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ORCIDBibTeX records: Richard Bonneau
@inproceedings{DBLP:conf/iclr/FreyBZKLHWRBCLG24,
author = {Nathan C. Frey and
Daniel Berenberg and
Karina Zadorozhny and
Joseph Kleinhenz and
Julien Lafrance{-}Vanasse and
Isidro H{\"{o}}tzel and
Yan Wu and
Stephen Ra and
Richard Bonneau and
Kyunghyun Cho and
Andreas Loukas and
Vladimir Gligorijevic and
Saeed Saremi},
title = {Protein Discovery with Discrete Walk-Jump Sampling},
booktitle = {The Twelfth International Conference on Learning Representations,
{ICLR} 2024, Vienna, Austria, May 7-11, 2024},
publisher = {OpenReview.net},
year = {2024},
url = {https://openreview.net/forum?id=zMPHKOmQNb},
timestamp = {Mon, 29 Jul 2024 16:19:40 +0200},
biburl = {https://dblp.org/rec/conf/iclr/FreyBZKLHWRBCLG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JokinenDHGMBHL23,
author = {Emmi Jokinen and
Alexandru Dumitrescu and
Jani Huuhtanen and
Vladimir Gligorijevic and
Satu Mustjoki and
Richard Bonneau and
Markus Heinonen and
Harri L{\"{a}}hdesm{\"{a}}ki},
title = {TCRconv: predicting recognition between {T} cell receptors and epitopes
using contextualized motifs},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac788},
doi = {10.1093/BIOINFORMATICS/BTAC788},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JokinenDHGMBHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icwsm/BuntainBNT23,
author = {Cody Buntain and
Richard Bonneau and
Jonathan Nagler and
Joshua A. Tucker},
editor = {Yu{-}Ru Lin and
Meeyoung Cha and
Daniele Quercia},
title = {Measuring the Ideology of Audiences for Web Links and Domains Using
Differentially Private Engagement Data},
booktitle = {Proceedings of the Seventeenth International {AAAI} Conference on
Web and Social Media, {ICWSM} 2023, Limassol, Cyprus, June 5-8, 2023},
pages = {72--83},
publisher = {{AAAI} Press},
year = {2023},
url = {https://doi.org/10.1609/icwsm.v17i1.22127},
doi = {10.1609/ICWSM.V17I1.22127},
timestamp = {Mon, 03 Jun 2024 16:33:42 +0200},
biburl = {https://dblp.org/rec/conf/icwsm/BuntainBNT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/AhdritzBKJBFWRB23,
author = {Gustaf Ahdritz and
Nazim Bouatta and
Sachin Kadyan and
Lukas Jarosch and
Daniel Berenberg and
Ian Fisk and
Andrew M. Watkins and
Stephen Ra and
Richard Bonneau and
Mohammed AlQuraishi},
editor = {Alice Oh and
Tristan Naumann and
Amir Globerson and
Kate Saenko and
Moritz Hardt and
Sergey Levine},
title = {OpenProteinSet: Training data for structural biology at scale},
booktitle = {Advances in Neural Information Processing Systems 36: Annual Conference
on Neural Information Processing Systems 2023, NeurIPS 2023, New Orleans,
LA, USA, December 10 - 16, 2023},
year = {2023},
url = {http://papers.nips.cc/paper\_files/paper/2023/hash/0eb82171240776fe19da498bef3b1abe-Abstract-Datasets\_and\_Benchmarks.html},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/nips/AhdritzBKJBFWRB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/MartinkusLLLHRW23,
author = {Karolis Martinkus and
Jan Ludwiczak and
Wei{-}Ching Liang and
Julien Lafrance{-}Vanasse and
Isidro H{\"{o}}tzel and
Arvind Rajpal and
Yan Wu and
Kyunghyun Cho and
Richard Bonneau and
Vladimir Gligorijevic and
Andreas Loukas},
editor = {Alice Oh and
Tristan Naumann and
Amir Globerson and
Kate Saenko and
Moritz Hardt and
Sergey Levine},
title = {AbDiffuser: full-atom generation of in-vitro functioning antibodies},
booktitle = {Advances in Neural Information Processing Systems 36: Annual Conference
on Neural Information Processing Systems 2023, NeurIPS 2023, New Orleans,
LA, USA, December 10 - 16, 2023},
year = {2023},
url = {http://papers.nips.cc/paper\_files/paper/2023/hash/801ec05b0aae9fcd2ef35c168bd538e0-Abstract-Conference.html},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/nips/MartinkusLLLHRW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2306-12360,
author = {Nathan C. Frey and
Daniel Berenberg and
Karina Zadorozhny and
Joseph Kleinhenz and
Julien Lafrance{-}Vanasse and
Isidro H{\"{o}}tzel and
Yan Wu and
Stephen Ra and
Richard Bonneau and
Kyunghyun Cho and
Andreas Loukas and
Vladimir Gligorijevic and
Saeed Saremi},
title = {Protein Discovery with Discrete Walk-Jump Sampling},
