{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T07:03:32Z","timestamp":1771571012659,"version":"3.50.1"},"reference-count":51,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2018,5,1]],"date-time":"2018-05-01T00:00:00Z","timestamp":1525132800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2018,5,1]],"date-time":"2018-05-01T00:00:00Z","timestamp":1525132800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2018,3,9]],"date-time":"2018-03-09T00:00:00Z","timestamp":1520553600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"crossref","award":["NNF14OC0011269"],"award-info":[{"award-number":["NNF14OC0011269"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"crossref","award":["NNF10CC1016517"],"award-info":[{"award-number":["NNF10CC1016517"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"crossref"}]},{"name":"German Ministry of Education and Research","award":["031A343A"],"award-info":[{"award-number":["031A343A"]}]},{"name":"The Danish Agency for Science, Technology and Innovation","award":["3039-00003B INNOFOND_SP"],"award-info":[{"award-number":["3039-00003B INNOFOND_SP"]}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Metabolic Engineering"],"published-print":{"date-parts":[[2018,5]]},"DOI":"10.1016\/j.ymben.2018.03.006","type":"journal-article","created":{"date-parts":[[2018,3,10]],"date-time":"2018-03-10T20:13:37Z","timestamp":1520712817000},"page":"73-82","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":56,"special_numbering":"C","title":["Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae"],"prefix":"10.1016","volume":"47","author":[{"given":"Tomas","family":"Strucko","sequence":"first","affiliation":[]},{"given":"Katharina","family":"Zirngibl","sequence":"additional","affiliation":[]},{"given":"Filipa","family":"Pereira","sequence":"additional","affiliation":[]},{"given":"Eleni","family":"Kafkia","sequence":"additional","affiliation":[]},{"given":"Elsayed T.","family":"Mohamed","sequence":"additional","affiliation":[]},{"given":"Mandy","family":"Rettel","sequence":"additional","affiliation":[]},{"given":"Frank","family":"Stein","sequence":"additional","affiliation":[]},{"given":"Adam M.","family":"Feist","sequence":"additional","affiliation":[]},{"given":"Paula","family":"Jouhten","sequence":"additional","affiliation":[]},{"given":"Kiran Raosaheb","family":"Patil","sequence":"additional","affiliation":[]},{"given":"Jochen","family":"Forster","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"key":"10.1016\/j.ymben.2018.03.006_bib1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"10.1016\/j.ymben.2018.03.006_bib2","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq \u2013 a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ymben.2018.03.006_bib3","unstructured":"Andrews, S., 2010. FastQC: A Quality Control Tool For High Throughput Sequence Data. \u3008http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/\u3009 (Accessed 29 January 2018)."},{"key":"10.1016\/j.ymben.2018.03.006_bib4","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1038\/nrg3564","article-title":"Genome dynamics during experimental evolution","volume":"14","author":"Barrick","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.ymben.2018.03.006_bib5","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1007\/s002940050515","article-title":"UBC13, a DNA-damage-inducible gene, is a member of the error-free postreplication repair pathway in Saccharomyces cerevisiae","volume":"37","author":"Brusky","year":"2000","journal-title":"Curr. Genet."},{"key":"10.1016\/j.ymben.2018.03.006_bib6","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.biotechadv.2008.07.006","article-title":"Glycerol: a promising and abundant carbon source for industrial microbiology","volume":"27","author":"da Silva","year":"2009","journal-title":"Biotechnol. Adv."},{"key":"10.1016\/j.ymben.2018.03.006_bib7","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"DePristo","year":"2011","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ymben.2018.03.006_bib8","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1534\/genetics.112.140467","article-title":"The ubiquitin-proteasome system of Saccharomyces cerevisiae","volume":"192","author":"Finley","year":"2012","journal-title":"Genetics"},{"key":"10.1016\/j.ymben.2018.03.006_bib9","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1101\/gr.234503","article-title":"Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network","volume":"13","author":"F\u00f6rster","year":"2003","journal-title":"Genome Res."