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ORCIDBibTeX records: William Stafford Noble
@article{DBLP:journals/bioinformatics/VaroquauxNV23,
author = {Nelle Varoquaux and
William S. Noble and
Jean{-}Philippe Vert},
title = {Inference of 3D genome architecture by modeling overdispersion of
Hi-C data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac838},
doi = {10.1093/BIOINFORMATICS/BTAC838},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VaroquauxNV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LinKHBN23,
author = {Andy Lin and
Brooke L. Deatherage Kaiser and
Janine R. Hutchison and
Jeffrey A. Bilmes and
William Stafford Noble},
title = {MS1Connect: a mass spectrometry run similarity measure},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad058},
doi = {10.1093/BIOINFORMATICS/BTAD058},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LinKHBN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/Noble23,
author = {William Stafford Noble},
title = {Ten simple rules for defining a computational biology project},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {1},
year = {2023},
url = {https://doi.org/10.1371/journal.pcbi.1010786},
doi = {10.1371/JOURNAL.PCBI.1010786},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/Noble23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/MinDGN23,
author = {Alan Min and
Timothy Durham and
Louis Gevirtzman and
William Stafford Noble},
title = {Matrix prior for data transfer between single cell data types in latent
Dirichlet allocation},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {5},
year = {2023},
url = {https://doi.org/10.1371/journal.pcbi.1011049},
doi = {10.1371/JOURNAL.PCBI.1011049},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/MinDGN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/BaurSSZ0MSNR23,
author = {Brittany Baur and
Junha Shin and
Jacob Schreiber and
Shilu Zhang and
Yi Zhang and
Mohith Manjunath and
Jun S. Song and
William Stafford Noble and
Sushmita Roy},
title = {Leveraging epigenomes and three-dimensional genome organization for
interpreting regulatory variation},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {7},
year = {2023},
url = {https://doi.org/10.1371/journal.pcbi.1011286},
doi = {10.1371/JOURNAL.PCBI.1011286},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/BaurSSZ0MSNR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2309-15319,
author = {Winston Chen and
William Stafford Noble and
Yang Young Lu},
title = {DeepROCK: Error-controlled interaction detection in deep neural networks},
journal = {CoRR},
volume = {abs/2309.15319},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2309.15319},
doi = {10.48550/ARXIV.2309.15319},
eprinttype = {arXiv},
eprint = {2309.15319},
timestamp = {Tue, 17 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2309-15319.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/DemetciSSNS22,
author = {Pinar Demetci and
Rebecca Santorella and
Bj{\"{o}}rn Sandstede and
William Stafford Noble and
Ritambhara Singh},
title = {{SCOT:} Single-Cell Multi-Omics Alignment with Optimal Transport},
journal = {J. Comput. Biol.},
volume = {29},
number = {1},
pages = {3--18},
year = {2022},
url = {https://doi.org/10.1089/cmb.2021.0446},
doi = {10.1089/CMB.2021.0446},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/DemetciSSNS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/DemetciSSNS22a,
author = {Pinar Demetci and
Rebecca Santorella and
Bj{\"{o}}rn Sandstede and
William Stafford Noble and
Ritambhara Singh},
title = {Single-Cell Multiomics Integration by {SCOT}},
journal = {J. Comput. Biol.},
volume = {29},
number = {1},
pages = {19--22},
year = {2022},
url = {https://doi.org/10.1089/cmb.2021.0477},
doi = {10.1089/CMB.2021.0477},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/DemetciSSNS22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ZhangMVN22,
author = {Ran Zhang and
Laetitia Meng{-}Papaxanthos and
Jean{-}Philippe Vert and
William Stafford Noble},
title = {Multimodal Single-Cell Translation and Alignment with Semi-Supervised
Learning},
journal = {J. Comput. Biol.},
volume = {29},
number = {11},
pages = {1198--1212},
year = {2022},
url = {https://doi.org/10.1089/cmb.2022.0264},
doi = {10.1089/CMB.2022.0264},
timestamp = {Sun, 15 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/ZhangMVN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/YilmazFBON22,
author = {Melih Yilmaz and
William Fondrie and
Wout Bittremieux and
Sewoong Oh and
William S. Noble},
editor = {Kamalika Chaudhuri and
Stefanie Jegelka and
Le Song and
Csaba Szepesv{\'{a}}ri and
Gang Niu and
Sivan Sabato},
title = {De novo mass spectrometry peptide sequencing with a transformer model},
booktitle = {International Conference on Machine Learning, {ICML} 2022, 17-23 July
2022, Baltimore, Maryland, {USA}},
series = {Proceedings of Machine Learning Research},
volume = {162},
pages = {25514--25522},
publisher = {{PMLR}},
year = {2022},
url = {https://proceedings.mlr.press/v162/yilmaz22a.html},
timestamp = {Tue, 12 Jul 2022 17:36:52 +0200},
biburl = {https://dblp.org/rec/conf/icml/YilmazFBON22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isit/MazoojiKNS22,
author = {Kayvon Mazooji and
Sreeram Kannan and
William Stafford Noble and
Ilan Shomorony},
title = {Fundamental Limits of Multi-Sample Flow Graph Decomposition},
booktitle = {{IEEE} International Symposium on Information Theory, {ISIT} 2022,
Espoo, Finland, June 26 - July 1, 2022},
pages = {2403--2408},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/ISIT50566.2022.9834518},
doi = {10.1109/ISIT50566.2022.9834518},
timestamp = {Mon, 08 Aug 2022 16:44:13 +0200},
biburl = {https://dblp.org/rec/conf/isit/MazoojiKNS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ZhangMVN22,
author = {Ran Zhang and
Laetitia Meng{-}Papaxanthos and
Jean{-}Philippe Vert and
William Stafford Noble},
editor = {Itsik Pe'er},
title = {Semi-supervised Single-Cell Cross-modality Translation Using Polarbear},
booktitle = {Research in Computational Molecular Biology - 26th Annual International
Conference, {RECOMB} 2022, San Diego, CA, USA, May 22-25, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13278},
pages = {20--35},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-04749-7\_2},
doi = {10.1007/978-3-031-04749-7\_2},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ZhangMVN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchreiberBN21,
author = {Jacob M. Schreiber and
Jeffrey A. Bilmes and
William Stafford Noble},
title = {Prioritizing transcriptomic and epigenomic experiments using an optimization
strategy that leverages imputed data},
journal = {Bioinform.},
volume = {37},
number = {4},
pages = {439--447},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa830},
doi = {10.1093/BIOINFORMATICS/BTAA830},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchreiberBN21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LinSN21,
author = {Dejun Lin and
Justin Sanders and
William Stafford Noble},
title = {HiCRep.py: fast comparison of Hi-C contact matrices in Python},
journal = {Bioinform.},
volume = {37},
number = {18},
pages = {2996--2997},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab097},
doi = {10.1093/BIOINFORMATICS/BTAB097},
timestamp = {Sun, 22 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LinSN21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuBRVN21,
author = {Yang Young Lu and
Jeff A. Bilmes and
Ricard A. Rodriguez{-}Mias and
Judit Vill{\'{e}}n and
William Stafford Noble},
title = {DIAmeter: matching peptides to data-independent acquisition mass spectrometry
data},
journal = {Bioinform.},
volume = {37},
number = {Supplement},
pages = {434--432},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab284},
doi = {10.1093/BIOINFORMATICS/BTAB284},
timestamp = {Tue, 21 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuBRVN21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/Lu0XN21,
author = {Yang Young Lu and
Wenbo Guo and
Xinyu Xing and
William Stafford Noble},
editor = {Marina Meila and
Tong Zhang},
title = {{DANCE:} Enhancing saliency maps using decoys},
booktitle = {Proceedings of the 38th International Conference on Machine Learning,
{ICML} 2021, 18-24 July 2021, Virtual Event},
series = {Proceedings of Machine Learning Research},
volume = {139},
pages = {7124--7133},
publisher = {{PMLR}},
year = {2021},
url = {http://proceedings.mlr.press/v139/lu21b.html},
timestamp = {Wed, 25 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icml/Lu0XN21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/LuYBN21,
author = {Yang Young Lu and
Timothy C. Yu and
Giancarlo Bonora and
William Stafford Noble},
editor = {Marina Meila and
Tong Zhang},
title = {{ACE:} Explaining cluster from an adversarial perspective},
booktitle = {Proceedings of the 38th International Conference on Machine Learning,
{ICML} 2021, 18-24 July 2021, Virtual Event},
series = {Proceedings of Machine Learning Research},
volume = {139},
pages = {7156--7167},
publisher = {{PMLR}},
year = {2021},
url = {http://proceedings.mlr.press/v139/lu21e.html},
timestamp = {Wed, 25 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icml/LuYBN21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jmlr/SchreiberBN20,
author = {Jacob M. Schreiber and
Jeffrey A. Bilmes and
William Stafford Noble},
title = {apricot: Submodular selection for data summarization in Python},
journal = {J. Mach. Learn. Res.},
volume = {21},
pages = {161:1--161:6},
year = {2020},
url = {http://jmlr.org/papers/v21/19-467.html},
timestamp = {Wed, 18 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jmlr/SchreiberBN20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/KimYBRLQLHWSDN20,
author = {Hyeon{-}Jin Kim and
Galip G{\"{u}}rkan Yardimci and
Giancarlo Bonora and
Vijay Ramani and
Jie Liu and
Ruolan Qiu and
Choli Lee and
Jennifer Hesson and
Carol B. Ware and
Jay Shendure and
Zhi{-}jun Duan and
William Stafford Noble},
title = {Capturing cell type-specific chromatin compartment patterns by applying
topic modeling to single-cell Hi-C data},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {9},
year = {2020},
url = {https://doi.org/10.1371/journal.pcbi.1008173},
doi = {10.1371/JOURNAL.PCBI.1008173},
timestamp = {Mon, 23 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/KimYBRLQLHWSDN20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/SchreiberDNB20,
author = {Jacob M. Schreiber and
Timothy J. Durham and
William S. Noble and
Jeffrey A. Bilmes},
title = {Avocado: Deep tensor factorization characterizes the human epigenome
via imputation of tens of thousands of functional experiments},
booktitle = {{BCB} '20: 11th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, Virtual Event, USA,
September 21-24, 2020},
pages = {37:1},
publisher = {{ACM}},
year = {2020},
url = {https://doi.org/10.1145/3388440.3414215},
doi = {10.1145/3388440.3414215},
timestamp = {Thu, 29 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/SchreiberDNB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/SchreiberHN20,
author = {Jacob M. Schreiber and
Deepthi Hegde and
William S. Noble},
title = {Zero-shot imputations across species are enabled through joint modeling
of human and mouse epigenomics},
booktitle = {{BCB} '20: 11th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, Virtual Event, USA,
September 21-24, 2020},
pages = {39:1--39:9},
publisher = {{ACM}},
year = {2020},
url = {https://doi.org/10.1145/3388440.3412412},
