Sceptic: pseudotime analysis for time-series single-cell sequencing and imaging data.

William Stafford Noble William S. Noble William Noble Grundy University of Washington, Seattle, USA https://noble.gs.washington.edu/~wnoble/ https://scholar.google.com/citations?user=plt2_DsAAAAJ https://zbmath.org/authors/?q=ai:stafford-noble.william https://mathscinet.ams.org/mathscinet/MRAuthorID/721261 https://mathgenealogy.org/id.php?id=121369 https://orcid.org/0000-0001-7283-4715 https://www.wikidata.org/entity/Q29053213 https://id.loc.gov/authorities/names/n2010180530 https://en.wikipedia.org/wiki/William_Stafford_Noble Gang Li 0034 Hyeon-Jin Kim Sriram Pendyala Ran Zhang Jean-Philippe Vert Christine Disteche Xinxian Deng Douglas Fowler William S. Noble Sceptic: pseudotime analysis for time-series single-cell sequencing and imaging data. 2025 June https://doi.org/10.5281/zenodo.15746650 Zenodo streams/repo/zenodo Gang Li 0034 Hyeon-Jin Kim Sriram Pendyala Ran Zhang Jean-Philippe Vert Christine Disteche Xinxian Deng Douglas Fowler William S. Noble Sceptic: pseudotime analysis for time-series single-cell sequencing and imaging data. 2025 June https://doi.org/10.5281/zenodo.15729887 Zenodo streams/repo/zenodo Huaizhi Qu Xiao Wang 0013 Yuanyuan Zhang Sheng Wang 0012 William S. Noble Tianlong Chen 0001 Data for "CryoNeRF: neural radiance field for homogeneous and heterogeneous cryo-EM reconstruction". 2025 January https://doi.org/10.5281/zenodo.14600230 Zenodo streams/repo/zenodo data/11/QuWZwNC25b Huaizhi Qu Xiao Wang 0013 Yuanyuan Zhang Sheng Wang 0012 William S. Noble Tianlong Chen 0001 Data for "CryoNeRF: neural radiance field for homogeneous and heterogeneous cryo-EM reconstruction". 2025 January https://doi.org/10.5281/zenodo.14602456 Zenodo streams/repo/zenodo data/11/QuWZwNC25b Anupama Jha Borislav H. Hristov Xiao Wang 0013 Sheng Wang 0012 William Greenleaf Anshul Kundaje Erez S. Lieberman Aiden Alessandro Bertero William Stafford Noble Example dataset for prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC. Zenodo 2025 July https://doi.org/10.5281/zenodo.15839236 streams/repo/zenodo

Justin Sanders Melih Yilmaz Jacob H. Russell Wout Bittremieux William Fondrie Nicholas M. Riley Sewoong Oh William Stafford Noble Foundation model for mass spectrometry proteomics. 2025 May abs/2505.10848 CoRR https://doi.org/10.48550/arXiv.2505.10848 db/journals/corr/corr2505.html#abs-2505-10848 streams/journals/corr

Yang Young Lu William Stafford Noble Uri Keich A BLAST from the past: revisiting blastp's E-value. 2024 40 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btae729 db/journals/bioinformatics/bioinformatics40.html#LuNK24

Varun Ananth Justin Sanders Melih Yilmaz Bo Wen Sewoong Oh William Stafford Noble A learned score function improves the power of mass spectrometry database search. i410-i417 2024 40 Bioinform. Supplement_1 https://doi.org/10.1093/bioinformatics/btae218 db/journals/bioinformatics/bioinformatics40.html#AnanthSYWON24

Tangqi Fang Yifeng Liu 0004 Addie Woicik Minsi Lu Anupama Jha Xiao Wang 0013 Gang Li 0034 Borislav H. Hristov Zixuan Liu 0001 Hanwen Xu William S. Noble Sheng Wang 0012 Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model. i471-i480 2024 40 Bioinform. Supplement_1 https://doi.org/10.1093/bioinformatics/btae211 db/journals/bioinformatics/bioinformatics40.html#FangLWLJWLHLXN024

Jack Freestone Lukas Käll William Stafford Noble Uri Keich Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis. 448-453 2024 RECOMB https://doi.org/10.1007/978-1-0716-3989-4_50 conf/recomb/2024 db/conf/recomb/recomb2024.html#FreestoneKNK24

Winston Chen Yifan Jiang William Stafford Noble Yang Young Lu Error-controlled non-additive interaction discovery in machine learning models. 2024 abs/2408.17016 CoRR https://doi.org/10.48550/arXiv.2408.17016 db/journals/corr/corr2408.html#abs-2408-17016 streams/journals/corr

Nelle Varoquaux William S. Noble Jean-Philippe Vert Inference of 3D genome architecture by modeling overdispersion of Hi-C data. 2023 January 39 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btac838 db/journals/bioinformatics/bioinformatics39.html#VaroquauxNV23

Andy Lin Brooke L. Deatherage Kaiser Janine R. Hutchison Jeffrey A. Bilmes William Stafford Noble MS1Connect: a mass spectrometry run similarity measure. 2023 February 39 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btad058 db/journals/bioinformatics/bioinformatics39.html#LinKHBN23

Laetitia Meng-Papaxanthos Ran Zhang Gang Li 0034 Marco Cuturi William Stafford Noble Jean-Philippe Vert LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis. 2023 39 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btad420 db/journals/bioinformatics/bioinformatics39.html#Meng-Papaxanthos23

William Stafford Noble Ten simple rules for defining a computational biology project. 2023 January 19 PLoS Comput. Biol. 1 https://doi.org/10.1371/journal.pcbi.1010786 https://www.wikidata.org/entity/Q117013749 db/journals/ploscb/ploscb19.html#Noble23

Alan Min Timothy Durham Louis Gevirtzman William Stafford Noble Matrix prior for data transfer between single cell data types in latent Dirichlet allocation. 2023 19 PLoS Comput. Biol. 5 https://doi.org/10.1371/journal.pcbi.1011049 db/journals/ploscb/ploscb19.html#MinDGN23

Brittany Baur Junha Shin Jacob Schreiber Shilu Zhang Yi Zhang 0055 Mohith Manjunath Jun S. Song William Stafford Noble Sushmita Roy Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation. 2023 19 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1011286 db/journals/ploscb/ploscb19.html#BaurSSZ0MSNR23

Winston Chen William Stafford Noble Yang Young Lu DeepROCK: Error-controlled interaction detection in deep neural networks. 2023 abs/2309.15319 CoRR https://doi.org/10.48550/arXiv.2309.15319 db/journals/corr/corr2309.html#abs-2309-15319

Borislav H. Hristov Jeff A. Bilmes William Stafford Noble Linking cells across single-cell modalities by synergistic matching of neighborhood structure. ii148-ii154 2022 38 Bioinform. Supplement_2 https://doi.org/10.1093/bioinformatics/btac481 db/journals/bioinformatics/bioinformatics38.html#HristovBN22

Jack Freestone Temana Short William Stafford Noble Uri Keich Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition. ii82-ii88 2022 38 Bioinform. Supplement_2 https://doi.org/10.1093/bioinformatics/btac471 db/journals/bioinformatics/bioinformatics38.html#FreestoneSNK22

Pinar Demetci Rebecca Santorella Björn Sandstede William Stafford Noble Ritambhara Singh SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport. 3-18 2022 29 J. Comput. Biol. 1 https://doi.org/10.1089/cmb.2021.0446 db/journals/jcb/jcb29.html#DemetciSSNS22

Pinar Demetci Rebecca Santorella Björn Sandstede William Stafford Noble Ritambhara Singh Single-Cell Multiomics Integration by SCOT. 19-22 2022 29 J. Comput. Biol. 1 https://doi.org/10.1089/cmb.2021.0477 db/journals/jcb/jcb29.html#DemetciSSNS22a

Ran Zhang Laetitia Meng-Papaxanthos Jean-Philippe Vert William Stafford Noble Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning. 1198-1212 2022 29 J. Comput. Biol. 11 https://doi.org/10.1089/cmb.2022.0264 db/journals/jcb/jcb29.html#ZhangMVN22

Melih Yilmaz William Fondrie Wout Bittremieux Sewoong Oh William S. Noble De novo mass spectrometry peptide sequencing with a transformer model. 25514-25522 2022 ICML https://proceedings.mlr.press/v162/yilmaz22a.html conf/icml/2022 db/conf/icml/icml2022.html#YilmazFBON22 Kayvon Mazooji Sreeram Kannan William Stafford Noble Ilan Shomorony Fundamental Limits of Multi-Sample Flow Graph Decomposition. 2403-2408 2022 ISIT https://doi.org/10.1109/ISIT50566.2022.9834518 conf/isit/2022 db/conf/isit/isit2022.html#MazoojiKNS22 Ran Zhang Laetitia Meng-Papaxanthos Jean-Philippe Vert William Stafford Noble Semi-supervised Single-Cell Cross-modality Translation Using Polarbear. 20-35 2022 RECOMB https://doi.org/10.1007/978-3-031-04749-7_2 conf/recomb/2022 db/conf/recomb/recomb2022.html#ZhangMVN22 Laetitia Meng-Papaxanthos Ran Zhang Gang Li 0034 Marco Cuturi William Stafford Noble Jean-Philippe Vert Software for Large Scale MMD-MA. 2022 January https://doi.org/10.5281/zenodo.8076311 Zenodo streams/repo/zenodo

