{"entity": "researcher", "timestamp": "2026-08-20T22:06:27.685Z", "family": "Tafur Rangel", "given": "Albert", "initials": "A", "orcid": "0000-0002-9428-183X", "affiliations": ["Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.", "Novo Nordisk Foundation Center for Biosustainability, Technology University of Denmark, Lyngby, Denmark."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/6bb75f8d7aa64fdda5093249081d4bb2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/6bb75f8d7aa64fdda5093249081d4bb2"}}, "publications": [{"entity": "publication", "iuid": "b97e47ebc84d4a59992a5f50250b98d3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b97e47ebc84d4a59992a5f50250b98d3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b97e47ebc84d4a59992a5f50250b98d3"}}, "title": "Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community.", "authors": [{"family": "Zhang", "given": "Chengyu", "initials": "C", "orcid": "0009-0004-3006-9073", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9867421acdbf4aa8a585fb8e255f21ad.json"}}, {"family": "S\u00e1nchez", "given": "Benjam\u00edn J", "initials": "BJ", "orcid": "0000-0001-6093-4110", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5c008a0fbd646fab02156701275efbc.json"}}, {"family": "Li", "given": "Feiran", "initials": "F", "orcid": "0000-0001-9155-5260", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/638ad58b8b28497a83955cea3c7dee17.json"}}, {"family": "Eiden", "given": "Cheng Wei Quan", "initials": "CWQ"}, {"family": "Scott", "given": "William T", "initials": "WT", "orcid": "0000-0002-4029-2998", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e441c588fbe240618e748097d4b01b82.json"}}, {"family": "Liebal", "given": "Ulf W", "initials": "UW"}, {"family": "Blank", "given": "Lars M", "initials": "LM", "orcid": "0000-0003-0961-4976", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/743160679cc94ffbb978080251a9f6bc.json"}}, {"family": "Mengers", "given": "Hendrik G", "initials": "HG"}, {"family": "Anton", "given": "Mihail", "initials": "M", "orcid": "0000-0002-7753-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/733c89e6b386409392abf45608738222.json"}}, {"family": "Rangel", "given": "Albert Tafur", "initials": "AT", "orcid": "0000-0002-9428-183X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6bb75f8d7aa64fdda5093249081d4bb2.json"}}, {"family": "Mendoza", "given": "Sebasti\u00e1n N", "initials": "SN", "orcid": "0000-0002-2192-5569", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e86dce914d4f9e864618fb15905d85.json"}}, {"family": "Zhang", "given": "Lixin", "initials": "L"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Lu", "given": "Hongzhong", "initials": "H", "orcid": "0009-0005-8555-1841", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48fa3bb35c724824bc18e1e5c23c1403.json"}}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ", "orcid": "0000-0002-3593-5792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/182c8731b6744479864cc75ced13d229.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "volume": "20", "issue": "10", "pages": "1134-1150", "issn-l": "1744-4292"}, "abstract": "Genome-scale metabolic models (GEMs) can facilitate metabolism-focused multi-omics integrative analysis. Since Yeast8, the yeast-GEM of Saccharomyces cerevisiae, published in 2019, has been continuously updated by the community. This has increased the quality and scope of the model, culminating now in Yeast9. To evaluate its predictive performance, we generated 163 condition-specific GEMs constrained by single-cell transcriptomics from osmotic pressure or reference conditions. Comparative flux analysis showed that yeast adapting to high osmotic pressure benefits from upregulating fluxes through central carbon metabolism. Furthermore, combining Yeast9 with proteomics revealed metabolic rewiring underlying its preference for nitrogen sources. Lastly, we created strain-specific GEMs (ssGEMs) constrained by transcriptomics for 1229 mutant strains. Well able to predict the strains' growth rates, fluxomics from those large-scale ssGEMs outperformed transcriptomics in predicting functional categories for all studied genes in machine learning models. Based on those findings we anticipate that Yeast9 will continue to empower systems biology studies of yeast metabolism.", "doi": "10.1038/s44320-024-00060-7", "pmid": "39134886", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11450192"}, {"db": "pii", "key": "10.1038/s44320-024-00060-7"}], "notes": [], "created": "2026-08-20T09:26:45.708Z", "modified": "2026-08-20T09:26:46.054Z"}, {"entity": "publication", "iuid": "cef4608c83e9440c95c053a6566c0966", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cef4608c83e9440c95c053a6566c0966.