doi = {10.1145/3388440.3412412},
timestamp = {Fri, 13 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/SchreiberHN20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/SinghDBRLFDDSDN20,
author = {Ritambhara Singh and
Pinar Demetci and
Giancarlo Bonora and
Vijay Ramani and
Choli Lee and
He Fang and
Zhi{-}jun Duan and
Xinxian Deng and
Jay Shendure and
Christine Disteche and
William Stafford Noble},
title = {Unsupervised manifold alignment for single-cell multi-omics data},
booktitle = {{BCB} '20: 11th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, Virtual Event, USA,
September 21-24, 2020},
pages = {40:1--40:10},
publisher = {{ACM}},
year = {2020},
url = {https://doi.org/10.1145/3388440.3412410},
doi = {10.1145/3388440.3412410},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/SinghDBRLFDDSDN20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/YangBN20,
author = {Wei Yang and
Jeffrey A. Bilmes and
William Stafford Noble},
title = {Submodular sketches of single-cell RNA-seq measurements},
booktitle = {{BCB} '20: 11th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, Virtual Event, USA,
September 21-24, 2020},
pages = {61:1--61:6},
publisher = {{ACM}},
year = {2020},
url = {https://doi.org/10.1145/3388440.3412409},
doi = {10.1145/3388440.3412409},
timestamp = {Fri, 13 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/YangBN20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/EmeryHNK20,
author = {Kristen Emery and
Syamand Hasam and
William Stafford Noble and
Uri Keich},
editor = {Russell Schwartz},
title = {Multiple Competition-Based {FDR} Control and Its Application to Peptide
Detection},
booktitle = {Research in Computational Molecular Biology - 24th Annual International
Conference, {RECOMB} 2020, Padua, Italy, May 10-13, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12074},
pages = {54--71},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-45257-5\_4},
doi = {10.1007/978-3-030-45257-5\_4},
timestamp = {Mon, 04 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/EmeryHNK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2002-00526,
author = {Yang Lu and
Wenbo Guo and
Xinyu Xing and
William Stafford Noble},
title = {Robust saliency maps with decoy-enhanced saliency score},
journal = {CoRR},
volume = {abs/2002.00526},
year = {2020},
url = {https://arxiv.org/abs/2002.00526},
eprinttype = {arXiv},
eprint = {2002.00526},
timestamp = {Mon, 22 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2002-00526.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GabereN19,
author = {Musa Nur Gabere and
William Stafford Noble},
title = {Response to comments on 'Empirical comparison of web-based antimicrobial
peptide prediction tools'},
journal = {Bioinform.},
volume = {35},
number = {15},
pages = {2695--2696},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty1024},
doi = {10.1093/BIOINFORMATICS/BTY1024},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GabereN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChengGNB19,
author = {Alice Cheng and
Charles E. Grant and
William S. Noble and
Timothy L. Bailey},
title = {MoMo: discovery of statistically significant post-translational modification
motifs},
journal = {Bioinform.},
volume = {35},
number = {16},
pages = {2774--2782},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty1058},
doi = {10.1093/BIOINFORMATICS/BTY1058},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChengGNB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jossw/MommertKVLGSDGN19,
author = {Michael Mommert and
Michael S. P. Kelley and
Miguel de Val{-}Borro and
Jian{-}Yang Li and
Giannina Guzman and
Brigitta M. Sipocz and
Josef Durech and
Mikael Granvik and
William S. Noble and
Nick Moskovitz and
Antti Penttil{\"{a}} and
Nalin Samarasinha},
title = {sbpy: {A} Python module for small-body planetary astronomy},
journal = {J. Open Source Softw.},
volume = {4},
number = {38},
pages = {1426},
year = {2019},
url = {https://doi.org/10.21105/joss.01426},
doi = {10.21105/JOSS.01426},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jossw/MommertKVLGSDGN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ReadCLRN19,
author = {David F. Read and
Kate Cook and
Yang Young Lu and
Karine G. Le Roch and
William Stafford Noble},
title = {Predicting gene expression in the human malaria parasite Plasmodium
falciparum using histone modification, nucleosome positioning, and
3D localization features},
journal = {PLoS Comput. Biol.},
volume = {15},
number = {9},
year = {2019},
url = {https://doi.org/10.1371/journal.pcbi.1007329},
doi = {10.1371/JOURNAL.PCBI.1007329},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/ReadCLRN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/BaiBN19,
author = {Wenruo Bai and
Jeffrey A. Bilmes and
William S. Noble},
title = {Submodular Generalized Matching for Peptide Identification in Tandem
Mass Spectrometry},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {16},
number = {4},
pages = {1168--1181},
year = {2019},
url = {https://doi.org/10.1109/TCBB.2018.2822280},
doi = {10.1109/TCBB.2018.2822280},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/BaiBN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/LiuHSVN19,
author = {Jie Liu and
Yuanhao Huang and
Ritambhara Singh and
Jean{-}Philippe Vert and
William Stafford Noble},
editor = {Katharina T. Huber and
Dan Gusfield},
title = {Jointly Embedding Multiple Single-Cell Omics Measurements},
booktitle = {19th International Workshop on Algorithms in Bioinformatics, {WABI}
2019, September 8-10, 2019, Niagara Falls, NY, {USA}},
series = {LIPIcs},
volume = {143},
pages = {10:1--10:13},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2019},
url = {https://doi.org/10.4230/LIPIcs.WABI.2019.10},
doi = {10.4230/LIPICS.WABI.2019.10},
timestamp = {Mon, 23 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/LiuHSVN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/CauerYVVN19,
author = {Alexandra Gesine Cauer and
G{\"{u}}rkan Yardimci and
Jean{-}Philippe Vert and
Nelle Varoquaux and
William Stafford Noble},
editor = {Katharina T. Huber and
Dan Gusfield},
title = {Inferring Diploid 3D Chromatin Structures from Hi-C Data},
booktitle = {19th International Workshop on Algorithms in Bioinformatics, {WABI}
2019, September 8-10, 2019, Niagara Falls, NY, {USA}},
series = {LIPIcs},
volume = {143},
pages = {11:1--11:13},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2019},
url = {https://doi.org/10.4230/LIPIcs.WABI.2019.11},
doi = {10.4230/LIPICS.WABI.2019.11},
timestamp = {Mon, 23 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/CauerYVVN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1906-03543,
author = {Jacob M. Schreiber and
Jeffrey A. Bilmes and
William Stafford Noble},
title = {apricot: Submodular selection for data summarization in Python},
journal = {CoRR},
volume = {abs/1906.03543},
year = {2019},
url = {http://arxiv.org/abs/1906.03543},
eprinttype = {arXiv},
eprint = {1906.03543},
timestamp = {Fri, 14 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1906-03543.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChanLRBNH18,
author = {Rachel C. W. Chan and
Maxwell W. Libbrecht and
Eric G. Roberts and
Jeffrey A. Bilmes and
William Stafford Noble and
Michael M. Hoffman},
title = {Segway 2.0: Gaussian mixture models and minibatch training},
journal = {Bioinform.},
volume = {34},
number = {4},
pages = {669--671},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx603},
doi = {10.1093/BIOINFORMATICS/BTX603},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChanLRBNH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuLYN18,
author = {Jie Liu and
Dejun Lin and
Galip G{\"{u}}rkan Yardimci and
William Stafford Noble},
title = {Unsupervised embedding of single-cell Hi-C data},
journal = {Bioinform.},
volume = {34},
number = {13},
pages = {i96--i104},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty285},
doi = {10.1093/BIOINFORMATICS/BTY285},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuLYN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UrsuBTWYNK18,
author = {Oana Ursu and
Nathan Boley and
Maryna Taranova and
Y. X. Rachel Wang and
Galip G{\"{u}}rkan Yardimci and
William Stafford Noble and
Anshul Kundaje},
title = {GenomeDISCO: a concordance score for chromosome conformation capture
experiments using random walks on contact map graphs},
journal = {Bioinform.},
volume = {34},
number = {16},
pages = {2701--2707},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty164},
doi = {10.1093/BIOINFORMATICS/BTY164},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/UrsuBTWYNK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/SurMJNM18,
author = {Aakash Sur and
Jackie McDonald and
Bryan Jensen and
William S. Noble and
Peter J. Myler},
title = {Unveiling Elements of Genomic Architecture with Genome Wide Chromatin
Conformation Capture},
booktitle = {{AMIA} 2018, American Medical Informatics Association Annual Symposium,
San Francisco, CA, November 3-7, 2018},
publisher = {{AMIA}},
year = {2018},
url = {https://knowledge.amia.org/67852-amia-1.4259402/t006-1.4263223/t006-1.4263224/2976805-1.4263273/2976877-1.4263270},
timestamp = {Wed, 17 Apr 2024 11:47:15 +0200},
biburl = {https://dblp.org/rec/conf/amia/SurMJNM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/LibbrechtBN18,
author = {Maxwell W. Libbrecht and
Jeffrey A. Bilmes and
William Stafford Noble},
editor = {Amarda Shehu and
Cathy H. Wu and
Christina Boucher and
Jing Li and
Hongfang Liu and
Mihai Pop},
title = {Choosing Non-redundant Representative Subsets Of Protein Sequence
Data Sets Using Submodular Optimization},
booktitle = {Proceedings of the 2018 {ACM} International Conference on Bioinformatics,
Computational Biology, and Health Informatics, {BCB} 2018, Washington,
DC, USA, August 29 - September 01, 2018},
pages = {566},
publisher = {{ACM}},
year = {2018},
url = {https://doi.org/10.1145/3233547.3233717},
doi = {10.1145/3233547.3233717},
timestamp = {Wed, 21 Nov 2018 12:44:25 +0100},
biburl = {https://dblp.org/rec/conf/bcb/LibbrechtBN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/BaiNB18,
author = {Wenruo Bai and
William Stafford Noble and
Jeff A. Bilmes},
editor = {Samy Bengio and
Hanna M. Wallach and
Hugo Larochelle and
Kristen Grauman and
Nicol{\`{o}} Cesa{-}Bianchi and
Roman Garnett},
title = {Submodular Maximization via Gradient Ascent: The Case of Deep Submodular
Functions},
booktitle = {Advances in Neural Information Processing Systems 31: Annual Conference
on Neural Information Processing Systems 2018, NeurIPS 2018, December
3-8, 2018, Montr{\'{e}}al, Canada},
pages = {7989--7999},
year = {2018},
url = {https://proceedings.neurips.cc/paper/2018/hash/b43a6403c17870707ca3c44984a2da22-Abstract.html},
timestamp = {Mon, 16 May 2022 15:41:51 +0200},
biburl = {https://dblp.org/rec/conf/nips/BaiNB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/LuFLN18,
author = {Yang Young Lu and
Yingying Fan and
Jinchi Lv and
William Stafford Noble},
editor = {Samy Bengio and
Hanna M. Wallach and
Hugo Larochelle and
Kristen Grauman and
Nicol{\`{o}} Cesa{-}Bianchi and
Roman Garnett},
title = {DeepPINK: reproducible feature selection in deep neural networks},
booktitle = {Advances in Neural Information Processing Systems 31: Annual Conference
on Neural Information Processing Systems 2018, NeurIPS 2018, December
3-8, 2018, Montr{\'{e}}al, Canada},
pages = {8690--8700},
year = {2018},
url = {https://proceedings.neurips.cc/paper/2018/hash/29daf9442f3c0b60642b14c081b4a556-Abstract.html},