Jacob M. Schreiber Jeffrey A. Bilmes William Stafford Noble Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data. 439-447 2021 37 Bioinform. 4 https://doi.org/10.1093/bioinformatics/btaa830 https://www.wikidata.org/entity/Q99613900 db/journals/bioinformatics/bioinformatics37.html#SchreiberBN21

Dejun Lin Justin Sanders William Stafford Noble HiCRep.py: fast comparison of Hi-C contact matrices in Python. 2996-2997 2021 37 Bioinform. 18 https://doi.org/10.1093/bioinformatics/btab097 https://www.wikidata.org/entity/Q122702146 db/journals/bioinformatics/bioinformatics37.html#LinSN21

Yang Young Lu Jeff A. Bilmes Ricard A. Rodriguez-Mias Judit Villén William Stafford Noble DIAmeter: matching peptides to data-independent acquisition mass spectrometry data. 434-432 2021 37 Bioinform. Supplement https://doi.org/10.1093/bioinformatics/btab284 db/journals/bioinformatics/bioinformatics37.html#LuBRVN21

Yang Young Lu Wenbo Guo 0002 Xinyu Xing 0001 William Stafford Noble DANCE: Enhancing saliency maps using decoys. 7124-7133 2021 ICML http://proceedings.mlr.press/v139/lu21b.html conf/icml/2021 db/conf/icml/icml2021.html#Lu0XN21 Yang Young Lu Timothy C. Yu Giancarlo Bonora William Stafford Noble ACE: Explaining cluster from an adversarial perspective. 7156-7167 2021 ICML http://proceedings.mlr.press/v139/lu21e.html conf/icml/2021 db/conf/icml/icml2021.html#LuYBN21

Jacob M. Schreiber Jeffrey A. Bilmes William Stafford Noble apricot: Submodular selection for data summarization in Python. 161:1-161:6 2020 21 J. Mach. Learn. Res. https://jmlr.org/papers/v21/19-467.html db/journals/jmlr/jmlr21.html#SchreiberBN20

Hyeon-Jin Kim Galip Gürkan Yardimci Giancarlo Bonora Vijay Ramani Jie Liu 0045 Ruolan Qiu Choli Lee Jennifer Hesson Carol B. Ware Jay Shendure Zhi-jun Duan William Stafford Noble Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. 2020 16 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1008173 https://www.wikidata.org/entity/Q99568702 db/journals/ploscb/ploscb16.html#KimYBRLQLHWSDN20

Jacob M. Schreiber Timothy J. Durham William S. Noble Jeffrey A. Bilmes Avocado: Deep tensor factorization characterizes the human epigenome via imputation of tens of thousands of functional experiments. 37:1 2020 BCB https://doi.org/10.1145/3388440.3414215 conf/bcb/2020 db/conf/bcb/bcb2020.html#SchreiberDNB20 Jacob M. Schreiber Deepthi Hegde William S. Noble Zero-shot imputations across species are enabled through joint modeling of human and mouse epigenomics. 39:1-39:9 2020 BCB https://doi.org/10.1145/3388440.3412412 conf/bcb/2020 db/conf/bcb/bcb2020.html#SchreiberHN20 Ritambhara Singh Pinar Demetci Giancarlo Bonora Vijay Ramani Choli Lee He Fang Zhi-jun Duan Xinxian Deng Jay Shendure Christine Disteche William Stafford Noble Unsupervised manifold alignment for single-cell multi-omics data. 40:1-40:10 2020 BCB https://doi.org/10.1145/3388440.3412410 https://www.wikidata.org/entity/Q112759787 conf/bcb/2020 db/conf/bcb/bcb2020.html#SinghDBRLFDDSDN20 Wei Yang Jeffrey A. Bilmes William Stafford Noble Submodular sketches of single-cell RNA-seq measurements. 61:1-61:6 2020 BCB https://doi.org/10.1145/3388440.3412409 conf/bcb/2020 db/conf/bcb/bcb2020.html#YangBN20 Kristen Emery Syamand Hasam William Stafford Noble Uri Keich Multiple Competition-Based FDR Control and Its Application to Peptide Detection. 54-71 2020 RECOMB https://doi.org/10.1007/978-3-030-45257-5_4 conf/recomb/2020 db/conf/recomb/recomb2020.html#EmeryHNK20

Yang Lu Wenbo Guo 0002 Xinyu Xing 0001 William Stafford Noble Robust saliency maps with decoy-enhanced saliency score. 2020 abs/2002.00526 CoRR https://arxiv.org/abs/2002.00526 db/journals/corr/corr2002.html#abs-2002-00526

Musa Nur Gabere William Stafford Noble Response to comments on 'Empirical comparison of web-based antimicrobial peptide prediction tools'. 2695-2696 2019 35 Bioinform. 15 https://doi.org/10.1093/bioinformatics/bty1024 https://www.wikidata.org/entity/Q62843864 db/journals/bioinformatics/bioinformatics35.html#GabereN19

Alice Cheng Charles E. Grant William S. Noble Timothy L. Bailey MoMo: discovery of statistically significant post-translational modification motifs. 2774-2782 2019 35 Bioinform. 16 https://doi.org/10.1093/bioinformatics/bty1058 https://www.wikidata.org/entity/Q62843858 db/journals/bioinformatics/bioinformatics35.html#ChengGNB19

Michael Mommert Michael S. P. Kelley Miguel de Val-Borro Jian-Yang Li Giannina Guzman Brigitta M. Sipocz Josef Durech Mikael Granvik William S. Noble Nick Moskovitz Antti Penttilä Nalin Samarasinha sbpy: A Python module for small-body planetary astronomy. 1426 2019 4 J. Open Source Softw. 38 https://doi.org/10.21105/joss.01426 https://www.wikidata.org/entity/Q104708444 db/journals/jossw/jossw4.html#MommertKVLGSDGN19

David F. Read Kate Cook Yang Young Lu Karine G. Le Roch William Stafford Noble Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features. 2019 15 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1007329 https://www.wikidata.org/entity/Q90059865 db/journals/ploscb/ploscb15.html#ReadCLRN19

Wenruo Bai Jeffrey A. Bilmes William S. Noble Submodular Generalized Matching for Peptide Identification in Tandem Mass Spectrometry. 1168-1181 2019 16 IEEE ACM Trans. Comput. Biol. Bioinform. 4 https://doi.org/10.1109/TCBB.2018.2822280 https://www.wikidata.org/entity/Q89555456 db/journals/tcbb/tcbb16.html#BaiBN19

Jie Liu 0045 Yuanhao Huang Ritambhara Singh Jean-Philippe Vert William Stafford Noble Jointly Embedding Multiple Single-Cell Omics Measurements. 10:1-10:13 2019 WABI https://doi.org/10.4230/LIPIcs.WABI.2019.10 conf/wabi/2019 db/conf/wabi/wabi2019.html#LiuHSVN19 Alexandra Gesine Cauer Gürkan Yardimci Jean-Philippe Vert Nelle Varoquaux William Stafford Noble Inferring Diploid 3D Chromatin Structures from Hi-C Data. 11:1-11:13 2019 WABI https://doi.org/10.4230/LIPIcs.WABI.2019.11 conf/wabi/2019 db/conf/wabi/wabi2019.html#CauerYVVN19

Jacob M. Schreiber Jeffrey A. Bilmes William Stafford Noble apricot: Submodular selection for data summarization in Python. 2019 abs/1906.03543 CoRR http://arxiv.org/abs/1906.03543 db/journals/corr/corr1906.html#abs-1906-03543

Rachel C. W. Chan Maxwell W. Libbrecht Eric G. Roberts Jeffrey A. Bilmes William Stafford Noble Michael M. Hoffman Segway 2.0: Gaussian mixture models and minibatch training. 669-671 2018 34 Bioinform. 4 https://doi.org/10.1093/bioinformatics/btx603 https://www.wikidata.org/entity/Q47447161 db/journals/bioinformatics/bioinformatics34.html#ChanLRBNH18

Jie Liu 0045 Dejun Lin Galip Gürkan Yardimci William Stafford Noble Unsupervised embedding of single-cell Hi-C data. i96-i104 2018 34 Bioinform. 13 https://doi.org/10.1093/bioinformatics/bty285 https://www.wikidata.org/entity/Q55514143 db/journals/bioinformatics/bioinformatics34.html#LiuLYN18

