Noble Research Lab: Publications and software

y Noble Research Lab: Publications and software

Publications and software

2016
2024

Submitted

Maria Chernigovskaya, Khang Le Quy, 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. "Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases." bioRxiv

Jack Freestone, William Stafford Noble, Uri Keich. "A semi-supervised framework for diverse multiple hypothesis testing scenarios." arXiv

Evan E. Kania, Aidan Fenix, Daphnée M Marciniak, Qiaoyi Lin, Sara Bianchi, Borislav Hristov, Mr Shuai Li, Conor K Camplisson, Rose Fields, Professor Brian J. Beliveau, Devin K. Schweppe, William S Noble, Professor Shao-En Ong, Professor Alessandro Bertero, Charles E Murry, David Shechner. "Nascent transcript O-MAP reveals the molecular architecture of a single-locus subnuclear compartment built by RBM20 and the TTN RNA." bioRxiv

Alexander J. Solivais, Hannah Boekweg, Lloyd M. Smith, William Stafford Noble, Micharl R. Shortreed, Samuel H. Payne, Uri Keich. "Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation." bioRxiv
FlashLFQ

Bo Wen, Chris Hsu, Wen-Feng Zeng, Michael Riffle, Alexis Chang, Miranda Mudge, Brook Nunn, Matthew D. Berg, Judit Villen, Michael J. MacCoss, William Stafford Noble. "Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics." bioRxiv
Carafe

Anupama Jha, Borislav Hristov, Xiao Wang, Sheng Wang, William J. Greenleaf, Anshul Kundaje, Erez Lieberman Aiden, Alessandro Bertero, William Stafford Noble. "Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC." bioRxiv.
TwinC

The 4D Nucleome Consortium, Job Dekker, Betul Akgol Oksuz, Yang Zhang, Ye Wang, Miriam K. Minsk, Shuzhen Kuang, Liyan Yang, Johan H. Gibcus, Nils Krietenstein, Oliver Rando, Jie Xu, Derek H. Janssens, Steven Henikoff, Alexander Kukalev, Andrea Willemin, 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 Szabo, Christoph J. Thieme, Teresa Szczepinska, Mateusz Chilinski, 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 Park, Burak H. Alver, Andrew Schroeder, Rahi Navelkar, Clara Bakker, William Ronchetti, Shannon Ehmsen, Alex 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. "An integrated view of the structure and function of the human 4D nucleome." bioRxiv.

Gang Li, Eva K. Nichols, Valentino E. Browning, Nicolas J. Longhi, Conor Camplisson, Brian J. Beliveau, and William Stafford Noble. "Predicting cell cycle stage from 3D single-cell nuclear-stained images." bioRxiv.
CellCycleNet

Jack Freestone, Lukas Kall, William Stafford Noble, Uri Keich. "How to train a post-processor for tandem mass spectrometry proteomics database search while maintaining control of the false discovery rate." bioRxiv.
Percolator-RESET

Lincoln Harris, William Stafford Noble. "Imputation of cancer proteomics data with a deep model that learns from many datasets." bioRxiv.
Lupine

Ran Zhang, Cx Qiu, Gala Filippova, Gang Li, Jay Shendure, Jean-Philippe Vert, Xinxian Deng, Christine Disteche, William Stafford Noble. "Multi-condition and multi-modal temporal profile inference during mouse embryonic development." bioRxiv.
Sunbear

Mitchell R. Vollger, Elliott G. Swanson, Shane J. Neph, Jane Ranchalis, Katherine M. Munson, Ching-Huang Ho, Adriana E. Sedeno-Cortes, William E. Fondrie, Stephanie C. Bohaczuk, Yizi Mao, Nancy L. Parmalee, Benjamin J. Mallory, William T. Harvey, Younjun Kwon, Gage H. Garcia, Kendra Hoekzema, Jeffrey G. Meyer, Mine Cicek, Evan E. Eichler, William Stafford Noble, Daniela M. Witten, James T. Bennett, John P. Ray, Andrew B. Stergachis. "A haplotype-resolved view of human gene regulation." bioRxiv.

