{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:34Z","timestamp":1753875814717,"version":"3.41.2"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,5,19]],"date-time":"2025-05-19T00:00:00Z","timestamp":1747612800000},"content-version":"vor","delay-in-days":144,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Portuguese Foundation for Science and Technology"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The increasing availability of high-throughput technologies in systems biology has advanced predictive tools like genome-scale metabolic models. Despite this progress, integrating omics data to create accurate, context-specific metabolic models for different tissues or cells remains challenging. A significant issue is that many existing tools rely on proprietary software, which limits accessibility. We introduce TROPPO, an open-source Python library designed to overcome these challenges. TROPPO supports a wide range of context-specific reconstruction algorithms, provides validation methods for assessing generated models, and includes gap-filling algorithms to ensure model consistency, integrating well with other constraint-based tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>TROPPO is implemented in Python and is freely available at https:\/\/github.com\/BioSystemsUM\/TROPPO and https:\/\/pypi.org\/project\/TROPPO\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioadv\/vbaf113","type":"journal-article","created":{"date-parts":[[2025,5,19]],"date-time":"2025-05-19T15:35:45Z","timestamp":1747668945000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>TROPPO<\/i>: tissue-specific reconstruction and phenotype prediction using omics data"],"prefix":"10.1093","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2255-8983","authenticated-orcid":false,"given":"Alexandre","family":"Oliveira","sequence":"first","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057,","place":["Portugal"]}]},{"given":"Jorge","family":"Ferreira","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057,","place":["Portugal"]}]},{"given":"V\u00edtor","family":"Vieira","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057,","place":["Portugal"]}]},{"given":"Bruno","family":"S\u00e1","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8439-8172","authenticated-orcid":false,"given":"Miguel","family":"Rocha","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057,","place":["Portugal"]},{"name":"LABBELS\u2014Associate Laboratory , Braga 4710-057,","place":["Portugal"]}]}],"member":"286","published-online":{"date-parts":[[2025,5,19]]},"reference":[{"key":"2025063009161346700_vbaf113-B1","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1002\/msb.145122","article-title":"Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling","volume":"10","author":"Agren","year":"2014","journal-title":"Mol Syst Biol"},{"key":"2025063009161346700_vbaf113-B2","doi-asserted-by":"crossref","first-page":"108052","DOI":"10.1016\/j.compbiomed.2024.108052","article-title":"Reconstruction of cell-specific models capturing the influence of metabolism on DNA methylation in cancer","volume":"170","author":"Barata","year":"2024","journal-title":"Comput Biol Med"},{"key":"2025063009161346700_vbaf113-B3","doi-asserted-by":"crossref","first-page":"105177","DOI":"10.1016\/j.compbiomed.2021.105177","article-title":"Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells","volume":"142","author":"Barata","year":"2022","journal-title":"Comput Biol Med"},{"key":"2025063009161346700_vbaf113-B4","doi-asserted-by":"crossref","first-page":"e1000082","DOI":"10.1371\/journal.pcbi.1000082","article-title":"Context-specific metabolic networks are consistent with experiments","volume":"4","author":"Becker","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"2025063009161346700_vbaf113-B5","doi-asserted-by":"crossref","first-page":"bbad387","DOI":"10.1093\/bib\/bbad387","article-title":"COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery","volume":"24","author":"Bessell","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025063009161346700_vbaf113-B6","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nbt.4072","article-title":"Recon3d enables a three-dimensional view of gene variation in human metabolism","volume":"36","author":"Brunk","year":"2018","journal-title":"Nature Biotechnology"},{"key":"2025063009161346700_vbaf113-B7","doi-asserted-by":"crossref","first-page":"e1000489","DOI":"10.1371\/journal.pcbi.1000489","article-title":"Interpreting expression data with metabolic flux models: predicting mycobacterium tuberculosis mycolic acid production","volume":"5","author":"Colijn","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"2025063009161346700_vbaf113-B8","doi-asserted-by":"crossref","first-page":"e1011499","DOI":"10.1371\/journal.pcbi.1011499","article-title":"The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber","volume":"19","author":"Cunha","year":"2023","journal-title":"PLoS Comput Biol"},{"key":"2025063009161346700_vbaf113-B9","doi-asserted-by":"crossref","first-page":"6319","DOI":"10.1038\/s41467-020-20139-7","article-title":"Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection","volume":"11","author":"Desai","year":"2020","journal-title":"Nat Commun"},{"key":"2025063009161346700_vbaf113-B10","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":"Ebrahim","year":"2013","journal-title":"BMC