},{"key":"10.1016\/j.ymben.2018.03.006_bib10","doi-asserted-by":"crossref","first-page":"e55","DOI":"10.1093\/nar\/gkm106","article-title":"USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products","volume":"35","author":"Geu-Flores","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymben.2018.03.006_bib11","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/nprot.2007.13","article-title":"High-efficiency yeast transformation using the LiAc\/SS carrier DNA\/PEG method","volume":"2","author":"Gietz","year":"2007","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.ymben.2018.03.006_bib12","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1038\/ng1906","article-title":"Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale","volume":"38","author":"Herring","year":"2006","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ymben.2018.03.006_bib13","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s13068-016-0696-6","article-title":"The sole introduction of two single-point mutations establishes glycerol utilization in Saccharomyces cerevisiae CEN.PK derivatives","volume":"10","author":"Ho","year":"2017","journal-title":"Biotechnol. Biofuels"},{"key":"10.1016\/j.ymben.2018.03.006_bib14","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1016\/S0092-8674(00)80575-9","article-title":"Noncanonical MMS2-encoded ubiquitin-conjugating enzyme functions in assembly of novel polyubiquitin chains for DNA repair","volume":"96","author":"Hofmann","year":"1999","journal-title":"Cell"},{"key":"10.1016\/j.ymben.2018.03.006_bib15","doi-asserted-by":"crossref","DOI":"10.1016\/0168-9525(90)90190-H","article-title":"Rapid assessment of S. cerevisiae mating type by PCR","volume":"6","author":"Illuxley","year":"1990","journal-title":"Trends Genet."},{"key":"10.1016\/j.ymben.2018.03.006_bib16","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.ymben.2015.01.008","article-title":"Multiplex metabolic pathway engineering using CRISPR\/Cas9 in Saccharomyces cerevisiae","volume":"28","author":"Jako\u010di\u016bnas","year":"2015","journal-title":"Metab. Eng."},{"key":"10.1016\/j.ymben.2018.03.006_bib17","doi-asserted-by":"crossref","first-page":"fow080","DOI":"10.1093\/femsyr\/fow080","article-title":"Saccharomyces cerevisiae metabolism in ecological context","volume":"16","author":"Jouhten","year":"2016","journal-title":"FEMS Yeast Res."},{"key":"10.1016\/j.ymben.2018.03.006_bib18","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.ymben.2006.08.001","article-title":"Data correction strategy for metabolomics analysis using gas chromatography\u2013mass spectrometry","volume":"9","author":"Kanani","year":"2007","journal-title":"Metab. Eng."},{"key":"10.1016\/j.ymben.2018.03.006_bib19","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1038\/ng.280","article-title":"Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae","volume":"40","author":"Kao","year":"2008","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ymben.2018.03.006_bib20","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"Kim","year":"2013","journal-title":"Genome Biol."},{"key":"10.1016\/j.ymben.2018.03.006_bib21","doi-asserted-by":"crossref","first-page":"2169","DOI":"10.1021\/ac302881e","article-title":"Evaluation and optimization of metabolome sample preparation methods for Saccharomyces cerevisiae","volume":"85","author":"Kim","year":"2013","journal-title":"Anal. Chem."},{"key":"10.1016\/j.ymben.2018.03.006_bib22","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1016\/j.ymben.2016.10.008","article-title":"Towards the exploitation of glycerol's high reducing power in Saccharomyces cerevisiae-based bioprocesses","volume":"38","author":"Klein","year":"2016","journal-title":"Metab. Eng."},{"key":"10.1016\/j.ymben.2018.03.006_bib23","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.meteno.2016.09.001","article-title":"The expression of glycerol facilitators from various yeast species improves growth on glycerol of Saccharomyces cerevisiae","volume":"3","author":"Klein","year":"2016","journal-title":"Metab. Eng. Commun."},{"key":"10.1016\/j.ymben.2018.03.006_bib24","doi-asserted-by":"crossref","first-page":"e1003972","DOI":"10.1371\/journal.pgen.1003972","article-title":"Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment","volume":"9","author":"Kvitek","year":"2013","journal-title":"PLoS Genet."