Bonnie Berger | JRNLClub

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Bonnie Berger

Highly Cited Researcher2025

Massachusetts Institute of Technology

Collaboration network ORCID

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Recent publications · auto-generated until this profile is claimed

Bonnie Berger Oct 1, 2026

New paperauto

Paper

Learning how single cells respond to perturbations

Sources

Recognition: Clarivate Highly Cited Researchers 2025 - Cross-Field. See the roster on JRNLClub.
Publications & citations: OpenAlex A5044078921 - works, citation counts, co-authors, and research topics.
Affiliations & identity: ORCID 0000-0002-2724-7228 - employment history, curated by the researcher.

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Molecular Cell · 2026 · Ekin Deniz Aksu, Bonnie Berger

Bonnie Berger Sep 25, 2026

New paperauto

Paper

ProPGen v0.0.1-preprint: code for Phenotypic noise drives evolutionary dynamics in adapting populations

Zenodo (CERN European Organization for Nuclear Research) · 2026 · Vaibhav Mohanty, Anna Sappington, Eugene I. Shakhnovich et al.

Bonnie Berger Aug 26, 2026

New paperauto

Paper

BatchRefiner: fast, significant improvement in batch integration of single-cell embeddings with ensemble refinement

bioRxiv (Cold Spring Harbor Laboratory) · 2026 · Schäffer DE, Kang H, Aksu ED et al.

Bonnie Berger Jul 17, 2026

New paperauto

Paper

Foundation model reveals the shared organization of transcription and topologically associating domains

Cell Systems · 2026 · Huan Liang, Bonnie Berger, Rohit Singh

Bonnie Berger Jun 10, 2026

New paperauto

Paper

Promera: a unified model for biomolecular structure prediction, filtering, and design

bioRxiv (Cold Spring Harbor Laboratory) · 2026 · Bowen Jing, Mihir Bafna, Daniel Diaz et al.

Bonnie Berger Jun 1, 2026

New paperauto

Paper

Thousandfold Expansion Microscopy

bioRxiv (Cold Spring Harbor Laboratory) · 2026 · Helena Hu, Donatus Krah, Antonios Ntolkeras et al.

Bonnie Berger May 29, 2026

New paperauto

Paper

SwitchCraft: A Programmatic Framework for Designing State-Switching Proteins

PubMed · 2026 · Bowen Jing, Mihir Bafna, Anisha Parsan et al.

Bonnie Berger Apr 2, 2026

New paperauto

Paper

AI-based methods for simulating, sampling, and predicting protein ensembles

Current Opinion in Structural Biology · 2026 · Bowen Jing, Bonnie Berger, Tommi Jaakkola

Bonnie Berger Mar 16, 2026

New paperauto

Paper

Evolutionary dynamics under phenotypic uncertainty

bioRxiv (Cold Spring Harbor Laboratory) · 2026 · Vaibhav Mohanty, Anna Sappington, Eugene I Shakhnovich et al.

Bonnie Berger Mar 14, 2026

New paperauto

Paper

Urban Incident Prediction with Graph Neural Networks: Integrating Government Ratings and Crowdsourced Reports

Proceedings of the AAAI Conference on Artificial Intelligence · 2026 · Sidhika Balachandar, Shuvom Sadhuka, Bonnie Berger et al.

Research Statement

AI generated · 6h ago

Bonnie Berger's indexed work centers on computational methods for protein structure, single-cell genomics, and cryo-EM analysis. Her senior-authored contributions include positive-unlabeled convolutional networks for particle picking in cryo-electron micrographs, a widely cited approach to automating a bottleneck in structure determination, and Scanorama, a method for integrating heterogeneous single-cell transcriptomes. Earlier work on coiled-coil prediction from pairwise residue correlations established a lasting thread in sequence-based structure prediction, while her first-authored result on the hydrophobic-hydrophilic model's NP-completeness framed protein folding as a computational problem. Beyond these, Berger contributed as a middle author to large collaborative efforts, including work identifying ACE2 as an interferon-stimulated gene in human airway epithelial cells and neural-network reconstruction of heterogeneous cryo-EM structures via CryoDRGN. Her portfolio spans sequence-level prediction, network alignment, and deep-learning tools for imaging and transcriptomics, suggesting a consistent focus on algorithmic methods that make complex biological data tractable.

Most Cited Works

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 Methods2019

2,034Citations

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

Brian Hie, Bryan Bryson, Bonnie Berger

Nature Biotechnology2019

968Citations

MultiCoil: A program for predicting two‐and three‐stranded coiled coils

Research Areas

Genomics and Phylogenetic StudiesProtein Structure and DynamicsBioinformatics and Genomic NetworksMachine Learning in BioinformaticsEnzyme Structure and Function

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Record matching

Crossref, Europe PMC, and PubMed, used to reconcile DOIs, PMIDs, and divergent citation counts across sources. All sources

Research statement

Written by a language model from the publications and outputs listed on this page. Not written or reviewed by the researcher.

Snapshot

Data as of 29 Oct 2026. Counts change as sources are reindexed.

E Wolf, P S Kim, B Berger

Protein Science1997

720Citations

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

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

Nature Methods2021

706Citations

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

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

Nature Communications2020

634Citations