timestamp = {Thu, 21 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/nips/LuFLN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1809-01185,
author = {Yang Young Lu and
Yingying Fan and
Jinchi Lv and
William Stafford Noble},
title = {DeepPINK: reproducible feature selection in deep neural networks},
journal = {CoRR},
volume = {abs/1809.01185},
year = {2018},
url = {http://arxiv.org/abs/1809.01185},
eprinttype = {arXiv},
eprint = {1809.01185},
timestamp = {Fri, 05 Oct 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1809-01185.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GabereN17,
author = {Musa Nur Gabere and
William Stafford Noble},
title = {Empirical comparison of web-based antimicrobial peptide prediction
tools},
journal = {Bioinform.},
volume = {33},
number = {13},
pages = {1921--1929},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx081},
doi = {10.1093/BIOINFORMATICS/BTX081},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GabereN17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YanYYNG17,
author = {Koon{-}Kiu Yan and
Galip G{\"{u}}rkan Yardimci and
Chengfei Yan and
William S. Noble and
Mark Gerstein},
title = {HiC-spector: a matrix library for spectral and reproducibility analysis
of Hi-C contact maps},
journal = {Bioinform.},
volume = {33},
number = {14},
pages = {2199--2201},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx152},
doi = {10.1093/BIOINFORMATICS/BTX152},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YanYYNG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaYRN17,
author = {Wenxiu Ma and
Lin Yang and
Remo Rohs and
William Stafford Noble},
title = {{DNA} sequence+shape kernel enables alignment-free modeling of transcription
factor binding},
journal = {Bioinform.},
volume = {33},
number = {19},
pages = {3003--3010},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx336},
doi = {10.1093/BIOINFORMATICS/BTX336},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaYRN17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/peerj-cs/SchreiberN17,
author = {Jacob M. Schreiber and
William S. Noble},
title = {Finding the optimal Bayesian network given a constraint graph},
journal = {PeerJ Comput. Sci.},
volume = {3},
pages = {e122},
year = {2017},
url = {https://doi.org/10.7717/peerj-cs.122},
doi = {10.7717/PEERJ-CS.122},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/peerj-cs/SchreiberN17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/Noble17,
author = {William Stafford Noble},
title = {Ten simple rules for writing a response to reviewers},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {10},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005730},
doi = {10.1371/JOURNAL.PCBI.1005730},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/Noble17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iclr/WangCBN17,
author = {Shengjie Wang and
Haoran Cai and
Jeff A. Bilmes and
William S. Noble},
title = {Training Compressed Fully-Connected Networks with a Density-Diversity
Penalty},
booktitle = {5th International Conference on Learning Representations, {ICLR} 2017,
Toulon, France, April 24-26, 2017, Conference Track Proceedings},
publisher = {OpenReview.net},
year = {2017},
url = {https://openreview.net/forum?id=Hku9NK5lx},
timestamp = {Thu, 25 Jul 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iclr/WangCBN17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/KeichN17,
author = {Uri Keich and
William Stafford Noble},
editor = {S{\"{u}}leyman Cenk Sahinalp},
title = {Progressive Calibration and Averaging for Tandem Mass Spectrometry
Statistical Confidence Estimation: Why Settle for a Single Decoy?},
booktitle = {Research in Computational Molecular Biology - 21st Annual International
Conference, {RECOMB} 2017, Hong Kong, China, May 3-7, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10229},
pages = {99--116},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-56970-3\_7},
doi = {10.1007/978-3-319-56970-3\_7},
timestamp = {Sat, 30 May 2020 20:04:52 +0200},
biburl = {https://dblp.org/rec/conf/recomb/KeichN17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/ml/NobleL17,
author = {William Stafford Noble and
Christina S. Leslie},
editor = {Claude Sammut and
Geoffrey I. Webb},
title = {Learning Models of Biological Sequences},
booktitle = {Encyclopedia of Machine Learning and Data Mining},
pages = {723--729},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-1-4899-7687-1\_468},
doi = {10.1007/978-1-4899-7687-1\_468},
timestamp = {Wed, 12 Jul 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/ml/NobleL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/peerjpre/SchreiberN17,
author = {Jacob M. Schreiber and
William S. Noble},
title = {Finding the optimal bayesian network given a constraint graph},
journal = {PeerJ Prepr.},
volume = {5},
pages = {e2872},
year = {2017},
url = {https://doi.org/10.7287/peerj.preprints.2872v1},
doi = {10.7287/PEERJ.PREPRINTS.2872V1},
timestamp = {Thu, 09 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/peerjpre/SchreiberN17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrantJBN16,
author = {Charles E. Grant and
James Johnson and
Timothy L. Bailey and
William Stafford Noble},
title = {{MCAST:} scanning for \emph{cis}-regulatory motif clusters},
journal = {Bioinform.},
volume = {32},
number = {8},
pages = {1217--1219},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv750},
doi = {10.1093/BIOINFORMATICS/BTV750},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrantJBN16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangHBN16,
author = {Shengjie Wang and
John T. Halloran and
Jeff A. Bilmes and
William S. Noble},
title = {Faster and more accurate graphical model identification of tandem
mass spectra using trellises},
journal = {Bioinform.},
volume = {32},
number = {12},
pages = {322--331},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw269},
doi = {10.1093/BIOINFORMATICS/BTW269},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangHBN16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/BaiBN16,
author = {Wenruo Bai and
Jeffrey A. Bilmes and
William S. Noble},
title = {Bipartite matching generalizations for peptide identification in tandem
mass spectrometry},
booktitle = {Proceedings of the 7th {ACM} International Conference on Bioinformatics,
Computational Biology, and Health Informatics, {BCB} 2016, Seattle,
WA, USA, October 2-5, 2016},
pages = {327--336},
publisher = {{ACM}},
year = {2016},
url = {https://doi.org/10.1145/2975167.2975201},
doi = {10.1145/2975167.2975201},
timestamp = {Tue, 06 Nov 2018 16:59:10 +0100},
biburl = {https://dblp.org/rec/conf/bcb/BaiBN16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BaileyJGN15,
author = {Timothy L. Bailey and
James Johnson and
Charles E. Grant and
William S. Noble},
title = {The {MEME} Suite},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Webserver-Issue},
pages = {W39--W49},
year = {2015},
url = {https://doi.org/10.1093/nar/gkv416},
doi = {10.1093/NAR/GKV416},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BaileyJGN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pnas/YardimciN15,
author = {Galip G{\"{u}}rkan Yardimci and
William Stafford Noble},
title = {Predictive model of 3D domain formation via CTCF-mediated extrusion},
journal = {Proc. Natl. Acad. Sci. {USA}},
volume = {112},
number = {47},
pages = {14404--14405},
year = {2015},
url = {https://doi.org/10.1073/pnas.1519849112},
doi = {10.1073/PNAS.1519849112},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pnas/YardimciN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/AydinBN15,
author = {Zafer Aydin and
David Baker and
William Stafford Noble},
editor = {Oscar Pastor and
Christine Sinoquet and
Ana L. N. Fred and
Hugo Gamboa and
Dirk Elias},
title = {Constructing Structural Profiles for Protein Torsion Angle Prediction},
booktitle = {{BIOINFORMATICS} 2015 - Proceedings of the International Conference
on Bioinformatics Models, Methods and Algorithms, Lisbon, Portugal,
12-15 January, 2015},
pages = {26--35},
publisher = {SciTePress},
year = {2015},
timestamp = {Thu, 21 Jan 2021 13:58:22 +0100},
biburl = {https://dblp.org/rec/conf/biostec/AydinBN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/AydinBN15a,
author = {Zafer Aydin and
David Baker and
William Stafford Noble},
editor = {Ana L. N. Fred and
Hugo Gamboa and
Dirk Elias},
title = {Template Scoring Methods for Protein Torsion Angle Prediction},
booktitle = {Biomedical Engineering Systems and Technologies - 8th International
Joint Conference, {BIOSTEC} 2015, Lisbon, Portugal, January 12-15,
2015, Revised Selected Papers},
series = {Communications in Computer and Information Science},
volume = {574},
pages = {206--223},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-27707-3\_13},
doi = {10.1007/978-3-319-27707-3\_13},
timestamp = {Sun, 02 Jun 2019 21:12:03 +0200},
biburl = {https://dblp.org/rec/conf/biostec/AydinBN15a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/LibbrechtHBN15,
author = {Maxwell W. Libbrecht and
Michael M. Hoffman and
Jeff A. Bilmes and
William Stafford Noble},
editor = {Francis R. Bach and
David M. Blei},
title = {Entropic Graph-based Posterior Regularization},
booktitle = {Proceedings of the 32nd International Conference on Machine Learning,
{ICML} 2015, Lille, France, 6-11 July 2015},
series = {{JMLR} Workshop and Conference Proceedings},
volume = {37},
pages = {1992--2001},
publisher = {JMLR.org},
year = {2015},
url = {http://proceedings.mlr.press/v37/libbrecht15.html},
timestamp = {Wed, 29 May 2019 08:41:45 +0200},
biburl = {https://dblp.org/rec/conf/icml/LibbrechtHBN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VaroquauxANV14,
author = {Nelle Varoquaux and
Ferhat Ay and
William Stafford Noble and
Jean{-}Philippe Vert},
title = {A statistical approach for inferring the 3D structure of the genome},
journal = {Bioinform.},
volume = {30},
number = {12},
pages = {26--33},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu268},
doi = {10.1093/BIOINFORMATICS/BTU268},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VaroquauxANV14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/HoJLALISMTAPGKR14,
author = {Joshua Wing Kei Ho and
Youngsook L. Jung and
Tao Liu and
Burak Han Alver and
Soohyun Lee and
Kohta Ikegami and
Kyung{-}Ah Sohn and
Aki Minoda and
Michael Y. Tolstorukov and
Alex Appert and
Stephen C. J. Parker and
Tingting Gu and
Anshul Kundaje and
Nicole C. Riddle and
Eric Bishop and
Thea A. Egelhofer and
Sheng'en Shawn Hu and
Artyom A. Alekseyenko and
Andreas Rechtsteiner and
Dalal Asker and
Jason A. Belsky and
Sarah K. Bowman and
Q. Brent Chen and
Ron A.{-}J. Chen and
Daniel S. Day and
Yan Dong and
Andrea C. Dose and
Xikun Duan and
Charles B. Epstein and
Sevinc Ercan and
Elise A. Feingold and
Francesco Ferrari and
Jacob M. Garrigues and
Nils Gehlenborg and
Peter J. Good and
Psalm Haseley and
Daniel He and
Moritz Herrmann and
Michael M. Hoffman and
Tess E. Jeffers and
Peter V. Kharchenko and
Paulina Kolasinska{-}Zwierz and
Chitra V. Kotwaliwale and
Nischay Kumar and
Sasha A. Langley and
Erica Larschan and
Isabel Latorre and
Maxwell W. Libbrecht and
Xueqiu Lin and
Richard Park and
Michael J. Pazin and
Hoang N. Pham and
Annette Plachetka and
Bo Qin and
Yuri B. Schwartz and
Noam Shoresh and
Przemyslaw Stempor and
Anne Vielle and
Chengyang Wang and
Christina M. Whittle and
Huiling Xue and
Robert E. Kingston and
Ju Han Kim and
