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Bonnie Berger

massachusetts institute of technology

85H-index
515Paper Count
3.4WCitation Count
Published Papers 133
Publication Date
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Foundation model reveals the shared organization of transcription and topologically associating domains
errCell Systems
IF7.7
err2026-07-17
err0
PREAI
errHuan Liang; Bonnie Berger; Rohit Singh
errShare
errSave
AI-based methods for simulating, sampling, and predicting protein ensembles
errCurrent Opinion in Structural Biology
IF7
err2026-04-02
err0
PREAI
errBowen Jing; Bonnie Berger; Tommi Jaakkola
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errSave
Learning the language of protein-protein interactions
errNature Communications
IF15.7
err2026-01-07
err0
errOAAI
errVarun Ullanat; Bowen Jing; Samuel Sledzieski; Bonnie Berger
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errSave
Single-cell and spatial profiling highlights TB-induced myofibroblasts as drivers of lung pathology
errJournal of Experimental Medicine
IF10.6
err2026-01-05
err3
PREAI
errMbano, Ian M.; Liu, Nuo; Wadsworth II, Marc H.; Chambers, Mark J.; Mpotje, Thabo; Asowata, Osaretin E.; Nyquist, Sarah K.; Nargan, Kievershen; Ramsuran, Duran; Karim, Farina; Hughes, Travis K.; Bromley, Joshua D.; Krause, Robert; Naidoo, Threnesan; Tezera, Liku B.; Reichmann, Michaela T.; Ganchua, Sharie Keanne; Kloverpris, Henrik N.; Dullabh, Kaylesh J.; Madansein, Rajhmun; Triana, Sergio; Steyn, Adrie J. C.; Berger, Bonnie; Marakalala, Mohlopheni J.; Fortune, Sarah M.; Flynn, JoAnne L.; Elkington, Paul T.; Shalek, Alex K.; Leslie, Alasdair
errShare
errSave
RECOMB 2025 Special Issue
errGENOME RESEARCH
IF5.5
err2025-12-01
err0
PREAI
errSankararaman, Sriram; Berger, Bonnie
errShare
errSave
Graph-based deep reinforcement learning for haplotype assembly with Ralphi
errGENOME RESEARCH
IF5.5
err2025-12-01
err1
PREAI
errBattistella, Enzo; Maheshwari, Anant; Ekim, Baris; Berger, Bonnie; Popic, Victoria
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errSave
Single-cell profiling reveals a role for tuberculosis-induced myofibroblasts in the immunopathology of infected lungs
errJOURNAL OF IMMUNOLOGY
IF3.4
err2025-11-01
err0
PREAI
errLiu, Nuo; Mbano, Ian Maheti; Wardsworth, Marc; Chambers, Mark; Mpotje, Thabo; Asowata, Osaretin; Nyquist, Sarah; Nargan, Kievershen; Ramsuran, Duran; Karim, Farina; Hughes, Travis; Bromley, Joshua; Krause, Robert; Tezera, Liku; Reichmann, Michaela; Keanne, Sharie; Ganchua, C.; Kloverpris, Henrik; Dullabh, Kaylesh; Madansein, Rajhmun; Triana, Sergio; Steyn, Adrie; Berger, Bonnie; Marakalala, Mohlopheni; Fortune, Sarah; Flynn, Joanne L.; Elkington, Paul T.; Shalek, Alex K.; Leslie, Alasdair
errShare
errSave
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT
errBIOINFORMATICS
IF5.4
err2025-10-01
err0
PREAI
errSchaffer, Daniel E.; Sledzieski, Samuel; Cowen, Lenore; Berger, Bonnie
errShare
errSave
CD4+T cells re-wire granuloma cellularity and regulatory networks to promote immunomodulation following Mtb reinfection
errIMMUNITY
IF26.3
err2024-10-01
err0
errOAAI
errBromley, Joshua D.; Ganchua, Sharie Keanne C.; Nyquist, Sarah K.; Maiello, Pauline; Chao, Michael; Borish, H. Jacob; Rodgers, Mark; Tomko, Jaime; Kracinovsky, Kara; Mugahid, Douaa; Nguyen, Son; Wang, Qianchang Dennis; Rosenberg, Jacob M.; Klein, Edwin C.; Gideon, Hannah P.; Floyd-O'Sullivan, Roisin; Berger, Bonnie; Scanga, Charles A.; Lin, Philana Ling; Fortune, Sarah M.; Shalek, Alex K.; Flynn, JoAnne L.
errShare
