Publications

*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).