Richard Bonneau

54 papers A* 5A 1C 1Misc 2Journal 42Unranked 2

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins. CoRR Frédéric A. Dreyer, Jan Ludwiczak, Karolis Martinkus, Brennan Abanades, Robert G. Alberstein, Pan Kessel, Pranav Rao, Jae Hyeon Lee, Richard Bonneau, Andrew M. Watkins, Franziska Seeger
2025	A*	`conf`	Generalists vs. Specialists: Evaluating LLMs on Highly-Constrained Biophysical Sequence Optimization Tasks. ICML Angelica Chen, Samuel Don Stanton, Frances Ding, Robert G. Alberstein, Andrew Martin Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey
2025	J	`jnl`	Pharmacophore-based design by learning on voxel grids. CoRR Omar Mahmood, Pedro O. Pinheiro, Richard Bonneau, Saeed Saremi, Vishnu Sresht
2025	J	`jnl`	Tokenized and continuous embedding compressions of protein sequence and structure. Patterns Amy X. Lu, Wilson Yan, Kevin K. Yang, Vladimir Gligorijevic, Kyunghyun Cho, Pieter Abbeel, Richard Bonneau, Nathan C. Frey
2025	J	`jnl`	Unified all-atom molecule generation with neural fields. CoRR Matthieu Kirchmeyer, Pedro O. Pinheiro, Emma Willett, Karolis Martinkus, Joseph Kleinhenz, Emily K. Makowski, Andrew M. Watkins, Vladimir Gligorijevic, Richard Bonneau, Saeed Saremi
2025	J	`jnl`	deepNGS navigator: exploring antibody NGS datasets using deep contrastive learning. Bioinform. Homa Mohammadi Peyhani, Edith Lee, Richard Bonneau, Vladimir Gligorijevic, Jae Hyeon Lee
2024	J	`jnl`	LLMs are Highly-Constrained Biophysical Sequence Optimizers. CoRR Angelica Chen, Samuel Don Stanton, Robert G. Alberstein, Andrew M. Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey
2024	A*	`conf`	Protein Discovery with Discrete Walk-Jump Sampling. ICLR Nathan C. Frey, Daniel Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hötzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi
2023	J	`jnl`	AbDiffuser: Full-Atom Generation of In-Vitro Functioning Antibodies. CoRR Karolis Martinkus, Jan Ludwiczak, Kyunghyun Cho, Wei-Ching Liang, Julien Lafrance-Vanasse, Isidro Hötzel, Arvind Rajpal, Yan Wu, Richard Bonneau, Vladimir Gligorijevic, Andreas Loukas
2023	A*	`conf`	AbDiffuser: full-atom generation of in-vitro functioning antibodies. NeurIPS Karolis Martinkus, Jan Ludwiczak, Wei-Ching Liang, Julien Lafrance-Vanasse, Isidro Hötzel, Arvind Rajpal, Yan Wu, Kyunghyun Cho, Richard Bonneau, Vladimir Gligorijevic, Andreas Loukas
2023	A	`conf`	Measuring the Ideology of Audiences for Web Links and Domains Using Differentially Private Engagement Data. ICWSM Cody Buntain, Richard Bonneau, Jonathan Nagler, Joshua A. Tucker
2023	A*	`conf`	OpenProteinSet: Training data for structural biology at scale. NeurIPS Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
2023	J	`jnl`	OpenProteinSet: Training data for structural biology at scale. CoRR Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
2023	J	`jnl`	Protein Discovery with Discrete Walk-Jump Sampling. CoRR Nathan C. Frey, Daniel Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hötzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi
2023	J	`jnl`	TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs. Bioinform. Emmi Jokinen, Alexandru Dumitrescu, Jani Huuhtanen, Vladimir Gligorijevic, Satu Mustjoki, Richard Bonneau, Markus Heinonen, Harri Lähdesmäki
2022	J	`jnl`	A Pareto-optimal compositional energy-based model for sampling and optimization of protein sequences. CoRR Natasa Tagasovska, Nathan C. Frey, Andreas Loukas, Isidro Hötzel, Julien Lafrance-Vanasse, Ryan Lewis Kelly, Yan Wu, Arvind Rajpal, Richard Bonneau, Kyunghyun Cho, Stephen Ra, Vladimir Gligorijevic
2022	A*	`conf`	Dictionary-Assisted Supervised Contrastive Learning. EMNLP Patrick Y. Wu, Richard Bonneau, Joshua A. Tucker, Jonathan Nagler
2022	J	`jnl`	Dictionary-Assisted Supervised Contrastive Learning. CoRR Patrick Y. Wu, Richard Bonneau, Joshua A. Tucker, Jonathan Nagler
