{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:57Z","timestamp":1772138097554,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,10,4]],"date-time":"2019-10-04T00:00:00Z","timestamp":1570147200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Department of Science and Technology, India"},{"name":"INSPIRE Faculty Fellowship","award":["IFA 12-ENG-34"],"award-info":[{"award-number":["IFA 12-ENG-34"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Thermodynamic analysis of biological reaction networks requires the availability of accurate and consistent values of Gibbs free energies of reaction and formation. These Gibbs energies can be measured directly via the careful design of experiments or can be computed from the curated Gibbs free energy databases. However, the computed Gibbs free energies of reactions and formations do not satisfy the thermodynamic constraints due to the compounding effect of measurement errors in the experimental data. The propagation of these errors can lead to a false prediction of pathway feasibility and uncertainty in the estimation of thermodynamic parameters.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>This work proposes a data reconciliation framework for thermodynamically consistent estimation of Gibbs free energies of reaction, formation and group contributions from experimental data. In this framework, we formulate constrained optimization problems that reduce measurement errors and their effects on the estimation of Gibbs energies such that the thermodynamic constraints are satisfied. When a subset of Gibbs free energies of formations is unavailable, it is shown that the accuracy of their resulting estimates is better than that of existing empirical prediction methods. Moreover, we also show that the estimation of group contributions can be improved using this approach. Further, we provide guidelines based on this approach for performing systematic experiments to estimate unknown Gibbs formation energies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The MATLAB code for the executing the proposed algorithm is available for free on the GitHub repository: https:\/\/github.com\/samansalike\/DR-thermo.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz741","type":"journal-article","created":{"date-parts":[[2019,9,28]],"date-time":"2019-09-28T20:54:46Z","timestamp":1569704086000},"page":"1219-1225","source":"Crossref","is-referenced-by-count":8,"title":["Thermodynamically consistent estimation of Gibbs free energy from data: data reconciliation approach"],"prefix":"10.1093","volume":"36","author":[{"given":"Saman","family":"Salike","sequence":"first","affiliation":[{"name":"Department of Chemical Engineering, National Institute of Technology , Tiruchirappalli 620015, India"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0928-6028","authenticated-orcid":false,"given":"Nirav","family":"Bhatt","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences , India"},{"name":"Initiative for Biological Systems Engineering (IBSE) , India"},{"name":"Robert Bosch Centre for Data Science and Artificial Intelligence (RBC-DSAI), Indian Institute of Technology Madras , Chennai 600036, India"}]}],"member":"286","published-online":{"date-parts":[[2019,10,4]]},"reference":[{"key":"2023013110132990900_btz741-B1","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1351\/pac199466081641","article-title":"Recommendations for nomenclature and tables in biochemical thermodynamics (IUPAC recommendations 1994)","volume":"66","author":"Alberty","year":"1994","journal-title":"Pure Appl. Chem"},{"key":"2023013110132990900_btz741-B2","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1006\/abbi.1998.0638","article-title":"Calculation of standard transformed Gibbs energies and standard transformed enthalpies of biochemical reactants","volume":"353","author":"Alberty","year":"1998","journal-title":"Arch. Biochem. Biophys"},{"key":"2023013110132990900_btz741-B3","volume-title":"Thermodynamics of Biochemical Reactions","author":"Alberty","year":"2005"},{"key":"2023013110132990900_btz741-B4","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.copbio.2015.08.021","article-title":"Heading in the right direction: thermodynamics-based network analysis and pathway engineering","volume":"36","author":"Ataman","year":"2015","journal-title":"Curr. Opin. Biotechnol"},{"key":"2023013110132990900_btz741-B5","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1002\/btpr.143","article-title":"Data reconciliation of concentration estimates from mid-infrared and dielectric spectral measurements for improved on-line monitoring of bioprocesses","volume":"25","author":"Dabros","year":"2009","journal-title":"Biotechnol. Progr"},{"key":"2023013110132990900_btz741-B6","doi-asserted-by":"crossref","first-page":"16653","DOI":"10.1016\/S0021-9258(18)66615-3","article-title":"The role of formylmethanofuran: tetrahydromethanopterin formyltransferase in methanogenesis from carbon dioxide","volume":"261","author":"Donnelly","year":"1986","journal-title":"J. Biol. Chem"},{"key":"2023013110132990900_btz741-B7","doi-asserted-by":"crossref","first-page":"2691","DOI":"10.1016\/j.bpj.2018.04.030","article-title":"Temperature-dependent estimation of Gibbs energies using an updated group-contribution method","volume":"114","author":"Du","year":"2018","journal-title":"Biophys. J"},{"key":"2023013110132990900_btz741-B8","doi-asserted-by":"crossref","first-page":"121.","DOI":"10.1038\/msb4100155","article-title":"A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information","volume":"3","author":"Feist","year":"2007","journal-title":"Mol. Syst. Biol"},{"key":"2023013110132990900_btz741-B9","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1002\/bit.22285","article-title":"Thermodynamic analysis of biodegradation pathways","volume":"103","author":"Finley","year":"2009","journal-title":"Biotechnol. Bioeng"},{"key":"2023013110132990900_btz741-B10","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1186\/1756-0500-3-125","article-title":"Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling","volume":"3","author":"Garg","year":"2010","journal-title":"BMC