Research

David Froelicher, Hyunghoon Cho, Manaswitha Edupalli, Joao Sa Sousa, Jean-Philippe Bossuat, Apostolos Pyrgelis, Juan R. Troncoso-Pastoriza, Bonnie Berger, Jean-Pierre Hubaux

2023 IEEE Symposium on Security and Privacy (SP) · 01 May 2023 · doi:10.1109/SP46215.2023.10179350

Learning the Language of Antibody Hypervariability

Rohit Singh, Chiho Im, Yu Qiu, Brian Mackness, Abhinav Gupta, …, Lena Erlach, Maria Wendt, Yves Fomekong Nanfack, Bryan Bryson, Bonnie Berger

Cold Spring Harbor Laboratory · 28 Apr 2023 · doi:10.1101/2023.04.26.538476

Source

Unveiling causal regulatory mechanisms through cell-state parallax

Alexander Po-Yen Wu, Rohit Singh, Christopher Walsh, Bonnie Berger

Cold Spring Harbor Laboratory · 03 Mar 2023 · doi:10.1101/2023.03.02.530529

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Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing

Haris Smajlović, Ariya Shajii, Bonnie Berger, Hyunghoon Cho, Ibrahim Numanagić

Genome Biology · 11 Jan 2023 · doi:10.1186/s13059-022-02841-5

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EigenFold: Generative Protein Structure Prediction with Diffusion Models

Bowen Jing, Ezra Erives, Peter Pao-Huang, Gabriele Corso, Bonnie Berger, Tommi Jaakkola

arXiv · 01 Jan 2023 · doi:10.48550/arXiv.2304.02198

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Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms

Bowen Jing, Tommi Jaakkola, Bonnie Berger

arXiv · 01 Jan 2023 · doi:10.48550/arXiv.2312.04323

Source

2022

Learning the Drug-Target Interaction Lexicon

Rohit Singh, Samuel Sledzieski, Lenore Cowen, Bonnie Berger

Cold Spring Harbor Laboratory · 10 Dec 2022 · doi:10.1101/2022.12.06.519374

Source

Navigating bottlenecks and trade-offs in genomic data analysis

Bonnie Berger, Yun William Yu

Nature Reviews Genetics · 07 Dec 2022 · doi:10.1038/s41576-022-00551-z

Secure and Federated Genome-Wide Association Studies for Biobank-Scale Datasets

Hyunghoon Cho, David Froelicher, Jeffrey Chen, Manaswitha Edupalli, Apostolos Pyrgelis, Juan R. Troncoso-Pastoriza, Jean-Pierre Hubaux, Bonnie Berger

Cold Spring Harbor Laboratory · 02 Dec 2022 · doi:10.1101/2022.11.30.518537

Source

Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN

Laurel F. Kinman, Barrett M. Powell, Ellen D. Zhong, Bonnie Berger, Joseph H. Davis

Nature Protocols · 14 Nov 2022 · doi:10.1038/s41596-022-00763-x

Adapting protein language models for rapid DTI prediction

Samuel Sledzieski, Rohit Singh, Lenore Cowen, Bonnie Berger

Cold Spring Harbor Laboratory · 04 Nov 2022 · doi:10.1101/2022.11.03.515084

Contrasting drugs from decoys

Samuel Sledzieski, Rohit Singh, Lenore Cowen, Bonnie Berger

Cold Spring Harbor Laboratory · 04 Nov 2022 · doi:10.1101/2022.11.03.515086

Source

CryoDRGN2: Ab Initio Neural Reconstruction of Dynamic Protein Complexes

Ellen D Zhong, Adam Lerer, Joseph H Davis, Bonnie Berger

Microscopy and Microanalysis · 01 Aug 2022 · doi:10.1017/S1431927622005062

Prioritizing transcription factor perturbations from single-cell transcriptomics

Rohit Singh, Joshua Shing Shun Li, Sudhir Gopal Tattikota, Yifang Liu, Jun Xu, Yanhui Hu, Norbert Perrimon, Bonnie Berger

Cold Spring Harbor Laboratory · 30 Jun 2022 · doi:10.1101/2022.06.27.497786

Genome-wide mapping of somatic mutation rates uncovers drivers of cancer

Maxwell A. Sherman, Adam U. Yaari, Oliver Priebe, Felix Dietlein, Po-Ru Loh, Bonnie Berger

Nature Biotechnology · 20 Jun 2022 · doi:10.1038/s41587-022-01353-8

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Secure and federated linear mixed model association tests

Jeffrey Chen, Manaswitha Edupalli, Bonnie Berger, Hyunghoon Cho

Cold Spring Harbor Laboratory · 24 May 2022 · doi:10.1101/2022.05.20.492837

Cellular and transcriptional diversity over the course of human lactation

Sarah K. Nyquist, Patricia Gao, Tessa K. J. Haining, Michael R. Retchin, Yarden Golan, …, Nadav Ahituv, Micaela E. Martinez, Alex K. Shalek, Bonnie Berger, Brittany A. Goods

Proceedings of the National Academy of Sciences · 04 Apr 2022 · doi:10.1073/pnas.2121720119

Source

Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization

Sisi Shan, Shitong Luo, Ziqing Yang, Junxian Hong, Yufeng Su, …, Xuanling Shi, Qi Zhang, Bonnie Berger, Linqi Zhang, Jian Peng

Proceedings of the National Academy of Sciences · 01 Mar 2022 · doi:10.1073/pnas.2122954119