journal = {CoRR},
volume = {abs/2306.12360},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2306.12360},
doi = {10.48550/ARXIV.2306.12360},
eprinttype = {arXiv},
eprint = {2306.12360},
timestamp = {Fri, 23 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2306-12360.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2308-05027,
author = {Karolis Martinkus and
Jan Ludwiczak and
Kyunghyun Cho and
Wei{-}Ching Liang and
Julien Lafrance{-}Vanasse and
Isidro H{\"{o}}tzel and
Arvind Rajpal and
Yan Wu and
Richard Bonneau and
Vladimir Gligorijevic and
Andreas Loukas},
title = {AbDiffuser: Full-Atom Generation of In-Vitro Functioning Antibodies},
journal = {CoRR},
volume = {abs/2308.05027},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2308.05027},
doi = {10.48550/ARXIV.2308.05027},
eprinttype = {arXiv},
eprint = {2308.05027},
timestamp = {Thu, 24 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2308-05027.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2308-05326,
author = {Gustaf Ahdritz and
Nazim Bouatta and
Sachin Kadyan and
Lukas Jarosch and
Daniel Berenberg and
Ian Fisk and
Andrew M. Watkins and
Stephen Ra and
Richard Bonneau and
Mohammed AlQuraishi},
title = {OpenProteinSet: Training data for structural biology at scale},
journal = {CoRR},
volume = {abs/2308.05326},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2308.05326},
doi = {10.48550/ARXIV.2308.05326},
eprinttype = {arXiv},
eprint = {2308.05326},
timestamp = {Thu, 24 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2308-05326.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YiCB22,
author = {Ren Yi and
Kyunghyun Cho and
Richard Bonneau},
title = {NetTIME: a multitask and base-pair resolution framework for improved
transcription factor binding site prediction},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4762--4770},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac569},
doi = {10.1093/BIOINFORMATICS/BTAC569},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YiCB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/emnlp/WuBTN22,
author = {Patrick Y. Wu and
Richard Bonneau and
Joshua A. Tucker and
Jonathan Nagler},
editor = {Yoav Goldberg and
Zornitsa Kozareva and
Yue Zhang},
title = {Dictionary-Assisted Supervised Contrastive Learning},
booktitle = {Proceedings of the 2022 Conference on Empirical Methods in Natural
Language Processing, {EMNLP} 2022, Abu Dhabi, United Arab Emirates,
December 7-11, 2022},
pages = {10217--10235},
publisher = {Association for Computational Linguistics},
year = {2022},
url = {https://doi.org/10.18653/v1/2022.emnlp-main.696},
doi = {10.18653/V1/2022.EMNLP-MAIN.696},
timestamp = {Thu, 10 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/emnlp/WuBTN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2205-04259,
author = {Daniel Berenberg and
Jae Hyeon Lee and
Simon Kelow and
Ji Won Park and
Andrew M. Watkins and
Vladimir Gligorijevic and
Richard Bonneau and
Stephen Ra and
Kyunghyun Cho},
title = {Multi-segment preserving sampling for deep manifold sampler},
journal = {CoRR},
volume = {abs/2205.04259},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2205.04259},
doi = {10.48550/ARXIV.2205.04259},
eprinttype = {arXiv},
eprint = {2205.04259},
timestamp = {Wed, 11 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2205-04259.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2210-04096,
author = {Ji Won Park and
Samuel Stanton and
Saeed Saremi and
Andrew M. Watkins and
Henri Dwyer and
Vladimir Gligorijevic and
Richard Bonneau and
Stephen Ra and
Kyunghyun Cho},
title = {PropertyDAG: Multi-objective Bayesian optimization of partially ordered,
mixed-variable properties for biological sequence design},
journal = {CoRR},
volume = {abs/2210.04096},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2210.04096},
doi = {10.48550/ARXIV.2210.04096},
eprinttype = {arXiv},
eprint = {2210.04096},
timestamp = {Wed, 12 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2210-04096.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2210-10838,
author = {Natasa Tagasovska and
Nathan C. Frey and
Andreas Loukas and
Isidro H{\"{o}}tzel and
Julien Lafrance{-}Vanasse and
Ryan Lewis Kelly and
Yan Wu and
Arvind Rajpal and
