Brian Hie


*Equal contribution. Corresponding author.

B. Hie*, S. Candido*, Z. Lin, O. Kabeli, R. Rao, N. Smetanin, T. Sercu, and A. Rives.
“A high-level programming language for generative protein design.”
bioRxiv, DOI:10.1101/2022.12.21.521526 (2022). [Code]


*Equal contribution. Corresponding author.

B. Hie, V. Shanker, D. Xu, T.U.J. Bruun, P.A. Weidenbacher, S. Tang, W. Wu, J.E. Pak, and P.S. Kim.
“Efficient evolution of human antibodies from general protein language models.”
Nature Biotechnology, DOI:10.1038/s41587-023-01763-2 (2023). [Code]

Z. Lin*, H. Akin*, R. Rao*, B. Hie*, Z. Zhu, W. Lu, N. Smetanin, R. Verkuil, O. Kabeli, Y. Shmueli, A. dos Santos Costa, M. Fazel-Zarandi, T. Sercu, S. Candido, and A. Rives.
“Evolutionary-scale prediction of atomic level protein structure with a language model.”
Science, 379:6637 (2023). [Code]

B. Hie, K.K. Yang, and P.S. Kim.
“Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins.”
Cell Systems, 13:4 (2022). [Code]

M.C. Maher, I. Bartha, S. Weaver, J. di Iulio, E. Ferri, L. Soriaga, F.A. Lempp, B. Hie, B. Bryson, B. Berger, D.L. Robertson, G. Snell, D. Corti, H.W. Virgin, S.L. Kosakovsky Pond, and A. Telenti.
“Predicting the mutational drivers of future SARS-CoV-2 variants of concern.”
Science Translational Medicine, DOI: 10.1126/scitranslmed.abk3445 (2022).

B. Hie and K. Yang.
“Adaptive machine learning for protein engineering.”
Current Opinion in Structural Biology, 72:145-152 (2022).

B. Hie.
“Algorithms for understanding and fighting infectious disease.”
Massachusetts Institute of Technology, Doctoral Thesis (2021).

R. Singh*, B. Hie*, A. Narayan, and B. Berger.
“Schema: Metric learning enables interpretable synthesis of heterogeneous single-cell modalities.”
Genome Biology, 22:131 (2021). [Code]

B. Hie, E. Zhong, B. Berger, and B. Bryson.
“Learning the language of viral evolution and escape.”
Science, 371:6526 (2021). A previous version appeared at NeurIPS 2020. [Code]

B. Hie, B. Bryson, and B. Berger.
“Leveraging uncertainty in machine learning accelerates biological discovery and design.”
Cell Systems, 11:5 (2020). [Code]

B. Hie*, J. Peters*, S. Nyquist*, A. Shalek, B. Berger, and B. Bryson.
“Computational methods for single-cell RNA sequencing.”
Annual Review of Biomedical Data Science, 3:1 (2020).

B. Hie*, H. Cho*, B. DeMeo, B. Bryson, and B. Berger.
“Geometric sketching compactly summarizes the single-cell transcriptomic landscape.”
Cell Systems, 8:6 (2019). A previous version appeared at RECOMB 2019. [Code]

B. Hie, B. Bryson, and B. Berger.
“Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.”
Nature Biotechnology, 37:685-691 (2019). [Code]

A.K. Tehranchi, B. Hie, M. Dacre, I.M. Kaplow, K.P. Pettie, P.A. Combs, and H.B. Fraser.
“Fine-mapping cis-regulatory variants in diverse human populations.”
eLife, 8:e39595 (2019).

B. Hie*, H. Cho*, and B. Berger.
“Realizing private and practical pharmacological collaboration.”
Science, 362:6417 (2018). [Code]

A.K. Tehranchi, M. Myrthil, T. Martin, B. Hie, D. Golan, and H.B. Fraser.
“Pooled ChIP-seq links variation in transcription factor binding to complex disease risk.”
Cell, 165:3 (2016).