Bonnie Berger

Also affiliated with Harvard University, Moscow Institute of Thermal Technology, Massachusetts Institute of Technology

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

7.8Author DataRank

Indexed papers

3in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 3 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

The scverse project provides a computational ecosystem for single-cell omics data analysis

Nature Biotechnology(2023)10.1038/s41587-023-01733-8

Top 4%

5.4DataRank

Top 4%353 citations

Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso +29 more

Papers

Driven by 101 papers — median percentile 94. Top paper: “SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues”.

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

Cell(2020)10.1016/j.cell.2020.04.035

N/A

14.1DataRank · unranked

2492 citations

Samuel J. Allon, Sarah K. Nyquist, Ian Mbano, Vincent N. Miao, Constantine N. Tzouanas +92 more

Learning the protein language: Evolution, structure, and function

Cell Systems(2021)10.1016/j.cels.2021.05.017

N/A

10.3DataRank · unranked

543 citations

Bonnie Berger, Tristan Bepler

The scverse project provides a computational ecosystem for single-cell omics data analysis

Nature Biotechnology(2023)10.1038/s41587-023-01733-8

Top 4%

5.4DataRank

Top 4%353 citations

Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso +29 more

Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery

Journal of Computational Biology(2004)10.1089/1066527041410319

N/A

5.0DataRank · unranked

105 citations

Nick Patterson, Bonnie Berger, Matthew E. Hurles, Bruce W. Birren, Sharon L. R. Kardia

Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control

Immunity(2022)10.1016/j.immuni.2022.04.004

N/A

4.8DataRank · unranked

294 citations

Travis K. Hughes, Constantine N. Tzouanas, Marc H. Wadsworth, Ang A. Tu, Todd M. Gierahn +38 more

Contrastive learning in protein language space predicts interactions between drugs and protein targets

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2220778120

N/A

4.5DataRank · unranked

191 citations

Samuel Sledzieski, Bryan D. Bryson, Lenore Cowen, Bonnie Berger, Rohit Singh

Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection

Nature Medicine(2020)10.1038/s41591-020-0799-2

N/A

3.9DataRank · unranked

175 citations

Toby P. Aicher, Daniel Muema, Shaina L. Carroll, José Ordovás-Montañés, Vincent N. Miao +16 more

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Science(2010)10.1126/science.1198374

Top 9%

2.4DataRank

Top 9%1089 citations

Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Yanxiao Zhang, Richard S. Sandstrom +172 more

Cellular and transcriptional diversity over the course of human lactation

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2121720119

N/A

1.5DataRank · unranked

70 citations

Patricia Gao, Tessa K. J. Haining, Michael R. Retchin, Yarden Golan, Riley S. Drake +8 more

Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens

Molecular Cell(2023)10.1016/j.molcel.2023.03.013

N/A

1.2DataRank · unranked

47 citations

Oana Ursu, Alexander P. Wu, Evan B. Winter, Michael S. Cuoco, Sai Ma +7 more

Efficient Bayesian mixed-model analysis increases association power in large cohorts

Nature Genetics(2015)10.1038/ng.3190

N/A

1.1DataRank · unranked

1781 citations

George Tucker, Brendan K Bulik-Sullivan, Bjarni J. Vilhjálmsson, Hilary K. Finucane, Rany M. Salem +9 more

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

Nature Communications(2020)10.1038/s41467-020-18952-1

N/A

0.960DataRank · unranked

601 citations

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

Compact Integration of Multi-Network Topology for Functional Analysis of Genes

Cell Systems(2016)10.1016/j.cels.2016.10.017

N/A

0.837DataRank · unranked

264 citations

Bonnie Berger, Jian Peng, Hyunghoon Cho

Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation

Science Immunology(2021)10.1126/sciimmunol.abb7221

N/A

0.776DataRank · unranked

176 citations

José Ordovás-Montañés, Samuel J. Allon, Kathleen M. Buchheit, Marko Vukovic, Tahereh Derakhshan +17 more

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

Cell Systems(2021)10.1016/j.cels.2021.08.009

N/A

0.727DataRank · unranked

126 citations

Bonnie Berger, Rayan Chikhi, Barış Ekim

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

Nature Communications(2020)10.1038/s41467-020-18320-z

N/A

0.695DataRank · unranked

22 citations

Deniz Yorukoglu, Lillian Zhang, Sarah K. Nyquist, Alex K. Shalek, Sharon L. R. Kardia +4 more