Richard Bonneau and
Kyunghyun Cho and
Stephen Ra and
Vladimir Gligorijevic},
title = {A Pareto-optimal compositional energy-based model for sampling and
optimization of protein sequences},
journal = {CoRR},
volume = {abs/2210.10838},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2210.10838},
doi = {10.48550/ARXIV.2210.10838},
eprinttype = {arXiv},
eprint = {2210.10838},
timestamp = {Tue, 25 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2210-10838.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2210-15172,
author = {Patrick Y. Wu and
Richard Bonneau and
Joshua A. Tucker and
Jonathan Nagler},
title = {Dictionary-Assisted Supervised Contrastive Learning},
journal = {CoRR},
volume = {abs/2210.15172},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2210.15172},
doi = {10.48550/ARXIV.2210.15172},
eprinttype = {arXiv},
eprint = {2210.15172},
timestamp = {Wed, 02 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2210-15172.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BarotGCB21,
author = {Meet Barot and
Vladimir Gligorijevic and
Kyunghyun Cho and
Richard Bonneau},
title = {NetQuilt: deep multispecies network-based protein function prediction
using homology-informed network similarity},
journal = {Bioinform.},
volume = {37},
number = {16},
pages = {2414--2422},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab098},
doi = {10.1093/BIOINFORMATICS/BTAB098},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BarotGCB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DalyGB21,
author = {Aidan C. Daly and
Krzysztof J. Geras and
Richard Bonneau},
title = {A convolutional neural network for common coordinate registration
of high-resolution histology images},
journal = {Bioinform.},
volume = {37},
number = {22},
pages = {4216--4226},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab447},
doi = {10.1093/BIOINFORMATICS/BTAB447},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DalyGB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pacmhci/BuntainBNT21,
author = {Cody Buntain and
Richard Bonneau and
Jonathan Nagler and
Joshua A. Tucker},
title = {YouTube Recommendations and Effects on Sharing Across Online Social
Platforms},
journal = {Proc. {ACM} Hum. Comput. Interact.},
volume = {5},
number = {{CSCW1}},
pages = {11:1--11:26},
year = {2021},
url = {https://doi.org/10.1145/3449085},
doi = {10.1145/3449085},
timestamp = {Wed, 09 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/pacmhci/BuntainBNT21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/TjarnbergMJSCCB21,
author = {Andreas Tj{\"{a}}rnberg and
Omar Mahmood and
Christopher A. Jackson and
Giuseppe{-}Antonio Saldi and
Kyunghyun Cho and
Lionel A. Christiaen and
Richard A. Bonneau},
title = {Optimal tuning of weighted kNN- and diffusion-based methods for denoising
single cell genomics data},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {1},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1008569},
doi = {10.1371/JOURNAL.PCBI.1008569},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/TjarnbergMJSCCB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/DillonBABBBDDEE21,
author = {Matthew R. Dillon and
Evan Bolyen and
Anja Adamov and
Aeriel Belk and
Emily Borsom and
Zachary Burcham and
Justine W. Debelius and
Heather Deel and
Alex Emmons and
Mehrbod Estaki and
Chloe Herman and
Christopher R. Keefe and
Jamie T. Morton and
Renato R. M. Oliveira and
Andrew Sanchez and
Anthony Simard and
Yoshiki Vazquez{-}Baeza and
Michal Ziemski and
Hazuki E. Miwa and
Terry A. Kerere and
Carline Coote and
Richard Bonneau and
Rob Knight and
Guilherme Oliveira and
Piraveen Gopalasingam and
Benjamin D. Kaehler and
Emily K. Cope and
Jessica L. Metcalf and
Michael S. Robeson II and
Nicholas A. Bokulich and
J. Gregory Caporaso},
title = {Experiences and lessons learned from two virtual, hands-on microbiome
bioinformatics workshops},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {6},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1009056},
doi = {10.1371/JOURNAL.PCBI.1009056},
timestamp = {Sun, 28 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/DillonBABBBDDEE21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/www/ChenARFNTB21,
author = {Zhouhan Chen and
