Richard Bonneau

发表

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

Kyunghyun Cho, Ren Yi, Richard Bonneau, 2022, Bioinformatics.

EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

Nathan C Frey, A. Regev, Payman Yadollahpour, 2022, bioRxiv.

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

Kyunghyun Cho, Ren Yi, Richard Bonneau, 2021, bioRxiv.

A Pareto-optimal compositional energy-based model for sampling and optimization of protein sequences

Ryan L Kelly, Nathan C Frey, Ryan L. Kelly, 2022, ArXiv.

OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

Brian D. Weitzner, Marta M. Stepniewska-Dziubinska, Stella Rose Biderman, 2022, bioRxiv.

PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design

Saeed Saremi, A. Watkins, V. Gligorijević, 2022, ArXiv.

OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

Brian D. Weitzner, Marta M. Stepniewska-Dziubinska, Stella Rose Biderman, 2022, bioRxiv.

Probabilistic Matrix Factorization for Gene Regulatory Network Inference

Kyunghyun Cho, Kyunghyun Cho, Claudia Skok Gibbs, 2022 .

EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

Nathan C Frey, A. Regev, Payman Yadollahpour, 2023, bioRxiv.

Function-guided protein design by deep manifold sampling

A. Watkins, V. Gligorijević, Daniel Berenberg, 2021, bioRxiv.

Multi-segment preserving sampling for deep manifold sampler

Ji Won Park, A. Watkins, Daniel Berenberg, 2022, ArXiv.

Protein Discovery with Discrete Walk-Jump Sampling

Nathan C Frey, Andreas Loukas, Y. Wu, 2023, 2306.12360.

OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

Brian D. Weitzner, Marta M. Stepniewska-Dziubinska, Stella Rose Biderman, 2023, bioRxiv.

OpenProteinSet: Training data for structural biology at scale

Daniel Berenberg, Ian Fisk, Mohammed AlQuraishi, 2023, NeurIPS.

AbDiffuser: Full-Atom Generation of In-Vitro Functioning Antibodies

Andreas Loukas, Y. Wu, V. Gligorijević, 2023, NeurIPS.

A Variational Inference Approach to Single-Cell Gene Regulatory Network Inference using Probabilistic Matrix Factorization

Kyunghyun Cho, O. Mahmood, Richard Bonneau, 2023, bioRxiv.

Protein remote homology detection and structural alignment using deep learning

Kyunghyun Cho, V. Gligorijević, Daniel Berenberg, 2023, Nature biotechnology.

Predicting recognition between T cell receptors and epitopes using contextualized motifs

H. Lähdesmäki, S. Mustjoki, Markus Heinonen, 2022, bioRxiv.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Tapio Salakoski, Paolo Fontana, Silvio C. E. Tosatto, 2016, Genome Biology.

Learning accurate representations of microbe-metabolite 1 interactions

James R. Foulds, Y. Vázquez-Baeza, A. Watters, 2019 .