2022	J	`jnl`	High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0. Bioinform. Claudia Skok Gibbs, Christopher A. Jackson, Giuseppe-Antonio Saldi, Andreas Tjärnberg, Aashna Shah, Aaron Watters, Nicholas De Veaux, Konstantine Tchourine, Ren Yi, Tymor Hamamsy, Dayanne M. Castro, Nicholas Carriero, Bram L. Gorissen, David Gresham, Emily R. Miraldi, Richard Bonneau
2022	J	`jnl`	Multi-segment preserving sampling for deep manifold sampler. CoRR Daniel Berenberg, Jae Hyeon Lee, Simon Kelow, Ji Won Park, Andrew M. Watkins, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho
2022	J	`jnl`	NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction. Bioinform. Ren Yi, Kyunghyun Cho, Richard Bonneau
2022	J	`jnl`	PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design. CoRR Ji Won Park, Samuel Stanton, Saeed Saremi, Andrew M. Watkins, Henri Dwyer, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho
2021	J	`jnl`	A convolutional neural network for common coordinate registration of high-resolution histology images. Bioinform. Aidan C. Daly, Krzysztof J. Geras, Richard Bonneau
2021	—	`conf`	An Automatic Framework to Continuously Monitor Multi-Platform Information Spread. MISINFO@WWW Zhouhan Chen, Kevin Aslett, Jen Rosiere Reynolds, Juliana Freire, Jonathan Nagler, Joshua A. Tucker, Richard Bonneau
2021	J	`jnl`	Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLoS Comput. Biol. Matthew R. Dillon, Evan Bolyen, Anja Adamov, Aeriel Belk, Emily Borsom, Zachary Burcham, Justine W. Debelius, Heather Deel, Alex Emmons, Mehrbod Estaki, Chloe Herman, Christopher R. Keefe, Jamie T. Morton, Renato R. M. Oliveira, Andrew Sanchez, Anthony Simard, Yoshiki Vazquez-Baeza, Michal Ziemski, Hazuki E. Miwa, Terry A. Kerere, Carline Coote, Richard Bonneau, Rob Knight, Guilherme Oliveira, Piraveen Gopalasingam, Benjamin D. Kaehler, Emily K. Cope, Jessica L. Metcalf, Michael S. Robeson II, Nicholas A. Bokulich, J. Gregory Caporaso
2021	J	`jnl`	NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity. Bioinform. Meet Barot, Vladimir Gligorijevic, Kyunghyun Cho, Richard Bonneau
2021	J	`jnl`	YouTube Recommendations and Effects on Sharing Across Online Social Platforms. Proc. ACM Hum. Comput. Interact. Cody Buntain, Richard Bonneau, Jonathan Nagler, Joshua A. Tucker
2020	J	`jnl`	Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput. Biol. Julia Koehler Leman, Brian D. Weitzner, P. Douglas Renfrew, Steven M. Lewis, Rocco Moretti, Andrew M. Watkins, Vikram Khipple Mulligan, Sergey Lyskov, Jared Adolf-Bryfogle, Jason W. Labonte, Justyna Krys, RosettaCommons Consortium, Christopher Bystroff, William R. Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland L. Dunbrack Jr., Tanja Kortemme, Andrew Leaver-Fay, Charlie E. M. Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J. Gray, Richard Bonneau
2020	J	`jnl`	YouTube Recommendations and Effects on Sharing Across Online Social Platforms. CoRR Cody Buntain, Richard Bonneau, Jonathan Nagler, Joshua A. Tucker
2019	J	`jnl`	Multi-study inference of regulatory networks for more accurate models of gene regulation. PLoS Comput. Biol. Dayanne M. Castro, Nicholas R. de Veaux, Emily R. Miraldi, Richard Bonneau
2019	J	`jnl`	Towards region-specific propagation of protein functions. Bioinform. Da Chen Emily Koo, Richard Bonneau
2018	J	`jnl`	Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. Bioinform. Tarmo Äijö, Christian L. Müller, Richard Bonneau
2018	J	`jnl`	deepNF: deep network fusion for protein function prediction. Bioinform. Vladimir Gligorijevic, Meet Barot, Richard Bonneau
2017	J	`jnl`	Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP. BMC Bioinform. Julia Koehler Leman, Sergey Lyskov, Richard Bonneau
2017	J	`jnl`	Detecting Bots on Russian Political Twitter. Big Data Denis Stukal, Sergey Sanovich, Richard Bonneau, Joshua A. Tucker
2017	J	`jnl`	Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. PLoS Comput. Biol. Kevin Drew, Christian L. Müller, Richard Bonneau, Edward M. Marcotte
