Jakub Otwinowski
Associate Research ScientistCards
About
Research
Publications
2024
Learning the shape of protein microenvironments with a holographic convolutional neural network
Pun M, Ivanov A, Bellamy Q, Montague Z, LaMont C, Bradley P, Otwinowski J, Nourmohammad A. Learning the shape of protein microenvironments with a holographic convolutional neural network. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2300838121. PMID: 38300863, PMCID: PMC10861886, DOI: 10.1073/pnas.2300838121.Peer-Reviewed Original ResearchContrastive losses as generalized models of global epistasis
Brookes D, Otwinowski J, Sinai S. Contrastive losses as generalized models of global epistasis. 2024, 93374-93405. DOI: 10.52202/079017-2962.Peer-Reviewed Original Research
2021
Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19
Montague Z, Lv H, Otwinowski J, DeWitt W, Isacchini G, Yip G, Ng W, Tsang O, Yuan M, Liu H, Wilson I, Peiris J, Wu N, Nourmohammad A, Mok C. Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19. Cell Reports 2021, 35: 109173. PMID: 33991510, PMCID: PMC8106887, DOI: 10.1016/j.celrep.2021.109173.Peer-Reviewed Original Research
2020
Information-Geometric Optimization with Natural Selection
Otwinowski J, LaMont C, Nourmohammad A. Information-Geometric Optimization with Natural Selection. Entropy 2020, 22: 967. PMID: 33286736, PMCID: PMC7597266, DOI: 10.3390/e22090967.Peer-Reviewed Original ResearchMajor antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape
Wu N, Otwinowski J, Thompson A, Nycholat C, Nourmohammad A, Wilson I. Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape. Nature Communications 2020, 11: 1233. PMID: 32144244, PMCID: PMC7060233, DOI: 10.1038/s41467-020-15102-5.Peer-Reviewed Original ResearchAnimalsAntigens, ViralBinding SitesCrystallography, X-RayDNA Mutational AnalysisDogsEvolution, MolecularHEK293 CellsHemagglutinin Glycoproteins, Influenza VirusHumansInfluenza A Virus, H3N2 SubtypeMadin Darby Canine Kidney CellsMutationProtein DomainsReceptors, Cell SurfaceReverse Transcriptase Polymerase Chain ReactionRNA, ViralSequence Analysis, DNA
2019
Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1
Nourmohammad A, Otwinowski J, Łuksza M, Mora T, Walczak A. Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1. Molecular Biology And Evolution 2019, 36: 2184-2194. PMID: 31209469, PMCID: PMC6759071, DOI: 10.1093/molbev/msz143.Peer-Reviewed Original Research
2018
Biophysical Inference of Epistasis and the Effects of Mutations on Protein Stability and Function
Otwinowski J. Biophysical Inference of Epistasis and the Effects of Mutations on Protein Stability and Function. Molecular Biology And Evolution 2018, 35: 2345-2354. PMID: 30085303, PMCID: PMC6188545, DOI: 10.1093/molbev/msy141.Peer-Reviewed Original ResearchInferring the shape of global epistasis
Otwinowski J, McCandlish D, Plotkin J. Inferring the shape of global epistasis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2018, 115: e7550-e7558. PMID: 30037990, PMCID: PMC6094095, DOI: 10.1073/pnas.1804015115.Peer-Reviewed Original Research
2016
Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections
Nourmohammad A, Otwinowski J, Plotkin J. Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections. PLOS Genetics 2016, 12: e1006171. PMID: 27442127, PMCID: PMC4956326, DOI: 10.1371/journal.pgen.1006171.Peer-Reviewed Original Research
2015
Detecting epistasis from an ensemble of adapting populations
McCandlish D, Otwinowski J, Plotkin J. Detecting epistasis from an ensemble of adapting populations. Evolution 2015, 69: 2359-2370. PMID: 26194030, PMCID: PMC5656054, DOI: 10.1111/evo.12735.Peer-Reviewed Original Research