Res. Notes"},{"key":"2023013110132990900_btz741-B11","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.pisc.2014.02.001","article-title":"Standards in biothermodynamics","volume":"1","author":"Goldberg","year":"2014","journal-title":"Perspect. Sci"},{"key":"2023013110132990900_btz741-B12","doi-asserted-by":"crossref","first-page":"2874","DOI":"10.1093\/bioinformatics\/bth314","article-title":"Thermodynamics of enzyme-catalyzed reactions \u2013 a database for quantitative biochemistry","volume":"20","author":"Goldberg","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013110132990900_btz741-B13","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1063\/1.2789450","article-title":"Thermodynamics of enzyme-catalyzed reactions: part 7-2007 update","volume":"36","author":"Goldberg","year":"2007","journal-title":"J. Phys. Chem. Ref. Data"},{"key":"2023013110132990900_btz741-B14","doi-asserted-by":"crossref","first-page":"1603","DOI":"10.1093\/bioinformatics\/bti213","article-title":"Exploring the diversity of complex metabolic networks","volume":"21","author":"Hatzimanikatis","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013110132990900_btz741-B15","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1529\/biophysj.105.071720","article-title":"Genome-scale thermodynamic analysis of Escherichia coli metabolism","volume":"90","author":"Henry","year":"2006","journal-title":"Biophys. J"},{"key":"2023013110132990900_btz741-B16","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1529\/biophysj.106.093138","article-title":"Thermodynamics-based metabolic flux analysis","volume":"92","author":"Henry","year":"2007","journal-title":"Biophys. J"},{"key":"2023013110132990900_btz741-B17","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1007\/978-1-84996-106-6_2","volume-title":"Advanced Control and Supervision of Mineral Processing Plants","author":"Hodouin","year":"2010"},{"key":"2023013110132990900_btz741-B18","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1529\/biophysj.107.124784","article-title":"Group contribution method for thermodynamic analysis of complex metabolic networks","volume":"95","author":"Jankowski","year":"2008","journal-title":"Biophys. J"},{"key":"2023013110132990900_btz741-B19","doi-asserted-by":"crossref","first-page":"7022.","DOI":"10.1038\/srep07022","article-title":"Quantum chemical approach to estimating the thermodynamics of metabolic reactions","volume":"4","author":"Jinich","year":"2014","journal-title":"Sci. Rep"},{"key":"2023013110132990900_btz741-B20","doi-asserted-by":"crossref","first-page":"291.","DOI":"10.1038\/nrmicro2737","article-title":"Constraining the metabolic genotype\u2013phenotype relationship using a phylogeny of in silico methods","volume":"10","author":"Lewis","year":"2012","journal-title":"Nat. Rev. Microbiol"},{"key":"2023013110132990900_btz741-B21","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.copbio.2014.12.019","article-title":"Computational methods in metabolic engineering for strain design","volume":"34","author":"Long","year":"2015","journal-title":"Curr. Opin. Biotechnol"},{"key":"2023013110132990900_btz741-B22","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1002\/bit.20572","article-title":"How reliable are thermodynamic feasibility statements of biochemical pathways?","volume":"92","author":"Maskow","year":"2005","journal-title":"Biotechnol. Bioeng"},{"key":"2023013110132990900_btz741-B23","doi-asserted-by":"crossref","first-page":"1070","DOI":"10.1002\/bit.260361013","article-title":"Group contributions for estimating standard Gibbs energies of formation of biochemical compounds in aqueous solution","volume":"36","author":"Mavrovouniotis","year":"1990","journal-title":"Biotechnol. Bioeng"},{"key":"2023013110132990900_btz741-B24","doi-asserted-by":"crossref","first-page":"14440","DOI":"10.1016\/S0021-9258(18)98705-3","article-title":"Estimation of standard Gibbs energy changes of biotransformations","volume":"266","author":"Mavrovouniotis","year":"1991","journal-title":"J. Biol. Chem"},{"key":"2023013110132990900_btz741-B25","volume-title":"Detection: An Intelligent Use of Process Data","author":"Narasimhan","year":"1999"},{"key":"2023013110132990900_btz741-B26","doi-asserted-by":"crossref","first-page":"125.","DOI":"10.1038\/s42255-018-0006-7","article-title":"An upper limit on Gibbs energy dissipation governs cellular metabolism","volume":"1","author":"Niebel","year":"2019","journal-title":"Nat. Metab"},{"key":"2023013110132990900_btz741-B27","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1093\/bioinformatics\/bts317","article-title":"An integrated open framework for thermodynamics of reactions that combines accuracy and coverage","volume":"28","author":"Noor","year":"2012","journal-title":"Bioinformatics"},{"key":"2023013110132990900_btz741-B28","doi-asserted-by":"crossref","first-page":"e1003098.","DOI":"10.1371\/journal.pcbi.1003098","article-title":"Consistent estimation of Gibbs energy using component contributions","volume":"9","author":"Noor","year":"2013","journal-title":"PLoS Comput. Biol"},{"key":"2023013110132990900_btz741-B29","doi-asserted-by":"crossref","first-page":"2377","DOI":"10.1099\/00221287-144-9-2377","article-title":"Biochemistry of methanogenesis: a tribute to Marjory Stephenson: 1998 Marjory Stephenson Prize Lecture","volume":"144","author":"Thauer","year":"1998","journal-title":"Microbiology"},{"key":"2023013110132990900_btz741-B30","author":"Wagman","year":"1982"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz741\/30989938\/btz741.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/4\/1219\/48982433\/bioinformatics_36_4_1219.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/4\/1219\/48982433\/bioinformatics_36_4_1219.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T15:12:06Z","timestamp":1675177926000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/4\/1219\/5581400"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,10,4]]},"references-count":30,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2020,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz741","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/492819","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,2,15]]},"published":{"date-parts":[[2019,10,4]]}}}