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cef4608c83e9440c95c053a6566c0966"}}, "title": "Biosynthesis of Hesperetin, Homoeriodictyol, and Homohesperetin in a Transcriptomics-Driven Engineered Strain of Streptomyces albidoflavus.", "authors": [{"family": "P\u00e9rez-Valero", "given": "\u00c1lvaro", "initials": "\u00c1", "orcid": "0000-0002-4560-3847", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baf089bccd254e1395b70a27aa8dbf15.json"}}, {"family": "Serna-Diestro", "given": "Juan", "initials": "J", "orcid": "0000-0003-1820-8064", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43c4c902f8d84755ab8bd508098232aa.json"}}, {"family": "Tafur Rangel", "given": "Albert", "initials": "A", "orcid": "0000-0002-9428-183X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6bb75f8d7aa64fdda5093249081d4bb2.json"}}, {"family": "Barbuto Ferraiuolo", "given": "Simona", "initials": "S", "orcid": "0000-0002-9126-5869", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76cd5ed4ff5542a78fbaa277fdf3da05.json"}}, {"family": "Schiraldi", "given": "Chiara", "initials": "C", "orcid": "0000-0002-1066-843X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed1f5d32a0674d26be4400ff1945d1ad.json"}}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ", "orcid": "0000-0002-3593-5792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/182c8731b6744479864cc75ced13d229.json"}}, {"family": "Villar", "given": "Claudio J", "initials": "CJ"}, {"family": "Lomb\u00f3", "given": "Felipe", "initials": "F", "orcid": "0000-0002-6680-6723", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c0fb391d3df455ba3b1556543a423e9.json"}}], "type": "journal article", "published": "2024-04-05", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "25", "issue": "7", "issn-l": null}, "abstract": "Flavonoids exhibit various bioactivities including anti-oxidant, anti-tumor, anti-inflammatory, and anti-viral properties. Methylated flavonoids are particularly significant due to their enhanced oral bioavailability, improved intestinal absorption, and greater stability. The heterologous production of plant flavonoids in bacterial factories involves the need for enough biosynthetic precursors to allow for high production levels. These biosynthetic precursors are malonyl-CoA and l-tyrosine. In this work, to enhance flavonoid biosynthesis in Streptomyces albidoflavus, we conducted a transcriptomics study for the identification of candidate genes involved in l-tyrosine catabolism. The hypothesis was that the bacterial metabolic machinery would detect an excess of this amino acid if supplemented with the conventional culture medium and would activate the genes involved in its catabolism towards energy production. Then, by inactivating those overexpressed genes (under an excess of l-tyrosine), it would be possible to increase the intracellular pools of this precursor amino acid and eventually the final flavonoid titers in this bacterial factory. The RNAseq data analysis in the S. albidoflavus wild-type strain highlighted the hppD gene encoding 4-hydroxyphenylpyruvate dioxygenase as a promising target for knock-out, exhibiting a 23.2-fold change (FC) in expression upon l-tyrosine supplementation in comparison to control cultivation conditions. The subsequent knock-out of the hppD gene in S. albidoflavus resulted in a 1.66-fold increase in the naringenin titer, indicating enhanced flavonoid biosynthesis. Leveraging the improved strain of S. albidoflavus, we successfully synthesized the methylated flavanones hesperetin, homoeriodictyol, and homohesperetin, achieving titers of 2.52 mg/L, 1.34 mg/L, and 0.43 mg/L, respectively. In addition, the dimethoxy flavanone homohesperetin was produced as a byproduct of the endogenous metabolism of S. albidoflavus. To our knowledge, this is the first time that hppD deletion was utilized as a strategy to augment the biosynthesis of flavonoids. Furthermore, this is the first report where hesperetin and homoeriodictyol have been synthesized from l-tyrosine as a precursor. Therefore, transcriptomics is, in this case, a successful approach for the identification of catabolism reactions affecting key precursors during flavonoid biosynthesis, allowing the generation of enhanced production strains.", "doi": "10.3390/ijms25074053", "pmid": "38612864", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11012174"}, {"db": "pii", "key": "ijms25074053"}], "notes": [], "created": "2026-08-20T13:41:44.609Z", "modified": "2026-08-20T13:41:44.866Z"}, {"entity": "publication", "iuid": "fa8f0b2e9e654bd1a0728a072024b326", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fa8f0b2e9e654bd1a0728a072024b326.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fa8f0b2e9e654bd1a0728a072024b326"}}, "title": "Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0.", "authors": [{"family": "Chen", "given": "Yu", "initials": "Y", "orcid": "0000-0003-3326-9068", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d5b3f948bb84c05a28b5feeb3738128.json"}}, {"family": "Gustafsson", "given": "Johan", "initials": "J", "orcid": "0000-0001-5072-2659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39eef1abb23c4ecab986fe0646830f07.json"}}, {"family": "Tafur Rangel", "given": "Albert", "initials": "A", "orcid": "0000-0002-9428-183X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6bb75f8d7aa64fdda5093249081d4bb2.json"}}, {"family": "Anton", "given": "Mihail", "initials": "M", "orcid": "0000-0002-7753-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/733c89e6b386409392abf45608738222.json"}}, {"family": "Domenzain", "given": "Iv\u00e1n", "initials": "I", "orcid": "0000-0002-5322-2040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/588d2eed593448689fd63a7e656b5615.json"}}, {"family": "Kittikunapong", "given": "Cheewin", "initials": "C"}, {"family": "Li", "given": "Feiran", "initials": "F", "orcid": "0000-0001-9155-5260", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/638ad58b8b28497a83955cea3c7dee17.json"}}, {"family": "Yuan", "given": "Le", "initials": "L", "orcid": "0000-0003-3317-9011", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb344bfa13e345bd8632a85d937f09df.