Richard Bonneau

Associated Press

Biochemistry, Genetics and Molecular BiologySocial Sciences

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 5%percentile

0.460Author DataRank

Indexed papers

4in 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 4 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.

Tissue and cellular spatiotemporal dynamics in colon aging

Nature Biotechnology(2025)10.1038/s41587-025-02830-6

Top 61%

0.241DataRank

Top 61%4 citations

Francesco Cambuli, Tarmo Äijö, Britta Lötstedt, Nemanja Despot Marjanovic, Sara Fernández‐García +11 more

Papers

Driven by 60 papers — median percentile 38. Top paper: “Structure-based protein function prediction using graph convolutional networks”.

Structure-based protein function prediction using graph convolutional networks

Nature Communications(2021)10.1038/s41467-021-23303-9

N/A

10.3DataRank · unranked

937 citations

P. Douglas Renfrew, Tomasz Kościółek, Julia Koehler Leman, Daniel Berenberg, Tommi Vatanen +9 more

Protein remote homology detection and structural alignment using deep learning

Nature Biotechnology(2023)10.1038/s41587-023-01917-2

N/A

3.6DataRank · unranked

155 citations

James T. Morton, Robert Blackwell, Daniel Berenberg, Nicholas Carriero, Vladimir Gligorijević +5 more

NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health

Nature Aging(2022)10.1038/s43587-022-00326-5

N/A

2.1DataRank · unranked

128 citations

Patty J. Lee, Christopher C. Benz, Philip D. Blood, Katy Börner, Judith Campisi +93 more

High-density spatial transcriptomics arrays for in situ tissue profiling

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/563338

N/A

1.9DataRank · unranked

25 citations

Johanna Klughammer, Linnea Stenbeck, Fredrik Salmén, Tarmo Äijö, Richard Bonneau +9 more

High-definition spatial transcriptomics for in situ tissue profiling

Nature Methods(2019)10.1038/s41592-019-0548-y

N/A

1.1DataRank · unranked

1196 citations

Gökçen Eraslan, Fredrik Salmén, Johanna Klughammer, Linnea Stenbeck, Denis Schapiro +13 more

SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

The Science of The Total Environment(2021)10.1016/j.scitotenv.2021.150121

N/A

0.859DataRank · unranked

305 citations

Amy Xiao, Jianbo Zhang, Katya Moniz, Noriko Endo, Federica Armas +23 more

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

eLife(2020)10.7554/elife.51254

N/A

0.754DataRank · unranked

151 citations

Dayanne M Castro, Giuseppe-Antonio Saldi, Richard Bonneau, David Gresham, Christopher A. Jackson

SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

medRxiv(2020)10.1101/2020.06.15.20117747

N/A

0.741DataRank · unranked

139 citations

Amy Xiao, Jianbo Zhang, Katya Moniz, Noriko Endo, Federica Armas +23 more

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation

Nature Immunology(2017)10.1038/ni.3683

N/A

0.729DataRank · unranked

128 citations

Emily R. Miraldi, Maria Pokrovskii, Asaf Madi, Nir Yosef, Ivo Wortman +10 more

Sequence-structure-function relationships in the microbial protein universe

Nature Communications(2023)10.1038/s41467-023-37896-w

N/A

0.700DataRank · unranked

105 citations

Paweł Szczerbiak, P. Douglas Renfrew, Vladimir Gligorijević, Daniel Berenberg, Tommi Vatanen +11 more

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection

Microbiome(2020)10.1186/s40168-020-00803-2

N/A

0.665DataRank · unranked

83 citations

Christian V. Forst, Aubree Gordon, Gabrielle Gussin, Adam Geber, Porfirio J. Fernandez +8 more

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2012800118

N/A

0.657DataRank · unranked

79 citations

Sean D. Workman, Tianjun Sun, Stephen Rettie, Xinting Li, L.J. Worrall +12 more

Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop

Journal of Allergy and Clinical Immunology(2024)10.1016/j.jaci.2024.01.014

N/A

0.637DataRank · unranked

20 citations

Patrice M. Becker, Matthew C. Altman, Jessica Lasky‐Su, Carole Ober, Karsten Zengler +25 more