Oana Ursu Nathan Boley Maryna Taranova Y. X. Rachel Wang Galip Gürkan Yardimci William Stafford Noble Anshul Kundaje GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs. 2701-2707 2018 34 Bioinform. 16 https://doi.org/10.1093/bioinformatics/bty164 https://www.wikidata.org/entity/Q57991438 db/journals/bioinformatics/bioinformatics34.html#UrsuBTWYNK18

Aakash Sur Jackie McDonald Bryan Jensen William S. Noble Peter J. Myler Unveiling Elements of Genomic Architecture with Genome Wide Chromatin Conformation Capture. 2018 AMIA https://knowledge.amia.org/67852-amia-1.4259402/t006-1.4263223/t006-1.4263224/2976805-1.4263273/2976877-1.4263270 conf/amia/2018 db/conf/amia/amia2018.html#SurMJNM18 Maxwell W. Libbrecht Jeffrey A. Bilmes William Stafford Noble Choosing Non-redundant Representative Subsets Of Protein Sequence Data Sets Using Submodular Optimization. 566 2018 BCB https://doi.org/10.1145/3233547.3233717 conf/bcb/2018 db/conf/bcb/bcb2018.html#LibbrechtBN18 Wenruo Bai William Stafford Noble Jeff A. Bilmes Submodular Maximization via Gradient Ascent: The Case of Deep Submodular Functions. 7989-7999 2018 NeurIPS https://proceedings.neurips.cc/paper/2018/hash/b43a6403c17870707ca3c44984a2da22-Abstract.html http://papers.nips.cc/paper/8022-submodular-maximization-via-gradient-ascent-the-case-of-deep-submodular-functions conf/nips/2018 db/conf/nips/nips2018.html#BaiNB18 Yang Young Lu Yingying Fan Jinchi Lv William Stafford Noble DeepPINK: reproducible feature selection in deep neural networks. 8690-8700 2018 NeurIPS https://proceedings.neurips.cc/paper/2018/hash/29daf9442f3c0b60642b14c081b4a556-Abstract.html http://papers.nips.cc/paper/8085-deeppink-reproducible-feature-selection-in-deep-neural-networks conf/nips/2018 db/conf/nips/nips2018.html#LuFLN18

Yang Young Lu Yingying Fan Jinchi Lv William Stafford Noble DeepPINK: reproducible feature selection in deep neural networks. 2018 abs/1809.01185 CoRR http://arxiv.org/abs/1809.01185 db/journals/corr/corr1809.html#abs-1809-01185

Musa Nur Gabere William Stafford Noble Empirical comparison of web-based antimicrobial peptide prediction tools. 1921-1929 2017 33 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btx081 https://www.wikidata.org/entity/Q38958910 db/journals/bioinformatics/bioinformatics33.html#GabereN17

Koon-Kiu Yan Galip Gürkan Yardimci Chengfei Yan William S. Noble Mark Gerstein HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps. 2199-2201 2017 33 Bioinform. 14 https://doi.org/10.1093/bioinformatics/btx152 https://www.wikidata.org/entity/Q36332177 db/journals/bioinformatics/bioinformatics33.html#YanYYNG17

Wenxiu Ma Lin Yang Remo Rohs William Stafford Noble DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding. 3003-3010 2017 33 Bioinform. 19 https://doi.org/10.1093/bioinformatics/btx336 https://www.wikidata.org/entity/Q38765570 db/journals/bioinformatics/bioinformatics33.html#MaYRN17

Jacob M. Schreiber William S. Noble Finding the optimal Bayesian network given a constraint graph. e122 2017 3 PeerJ Comput. Sci. https://doi.org/10.7717/peerj-cs.122 https://www.wikidata.org/entity/Q110950396 db/journals/peerj-cs/peerj-cs3.html#SchreiberN17

William Stafford Noble Ten simple rules for writing a response to reviewers. 2017 13 PLoS Comput. Biol. 10 https://doi.org/10.1371/journal.pcbi.1005730 https://www.wikidata.org/entity/Q46236365 db/journals/ploscb/ploscb13.html#Noble17

Shengjie Wang 0001 Haoran Cai Jeff A. Bilmes William S. Noble Training Compressed Fully-Connected Networks with a Density-Diversity Penalty. 2017 ICLR (Poster) https://openreview.net/forum?id=Hku9NK5lx conf/iclr/2017 db/conf/iclr/iclr2017.html#WangCBN17 Uri Keich William Stafford Noble Progressive Calibration and Averaging for Tandem Mass Spectrometry Statistical Confidence Estimation: Why Settle for a Single Decoy? 99-116 2017 RECOMB https://doi.org/10.1007/978-3-319-56970-3_7 https://www.wikidata.org/entity/Q89856611 conf/recomb/2017 db/conf/recomb/recomb2017.html#KeichN17 William Stafford Noble Christina S. Leslie Learning Models of Biological Sequences. 723-729 2017 Encyclopedia of Machine Learning and Data Mining https://doi.org/10.1007/978-1-4899-7687-1_468 reference/ml/2017 db/reference/ml/ml2017.html#NobleL17 Rachel C. W. Chan Maxwell W. Libbrecht Eric G. Roberts Jeffrey A. Bilmes William Stafford Noble Michael M. Hoffman Segway 2.0 Application Note Datasets. 2017 June https://doi.org/10.5281/zenodo.854778 Zenodo streams/repo/zenodo Rachel C. W. Chan Maxwell W. Libbrecht Eric G. Roberts Jeffrey A. Bilmes William Stafford Noble Michael M. Hoffman Segway 2.0 Application Note Scripts. 2017 June https://doi.org/10.5281/zenodo.854764 Zenodo streams/repo/zenodo

Jacob M. Schreiber William S. Noble Finding the optimal bayesian network given a constraint graph. e2872 2017 5 PeerJ Prepr. https://doi.org/10.7287/peerj.preprints.2872v1 https://www.wikidata.org/entity/Q60347306 db/journals/peerjpre/peerjpre5.html#SchreiberN17

Charles E. Grant James Johnson Timothy L. Bailey William Stafford Noble MCAST: scanning for cis-regulatory motif clusters. 1217-1219 2016 32 Bioinform. 8 https://doi.org/10.1093/bioinformatics/btv750 https://www.wikidata.org/entity/Q37002983 db/journals/bioinformatics/bioinformatics32.html#GrantJBN16

Shengjie Wang 0001 John T. Halloran Jeff A. Bilmes William S. Noble Faster and more accurate graphical model identification of tandem mass spectra using trellises. 322-331 2016 32 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btw269 https://www.wikidata.org/entity/Q37005515 db/journals/bioinformatics/bioinformatics32.html#WangHBN16

Wenruo Bai Jeffrey A. Bilmes William S. Noble Bipartite matching generalizations for peptide identification in tandem mass spectrometry. 327-336 2016 BCB https://doi.org/10.1145/2975167.2975201 conf/bcb/2016 db/conf/bcb/bcb2016.html#BaiBN16

Timothy L. Bailey James Johnson Charles E. Grant William S. Noble The MEME Suite. W39-W49 2015 43 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkv416 https://www.wikidata.org/entity/Q35810173 db/journals/nar/nar43.html#BaileyJGN15

Galip Gürkan Yardimci William Stafford Noble Predictive model of 3D domain formation via CTCF-mediated extrusion. 14404-14405 2015 112 Proc. Natl. Acad. Sci. USA 47 https://doi.org/10.1073/pnas.1519849112 https://www.wikidata.org/entity/Q36331983 db/journals/pnas/pnas112.html#YardimciN15

Zafer Aydin David Baker 0001 William Stafford Noble Constructing Structural Profiles for Protein Torsion Angle Prediction. 26-35 2015 BIOINFORMATICS conf/biostec/2015bi db/conf/biostec/bioinformatics2015.html#AydinBN15 Zafer Aydin David Baker 0001 William Stafford Noble Template Scoring Methods for Protein Torsion Angle Prediction. 206-223 2015 BIOSTEC (Selected Papers) https://doi.org/10.1007/978-3-319-27707-3_13 conf/biostec/2015ccis db/conf/biostec/biostec2015ccis.html#AydinBN15a Maxwell W. Libbrecht Michael M. Hoffman Jeff A. Bilmes William Stafford Noble Entropic Graph-based Posterior Regularization. 1992-2001 2015 ICML http://proceedings.mlr.press/v37/libbrecht15.html conf/icml/2015 db/conf/icml/icml2015.html#LibbrechtHBN15

Nelle Varoquaux Ferhat Ay William Stafford Noble Jean-Philippe Vert A statistical approach for inferring the 3D structure of the genome. 26-33 2014 30 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btu268 https://www.wikidata.org/entity/Q34424959 db/journals/bioinformatics/bioinformatics30.html#VaroquauxANV14

