Jakub Otwinowski
Jakub Otwinowski
Dyno Therapeutics
Подтвержден адрес электронной почты в домене dynotx.com
Inferring the shape of global epistasis
J Otwinowski, DM McCandlish, JB Plotkin
Proceedings of the National Academy of Sciences 115 (32), E7550-E7558, 2018
Direct observation of colloidal aggregation by critical Casimir forces
D Bonn, J Otwinowski, S Sacanna, H Guo, G Wegdam, P Schall
Physical review letters 103 (15), 156101, 2009
Inferring fitness landscapes by regression produces biased estimates of epistasis
J Otwinowski, JB Plotkin
Proceedings of the National Academy of Sciences 111 (22), E2301-E2309, 2014
Host-pathogen coevolution and the emergence of broadly neutralizing antibodies in chronic infections
A Nourmohammad, J Otwinowski, JB Plotkin
PLoS genetics 12 (7), e1006171, 2016
Biophysical inference of epistasis and the effects of mutations on protein stability and function
J Otwinowski
Molecular biology and evolution 35 (10), 2345-2354, 2018
Genotype to Phenotype Mapping and the Fitness Landscape of the E. coli lac Promoter
J Otwinowski, I Nemenman
PloS one 8 (5), e61570, 2013
Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape
NC Wu, J Otwinowski, AJ Thompson, CM Nycholat, A Nourmohammad, ...
Nature communications 11 (1), 1233, 2020
Fierce selection and interference in B-cell repertoire response to chronic HIV-1
A Nourmohammad, J Otwinowski, M Łuksza, T Mora, AM Walczak
Molecular Biology and Evolution 36 (10), 2184–2194, 2019
Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19
Z Montague, H Lv, J Otwinowski, WS DeWitt, G Isacchini, GK Yip, WW Ng, ...
Cell Reports 35 (8), 2021
Novel techniques of laser acceleration: from structures to plasmas
S Kalmykov, O Polomarov, D Korobkin, J Otwinowski, J Power, G Shvets
Philosophical Transactions of the Royal Society A: Mathematical, Physical …, 2006
Clonal interference and Mullerʼs ratchet in spatial habitats
J Otwinowski, J Krug
Physical biology 11 (5), 056003, 2014
Design of an optimal combination therapy with broadly neutralizing antibodies to suppress HIV-1
C LaMont, J Otwinowski, K Vanshylla, H Gruell, F Klein, ...
Elife 11, e76004, 2022
Detecting epistasis from an ensemble of adapting populations
DM McCandlish, J Otwinowski, JB Plotkin
Evolution 69 (9), 2359-2370, 2015
Accumulation of beneficial mutations in one dimension
J Otwinowski, S Boettcher
Physical Review E 84 (1), 011925, 2011
A totally asymmetric exclusion process with hierarchical long range connections
J Otwinowski, S Boettcher
Journal of Statistical Mechanics: Theory and Experiment 2009 (07), P07010, 2009
Learning the shape of protein microenvironments with a holographic convolutional neural network
MN Pun, A Ivanov, Q Bellamy, Z Montague, C LaMont, P Bradley, ...
Proceedings of the National Academy of Sciences 121 (6), e2300838121, 2024
Speeding up evolutionary search by small fitness fluctuations
J Otwinowski, S Tanase-Nicola, I Nemenman
Journal of statistical physics 144, 367-378, 2011
Information-geometric optimization with natural selection
J Otwinowski, C LaMont
Entropy, 2020
Contrastive losses as generalized models of global epistasis
DH Brookes, J Otwinowski, S Sinai
arXiv preprint arXiv:2305.03136, 2023
Learning the shape of the immune and protein universe
A Nourmohammad, M Pun, GM Visani, A Ivanov, Q Bellamy, Z Montague, ...
Bulletin of the American Physical Society, 2024
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