Bradley E. Bernstein and
Abby F. Dernburg and
Vincenzo Pirrotta and
Mitzi I. Kuroda and
William S. Noble and
Thomas D. Tullius and
Manolis Kellis and
David M. MacAlpine and
Susan Strome and
Sarah C. R. Elgin and
Xiaole Shirley Liu and
Jason D. Lieb and
Julie Ahringer and
Gary H. Karpen and
Peter J. Park},
title = {Comparative analysis of metazoan chromatin organization Open},
journal = {Nat.},
volume = {512},
number = {7515},
pages = {449--452},
year = {2014},
url = {https://doi.org/10.1038/nature13415},
doi = {10.1038/NATURE13415},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nature/HoJLALISMTAPGKR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ZareWHWSNSWBN14,
author = {Habil Zare and
Junfeng Wang and
Alex Hu and
Kris Weber and
Joshua D. Smith and
Deborah A. Nickerson and
ChaoZhong Song and
Daniela M. Witten and
C. Anthony Blau and
William Stafford Noble},
title = {Inferring Clonal Composition from Multiple Sections of a Breast Cancer},
journal = {PLoS Comput. Biol.},
volume = {10},
number = {7},
year = {2014},
url = {https://doi.org/10.1371/journal.pcbi.1003703},
doi = {10.1371/JOURNAL.PCBI.1003703},
timestamp = {Thu, 25 Nov 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/ZareWHWSNSWBN14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/uai/HalloranBN14,
author = {John T. Halloran and
Jeff A. Bilmes and
William Stafford Noble},
editor = {Nevin L. Zhang and
Jin Tian},
title = {Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry},
booktitle = {Proceedings of the Thirtieth Conference on Uncertainty in Artificial
Intelligence, {UAI} 2014, Quebec City, Quebec, Canada, July 23-27,
2014},
pages = {320--329},
publisher = {{AUAI} Press},
year = {2014},
url = {https://dslpitt.org/uai/displayArticleDetails.jsp?mmnu=1\&\#38;smnu=2\&\#38;article\_id=2467\&\#38;proceeding\_id=30},
timestamp = {Wed, 03 Feb 2021 11:09:27 +0100},
biburl = {https://dblp.org/rec/conf/uai/HalloranBN14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/HoffmanBWWBN13,
author = {Michael M. Hoffman and
Orion J. Buske and
Jie Wang and
Zhiping Weng and
Jeff A. Bilmes and
William Stafford Noble},
editor = {Jing Gao},
title = {Unsupervised pattern discovery in human chromatin structure through
genomic segmentation},
booktitle = {{ACM} Conference on Bioinformatics, Computational Biology and Biomedical
Informatics. {ACM-BCB} 2013, Washington, DC, USA, September 22-25,
2013},
pages = {813},
publisher = {{ACM}},
year = {2013},
url = {https://doi.org/10.1145/2506583.2506701},
doi = {10.1145/2506583.2506701},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/HoffmanBWWBN13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/HarteminkKNW13,
author = {Alexander J. Hartemink and
Manolis Kellis and
William Stafford Noble and
Zhiping Weng},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Session Introduction},
booktitle = {Biocomputing 2013: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2013},
pages = {65--68},
publisher = {World Scientific Publishing},
year = {2013},
url = {http://psb.stanford.edu/psb-online/proceedings/psb13/intro-epigenomics.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/HarteminkKNW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Cuellar-PartidaBMWNB12,
author = {Gabriel Cu{\'{e}}llar{-}Partida and
Fabian A. Buske and
Robert C. McLeay and
Tom Whitington and
William Stafford Noble and
Timothy L. Bailey},
title = {Epigenetic priors for identifying active transcription factor binding
sites},
journal = {Bioinform.},
volume = {28},
number = {1},
pages = {56--62},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/btr614},
doi = {10.1093/BIOINFORMATICS/BTR614},
timestamp = {Wed, 22 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Cuellar-PartidaBMWNB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/McIlwainMBRMN12,
author = {Sean McIlwain and
Michael Mathews and
Michael Bereman and
Edwin W. Rubel and
Michael J. MacCoss and
William Stafford Noble},
title = {Estimating relative abundances of proteins from shotgun proteomics
data},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {308},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-308},
doi = {10.1186/1471-2105-13-308},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/McIlwainMBRMN12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GranholmNK12,
author = {Viktor Granholm and
William Stafford Noble and
Lukas K{\"{a}}ll},
title = {A cross-validation scheme for machine learning algorithms in shotgun
proteomics},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-16}},
pages = {S3},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S16-S3},
doi = {10.1186/1471-2105-13-S16-S3},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GranholmNK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/NobleM12,
author = {William Stafford Noble and
Michael J. MacCoss},
title = {Computational and Statistical Analysis of Protein Mass Spectrometry
Data},
journal = {PLoS Comput. Biol.},
volume = {8},
number = {1},
year = {2012},
url = {https://doi.org/10.1371/journal.pcbi.1002296},
doi = {10.1371/JOURNAL.PCBI.1002296},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/NobleM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/SerangN12,
author = {Oliver Serang and
William Stafford Noble},
title = {Faster Mass Spectrometry-Based Protein Inference: Junction Trees Are
More Efficient than Sampling and Marginalization by Enumeration},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {3},
pages = {809--817},
year = {2012},
url = {https://doi.org/10.1109/TCBB.2012.26},
doi = {10.1109/TCBB.2012.26},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/SerangN12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/RyuGNM12,
author = {Soyoung Ryu and
David R. Goodlett and
William S. Noble and
Vladimir N. Minin},
title = {A statistical approach to peptide identification from clustered tandem
mass spectrometry data},
booktitle = {2012 {IEEE} International Conference on Bioinformatics and Biomedicine
Workshops, {BIBMW} 2012, Philadelphia, USA, October 4-7, 2012},
pages = {648--653},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/BIBMW.2012.6470214},
doi = {10.1109/BIBMW.2012.6470214},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/RyuGNM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/NobleBDDM12,
author = {William Stafford Noble and
C. Anthony Blau and
Job Dekker and
Zhi{-}jun Duan and
Yi Mao},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {The Structure and Function of Chromatin and Chromosomes},
booktitle = {Biocomputing 2012: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2012},
pages = {434--440},
publisher = {World Scientific Publishing},
year = {2012},
url = {http://psb.stanford.edu/psb-online/proceedings/psb12/wkshop-sfcc.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/NobleBDDM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/uai/SinghHBKN12,
author = {Ajit P. Singh and
John T. Halloran and
Jeff A. Bilmes and
Katrin Kirchhoff and
William Stafford Noble},
editor = {Nando de Freitas and
Kevin P. Murphy},
title = {Spectrum Identification using a Dynamic Bayesian Network Model of
Tandem Mass Spectra},
booktitle = {Proceedings of the Twenty-Eighth Conference on Uncertainty in Artificial
Intelligence, Catalina Island, CA, USA, August 14-18, 2012},
pages = {775--785},
publisher = {{AUAI} Press},
year = {2012},
url = {https://dslpitt.org/uai/displayArticleDetails.jsp?mmnu=1\&\#38;smnu=2\&\#38;article\_id=2343\&\#38;proceeding\_id=28},
timestamp = {Mon, 23 Nov 2020 08:36:48 +0100},
biburl = {https://dblp.org/rec/conf/uai/SinghHBKN12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1210-4904,
author = {Ajit P. Singh and
John T. Halloran and
Jeff A. Bilmes and
Katrin Kirchhoff and
William Stafford Noble},
title = {Spectrum Identification using a Dynamic Bayesian Network Model of
Tandem Mass Spectra},
journal = {CoRR},
volume = {abs/1210.4904},
year = {2012},
url = {http://arxiv.org/abs/1210.4904},
eprinttype = {arXiv},
eprint = {1210.4904},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1210-4904.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrantBN11,
author = {Charles E. Grant and
Timothy L. Bailey and
William Stafford Noble},
title = {{FIMO:} scanning for occurrences of a given motif},
journal = {Bioinform.},
volume = {27},
number = {7},
pages = {1017--1018},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr064},
doi = {10.1093/BIOINFORMATICS/BTR064},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrantBN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TanakaBGNK11,
author = {Emi Tanaka and
Timothy L. Bailey and
Charles E. Grant and
William Stafford Noble and
Uri Keich},
title = {Improved similarity scores for comparing motifs},
journal = {Bioinform.},
volume = {27},
number = {12},
pages = {1603--1609},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr257},
doi = {10.1093/BIOINFORMATICS/BTR257},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TanakaBGNK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AydinSBN11,
author = {Zafer Aydin and
Ajit P. Singh and
Jeff A. Bilmes and
William Stafford Noble},
title = {Learning sparse models for a dynamic Bayesian network classifier of
protein secondary structure},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {154},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-154},
doi = {10.1186/1471-2105-12-154},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AydinSBN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BuskeHPRN11,
author = {Orion J. Buske and
Michael M. Hoffman and
Nadia Ponts and
Karine G. Le Roch and
William Stafford Noble},
title = {Exploratory analysis of genomic segmentations with Segtools},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {415},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-415},
doi = {10.1186/1471-2105-12-415},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BuskeHPRN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/MelvinWNL11,
author = {Iain Melvin and
Jason Weston and
William Stafford Noble and
Christina S. Leslie},
title = {Detecting Remote Evolutionary Relationships among Proteins by Large-Scale
Semantic Embedding},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {1},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1001047},
doi = {10.1371/JOURNAL.PCBI.1001047},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/MelvinWNL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/NobleDASMKLSFB11,
author = {William Stafford Noble and
Zhi{-}jun Duan and
Mirela Andronescu and
Kevin Schutz and
Sean McIlwain and
Yoo Jung Kim and
Choli Lee and
Jay Shendure and
Stanley Fields and
C. Anthony Blau},
editor = {Vineet Bafna and
S{\"{u}}leyman Cenk Sahinalp},
title = {A Three-Dimensional Model of the Yeast Genome},
booktitle = {Research in Computational Molecular Biology - 15th Annual International
Conference, {RECOMB} 2011, Vancouver, BC, Canada, March 28-31, 2011.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6577},
pages = {320},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-20036-6\_28},
doi = {10.1007/978-3-642-20036-6\_28},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/NobleDASMKLSFB11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/daglib/p/QiN11,
author = {Yanjun Qi and
William Stafford Noble},
editor = {Henry Horng{-}Shing Lu and
Bernhard Sch{\"{o}}lkopf and
Hongyu Zhao},
title = {Protein Interaction Networks: Protein Domain Interaction and Protein
Function Prediction},
