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Evaluation of methods for modeling transcription factor sequence specificity.
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium; Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR. Weirauch MT, et al. Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486. Epub 2013 Jan 27. Nat Biotechnol. 2013. PMID: 23354101 Free PMC article.
Bayesian metabolic flux analysis reveals intracellular flux couplings.
Heinonen M, Osmala M, Mannerström H, Wallenius J, Kaski S, Rousu J, Lähdesmäki H. Heinonen M, et al. Among authors: lahdesmaki h. Bioinformatics. 2019 Jul 15;35(14):i548-i557. doi: 10.1093/bioinformatics/btz315. Bioinformatics. 2019. PMID: 31510676 Free PMC article.
Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods.
Voutilainen S, Heinonen M, Andberg M, Jokinen E, Maaheimo H, Pääkkönen J, Hakulinen N, Rouvinen J, Lähdesmäki H, Kaski S, Rousu J, Penttilä M, Koivula A. Voutilainen S, et al. Among authors: lahdesmaki h. Appl Microbiol Biotechnol. 2020 Dec;104(24):10515-10529. doi: 10.1007/s00253-020-10960-x. Epub 2020 Nov 4. Appl Microbiol Biotechnol. 2020. PMID: 33147349 Free PMC article.
Predicting recognition between T cell receptors and epitopes with TCRGP.
Jokinen E, Huuhtanen J, Mustjoki S, Heinonen M, Lähdesmäki H. Jokinen E, et al. Among authors: lahdesmaki h. PLoS Comput Biol. 2021 Mar 25;17(3):e1008814. doi: 10.1371/journal.pcbi.1008814. eCollection 2021 Mar. PLoS Comput Biol. 2021. PMID: 33764977 Free PMC article.
130 results