Kevin Aslett and
Jen Rosiere Reynolds and
Juliana Freire and
Jonathan Nagler and
Joshua A. Tucker and
Richard Bonneau},
editor = {Llu{\'{\i}}s Garcia Pueyo and
Anand Bhaskar and
Prathyusha Senthil Kumar and
Panayiotis Tsaparas and
Kiran Garimella and
Yu Sun and
Francesco Bonchi},
title = {An Automatic Framework to Continuously Monitor Multi-Platform Information
Spread},
booktitle = {Proceedings of the Workshop on Misinformation Integrity in Social
Networks 2021 co-located with 30th The Web Conference (TheWebConf
2021), Ljubljana, Slovenia, April 15, 2021},
series = {{CEUR} Workshop Proceedings},
volume = {2890},
publisher = {CEUR-WS.org},
year = {2021},
url = {http://ceur-ws.org/Vol-2890/paper3.pdf},
timestamp = {Tue, 05 Sep 2023 08:59:57 +0200},
biburl = {https://dblp.org/rec/conf/www/ChenARFNTB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LemanWRLMWMLALK20,
author = {Julia Koehler Leman and
Brian D. Weitzner and
P. Douglas Renfrew and
Steven M. Lewis and
Rocco Moretti and
Andrew M. Watkins and
Vikram Khipple Mulligan and
Sergey Lyskov and
Jared Adolf{-}Bryfogle and
Jason W. Labonte and
Justyna Krys and
RosettaCommons Consortium and
Christopher Bystroff and
William R. Schief and
Dominik Gront and
Ora Schueler{-}Furman and
David Baker and
Philip Bradley and
Roland L. Dunbrack Jr. and
Tanja Kortemme and
Andrew Leaver{-}Fay and
Charlie E. M. Strauss and
Jens Meiler and
Brian Kuhlman and
Jeffrey J. Gray and
Richard Bonneau},
title = {Better together: Elements of successful scientific software development
in a distributed collaborative community},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {5},
year = {2020},
url = {https://doi.org/10.1371/journal.pcbi.1007507},
doi = {10.1371/JOURNAL.PCBI.1007507},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/LemanWRLMWMLALK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2003-00970,
author = {Cody Buntain and
Richard Bonneau and
Jonathan Nagler and
Joshua A. Tucker},
title = {YouTube Recommendations and Effects on Sharing Across Online Social
Platforms},
journal = {CoRR},
volume = {abs/2003.00970},
year = {2020},
url = {https://arxiv.org/abs/2003.00970},
eprinttype = {arXiv},
eprint = {2003.00970},
timestamp = {Tue, 10 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2003-00970.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KooB19,
author = {Da Chen Emily Koo and
Richard Bonneau},
title = {Towards region-specific propagation of protein functions},
journal = {Bioinform.},
volume = {35},
number = {10},
pages = {1737--1744},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty834},
doi = {10.1093/BIOINFORMATICS/BTY834},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KooB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/CastroVMB19,
author = {Dayanne M. Castro and
Nicholas R. de Veaux and
Emily R. Miraldi and
Richard Bonneau},
title = {Multi-study inference of regulatory networks for more accurate models
of gene regulation},
journal = {PLoS Comput. Biol.},
volume = {15},
number = {1},
year = {2019},
url = {https://doi.org/10.1371/journal.pcbi.1006591},
doi = {10.1371/JOURNAL.PCBI.1006591},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/CastroVMB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AijoMB18,
author = {Tarmo {\"{A}}ij{\"{o}} and
Christian L. M{\"{u}}ller and
Richard Bonneau},
title = {Temporal probabilistic modeling of bacterial compositions derived
from 16S rRNA sequencing},
journal = {Bioinform.},
volume = {34},
number = {3},
pages = {372--380},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx549},
doi = {10.1093/BIOINFORMATICS/BTX549},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AijoMB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GligorijevicBB18,
author = {Vladimir Gligorijevic and
Meet Barot and
Richard Bonneau},
title = {deepNF: deep network fusion for protein function prediction},
journal = {Bioinform.},
volume = {34},
number = {22},
pages = {3873--3881},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty440},
doi = {10.1093/BIOINFORMATICS/BTY440},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GligorijevicBB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bigdata/StukalSBT17,
author = {Denis Stukal and