booktitle = {Handbook of Statistical Bioinformatics},
series = {Springer Handbooks of Computational Statistics},
pages = {427--459},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-16345-6\_21},
doi = {10.1007/978-3-642-16345-6\_21},
timestamp = {Wed, 14 Nov 2018 10:12:21 +0100},
biburl = {https://dblp.org/rec/books/daglib/p/QiN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HoffmanBN10,
author = {Michael M. Hoffman and
Orion J. Buske and
William Stafford Noble},
title = {The Genomedata format for storing large-scale functional genomics
data},
journal = {Bioinform.},
volume = {26},
number = {11},
pages = {1458--1459},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq164},
doi = {10.1093/BIOINFORMATICS/BTQ164},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HoffmanBN10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenHBHN10,
author = {Xiaoyu Chen and
Michael M. Hoffman and
Jeff A. Bilmes and
Jay R. Hesselberth and
William Stafford Noble},
title = {A dynamic Bayesian network for identifying protein-binding footprints
from single molecule-based sequencing data},
journal = {Bioinform.},
volume = {26},
number = {12},
pages = {334--342},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq175},
doi = {10.1093/BIOINFORMATICS/BTQ175},
timestamp = {Tue, 01 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenHBHN10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AydinMWN10,
author = {Zafer Aydin and
John I. Murray and
Robert H. Waterston and
William Stafford Noble},
title = {Using machine learning to speed up manual image annotation: application
to a 3D imaging protocol for measuring single cell gene expression
in the developing \emph{C. elegans} embryo},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {84},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-84},
doi = {10.1186/1471-2105-11-84},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AydinMWN10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HueRVN10,
author = {Martial Hue and
Michael Riffle and
Jean{-}Philippe Vert and
William Stafford Noble},
title = {Large-scale prediction of protein-protein interactions from structures},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {144},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-144},
doi = {10.1186/1471-2105-11-144},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HueRVN10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cominfsys/GrammKNSWY10,
author = {Jens Gramm and
Richard M. Karp and
William S. Noble and
Roded Sharan and
Qianfei Wang and
Nir Yosef},
title = {Prediction of Phenotype Information from Genotype Data},
journal = {Commun. Inf. Syst.},
volume = {10},
number = {2},
pages = {99--114},
year = {2010},
url = {https://doi.org/10.4310/cis.2010.v10.n2.a3},
doi = {10.4310/CIS.2010.V10.N2.A3},
timestamp = {Wed, 16 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cominfsys/GrammKNSWY10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ReynoldsBN10,
author = {Sheila M. Reynolds and
Jeff A. Bilmes and
William Stafford Noble},
title = {Learning a Weighted Sequence Model of the Nucleosome Core and Linker
Yields More Accurate Predictions in \emph{Saccharomyces cerevisiae}
and \emph{Homo sapiens}},
journal = {PLoS Comput. Biol.},
volume = {6},
number = {7},
year = {2010},
url = {https://doi.org/10.1371/journal.pcbi.1000834},
doi = {10.1371/JOURNAL.PCBI.1000834},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ReynoldsBN10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/AgiusACNL10,
author = {Phaedra Agius and
Aaron Arvey and
William Chang and
William Stafford Noble and
Christina S. Leslie},
title = {High Resolution Models of Transcription Factor-DNA Affinities Improve
\emph{In Vitro} and \emph{In Vivo} Binding Predictions},
journal = {PLoS Comput. Biol.},
volume = {6},
number = {9},
year = {2010},
url = {https://doi.org/10.1371/journal.pcbi.1000916},
doi = {10.1371/JOURNAL.PCBI.1000916},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/AgiusACNL10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ReynoldsWBN10,
author = {Sheila M. Reynolds and
Zhiping Weng and
Jeff A. Bilmes and
William Stafford Noble},
editor = {Bonnie Berger},
title = {Predicting Nucleosome Positioning Using Multiple Evidence Tracks},
booktitle = {Research in Computational Molecular Biology, 14th Annual International
Conference, {RECOMB} 2010, Lisbon, Portugal, April 25-28, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6044},
pages = {441--455},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-12683-3\_29},
doi = {10.1007/978-3-642-12683-3\_29},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ReynoldsWBN10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/ml/NobleL10,
author = {William Stafford Noble and
Christina S. Leslie},
editor = {Claude Sammut and
Geoffrey I. Webb},
title = {Learning Models of Biological Sequences},
booktitle = {Encyclopedia of Machine Learning},
pages = {590--594},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-0-387-30164-8\_463},
doi = {10.1007/978-0-387-30164-8\_463},
timestamp = {Wed, 14 Nov 2018 10:51:34 +0100},
biburl = {https://dblp.org/rec/reference/ml/NobleL10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MelvinWLN09,
author = {Iain Melvin and
Jason Weston and
Christina S. Leslie and
William Stafford Noble},
title = {{RANKPROP:} a web server for protein remote homology detection},
journal = {Bioinform.},
volume = {25},
number = {1},
pages = {121--122},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btn567},
doi = {10.1093/BIOINFORMATICS/BTN567},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MelvinWLN09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KallSN09,
author = {Lukas K{\"{a}}ll and
John D. Storey and
William Stafford Noble},
title = {{QVALITY:} non-parametric estimation of \emph{q}-values and posterior
error probabilities},
journal = {Bioinform.},
volume = {25},
number = {7},
pages = {964--966},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp021},
doi = {10.1093/BIOINFORMATICS/BTP021},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KallSN09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HawkinsGNB09,
author = {John Hawkins and
Charles E. Grant and
William Stafford Noble and
Timothy L. Bailey},
title = {Assessing phylogenetic motif models for predicting transcription factor
binding sites},
journal = {Bioinform.},
volume = {25},
number = {12},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp201},
doi = {10.1093/BIOINFORMATICS/BTP201},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HawkinsGNB09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BaileyBBFGCRLN09,
author = {Timothy L. Bailey and
Mikael Bod{\'{e}}n and
Fabian A. Buske and
Martin C. Frith and
Charles E. Grant and
Luca Clementi and
Jingyuan Ren and
Wilfred W. Li and
William Stafford Noble},
title = {{MEME} {SUITE:} tools for motif discovery and searching},
journal = {Nucleic Acids Res.},
volume = {37},
number = {Web-Server-Issue},
pages = {202--208},
year = {2009},
url = {https://doi.org/10.1093/nar/gkp335},
doi = {10.1093/NAR/GKP335},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BaileyBBFGCRLN09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/Noble09,
author = {William Stafford Noble},
title = {A Quick Guide to Organizing Computational Biology Projects},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {7},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000424},
doi = {10.1371/JOURNAL.PCBI.1000424},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/Noble09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ReynoldsBN09,
author = {Sheila M. Reynolds and
Jeff A. Bilmes and
William Stafford Noble},
editor = {Serafim Batzoglou},
title = {On the Relationship between {DNA} Periodicity and Local Chromatin
Structure},
booktitle = {Research in Computational Molecular Biology, 13th Annual International
Conference, {RECOMB} 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5541},
pages = {434--450},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02008-7\_31},
doi = {10.1007/978-3-642-02008-7\_31},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ReynoldsBN09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LianTTSNL08,
author = {Heng Lian and
William A. Thompson and
Robert E. Thurman and
John A. Stamatoyannopoulos and
William Stafford Noble and
Charles E. Lawrence},
title = {Automated mapping of large-scale chromatin structure in {ENCODE}},
journal = {Bioinform.},
volume = {24},
number = {17},
pages = {1911--1916},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn335},
doi = {10.1093/BIOINFORMATICS/BTN335},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LianTTSNL08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MelvinWLN08,
author = {Iain Melvin and
Jason Weston and
Christina S. Leslie and
William Stafford Noble},
title = {Combining classifiers for improved classification of proteins from
sequence or structure},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-389},
doi = {10.1186/1471-2105-9-389},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MelvinWLN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/QiuN08,
author = {Jian Qiu and
William Stafford Noble},
title = {Predicting Co-Complexed Protein Pairs from Heterogeneous Data},
journal = {PLoS Comput. Biol.},
volume = {4},
number = {4},
year = {2008},
url = {https://doi.org/10.1371/journal.pcbi.1000054},
doi = {10.1371/JOURNAL.PCBI.1000054},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/QiuN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/GuptaDTKSN08,
author = {Shobhit Gupta and
Jonathan H. Dennis and
Robert E. Thurman and
Robert E. Kingston and
John A. Stamatoyannopoulos and
William Stafford Noble},
title = {Predicting Human Nucleosome Occupancy from Primary Sequence},
journal = {PLoS Comput. Biol.},
volume = {4},
number = {8},
year = {2008},
url = {https://doi.org/10.1371/journal.pcbi.1000134},
doi = {10.1371/JOURNAL.PCBI.1000134},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/GuptaDTKSN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ReynoldsKRBN08,
author = {Sheila M. Reynolds and
Lukas K{\"{a}}ll and
Michael Riffle and
Jeff A. Bilmes and
William Stafford Noble},
title = {Transmembrane Topology and Signal Peptide Prediction Using Dynamic
Bayesian Networks},
journal = {PLoS Comput. Biol.},
volume = {4},
number = {11},
year = {2008},
url = {https://doi.org/10.1371/journal.pcbi.1000213},
doi = {10.1371/JOURNAL.PCBI.1000213},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ReynoldsKRBN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/KallSN08,
author = {Lukas K{\"{a}}ll and
John D. Storey and
William Stafford Noble},
title = {Non-parametric estimation of posterior error probabilities associated
with peptides identified by tandem mass spectrometry},
booktitle = {ECCB'08 Proceedings, Seventh European Conference on Computational
Biology, 22-26 September 2008, Cagliari, Italy},
pages = {42--48},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn294},
doi = {10.1093/BIOINFORMATICS/BTN294},
timestamp = {Fri, 30 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eccb/KallSN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/YosefSN08,
author = {Nir Yosef and
Roded Sharan and
William Stafford Noble},
title = {Improved network-based identification of protein orthologs},
booktitle = {ECCB'08 Proceedings, Seventh European Conference on Computational
Biology, 22-26 September 2008, Cagliari, Italy},
