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William Stafford Noble

university of washington

107H-index
613Paper Count
8.3WCitation Count
Published Papers 192
Publication Date
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A generalizable Hi-C foundation model for chromatin architecture, single-cell and multiomics analysis across species
errNature Methods
IF32.1
err2026-06-15
err0
PREAI
errXiao Wang; Yuanyuan Zhang; Suhita Ray; Anupama Jha; Tangqi Fang; Shengqi Hang; Sergei Doulatov; William S. Noble; Sheng Wang
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errSave
Label-Free Quantification in the Crux Toolkit
errJournal of Proteome Research
IF3.6
err2026-06-11
err0
PREAI
errFrank Lawrence Nii Adoquaye Acquaye; Bo Wen; Charles E. Grant; William S. Noble; Attila Kertesz-Farkas
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errSave
Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC
errNature Communications
IF15.7
err2026-04-20
err0
errOAAI
errAnupama Jha; Borislav Hristov; Xiao Wang; Sheng Wang; William J. Greenleaf; Anshul Kundaje; Erez Lieberman Aiden; Alessandro Bertero; William Stafford Noble
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An integrated view of the structure and function of the human 4D nucleome
errNature
IF48.5
err2025-12-17
err0
errOAAI
errJob Dekker; Betul Akgol Oksuz; Yang Zhang; Ye Wang; Miriam K. Minsk; Shuzhen Kuang; Liyan Yang; Johan H. Gibcus; Nils Krietenstein; Oliver J. Rando; Jie Xu; Derek H. Janssens; Steven Henikoff; Alexander Kukalev; Willemin Andréa; Warren Winick-Ng; Rieke Kempfer; Ana Pombo; Miao Yu; Pradeep Kumar; Liguo Zhang; Andrew S. Belmont; Takayo Sasaki; Tom van Schaik; Laura Brueckner; Daan Peric-Hupkes; Bas van Steensel; Ping Wang; Haoxi Chai; Minji Kim; Yijun Ruan; Ran Zhang; Sofia A. Quinodoz; Prashant Bhat; Mitchell Guttman; Wenxin Zhao; Shu Chien; Yuan Liu; Sergey V. Venev; Dariusz Plewczynski; Ibai Irastorza Azcarate; Dominik Szabó; Christoph J. Thieme; Teresa Szczepińska; Mateusz Chiliński; Kaustav Sengupta; Mattia Conte; Andrea Esposito; Alex Abraham; Ruochi Zhang; Yuchuan Wang; Xingzhao Wen; Qiuyang Wu; Yang Yang; Jie Liu; Lorenzo Boninsegna; Asli Yildirim; Yuxiang Zhan; Andrea Maria Chiariello; Simona Bianco; Lindsay Lee; Ming Hu; Yun Li; R. Jordan Barnett; Ashley L. Cook; Daniel J. Emerson; Claire Marchal; Peiyao Zhao; Peter J. Park; Burak H. Alver; Andrew J. Schroeder; Rahi Navelkar; Clara Bakker; William Ronchetti; Shannon Ehmsen; Alexander D. Veit; Nils Gehlenborg; Ting Wang; Daofeng Li; Xiaotao Wang; Mario Nicodemi; Bing Ren; Sheng Zhong; Jennifer E. Phillips-Cremins; David M. Gilbert; Katherine S. Pollard; Frank Alber; Jian Ma; William S. Noble; Feng Yue
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Proteomics data imputation with a deep model that learns from many datasets
errMolecular & Cellular Proteomics
IF5.5
err2025-11-18
err0
errOAAI
errLincoln Harris; William S. Noble
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errSave
Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases
errCell Systems
IF7.7
err2025-11-12
err0
errOAAI
errMaria Chernigovskaya; Khang Lê Quý; Maria Stensland; Sachin Singh; Rowan Nelson; Melih Yilmaz; Konstantinos Kalogeropoulos; Pavel Sinitcyn; Anand Patel; Natalie Castellana; Stefano Bonissone; Stian Foss; Jan Terje Andersen; Geir Kjetil Sandve; Timothy Patrick Jenkins; William S. Noble; Tuula A. Nyman; Igor Snapkow; Victor Greiff
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errSave
Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics
errNature Communications
IF15.7
err2025-11-06
err0
errOAAI
errBo Wen; Chris Hsu; David Shteynberg; Wen-Feng Zeng; Michael Riffle; Alexis Chang; Miranda C. Mudge; Brook L. Nunn; Brendan X. MacLean; Matthew D. Berg; Judit Villén; Michael J. MacCoss; William S. Noble
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errSave
Multicondition and multimodal temporal profile inference during mouse embryonic development
errGENOME RESEARCH
IF5.5
err2025-10-01
err0
errOAAI
errZhang, Ran; Qiu, Chengxiang; Filippova, Galina N.; Li, Gang; Shendure, Jay; Vert, Jean-Philippe; Deng, Xinxian; Noble, William Stafford; Disteche, Christine M.
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errSave
Predicting chromatin conformation contact maps
errPLOS ONE
IF2.6
err2025-09-29
err0
PREAI
errMin, Alan; Schreiber, Jacob; Kundaje, Anshul; Noble, William S.
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errSave
Error-controlled non-additive interaction discovery in machine learning models
errNature Machine Intelligence
IF23.9
err2025-09-22
err0
errOAAI
errWinston Chen; Yifan Jiang; William Stafford Noble; Yang Young Lu