Sergey Sanovich and
Richard Bonneau and
Joshua A. Tucker},
title = {Detecting Bots on Russian Political Twitter},
journal = {Big Data},
volume = {5},
number = {4},
pages = {310--324},
year = {2017},
url = {https://doi.org/10.1089/big.2017.0038},
doi = {10.1089/BIG.2017.0038},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bigdata/StukalSBT17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LemanLB17,
author = {Julia Koehler Leman and
Sergey Lyskov and
Richard Bonneau},
title = {Computing structure-based lipid accessibility of membrane proteins
with mp{\_}lipid{\_}acc in RosettaMP},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {115:1--115:9},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1541-z},
doi = {10.1186/S12859-017-1541-Z},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LemanLB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/DrewMBM17,
author = {Kevin Drew and
Christian L. M{\"{u}}ller and
Richard Bonneau and
Edward M. Marcotte},
title = {Identifying direct contacts between protein complex subunits from
their conditional dependence in proteomics datasets},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {10},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005625},
doi = {10.1371/JOURNAL.PCBI.1005625},
timestamp = {Thu, 04 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/DrewMBM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/BhardwajMBGHCBP16,
author = {Gaurav Bhardwaj and
Vikram Khipple Mulligan and
Christopher D. Bahl and
Jason M. Gilmore and
Peta J. Harvey and
Olivier Cheneval and
Garry W. Buchko and
Surya V. S. R. K. Pulavarti and
Quentin Kaas and
Alexander Eletsky and
Po{-}Ssu Huang and
William A. Johnsen and
Per Greisen and
Gabriel J. Rocklin and
Yifan Song and
Thomas W. Linsky and
Andrew M. Watkins and
Stephen A. Rettie and
Xianzhong Xu and
Lauren P. Carter and
Richard Bonneau and
James M. Olson and
Evangelos A. Coutsias and
Colin E. Correnti and
Thomas Szyperski and
David J. Craik and
David Baker},
title = {Accurate \emph{de novo} design of hyperstable constrained peptides},
journal = {Nat.},
volume = {538},
number = {7625},
pages = {329--335},
year = {2016},
url = {https://doi.org/10.1038/nature19791},
doi = {10.1038/NATURE19791},
timestamp = {Thu, 09 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nature/BhardwajMBGHCBP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/RaviramRMMBFSPS16,
author = {Ramya Raviram and
Pedro P. Rocha and
Christian L. M{\"{u}}ller and
Emily R. Miraldi and
Sana Badri and
Yi Fu and
Emily Swanzey and
Charlotte Proudhon and
Valentina Snetkova and
Richard Bonneau and
Jane A. Skok},
title = {4C-ker: {A} Method to Reproducibly Identify Genome-Wide Interactions
Captured by 4C-Seq Experiments},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {3},
year = {2016},
url = {https://doi.org/10.1371/journal.pcbi.1004780},
doi = {10.1371/JOURNAL.PCBI.1004780},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/RaviramRMMBFSPS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LamWMCB16,
author = {Kari Y. Lam and
Zachary M. Westrick and
Christian L. M{\"{u}}ller and
Lionel A. Christiaen and
Richard Bonneau},
title = {Fused Regression for Multi-source Gene Regulatory Network Inference},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {12},
year = {2016},
url = {https://doi.org/10.1371/journal.pcbi.1005157},
doi = {10.1371/JOURNAL.PCBI.1005157},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/LamWMCB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/Aphinyanaphongs16,
author = {Yin Aphinyanaphongs and
Armine Lulejian and
Duncan Penfold{-}Brown and
Richard Bonneau and
Paul Krebs},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein and
Marylyn D. Ritchie},
title = {Text Classification for Automatic Detection of E-Cigarette Use and
Use for Smoking Cessation from Twitter: {A} Feasibility Pilot},
booktitle = {Biocomputing 2016: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 4-8, 2016},
pages = {480--491},
year = {2016},
url = {http://psb.stanford.edu/psb-online/proceedings/psb16/aphinyanaphongs.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/Aphinyanaphongs16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/cu/p/TuckerNMBPB16,
