RB
Richard Bonneau
bioinformaticsSoftwareGene Regulatory NetworksAlgorithmssystems biologyModels, Molecularcs.LGgenomicsModels, BiologicalModels, Genetic
On Valency
published · living versionsW_fwzmgj9y·v1 · currentpublished
iGC: Antibody Optimization via Reinforcement Learning over a Learned Somatic Hypermutation Prior
with Thao Nguyen, Robert G. Alberstein, Ewa Nowara, Homa MohammadiPeyhani +8
1 version
Preprints & journals
280 papers in the corpus · 1983–2026MIMOSA: Guiding De Novo Antibody Design with Natural Interaction Fingerprints10.64898/2026.09.24.753155v1 · Abanades, B., Roncoli, A., Bhagawati, M. et al.2026 · 0 citationsbioRxiv
GLM-Prior: a genomic language model for transferable sequence-derived priors in gene regulatory network inference.42791261 · Skok Gibbs, Claudia, Chen, Angelica, Bonneau, Richard et al.2026 · 0 citationsNature communications. 2026;17(1)
DyAb: sequence-based antibody design and property prediction in a low-data regime.42665538 · Lin, Joshua Yao-Yu, Hofmann, Jennifer L, Leaver-Fay, Andrew et al.2026 · 2 citationsmAbs. 2026;18(1):2717460
Moving from Association to Causation: Instrumental factor models for causal inference in high-dimensional multi-omics data10.64898/2025.12.26.696613v1 · Mishra, A. K., Badri, M., Coler, E. A. et al.2025 · 0 citationsbioRxiv
Conformation-aware structure prediction of antigen-recognizing immune proteins.41378904 · Dreyer, Frédéric A, Ludwiczak, Jan, Martinkus, Karolis et al.2025 · 4 citationsmAbs. 2026;18(1):2602217
Unified all-atom molecule generation with neural fields2511.15906v1 · Matthieu Kirchmeyer, Pedro O. Pinheiro, Emma Willett et al.2025 · 0 citationsarXiv
Pharmacophore-based design by learning on voxel grids2512.02031v1 · Omar Mahmood, Pedro O. Pinheiro, Richard Bonneau et al.2025 · 0 citationsarXiv
CDR Conformation Aware Antibody Sequence Design with ConformAb10.1101/2025.11.12.688095v1 · Sinha, I., Stanton, S., Lillington, S. et al.2025 · 1 citationbioRxiv
PlasmoFP: leveraging deep learning to predict protein function of uncharacterized proteins across the malaria parasite genus.41279499 · Srivastava, Harsh R, Berenberg, Daniel, Qassab, Omar et al.2025 · 1 citationbioRxiv : the preprint server for biology. 2025
Property Enhancer - a data efficient multi-objective approach for functional antibody optimization10.1101/2025.10.08.681101v1 · Tagasovska, N., Ludwiczak, J., Loukas, A. et al.2025 · 0 citationsbioRxiv
A Validated Regulatory Network for Th17 Cell Specification.40992377 · Ciofani, Maria, Madar, Aviv, Galan, Carolina et al.2025 · 0 citationsCell. 2025;188(21):6096
Dynamic Gene Regulatory Network Inference with Interpretable, Biophysically-Motivated Neural ODEs10.1101/2025.09.19.676870v1 · Beheler-Amass, M., Jackson, C. A., Gresham, D. et al.2025 · 3 citationsbioRxiv
deepNGS navigator: exploring antibody NGS datasets using deep contrastive learning.40796135 · MohammadiPeyhani, Homa, Lee, Edith, Bonneau, Richard et al.2025 · 1 citationBioinformatics (Oxford, England). 2025;41(9)
Deep Evolutionary Fitness Inference for Variant Nomination from Directed Evolution10.1101/2025.07.22.666175v1 · Shen, M. W., Diamant, N., Helmling, C. et al.2025 · 0 citationsbioRxiv
Comparative genomics of the parasite Trichomonas vaginalis reveals genes involved in spillover from birds to humans.40707449 · Sullivan, Steven A, Orosco, Jordan C, Callejas-Hernández, Francisco et al.2025 · 5 citationsNature communications. 2025;16(1):6487
