Richard Bonneau
Orcid: 0000-0003-4354-7906
According to our database1,
Richard Bonneau
authored at least 43 papers
between 2006 and 2023.
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Bibliography
2023
TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs.
Bioinform., January, 2023
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
Measuring the Ideology of Audiences for Web Links and Domains Using Differentially Private Engagement Data.
Proceedings of the Seventeenth International AAAI Conference on Web and Social Media, 2023
2022
NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction.
Bioinform., October, 2022
A Pareto-optimal compositional energy-based model for sampling and optimization of protein sequences.
CoRR, 2022
PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design.
CoRR, 2022
Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, 2022
2021
A convolutional neural network for common coordinate registration of high-resolution histology images.
Bioinform., November, 2021
Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data.
PLoS Comput. Biol., 2021
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.
PLoS Comput. Biol., 2021
Proc. ACM Hum. Comput. Interact., 2021
NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity.
Bioinform., 2021
Proceedings of the Workshop on Misinformation Integrity in Social Networks 2021 co-located with 30th The Web Conference (TheWebConf 2021), 2021
2020
Better together: Elements of successful scientific software development in a distributed collaborative community.
PLoS Comput. Biol., 2020
2019
Multi-study inference of regulatory networks for more accurate models of gene regulation.
PLoS Comput. Biol., 2019
2018
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing.
Bioinform., 2018
2017
Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.
PLoS Comput. Biol., 2017
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP.
BMC Bioinform., 2017
2016
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.
PLoS Comput. Biol., 2016
PLoS Comput. Biol., 2016
Text Classification for Automatic Detection of E-Cigarette Use and Use for Smoking Cessation from Twitter: A Feasibility Pilot.
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016
Proceedings of the Computational Social Science: Discovery and Prediction, 2016
2015
PLoS Comput. Biol., 2015
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., 2015
Inter-species pathway perturbation prediction via data-driven detection of functional homology.
Bioinform., 2015
Proceedings of the IEEE International Conference on Data Mining Workshop, 2015
2014
Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks.
IEEE Trans. Vis. Comput. Graph., 2014
PLoS Comput. Biol., 2014
2013
Parametric Bayesian priors and better choice of negative examples improve protein function prediction.
Bioinform., 2013
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks.
Bioinform., 2013
2012
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012
2011
Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters.
PLoS Comput. Biol., 2011
2008
Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering, 2008
2007
2006
The Gaggle: An open-source software system for integrating bioinformatics software and data sources.
BMC Bioinform., 2006
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks.
BMC Bioinform., 2006