Joshua Wing Kei Ho Youngsook L. Jung Tao Liu 0022 Burak Han Alver Soohyun Lee Kohta Ikegami Kyung-Ah Sohn Aki Minoda Michael Y. Tolstorukov Alex Appert Stephen C. J. Parker Tingting Gu Anshul Kundaje Nicole C. Riddle Eric Bishop Thea A. Egelhofer Sheng'en Shawn Hu Artyom A. Alekseyenko Andreas Rechtsteiner Dalal Asker Jason A. Belsky Sarah K. Bowman Q. Brent Chen Ron A.-J. Chen Daniel S. Day Yan Dong Andrea C. Dose Xikun Duan Charles B. Epstein Sevinc Ercan Elise A. Feingold Francesco Ferrari Jacob M. Garrigues Nils Gehlenborg Peter J. Good Psalm Haseley Daniel He Moritz Herrmann Michael M. Hoffman Tess E. Jeffers Peter V. Kharchenko Paulina Kolasinska-Zwierz Chitra V. Kotwaliwale Nischay Kumar Sasha A. Langley Erica Larschan Isabel Latorre Maxwell W. Libbrecht Xueqiu Lin Richard Park Michael J. Pazin Hoang N. Pham Annette Plachetka Bo Qin Yuri B. Schwartz Noam Shoresh Przemyslaw Stempor Anne Vielle Chengyang Wang Christina M. Whittle Huiling Xue Robert E. Kingston Ju Han Kim Bradley E. Bernstein Abby F. Dernburg Vincenzo Pirrotta Mitzi I. Kuroda William S. Noble Thomas D. Tullius Manolis Kellis David M. MacAlpine Susan Strome Sarah C. R. Elgin Xiaole Shirley Liu Jason D. Lieb Julie Ahringer Gary H. Karpen Peter J. Park Comparative analysis of metazoan chromatin organization Open. 449-452 2014 512 Nat. 7515 https://doi.org/10.1038/nature13415 https://www.wikidata.org/entity/Q34486035 db/journals/nature/nature512.html#HoJLALISMTAPGKR14

Habil Zare Junfeng Wang Alex Hu Kris Weber Joshua D. Smith Deborah A. Nickerson ChaoZhong Song Daniela M. Witten C. Anthony Blau William Stafford Noble Inferring Clonal Composition from Multiple Sections of a Breast Cancer. 2014 10 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1003703 https://www.wikidata.org/entity/Q21145293 db/journals/ploscb/ploscb10.html#ZareWHWSNSWBN14

John T. Halloran Jeff A. Bilmes William Stafford Noble Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry. 320-329 2014 UAI https://dslpitt.org/uai/displayArticleDetails.jsp?mmnu=1&smnu=2&article_id=2467&proceeding_id=30 conf/uai/2014 db/conf/uai/uai2014.html#HalloranBN14 Michael M. Hoffman Orion J. Buske Jie Wang Zhiping Weng Jeff A. Bilmes William Stafford Noble Unsupervised pattern discovery in human chromatin structure through genomic segmentation. 813 2013 BCB https://doi.org/10.1145/2506583.2506701 conf/bcb/2013 db/conf/bcb/bcb2013.html#HoffmanBWWBN13 Alexander J. Hartemink Manolis Kellis William Stafford Noble Zhiping Weng Session Introduction. 65-68 2013 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb13/intro-epigenomics.pdf conf/psb/2013 db/conf/psb/psb2013.html#HarteminkKNW13

Gabriel Cuéllar-Partida Fabian A. Buske Robert C. McLeay Tom Whitington William Stafford Noble Timothy L. Bailey Epigenetic priors for identifying active transcription factor binding sites. 56-62 2012 28 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btr614 https://www.wikidata.org/entity/Q24623379 db/journals/bioinformatics/bioinformatics28.html#Cuellar-PartidaBMWNB12

Sean McIlwain Michael Mathews Michael Bereman Edwin W. Rubel Michael J. MacCoss William Stafford Noble Estimating relative abundances of proteins from shotgun proteomics data. 308 2012 13 BMC Bioinform. https://doi.org/10.1186/1471-2105-13-308 https://www.wikidata.org/entity/Q30577922 db/journals/bmcbi/bmcbi13.html#McIlwainMBRMN12

Viktor Granholm William Stafford Noble Lukas Käll A cross-validation scheme for machine learning algorithms in shotgun proteomics. S3 2012 13 BMC Bioinform. S-16 https://doi.org/10.1186/1471-2105-13-S16-S3 https://www.wikidata.org/entity/Q34486815 db/journals/bmcbi/bmcbi13S.html#GranholmNK12

William Stafford Noble Michael J. MacCoss Computational and Statistical Analysis of Protein Mass Spectrometry Data. 2012 8 PLoS Comput. Biol. 1 https://doi.org/10.1371/journal.pcbi.1002296 https://www.wikidata.org/entity/Q34145620 db/journals/ploscb/ploscb8.html#NobleM12

Oliver Serang William Stafford Noble Faster Mass Spectrometry-Based Protein Inference: Junction Trees Are More Efficient than Sampling and Marginalization by Enumeration. 809-817 2012 9 IEEE ACM Trans. Comput. Biol. Bioinform. 3 https://doi.org/10.1109/TCBB.2012.26 https://doi.ieeecomputersociety.org/10.1109/TCBB.2012.26 https://dl.acm.org/doi/10.1109/TCBB.2012.26 https://www.wikidata.org/entity/Q34158195 db/journals/tcbb/tcbb9.html#SerangN12

Soyoung Ryu David R. Goodlett William S. Noble Vladimir N. Minin A statistical approach to peptide identification from clustered tandem mass spectrometry data. 648-653 2012 BIBM Workshops https://doi.org/10.1109/BIBMW.2012.6470214 https://doi.ieeecomputersociety.org/10.1109/BIBMW.2012.6470214 https://www.wikidata.org/entity/Q30653513 conf/bibm/2012w db/conf/bibm/bibmw2012.html#RyuGNM12 William Stafford Noble C. Anthony Blau Job Dekker Zhi-jun Duan Yi Mao The Structure and Function of Chromatin and Chromosomes. 434-440 2012 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb12/wkshop-sfcc.pdf conf/psb/2012 db/conf/psb/psb2012.html#NobleBDDM12 Ajit P. Singh John T. Halloran Jeff A. Bilmes Katrin Kirchhoff William Stafford Noble Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra. 775-785 2012 UAI https://dslpitt.org/uai/displayArticleDetails.jsp?mmnu=1&smnu=2&article_id=2343&proceeding_id=28 conf/uai/2012 db/conf/uai/uai2012.html#SinghHBKN12

Ajit P. Singh John T. Halloran Jeff A. Bilmes Katrin Kirchhoff William Stafford Noble Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra http://arxiv.org/abs/1210.4904 2012 CoRR abs/1210.4904 db/journals/corr/corr1210.html#abs-1210-4904

Charles E. Grant Timothy L. Bailey William Stafford Noble FIMO: scanning for occurrences of a given motif. 1017-1018 2011 27 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btr064 https://www.wikidata.org/entity/Q34729603 db/journals/bioinformatics/bioinformatics27.html#GrantBN11

Emi Tanaka Timothy L. Bailey Charles E. Grant William Stafford Noble Uri Keich Improved similarity scores for comparing motifs. 1603-1609 2011 27 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btr257 https://www.wikidata.org/entity/Q35019699 db/journals/bioinformatics/bioinformatics27.html#TanakaBGNK11

Zafer Aydin Ajit P. Singh Jeff A. Bilmes William Stafford Noble Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure. 154 2011 12 BMC Bioinform. https://doi.org/10.1186/1471-2105-12-154 https://www.wikidata.org/entity/Q28743494 db/journals/bmcbi/bmcbi12.html#AydinSBN11

Orion J. Buske Michael M. Hoffman Nadia Ponts Karine G. Le Roch William Stafford Noble Exploratory analysis of genomic segmentations with Segtools. 415 2011 12 BMC Bioinform. https://doi.org/10.1186/1471-2105-12-415 https://www.wikidata.org/entity/Q34058920 db/journals/bmcbi/bmcbi12.html#BuskeHPRN11

Iain Melvin Jason Weston William Stafford Noble Christina S. Leslie Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding. 2011 7 PLoS Comput. Biol. 1 https://doi.org/10.1371/journal.pcbi.1001047 https://www.wikidata.org/entity/Q28743231 db/journals/ploscb/ploscb7.html#MelvinWNL11

William Stafford Noble Zhi-jun Duan Mirela Andronescu Kevin Schutz Sean McIlwain Yoo Jung Kim Choli Lee Jay Shendure Stanley Fields C. Anthony Blau A Three-Dimensional Model of the Yeast Genome. 320 2011 RECOMB https://doi.org/10.1007/978-3-642-20036-6_28 conf/recomb/2011 db/conf/recomb/recomb2011.html#NobleDASMKLSFB11 Yanjun Qi William Stafford Noble Protein Interaction Networks: Protein Domain Interaction and Protein Function Prediction. 427-459 2011 Handbook of Statistical Bioinformatics https://doi.org/10.1007/978-3-642-16345-6_21 books/daglib/0026799 db/books/daglib/0026799.html#QiN11