Justin Sanders, Bo Wen, Paul Rudnick, Rich Johnson, Christine C. Wu, Sewoong Oh, Michael J. MacCoss, and William Stafford Noble. "A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data." bioRxiv.
Cascadia

Alan Min, Jacob M. Schreiber, Anshul Kundaje, William Stafford Noble. "Predicting chromatin conformation contact maps.". bioRxiv.
Sphinx

Gang Li, Hyeon-Jin Kim, Sriram Pendyala, Ran Zhang, Christine M. Disteche, Jean-Philippe Vert, Xinxian Deng, Doug Fowler, William Stafford Noble. "Pseudotime analysis for time-series single-cell sequencing and imaging data." bioRxiv.
Sceptic

Borislav Hristov, William Stafford Noble, Alessandro Bertero. "Systematic identification of inter-chromosomal interaction networks supports the existence of specialized RNA factories." bioRxiv.
trans-C

Vikram Agarwal, Fumitaka Inoue, Max Schubach, Beth K. Martin, Pyaree Mohan Dash, Zicong Zhang, Ajuni Sohota, William Stafford Noble, Galip Gurkan Yardimci, Martin Kircher, Jay Shendure, Nadav Ahituv. "Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types". bioRxiv.

Arya Ebadi, Dong Luo, Jack Freestone, William Stafford Noble, Uri Keich. "Bounding the FDP in competition-based control of the FDR." arXiv.

Gayani Batugedara, Xueqing M. Lu, Steven Abel, Zeinab Chahine, Borislav Hristov, Desiree Williams, Thomas Hollin, Tina Wang, Anthony Cort, Todd Lenz, Trevor Thompson, Jacques Prudhomme, Abai K. Tripathi, Guoyue Xu, Juliana Cudini, Sunil Dogga, Mara Lawniczak, William Stafford Noble, Photini Sinnis, Karine G Le Roch. "Deciphering the non-coding code of pathogenicity and sexual differentiation in the human malaria parasite." bioRxiv.

Ricard A. Rodriguez-Mias, Kyle N. Hess, Bianca Y. Ruiz, Ian R. Smith, Anthony S. Barente, Sarah M. Zimmerman, Yang Y. Lu, William Stafford Noble, Stanley Fields, Judit Villen. "Proteome-wide identification of amino acid substitutions deleterious for protein function." bioRxiv.

In press

Ran Zhang, Mu Yang, Jacob Schreiber, Diana R. O'Day, James Turner, Jay Shendure, William S. Noble, Christine M. Disteche, Xinxian Deng. "Cross-species imputation and comparison of single-cell transcriptomic profiles." Genome Biology.
Icebear

Winston Chen, Yifan Jiang, William Stafford Noble, Yang Y Lu. Error-controlled non-additive interaction discovery in machine learning models." Nature Machine Intelligence.

Bo Wen, Jack A. Freestone, Michael J. MacCoss, William Stafford Noble, Uri Keich. "Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment." Nature Methods.
FDRBench

He Fang, Ana R. Tronco, Giancarlo Bonora, Truong Nguyen, Jitendra Thakur, Joel B. Berletch, Galina N. Filippova, Steven Henikoff, Jay Shendure, William S. Noble, Christine M. Disteche, Xinxian Deng. "CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation." BMC Biology.

BL Nunn, E Timmins-Schiffman, MC Mudge, D Plubell, G Chebli, J Kubanek, M Riffle, WS Noble, E Harvey, TA Nunn, M Huntemann, A Clum, B Foster, B Foster, S Roux K Palaniappan, S Mukherjee, TBK Reddy, C Daum, A Copeland, IA Chen, NN Ivanova, NC Kyrpides, TG del Rio, EA Eloe-Fadrosh. "Microbial metagenomes across a complete phytoplankton bloom cycle: high-resolution sampling every 4 hours over 22 Days." Scientific Data. 11(1270), 2024.

Yang Lu, William Stafford Noble, Uri Keich. "A BLAST from the past: revisiting BLAST's E-value." Bioinformatics. 40(12):btae729, 2024.
SGPvalue

Wout Bittremieux, Varun Ananth, William Fondrie, Carlo Melendez, Marina Pominova, Justin Sanders, Bo Wen, Melih Yilmaz, William Stafford Noble. "Deep learning methods for de novo peptide sequencing." Mass Spectrometry Reviews.

Vianne R Gao, Rui Yang, Arnav Das, Renhe Luo, Hanzhi Luo, Dylan R McNally, Ioannis Karagiannidis, Martin A Rivas, Zhong-Min Wang, Darko Barisic, Alireza Karbalayghareh, Wilfred Wong, Yingqian A Zhan, Christopher R Chin, William S Noble, Jeff A Bilmes, Effie Apostolou, Michael G Kharas, Wendy Beguelin, Aaron D Viny, Danwei Huangfu, Alexander Y Rudensky, Ari M Melnick, Christina S Leslie. "ChromaFold predicts the 3D contact map from single-cell chromatin accessibility." Nature Communications.
ChromaFold

Vikram Agarwal, Fumitaka Inoue, Max Schubach, Dmitriy Penzar, Beth K. Martin, Pyaree Mohan Dash, Pia Keukeleure, Zicong Zhang, Ajuni Sohota, Jingjin Zhao, Ilias Georgakopoulos-Soares, William Stafford Noble, Galip Gurkan Yardimci, Ivan V. Kulakovskiy, Martin Kircher, Jay Shendure, Nadav Ahituv. "Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types". Nature.