},{"key":"10.1016\/j.ymben.2018.03.006_bib25","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1038\/nature12344","article-title":"Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations","volume":"500","author":"Lang","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.ymben.2018.03.006_bib26","doi-asserted-by":"crossref","first-page":"6720","DOI":"10.1128\/MCB.19.10.6720","article-title":"A transcriptional switch in the expression of yeast tricarboxylic acid cycle genes in response to a reduction or loss of respiratory function","volume":"19","author":"Liu","year":"1999","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.ymben.2018.03.006_bib27","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1186\/s12859-014-0366-2","article-title":"Rapid evaluation and quality control of next generation sequencing data with FaQCs","volume":"15","author":"Lo","year":"2014","journal-title":"BMC Bioinforma."},{"key":"10.1016\/j.ymben.2018.03.006_bib28","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq. 2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.ymben.2018.03.006_bib29","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/j.ymben.2003.09.002","article-title":"The effects of alternate optimal solutions in constraint-based genome-scale metabolic models","volume":"5","author":"Mahadevan","year":"2003","journal-title":"Metab. Eng."},{"key":"10.1016\/j.ymben.2018.03.006_bib30","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"10.1016\/j.ymben.2018.03.006_bib31","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"10.1016\/j.ymben.2018.03.006_bib32","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1007\/s10295-010-0878-3","article-title":"Generation of an evolved Saccharomyces cerevisiae strain with a high freeze tolerance and an improved ability to grow on glycerol","volume":"38","author":"Merico","year":"2011","journal-title":"J. Ind. Microbiol. Biotechnol."},{"key":"10.1016\/j.ymben.2018.03.006_bib33","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.ymben.2012.01.006","article-title":"Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform","volume":"14","author":"Mikkelsen","year":"2012","journal-title":"Metab. Eng."},{"key":"10.1016\/j.ymben.2018.03.006_bib34","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1093\/bioinformatics\/btu743","article-title":"CRISPRdirect: software for designing CRISPR\/Cas guide RNA with reduced off-target sites","volume":"31","author":"Naito","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ymben.2018.03.006_bib35","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/1475-2859-11-36","article-title":"De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology","volume":"11","author":"Nijkamp","year":"2012","journal-title":"Microb. Cell Fact."},{"key":"10.1016\/j.ymben.2018.03.006_bib36","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/1472-6750-10-21","article-title":"A mutant Pfu DNA polymerase designed for advanced uracil-excision DNA engineering","volume":"10","author":"N\u00f8rholm","year":"2010","journal-title":"BMC Biotechnol."},{"key":"10.1016\/j.ymben.2018.03.006_bib37","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1016\/j.biortech.2010.08.003","article-title":"Kinetic analysis of a Saccharomyces cerevisiae strain adapted for improved growth on glycerol: implications for the development of yeast bioprocesses on glycerol","volume":"102","author":"Ochoa-Estopier","year":"2011","journal-title":"Bioresour. Technol."},{"key":"10.1016\/j.ymben.2018.03.006_bib38","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/S0167-7799(97)01136-0","article-title":"On-line and in situ monitoring of biomass in submerged cultivations","volume":"15","author":"Olsson","year":"1997","journal-title":"Trends Biotechnol."