author = {Joshua A. Tucker and
Jonathan Nagler and
Megan Macduffee Metzger and
Pablo Barber{\'{a}} and
Duncan Penfold{-}Brown and
Richard Bonneau},
editor = {R. Michael Alvarez},
title = {Big Data, Social Media, and Protest: Foundations for a Research Agenda},
booktitle = {Computational Social Science: Discovery and Prediction},
series = {Analytical Methods for Social Research},
pages = {199--224},
publisher = {Cambridge University Press},
year = {2016},
url = {https://doi.org/10.1017/CBO9781316257340.009},
doi = {10.1017/CBO9781316257340.009},
timestamp = {Wed, 14 Jun 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/cu/p/TuckerNMBPB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HafemeisterRBMNRBT15,
author = {Christoph Hafemeister and
Roberto Romero and
Erhan Bilal and
Pablo Meyer and
Raquel Norel and
Kahn Rhrissorrakrai and
Richard Bonneau and
Adi L. Tarca},
title = {Inter-species pathway perturbation prediction via data-driven detection
of functional homology},
journal = {Bioinform.},
volume = {31},
number = {4},
pages = {501--508},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btu570},
doi = {10.1093/BIOINFORMATICS/BTU570},
timestamp = {Fri, 01 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HafemeisterRBMNRBT15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcmc/VaccariVBBJNT15,
author = {Cristian Vaccari and
Augusto Valeriani and
Pablo Barber{\'{a}} and
Richard Bonneau and
John T. Jost and
Jonathan Nagler and
Joshua A. Tucker},
title = {Political Expression and Action on Social Media: Exploring the Relationship
Between Lower- and Higher-Threshold Political Activities Among Twitter
Users in Italy},
journal = {J. Comput. Mediat. Commun.},
volume = {20},
number = {2},
pages = {221--239},
year = {2015},
url = {https://doi.org/10.1111/jcc4.12108},
doi = {10.1111/JCC4.12108},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcmc/VaccariVBBJNT15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/KurtzMMLBB15,
author = {Zachary D. Kurtz and
Christian L. M{\"{u}}ller and
Emily R. Miraldi and
Dan R. Littman and
Martin J. Blaser and
Richard A. Bonneau},
title = {Sparse and Compositionally Robust Inference of Microbial Ecological
Networks},
journal = {PLoS Comput. Biol.},
volume = {11},
number = {5},
year = {2015},
url = {https://doi.org/10.1371/journal.pcbi.1004226},
doi = {10.1371/JOURNAL.PCBI.1004226},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/KurtzMMLBB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icdm/YoungsSB15,
author = {Noah Youngs and
Dennis E. Shasha and
Richard Bonneau},
title = {Positive-Unlabeled Learning in the Face of Labeling Bias},
booktitle = {{IEEE} International Conference on Data Mining Workshop, {ICDMW} 2015,
Atlantic City, NJ, USA, November 14-17, 2015},
pages = {639--645},
publisher = {{IEEE} Computer Society},
year = {2015},
url = {https://doi.org/10.1109/ICDMW.2015.207},
doi = {10.1109/ICDMW.2015.207},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icdm/YoungsSB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/YoungsPBS14,
author = {Noah Youngs and
Duncan Penfold{-}Brown and
Richard Bonneau and
Dennis E. Shasha},
title = {Negative Example Selection for Protein Function Prediction: The NoGO
Database},
journal = {PLoS Comput. Biol.},
volume = {10},
number = {6},
year = {2014},
url = {https://doi.org/10.1371/journal.pcbi.1003644},
doi = {10.1371/JOURNAL.PCBI.1003644},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/YoungsPBS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tvcg/YuDCMAHMBS14,
author = {Bowen Yu and
Harish Doraiswamy and
Xi Chen and
Emily R. Miraldi and
Mario Luis Arrieta{-}Ortiz and
Christoph Hafemeister and
Aviv Madar and
Richard Bonneau and
Cl{\'{a}}udio T. Silva},
title = {Genotet: An Interactive Web-based Visual Exploration Framework to
Support Validation of Gene Regulatory Networks},
journal = {{IEEE} Trans. Vis. Comput. Graph.},
volume = {20},
number = {12},
pages = {1903--1912},
year = {2014},
url = {https://doi.org/10.1109/TVCG.2014.2346753},
doi = {10.1109/TVCG.2014.2346753},
timestamp = {Mon, 24 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tvcg/YuDCMAHMBS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GreenfieldHB13,