Michael M. Hoffman Orion J. Buske William Stafford Noble The Genomedata format for storing large-scale functional genomics data. 1458-1459 2010 26 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btq164 https://www.wikidata.org/entity/Q33569885 db/journals/bioinformatics/bioinformatics26.html#HoffmanBN10

Xiaoyu Chen Michael M. Hoffman Jeff A. Bilmes Jay R. Hesselberth William Stafford Noble A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. 334-342 2010 26 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btq175 https://www.wikidata.org/entity/Q33597335 db/journals/bioinformatics/bioinformatics26.html#ChenHBHN10

Zafer Aydin John I. Murray Robert H. Waterston William Stafford Noble Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo. 84 2010 11 BMC Bioinform. https://doi.org/10.1186/1471-2105-11-84 https://www.wikidata.org/entity/Q33530567 db/journals/bmcbi/bmcbi11.html#AydinMWN10

Martial Hue Michael Riffle Jean-Philippe Vert William Stafford Noble Large-scale prediction of protein-protein interactions from structures. 144 2010 11 BMC Bioinform. https://doi.org/10.1186/1471-2105-11-144 https://www.wikidata.org/entity/Q33542870 db/journals/bmcbi/bmcbi11.html#HueRVN10

Jens Gramm Richard M. Karp William S. Noble Roded Sharan Qianfei Wang Nir Yosef Prediction of Phenotype Information from Genotype Data. 99-114 2010 10 Commun. Inf. Syst. 2 https://doi.org/10.4310/cis.2010.v10.n2.a3 db/journals/cominfsys/cominfsys10.html#GrammKNSWY10

Sheila M. Reynolds Jeff A. Bilmes William Stafford Noble Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens. 2010 6 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1000834 https://www.wikidata.org/entity/Q33349451 db/journals/ploscb/ploscb6.html#ReynoldsBN10

Phaedra Agius Aaron Arvey William Chang William Stafford Noble Christina S. Leslie High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions. 2010 6 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1000916 https://www.wikidata.org/entity/Q33691422 db/journals/ploscb/ploscb6.html#AgiusACNL10

Sheila M. Reynolds Zhiping Weng Jeff A. Bilmes William Stafford Noble Predicting Nucleosome Positioning Using Multiple Evidence Tracks. 441-455 2010 RECOMB https://doi.org/10.1007/978-3-642-12683-3_29 conf/recomb/2010 db/conf/recomb/recomb2010.html#ReynoldsWBN10 William Stafford Noble Christina S. Leslie Learning Models of Biological Sequences. 590-594 2010 Encyclopedia of Machine Learning https://doi.org/10.1007/978-0-387-30164-8_463 reference/ml/2010 db/reference/ml/ml2010.html#NobleL10

Iain Melvin Jason Weston Christina S. Leslie William Stafford Noble RANKPROP: a web server for protein remote homology detection. 121-122 2009 25 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btn567 https://www.wikidata.org/entity/Q37090223 db/journals/bioinformatics/bioinformatics25.html#MelvinWLN09

Lukas Käll John D. Storey William Stafford Noble QVALITY: non-parametric estimation of q-values and posterior error probabilities. 964-966 2009 25 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btp021 https://www.wikidata.org/entity/Q42951705 db/journals/bioinformatics/bioinformatics25.html#KallSN09

John Hawkins Charles E. Grant William Stafford Noble Timothy L. Bailey Assessing phylogenetic motif models for predicting transcription factor binding sites. 2009 25 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btp201 https://www.wikidata.org/entity/Q43121061 db/journals/bioinformatics/bioinformatics25.html#HawkinsGNB09

Timothy L. Bailey Mikael Bodén Fabian A. Buske Martin C. Frith Charles E. Grant Luca Clementi Jingyuan Ren Wilfred W. Li William Stafford Noble MEME SUITE: tools for motif discovery and searching. 202-208 2009 37 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gkp335 https://www.wikidata.org/entity/Q29547204 db/journals/nar/nar37.html#BaileyBBFGCRLN09

William Stafford Noble A Quick Guide to Organizing Computational Biology Projects. 2009 5 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1000424 https://www.wikidata.org/entity/Q24273455 db/journals/ploscb/ploscb5.html#Noble09

Sheila M. Reynolds Jeff A. Bilmes William Stafford Noble On the Relationship between DNA Periodicity and Local Chromatin Structure. 434-450 2009 RECOMB https://doi.org/10.1007/978-3-642-02008-7_31 conf/recomb/2009 db/conf/recomb/recomb2009.html#ReynoldsBN09

Heng Lian William A. Thompson Robert E. Thurman John A. Stamatoyannopoulos William Stafford Noble Charles E. Lawrence Automated mapping of large-scale chromatin structure in ENCODE. 1911-1916 2008 24 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btn335 https://www.wikidata.org/entity/Q36844430 db/journals/bioinformatics/bioinformatics24.html#LianTTSNL08

Iain Melvin Jason Weston Christina S. Leslie William Stafford Noble Combining classifiers for improved classification of proteins from sequence or structure. 2008 9 BMC Bioinform. https://doi.org/10.1186/1471-2105-9-389 https://www.wikidata.org/entity/Q33371114 db/journals/bmcbi/bmcbi9.html#MelvinWLN08

Jian Qiu William Stafford Noble Predicting Co-Complexed Protein Pairs from Heterogeneous Data. 2008 4 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1000054 https://www.wikidata.org/entity/Q31153033 db/journals/ploscb/ploscb4.html#QiuN08

Shobhit Gupta Jonathan H. Dennis Robert E. Thurman Robert E. Kingston John A. Stamatoyannopoulos William Stafford Noble Predicting Human Nucleosome Occupancy from Primary Sequence. 2008 4 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.1000134 https://www.wikidata.org/entity/Q33363096 db/journals/ploscb/ploscb4.html#GuptaDTKSN08

Sheila M. Reynolds Lukas Käll Michael Riffle Jeff A. Bilmes William Stafford Noble Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks. 2008 4 PLoS Comput. Biol. 11 https://doi.org/10.1371/journal.pcbi.1000213 https://www.wikidata.org/entity/Q28473900 db/journals/ploscb/ploscb4.html#ReynoldsKRBN08

Lukas Käll John D. Storey William Stafford Noble Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. 42-48 2008 ECCB https://doi.org/10.1093/bioinformatics/btn294 https://www.wikidata.org/entity/Q42005545 conf/eccb/2008 db/conf/eccb/eccb2008.html#KallSN08 Nir Yosef Roded Sharan William Stafford Noble Improved network-based identification of protein orthologs. 200-206 2008 ECCB https://doi.org/10.1093/bioinformatics/btn277 https://www.wikidata.org/entity/Q44544127 conf/eccb/2008 db/conf/eccb/eccb2008.html#YosefSN08 Aaron A. Klammer Sheila M. Reynolds Jeff A. Bilmes Michael J. MacCoss William Stafford Noble Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. 348-356 2008 ISMB https://doi.org/10.1093/bioinformatics/btn189 https://www.wikidata.org/entity/Q30490288 conf/ismb/2008 db/conf/ismb/ismb2008.html#KlammerRBMN08 Robert E. Thurman William Stafford Noble John A. Stamatoyannopoulos Multi-Scale Correlations in Continuous Genomic Data. 201-215 2008 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb08/thurman.pdf conf/psb/2008 db/conf/psb/psb2008.html#ThurmanNS08

Jian Qiu Martial Hue Asa Ben-Hur Jean-Philippe Vert William Stafford Noble A structural alignment kernel for protein structures. 1090-1098 2007 23 Bioinform. 9 https://doi.org/10.1093/bioinformatics/btl642 https://www.wikidata.org/entity/Q38517015 db/journals/bioinformatics/bioinformatics23.html#QiuHBVN07

Nathan Day Andrew Hemmaplardh Robert E. Thurman John A. Stamatoyannopoulos William Stafford Noble Unsupervised segmentation of continuous genomic data. 1424-1426 2007 23 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btm096 https://www.wikidata.org/entity/Q31106817 db/journals/bioinformatics/bioinformatics23.html#DayHTSN07

Gal Chechik Christina S. Leslie William Stafford Noble Gunnar Rätsch Quaid Morris Koji Tsuda NIPS workshop on New Problems and Methods in Computational Biology. 2007 8 BMC Bioinform. S-10 https://doi.org/10.1186/1471-2105-8-S10-S1 https://www.wikidata.org/entity/Q45788614 db/journals/bmcbi/bmcbi8S.html#ChechikLNRMT07