Bo Wen, William Stafford Noble. "A multi-species benchmark for training and validating mass spectrometry proteomics machine learning models." Scientific Data.
Benchmark
Source code
Behind the paper

Carlo Melendez, Justin Sanders, Melih Yilmaz, Wout Bittremieux, William Fondrie, Sewoong Oh, William Stafford Noble. "Accounting for digestion enzyme bias in Casanovo." Journal of Proteome Research.
Casanovo
Data on Zenodo

Anupama Jha, Stephanie C. Bohaczuk, Yizi Mao, Jane Ranchalis, Benjamin J. Mallory, Alan T. Min, Morgan O. Hamm, Elliott Swanson, Connor Finkbeiner, Tony Li, Dale Whittington, William Stafford Noble, Andrew B. Stergachis, Mitchell R. Vollger. "Fibertools: fast and accurate DNA-m6A calling using single-molecule long-read sequencing." Genome Research.
Fibertools

Melih Yilmaz, William E. Fondrie, Wout Bittremieux, Carlo Melendez, Rowan Nelson, Varun Ananth, Sewoong Oh, William Stafford Noble. "Sequence-to-sequence translation from mass spectra to peptides with a transformer model." Nature Communications.
Casanovo

Jack Freestone, William Stafford Noble, Uri Keich. "Re-investigating the correctness of decoy-based false discovery rate control in proteomics tandem mass spectrometry." Journal of Proteome Research.

2024

William Stafford Noble. "Response to 'The perpetual motion machine of AI-generated data and the distraction of ChatGPT as a "scientist."'" Nature Biotechnology. 42:835-836, 2024.

Varun Ananth, Justin Sanders, Melih Yilmaz, Sewoong Oh and William Stafford Noble. "A learned score function improves the power of mass spectrometry database search." Bioinformatics (Proceedings of the ISMB). 40(Supplement_1):i410-i417, 2024.
Casanovo

Tanqi Fang, Yifeng Liu, Addie Woicik, Minsi Lu, Anupama Jha, Xiao Wang, Gang Li, Borislav Hristov, Zixuan Liu, Hanwen Xu, William Noble, Sheng Wang. "Enhancing Hi-C contact matrices for loop detection with Capricorn, a multi-view diffusion model". Bioinformatics (Proceedings of the ISMB). 40(Supplement_1):i471-i480, 2024.
Capricorn

Suchen Zheng, Nitya Thakkar, Hannah Harris, Megan Zhang, Susanna Liu, Mark Gerstein, Erez Lieberman-Aiden, M. Jordan Rowley, William Stafford Noble, Gamze Gursoy, Ritambhara Singh. "Predicting A/B compartments from histone modifications using deep learning." iScience. 27(5):109570, 2024.

Jack Freestone, William Stafford Noble, Uri Keich. "Analysis of tandem mass spectrometry data with CONGA: Combining Open and Narrow searches with Group-wise Analysis." Journal of Proteome Research 23(6):1894-1906, 2024.

Jack Freestone, William Stafford Noble, Uri Keich. "Reinvestigating the correctness of decoy-based false discovery rate control in proteomics tandem mass spectrometry" Journal of Proteome Research 23(6):1907-1914, 2024.

Andy Lin, Donovan See, Uri Keich, Wiliam E. Fondrie, William Stafford Noble. "Target-decoy false discovery rate estimation using Crema." Proteomics. 24(8):2300084, 2024.
Crema

Thomas Hollin, Steven Abel, Charles Banks, Borislav Hristov, Jacques Prudhomme, Kianna Hales, Laurence Florens, William Stafford Noble, Karine G. Le Roch. "Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes." Nature Communications. 15:1365, 2024.

Chengxiang Qiu, Beth K. Martin, Ian C. Welsh, Riza M. Daza, Truc-Mai Le, Xingfan Huang, Eva K. Nichols, Megan L. Taylor, Olivia Fulton, Diana R. O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M. Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B. Moens, David Kimelman, Junyue Cao, Alexander F. Schier, Malte Spielmann, Stephen A. Murray, Cole Trapnell, Jay Shendure. "A single cell timelapse of mouse development finds dramatic shifts at birth." Nature. 626:1084-1093, 2024

Robin Aguilar, Conor K. Camplisson, Qiaoyi Lin, Karen H. Miga, William S. Noble, Brian J. Beliveau. "Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes" Nature Communications. 15:1027, 2024.
TigerFISH

Daniel Mar, Ilona Babenko, Ran Zhang, William Stafford Noble, Oleg Denisenko, Tomas Vaisar, Karol Bomsztyk. "MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes." Laboratory Investigation. 104(1):100282, 2024.