2016	J	`jnl`	4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. PLoS Comput. Biol. Ramya Raviram, Pedro P. Rocha, Christian L. Müller, Emily R. Miraldi, Sana Badri, Yi Fu, Emily Swanzey, Charlotte Proudhon, Valentina Snetkova, Richard Bonneau, Jane A. Skok
2016	J	`jnl`	Accurate Nat. Gaurav Bhardwaj, Vikram Khipple Mulligan, Christopher D. Bahl, Jason M. Gilmore, Peta J. Harvey, Olivier Cheneval, Garry W. Buchko, Surya V. S. R. K. Pulavarti, Quentin Kaas, Alexander Eletsky, Po-Ssu Huang, William A. Johnsen, Per Greisen, Gabriel J. Rocklin, Yifan Song, Thomas W. Linsky, Andrew M. Watkins, Stephen A. Rettie, Xianzhong Xu, Lauren P. Carter, Richard Bonneau, James M. Olson, Evangelos A. Coutsias, Colin E. Correnti, Thomas Szyperski, David J. Craik, David Baker
2016	—	`ch.`	Big Data, Social Media, and Protest: Foundations for a Research Agenda. Computational Social Science Joshua A. Tucker, Jonathan Nagler, Megan Macduffee Metzger, Pablo Barberá, Duncan Penfold-Brown, Richard Bonneau
2016	J	`jnl`	Fused Regression for Multi-source Gene Regulatory Network Inference. PLoS Comput. Biol. Kari Y. Lam, Zachary M. Westrick, Christian L. Müller, Lionel A. Christiaen, Richard Bonneau
2016	Misc	`conf`	Text Classification for Automatic Detection of E-Cigarette Use and Use for Smoking Cessation from Twitter: A Feasibility Pilot. PSB Yin Aphinyanaphongs, Armine Lulejian, Duncan Penfold-Brown, Richard Bonneau, Paul Krebs
2015	J	`jnl`	Inter-species pathway perturbation prediction via data-driven detection of functional homology. Bioinform. Christoph Hafemeister, Roberto Romero, Erhan Bilal, Pablo Meyer, Raquel Norel, Kahn Rhrissorrakrai, Richard Bonneau, Adi L. Tarca
2015	J	`jnl`	Political Expression and Action on Social Media: Exploring the Relationship Between Lower- and Higher-Threshold Political Activities Among Twitter Users in Italy. J. Comput. Mediat. Commun. Cristian Vaccari, Augusto Valeriani, Pablo Barberá, Richard Bonneau, John T. Jost, Jonathan Nagler, Joshua A. Tucker
2015	—	`conf`	Positive-Unlabeled Learning in the Face of Labeling Bias. ICDM Workshops Noah Youngs, Dennis E. Shasha, Richard Bonneau
2014	J	`jnl`	Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks. IEEE Trans. Vis. Comput. Graph. Bowen Yu, Harish Doraiswamy, Xi Chen, Emily R. Miraldi, Mario Luis Arrieta-Ortiz, Christoph Hafemeister, Aviv Madar, Richard Bonneau, Cláudio T. Silva
2014	J	`jnl`	Negative Example Selection for Protein Function Prediction: The NoGO Database. PLoS Comput. Biol. Noah Youngs, Duncan Penfold-Brown, Richard Bonneau, Dennis E. Shasha
2013	J	`jnl`	Parametric Bayesian priors and better choice of negative examples improve protein function prediction. Bioinform. Noah Youngs, Duncan Penfold-Brown, Kevin Drew, Dennis E. Shasha, Richard Bonneau
2013	J	`jnl`	Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. Bioinform. Alex Greenfield, Christoph Hafemeister, Richard Bonneau
2012	Misc	`conf`	Session introduction. Pacific Symposium on Biocomputing Jason E. McDermott, Pascal Braun, Richard Bonneau, Daniel R. Hyduke
2011	J	`jnl`	Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters. PLoS Comput. Biol. Thadeous Kacmarczyk, Peter Waltman, Ashley Bate, Patrick Eichenberger, Richard Bonneau
2008	C	`conf`	Modeling gene regulation and spatial organization of sequence based motifs. BIBE Jochen Supper, Claas aufm Kampe, Dierk Wanke, Kenneth W. Berendzen, Klaus Harter, Richard Bonneau, Andreas Zell
2007	J	`jnl`	BioNetBuilder: automatic integration of biological networks. Bioinform. Iliana Avila-Campillo, Kevin Drew, John Lin, David J. Reiss, Richard Bonneau
2006	J	`jnl`	Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinform. David J. Reiss, Nitin S. Baliga, Richard Bonneau
2006	J	`jnl`	The Gaggle: An open-source software system for integrating bioinformatics software and data sources. BMC Bioinform. Paul T. Shannon, David J. Reiss, Richard Bonneau, Nitin S. Baliga