125-53



• Reyes LH, Almario MP, Kao KC (2011) Genomic library screens for genes involved in n-butanol tolerance in Escherichia coli. PLoS One 6:e17678



• 2010


• Tohsato Y, Baba T, Mazaki Y, Ito M, Wanner BL, Mori H (2010) Environmental dependency of gene knockouts on phenotype microarray analysis in Escherichia coli. J Bioinform Comput Biol 8 Suppl 1:83-99



• Desai KK, Miller BG (2010) Recruitment of genes and enzymes conferring resistance to the nonnatural toxin bromoacetate. Proc Natl Acad Sci U S A 107:17968-73



• Sanchez-Torres V, Maeda T, Wood TK (2010) Global regulator H-NS and lipoprotein NlpI influence production of extracellular DNA in Escherichia coli. Biochem Biophys Res Commun 401:197-202



• Gonidakis S, Finkel SE, Longo VD (2010) Genome-wide screen identifies Escherichia coli TCA-cycle-related mutants with extended chronological lifespan dependent on acetate metabolism and the hypoxia-inducible transcription factor ArcA. Aging Cell 9:868-81



• Zhou Y, Minami T, Honda K, Omasa T, Ohtake H (2010) Enhancement of recombinant enzyme activity in cpxA-deficient mutant of Escherichia coli. J Biosci Bioeng 110:403-7



• Wintermute EH, Silver PA (2010) Emergent cooperation in microbial metabolism. Mol Syst Biol 6:407



• Becket E, Chen F, Tamae C, Miller JH (2010) Determination of hypersensitivity to genotoxic agents among Escherichia coli single gene knockout mutants. DNA Repair (Amst) 9:949-57



• Maynard ND, Birch EW, Sanghvi JC, Chen L, Gutschow MV, Covert MW (2010) A forward-genetic screen and dynamic analysis of lambda phage host-dependencies reveals an extensive interaction network and a new anti-viral strategy. PLoS Genet 6:e1001017



• Liu A, Tran L, Becket E, Lee K, Chinn L, Park E, Tran K, Miller JH (2010) Antibiotic sensitivity profiles determined with an Escherichia coli gene knockout collection: generating an antibiotic bar code. Antimicrob Agents Chemother 54:1393-403



• Bakheet TM, Doig AJ (2010) Properties and identification of antibiotic drug targets. BMC Bioinformatics 11:195



• 2009


• 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 19:2308-16



• Babu M, Musso G, Díaz-Mejía JJ, Butland G, Greenblatt JF, Emili A (2009) Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes. Mol Biosyst 5:1439-55 Review



• Montero M, Eydallin G, Viale AM, Almagro G, Muñoz FJ, Rahimpour M, Sesma MT, Baroja-Fernández E, Pozueta-Romero J (2009) Escherichia coli glycogen metabolism is controlled by the PhoP-PhoQ regulatory system at submillimolar environmental Mg2+ concentrations, and is highly interconnected with a wide variety of cellular processes. Biochem J 424:129-41



• Williams JA, Luke J, Hodgson C (2009) Strain engineering by genome mass transfer: efficient chromosomal trait transfer method utilizing donor genomic DNA and recipient recombineering hosts. Mol Biotechnol 43:41-51



• Sharma O, Datsenko KA, Ess SC, Zhalnina MV, Wanner BL, Cramer WA (2009) Genome-wide screens: novel mechanisms in colicin import and cytotoxicity. Mol Microbiol 73:571-85



• 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



• Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, Takai Y, Honma M, Mori H, Tomita M (2009) Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Mol Syst Biol 5:306



• Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C (2009) Systematic mapping of genetic interaction networks. Annu Rev Genet 43:601-25 Review



• Rooney JP, George AD, Patil A, Begley U, Bessette E, Zappala MR, Huang X, Conklin DS, Cunningham RP, Begley TJ (2009) Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks. Genomics 93:42-51



• 2008


• Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL, Mori H, Weissman JS, Krogan NJ, Gross CA (2008) High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 5:781-7



• Silhavy TJ, Gitai Z (2008) Sex to the rescue. Nat Methods 5:759-60



• Butland G, Babu M, Díaz-Mejía JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H, Sheikh B, Moreno-Hagelseib G, Greenblatt JF, Emili A (2008) eSGA: E. coli synthetic genetic array analysis. Nat Methods 5:789-95



• Tamae C, Liu A, Kim K, Sitz D, Hong J, Becket E, Bui A, Solaimani P, Tran KP, Yang H, Miller JH (2008) Determination of antibiotic hypersensitivity among 4,000 single-gene-knockout mutants of Escherichia coli. J Bacteriol 190:5981-8



• Plaimas K, Mallm JP, Oswald M, Svara F, Sourjik V, Eils R, König R (2008) Machine learning based analyses on metabolic networks supports high-throughput knockout screens. BMC Syst Biol 2:67



• 2007


• Hobman JL, Patel MD, Hidalgo-Arroyo GA, Cariss SJ, Avison MB, Penn CW, Constantinidou C (2007) Comparative genomic hybridization detects secondary chromosomal deletions in Escherichia coli K-12 MG1655 mutants and highlights instability in the flhDC region. J Bacteriol 189:8786-92



• Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007) Multicopy suppression underpins metabolic evolvability. Mol Biol Evol 24:2716-22



• Inoue T, Shingaki R, Hirose S, Waki K, Mori H, Fukui K (2007) Genome-wide screening of genes required for swarming motility in Escherichia coli K-12. J Bacteriol 189:950-7



• 2006


• 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



• 2005


• Ito M, Baba T, Mori H, Mori H (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab Eng 7:318-27



• Arita M, Robert M, Tomita M (2005) All systems go: launching cell simulation fueled by integrated experimental biology data. Curr Opin Biotechnol 16:344-9 Review