Developmental dynamics of RNA translation in the human brain

Nature Neuroscience(2022)10.1038/s41593-022-01164-9

N/A

0.694DataRank · unranked

101 citations

Benjamin Finander, GiHun Choi, Ava C. Carter, Iva Pritišanac, Aqsa Alam +20 more

Democratizing protein language models with parameter-efficient fine-tuning

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2405840121

N/A

0.663DataRank · unranked

82 citations

Meghana Kshirsagar, Minkyung Baek, Rahul Dodhia, Juan Lavista Ferres, Bonnie Berger +1 more

Computational analysis of noncoding RNAs

WIREs RNA(2012)10.1002/wrna.1134

N/A

0.581DataRank · unranked

47 citations

Sebastian Will, David A. Hendrix, Loyal A. Goff, John L. Rinn, Bonnie Berger +2 more

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

Genome biology(2021)10.1186/s13059-021-02313-2

N/A

0.578DataRank · unranked

46 citations

Brian Hie, Ashwin Narayan, Bonnie Berger, Rohit Singh

MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis

Genome Biology(2012)10.1186/gb-2012-13-1-r6

N/A

0.561DataRank · unranked

41 citations

Deborah Hung, Prisca Liberali, Bonnie Berger, Sarah A. Stanley, Deborah T. Hung +1 more

Truly Privacy-Preserving Federated Analytics for Precision Medicine with Multiparty Homomorphic Encryption

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.24.432489

N/A

0.553DataRank · unranked

39 citations

Juan Ramón Troncoso-Pastoriza, Jean Louis Raisaro, Michel A. Cuendet, João Sá Sousa, Hyunghoon Cho +4 more

An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

Nature Communications(2014)10.1038/ncomms5893

N/A

0.546DataRank · unranked

37 citations

Jason Trigg, Prisca Liberali, Bonnie Berger, Leonid Chindelevitch

Sparse autoencoders uncover biologically interpretable features in protein language model representations

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2506316122

N/A

0.494DataRank · unranked

26 citations

Mihir Bafna, Eric J. Alm, Bonnie Berger, Onkar Singh Gujral

HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells

JCI Insight(2021)10.1172/jci.insight.148920

N/A

0.442DataRank · unranked

8 citations

Osaretin E. Asowata, Nicholas Herbert, Sarah K. Nyquist, Yenzekile Zungu, Alveera Singh +15 more

HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control

Frontiers in Immunology(2022)10.3389/fimmu.2022.912038

N/A

0.406DataRank · unranked

14 citations

Sarah K. Nyquist, Osaretin E. Asowata, Samuel W. Kazer, Alveera Singh, Abigail Ngoepe +21 more

Large mosaic copy number variations confer autism risk

medRxiv(2020)10.1101/2020.01.22.20017624

N/A

0.330DataRank · unranked

8 citations

Rachel E. Rodin, Giulio Genovese, Caroline Dias, Alison R. Barton, Ronen E. Mukamel +5 more

Microbial dynamics inference at ecosystem-scale

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.14.469105

N/A

0.312DataRank · unranked

7 citations

Younhun Kim, Sawal Acharya, David E. Kaplan, Nicholas DiBenedetto, Richard Lavin +5 more

Reply to “Do genome‐scale models need exact solvers or clearer standards?”

Molecular Systems Biology(2015)10.15252/msb.20156548

N/A

0.312DataRank · unranked

7 citations

Jason Trigg, Prisca Liberali, Bonnie Berger, Leonid Chindelevitch

Cellular and transcriptional diversity over the course of human lactation

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.13.468496

N/A

0.292DataRank · unranked

6 citations

Patricia Gao, Tessa K. J. Haining, Michael R. Retchin, Yarden Golan Maor, Riley S. Drake +8 more

Phylogenetic reconciliation reveals extensive ancestral recombination in Sarbecoviruses and the SARS-CoV-2 lineage

