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Rittmann","year":"2006","journal-title":"Environ Sci Technol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"14592","DOI":"10.1073\/pnas.1218447110","article-title":"Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass","volume":"110","author":"JJ Minty","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"e201210017","DOI":"10.5936\/csbj.201210017","article-title":"Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems","volume":"3","author":"HC Bernstein","year":"2012","journal-title":"Comput Struct Biotechnol J"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/1754-6834-6-59","article-title":"Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans\/yeast co-culture","volume":"6","author":"TR 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Lloyd","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"4468","DOI":"10.1128\/AEM.60.12.4468-4477.1994","article-title":"Coexistence among Epiphytic Bacterial Populations Mediated through Nutritional Resource Partitioning","volume":"60","author":"M Wilson","year":"1994","journal-title":"Appl Environ Microbiol"},{"key":"ref41","doi-asserted-by":"crossref","unstructured":"Zhao Q, Segre D, Paschalidisy IC. Optimal allocation of metabolic functions among organisms in a microbial ecosystem. 2016 IEEE 55th Conference on Decision and Control (CDC). 2016. <comment>doi: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/doi.org\/10.1109\/cdc.2016.7799357\" xlink:type=\"simple\">10.1109\/cdc.2016.7799357<\/ext-link><\/comment>","DOI":"10.1109\/CDC.2016.7799357"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1126\/science.aad0876","article-title":"SYNTHETIC BIOLOGY. Synthetic communities, the sum of parts","volume":"349","author":"BP Teague","year":"2015","journal-title":"Science"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"16181","DOI":"10.1038\/nmicrobiol.2016.181","article-title":"Bacterial evolution: Genomics of metabolic trade-offs","volume":"1","author":"MF Polz","year":"2016","journal-title":"Nat Microbiol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1038\/msb.2013.52","article-title":"Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction","volume":"9","author":"EJ O\u2019Brien","year":"2014","journal-title":"Mol Syst Biol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/j.ymben.2009.10.003","article-title":"Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli","volume":"12","author":"AM Feist","year":"2010","journal-title":"Metab Eng"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1093\/bioinformatics\/btp704","article-title":"Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways","volume":"26","author":"N Tepper","year":"2010","journal-title":"Bioinformatics"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/j.ymben.2009.10.003","article-title":"Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli","volume":"12","author":"AM Feist","year":"2010","journal-title":"Metab Eng"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1093\/bioinformatics\/btp704","article-title":"Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways","volume":"26","author":"N Tepper","year":"2010","journal-title":"Bioinformatics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1038\/msb.2011.65","article-title":"A comprehensive genome-scale reconstruction of Escherichia coli metabolism\u20142011","volume":"7","author":"JD Orth","year":"2011","journal-title":"Mol Syst Biol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1038\/nbt.3956","article-title":"iML1515, a knowledgebase that computes Escherichia coli traits","volume":"35","author":"JM Monk","year":"2017","journal-title":"Nat Biotechnol"},{"key":"ref51","article-title":"The social network of microorganisms\u2014how auxotrophies shape complex communities","author":"K Zengler","year":"2018","journal-title":"Nat Rev Microbiol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1042\/bj2340593","article-title":"The cloning and sequence analysis of the aspC and tyrB genes from Escherichia coli K12. Comparison of the primary structures of the aspartate aminotransferase and aromatic aminotransferase of E. coli with those of the pig aspartate aminotransferase isoenzymes","volume":"234","author":"IG Fotheringham","year":"1986","journal-title":"Biochem J"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1128\/JB.117.1.133-143.1974","article-title":"Mapping of the structural genes of the three aspartokinases and of the two homoserine dehydrogenases of Escherichia coli K-12","volume":"117","author":"J Th\u00e8ze","year":"1974","journal-title":"J Bacteriol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1093\/genetics\/51.2.167","article-title":"TOPOGRAPHY OF COTRANSDUCIBLE ARGININE MUTATIONS IN ESCHERICHIA COLI K-12","volume":"51","author":"N Glansdorff","year":"1965","journal-title":"Genetics"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1042\/bj1100589","article-title":"Positive control of sulphate reduction in Escherichia coli. 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Wild","year":"1985","journal-title":"Mol Gen Genet"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1007\/s10529-006-9163-y","article-title":"Genetic manipulation of a primary metabolic pathway for L-ornithine production in Escherichia coli","volume":"28","author":"Y-J Lee","year":"2006","journal-title":"Biotechnol Lett"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1128\/JB.142.1.221-228.1980","article-title":"Mutations in two unlinked genes are required to produce asparagine auxotrophy in Escherichia coli","volume":"142","author":"J Felton","year":"1980","journal-title":"J Bacteriol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1128\/jb.175.4.982-992.1993","article-title":"Structural genes for thiamine biosynthetic enzymes (thiCEFGH) in Escherichia coli K-12","volume":"175","author":"PB Vander Horn","year":"1993","journal-title":"J Bacteriol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1128\/JB.149.3.916-922.1982","article-title":"Genetic and biochemical analyses of pantothenate biosynthesis in Escherichia coli and Salmonella typhimurium","volume":"149","author":"JE Cronan Jr","year":"1982","journal-title":"J Bacteriol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1814","DOI":"10.1128\/JB.180.7.1814-1821.1998","article-title":"Identification and function of the pdxY gene, which encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5\u2019-phosphate biosynthesis in Escherichia coli K-12","volume":"180","author":"Y Yang","year":"1998","journal-title":"J Bacteriol"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"e26172","DOI":"10.1371\/journal.pone.0026172","article-title":"Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli","volume":"6","author":"D-H 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Struct"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"4769","DOI":"10.1021\/bi00182a004","article-title":"Refined 