Towards region-specific propagation of protein functions

Bioinformatics(2019)10.1093/bioinformatics/bty834

N/A

0.632DataRank · unranked

11 citations

Richard Bonneau, Da Chen Emily Koo

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Nature Communications(2021)10.1038/s41467-021-27222-7

N/A

0.500DataRank · unranked

27 citations

Sergey Lyskov, Steven M. Lewis, Jared Adolf‐Bryfogle, Rebecca F. Alford, Kyle A. Barlow +45 more

Lab-in-the-loop therapeutic antibody design with deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.19.639050

N/A

0.483DataRank · unranked

24 citations

Isidro Hötzel, Samuel D. Stanton, Ryan L. Kelly, Robert G. Alberstein, Emily K. Makowski +68 more

The 2010 Rosetta Developers Meeting: Macromolecular Prediction and Design Meets Reproducible Publishing

PLoS ONE(2011)10.1371/journal.pone.0022431

N/A

0.427DataRank · unranked

7 citations

Gabrielle Campbell, Charlie E. M. Strauss, Richard Bonneau, P. Douglas Renfrew

Sequence-structure-function relationships in the microbial protein universe

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.18.484903

N/A

0.360DataRank · unranked

10 citations

Paweł Szczerbiak, P. Douglas Renfrew, Vladimir Gligorijević, Daniel Berenberg, Tommi Vatanen +11 more

Tissue and cellular spatiotemporal dynamics in colon aging

Nature Biotechnology(2025)10.1038/s41587-025-02830-6

Top 61%

0.241DataRank

Top 61%4 citations

Francesco Cambuli, Tarmo Äijö, Britta Lötstedt, Nemanja Despot Marjanovic, Sara Fernández‐García +11 more

Tissue and cellular spatiotemporal dynamics in colon aging

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.22.590125

Top 63%

0.218DataRank

Top 63%3 citations

Francesco Cambuli, Tarmo Äijö, Britta Lötstedt, Nemanja Despot Marjanovic, Olena Kuksenko +11 more

Towards region-specific propagation of protein functions

bioRxiv (Cold Spring Harbor Laboratory)10.1101/275487

N/A

0.209DataRank · unranked

2 citations

Richard Bonneau, Da Chen Emily Koo

Comparative genomics of the parasite Trichomonas vaginalis reveals genes involved in spillover from birds to humans

Nature Communications(2025)10.1038/s41467-025-61483-w

N/A

0.208DataRank · unranked

3 citations

Jordan C. Orosco, Francisco Callejas‐Hernández, Frances Blow, Hayan Lee, T. Rhyker Ranallo-Benavidez +22 more

Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.22.629724

N/A

0.165DataRank · unranked

2 citations

Jordan C. Orosco, Francisco Callejas‐Hernández, Frances Blow, Hayan Lee, T. Rhyker Ranallo-Benavidez +21 more

Lower Airway Dysbiosis Affects Lung Cancer Progression

Cancer Discovery(2020)10.1158/2159-8290.cd-20-0263

N/A

0DataRank · unranked

309 citations

Benjamin G. Wu, Imran Sulaiman, Katherine Gershner, Rosemary Schluger, Yonghua Li +37 more

Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice

Cell Host & Microbe(2021)10.1016/j.chom.2021.06.014

N/A

0DataRank · unranked

57 citations

Yue Yin, Jincheng Wang, Thomas Battaglia, Kimberly A. Krautkramer, Wei Vivian Li +24 more

Viewing the US presidential electoral map through the lens of public health

PLoS ONE(2021)10.1371/journal.pone.0254001

N/A

0DataRank · unranked

16 citations

Michael Danziger, Jonathan Nagler, Richard Bonneau, Tymor Hamamsy

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

PLoS Computational Biology(2021)10.1371/journal.pcbi.1008569

N/A

0DataRank · unranked

31 citations

Omar Mahmood, Christopher A. Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel Christiaen +2 more

NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity

Bioinformatics(2021)10.1093/bioinformatics/btab098

N/A

0DataRank · unranked

31 citations

Vladimir Gligorijević, Kyunghyun Cho, Richard Bonneau, Meet Barot

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops

PLoS Computational Biology(2021)10.1371/journal.pcbi.1009056

N/A

0DataRank · unranked

6 citations

Evan Bolyen, A. K. Adamov, Aeriel D. Belk, Emily M. Borsom, Zachary M. Burcham +26 more