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.12.456131

N/A

0.208DataRank · unranked

3 citations

Samuel Sledzieski, Bonnie Berger, Yi-Chieh Wu, Mukul S. Bansal, Sumaira Zaman

Generative Modeling of Molecular Dynamics Trajectories

PubMed(2024)10.48550/arxiv.2409.17808

N/A

0.198DataRank · unranked

2 citations

H. Stärk, Tommi Jaakkola, Bonnie Berger, Bowen Jing

Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets

Lecture notes in computer science(2024)10.1007/978-1-0716-3989-4_19

N/A

0.113DataRank · unranked

1 citations

David Froelicher, Ricky Magner, Victoria Popic, Bonnie Berger, Hyunghoon Cho +1 more

mapquik: Efficient low-divergence mapping of long reads in minimizer space

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.23.521809

N/A

0DataRank · unranked

2 citations

Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi, Barış Ekim

Contrasting drugs from decoys

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.03.515086

N/A

0DataRank · unranked

1 citations

Rohit Singh, Lenore Cowen, Bonnie Berger, Samuel Sledzieski

Identification and characterization of the T cell receptor (TCR) repertoire of the Cynomolgus macaque ( Macaca Fascicularis )

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.30.486315

N/A

0DataRank · unranked

0 citations

Shayla Boyce, Sarah K. Nyquist, Tasneem Jivanjee, Samira Ibrahim, Joshua D. Bromley +10 more

CD8+ lymphocytes are critical for early control of tuberculosis in macaques

The Journal of Experimental Medicine(2023)10.1084/jem.20230707

N/A

0DataRank · unranked

88 citations

Sarah K. Nyquist, Michael C. Chao, Pauline Maiello, Amy J. Myers, Forrest Hopkins +22 more

split-intein Gal4 provides intersectional genetic labeling that is repressible by Gal80

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2304730120

N/A

0DataRank · unranked

36 citations

Haojiang Luan, Jun Xu, Rohit Singh, Neha Joshi, Tanuj Thakkar +4 more

TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions

Bioinformatics(2023)10.1093/bioinformatics/btad663

N/A

0DataRank · unranked

32 citations

Kapil Devkota, Rohit Singh, Lenore Cowen, Bonnie Berger, Samuel Sledzieski

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

Genome biology(2023)10.1186/s13059-022-02841-5

N/A

0DataRank · unranked

25 citations

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

SCA: recovering single-cell heterogeneity through information-based dimensionality reduction

Genome biology(2023)10.1186/s13059-023-02998-7

N/A

0DataRank · unranked

18 citations

Bonnie Berger, Benjamin DeMeo

sfkit: a web-based toolkit for secure and federated genomic analysis

Nucleic Acids Research(2023)10.1093/nar/gkad464

N/A

0DataRank · unranked

15 citations

David Froelicher, D. V. Loginov, David L. Bernick, Bonnie Berger, Hyunghoon Cho +1 more

Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome

PLoS ONE(2023)10.1371/journal.pone.0270965

N/A

0DataRank · unranked

10 citations

Nathanael Brenner, Samuel Sledzieski, Monsurat Olaosebikan, Liza M. Roger, Matthew Lynn-Goin +10 more

Lipophorin receptors genetically modulate neurodegeneration caused by reduction of Psn expression in the aging Drosophila brain

Genetics(2023)10.1093/genetics/iyad202

N/A

0DataRank · unranked

6 citations

Chen Zhang, Yuhao Wang, Jian Peng, Bonnie Berger, Norbert Perrimon +2 more

EigenFold: Generative Protein Structure Prediction with Diffusion Models

PubMed(2023)10.48550/arxiv.2304.02198

N/A

0DataRank · unranked

39 citations

Ezra Erives, Peter Pao-Huang, Gabriele Corso, Bonnie Berger, Tommi Jaakkola +1 more

Scalable and Privacy-Preserving Federated Principal Component Analysis

PubMed(2023)10.1109/sp46215.2023.10179350

N/A

0DataRank · unranked

25 citations

Hyunghoon Cho, Manaswitha Edupalli, João Sá Sousa, Jean-Philippe Bossuat, Apostolos Pyrgelis +4 more

Codon: A Compiler for High-Performance Pythonic Applications and DSLs

DSpace@MIT (Massachusetts Institute of Technology)(2023)10.1145/3578360.3580275

N/A

0DataRank · unranked

21 citations

Gabriel Ramı́rez, Haris Smajlović, Jessica M. Ray, Bonnie Berger, Saman Amarasinghe +2 more

