{ "abstracts": [], "container_id": "s3gm7274mfe6fcs7e3jterqlri", "contribs": [ { "extra": { "seq": "first" }, "index": 0, "raw_name": "Marc Harper", "role": "author" }, { "index": 1, "raw_name": "Luisa Gronenberg", "role": "author" }, { "index": 2, "raw_name": "James Liao", "role": "author" }, { "index": 3, "raw_name": "Christopher Lee", "role": "author" }, { "extra": { "seq": "first" }, "raw_name": "Mickaël Desvaux", "role": "editor" } ], "ext_ids": { "core": "44314049", "doi": "10.1371/journal.pone.0088072", "pmcid": "PMC3935835", "pmid": "24586303", "wikidata_qid": "Q35106021" }, "extra": { "crossref": { "license": [ { "URL": "http://creativecommons.org/licenses/by/4.0/", "content-version": "unspecified", "delay-in-days": 0, "start": "2014-02-26T00:00:00Z" } ], "type": "journal-article" } }, "ident": "cqkm3hyn3rgcng3d3alwtciwpq", "language": "en", "license_slug": "CC-BY", "pages": "e88072", "publisher": "Public Library of Science (PLoS)", "refs": [ { "container_name": "Microb Cell Fact", "extra": { "authors": [ "JJ Minty" ], "doi": "10.1186/1475-2859-10-18", "volume": "10" }, "index": 0, "key": "ref1", "locator": "18", "title": "Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli", "year": 2011 }, { "extra": { "unstructured": "Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, et al.. (2010) Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Sys Bio 6." }, "index": 1, "key": "ref2" }, { "extra": { "unstructured": "Umland TC, Schultz LW, MacDonald U, Beanan JM, Olson R, et al.. (2012) In vivo-validated essential genes identified in Acinetobacter baumannii by using human ascites overlap poorly with essential genes detected on laboratory media. mBio 3." }, "index": 2, "key": "ref3" }, { "container_name": "Genetics", "extra": { "authors": [ "S Sarin" ], "doi": "10.1534/genetics.110.116319", "volume": "185" }, "index": 3, "key": "ref4", "locator": "417", "title": "Analysis of multiple ethyl methanesulfonate-mutagenized Caenorhabditis elegans strains by whole-genome sequencing", "year": 2010 }, { "container_name": "Genetics", "extra": { "authors": [ "Y Zhu" ], "doi": "10.1534/genetics.112.141986", "volume": "192" }, "index": 4, "key": "ref5", "locator": "139", "title": "Gene discovery using mutagen-induced polymorphisms and deep sequencing: Application to plant disease resistance", "year": 2012 }, { "container_name": "PloS one", "extra": { "authors": [ "MA Harper" ], "doi": "10.1371/journal.pone.0016517" }, "index": 5, "key": "ref6", "locator": "e16517", "title": "Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants", "year": 2011 }, { "container_name": "PloS one", "extra": { "authors": [ "LH Reyes" ], "doi": "10.1371/journal.pone.0017678" }, "index": 6, "key": "ref7", "locator": "e17678", "title": "Genomic library screens for genes involved in n-butanol tolerance in Escherichia coli", "year": 2011 }, { "container_name": "Genome res", "extra": { "authors": [ "Y Erlich" ], "doi": "10.1101/gr.092957.109", "volume": "19" }, "index": 7, "key": "ref8", "locator": "1243", "title": "Dna sudoku - harnessing high- throughput sequencing for multiplexed specimen analysis", "year": 2009 }, { "container_name": "BMC bioinformatics", "extra": { "authors": [ "R Emanuele" ], "doi": "10.1186/1471-2105-13-239", "volume": "13" }, "index": 8, "key": "ref9", "locator": "239", "title": "SNP calling by sequencing pooled samples", "year": 2012 }, { "container_name": "Genome res", "extra": { "authors": [ "C Honisch" ], "doi": "10.1101/gr.2977704", "volume": "14" }, "index": 