author = {Alex Greenfield and
Christoph Hafemeister and
Richard Bonneau},
title = {Robust data-driven incorporation of prior knowledge into the inference
of dynamic regulatory networks},
journal = {Bioinform.},
volume = {29},
number = {8},
pages = {1060--1067},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt099},
doi = {10.1093/BIOINFORMATICS/BTT099},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GreenfieldHB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YoungsPDSB13,
author = {Noah Youngs and
Duncan Penfold{-}Brown and
Kevin Drew and
Dennis E. Shasha and
Richard Bonneau},
title = {Parametric Bayesian priors and better choice of negative examples
improve protein function prediction},
journal = {Bioinform.},
volume = {29},
number = {9},
pages = {1190--1198},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt110},
doi = {10.1093/BIOINFORMATICS/BTT110},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YoungsPDSB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/McDermottBBH12,
author = {Jason E. McDermott and
Pascal Braun and
Richard Bonneau and
Daniel R. Hyduke},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Session introduction},
booktitle = {Biocomputing 2012: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2012},
pages = {283--286},
publisher = {World Scientific Publishing},
year = {2012},
url = {http://psb.stanford.edu/psb-online/proceedings/psb12/intro-modeling.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/McDermottBBH12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/KacmarczykWBEB11,
author = {Thadeous Kacmarczyk and
Peter Waltman and
Ashley Bate and
Patrick Eichenberger and
Richard Bonneau},
title = {Comparative Microbial Modules Resource: Generation and Visualization
of Multi-species Biclusters},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {12},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1002228},
doi = {10.1371/JOURNAL.PCBI.1002228},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/KacmarczykWBEB11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/SupperKWBHBZ08,
author = {Jochen Supper and
Claas aufm Kampe and
Dierk Wanke and
Kenneth W. Berendzen and
Klaus Harter and
Richard Bonneau and
Andreas Zell},
title = {Modeling gene regulation and spatial organization of sequence based
motifs},
booktitle = {Proceedings of the 8th {IEEE} International Conference on Bioinformatics
and Bioengineering, {BIBE} 2008, October 8-10, 2008, Athens, Greece},
pages = {1--7},
publisher = {{IEEE}},
year = {2008},
url = {https://doi.org/10.1109/BIBE.2008.4696696},
doi = {10.1109/BIBE.2008.4696696},
timestamp = {Thu, 14 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibe/SupperKWBHBZ08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Avila-CampilloDLRB07,
author = {Iliana Avila{-}Campillo and
Kevin Drew and
John Lin and
David J. Reiss and
Richard Bonneau},
title = {BioNetBuilder: automatic integration of biological networks},
journal = {Bioinform.},
volume = {23},
number = {3},
pages = {392--393},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btl604},
doi = {10.1093/BIOINFORMATICS/BTL604},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Avila-CampilloDLRB07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShannonRBB06,
author = {Paul T. Shannon and
David J. Reiss and
Richard Bonneau and
Nitin S. Baliga},
title = {The Gaggle: An open-source software system for integrating bioinformatics
software and data sources},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {176},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-176},
doi = {10.1186/1471-2105-7-176},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ShannonRBB06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ReissBB06,
author = {David J. Reiss and
Nitin S. Baliga and
Richard Bonneau},
title = {Integrated biclustering of heterogeneous genome-wide datasets for
the inference of global regulatory networks},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {280},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-280},
doi = {10.1186/1471-2105-7-280},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ReissBB06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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