Jean-Philippe Vert Jian Qiu William Stafford Noble A new pairwise kernel for biological network inference with support vector machines. 2007 8 BMC Bioinform. S-10 https://doi.org/10.1186/1471-2105-8-S10-S8 https://www.wikidata.org/entity/Q33319512 db/journals/bmcbi/bmcbi8S.html#VertQN07

Iain Melvin Eugene Ie Rui Kuang Jason Weston William Stafford Noble Christina S. Leslie SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. 2007 8 BMC Bioinform. S-4 https://doi.org/10.1186/1471-2105-8-S4-S2 https://www.wikidata.org/entity/Q33287738 db/journals/bmcbi/bmcbi8S.html#MelvinIKWNL07

Iain Melvin Eugene Ie Jason Weston William Stafford Noble Christina S. Leslie Multi-class Protein Classification Using Adaptive Codes. 1557-1581 2007 8 J. Mach. Learn. Res. https://dl.acm.org/doi/10.5555/1314498.1314551 db/journals/jmlr/jmlr8.html#MelvinIWNL07

Aaron A. Klammer Xianhua Yi Michael J. MacCoss William Stafford Noble Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions. 459-472 2007 conf/recomb/2007 RECOMB https://doi.org/10.1007/978-3-540-71681-5_32 db/conf/recomb/recomb2007.html#KlammerYMN07

Darrin P. Lewis Tony Jebara William Stafford Noble Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure. 2753-2760 2006 22 Bioinform. 22 https://doi.org/10.1093/bioinformatics/btl475 https://www.wikidata.org/entity/Q31060397 db/journals/bioinformatics/bioinformatics22.html#LewisJN06

Asa Ben-Hur William Stafford Noble Choosing negative examples for the prediction of protein-protein interactions. 2006 7 BMC Bioinform. S-1 https://doi.org/10.1186/1471-2105-7-S1-S2 https://www.wikidata.org/entity/Q33244579 db/journals/bmcbi/bmcbi7S.html#Ben-HurN06

Jason Weston Rui Kuang Christina S. Leslie William Stafford Noble Protein Ranking by Semi-Supervised Network Propagation. 2006 7 BMC Bioinform. S-1 https://doi.org/10.1186/1471-2105-7-S1-S10 https://www.wikidata.org/entity/Q33244577 db/journals/bmcbi/bmcbi7S.html#WestonKLN06

Tobias P. Mann Richard Humbert John A. Stamatoyannopoulos William Stafford Noble Automated Validation of Polymerase Chain Reaction Amplicon Melting Curves. 299-316 2006 4 J. Bioinform. Comput. Biol. 2 https://doi.org/10.1142/S0219720006001989 https://www.wikidata.org/entity/Q51938452 db/journals/jbcb/jbcb4.html#MannHSN06

Darrin P. Lewis Tony Jebara William Stafford Noble Nonstationary kernel combination. 553-560 2006 conf/icml/2006 ICML https://doi.org/10.1145/1143844.1143914 db/conf/icml/icml2006.html#LewisJN06 Tobias P. Mann William Stafford Noble Efficient identification of DNA hybridization partners in a sequence database. 350-358 2006 conf/ismb/2006 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/btl240 https://www.wikidata.org/entity/Q38311121 db/conf/ismb/ismb2006.html#MannN06 Jason Weston Christina S. Leslie Eugene Ie William Stafford Noble Semi-Supervised Protein Classification Using Cluster Kernels. 342-360 2006 Semi-Supervised Learning https://doi.org/10.7551/mitpress/9780262033589.003.0019 books/mit/06/CSZ2006 db/books/collections/CSZ2006.html#WestonLIN06

Jean-Philippe Vert Jian Qiu William Stafford Noble Metric learning pairwise kernel for graph inference http://arxiv.org/abs/q-bio/0610040 2006 CoRR abs/q-bio/0610040 db/journals/corr/corr0610.html#abs-q-bio-0610040

Jason Weston Christina S. Leslie Eugene Ie Dengyong Zhou André Elisseeff William Stafford Noble Semi-supervised protein classification using cluster kernels. 3241-3247 2005 21 Bioinform. 15 https://doi.org/10.1093/bioinformatics/bti497 https://www.wikidata.org/entity/Q48487929 db/journals/bioinformatics/bioinformatics21.html#WestonLIZEN05

Rui Kuang Jason Weston William Stafford Noble Christina S. Leslie Motif-based protein ranking by network propagation. 3711-3718 2005 21 Bioinform. 19 https://doi.org/10.1093/bioinformatics/bti608 https://www.wikidata.org/entity/Q48479167 db/journals/bioinformatics/bioinformatics21.html#KuangWNL05

Charles X. Ling William Stafford Noble Qiang Yang 0001 Guest Editors' Introduction to the Special Issue: Machine Learning for Bioinformatics - Part 1. 81-82 2005 2 IEEE ACM Trans. Comput. Biol. Bioinform. 2 https://doi.org/10.1109/TCBB.2005.25 https://doi.ieeecomputersociety.org/10.1109/TCBB.2005.25 https://dl.acm.org/doi/10.1109/TCBB.2005.25 https://www.wikidata.org/entity/Q59678900 db/journals/tcbb/tcbb2.html#LingNY05

Charles X. Ling William Stafford Noble Qiang Yang 0001 Guest Editor's Introduction to the Special Issue: Machine Learning for Bioinformatics-Part 2. 177-178 2005 2 IEEE ACM Trans. Comput. Biol. Bioinform. 3 https://doi.org/10.1109/TCBB.2005.41 https://doi.ieeecomputersociety.org/10.1109/TCBB.2005.41 https://dl.acm.org/doi/10.1109/TCBB.2005.41 https://www.wikidata.org/entity/Q59678898 db/journals/tcbb/tcbb2.html#LingNY05a

Will Sheffler Eli Upfal John Sedivy William Stafford Noble A Learned Comparative Expression Measure for Affymetrix GeneChip DNA Microarrays. 144-154 2005 conf/csb/2005 CSB https://doi.org/10.1109/CSB.2005.5 https://doi.ieeecomputersociety.org/10.1109/CSB.2005.5 https://www.wikidata.org/entity/Q51588405 db/conf/csb/csb2005.html#ShefflerUSN05 Aaron A. Klammer Christine C. Wu Michael J. MacCoss William Stafford Noble Peptide Charge State Determination for Low-Resolution Tandem Mass Spectra. 175-185 2005 conf/csb/2005 CSB https://doi.org/10.1109/CSB.2005.44 https://doi.ieeecomputersociety.org/10.1109/CSB.2005.44 https://www.wikidata.org/entity/Q51953488 db/conf/csb/csb2005.html#KlammerWMN05 Tobias P. Mann Richard Humbert John A. Stamatoyannopoulos William Stafford Noble Automated Validation of Polymerase Chain Reactions Using Amplicon Melting Curves. 377-385 2005 conf/csb/2005 CSB https://doi.org/10.1109/CSB.2005.17 https://doi.ieeecomputersociety.org/10.1109/CSB.2005.17 https://www.wikidata.org/entity/Q51953440 db/conf/csb/csb2005.html#MannHSN05 Eugene Ie Jason Weston William Stafford Noble Christina S. Leslie Multi-class protein fold recognition using adaptive codes. 329-336 2005 conf/icml/2005 ICML https://doi.org/10.1145/1102351.1102393 db/conf/icml/icml2005.html#IeWNL05 Asa Ben-Hur William Stafford Noble Kernel methods for predicting protein-protein interactions. 38-46 2005 conf/ismb/2005 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/bti1016 https://www.wikidata.org/entity/Q38520179 db/conf/ismb/ismb2005.html#Ben-HurN05 William Stafford Noble Scott Kuehn Robert E. Thurman Man Yu John A. Stamatoyannopoulos Predicting the in vivo signature of human gene regulatory sequence. 328-343 2005 conf/ismb/2005 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/bti1047 https://www.wikidata.org/entity/Q46551428 db/conf/ismb/ismb2005.html#NobleKTYS05 Jean-Philippe Vert Robert E. Thurman William Stafford Noble Kernels for gene regulatory regions. 2005 conf/nips/2005 NIPS https://proceedings.neurips.cc/paper/2005/hash/bd1354624fbae3b2149878941c60df99-Abstract.html http://papers.nips.cc/paper/2861-kernels-for-gene-regulatory-regions db/conf/nips/nips2005.html#VertTN05 1401-1408

Christina S. Leslie Eleazar Eskin Adiel Cohen Jason Weston William Stafford Noble Mismatch string kernels for discriminative protein classification. 2004 20 Bioinform. 4 https://doi.org/10.1093/bioinformatics/btg431 https://www.wikidata.org/entity/Q42620879 db/journals/bioinformatics/bioinformatics20.html#LeslieECWN04 467-476

Paul Pavlidis Ilan Wapinski William Stafford Noble Support vector machine classification on the web. 2004 20 Bioinform. 4 https://doi.org/10.1093/bioinformatics/btg461 https://www.wikidata.org/entity/Q45966840 db/journals/bioinformatics/bioinformatics20.html#PavlidisWN04 586-587