Syst Biol"},{"key":"2025063009161346700_vbaf113-B11","first-page":"491","article-title":"Generalized framework for context-specific metabolic model extraction methods","volume":"5","author":"Est\u00e9vez","year":"2014","journal-title":"Front Plant Sci"},{"key":"2025063009161346700_vbaf113-B12","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1038\/s41579-020-00440-4","article-title":"Reconstructing organisms in silico: genome-scale models and their emerging applications","volume":"18","author":"Fang","year":"2020","journal-title":"Nat Rev Microbiol"},{"key":"2025063009161346700_vbaf113-B13","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1126\/science.aaz1776","article-title":"The GTEx Consortium atlas of genetic regulatory effects across human tissues","volume":"369","author":"GTEx Consortium","year":"2020","journal-title":"Science"},{"key":"2025063009161346700_vbaf113-B14","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/s41596-018-0098-2","article-title":"Creation and analysis of biochemical constraint-based models using the cobra toolbox v. 3.0","volume":"14","author":"Heirendt","year":"2019","journal-title":"Nat Protoc"},{"year":"2023","author":"Machado","key":"2025063009161346700_vbaf113-B15"},{"key":"2025063009161346700_vbaf113-B16","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.cell.2019.12.023","article-title":"Quantitative proteomics of the cancer cell line encyclopedia","volume":"180","author":"Nusinow","year":"2020","journal-title":"Cell"},{"key":"2025063009161346700_vbaf113-B17","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.ifacol.2024.10.016","article-title":"Metabolic modelling reveals key pathways in Covid-19 in an effort to drive drug purposing","volume":"58","author":"Oliveira","year":"2024","journal-title":"IFAC-PapersOnLine"},{"key":"2025063009161346700_vbaf113-B18","doi-asserted-by":"crossref","first-page":"2494","DOI":"10.1093\/bioinformatics\/btab013","article-title":"MEWpy: a computational strain optimization workbench in Python","volume":"37","author":"Pereira","year":"2021","journal-title":"Bioinformatics"},{"key":"2025063009161346700_vbaf113-B19","doi-asserted-by":"crossref","first-page":"eaaz1482","DOI":"10.1126\/scisignal.aaz1482","article-title":"An atlas of human metabolism","volume":"13","author":"Robinson","year":"2020","journal-title":"Sci Signal"},{"key":"2025063009161346700_vbaf113-B20","doi-asserted-by":"crossref","first-page":"e1012506","DOI":"10.1371\/journal.pcbi.1012506","article-title":"A diel multi-tissue genome-scale metabolic model of Vitis vinifera","volume":"20","author":"Sampaio","year":"2024","journal-title":"PLoS Comput Biol"},{"key":"2025063009161346700_vbaf113-B21","doi-asserted-by":"crossref","first-page":"e1004808","DOI":"10.1371\/journal.pcbi.1004808","article-title":"Reconstruction of tissue-specific metabolic networks using CORDA","volume":"12","author":"Schultz","year":"2016","journal-title":"PLoS Comput Biol"},{"year":"2018","author":"Sonnenschein","key":"2025063009161346700_vbaf113-B22"},{"key":"2025063009161346700_vbaf113-B23","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/s12859-020-3440-y","article-title":"SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks","volume":"21","author":"Tefagh","year":"2020","journal-title":"BMC Bioinformatics"},{"key":"2025063009161346700_vbaf113-B24","doi-asserted-by":"crossref","first-page":"5361","DOI":"10.1093\/bioinformatics\/btz598","article-title":"CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models","volume":"35","author":"Vieira","year":"2019","journal-title":"Bioinformatics"},{"key":"2025063009161346700_vbaf113-B25","doi-asserted-by":"crossref","first-page":"e1009294","DOI":"10.1371\/journal.pcbi.1009294","article-title":"A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale","volume":"18","author":"Vieira","year":"2022","journal-title":"PLoS Comput Biol"},{"key":"2025063009161346700_vbaf113-B26","doi-asserted-by":"crossref","first-page":"e1003424","DOI":"10.1371\/journal.pcbi.1003424","article-title":"Fast reconstruction of compact context-specific metabolic network models","volume":"10","author":"Vlassis","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"2025063009161346700_vbaf113-B27","doi-asserted-by":"crossref","first-page":"3140","DOI":"10.1093\/bioinformatics\/btq602","article-title":"iMAT: an integrative metabolic analysis tool","volume":"26","author":"Zur","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics Advances"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/advance-article-pdf\/doi\/10.1093\/bioadv\/vbaf113\/63235915\/vbaf113.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/5\/1\/vbaf113\/63235915\/vbaf113.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/5\/1\/vbaf113\/63235915\/vbaf113.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T13:16:22Z","timestamp":1751289382000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article\/doi\/10.1093\/bioadv\/vbaf113\/8137837"}},"subtitle":[],"editor":[{"given":"Yoshihiro","family":"Yamanishi","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,12,26]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,12,26]]}},"URL":"https:\/\/doi.org\/10.1093\/bioadv\/vbaf113","relation":{},"ISSN":["2635-0041"],"issn-type":[{"type":"electronic","value":"2635-0041"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2024,12,26]]},"article-number":"vbaf113"}}