Distinct Cellular Phenotypes of Language and Executive Decline in Amyotrophic Lateral Sclerosis.40060539 · Petrescu, Joana, Roque, Cláudio Gouveia, Jackson, Christopher A et al.2026 · 4 citationsbioRxiv : the preprint server for biology. 2025
Tokenized and continuous embedding compressions of protein sequence and structure.40575127 · Lu, Amy X, Yan, Wilson, Yang, Kevin K et al.2025 · 13 citationsPatterns (New York, N.Y.). 2025;6(6):101289
Genome-wide expression gradient estimation based on local pseudotime in single cell RNA sequencing10.1101/2025.05.01.650773v1 · Tjaernberg, A., Jackson, C., Bonneau, R. et al.2025 · 0 citationsbioRxiv
Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans.39763951 · Sullivan, Steven A, Orosco, Jordan C, Callejas-Hernández, Francisco et al.2025 · 2 citationsbioRxiv : the preprint server for biology. 2024
Controllable All-Atom Protein Generation with Latent Diffusion10.1101/2024.12.02.626353v3 · Lu, A. X., Yan, W., Robinson, S. A. et al.2024 · 5 citationsbioRxiv
Measuring receptivity to misinformation at scale on a social media platform.39381645 · Tokita, Christopher K, Aslett, Kevin, Godel, William P et al.2026 · 10 citationsPNAS nexus. 2024;3(10):pgae396
Cramming Protein Language Model Training in 24 GPU Hours10.1101/2024.05.14.594108v1 · Frey, N. C., Joren, T., Ismail, A. et al.2024 · 3 citationsbioRxiv
OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.38744917 · Ahdritz, Gustaf, Bouatta, Nazim, Floristean, Christina et al.2024 · 439 citationsNature methods. 2024;21(8):1514-1524
Tissue and cellular spatiotemporal dynamics in colon aging.38712088 · Daly, Aidan C, Cambuli, Francesco, Äijö, Tarmo et al.2025 · 10 citationsbioRxiv : the preprint server for biology. 2024
Correction to "Computational Prediction of Coiled-Coil Protein Gelation Dynamics and Structure".38630987 · Britton, Dustin, Christians, Luc F, Liu, Chengliang et al.2024 · 0 citationsBiomacromolecules. 2024;25(5):3214
PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization.38589899 · Skok Gibbs, Claudia, Mahmood, Omar, Bonneau, Richard et al.2024 · 18 citationsGenome biology. 2024;25(1):88
Computational Design of Phosphotriesterase Improves V-Agent Degradation Efficiency.38426687 · Kronenberg, Jacob, Chu, Stanley, Olsen, Andrew et al.2024 · 4 citationsChemistryOpen. 2024;13(7):e202300263
Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases.38464323 · Jin, Dong-Min, Morton, James T, Bonneau, Richard2026 · 22 citationsbioRxiv : the preprint server for biology. 2024
Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop.38295882 · Bunyavanich, Supinda, Becker, Patrice M, Altman, Matthew C et al.2024 · 20 citationsThe Journal of allergy and clinical immunology. 2024;153(4):954-968
Supercharged Phosphotriesterase for improved Paraoxon activity.39292622 · Kronenberg, Jacob, Britton, Dustin, Halvorsen, Leif et al.2025 · 2 citationsProtein engineering, design & selection : PEDS. 2024;37
Computational Prediction of Coiled-Coil Protein Gelation Dynamics and Structure.38110299 · Britton, Dustin, Christians, Luc F, Liu, Chengliang et al.2024 · 18 citationsBiomacromolecules. 2024;25(1):258-271
Learning sequence, structure, and function representations of proteins with language models.38045331 · Hamamsy, Tymor, Barot, Meet, Morton, James T et al.2023 · 10 citationsbioRxiv : the preprint server for biology. 2023
Protein-Engineered Fibers For Drug Encapsulation Traceable via 19F Magnetic Resonance.38037605 · Britton, Dustin, Legocki, Jakub, Aristizabal, Orlando et al.2024 · 6 citationsACS applied nano materials. 2023;6(22):21245-21257
Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression.37790443 · Jackson, Christopher A, Beheler-Amass, Maggie, Tjärnberg, Andreas et al.2024 · 3 citationsbioRxiv : the preprint server for biology. 2023
Protein remote homology detection and structural alignment using deep learning.37679542 · Hamamsy, Tymor, Morton, James T, Blackwell, Robert et al.2024 · 144 citationsNature biotechnology. 2024;42(6):975-985
OpenProteinSet: Training data for structural biology at scale2308.05326v1 · Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan et al.2023 · 20 citationsarXiv
OpenProteinSet: Training data for structural biology at scale.37608940 · Ahdritz, Gustaf, Bouatta, Nazim, Kadyan, Sachin et al.2024 · 20 citationsArXiv. 2023
AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies2308.05027v2 · Karolis Martinkus, Jan Ludwiczak, Kyunghyun Cho et al.2023 · 24 citationsarXiv
Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles.37365313 · Morton, James T, Jin, Dong-Min, Mills, Robert H et al.2023 · 224 citationsNature neuroscience. 2023;26(7):1208-1217
CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection.37330554 · Zhang, Lingdi, Rahman, Jahan, Chung, Matthew et al.2023 · 6 citationsMicrobiome. 2023;11(1):136
Protein Discovery with Discrete Walk-Jump Sampling2306.12360v2 · Nathan C. Frey, Daniel Berenberg, Karina Zadorozhny et al.2023 · 5 citationsThe Twelfth International Conference on Learning Representations, 2024
Sequence-structure-function relationships in the microbial protein universe.37100781 · Koehler Leman, Julia, Szczerbiak, Pawel, Renfrew, P Douglas et al.2023 · 105 citationsNature communications. 2023;14(1):2351
Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method.37010293 · Maranga, Mary, Szczerbiak, Pawel, Bezshapkin, Valentyn et al.2023 · 52 citationsmSystems. 2023;8(2):e0117822
Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference.36778259 · Tjärnberg, Andreas, Beheler-Amass, Maggie, Jackson, Christopher A et al.2024 · 10 citationsbioRxiv : the preprint server for biology. 2023
Fluorescent azobenzene-confined coiled-coil mesofibers.36538008 · Punia, Kamia, Britton, Dustin, Hüll, Katharina et al.2023 · 6 citationsSoft matter. 2023;19(3):497-501
Exposure to the Russian Internet Research Agency foreign influence campaign on Twitter in the 2016 US election and its relationship to attitudes and voting behavior.36624094 · Eady, Gregory, Paskhalis, Tom, Zilinsky, Jan et al.2023 · 125 citationsNature communications. 2023;14(1):62
TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs.36477794 · Jokinen, Emmi, Dumitrescu, Alexandru, Huuhtanen, Jani et al.2023 · 30 citationsBioinformatics (Oxford, England). 2023;39(1)
Specificities of Modeling of Membrane Proteins Using Multi-Template Homology Modeling.36959446 · Koehler Leman, Julia, Bonneau, Richard2023 · 3 citationsMethods in molecular biology (Clifton, N.J.). 2023;2627:141-166
Coordinated control of neuronal differentiation and wiring by sustained transcription factors.36480601 · Özel, Mehmet Neset, Gibbs, Claudia Skok, Holguera, Isabel et al.2023 · 57 citationsScience (New York, N.Y.). 2022;378(6626):eadd1884
Alterations in the cutaneous microbiome of patients with psoriasis and psoriatic arthritis reveal similarities between non-lesional and lesional skin.36600182 · Boix-Amorós, Alba, Badri, Michelle H, Manasson, Julia et al.2023 · 50 citationsAnnals of the rheumatic diseases. 2023;82(4):507-514
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