Wei Wu William Stafford Noble Genomic data visualization on the Web. 1804-1805 2004 20 Bioinform. 11 https://doi.org/10.1093/bioinformatics/bth154 https://www.wikidata.org/entity/Q30908836 db/journals/bioinformatics/bioinformatics20.html#WuN04

Gert R. G. Lanckriet Tijl De Bie Nello Cristianini Michael I. Jordan William Stafford Noble A statistical framework for genomic data fusion. 2626-2635 2004 20 Bioinform. 16 https://doi.org/10.1093/bioinformatics/bth294 https://www.wikidata.org/entity/Q30929198 db/journals/bioinformatics/bioinformatics20.html#LanckrietBCJN04

Koji Tsuda William Stafford Noble Learning kernels from biological networks by maximizing entropy. 326-333 2004 conf/ismb/2004 ISMB/ECCB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/bth906 https://www.wikidata.org/entity/Q48533625 db/conf/ismb/ismb2004.html#TsudaN04 Gert R. G. Lanckriet Minghua Deng Nello Cristianini Michael I. Jordan William Stafford Noble Kernel-Based Data Fusion and Its Application to Protein Function Prediction in Yeast. 300-311 2004 conf/psb/2004 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb04/lanckriet.pdf db/conf/psb/psb2004.html#LanckrietDCJN04

Paul Pavlidis William Stafford Noble Matrix2png: a utility for visualizing matrix data. 295-296 2003 19 Bioinform. 2 db/journals/bioinformatics/bioinformatics19.html#PavlidisN03 https://doi.org/10.1093/bioinformatics/19.2.295 https://www.wikidata.org/entity/Q30763076

Paul Pavlidis Qinghong Li William Stafford Noble The effect of replication on gene expression microarray experiments. 1620-1627 2003 19 Bioinform. 13 db/journals/bioinformatics/bioinformatics19.html#PavlidisLN03 https://doi.org/10.1093/bioinformatics/btg227 https://www.wikidata.org/entity/Q48228979

Shawn M. Gomez William Stafford Noble Andrey Rzhetsky Learning to predict protein-protein interactions from protein sequences. 1875-1881 2003 19 Bioinform. 15 db/journals/bioinformatics/bioinformatics19.html#GomezNR03 https://doi.org/10.1093/bioinformatics/btg352 https://www.wikidata.org/entity/Q47446623

Jie Qin Darrin P. Lewis William Stafford Noble Kernel hierarchical gene clustering from microarray expression data. 2097-2104 2003 19 Bioinform. 16 db/journals/bioinformatics/bioinformatics19.html#QinLN03 https://doi.org/10.1093/bioinformatics/btg288 https://www.wikidata.org/entity/Q33194479

Eleazar Eskin William Stafford Noble Yoram Singer Protein Family Classification Using Sparse Markov Transducers. 187-213 2003 10 J. Comput. Biol. 2 db/journals/jcb/jcb10.html#EskinNS03 https://doi.org/10.1089/106652703321825964 https://www.wikidata.org/entity/Q47837919

Li Liao William Stafford Noble Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships. 857-868 2003 10 J. Comput. Biol. 6 https://doi.org/10.1089/106652703322756113 https://www.wikidata.org/entity/Q51023320 db/journals/jcb/jcb10.html#LiaoN03

Timothy L. Bailey William Stafford Noble Searching for statistically significant regulatory modules. 16-25 2003 conf/eccb/2003 ECCB db/conf/eccb/eccb2003.html#BaileyN03 https://doi.org/10.1093/bioinformatics/btg1054 Jason Weston Christina S. Leslie Dengyong Zhou André Elisseeff William Stafford Noble Semi-supervised Protein Classification Using Cluster Kernels. 2003 conf/nips/2003 NIPS https://proceedings.neurips.cc/paper/2003/hash/12ffb0968f2f56e51a59a6beb37b2859-Abstract.html http://papers.nips.cc/paper/2496-semi-supervised-protein-classification-using-cluster-kernels db/conf/nips/nips2003.html#WestonLZEN03 595-602

Paul Pavlidis Jason Weston Jinsong Cai William Stafford Noble Learning Gene Functional Classifications from Multiple Data Types. 401-411 2002 9 J. Comput. Biol. 2 db/journals/jcb/jcb9.html#PavlidisWCN02 https://doi.org/10.1089/10665270252935539 https://www.wikidata.org/entity/Q30693068

Eleazar Eskin William Stafford Noble Yoram Singer Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences. 775-791 2002 9 J. Comput. Biol. 6 db/journals/jcb/jcb9.html#EskinNS02 https://doi.org/10.1089/10665270260518263 https://www.wikidata.org/entity/Q48603899

Bernhard Schölkopf Jason Weston Eleazar Eskin Christina S. Leslie William Stafford Noble A Kernel Approach for Learning from almost Orthogonal Patterns. 511-528 2002 conf/ecml/2002 ECML https://doi.org/10.1007/3-540-36755-1_44 db/conf/ecml/ecml2002.html#ScholkopfWELN02 Christina S. Leslie Eleazar Eskin Jason Weston William Stafford Noble Mismatch String Kernels for SVM Protein Classification. 1417-1424 2002 conf/nips/2002 NIPS https://proceedings.neurips.cc/paper/2002/hash/12b1e42dc0746f22cf361267de07073f-Abstract.html http://papers.nips.cc/paper/2179-mismatch-string-kernels-for-svm-protein-classification db/conf/nips/nips2002.html#LeslieEWN02 Bernhard Schölkopf Jason Weston Eleazar Eskin Christina S. Leslie William Stafford Noble A Kernel Approach for Learning from Almost Orthogonal Patterns. 494-511 2002 conf/pkdd/2002 PKDD https://doi.org/10.1007/3-540-45681-3_42 db/conf/pkdd/pkdd2002.html#ScholkopfWELN02 Paul Pavlidis Darrin P. Lewis William Stafford Noble Exploring Gene Expression Data with Class Scores. 474-485 2002 conf/psb/2002 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb02/pavlidis.pdf db/conf/psb/psb2002.html#PavlidisLN02 Christina S. Leslie Eleazar Eskin William Stafford Noble The Spectrum Kernel: A String Kernel for SVM Protein Classification. 566-575 2002 conf/psb/2002 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb02/leslie.pdf db/conf/psb/psb2002.html#LeslieEN02 Li Liao William Stafford Noble Combining pairwise sequence similarity and support vector machines for remote protein homology detection. 225-232 2002 conf/recomb/2002 RECOMB https://doi.org/10.1145/565196.565225 db/conf/recomb/recomb2002.html#LiaoN02 Eleazar Eskin William Noble Grundy Yoram Singer Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences. 65-73 2001 conf/ismb/2001 ISMB (Supplement of Bioinformatics) db/conf/ismb/ismb2001.html#EskinGS01 https://doi.org/10.1093/bioinformatics/17.suppl_1.s65 Paul Pavlidis Christopher Tang William Stafford Noble Classification of genes using probabilistic models of microarray expression profiles. 15-21 2001 conf/kdd/2001bio BIOKDD http://www.cs.rpi.edu/~zaki/BIOKDD01/pavlidis.ps.gz db/conf/kdd/biokdd2001.html#PavlidisTN01 Paul Pavlidis Terrence S. Furey M. Liberto David Haussler William Noble Grundy Promoter Region-Based Classification of Genes. 151-164 2001 conf/psb/2001 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb01/pavlidis.pdf db/conf/psb/psb2001.html#PavlidisFLHG01 Paul Pavlidis Jason Weston Jinsong Cai William Noble Grundy Gene functional classification from heterogeneous data. 249-255 2001 conf/recomb/2001 RECOMB https://doi.org/10.1145/369133.369228 db/conf/recomb/recomb2001.html#PavlidisWCG01 Eleazar Eskin William Noble Grundy Yoram Singer Protein Family Classification Using Sparse Markov Transducers. 134-145 2000 conf/ismb/2000 ISMB db/conf/ismb/ismb2000.html#EskinGS00 http://www.aaai.org/Library/ISMB/2000/ismb00-014.php

William Noble Grundy Timothy L. Bailey Family pairwise search with embedded motif models. 463-470 1999 15 Bioinform. 6 db/journals/bioinformatics/bioinformatics15.html#GrundyB99 https://doi.org/10.1093/bioinformatics/15.6.463 https://www.wikidata.org/entity/Q41675434

Timothy L. Bailey William Noble Grundy Classifying proteins by family using the product of correlated p-values. 10-14 1999 conf/recomb/1999 RECOMB https://doi.org/10.1145/299432.299444 db/conf/recomb/recomb1999.html#BaileyG99 Timothy L. Bailey Michael E. Baker Charles Elkan William Noble Grundy MEME, MAST, and Meta-MEME: New Tools for Motif Discovery in Protein Sequences. 30-54 1999 books/ox/WangSS99 Pattern Discovery in Biomolecular Data db/books/collections/Wang99.html#BaileyBEG99