errSave
Privacy-Enhancing Technologies in Biomedical Data Science
errANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE
IF6
err2024-08-23
err0
errOAAI
errCho, Hyunghoon; Froelicher, David; Dokmai, Natnatee; Nandi, Anupama; Sadhuka, Shuvom; Hong, Matthew M.; Berger, Bonnie
errShare
errSave
Secure discovery of genetic relatives across large-scale and distributed genomic data sets
errGENOME RESEARCH
IF5.5
err2024-08-07
err1
errOAAI
errHong, Matthew M.; Froelicher, David; Magner, Ricky; Popic, Victoria; Berger, Bonnie; Cho, Hyunghoon
errShare
errSave
Democratizing protein language models with parameter-efficient fine-tuning
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2024-06-20
err5
errOAAI
errSledzieski, Samuel; Kshirsagar, Meghana; Baek, Minkyung; Dodhia, Rahul; Ferres, Juan Lavista; Berger, Bonnie
errShare
errSave
Scanorama: integrating large and diverse single-cell transcriptomic datasets
errNATURE PROTOCOLS
IF16
err2024-06-06
err0
errOAAI
errHie, Brian L.; Kim, Soochi; Rando, Thomas A.; Bryson, Bryan; Berger, Bonnie
errShare
errSave
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors
errCELL SYSTEMS
IF7.7
err2024-05-01
err0
PREAI
errSingh, Rohit; Wu, Alexander P.; Mudide, Anish; Berger, Bonnie
errShare
errSave
Lipophorin receptors genetically modulate neurodegeneration caused by reduction of Psn expression in the aging Drosophila brain
errGENETICS
IF5.1
err2023-11-23
err1
errOAAI
errKang, Jongkyun; Zhang, Chen; Wang, Yuhao; Peng, Jian; Berger, Bonnie; Perrimon, Norbert; Shen, Jie
errShare
errSave
CD8+ lymphocytes are critical for early control of tuberculosis in macaques
errJOURNAL OF EXPERIMENTAL MEDICINE
IF10.6
err2023-10-16
err13
errOAAI
errWinchell, Caylin G.; Nyquist, Sarah K.; Chao, Michael C.; Maiello, Pauline; Myers, Amy J.; Hopkins, Forrest; Chase, Michael; Gideon, Hannah P.; Patel, Kush V.; Bromley, Joshua D.; Simonson, Andrew W.; Floyd-O'Sullivan, Roisin; Wadsworth, Marc; Rosenberg, Jacob M.; Uddin, Rockib; Hughes, Travis; Kelly, Ryan J.; Griffo, Josephine; Tomko, Jaime; Klein, Edwin; Berger, Bonnie; Scanga, Charles A.; Mattila, Joshua; Fortune, Sarah M.; Shalek, Alex K.; Lin, Philana Ling; Flynn, JoAnne L.
errShare
errSave
SCA: recovering single-cell heterogeneity through information-based dimensionality reduction
errGENOME BIOLOGY
IF9.4
err2023-08-25
err2
errOAAI
errDemeo, Benjamin; Berger, Bonnie
errShare
errSave
Efficient minimizer orders for large values of k using minimum decycling sets
errGENOME RESEARCH
IF5.5
err2023-08-09
err5
errOAAI
errPellow, David; Pu, Lianrong; Ekim, Baris; Kotlar, Lior; Berger, Bonnie; Shamir, Ron; Orenstein, Yaron
errShare
errSave
Efficient mapping of accurate long reads in minimizer space with mapquik
errGENOME RESEARCH
IF5.5
err2023-06-30
err8
errOAAI
errEkim, Baris; Sahlin, Kristoffer; Medvedev, Paul; Berger, Bonnie; Chikhi, Rayan
errShare
errSave
Contrastive learning in protein language space predicts interactions between drugs and protein targets
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2023-06-08
err45
errOAAI
errSingh, Rohit; Sledzieski, Samuel; Bryson, Bryan; Cowen, Lenore; Berger, Bonnie
errShare
errSave

Research Directions

No research directions
Co-authors
Cooperation Journals
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Eric S. Lander
H-index: 271 · Papers: 897
P
Paul M. Ridker
H-index: 226 · Papers: 1.4K
A
Aviv Regev
H-index: 208 · Papers: 965
C
Carl H. June
H-index: 177 · Papers: 1.4K
J
John A. Rogers
H-index: 166 · Papers: 1.1K
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