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Sam Sinai
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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
2752019
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
2702019
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
2092021
Variational auto-encoding of protein sequences
S Sinai, E Kelsic, GM Church, MA Nowak
NeurIPS 2017 MLCB workshop, 2017
782017
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
532020
A primer on model-guided exploration of fitness landscapes for biological sequence design
S Sinai, ED Kelsic
arXiv preprint arXiv:2010.10614, 2020
272020
Generative AAV capsid diversification by latent interpolation
S Sinai, N Jain, GM Church, ED Kelsic
bioRxiv, 2021.04. 16.440236, 2021
252021
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
242014
Turbulent coherent structures and early life below the Kolmogorov scale
MS Krieger, S Sinai, MA Nowak
Nature communications 11 (1), 2192, 2020
152020
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
142021
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
92018
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
72017
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
6*2024
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
32022
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
22018
Contrastive losses as generalized models of global epistasis
DH Brookes, J Otwinowski, S Sinai
arXiv preprint arXiv:2305.03136, 2023
12023
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
12021
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
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