Richard Bonneau

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 32

Top Topics

Conditional Dependence

Protein Function

Probabilistic Modeling

Top Venues

PLoS Comput. Biol.

Publications

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
Protein Discovery with Discrete Walk-Jump Sampling. ICLR (2024)
Karolis Martinkus, Jan Ludwiczak, Kyunghyun Cho, Wei-Ching Liang, Julien Lafrance-Vanasse, Isidro Hötzel, Arvind Rajpal, Yan Wu, Richard Bonneau, Vladimir Gligorijevic, Andreas Loukas
AbDiffuser: Full-Atom Generation of In-Vitro Functioning Antibodies. CoRR (2023)
Karolis Martinkus, Jan Ludwiczak, Wei-Ching Liang, Julien Lafrance-Vanasse, Isidro Hötzel, Arvind Rajpal, Yan Wu, Kyunghyun Cho, Richard Bonneau, Vladimir Gligorijevic, Andreas Loukas
AbDiffuser: full-atom generation of in-vitro functioning antibodies. NeurIPS (2023)
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
Protein Discovery with Discrete Walk-Jump Sampling. CoRR (2023)
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
OpenProteinSet: Training data for structural biology at scale. CoRR (2023)
Cody Buntain, Richard Bonneau, Jonathan Nagler, Joshua A. Tucker
Measuring the Ideology of Audiences for Web Links and Domains Using Differentially Private Engagement Data. ICWSM (2023)
Emmi Jokinen, Alexandru Dumitrescu, Jani Huuhtanen, Vladimir Gligorijevic, Satu Mustjoki, Richard Bonneau, Markus Heinonen, Harri Lähdesmäki
TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs. Bioinform. 39 (1) (2023)
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
OpenProteinSet: Training data for structural biology at scale. NeurIPS (2023)
Ji Won Park, Samuel Stanton, Saeed Saremi, Andrew M. Watkins, Henri Dwyer, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho
PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design. CoRR (2022)
Ren Yi, Kyunghyun Cho, Richard Bonneau
NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction. Bioinform. 38 (20) (2022)
Patrick Y. Wu, Richard Bonneau, Joshua A. Tucker, Jonathan Nagler
Dictionary-Assisted Supervised Contrastive Learning. CoRR (2022)
Patrick Y. Wu, Richard Bonneau, Joshua A. Tucker, Jonathan Nagler
Dictionary-Assisted Supervised Contrastive Learning. EMNLP (2022)
Daniel Berenberg, Jae Hyeon Lee, Simon Kelow, Ji Won Park, Andrew M. Watkins, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho
Multi-segment preserving sampling for deep manifold sampler. CoRR (2022)
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
A Pareto-optimal compositional energy-based model for sampling and optimization of protein sequences. CoRR (2022)
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
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLoS Comput. Biol. 17 (6) (2021)
Aidan C. Daly, Krzysztof J. Geras, Richard Bonneau
A convolutional neural network for common coordinate registration of high-resolution histology images. Bioinform. 37 (22) (2021)
Cody Buntain, Richard Bonneau, Jonathan Nagler, Joshua A. Tucker
YouTube Recommendations and Effects on Sharing Across Online Social Platforms. Proc. ACM Hum. Comput. Interact. 5 (CSCW1) (2021)
Zhouhan Chen, Kevin Aslett, Jen Rosiere Reynolds, Juliana Freire, Jonathan Nagler, Joshua A. Tucker, Richard Bonneau
An Automatic Framework to Continuously Monitor Multi-Platform Information Spread. MISINFO@WWW (2021)
Meet Barot, Vladimir Gligorijevic, Kyunghyun Cho, Richard Bonneau
NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity. Bioinform. 37 (16) (2021)
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
Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput. Biol. 16 (5) (2020)
Cody Buntain, Richard Bonneau, Jonathan Nagler, Joshua A. Tucker
YouTube Recommendations and Effects on Sharing Across Online Social Platforms. CoRR (2020)
Da Chen Emily Koo, Richard Bonneau
Towards region-specific propagation of protein functions. Bioinform. 35 (10) (2019)