Efficient minimizer orders for large values of k using minimum decycling sets

Genome Research(2023)10.1101/gr.277644.123

N/A

0DataRank · unranked

19 citations

Lianrong Pu, Barış Ekim, Lior Kotlar, Bonnie Berger, Ron Shamir +2 more

Efficient mapping of accurate long reads in minimizer space with mapquik

Genome Research(2023)10.1101/gr.277679.123

N/A

0DataRank · unranked

17 citations

Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi, Barış Ekim

Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.09.566187

N/A

0DataRank · unranked

15 citations

Meghana Kshirsagar, Minkyung Baek, Bonnie Berger, Rahul Dodhia, Juan Lavista Ferres +1 more

Assessing transcriptomic reidentification risks using discriminative sequence models

Genome Research(2023)10.1101/gr.277699.123

N/A

0DataRank · unranked

8 citations

Daniel Fridman, Bonnie Berger, Hyunghoon Cho, Shuvom Sadhuka

Assessing transcriptomic re-identification risks using discriminative sequence models

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.13.536784

N/A

0DataRank · unranked

3 citations

Daniel Fridman, Bonnie Berger, Hyunghoon Cho, Shuvom Sadhuka

split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.24.534001

N/A

0DataRank · unranked

1 citations

Haojiang Luan, Jun Xu, Rohit Singh, Neha Joshi, Tanuj Thakkar +4 more

Strain tracking with uncertainty quantification

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.25.525531

N/A

0DataRank · unranked

0 citations

Colin J. Worby, Sawal Acharya, Lucas R. van Dijk, Daniel Alfonsetti, Zackary Gromko +8 more

Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms

PubMed(2023)10.48550/arxiv.2312.04323

N/A

0DataRank · unranked

0 citations

Tommi Jaakkola, Bonnie Berger, Bowen Jing

Scanorama: integrating large and diverse single-cell transcriptomic datasets

Nature Protocols(2024)10.1038/s41596-024-00991-3

N/A

0DataRank · unranked

42 citations

Soochi Kim, Thomas A. Rando, Bryan D. Bryson, Bonnie Berger, Brian Hie

CD4+ T cells re-wire granuloma cellularity and regulatory networks to promote immunomodulation following Mtb reinfection

Immunity(2024)10.1016/j.immuni.2024.08.002

N/A

0DataRank · unranked

41 citations

Sharie Keanne C. Ganchua, Sarah K. Nyquist, Pauline Maiello, Michael C. Chao, H. Jacob Borish +17 more

Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors

Cell Systems(2024)10.1016/j.cels.2024.04.005

N/A

0DataRank · unranked

26 citations

Alexander P. Wu, Anish Mudide, Bonnie Berger, Rohit Singh

Privacy-Enhancing Technologies in Biomedical Data Science

Annual Review of Biomedical Data Science(2024)10.1146/annurev-biodatasci-120423-120107

N/A

0DataRank · unranked

26 citations

David Froelicher, Natnatee Dokmai, Anupama Nandi, Shuvom Sadhuka, Matthew M. Hong +2 more

AlphaFold Meets Flow Matching for Generating Protein Ensembles

arXiv (Cornell University)(2024)10.48550/arxiv.2402.04845

N/A

0DataRank · unranked

82 citations

Bonnie Berger, Tommi Jaakkola, Bowen Jing

Secure discovery of genetic relatives across large-scale and distributed genomic data sets

Genome Research(2024)10.1101/gr.279057.124

N/A

0DataRank · unranked

5 citations

David Froelicher, Ricky Magner, Victoria Popic, Bonnie Berger, Hyunghoon Cho +1 more

Secure and federated genome-wide association studies for biobank-scale datasets

Nature Genetics(2025)10.1038/s41588-025-02109-1

N/A

0DataRank · unranked

20 citations

David Froelicher, Jeffrey Chen, Manaswitha Edupalli, Apostolos Pyrgelis, Juan Ramón Troncoso-Pastoriza +3 more

Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain

Nature Microbiology(2025)10.1038/s41564-025-01983-z

N/A

0DataRank · unranked

5 citations

Colin J. Worby, Sawal Acharya, Lucas R. van Dijk, Daniel Alfonsetti, Zackary Gromko +8 more