William Noble Grundy Homology Detection via Family Pairwise Search. 479-491 1998 5 J. Comput. Biol. 3 db/journals/jcb/jcb5.html#Grundy98 https://doi.org/10.1089/cmb.1998.5.479 https://www.wikidata.org/entity/Q38549689

William Noble Grundy Family-based homology detection via pairwise sequence comparison. 94-100 1998 conf/recomb/1998 RECOMB https://doi.org/10.1145/279069.279098 db/conf/recomb/recomb1998.html#Grundy98

William Noble Grundy Timothy L. Bailey Charles Elkan Michael E. Baker Meta-MEME: motif-based hidden Markov models of protein families. 397-406 1997 13 Comput. Appl. Biosci. 4 db/journals/bioinformatics/bioinformatics13.html#GrundyBEB97 https://doi.org/10.1093/bioinformatics/13.4.397 https://www.wikidata.org/entity/Q46764870

William Noble Grundy Timothy L. Bailey Charles Elkan ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. 303-310 1996 12 Comput. Appl. Biosci. 4 db/journals/bioinformatics/bioinformatics12.html#GrundyBE96 https://doi.org/10.1093/bioinformatics/12.4.303

John Batali William Noble Grundy Modeling the Evolution of Motivation. 235-270 1996 4 Evol. Comput. 3 db/journals/ec/ec4.html#BataliG96 https://doi.org/10.1162/evco.1996.4.3.235

Phaedra Agius Julie Ahringer Erez S. Lieberman Aiden Artyom A. Alekseyenko Burak Han Alver Varun Ananth Mirela Andronescu Alex Appert Aaron Arvey Dalal Asker Ferhat Ay Zafer Aydin Wenruo Bai Timothy L. Bailey David Baker 0001 Michael E. Baker John Batali Brittany Baur Jason A. Belsky Asa Ben-Hur Michael Bereman Bradley E. Bernstein Alessandro Bertero Tijl De Bie Jeff A. BilmesJeffrey A. Bilmes Eric Bishop Wout Bittremieux C. Anthony Blau Mikael Bodén Nathan Boley Giancarlo Bonora Sarah K. Bowman Fabian A. Buske Orion J. Buske Haoran Cai Jinsong Cai Alexandra Gesine Cauer Rachel C. W. Chan William Chang Gal Chechik Q. Brent Chen Ron A.-J. Chen Tianlong Chen 0001 Winston Chen Xiaoyu Chen Alice Cheng Luca Clementi Adiel Cohen Kate Cook Nello Cristianini Gabriel Cuéllar-Partida Marco Cuturi Daniel S. Day Nathan Day Job Dekker Pinar Demetci Minghua Deng Xinxian Deng Jonathan H. Dennis Abby F. Dernburg Christine Disteche Yan Dong Andrea C. Dose Xikun Duan Zhi-jun Duan Josef Durech Timothy Durham Timothy J. Durham Thea A. Egelhofer Sarah C. R. Elgin André Elisseeff Charles Elkan Kristen Emery Charles B. Epstein Sevinc Ercan Eleazar Eskin Yingying Fan He Fang Tangqi Fang Elise A. Feingold Francesco Ferrari Stanley Fields William Fondrie Douglas Fowler Jack Freestone Martin C. Frith Terrence S. Furey Musa Nur Gabere Jacob M. Garrigues Nils Gehlenborg Mark Gerstein Louis Gevirtzman Shawn M. Gomez Peter J. Good David R. Goodlett Jens Gramm Viktor Granholm Charles E. Grant Mikael Granvik William Greenleaf Tingting Gu Wenbo Guo 0002 Shobhit Gupta Giannina Guzman John T. Halloran Alexander J. Hartemink Syamand Hasam Psalm Haseley David Haussler John Hawkins Daniel He Deepthi Hegde Andrew Hemmaplardh Moritz Herrmann Jay R. Hesselberth Jennifer Hesson Joshua W. K. HoJoshua Wing Kei Ho Michael M. Hoffman Borislav H. Hristov Alex Hu Sheng'en HuSheng'en Shawn Hu Yuanhao Huang Martial Hue Richard Humbert Janine R. Hutchison Eugene Ie Kohta Ikegami Tony Jebara Tess E. Jeffers Bryan Jensen Anupama Jha Yifan Jiang James Johnson Michael I. Jordan Youngsook L. Jung Brooke L. Deatherage Kaiser Lukas Käll Sreeram Kannan Richard M. Karp Gary H. Karpen Uri Keich Michael S. P. Kelley Manolis Kellis Peter V. Kharchenko Hyeonjin KimHyeon-Jin Kim Ju Han Kim Yoo Jung Kim Robert E. Kingston Katrin Kirchhoff Aaron A. Klammer Paulina Kolasinska-Zwierz Chitra V. Kotwaliwale Rui Kuang Scott Kuehn Nischay Kumar Anshul Kundaje Mitzi I. Kuroda Gert R. G. Lanckriet Sasha A. Langley Erica Larschan Isabel Latorre Charles E. Lawrence Choli Lee Soohyun Lee Christina S. Leslie Darrin P. Lewis Gang Li 0034 Jian-Yang Li Qinghong Li Wilfred W. Li Heng Lian Li Liao Maxwell W. Libbrecht M. Liberto Jason D. Lieb Andy Lin Dejun Lin Xueqiu Lin Charles Ling 0001Charles X. Ling Jie Liu 0045 Tao Liu 0022 Xiaole Shirley Liu Yifeng Liu 0004 Zixuan Liu 0001 Minsi Lu Yang Lu Yang Young Lu Jinchi Lv Wenxiu Ma David M. MacAlpine Michael J. MacCoss Mohith Manjunath Tobias P. Mann Yi Mao Michael Mathews Kayvon Mazooji Jackie McDonald Sean McIlwain Robert C. McLeay Iain Melvin Laetitia Meng-Papaxanthos Alan Min Volodymyr M. MininVladimir N. Minin Aki Minoda Michael Mommert Quaid Morris Nick Moskovitz John I. Murray Peter J. Myler Deborah A. Nickerson Sewoong Oh Peter J. Park Richard Park Stephen C. J. Parker Paul Pavlidis Michael J. Pazin Sriram Pendyala Antti Penttilä Hoang N. Pham Vincenzo Pirrotta Annette Plachetka Nadia Ponts Yanjun Qi Bo Qin Jie Qin Jian Qiu Ruolan Qiu Huaizhi Qu Vijay Ramani Gunnar Rätsch David F. Read Andreas Rechtsteiner Jingyuan Ren Sheila M. Reynolds Nicole C. Riddle Michael Riffle Nicholas M. Riley Eric G. Roberts Karine G. Le Roch Ricard A. Rodriguez-Mias Remo Rohs Sushmita Roy Edwin W. Rubel Jacob H. Russell Soyoung Ryu Andrey Rzhetsky Nalin Samarasinha Justin Sanders Björn Sandstede Rebecca Santorella Bernhard Schölkopf Jacob Schreiber Jacob M. Schreiber Kevin Schutz Yuri B. Schwartz John Sedivy Oliver Serang Roded Sharan Will Sheffler Jay Shendure Junha Shin Ilan Shomorony Noam Shoresh Temana Short Yoram Singer Ajit P. Singh Ritambhara Singh Brigitta M. Sipocz Joshua D. Smith Kyung-Ah Sohn ChaoZhong Song Jun S. Song John A. Stamatoyannopoulos Przemyslaw Stempor John D. Storey Susan Strome Aakash Sur Emi Tanaka Christopher Tang Maryna Taranova William A. Thompson Robert E. Thurman Michael TolstorukovMichael Y. Tolstorukov Koji Tsuda Thomas D. Tullius Eli Upfal Oana Ursu Miguel de Val-Borro Nelle Varoquaux Jean-Philippe Vert Anne Vielle Judit Villén Chengyang Wang Jie Wang Junfeng Wang Qianfei Wang Sheng Wang 0012 Shengjie Wang 0001 Xiao Wang 0013 Y. X. Rachel Wang Ilan Wapinski Carol B. Ware Robert H. Waterston Kris Weber Bo Wen Zhiping Weng Jason Weston Tom Whitington Christina M. Whittle Daniela M. Witten Addie Woicik Christine C. Wu Wei Wu Xinyu Xing 0001 Hanwen Xu Huiling Xue Chengfei Yan Koon-Kiu Yan Lin Yang Qiang Yang 0001 Wei Yang Galip Gürkan YardimciGürkan Yardimci Xianhua Yi Melih Yilmaz Nir Yosef Man Yu Timothy C. Yu Habil Zare Ran Zhang Shilu Zhang Yi Zhang 0055 Yuanyuan Zhang Dengyong Zhou