Source

2021

Deciphering the species-level structure of topologically associating domains

Rohit Singh, Bonnie Berger

Cold Spring Harbor Laboratory · 29 Oct 2021 · doi:10.1101/2021.10.28.466333

Source

Scalable Multimer Structure Prediction using Diffusion Models

Peter Pao-Huang, Bowen Jing, Bonnie Berger

NeurIPS 2023 AI for Science Workshop · 28 Oct 2021 · [no id info]

Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer

Barış Ekim, Bonnie Berger, Rayan Chikhi

Cell Systems · 01 Oct 2021 · doi:10.1016/j.cels.2021.08.009

Source

D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions

Samuel Sledzieski, Rohit Singh, Lenore Cowen, Bonnie Berger

Cell Systems · 01 Oct 2021 · doi:10.1016/j.cels.2021.08.010

Source

A Python-based programming language for high-performance computational genomics

Ariya Shajii, Ibrahim Numanagić, Alexander T. Leighton, Haley Greenyer, Saman Amarasinghe, Bonnie Berger

Nature Biotechnology · 19 Jul 2021 · doi:10.1038/s41587-021-00985-6

Source

Bayesian information sharing enhances detection of regulatory associations in rare cell types

Alexander P Wu, Jian Peng, Bonnie Berger, Hyunghoon Cho

Bioinformatics · 01 Jul 2021 · doi:10.1093/bioinformatics/btab269

Source

Levenshtein Distance, Sequence Comparison and Biological Database Search

Bonnie Berger, Michael S. Waterman, Yun William Yu

IEEE Transactions on Information Theory · 01 Jun 2021 · doi:10.1109/TIT.2020.2996543

Learning the protein language: Evolution, structure, and function

Tristan Bepler, Bonnie Berger

Cell Systems · 01 Jun 2021 · doi:10.1016/j.cels.2021.05.017

Source

Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities

Rohit Singh, Brian L. Hie, Ashwin Narayan, Bonnie Berger

Genome Biology · 03 May 2021 · doi:10.1186/s13059-021-02313-2

Source

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks

Ellen D. Zhong, Tristan Bepler, Bonnie Berger, Joseph H. Davis

Nature Methods · 01 Feb 2021 · doi:10.1038/s41592-020-01049-4

Source

Assessing single-cell transcriptomic variability through density-preserving data visualization

Ashwin Narayan, Bonnie Berger, Hyunghoon Cho

Nature Biotechnology · 18 Jan 2021 · doi:10.1038/s41587-020-00801-7

Source

Learning the language of viral evolution and escape

Brian Hie, Ellen D. Zhong, Bonnie Berger, Bryan Bryson

Science · 15 Jan 2021 · doi:10.1126/science.abd7331

Source

Exploring generative atomic models in cryo-EM reconstruction

Ellen D. Zhong, Adam Lerer, Joseph H. Davis, Bonnie Berger

arXiv · 01 Jan 2021 · doi:10.48550/arXiv.2107.01331

2020

Learning mutational semantics

Brian Hie, Ellen Zhong, Bryan Bryson, Bonnie Berger

Advances in Neural Information Processing Systems · 12 Dec 2020 · [no id info]

Source

Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design

Brian Hie, Bryan D. Bryson, Bonnie Berger

Cell Systems · 01 Nov 2020 · doi:10.1016/j.cels.2020.09.007

Source

Topaz-Denoise: general deep denoising models for cryoEM and cryoET

Tristan Bepler, Kotaro Kelley, Alex J. Noble, Bonnie Berger

Nature Communications · 15 Oct 2020 · doi:10.1038/s41467-020-18952-1

Source

Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

Emily Berger, Deniz Yorukoglu, Lillian Zhang, Sarah K. Nyquist, Alex K. Shalek, Manolis Kellis, Ibrahim Numanagić, Bonnie Berger

Nature Communications · 16 Sep 2020 · doi:10.1038/s41467-020-18320-z

Source

Computational Methods for Single-Cell RNA Sequencing

Brian Hie, Joshua Peters, Sarah K. Nyquist, Alex K. Shalek, Bonnie Berger, Bryan D. Bryson

Annual Review of Biomedical Data Science · 20 Jul 2020 · doi:10.1146/annurev-biodatasci-012220-100601

Hopper: a mathematically optimal algorithm for sketching biological data

Benjamin DeMeo, Bonnie Berger

Bioinformatics · 01 Jul 2020 · doi:10.1093/bioinformatics/btaa408

Source

Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs

Hyunghoon Cho, Sean Simmons, Ryan Kim, Bonnie Berger

Cell Systems · 01 May 2020 · doi:10.1016/j.cels.2020.03.006

Source

Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads

Sumaiya Nazeen, Yun William Yu, Bonnie Berger

Genome Biology · 24 Feb 2020 · doi:10.1186/s13059-020-1933-7

Source

A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets

Barış Ekim, Bonnie Berger, Yaron Orenstein

Lecture Notes in Computer Science · 01 Jan 2020 · doi:10.1007/978-3-030-45257-5_3

Source

2019

Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation

Luke A D Hutchison, Bonnie Berger, Isaac S Kohane

Bioinformatics · 20 Dec 2019 · doi:10.1093/bioinformatics/btz864

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

Tristan Bepler, Andrew Morin, Micah Rapp, Julia Brasch, Lawrence Shapiro, Alex J. Noble, Bonnie Berger

Nature Methods · 07 Oct 2019 · doi:10.1038/s41592-019-0575-8

Source

Emerging technologies towards enhancing privacy in genomic data sharing

Bonnie Berger, Hyunghoon Cho

Genome Biology · 02 Jul 2019 · doi:10.1186/s13059-019-1741-0