pages = {200--206},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn277},
doi = {10.1093/BIOINFORMATICS/BTN277},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eccb/YosefSN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/KlammerRBMN08,
author = {Aaron A. Klammer and
Sheila M. Reynolds and
Jeff A. Bilmes and
Michael J. MacCoss and
William Stafford Noble},
title = {Modeling peptide fragmentation with dynamic Bayesian networks for
peptide identification},
booktitle = {Proceedings 16th International Conference on Intelligent Systems for
Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008},
pages = {348--356},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn189},
doi = {10.1093/BIOINFORMATICS/BTN189},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/KlammerRBMN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/ThurmanNS08,
author = {Robert E. Thurman and
William Stafford Noble and
John A. Stamatoyannopoulos},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Multi-Scale Correlations in Continuous Genomic Data},
booktitle = {Biocomputing 2008, Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, 4-8 January 2008},
pages = {201--215},
publisher = {World Scientific},
year = {2008},
url = {http://psb.stanford.edu/psb-online/proceedings/psb08/thurman.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/ThurmanNS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QiuHBVN07,
author = {Jian Qiu and
Martial Hue and
Asa Ben{-}Hur and
Jean{-}Philippe Vert and
William Stafford Noble},
title = {A structural alignment kernel for protein structures},
journal = {Bioinform.},
volume = {23},
number = {9},
pages = {1090--1098},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btl642},
doi = {10.1093/BIOINFORMATICS/BTL642},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/QiuHBVN07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DayHTSN07,
author = {Nathan Day and
Andrew Hemmaplardh and
Robert E. Thurman and
John A. Stamatoyannopoulos and
William Stafford Noble},
title = {Unsupervised segmentation of continuous genomic data},
journal = {Bioinform.},
volume = {23},
number = {11},
pages = {1424--1426},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm096},
doi = {10.1093/BIOINFORMATICS/BTM096},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DayHTSN07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChechikLNRMT07,
author = {Gal Chechik and
Christina S. Leslie and
William Stafford Noble and
Gunnar R{\"{a}}tsch and
Quaid Morris and
Koji Tsuda},
title = {{NIPS} workshop on New Problems and Methods in Computational Biology},
journal = {{BMC} Bioinform.},
volume = {8},
number = {{S-10}},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-S10-S1},
doi = {10.1186/1471-2105-8-S10-S1},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChechikLNRMT07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VertQN07,
author = {Jean{-}Philippe Vert and
Jian Qiu and
William Stafford Noble},
title = {A new pairwise kernel for biological network inference with support
vector machines},
journal = {{BMC} Bioinform.},
volume = {8},
number = {{S-10}},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-S10-S8},
doi = {10.1186/1471-2105-8-S10-S8},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/VertQN07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MelvinIKWNL07,
author = {Iain Melvin and
Eugene Ie and
Rui Kuang and
Jason Weston and
William Stafford Noble and
Christina S. Leslie},
title = {SVM-Fold: a tool for discriminative multi-class protein fold and superfamily
recognition},
journal = {{BMC} Bioinform.},
volume = {8},
number = {{S-4}},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-S4-S2},
doi = {10.1186/1471-2105-8-S4-S2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MelvinIKWNL07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jmlr/MelvinIWNL07,
author = {Iain Melvin and
Eugene Ie and
Jason Weston and
William Stafford Noble and
Christina S. Leslie},
title = {Multi-class Protein Classification Using Adaptive Codes},
journal = {J. Mach. Learn. Res.},
volume = {8},
pages = {1557--1581},
year = {2007},
url = {https://dl.acm.org/doi/10.5555/1314498.1314551},
doi = {10.5555/1314498.1314551},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jmlr/MelvinIWNL07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/KlammerYMN07,
author = {Aaron A. Klammer and
Xianhua Yi and
Michael J. MacCoss and
William Stafford Noble},
editor = {Terence P. Speed and
Haiyan Huang},
title = {Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum
Identification for Diverse Chromatography Conditions},
booktitle = {Research in Computational Molecular Biology, 11th Annual International
Conference, {RECOMB} 2007, Oakland, CA, USA, April 21-25, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4453},
pages = {459--472},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-71681-5\_32},
doi = {10.1007/978-3-540-71681-5\_32},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/KlammerYMN07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LewisJN06,
author = {Darrin P. Lewis and
Tony Jebara and
William Stafford Noble},
title = {Support vector machine learning from heterogeneous data: an empirical
analysis using protein sequence and structure},
journal = {Bioinform.},
volume = {22},
number = {22},
pages = {2753--2760},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl475},
doi = {10.1093/BIOINFORMATICS/BTL475},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LewisJN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Ben-HurN06,
author = {Asa Ben{-}Hur and
William Stafford Noble},
title = {Choosing negative examples for the prediction of protein-protein interactions},
journal = {{BMC} Bioinform.},
volume = {7},
number = {{S-1}},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-S1-S2},
doi = {10.1186/1471-2105-7-S1-S2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/Ben-HurN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WestonKLN06,
author = {Jason Weston and
Rui Kuang and
Christina S. Leslie and
William Stafford Noble},
title = {Protein Ranking by Semi-Supervised Network Propagation},
journal = {{BMC} Bioinform.},
volume = {7},
number = {{S-1}},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-S1-S10},
doi = {10.1186/1471-2105-7-S1-S10},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WestonKLN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/MannHSN06,
author = {Tobias P. Mann and
Richard Humbert and
John A. Stamatoyannopoulos and
William Stafford Noble},
title = {Automated Validation of Polymerase Chain Reaction Amplicon Melting
Curves},
journal = {J. Bioinform. Comput. Biol.},
volume = {4},
number = {2},
pages = {299--316},
year = {2006},
url = {https://doi.org/10.1142/S0219720006001989},
doi = {10.1142/S0219720006001989},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/MannHSN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/LewisJN06,
author = {Darrin P. Lewis and
Tony Jebara and
William Stafford Noble},
editor = {William W. Cohen and
Andrew W. Moore},
title = {Nonstationary kernel combination},
booktitle = {Machine Learning, Proceedings of the Twenty-Third International Conference
{(ICML} 2006), Pittsburgh, Pennsylvania, USA, June 25-29, 2006},
series = {{ACM} International Conference Proceeding Series},
volume = {148},
pages = {553--560},
publisher = {{ACM}},
year = {2006},
url = {https://doi.org/10.1145/1143844.1143914},
doi = {10.1145/1143844.1143914},
timestamp = {Tue, 19 Nov 2019 09:25:06 +0100},
biburl = {https://dblp.org/rec/conf/icml/LewisJN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/MannN06,
author = {Tobias P. Mann and
William Stafford Noble},
title = {Efficient identification of {DNA} hybridization partners in a sequence
database},
booktitle = {Proceedings 14th International Conference on Intelligent Systems for
Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006},
pages = {350--358},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl240},
doi = {10.1093/BIOINFORMATICS/BTL240},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/MannN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/mit/06/WestonLIN06,
author = {Jason Weston and
Christina S. Leslie and
Eugene Ie and
William Stafford Noble},
editor = {Olivier Chapelle and
Bernhard Sch{\"{o}}lkopf and
Alexander Zien},
title = {Semi-Supervised Protein Classification Using Cluster Kernels},
booktitle = {Semi-Supervised Learning},
pages = {342--360},
publisher = {The {MIT} Press},
year = {2006},
url = {https://doi.org/10.7551/mitpress/9780262033589.003.0019},
doi = {10.7551/MITPRESS/9780262033589.003.0019},
timestamp = {Mon, 22 Jul 2019 15:58:13 +0200},
biburl = {https://dblp.org/rec/books/mit/06/WestonLIN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-q-bio-0610040,
author = {Jean{-}Philippe Vert and
Jian Qiu and
William Stafford Noble},
title = {Metric learning pairwise kernel for graph inference},
journal = {CoRR},
volume = {abs/q-bio/0610040},
year = {2006},
url = {http://arxiv.org/abs/q-bio/0610040},
eprinttype = {arXiv},
eprint = {q-bio/0610040},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-q-bio-0610040.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WestonLIZEN05,
author = {Jason Weston and
Christina S. Leslie and
Eugene Ie and
Dengyong Zhou and
Andr{\'{e}} Elisseeff and
William Stafford Noble},
title = {Semi-supervised protein classification using cluster kernels},
journal = {Bioinform.},
volume = {21},
number = {15},
pages = {3241--3247},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti497},
doi = {10.1093/BIOINFORMATICS/BTI497},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WestonLIZEN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KuangWNL05,
author = {Rui Kuang and
Jason Weston and
William Stafford Noble and
Christina S. Leslie},
title = {Motif-based protein ranking by network propagation},
journal = {Bioinform.},
volume = {21},
number = {19},
pages = {3711--3718},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti608},
doi = {10.1093/BIOINFORMATICS/BTI608},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KuangWNL05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LingNY05,
author = {Charles X. Ling and
William Stafford Noble and
Qiang Yang},
title = {Guest Editors' Introduction to the Special Issue: Machine Learning
for Bioinformatics - Part 1},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {2},
number = {2},
pages = {81--82},
year = {2005},
url = {https://doi.org/10.1109/TCBB.2005.25},
doi = {10.1109/TCBB.2005.25},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LingNY05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LingNY05a,
author = {Charles X. Ling and
William Stafford Noble and
Qiang Yang},
title = {Guest Editor's Introduction to the Special Issue: Machine Learning
for Bioinformatics-Part 2},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {2},
number = {3},
pages = {177--178},
year = {2005},
url = {https://doi.org/10.1109/TCBB.2005.41},
doi = {10.1109/TCBB.2005.41},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LingNY05a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/ShefflerUSN05,
author = {Will Sheffler and
Eli Upfal and
John Sedivy and
William Stafford Noble},
title = {A Learned Comparative Expression Measure for Affymetrix GeneChip {DNA}
Microarrays},
booktitle = {Fourth International {IEEE} Computer Society Computational Systems
Bioinformatics Conference, {CSB} 2005, Stanford, CA, USA, August 8-11,
2005},
pages = {144--154},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/CSB.2005.5},