9, "key": "ref10", "locator": "2495", "title": "High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12", "year": 2004 }, { "container_name": "PNAS", "extra": { "authors": [ "GJ Velicer" ], "doi": "10.1073/pnas.0510740103", "volume": "103" }, "index": 10, "key": "ref11", "locator": "8107", "title": "Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor", "year": 2006 }, { "container_name": "Genome res", "extra": { "authors": [ "DR Smith" ], "doi": "10.1101/gr.077776.108", "volume": "18" }, "index": 11, "key": "ref12", "locator": "1638", "title": "Rapid whole-genome mutational profiling using next-generation sequencing technologies", "year": 2008 }, { "container_name": "J bacteriology", "extra": { "authors": [ "J Klockgether" ], "doi": "10.1128/jb.01515-09", "volume": "192" }, "index": 12, "key": "ref13", "locator": "1113", "title": "Genome diversity of Pseudomonas aeruginosa pao1 laboratory strains", "year": 2010 }, { "container_name": "App Env microbiology", "extra": { "authors": [ "DH Lee" ], "doi": "10.1128/aem.00373-10", "volume": "76" }, "index": 13, "key": "ref14", "locator": "4158", "title": "Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a nonnative carbon source, l-1, 2-propanediol", "year": 2010 }, { "container_name": "PloS one", "extra": { "authors": [ "PE Chen" ], "doi": "10.1371/journal.pone.0012397" }, "index": 14, "key": "ref15", "locator": "e12397", "title": "Rapid identification of ge- netic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing", "year": 2010 }, { "container_name": "Nature genetics", "extra": { "authors": [ "CD Herring" ], "doi": "10.1038/ng1906", "volume": "38" }, "index": 15, "key": "ref16", "locator": "1406", "title": "Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale", "year": 2006 }, { "container_name": "Genome Biol", "extra": { "authors": [ "TM Conrad" ], "doi": "10.1186/gb-2009-10-10-r118", "volume": "10" }, "index": 16, "key": "ref17", "locator": "R118", "title": "Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals exible selection of adaptive mutations", "year": 2009 }, { "container_name": "PLoS genetics", "extra": { "authors": [ "A Srivatsan" ], "doi": "10.1371/journal.pgen.1000139" }, "index": 17, "key": "ref18", "locator": "e1000139", "title": "High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies", "year": 2008 }, { "container_name": "Mutation Res", "extra": { "authors": [ "J Ohnishi" ], "doi": "10.1016/j.mrgentox.2007.10.003", "volume": "649" }, "index": 18, "key": "ref19", "locator": "239", "title": "Characterization of mutations induced by N-methyl-N'-nitro-N-nitrosoguanidine in an industrial Corynebacterium glutamicum strain", "year": 2008 }, { "container_name": "PNAS", "extra": { "authors": [ "S Le Crom" ], "doi": "10.1073/pnas.0905848106", "volume": "106" }, "index": 19, "key": "ref20", "locator": "16151", "title": "Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel dna sequencing", "year": 2009 }, { "container_name": "App Env microbiology", "extra": { "authors": [ "YP Chao" ], "volume": "59" }, "index": 20, "key": "ref21", "locator": "4261", "title": "Alteration of growth yield by overexpression of phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxykinase in Escherichia coli", "year": 1993 }, { "container_name": "App Env microbiology", "extra": { "authors": [ "P Kim" ], "doi": "10.1128/aem.70.2.1238-1241.2004", "volume": "70" }, "index": 21, "key": "ref22", "locator": "1238", "title": "Effect of overexpression of Actinobacillus suc- cinogenes phosphoenolpyruvate carboxykinase on succinate production in Escherichia coli", "year": 2004 }, { "container_name": "Annals of the