},{"key":"10.1016\/j.ymben.2018.03.006_bib39","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1002\/yea.1806","article-title":"Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae","volume":"27","author":"Partow","year":"2010","journal-title":"Yeast"},{"key":"10.1016\/j.ymben.2018.03.006_bib40","doi-asserted-by":"crossref","first-page":"i333","DOI":"10.1093\/bioinformatics\/bts378","article-title":"DELLY: structural variant discovery by integrated paired-end and split-read analysis","volume":"28","author":"Rausch","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ymben.2018.03.006_bib41","first-page":"2695","article-title":"Structure and regulation of KGD1, the structural gene for yeast alpha-ketoglutarate dehydrogenase","volume":"9","author":"Repetto","year":"1989","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.ymben.2018.03.006_bib42","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0076-6879(02)50954-X","article-title":"Getting started with yeast","volume":"350","author":"Sherman","year":"2002","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.ymben.2018.03.006_bib43","doi-asserted-by":"crossref","first-page":"1519","DOI":"10.1007\/s10295-015-1684-8","article-title":"EasyClone 2.0: expanded toolkit of integrative vectors for stable gene expression in industrial Saccharomyces cerevisiae strains","volume":"42","author":"Stovicek","year":"2015","journal-title":"J. Ind. Microbiol. Biotechnol."},{"key":"10.1016\/j.ymben.2018.03.006_bib44","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.meteno.2015.03.001","article-title":"CRISPR\u2013Cas system enables fast and simple genome editing of industrial Saccharomyces cerevisiae strains","volume":"2","author":"Stovicek","year":"2015","journal-title":"Metab. Eng. Commun."},{"key":"10.1016\/j.ymben.2018.03.006_bib45","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1186\/1471-2105-9-303","article-title":"A unified approach to false discovery rate estimation","volume":"9","author":"Strimmer","year":"2008","journal-title":"BMC Bioinforma."},{"key":"10.1016\/j.ymben.2018.03.006_bib46","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/j.ymben.2016.03.003","article-title":"Genetic determinants for enhanced glycerol growth of Saccharomyces cerevisiae","volume":"36","author":"Swinnen","year":"2016","journal-title":"Metab. Eng."},{"key":"10.1016\/j.ymben.2018.03.006_bib47","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/1754-6834-6-157","article-title":"Re-evaluation of glycerol utilization in Saccharomyces cerevisiae: characterization of an isolate that grows on glycerol without supporting supplements","volume":"6","author":"Swinnen","year":"2013","journal-title":"Biotechnol. Biofuels"},{"key":"10.1016\/j.ymben.2018.03.006_bib48","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1016\/S0092-8674(01)00387-7","article-title":"Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2\/Ubc13 heterodimer","volume":"105","author":"VanDemark","year":"2001","journal-title":"Cell"},{"key":"10.1016\/j.ymben.2018.03.006_bib49","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1002\/yea.320080703","article-title":"Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation","volume":"8","author":"Verduyn","year":"1992","journal-title":"Yeast"},{"key":"10.1016\/j.ymben.2018.03.006_bib50","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1126\/science.1243357","article-title":"Long-term dynamics of adaptation in asexual populations","volume":"342","author":"Wiser","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.ymben.2018.03.006_bib51","doi-asserted-by":"crossref","first-page":"e0173318","DOI":"10.1371\/journal.pone.0173318","article-title":"Coevolution with bacteria drives the evolution of aerobic fermentation in Lachancea kluyveri","volume":"12","author":"Zhou","year":"2017","journal-title":"PLoS One"}],"container-title":["Metabolic Engineering"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1096717617304032?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1096717617304032?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T22:58:33Z","timestamp":1761087513000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1096717617304032"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,5]]},"references-count":51,"alternative-id":["S1096717617304032"],"URL":"https:\/\/doi.org\/10.1016\/j.ymben.2018.03.006","relation":{},"ISSN":["1096-7176"],"issn-type":[{"value":"1096-7176","type":"print"}],"subject":[],"published":{"date-parts":[[2018,5]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae","name":"articletitle","label":"Article Title"},{"value":"Metabolic Engineering","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ymben.2018.03.006","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2018 The Authors. Published by Elsevier Inc. on behalf of International Metabolic Engineering Society.","name":"copyright","label":"Copyright"}]}}