1.89-A structure of the histidine-binding protein complexed with histidine and its relationship with many other active transport\/chemosensory proteins","volume":"33","author":"N Yao","year":"1994","journal-title":"Biochemistry"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"3343","DOI":"10.1099\/mic.0.29088-0","article-title":"The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation","volume":"152","author":"M Caldara","year":"2006","journal-title":"Microbiology"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"6409","DOI":"10.1016\/S0021-9258(18)42710-X","article-title":"Escherichia coli alpha-ketoglutarate permease is a constitutively expressed proton symporter","volume":"267","author":"W Seol","year":"1992","journal-title":"J Biol 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Role of the ammonium transporter AmtB and AmtB-GlnK complex formation","volume":"279","author":"A Javelle","year":"2004","journal-title":"J Biol Chem"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1046\/j.1365-2958.1996.6281349.x","article-title":"An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli","volume":"21","author":"WC van Heeswijk","year":"1996","journal-title":"Mol Microbiol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The Pfam protein families database: towards a more sustainable future","volume":"44","author":"RD Finn","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"6670","DOI":"10.1021\/bi049474r","article-title":"Crystal structure of the C-terminal domain of the two-component system transmitter protein nitrogen regulator II (NRII; NtrB), regulator of nitrogen assimilation in Escherichia coli","volume":"43","author":"Y Song","year":"2004","journal-title":"Biochemistry"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1093\/oxfordjournals.molbev.a026009","article-title":"Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment","volume":"15","author":"CJ Brown","year":"1998","journal-title":"Mol Biol Evol"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"e48","DOI":"10.1371\/journal.pgen.0020048","article-title":"On the mechanism of gene amplification induced under stress in Escherichia coli","volume":"2","author":"A Slack","year":"2006","journal-title":"PLoS Genet"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/1745-6150-4-46","article-title":"Evolution by leaps: gene duplication in bacteria","volume":"4","author":"MH Serres","year":"2009","journal-title":"Biol Direct"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"3214","DOI":"10.1128\/jb.172.6.3214-3220.1990","article-title":"Cloning and sequencing of a gene encoding a glutamate and aspartate carrier of Escherichia coli K-12","volume":"172","author":"B Wallace","year":"1990","journal-title":"J Bacteriol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"3329","DOI":"10.1128\/JB.01940-06","article-title":"Escherichia coli abg genes enable uptake and cleavage of the folate catabolite p-aminobenzoyl-glutamate","volume":"189","author":"EL Carter","year":"2007","journal-title":"J Bacteriol"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1016\/j.cels.2017.11.013","article-title":"Metabolic Models of Protein Allocation Call for the Kinetome","volume":"5","author":"A Nilsson","year":"2017","journal-title":"Cell Syst"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"13091","DOI":"10.1038\/ncomms13091","article-title":"Multi-omic data integration enables discovery of hidden biological regularities","volume":"7","author":"A Ebrahim","year":"2016","journal-title":"Nat Commun"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"3401","DOI":"10.1073\/pnas.1514240113","article-title":"Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements","volume":"113","author":"D Davidi","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"5252","DOI":"10.1038\/s41467-018-07652-6","article-title":"Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models","volume":"9","author":"D Heckmann","year":"2018","journal-title":"Nat Commun"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1038\/nrmicro1949","article-title":"Reconstruction of biochemical networks in microorganisms","volume":"7","author":"AM Feist","year":"2009","journal-title":"Nat Rev Microbiol"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.tibtech.2015.02.001","article-title":"Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis","volume":"33","author":"DB Kell","year":"2015","journal-title":"Trends Biotechnol"},{"key":"ref91","article-title":"Nanotube-mediated cross-feeding couples the metabolism of interacting bacterial cells","author":"S Shitut","year":"2017","journal-title":"Nanotube-mediated cross-feeding couples the metabolism of interacting bacterial cells"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1038\/s41467-017-01628-8","article-title":"Paradoxes in leaky microbial trade","volume":"8","author":"Y Kallus","year":"2017","journal-title":"Nat Commun"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/1752-0509-7-74","article-title":"COBRApy: COnstraints-Based Reconstruction and Analysis for Python","volume":"7","author":"A Ebrahim","year":"2013","journal-title":"BMC Syst Biol"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1186\/s12859-016-1240-1","article-title":"solveME: fast and reliable solution of nonlinear ME models","volume":"17","author":"L Yang","year":"2016","journal-title":"BMC Bioinformatics. bmcbioinformatics.biomedcentral. \u2026"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"40863","DOI":"10.1038\/srep40863","article-title":"Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression","volume":"7","author":"D Ma","year":"2017","journal-title":"Sci Rep"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1752-0509-6-30","article-title":"Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions","volume":"6","author":"JD Orth","year":"2012","journal-title":"BMC Syst Biol"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/s12859-017-1469-3","article-title":"AfterQC: automatic filtering, trimming, error removing and quality control for fastq data","volume":"18","author":"S Chen","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"ref98","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.01038-14","article-title":"Complete Genome Sequence of Escherichia coli BW25113","volume":"2","author":"F Grenier","year":"2014","journal-title":"Genome Announc"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"ref100","article-title":"ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation","author":"PV Phaneuf","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref102","doi-asserted-by":"crossref","unstructured":"Seabold S, Perktold J. Statsmodels: Econometric and statistical modeling with python. Proceedings of the 9th Python in Science Conference. 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