NYAS", "extra": { "authors": [ "JC Liao" ], "volume": "745" }, "index": 22, "key": "ref23", "locator": "21", "title": "Alteration of the biochemical valves in the central metabolism of Escherichia colia", "year": 1994 }, { "container_name": "J Bio Chem", "extra": { "authors": [ "S Fong" ], "doi": "10.1074/jbc.m510016200", "volume": "281" }, "index": 23, "key": "ref24", "locator": "8024", "title": "Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes", "year": 2006 }, { "container_name": "FEMS microbiology reviews", "extra": { "authors": [ "U Sauer" ], "volume": "29" }, "index": 24, "key": "ref25", "locator": "765", "title": "The pep-pyruvate-oxaloacetate node as the switch point for carbon ux distribution in bacteria", "year": 2005 }, { "container_name": "Biotechnology and bioengineering", "extra": { "authors": [ "Y Dharmadi" ], "doi": "10.1002/bit.21025", "volume": "94" }, "index": 25, "key": "ref26", "locator": "821", "title": "Anaerobic fermentation of glycerol by Escherichia coli : a new platform for metabolic engineering", "year": 2006 }, { "container_name": "PNAS", "extra": { "authors": [ "X Zhang" ], "doi": "10.1073/pnas.0905396106", "volume": "106" }, "index": 26, "key": "ref27", "locator": "20180", "title": "Metabolic evolution of energy-conserving pathways for succinate production in Escherichia coli", "year": 2009 }, { "container_name": "Appl microbiology and biotechnology", "extra": { "authors": [ "R Liu" ], "doi": "10.1007/s00253-012-3896-4", "volume": "94" }, "index": 27, "key": "ref28", "locator": "959", "title": "Fermentation of xylose to succinate by enhancement of ATP supply in metabolically engineered Escherichia coli", "year": 2012 }, { "container_name": "Bioprocess and biosystems engineering", "extra": { "authors": [ "S Park" ], "doi": "10.1007/s00449-012-0759-4", "volume": "36" }, "index": 28, "key": "ref29", "locator": "127", "title": "Oxaloacetate and malate production in engineered Escherichia coli by expression of codon-optimized phosphoenolpyruvate carboxylase2 gene from Dunaliella salina", "year": 2013 }, { "extra": { "doi": "10.1016/j.ymben.2012.07.001", "unstructured": "Zhang B, Skory C, Yang S (2012) Metabolic engineering of Rhizopus oryzae: Effects of overex- pressing pyc and pepc genes on fumaric acid biosynthesis from glucose. Metab eng." }, "index": 29, "key": "ref30" }, { "container_name": "App microbiology and biotechnology", "extra": { "authors": [ "HJ Kim" ], "doi": "10.1007/s00253-011-3779-0", "volume": "94" }, "index": 30, "key": "ref31", "locator": "1079", "title": "An engineered Escherichia coli having a high in- tracellular level of ATP and enhanced recombinant protein production", "year": 2012 }, { "extra": { "doi": "10.1007/s00253-004-1567-9", "unstructured": "Peng L, Shimizu K (2004) Effect of ppc gene knockout on the metabolism of Escherichia coli in view of gene expressions, enzyme activities and intracellular metabolite concentrations. Appl microbiology and biotechnology." }, "index": 31, "key": "ref32" }, { "container_name": "Angewandte Chemie International Edition in English", "extra": { "authors": [ "F Hucho" ], "doi": "10.1002/anie.197505911", "volume": "14" }, "index": 32, "key": "ref33", "locator": "591", "title": "The pyruvate dehydrogenase multienzyme complex", "year": 1975 }, { "container_name": "Nucleic acids res", "extra": { "authors": [ "IM Keseler" ], "doi": "10.1093/nar/gkn751", "volume": "37" }, "index": 33, "key": "ref34", "locator": "D464", "title": "Ecocyc: a comprehensive view of Escherichia coli biology", "year": 2009 }, { "container_name": "Nucleic