doi = {10.1109/CSB.2005.5},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/ShefflerUSN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/KlammerWMN05,
author = {Aaron A. Klammer and
Christine C. Wu and
Michael J. MacCoss and
William Stafford Noble},
title = {Peptide Charge State Determination for Low-Resolution Tandem Mass
Spectra},
booktitle = {Fourth International {IEEE} Computer Society Computational Systems
Bioinformatics Conference, {CSB} 2005, Stanford, CA, USA, August 8-11,
2005},
pages = {175--185},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/CSB.2005.44},
doi = {10.1109/CSB.2005.44},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/KlammerWMN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/MannHSN05,
author = {Tobias P. Mann and
Richard Humbert and
John A. Stamatoyannopoulos and
William Stafford Noble},
title = {Automated Validation of Polymerase Chain Reactions Using Amplicon
Melting Curves},
booktitle = {Fourth International {IEEE} Computer Society Computational Systems
Bioinformatics Conference, {CSB} 2005, Stanford, CA, USA, August 8-11,
2005},
pages = {377--385},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/CSB.2005.17},
doi = {10.1109/CSB.2005.17},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/MannHSN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/IeWNL05,
author = {Eugene Ie and
Jason Weston and
William Stafford Noble and
Christina S. Leslie},
editor = {Luc De Raedt and
Stefan Wrobel},
title = {Multi-class protein fold recognition using adaptive codes},
booktitle = {Machine Learning, Proceedings of the Twenty-Second International Conference
{(ICML} 2005), Bonn, Germany, August 7-11, 2005},
series = {{ACM} International Conference Proceeding Series},
volume = {119},
pages = {329--336},
publisher = {{ACM}},
year = {2005},
url = {https://doi.org/10.1145/1102351.1102393},
doi = {10.1145/1102351.1102393},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icml/IeWNL05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/Ben-HurN05,
author = {Asa Ben{-}Hur and
William Stafford Noble},
title = {Kernel methods for predicting protein-protein interactions},
booktitle = {Proceedings Thirteenth International Conference on Intelligent Systems
for Molecular Biology 2005, Detroit, MI, USA, 25-29 June 2005},
pages = {38--46},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti1016},
doi = {10.1093/BIOINFORMATICS/BTI1016},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/Ben-HurN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/NobleKTYS05,
author = {William Stafford Noble and
Scott Kuehn and
Robert E. Thurman and
Man Yu and
John A. Stamatoyannopoulos},
title = {Predicting the \emph{in vivo} signature of human gene regulatory sequence},
booktitle = {Proceedings Thirteenth International Conference on Intelligent Systems
for Molecular Biology 2005, Detroit, MI, USA, 25-29 June 2005},
pages = {328--343},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti1047},
doi = {10.1093/BIOINFORMATICS/BTI1047},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/NobleKTYS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/VertTN05,
author = {Jean{-}Philippe Vert and
Robert E. Thurman and
William Stafford Noble},
title = {Kernels for gene regulatory regions},
booktitle = {Advances in Neural Information Processing Systems 18 [Neural Information
Processing Systems, {NIPS} 2005, December 5-8, 2005, Vancouver, British
Columbia, Canada]},
pages = {1401--1408},
year = {2005},
url = {https://proceedings.neurips.cc/paper/2005/hash/bd1354624fbae3b2149878941c60df99-Abstract.html},
timestamp = {Mon, 16 May 2022 15:41:51 +0200},
biburl = {https://dblp.org/rec/conf/nips/VertTN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeslieECWN04,
author = {Christina S. Leslie and
Eleazar Eskin and
Adiel Cohen and
Jason Weston and
William Stafford Noble},
title = {Mismatch string kernels for discriminative protein classification},
journal = {Bioinform.},
volume = {20},
number = {4},
pages = {467--476},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/btg431},
doi = {10.1093/BIOINFORMATICS/BTG431},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeslieECWN04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PavlidisWN04,
author = {Paul Pavlidis and
Ilan Wapinski and
William Stafford Noble},
title = {Support vector machine classification on the web},
journal = {Bioinform.},
volume = {20},
number = {4},
pages = {586--587},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/btg461},
doi = {10.1093/BIOINFORMATICS/BTG461},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PavlidisWN04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuN04,
author = {Wei Wu and
William Stafford Noble},
title = {Genomic data visualization on the Web},
journal = {Bioinform.},
volume = {20},
number = {11},
pages = {1804--1805},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth154},
doi = {10.1093/BIOINFORMATICS/BTH154},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuN04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LanckrietBCJN04,
author = {Gert R. G. Lanckriet and
Tijl De Bie and
Nello Cristianini and
Michael I. Jordan and
William Stafford Noble},
title = {A statistical framework for genomic data fusion},
journal = {Bioinform.},
volume = {20},
number = {16},
pages = {2626--2635},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth294},
doi = {10.1093/BIOINFORMATICS/BTH294},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LanckrietBCJN04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/TsudaN04,
author = {Koji Tsuda and
William Stafford Noble},
title = {Learning kernels from biological networks by maximizing entropy},
booktitle = {Proceedings Twelfth International Conference on Intelligent Systems
for Molecular Biology/Third European Conference on Computational Biology
2004, Glasgow, UK, July 31-August 4, 2004},
pages = {326--333},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth906},
doi = {10.1093/BIOINFORMATICS/BTH906},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/TsudaN04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/LanckrietDCJN04,
author = {Gert R. G. Lanckriet and
Minghua Deng and
Nello Cristianini and
Michael I. Jordan and
William Stafford Noble},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany A. Jung and
Teri E. Klein},
title = {Kernel-Based Data Fusion and Its Application to Protein Function Prediction
in Yeast},
booktitle = {Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA,
6-10 January 2004},
pages = {300--311},
publisher = {World Scientific},
year = {2004},
url = {http://psb.stanford.edu/psb-online/proceedings/psb04/lanckriet.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/LanckrietDCJN04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PavlidisN03,
author = {Paul Pavlidis and
William Stafford Noble},
title = {Matrix2png: a utility for visualizing matrix data},
journal = {Bioinform.},
volume = {19},
number = {2},
pages = {295--296},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/19.2.295},
doi = {10.1093/BIOINFORMATICS/19.2.295},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PavlidisN03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PavlidisLN03,
author = {Paul Pavlidis and
Qinghong Li and
William Stafford Noble},
title = {The effect of replication on gene expression microarray experiments},
journal = {Bioinform.},
volume = {19},
number = {13},
pages = {1620--1627},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/btg227},
doi = {10.1093/BIOINFORMATICS/BTG227},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PavlidisLN03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GomezNR03,
author = {Shawn M. Gomez and
William Stafford Noble and
Andrey Rzhetsky},
title = {Learning to predict protein-protein interactions from protein sequences},
journal = {Bioinform.},
volume = {19},
number = {15},
pages = {1875--1881},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/btg352},
doi = {10.1093/BIOINFORMATICS/BTG352},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GomezNR03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QinLN03,
author = {Jie Qin and
Darrin P. Lewis and
William Stafford Noble},
title = {Kernel hierarchical gene clustering from microarray expression data},
journal = {Bioinform.},
volume = {19},
number = {16},
pages = {2097--2104},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/btg288},
doi = {10.1093/BIOINFORMATICS/BTG288},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/QinLN03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/EskinNS03,
author = {Eleazar Eskin and
William Stafford Noble and
Yoram Singer},
title = {Protein Family Classification Using Sparse Markov Transducers},
journal = {J. Comput. Biol.},
volume = {10},
number = {2},
pages = {187--213},
year = {2003},
url = {https://doi.org/10.1089/106652703321825964},
doi = {10.1089/106652703321825964},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/EskinNS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/LiaoN03,
author = {Li Liao and
William Stafford Noble},
title = {Combining Pairwise Sequence Similarity and Support Vector Machines
for Detecting Remote Protein Evolutionary and Structural Relationships},
journal = {J. Comput. Biol.},
volume = {10},
number = {6},
pages = {857--868},
year = {2003},
url = {https://doi.org/10.1089/106652703322756113},
doi = {10.1089/106652703322756113},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/LiaoN03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/BaileyN03,
author = {Timothy L. Bailey and
William Stafford Noble},
title = {Searching for statistically significant regulatory modules},
booktitle = {Proceedings of the European Conference on Computational Biology {(ECCB}
2003), September 27-30, 2003, Paris, France},
pages = {16--25},
year = {2003},
timestamp = {Mon, 27 Oct 2003 15:56:17 +0100},
biburl = {https://dblp.org/rec/conf/eccb/BaileyN03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/WestonLZEN03,
author = {Jason Weston and
Christina S. Leslie and
Dengyong Zhou and
Andr{\'{e}} Elisseeff and
William Stafford Noble},
editor = {Sebastian Thrun and
Lawrence K. Saul and
Bernhard Sch{\"{o}}lkopf},
title = {Semi-supervised Protein Classification Using Cluster Kernels},
booktitle = {Advances in Neural Information Processing Systems 16 [Neural Information
Processing Systems, {NIPS} 2003, December 8-13, 2003, Vancouver and
Whistler, British Columbia, Canada]},
pages = {595--602},
publisher = {{MIT} Press},
year = {2003},
url = {https://proceedings.neurips.cc/paper/2003/hash/12ffb0968f2f56e51a59a6beb37b2859-Abstract.html},
timestamp = {Mon, 16 May 2022 15:41:51 +0200},
biburl = {https://dblp.org/rec/conf/nips/WestonLZEN03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/PavlidisWCN02,
author = {Paul Pavlidis and
Jason Weston and
Jinsong Cai and
William Stafford Noble},
title = {Learning Gene Functional Classifications from Multiple Data Types},
journal = {J. Comput. Biol.},
volume = {9},
number = {2},
pages = {401--411},
year = {2002},
url = {https://doi.org/10.1089/10665270252935539},
doi = {10.1089/10665270252935539},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/PavlidisWCN02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/EskinNS02,
author = {Eleazar Eskin and
William Stafford Noble and
Yoram Singer},
title = {Using Substitution Matrices to Estimate Probability Distributions
for Biological Sequences},
journal = {J. Comput. Biol.},
volume = {9},