High performance single-cell gene regulatory network inference at scale: The Inferelator 3.0

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.03.442499

N/A

0DataRank · unranked

11 citations

Christopher A. Jackson, Giuseppe-Antonio Saldi, Andreas Tjärnberg, Aashna Shah, Aaron Watters +11 more

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.04.438423

N/A

0DataRank · unranked

4 citations

Sergey Lyskov, Steven M. Lewis, Jared Adolf‐Bryfogle, Rebecca F. Alford, Kyle A. Barlow +43 more

NetTIME: a Multitask and Base-pair Resolution Framework for Improved Transcription Factor Binding Site Prediction

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.29.446316

N/A

0DataRank · unranked

0 citations

Kyunghyun Cho, Richard Bonneau, Ren Yi

High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0

Bioinformatics(2022)10.1093/bioinformatics/btac117

N/A

0DataRank · unranked

79 citations

Christopher A. Jackson, Giuseppe-Antonio Saldi, Andreas Tjärnberg, Aashna Shah, Aaron Watters +11 more

Coordinated control of neuronal differentiation and wiring by sustained transcription factors

Science(2022)10.1126/science.add1884

N/A

0DataRank · unranked

51 citations

Claudia Skok Gibbs, Isabel Holguera, Mennah Soliman, Richard Bonneau, Claude Desplan +1 more

Engineered protein–iron oxide hybrid biomaterial for MRI-traceable drug encapsulation

Molecular Systems Design & Engineering(2022)10.1039/d2me00002d

N/A

0DataRank · unranked

10 citations

Dustin Britton, Teeba Jihad, Kamia Punia, Xuan Xie, Erika Delgado-Fukushima +10 more

NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction

Bioinformatics(2022)10.1093/bioinformatics/btac569

N/A

0DataRank · unranked

1 citations

Kyunghyun Cho, Richard Bonneau, Ren Yi

TM-Vec: template modeling vectors for fast homology detection and alignment

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.25.501437

N/A

0DataRank · unranked

16 citations

James T. Morton, Daniel Berenberg, Nicholas Carriero, Vladimir Gligorijević, Robert Blackwell +5 more

CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection

medRxiv(2022)10.1101/2022.08.11.22278625

N/A

0DataRank · unranked

0 citations

Jahan Rahman, Lauren Lashua, Aubree Gordon, Ángel Balmaseda, Guillermina Kuan +3 more

Computational Prediction of Coiled–Coil Protein Gelation Dynamics and Structure

Biomacromolecules(2023)10.1021/acs.biomac.3c00968

N/A

0DataRank · unranked

17 citations

Luc F. Christians, Chengliang Liu, Jakub Legocki, Yingxin Xiao, Michael Meleties +12 more

CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection

Microbiome(2023)10.1186/s40168-023-01568-0

N/A

0DataRank · unranked

5 citations

Jahan Rahman, Matthew Chung, Lauren Lashua, Aubree Gordon, Ángel Balmaseda +4 more

Protein-Engineered Fibers For Drug Encapsulation Traceable via 19F Magnetic Resonance

ACS Applied Nano Materials(2023)10.1021/acsanm.3c04357

N/A

0DataRank · unranked

4 citations

Jakub Legocki, Orlando Aristizábal, Orin Mishkit, Chengliang Liu, Sihan Jia +5 more

Learning sequence, structure, and function representations of proteins with language models

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.26.568742

N/A

0DataRank · unranked

11 citations

Meet Barot, James T. Morton, Martin Steinegger, Richard Bonneau, Kyunghyun Cho +1 more

PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization

Genome biology(2024)10.1186/s13059-024-03226-6

N/A

0DataRank · unranked

16 citations

Omar Mahmood, Richard Bonneau, Kyunghyun Cho, Claudia Skok Gibbs

Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference

Genome biology(2024)10.1186/s13059-023-03134-1

N/A

0DataRank · unranked

8 citations

Maggie Beheler-Amass, Christopher A. Jackson, Lionel Christiaen, David Gresham, Richard Bonneau +1 more

A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV

Cell Reports(2020)10.1016/j.celrep.2019.12.054

N/A

0DataRank · unranked

29 citations

Nicholas De Veaux, Alexander Rives, Xavier Lahaye, Sasha Lucas, Brieuc P. Pérot +11 more