acids res", "extra": { "authors": [ "D Nam" ], "doi": "10.1093/nar/gkq428", "volume": "38" }, "index": 34, "key": "ref35", "locator": "W749", "title": "GSA-SNP: a general approach for gene set analysis of polymorphisms", "year": 2010 }, { "container_name": "BMC Sys Bio", "extra": { "authors": [ "J Lee" ], "doi": "10.1186/1752-0509-5-s2-s11" }, "index": 35, "key": "ref36", "locator": "S11", "title": "SNP-PRAGE: SNP-based parametric robust analysis of gene set enrichment", "year": 2011 }, { "container_name": "Nature", "extra": { "authors": [ "JH McDonald" ], "doi": "10.1038/351652a0", "volume": "351" }, "index": 36, "key": "ref37", "locator": "652", "title": "Adaptive protein evolution at the Adh locus in Drosophila", "year": 1991 }, { "container_name": "Mutation Res", "extra": { "authors": [ "M Harper" ], "doi": "10.1016/j.mrfmmm.2011.10.011", "volume": "731" }, "index": 37, "key": "ref38", "locator": "64", "title": "Genome-wide analysis of mutagenesis bias and context sensitivity of n-methyl-n'-nitro-n-nitrosoguanidine (ntg)", "year": 2012 }, { "container_name": "FEMS microbiology letters", "extra": { "authors": [ "L Peng" ], "volume": "235" }, "index": 38, "key": "ref39", "locator": "17", "title": "Metabolic ux analysis for a ppc mutant Escherichia coli based on 13c-labelling experiments together with enzyme activity assays and intracellular metabolite measurements", "year": 2004 }, { "extra": { "doi": "10.1111/1574-6968.12109", "unstructured": "Fong NL, Lerman JA, Lam I, Palsson BO, Charusanti P (2013) Reconciling a salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant. FEMS microbiology letters." }, "index": 39, "key": "ref40" }, { "container_name": "J mol microbiology and biotechnology", "extra": { "authors": [ "AJ Cozzone" ], "doi": "10.1159/000089642" }, "index": 40, "key": "ref41", "locator": "132", "title": "Control of isocitrate dehydrogenase catalytic activity by protein phosphorylation in Escherichia coli", "year": 2006 }, { "container_name": "J bacteriology", "extra": { "authors": [ "SR Maloy" ], "volume": "149" }, "index": 41, "key": "ref42", "locator": "173", "title": "Genetic regulation of the glyoxylate shunt in Escherichia coli K-12", "year": 1982 }, { "container_name": "BMC microbiology", "extra": { "authors": [ "H Waegeman" ], "doi": "10.1186/1471-2180-11-70", "volume": "11" }, "index": 42, "key": "ref43", "locator": "70", "title": "Effect of iclr and arca knockouts on biomass formation and metabolic uxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3)", "year": 2011 }, { "container_name": "PNAS", "extra": { "authors": [ "R Teufel" ], "doi": "10.1073/pnas.1005399107", "volume": "107" }, "index": 43, "key": "ref44", "locator": "14390", "title": "Bacterial phenylalanine and phenylacetate catabolic pathway revealed", "year": 2010 }, { "container_name": "Microbiology and Mol Bio Rev", "extra": { "authors": [ "W Boos" ], "volume": "62" }, "index": 44, "key": "ref45", "locator": "204", "title": "Maltose/maltodextrin system of Escherichia coli : transport, metabolism, and regulation", "year": 1998 }, { "container_name": "Biotechnology and bioengineering", "extra": { "authors": [ "K Jantama" ], "doi": "10.1002/bit.21694", "volume": "99" }, "index": 45, "key": "ref46", "locator": "1140", "title": "Combining metabolic en- gineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate", "year": 2008 }, { "container_name": "Appl Env microbiology", "extra": { "authors": [ "R Chatterjee" ], "doi": "10.1128/aem.67.1.148-154.2001", "volume": "67" }, "index": 46, "key": "ref47", "locator": "148", "title": "Mutation