number = {6},
pages = {775--791},
year = {2002},
url = {https://doi.org/10.1089/10665270260518263},
doi = {10.1089/10665270260518263},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/EskinNS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ecml/ScholkopfWELN02,
author = {Bernhard Sch{\"{o}}lkopf and
Jason Weston and
Eleazar Eskin and
Christina S. Leslie and
William Stafford Noble},
editor = {Tapio Elomaa and
Heikki Mannila and
Hannu Toivonen},
title = {A Kernel Approach for Learning from almost Orthogonal Patterns},
booktitle = {Machine Learning: {ECML} 2002, 13th European Conference on Machine
Learning, Helsinki, Finland, August 19-23, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2430},
pages = {511--528},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-36755-1\_44},
doi = {10.1007/3-540-36755-1\_44},
timestamp = {Tue, 14 May 2019 10:00:54 +0200},
biburl = {https://dblp.org/rec/conf/ecml/ScholkopfWELN02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/LeslieEWN02,
author = {Christina S. Leslie and
Eleazar Eskin and
Jason Weston and
William Stafford Noble},
editor = {Suzanna Becker and
Sebastian Thrun and
Klaus Obermayer},
title = {Mismatch String Kernels for {SVM} Protein Classification},
booktitle = {Advances in Neural Information Processing Systems 15 [Neural Information
Processing Systems, {NIPS} 2002, December 9-14, 2002, Vancouver, British
Columbia, Canada]},
pages = {1417--1424},
publisher = {{MIT} Press},
year = {2002},
url = {https://proceedings.neurips.cc/paper/2002/hash/12b1e42dc0746f22cf361267de07073f-Abstract.html},
timestamp = {Mon, 16 May 2022 15:41:51 +0200},
biburl = {https://dblp.org/rec/conf/nips/LeslieEWN02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pkdd/ScholkopfWELN02,
author = {Bernhard Sch{\"{o}}lkopf and
Jason Weston and
Eleazar Eskin and
Christina S. Leslie and
William Stafford Noble},
editor = {Tapio Elomaa and
Heikki Mannila and
Hannu Toivonen},
title = {A Kernel Approach for Learning from Almost Orthogonal Patterns},
booktitle = {Principles of Data Mining and Knowledge Discovery, 6th European Conference,
{PKDD} 2002, Helsinki, Finland, August 19-23, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2431},
pages = {494--511},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45681-3\_42},
doi = {10.1007/3-540-45681-3\_42},
timestamp = {Tue, 14 May 2019 10:00:47 +0200},
biburl = {https://dblp.org/rec/conf/pkdd/ScholkopfWELN02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/PavlidisLN02,
author = {Paul Pavlidis and
Darrin P. Lewis and
William Stafford Noble},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {Exploring Gene Expression Data with Class Scores},
booktitle = {Proceedings of the 7th Pacific Symposium on Biocomputing, {PSB} 2002,
Lihue, Hawaii, USA, January 3-7, 2002},
pages = {474--485},
year = {2002},
url = {http://psb.stanford.edu/psb-online/proceedings/psb02/pavlidis.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/PavlidisLN02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/LeslieEN02,
author = {Christina S. Leslie and
Eleazar Eskin and
William Stafford Noble},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {The Spectrum Kernel: {A} String Kernel for {SVM} Protein Classification},
booktitle = {Proceedings of the 7th Pacific Symposium on Biocomputing, {PSB} 2002,
Lihue, Hawaii, USA, January 3-7, 2002},
pages = {566--575},
year = {2002},
url = {http://psb.stanford.edu/psb-online/proceedings/psb02/leslie.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/LeslieEN02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/LiaoN02,
author = {Li Liao and
William Stafford Noble},
editor = {Gene Myers and
Sridhar Hannenhalli and
David Sankoff and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {Combining pairwise sequence similarity and support vector machines
for remote protein homology detection},
booktitle = {Proceedings of the Sixth Annual International Conference on Computational
Biology, {RECOMB} 2002, Washington, DC, USA, April 18-21, 2002},
pages = {225--232},
publisher = {{ACM}},
year = {2002},
url = {https://doi.org/10.1145/565196.565225},
doi = {10.1145/565196.565225},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/LiaoN02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/EskinGS01,
author = {Eleazar Eskin and
William Noble Grundy and
Yoram Singer},
title = {Using mixtures of common ancestors for estimating the probabilities
of discrete events in biological sequences},
booktitle = {Proceedings of the Ninth International Conference on Intelligent Systems
for Molecular Biology, July 21-25, 2001, Copenhagen, Denmark},
pages = {65--73},
year = {2001},
timestamp = {Thu, 20 Jun 2002 11:09:36 +0200},
biburl = {https://dblp.org/rec/conf/ismb/EskinGS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kdd/PavlidisTN01,
author = {Paul Pavlidis and
Christopher Tang and
William Stafford Noble},
editor = {Mohammed Javeed Zaki and
Hannu Toivonen and
Jason Tsong{-}Li Wang},
title = {Classification of genes using probabilistic models of microarray expression
profiles},
booktitle = {Proceedings of the {ACM} {SIGKDD} Workshop on Data Mining in Bioinformatics
{(BIOKDD} 2001)},
pages = {15--21},
year = {2001},
url = {http://www.cs.rpi.edu/\%7Ezaki/BIOKDD01/pavlidis.ps.gz},
timestamp = {Fri, 23 Aug 2019 14:18:49 +0200},
biburl = {https://dblp.org/rec/conf/kdd/PavlidisTN01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/PavlidisFLHG01,
author = {Paul Pavlidis and
Terrence S. Furey and
M. Liberto and
David Haussler and
William Noble Grundy},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {Promoter Region-Based Classification of Genes},
booktitle = {Proceedings of the 6th Pacific Symposium on Biocomputing, {PSB} 2001,
Hawaii, USA, January 3-7, 2001},
pages = {151--164},
year = {2001},
url = {http://psb.stanford.edu/psb-online/proceedings/psb01/pavlidis.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/PavlidisFLHG01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/PavlidisWCG01,
author = {Paul Pavlidis and
Jason Weston and
Jinsong Cai and
William Noble Grundy},
editor = {Thomas Lengauer},
title = {Gene functional classification from heterogeneous data},
booktitle = {Proceedings of the Fifth Annual International Conference on Computational
Biology, {RECOMB} 2001, Montr{\'{e}}al, Qu{\'{e}}bec, Canada,
April 22-25, 2001},
pages = {249--255},
publisher = {{ACM}},
year = {2001},
url = {https://doi.org/10.1145/369133.369228},
doi = {10.1145/369133.369228},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/PavlidisWCG01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/EskinGS00,
author = {Eleazar Eskin and
William Noble Grundy and
Yoram Singer},
editor = {Philip E. Bourne and
Michael Gribskov and
Russ B. Altman and
Nancy Jensen and
Debra A. Hope and
Thomas Lengauer and
Julie C. Mitchell and
Eric D. Scheeff and
Chris Smith and
Shawn Strande and
Helge Weissig},
title = {Protein Family Classification Using Sparse Markov Transducers},
booktitle = {Proceedings of the Eighth International Conference on Intelligent
Systems for Molecular Biology, August 19-23, 2000, La Jolla / San
Diego, CA, {USA}},
pages = {134--145},
publisher = {{AAAI}},
year = {2000},
url = {http://www.aaai.org/Library/ISMB/2000/ismb00-014.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/EskinGS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrundyB99,
author = {William Noble Grundy and
Timothy L. Bailey},
title = {Family pairwise search with embedded motif models},
journal = {Bioinform.},
volume = {15},
number = {6},
pages = {463--470},
year = {1999},
url = {https://doi.org/10.1093/bioinformatics/15.6.463},
doi = {10.1093/BIOINFORMATICS/15.6.463},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrundyB99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/BaileyG99,
author = {Timothy L. Bailey and
William Noble Grundy},
editor = {Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {Classifying proteins by family using the product of correlated \emph{p}-values},
booktitle = {Proceedings of the Third Annual International Conference on Research
in Computational Molecular Biology, {RECOMB} 1999, Lyon, France, April
11-14, 1999},
pages = {10--14},
publisher = {{ACM}},
year = {1999},
url = {https://doi.org/10.1145/299432.299444},
doi = {10.1145/299432.299444},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/BaileyG99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/ox/Wang99/BaileyBEG99,
author = {Timothy L. Bailey and
Michael E. Baker and
Charles Elkan and
William Noble Grundy},
editor = {Jason Tsong{-}Li Wang and
Bruce A. Shapiro and
Dennis E. Shasha},
title = {MEME, MAST, and Meta-MEME: New Tools for Motif Discovery in Protein
Sequences},
booktitle = {Pattern Discovery in Biomolecular Data: Tools, Techniques and Applications},
pages = {30--54},
publisher = {Oxford University Press},
year = {1999},
timestamp = {Sat, 03 Aug 2019 18:41:48 +0200},
biburl = {https://dblp.org/rec/books/ox/Wang99/BaileyBEG99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Grundy98,
author = {William Noble Grundy},
title = {Homology Detection via Family Pairwise Search},
journal = {J. Comput. Biol.},
volume = {5},
number = {3},
pages = {479--491},
year = {1998},
url = {https://doi.org/10.1089/cmb.1998.5.479},
doi = {10.1089/CMB.1998.5.479},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/Grundy98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/Grundy98,
author = {William Noble Grundy},
editor = {Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {Family-based homology detection via pairwise sequence comparison},
booktitle = {Proceedings of the Second Annual International Conference on Research
in Computational Molecular Biology, {RECOMB} 1998, New York, NY, USA,
March 22-25, 1998},
pages = {94--100},
publisher = {{ACM}},
year = {1998},
url = {https://doi.org/10.1145/279069.279098},
doi = {10.1145/279069.279098},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/Grundy98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrundyBEB97,
author = {William Noble Grundy and
Timothy L. Bailey and
Charles Elkan and
Michael E. Baker},
title = {Meta-MEME: motif-based hidden Markov models of protein families},
journal = {Comput. Appl. Biosci.},
volume = {13},
number = {4},
pages = {397--406},
year = {1997},
url = {https://doi.org/10.1093/bioinformatics/13.4.397},
doi = {10.1093/BIOINFORMATICS/13.4.397},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrundyBEB97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrundyBE96,
author = {William Noble Grundy and
Timothy L. Bailey and
Charles Elkan},
title = {ParaMEME: a parallel implementation and a web interface for a {DNA}
and protein motif discovery tool},
journal = {Comput. Appl. Biosci.},
volume = {12},
number = {4},
pages = {303--310},
year = {1996},
url = {https://doi.org/10.1093/bioinformatics/12.4.303},
doi = {10.1093/BIOINFORMATICS/12.4.303},
timestamp = {Fri, 15 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrundyBE96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ec/BataliG96,
author = {John Batali and
William Noble Grundy},
title = {Modeling the Evolution of Motivation},
journal = {Evol. Comput.},
volume = {4},
number = {3},
pages = {235--270},
year = {1996},
url = {https://doi.org/10.1162/evco.1996.4.3.235},
doi = {10.1162/EVCO.1996.4.3.235},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ec/BataliG96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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