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DOME: recommendations for supervised machine learning validation in biology.

Walsh I, Fishman D, Garcia-Gasulla D, Titma T, Pollastri G; ELIXIR Machine Learning Focus Group, Harrow J, Psomopoulos FE, Tosatto SCE. Walsh I, et al. Among authors: psomopoulos fe. Nat Methods. 2021 Oct;18(10):1122-1127. doi: 10.1038/s41592-021-01205-4. Nat Methods. 2021. PMID: 34316068 Free article. No abstract available.

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TRIP - T cell receptor/immunoglobulin profiler.

Kotouza MT, Gemenetzi K, Galigalidou C, Vlachonikola E, Pechlivanis N, Agathangelidis A, Sandaltzopoulos R, Mitkas PA, Stamatopoulos K, Chatzidimitriou A, Psomopoulos FE; Hellenic Precision Medicine Network in Oncology. Kotouza MT, et al. Among authors: psomopoulos fe. BMC Bioinformatics. 2020 Sep 29;21(1):422. doi: 10.1186/s12859-020-03669-1. BMC Bioinformatics. 2020. PMID: 32993478 Free PMC article.

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Ancestral state reconstruction of metabolic pathways across pangenome ensembles.

Psomopoulos FE, van Helden J, Médigue C, Chasapi A, Ouzounis CA. Psomopoulos FE, et al. Microb Genom. 2020 Nov;6(11):mgen000429. doi: 10.1099/mgen.0.000429. Microb Genom. 2020. PMID: 32924924 Free PMC article.

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Eleven quick tips for finding research data.

Gregory K, Khalsa SJ, Michener WK, Psomopoulos FE, de Waard A, Wu M. Gregory K, et al. Among authors: psomopoulos fe. PLoS Comput Biol. 2018 Apr 12;14(4):e1006038. doi: 10.1371/journal.pcbi.1006038. eCollection 2018 Apr. PLoS Comput Biol. 2018. PMID: 29649206 Free PMC article. No abstract available.

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Author Correction: DOME: recommendations for supervised machine learning validation in biology.

Walsh I, Fishman D, Garcia-Gasulla D, Titma T, Pollastri G; ELIXIR Machine Learning Focus Group, Harrow J, Psomopoulos FE, Tosatto SCE. Walsh I, et al. Among authors: psomopoulos fe. Nat Methods. 2021 Nov;18(11):1409-1410. doi: 10.1038/s41592-021-01304-2. Nat Methods. 2021. PMID: 34556867 No abstract available.

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Combining Multiple RNA-Seq Data Analysis Algorithms Using Machine Learning Improves Differential Isoform Expression Analysis.

Dimopoulos AC, Koukoutegos K, Psomopoulos FE, Moulos P. Dimopoulos AC, et al. Among authors: psomopoulos fe. Methods Protoc. 2021 Sep 27;4(4):68. doi: 10.3390/mps4040068. Methods Protoc. 2021. PMID: 34698224 Free PMC article.

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BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution.

Psomopoulos FE, Vitsios DM, Baichoo S, Ouzounis CA. Psomopoulos FE, et al. Bioinformatics. 2017 May 1;33(9):1418-1420. doi: 10.1093/bioinformatics/btw813. Bioinformatics. 2017. PMID: 28453679

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Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles.

Psomopoulos FE, Mitkas PA, Ouzounis CA. Psomopoulos FE, et al. PLoS One. 2013;8(1):e52854. doi: 10.1371/journal.pone.0052854. Epub 2013 Jan 14. PLoS One. 2013. PMID: 23341912 Free PMC article.

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Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.

Duarte AM, Psomopoulos FE, Blanchet C, Bonvin AM, Corpas M, Franc A, Jimenez RC, de Lucas JM, Nyrönen T, Sipos G, Suhr SB. Duarte AM, et al. Among authors: psomopoulos fe. Front Genet. 2015 Jun 23;6:197. doi: 10.3389/fgene.2015.00197. eCollection 2015. Front Genet. 2015. PMID: 26157454 Free PMC article.

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The chlamydiales pangenome revisited: structural stability and functional coherence.

Psomopoulos FE, Siarkou VI, Papanikolaou N, Iliopoulos I, Tsaftaris AS, Promponas VJ, Ouzounis CA. Psomopoulos FE, et al. Genes (Basel). 2012 May 16;3(2):291-319. doi: 10.3390/genes3020291. Genes (Basel). 2012. PMID: 24704919 Free PMC article.

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