Unveiling causal regulatory mechanisms through cell-state parallax

Nature Communications(2025)10.1038/s41467-025-61337-5

N/A

0DataRank · unranked

5 citations

Rohit Singh, Christopher A. Walsh, Bonnie Berger, Alexander P. Wu

Learning ecosystem-scale dynamics from microbiome data with MDSINE2

Nature Microbiology(2025)10.1038/s41564-025-02112-6

N/A

0DataRank · unranked

5 citations

Younhun Kim, Sawal Acharya, David E. Kaplan, Nicholas DiBenedetto, Richard Lavin +5 more

Single-cell and spatial profiling highlights TB-induced myofibroblasts as drivers of lung pathology

The Journal of Experimental Medicine(2025)10.1084/jem.20251067

N/A

0DataRank · unranked

3 citations

Nuo Liu, Marc H. Wadsworth, Mark John. Chambers, Thabo Mpotje, Osaretin E. Asowata +25 more

Graph-based deep reinforcement learning for haplotype assembly with Ralphi

Genome Research(2025)10.1101/gr.280569.125

N/A

0DataRank · unranked

1 citations

Anant Maheshwari, Barış Ekim, Bonnie Berger, Victoria Popic, Enzo Battistella

Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT

Bioinformatics(2025)10.1093/bioinformatics/btaf564

N/A

0DataRank · unranked

0 citations

Samuel Sledzieski, Lenore Cowen, Bonnie Berger, Daniel E. Schäffer

Rapid and accurate prediction of protein homo-oligomer symmetry with Seq2Symm

Research Square(2024)10.21203/rs.3.rs-4215086/v1

N/A

0DataRank · unranked

6 citations

Artur Meller, Ian R. Humphreys, Samuel Sledzieski, Yixi Xu, Rahul Dodhia +7 more

Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design

Cell Systems(2020)10.1016/j.cels.2020.09.007

N/A

0DataRank · unranked

162 citations

Bryan D. Bryson, Bonnie Berger, Brian Hie

Levenshtein Distance, Sequence Comparison and Biological Database Search

IEEE Transactions on Information Theory(2020)10.1109/tit.2020.2996543

N/A

0DataRank · unranked

150 citations

Michael S. Waterman, Yun William Yu, Bonnie Berger

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

Cell Systems(2020)10.1016/j.cels.2020.03.006

N/A

0DataRank · unranked

27 citations

Sean K. Simmons, Ryan Kim, Bonnie Berger, Hyunghoon Cho

Hopper: a mathematically optimal algorithm for sketching biological data

Bioinformatics(2020)10.1093/bioinformatics/btaa408

N/A

0DataRank · unranked

22 citations

Bonnie Berger, Benjamin DeMeo

CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.27.003871

N/A

0DataRank · unranked

16 citations

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

A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.17.910513

N/A

0DataRank · unranked

11 citations

Bonnie Berger, Yaron Orenstein, Barış Ekim

Learning the language of viral evolution and escape

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.08.193946

N/A

0DataRank · unranked

7 citations

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

Learning with uncertainty for biological discovery and design

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.11.247072

N/A

0DataRank · unranked

5 citations

Bryan D. Bryson, Bonnie Berger, Brian Hie

Multimodal profiling of lung granulomas reveals cellular correlates of tuberculosis control

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.24.352492

N/A

0DataRank · unranked

5 citations

Travis K. Hughes, Constantine N. Tzouanas, Marc H. Wadsworth, Ang Andy Tu, Todd M. Gierahn +37 more

GM-CSF differentiation of human monocytes stabilizes macrophage state via oxidative signaling

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.29.318352

N/A

0DataRank · unranked

2 citations

Cal Gunnarsson, Gregory H. Babunovic, Armel Nibasumba, Ngomu Akeem Akilimali, Marc H. Wadsworth +8 more

Learning the language of viral evolution and escape

Science(2021)10.1126/science.abd7331

N/A

0DataRank · unranked

382 citations

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

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

Cell Systems(2021)10.1016/j.cels.2021.08.010

N/A

0DataRank · unranked

209 citations

Rohit Singh, Lenore Cowen, Bonnie Berger, Samuel Sledzieski

Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption

Nature Communications(2021)10.1038/s41467-021-25972-y

N/A

0DataRank · unranked

180 citations

Juan Ramón Troncoso-Pastoriza, Jean Louis Raisaro, Michel A. Cuendet, João Sá Sousa, Hyunghoon Cho +4 more