Supercharged Phosphotriesterase for improved Paraoxon activity

Protein Engineering Design and Selection(2024)10.1093/protein/gzae015

N/A

0DataRank · unranked

2 citations

Dustin Britton, Leif Halvorsen, Stanley Chu, Maria Jinu Kulapurathazhe, Jason N. Chen +5 more

Correction to “Computational Prediction of Coiled–Coil Protein Gelation Dynamics and Structure”

Biomacromolecules(2024)10.1021/acs.biomac.4c00448

N/A

0DataRank · unranked

0 citations

Luc F. Christians, Chengliang Liu, Jakub Legocki, Yingxin Xiao, Michael Meleties +12 more

Computational Design of Phosphotriesterase Improves V‐Agent Degradation Efficiency

ChemistryOpen(2024)10.1002/open.202300263

N/A

0DataRank · unranked

4 citations

Stanley Chu, Andrew J. Olsen, Dustin Britton, Leif Halvorsen, Shengbo Guo +12 more

OutPredict: multiple datasets can improve prediction of expression and inference of causality

Scientific Reports(2020)10.1038/s41598-020-63347-3

N/A

0DataRank · unranked

21 citations

Matthew D. Brooks, Richard Bonneau, Gloria M. Coruzzi, Dennis Shasha, Jacopo Cirrone

Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks

mSystems(2020)10.1128/msystems.00057-20

N/A

0DataRank · unranked

20 citations

Christoph Hafemeister, Bentley Shuster, Nitin S. Baliga, Richard Bonneau, Patrick Eichenberger +1 more

Better together: Elements of successful scientific software development in a distributed collaborative community

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007507

N/A

0DataRank · unranked

44 citations

Brian D. Weitzner, P. Douglas Renfrew, Steven M. Lewis, Rocco Moretti, Andrew M. Watkins +20 more

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.28.970202

N/A

0DataRank · unranked

8 citations

Omar Mahmood, Christopher A. Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel Christiaen +2 more

Twitter activity about treatments during the COVID-19 pandemic: case studies of remdesivir, hydroxychloroquine, and convalescent plasma

medRxiv(2020)10.1101/2020.06.18.20134668

N/A

0DataRank · unranked

5 citations

Richard Bonneau, Tymor Hamamsy

Author Correction: OutPredict: multiple datasets can improve prediction of expression and inference of causality

Scientific Reports(2020)10.1038/s41598-020-69883-2

N/A

0DataRank · unranked

1 citations

Matthew D. Brooks, Richard Bonneau, Gloria M. Coruzzi, Dennis Shasha, Jacopo Cirrone

CRISPR-Decryptr reveals cis-regulatory elements from noncoding perturbation screens

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.13.247007

N/A

0DataRank · unranked

0 citations

Tarmo Äijö, Mariano I. Gabitto, Nicholas Carriero, Neville E. Sanjana, Jane A. Skok +2 more

Inferring causal molecular networks: empirical assessment through a community-based effort

UNC Libraries(2020)10.17615/j5nb-5n89

N/A

0DataRank · unranked

0 citations

Steven M. Hill, Daoud Meerzaman, Venkateshan Kannan, Bahman Afsari, Takeshi Hase +95 more

Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)

UNC Libraries(2020)10.17615/7c93-y342

N/A

0DataRank · unranked

0 citations

Tanja Kortemme, Benjamin Borgo, James J. Havranek, Fang‐Chieh Chou, Bryan S. Der +12 more

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

UNC Libraries(2020)10.17615/6sk2-v510

N/A

0DataRank · unranked

0 citations

Matthew J. O’Meara, Philip Bradley, Maxim V. Shapovalov, Rhiju Das, Hahnbeom Park +15 more

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

UNC Libraries(2020)10.17615/xrww-m716

N/A

0DataRank · unranked

0 citations

Brooke N. Bullock, Richard Bonneau, Paramjit S. Arora, Kent Kirshenbaum, Timothy W. Craven +14 more

Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design

UNC Libraries(2020)10.17615/0jkp-vh25

N/A

0DataRank · unranked

0 citations

Brian Kuhlman, Eun Jung Choi, P.D. Renfrew, Richard Bonneau

Richard Bonneau

Indexed papers

Top data-sharing exemplar

Papers