of the ptsG gene results in increased production of succinate in fermentation of glucose by Escherichia coli", "year": 2001 }, { "container_name": "Appl Env Microbiology", "extra": { "authors": [ "X Zhang" ], "doi": "10.1128/aem.01758-09", "volume": "75" }, "index": 47, "key": "ref48", "locator": "7807", "title": "Reengineering Escherichia coli for succinate production in mineral salts medium", "year": 2009 }, { "extra": { "doi": "10.1109/iembs.2006.260828", "unstructured": "Fury W, Batliwalla F, Gregersen PK, Li W (2006) Overlapping probabilities of top ranking gene lists, hypergeometric distribution, and stringency of gene selection criterion. In: Engineering in Medicine and Biology Society, 2006. EMBS'06. 28th Annual International Conference of the IEEE. IEEE, pp. 5531–5534." }, "index": 48, "key": "ref49" }, { "extra": { "unstructured": "Silhavy TJ, Berman ML, Enquist LW (1984) Experiments with gene fusions. Cold Spring Harbor Laboratory Cold Spring Harbor, New York." }, "index": 49, "key": "ref50" }, { "container_name": "Metabolic engineering", "extra": { "authors": [ "S Atsumi" ], "doi": "10.1016/j.ymben.2007.08.003", "volume": "10" }, "index": 50, "key": "ref51", "locator": "305", "title": "Metabolic engineering of Escherichia coli for 1-butanol production", "year": 2008 }, { "extra": { "unstructured": "Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, et al.. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the keio collection. Mol Sys Bio 2." }, "index": 51, "key": "ref52" }, { "extra": { "unstructured": "Miller JH (1972) Experiments in molecular genetics, volume 60. Cold Spring Harbor Laboratory Cold Spring Harbor, New York." }, "index": 52, "key": "ref53" }, { "container_name": "Bioinformatics", "extra": { "authors": [ "H Li" ], "doi": "10.1093/bioinformatics/btp352", "volume": "25" }, "index": 53, "key": "ref54", "locator": "2078", "title": "The sequence alignment/map format and SAMtools", "year": 2009 }, { "container_name": "SciPy", "extra": { "authors": [ "C Lee" ] }, "index": 54, "key": "ref55", "locator": "62", "title": "Exploring the future of bioinformatics data sharing and mining with Pygr and Worldbase", "year": 2009 }, { "extra": { "unstructured": "Jones E, Oliphant T, Peterson P (2001) SciPy: Open source scientific tools for Python. Available: http://www.scipy.org/. Accessed 2014 Jan 1." }, "index": 55, "key": "ref56" }, { "extra": { "unstructured": "R Core Team (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Available: http://www.R-project.org. ISBN 3-900051-07-0." }, "index": 56, "key": "ref57" }, { "extra": { "doi": "10.1007/978-0-387-21822-9", "unstructured": "Ewens W (2004) Mathematical population genetics: I. Theoretical introduction, volume 27. Springer." }, "index": 57, "key": "ref58" }, { "extra": { "unstructured": "Cover TM, Thomas JA (2012) Elements of information theory. Wiley-interscience." }, "index": 58, "key": "ref59" }, { "container_name": "FEMS microbiology letters", "extra": { "authors": [ "L Peng" ], "doi": "10.1111/j.1574-6968.2004.tb09562.x", "volume": "235" }, "index": 59, "key": "ref60", "locator": "17", "title": "Metabolic ux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements", "year": 2006 } ], "release_date": "2014-02-26", "release_stage": "published", "release_type": "article-journal", "release_year": 2014, "revision": "cb5ba2a2-f669-4669-be42-8109c0c835f3", "state": "active", "title": "Comprehensive Detection of Genes Causing a Phenotype Using Phenotype Sequencing and Pathway Analysis", "work_id": "a5fegh5iyrfwpc32y33envrime" }