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

Nature Biotechnology(2021)10.1038/s41587-020-00801-7

N/A

0DataRank · unranked

175 citations

Bonnie Berger, Hyunghoon Cho, Ashwin Narayan

An engineered protein-phosphorylation toggle network with implications for endogenous network discovery

Science(2021)10.1126/science.aav0780

N/A

0DataRank · unranked

37 citations

Tristan Bepler, Brian Teague, Bonnie Berger, James R. Broach, Ron Weiss +1 more

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

Bioinformatics(2021)10.1093/bioinformatics/btab269

N/A

0DataRank · unranked

2 citations

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

Sequence-based prediction of protein-protein interactions: a structure-aware interpretable deep learning model

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.22.427866

N/A

0DataRank · unranked

30 citations

Rohit Singh, Lenore Cowen, Bonnie Berger, Samuel Sledzieski

Deciphering the species-level structure of topologically associating domains

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.28.466333

N/A

0DataRank · unranked

16 citations

Bonnie Berger, Rohit Singh

Developmental Dynamics of RNA Translation in the Human Brain

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.22.465170

N/A

0DataRank · unranked

8 citations

Benjamin Finander, GiHun Choi, Ava C. Carter, Iva Pritišanac, Aqsa Alam +18 more

Minimizer-space de Bruijn graphs

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.09.447586

N/A

0DataRank · unranked

3 citations

Bonnie Berger, Rayan Chikhi, Barış Ekim

Recovering Single-cell Heterogeneity Through Information-based Dimensionality Reduction

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.19.427303

N/A

0DataRank · unranked

2 citations

Bonnie Berger, Benjamin DeMeo

Learning the mutational landscape of the cancer genome

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.03.454669

N/A

0DataRank · unranked

0 citations

Adam Yaari, Oliver Priebe, Felix Dietlein, Po‐Ru Loh, Bonnie Berger +1 more

HIV-specific CD8 + T-cells in tonsils express exhaustive T RM -like signatures

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.04.467061

N/A

0DataRank · unranked

0 citations

Sarah K. Nyquist, Osaretin E. Asowata, Samuel W. Kazer, Alveera Singh, Abigail Ngoepe +21 more

Topsy-Turvy: integrating a global view into sequence-based PPI prediction

Bioinformatics(2022)10.1093/bioinformatics/btac258

N/A

0DataRank · unranked

94 citations

Kapil Devkota, Samuel Sledzieski, Bonnie Berger, Lenore Cowen, Rohit Singh

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

Nature Biotechnology(2022)10.1038/s41587-022-01353-8

N/A

0DataRank · unranked

86 citations

Adam Yaari, Oliver Priebe, Felix Dietlein, Po‐Ru Loh, Bonnie Berger +1 more

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

Nature Protocols(2022)10.1038/s41596-022-00763-x

N/A

0DataRank · unranked

79 citations

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

Navigating bottlenecks and trade-offs in genomic data analysis

Nature Reviews Genetics(2022)10.1038/s41576-022-00551-z

N/A

0DataRank · unranked

61 citations

Yun William Yu, Bonnie Berger

Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)

BMC Genomics(2022)10.1186/s12864-022-08867-0

N/A

0DataRank · unranked

9 citations

Sarah K. Nyquist, Shayla Boyce, Tasneem Jivanjee, Samira Ibrahim, Joshua D. Bromley +10 more

Conformational landscape of the yeast SAGA complex as revealed by cryo-EM

Scientific Reports(2022)10.1038/s41598-022-16391-0

N/A

0DataRank · unranked

8 citations

Joeseph Felt, Ellen D. Zhong, Bonnie Berger, Joseph H. Davis, Calvin K. Yip +1 more

Adapting protein language models for rapid DTI prediction

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.03.515084

N/A

0DataRank · unranked

12 citations

Rohit Singh, Lenore Cowen, Bonnie Berger, Samuel Sledzieski

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

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.09.503342

N/A

0DataRank · unranked

11 citations

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

Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.18.512766

N/A

0DataRank · unranked

4 citations

Alexander P. Wu, Anish Mudide, Bonnie Berger, Rohit Singh

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