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errSave
A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data
errNature Methods
IF32.1
err2025-07-01
err0
errOAAI
errJustin Sanders; Bo Wen; Paul A. Rudnick; Richard S. Johnson; Christine C. Wu; Michael Riffle; Sewoong Oh; Michael J. MacCoss; William Stafford Noble
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errSave
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment
errNature Methods
IF32.1
err2025-06-16
err0
errOAAI
errBo Wen; Jack Freestone; Michael Riffle; Michael J. MacCoss; William S. Noble; Uri Keich
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errSave
Predicting cell cycle stage from 3D single-cell nuclear-stained images
errLIFE SCIENCE ALLIANCE
IF2.9
err2025-04-03
err0
errOAAI
errLi, Gang; Nichols, Eva K.; Browning, Valentino E.; Longhi, Nicolas J.; Sanchez-Forman, Madison; Camplisson, Conor K.; Beliveau, Brian J.; Noble, William Stafford
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errSave
Open-Source and FAIR Research Software for Proteomics
errJOURNAL OF PROTEOME RESEARCH
IF3.6
err2025-04-01
err0
errOAAI
errPerez-Riverol, Yasset; Bittremieux, Wout; Noble, William S.; Martens, Lennart; Bilbao, Aivett; Lazear, Michael R.; Gruening, Bjorn; Katz, Daniel S.; MacCoss, Michael J.; Dai, Chengxin; Eng, Jimmy K.; Bouwmeester, Robbin; Shortreed, Michael R.; Audain, Enrique; Sachsenberg, Timo; Van Goey, Jeroen; Wallmann, Georg; Wen, Bo; Kall, Lukas; Fondrie, William E.
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errSave
CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation
errBMC BIOLOGY
IF4.5
err2025-03-03
err0
errOAAI
errFang, He; Tronco, Ana R.; Bonora, Giancarlo; Nguyen, Truong; Thakur, Jitendra; Berletch, Joel B.; Filippova, Galina N.; Henikoff, Steven; Shendure, Jay; Noble, William S.; Duan, Zhijun; Disteche, Christine M.; Deng, Xinxian
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How to Train a Postprocessor for Tandem Mass Spectrometry Proteomics Database Search While Maintaining Control of the False Discovery Rate
errJOURNAL OF PROTEOME RESEARCH
IF3.6
err2025-03-01
err0
errOAAI
errFreestone, Jack; Kall, Lukas; Noble, William Stafford; Keich, Uri
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errSave
Cross-species imputation and comparison of single-cell transcriptomic profiles
errGENOME BIOLOGY
IF9.4
err2025-02-26
err0
errOAAI
errZhang, Ran; Yang, Mu; Schreiber, Jacob; O'Day, Diana R.; Turner, James M. A.; Shendure, Jay; Noble, William Stafford; Disteche, Christine M.
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errSave
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles ( vol 24 , 79 , 2023)
errGENOME BIOLOGY
IF9.4
err2025-02-13
err0
errOAAI
errSchreiber, Jacob Matthew; Boix, Carles A.; Lee, Jin Wook; Li, Hongyang; Guan, Yuanfang; Chang, Chun-Chieh; Chang, Jen-Chien; Hawkins-Hooker, Alex; Schoelkopf, Bernhard; Schweikert, Gabriele; Carulla, Mateo Rojas; Canakoglu, Arif; Guzzo, Francesco; Nanni, Luca; Masseroli, Marco; Carman, Mark James; Pinoli, Pietro; Hong, Chenyang; Yip, Kevin Y.; Spence, Jefrey P.; Batra, Sanjit Singh; Song, Yun S.; Mahony, Shaun; Zhang, Zheng; Tan, Wuwei; Shen, Yang; Sun, Yuanfei; Shi, Minyi; Adrian, Jessika; Sandstrom, Richard S.; Farrell, Nina P.; Halow, Jessica M.; Lee, Kristen; Jiang, Lixia; Yang, Xinqiong; Epstein, Charles B.; Strattan, J. Seth; Bernstein, Bradley E.; Snyder, Michael P.; Kellis, Manolis; Noble, William S.; Kundaje, Anshul Bharat; ENCODE Imputat Challenge Participants
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Deep Learning Methods for De Novo Peptide Sequencing
errMASS SPECTROMETRY REVIEWS
IF6.6
err2024-11-29
err0
PREAI
errBittremieux, Wout; Ananth, Varun; Fondrie, William E.; Melendez, Carlo; Pominova, Marina; Sanders, Justin; Wen, Bo; Yilmaz, Melih; Noble, William S.
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errSave
ChromaFold predicts the 3D contact map from single-cell chromatin accessibility
errNATURE COMMUNICATIONS
IF15.7
err2024-11-01
err1
errOAAI
errGao, Vianne R.; Yang, Rui; Das, Arnav; Luo, Renhe; Luo, Hanzhi; McNally, Dylan R.; Karagiannidis, Ioannis; Rivas, Martin A.; Wang, Zhong-Min; Barisic, Darko; Karbalayghareh, Alireza; Wong, Wilfred; Zhan, Yingqian A.; Chin, Christopher R.; Noble, William S.; Bilmes, Jeff A.; Apostolou, Effie; Kharas, Michael G.; Beguelin, Wendy; Viny, Aaron D.; Huangfu, Danwei; Rudensky, Alexander Y.; Melnick, Ari M.; Leslie, Christina S.
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Research Directions

No research directions
Co-authors
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