Dayanne M. Castro, Nicholas R. de Veaux, Emily R. Miraldi, Richard Bonneau
Multi-study inference of regulatory networks for more accurate models of gene regulation. PLoS Comput. Biol. 15 (1) (2019)
Vladimir Gligorijevic, Meet Barot, Richard Bonneau
deepNF: deep network fusion for protein function prediction. Bioinform. 34 (22) (2018)
Tarmo Äijö, Christian L. Müller, Richard Bonneau
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. Bioinform. 34 (3) (2018)
Kevin Drew, Christian L. Müller, Richard Bonneau, Edward M. Marcotte
Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. PLoS Comput. Biol. 13 (10) (2017)
Denis Stukal, Sergey Sanovich, Richard Bonneau, Joshua A. Tucker
Detecting Bots on Russian Political Twitter. Big Data 5 (4) (2017)
Julia Koehler Leman, Sergey Lyskov, Richard Bonneau
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP. BMC Bioinform. 18 (1) (2017)
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
design of hyperstable constrained peptides. Nat. 538 (7625) (2016)
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
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. PLoS Comput. Biol. 12 (3) (2016)
Yin Aphinyanaphongs, Armine Lulejian, Duncan Penfold-Brown, Richard Bonneau, Paul Krebs
Text Classification for Automatic Detection of E-Cigarette Use and Use for Smoking Cessation from Twitter: A Feasibility Pilot. PSB (2016)
Kari Y. Lam, Zachary M. Westrick, Christian L. Müller, Lionel A. Christiaen, Richard Bonneau
Fused Regression for Multi-source Gene Regulatory Network Inference. PLoS Comput. Biol. 12 (12) (2016)
Cristian Vaccari, Augusto Valeriani, Pablo Barberá, Richard Bonneau, John T. Jost, Jonathan Nagler, Joshua A. Tucker
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. 20 (2) (2015)
Noah Youngs, Dennis E. Shasha, Richard Bonneau
Positive-Unlabeled Learning in the Face of Labeling Bias. ICDM Workshops (2015)
Christoph Hafemeister, Roberto Romero, Erhan Bilal, Pablo Meyer, Raquel Norel, Kahn Rhrissorrakrai, Richard Bonneau, Adi L. Tarca
Inter-species pathway perturbation prediction via data-driven detection of functional homology. Bioinform. 31 (4) (2015)
Noah Youngs, Duncan Penfold-Brown, Richard Bonneau, Dennis E. Shasha
Negative Example Selection for Protein Function Prediction: The NoGO Database. PLoS Comput. Biol. 10 (6) (2014)
Bowen Yu, Harish Doraiswamy, Xi Chen, Emily R. Miraldi, Mario Luis Arrieta-Ortiz, Christoph Hafemeister, Aviv Madar, Richard Bonneau, Cláudio T. Silva
Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks. IEEE Trans. Vis. Comput. Graph. 20 (12) (2014)
Noah Youngs, Duncan Penfold-Brown, Kevin Drew, Dennis E. Shasha, Richard Bonneau
Parametric Bayesian priors and better choice of negative examples improve protein function prediction. Bioinform. 29 (9) (2013)
Alex Greenfield, Christoph Hafemeister, Richard Bonneau
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. Bioinform. 29 (8) (2013)
Jason E. McDermott, Pascal Braun, Richard Bonneau, Daniel R. Hyduke
Session introduction. Pacific Symposium on Biocomputing (2012)
Thadeous Kacmarczyk, Peter Waltman, Ashley Bate, Patrick Eichenberger, Richard Bonneau
Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters. PLoS Comput. Biol. 7 (12) (2011)
Jochen Supper, Claas aufm Kampe, Dierk Wanke, Kenneth W. Berendzen, Klaus Harter, Richard Bonneau, Andreas Zell
Modeling gene regulation and spatial organization of sequence based motifs. BIBE (2008)
Iliana Avila-Campillo, Kevin Drew, John Lin, David J. Reiss, Richard Bonneau
BioNetBuilder: automatic integration of biological networks. Bioinform. 23 (3) (2007)
Paul T. Shannon, David J. Reiss, Richard Bonneau, Nitin S. Baliga
The Gaggle: An open-source software system for integrating bioinformatics software and data sources. BMC Bioinform. 7 (2006)
David J. Reiss, Nitin S. Baliga, Richard Bonneau
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinform. 7 (2006)