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Richard Bonneau
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2020 – today
- 2024
- [c10]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 - [i9]Angelica Chen, Samuel Don Stanton, Robert G. Alberstein, Andrew M. Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey:
LLMs are Highly-Constrained Biophysical Sequence Optimizers. CoRR abs/2410.22296 (2024) - 2023
- [j29]Emmi Jokinen
, Alexandru Dumitrescu
TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs. Bioinform. 39(1) (2023) - [c9]Cody Buntain
Measuring the Ideology of Audiences for Web Links and Domains Using Differentially Private Engagement Data. ICWSM 2023: 72-83 - [c8]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 - [c7]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 - [i8]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 abs/2306.12360 (2023) - [i7]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 abs/2308.05027 (2023) - [i6]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 abs/2308.05326 (2023) - 2022
- [j28]Ren Yi
NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction. Bioinform. 38(20): 4762-4770 (2022) - [c6]Patrick Y. Wu, Richard Bonneau, Joshua A. Tucker, Jonathan Nagler:
Dictionary-Assisted Supervised Contrastive Learning. EMNLP 2022: 10217-10235 - [i5]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 abs/2205.04259 (2022) - [i4]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 abs/2210.04096 (2022) - [i3]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 abs/2210.10838 (2022) - [i2]Patrick Y. Wu, Richard Bonneau, Joshua A. Tucker, Jonathan Nagler:
Dictionary-Assisted Supervised Contrastive Learning. CoRR abs/2210.15172 (2022) - 2021
- [j27]Meet Barot
NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity. Bioinform. 37(16): 2414-2422 (2021) - [j26]Aidan C. Daly
A convolutional neural network for common coordinate registration of high-resolution histology images. Bioinform. 37(22): 4216-4226 (2021) - [j25]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): 11:1-11:26 (2021) - [j24]Andreas Tjärnberg
Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data. PLoS Comput. Biol. 17(1) (2021) - [j23]Matthew R. Dillon
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLoS Comput. Biol. 17(6) (2021) - [c5]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 - 2020
- [j22]Julia Koehler Leman
Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput. Biol. 16(5) (2020) - [i1]Cody Buntain, Richard Bonneau, Jonathan Nagler, Joshua A. Tucker:
YouTube Recommendations and Effects on Sharing Across Online Social Platforms. CoRR abs/2003.00970 (2020)
2010 – 2019
- 2019
- [j21]Da Chen Emily Koo
Towards region-specific propagation of protein functions. Bioinform. 35(10): 1737-1744 (2019) - [j20]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) - 2018
- [j19]Tarmo Äijö
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. Bioinform. 34(3): 372-380 (2018) - [j18]Vladimir Gligorijevic, Meet Barot, Richard Bonneau:
deepNF: deep network fusion for protein function prediction. Bioinform. 34(22): 3873-3881 (2018) - 2017
- [j17]Denis Stukal, Sergey Sanovich
Detecting Bots on Russian Political Twitter. Big Data 5(4): 310-324 (2017) - [j16]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): 115:1-115:9 (2017) - [j15]Kevin Drew
Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. PLoS Comput. Biol. 13(10) (2017) - 2016
- [j14]Gaurav Bhardwaj, Vikram Khipple Mulligan, Christopher D. Bahl
Accurate de novo design of hyperstable constrained peptides. Nat. 538(7625): 329-335 (2016) - [j13]Ramya Raviram, Pedro P. Rocha
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. PLoS Comput. Biol. 12(3) (2016) - [j12]Kari Y. Lam, Zachary M. Westrick, Christian L. Müller, Lionel A. Christiaen
Fused Regression for Multi-source Gene Regulatory Network Inference. PLoS Comput. Biol. 12(12) (2016) - [c4]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: 480-491 - [p1]Joshua A. Tucker, Jonathan Nagler, Megan Macduffee Metzger, Pablo Barberá
Big Data, Social Media, and Protest: Foundations for a Research Agenda. Computational Social Science 2016: 199-224 - 2015
- [j11]Christoph Hafemeister
Inter-species pathway perturbation prediction via data-driven detection of functional homology. Bioinform. 31(4): 501-508 (2015) - [j10]Cristian Vaccari, Augusto Valeriani, Pablo Barberá
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): 221-239 (2015) - [j9]Zachary D. Kurtz, Christian L. Müller, Emily R. Miraldi, Dan R. Littman, Martin J. Blaser, Richard A. Bonneau:
Sparse and Compositionally Robust Inference of Microbial Ecological Networks. PLoS Comput. Biol. 11(5) (2015) - [c3]Noah Youngs, Dennis E. Shasha, Richard Bonneau:
Positive-Unlabeled Learning in the Face of Labeling Bias. ICDM Workshops 2015: 639-645 - 2014
- [j8]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) - [j7]Bowen Yu, Harish Doraiswamy, Xi Chen, Emily R. Miraldi, Mario Luis Arrieta-Ortiz, Christoph Hafemeister
Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks. IEEE Trans. Vis. Comput. Graph. 20(12): 1903-1912 (2014) - 2013
- [j6]Alex Greenfield, Christoph Hafemeister
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. Bioinform. 29(8): 1060-1067 (2013) - [j5]Noah Youngs, Duncan Penfold-Brown, Kevin Drew
Parametric Bayesian priors and better choice of negative examples improve protein function prediction. Bioinform. 29(9): 1190-1198 (2013) - 2012
- [c2]Jason E. McDermott, Pascal Braun, Richard Bonneau, Daniel R. Hyduke:
Session introduction. Pacific Symposium on Biocomputing 2012: 283-286 - 2011
- [j4]Thadeous Kacmarczyk, Peter Waltman, Ashley Bate, Patrick Eichenberger
Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters. PLoS Comput. Biol. 7(12) (2011)
2000 – 2009
- 2008
- [c1]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: 1-7 - 2007
- [j3]Iliana Avila-Campillo, Kevin Drew
BioNetBuilder: automatic integration of biological networks. Bioinform. 23(3): 392-393 (2007) - 2006
- [j2]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: 176 (2006) - [j1]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: 280 (2006)
Coauthor Index
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last updated on 2024-12-01 00:17 CET by the dblp team
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