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ", "orcid": "0000-0002-3593-5792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/182c8731b6744479864cc75ced13d229.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Nat Protoc", "issn": "1750-2799", "volume": "19", "issue": "3", "pages": "629-667", "issn-l": null}, "abstract": "Genome-scale metabolic models (GEMs) are computational representations that enable mathematical exploration of metabolic behaviors within cellular and environmental constraints. Despite their wide usage in biotechnology, biomedicine and fundamental studies, there are many phenotypes that GEMs are unable to correctly predict. GECKO is a method to improve the predictive power of a GEM by incorporating enzymatic constraints using kinetic and omics data. GECKO has enabled reconstruction of enzyme-constrained metabolic models (ecModels) for diverse organisms, which show better predictive performance than conventional GEMs. In this protocol, we describe how to use the latest version GECKO 3.0; the procedure has five stages: (1) expansion from a starting metabolic model to an ecModel structure, (2) integration of enzyme turnover numbers into the ecModel structure, (3) model tuning, (4) integration of proteomics data into the ecModel and (5) simulation and analysis of ecModels. GECKO 3.0 incorporates deep learning-predicted enzyme kinetics, paving the way for improved metabolic models for virtually any organism and cell line in the absence of experimental data. The time of running the whole protocol is organism dependent, e.g., ~5 h for yeast.", "doi": "10.1038/s41596-023-00931-7", "pmid": "38238583", "labels": [], "xrefs": [{"db": "pii", "key": "10.1038/s41596-023-00931-7"}], "notes": [], "created": "2026-08-20T09:03:59.144Z", "modified": "2026-08-20T09:03:59.381Z"}, {"entity": "publication", "iuid": "d92c183b3bbb4c5d8025246440b4ebd0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d92c183b3bbb4c5d8025246440b4ebd0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d92c183b3bbb4c5d8025246440b4ebd0"}}, "title": "Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data", "authors": [{"family": "Zhang", "given": "Chengyu", "initials": "C"}, {"family": "S\u00e1nchez", "given": "Benjam\u00edn J", "initials": "BJ", "orcid": "0000-0002-1774-0908", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3b8d097b42c469c8aafee4b56473349.json"}}, {"family": "Li", "given": "Feiran", "initials": "F", "orcid": "0000-0001-9155-5260", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/638ad58b8b28497a83955cea3c7dee17.json"}}, {"family": "Eiden", "given": "Cheng Wei Quan", "initials": "CWQ"}, {"family": "Scott", "given": "William T", "initials": "WT", "orcid": "0000-0002-4029-2998", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e441c588fbe240618e748097d4b01b82.json"}}, {"family": "Liebal", "given": "Ulf W", "initials": "UW", "orcid": "0000-0001-5172-7339", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1aec71f590f43bbad4f16de716869b1.json"}}, {"family": "Blank", "given": "Lars M", "initials": "LM", "orcid": "0000-0003-0961-4976", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/743160679cc94ffbb978080251a9f6bc.json"}}, {"family": "Mengers", "given": "Hendrik G", "initials": "HG", "orcid": "0000-0002-5098-164X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f8937ca404445388bb360bfa81c2f8f.json"}}, {"family": "Anton", "given": "Mihail", "initials": "M", "orcid": "0000-0002-7753-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/733c89e6b386409392abf45608738222.json"}}, {"family": "Rangel", "given": "Albert Tafur", "initials": "AT", "orcid": "0000-0002-9428-183X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6bb75f8d7aa64fdda5093249081d4bb2.json"}}, {"family": "Mendoza", "given": "Sebasti\u00e1n N", "initials": "SN"}, {"family": "Zhang", "given": "Lixin", "initials": "L"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Lu", "given": "Hongzhong", "initials": "H"}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ", "orcid": "0000-0002-3593-5792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/182c8731b6744479864cc75ced13d229.json"}}], "type": "posted-content", "published": "2023-12-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.12.03.569754", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:50:40.338Z", "modified": "2026-08-20T10:50:40.475Z"}]}