Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design PJ Ogden*, ED Kelsic*, S Sinai, GM Church
Science 366 (6469), 1139-1143, 2019
283 2019 Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen MP Menden, D Wang, MJ Mason, B Szalai, KC Bulusu, Y Guan, T Yu, ...
Nature communications 10 (1), 1-17, 2019
273 2019 Deep diversification of an AAV capsid protein by machine learning DH Bryant*, A Bashir*, S Sinai*, NK Jain, PJ Ogden, PF Riley, GM Church, ...
Nature Biotechnology, 1-6, 2021
213 2021 Variational auto-encoding of protein sequences S Sinai, E Kelsic, GM Church, MA Nowak
NeurIPS 2017 MLCB workshop, 2017
78 2017 AdaLead: A simple and robust adaptive greedy search algorithm for sequence design S Sinai*, R Wang*, A Whatley*, S Slocum, E Locane, ED Kelsic
arXiv preprint arXiv:2010.02141, 2020
55 2020 A primer on model-guided exploration of fitness landscapes for biological sequence design S Sinai, ED Kelsic
arXiv preprint arXiv:2010.10614, 2020
28 2020 Generative AAV capsid diversification by latent interpolation S Sinai, N Jain, GM Church, ED Kelsic
bioRxiv, 2021.04. 16.440236, 2021
25 2021 Computer simulations of cellular group selection reveal mechanism for sustaining cooperation AJ Markvoort, S Sinai, MA Nowak
Journal of theoretical biology 357, 123-133, 2014
24 2014 Overcoming immunological challenges limiting capsid-mediated gene therapy with machine learning AZ Wec, KS Lin, JC Kwasnieski, S Sinai, J Gerold, ED Kelsic
Frontiers in Immunology 12, 674021, 2021
15 2021 Turbulent coherent structures and early life below the Kolmogorov scale MS Krieger, S Sinai, MA Nowak
Nature communications 11 (1), 2192, 2020
15 2020 Primordial sex facilitates the emergence of evolution S Sinai*, J Olejarz*, IA Neagu, MA Nowak
Journal of The Royal Society Interface 15 (139), 20180003, 2018
9 2018 Protein design using structure-based residue preferences D Ding, AY Shaw, S Sinai, N Rollins, N Prywes, DF Savage, MT Laub, ...
Nature Communications 15 (1), 1639, 2024
8 * 2024 Prebiotic selection for motifs in a model of template-free elongation of polymers within compartments G Kinsler*, S Sinai*, NK Lee, MA Nowak
PloS one 12 (7), e0180208, 2017
7 2017 Forecasting labels under distribution-shift for machine-guided sequence design LB Wheelock, S Malina, J Gerold, S Sinai
Machine Learning in Computational Biology, 166-180, 2022
3 2022 Deep Search: Next-Gen Strategies for Accelerating AAV Capsid Engineering E Kelsic, S Sinai, P Ogden, M Nowak, G Church
MOLECULAR THERAPY 26 (5), 168-168, 2018
2 2018 Contrastive losses as generalized models of global epistasis DH Brookes, J Otwinowski, S Sinai
arXiv preprint arXiv:2305.03136, 2023
1 2023 Efficient design of optimized AAV capsids using multi-property machine learning models trained across cells, organs and species S Abestesh, I Akartuna, A Brown, M Cramer, F Damani, J Gerold, J Gorns, ...
MOLECULAR THERAPY 29 (4), 12-12, 2021
1 2021 Improved dependoparvovirus production compositions and methods J Gerold, E Kelsic, S Sinai, A Veres, S Wolock
US Patent App. 18/042,890, 2023
2023 Beyond the training set: an intuitive method for detecting distribution shift in model-based optimization F Damani, DH Brookes, T Sternlieb, C Webster, S Malina, R Jajoo, K Lin, ...
arXiv preprint arXiv:2311.05363, 2023
2023 Generative design for gene therapy: An validated method F Damani, D Brookes, J Chan, R Jajoo, A Mijalis, J Samson, F Vadan, ...
NeurIPS 2023 Generative AI and Biology (GenBio) Workshop, 2023
2023