2023

Laetitia Meng-Papaxanthos, Ran Zhang, Gang Li, Marco Cuturi, William Stafford Noble, Jean-Philippe Vert. "LSMMD-MA: Scaling multimodal data integration for single-cell genomics data analysis." Bioinformatics. 39(7):btad420, 2023.
LSMMD-MA

Brittany Baur, Jacob Schreiber, Junha Shin, Shilu Zhang, Yi Zhang, Mohith Manjunath, Jun S. Song, William Stafford Noble, Sushmita Roy. "Leveraging public epigenomic datasets to examine the role of regulatory variation in the three-dimensional organization of the genome." PLOS Computational Biology. 19(7):e1011286, 2023.

Arya Ebadi, Jack Freestone, William Stafford Noble, Uri Keich. "Bridging the false discovery gap." Journal of Proteome Research. 22(7):2172-2178, 2023.

Rui Yang, Arnav Das, Vianne R. Gao, Alirezah Karbalayghareh, William Stafford Noble, Jeff A. Bilmes, Christina S. Leslie. "Epiphany: predicting Hi-C contact maps from 1D epigenomic signals." Genome Biology. 24:134, 2023.

Alan Min, Timothy J. Durham, Louis Gevirtzmann, William Stafford Noble. "Matrix prior for data transfer between single cell data types in latent Dirichlet allocation." PLOS Computational Biology. 19(5):e1011049, 2023.
lda_matrix_prior

Huiya Gu, Hannah Harris, Moshe Olshansky, Yossi Eliaz, Akshay Krishna, Achyuth Kalluchi, Mozes Jacobs, Gesine Cauer, Melanie Pham, Suhas S.P. Rao, Olga Dudchenko, Arina Omer, Kiana Mohajeri, Sungjae Kim, Michael H Nichols, Eric S Davis, Devika Udupa, Aviva Presser Aiden, Victor G Corces, Douglas H Phanstiel, William Stafford Noble, Jeong-Sun Seo, Michael E Talkowski, Erez Lieberman Aiden, M Jordan Rowley. "Chromatin alternates between A and B compartments at kilobase scale for subgenic organization." Nature Communications. 14:3033, 2023.

Dong Luo, Yilun He, Kristen Emery, William Stafford Noble, Uri Keich. "Competition-based control of the false discovery proportion." Biometrics. 79(4):3472-3483, 2023.

Lincoln Harris, William Fondrie, Sewoong Oh, William Noble. "Evaluating proteomics imputation methods with improved criteria" Journal of Proteome Research. 22(11):3427-3438, 2023.

J Rozowsky, J Drenkow, YT Yang, G Gursoy, T Galeev, B Borsari, CB Epstein, K Xiong, J Xu, J Gao, K Yu, A Berthel, Z Chen, F Navarro, J Liu, MS Sun, J Wright, J Chang, CJF Cameron, N Shoresh, E Gaskell, J Adrian, S Aganezov, G Balderrama-Gutierrez, S Banskota, GB Corona, S Chee, SB Chhetri, GCC Martins, C Danyko, CA Davis, D Farid, NP Farrell, I Gabdank, Y Gofin, DU Gorkin, M Gu, V Hecht, BC Hitz, R Issner, M Kirsche, X Kong, BR Lam, S Li, B Li, T Li, X Li, K Zin Lin, R Luo, M Mackiewicz, JE Moore, J Mudge, N Nelson, C Nusbaum, I Popov, HE Pratt, Y Qiu, S Ramakrishnan, J Raymond, L Salichos, A Scavelli, JM Schreiber, FJ Sedlazeck, LH See, RM Sherman, X Shi, M Shi, CA Sloan, JS Strattan, Z Tan, FY Tanaka, A Vlasova, J Wang, J Werner, B Williams, MXu, C Yan, L Yu, C Zaleski, J Zhang, JM Cherry, EM Mendenhall, WS Noble, Z Weng, ME Levine, A Dobin, B Wold, A Mortazavi, B Ren, J Gillis, RM Myers, MP Snyder, J Choudhary, A Milosavljevic, MC Schatz, R Guigo, BE Bernstein, TR Gingeras, M Gerstein. "The EN-TEx resource of multi-tissue personal epigenomes and variant-impact models." Cell. 186(7):P1493-1511, 2023.

Job Dekker, Frank Alber, Sarah Aufmkolk, Brian J. Beliveau, Benoit G Bruneau, Andrew Belmont, Lacramioara Bintu, Alistair Boettiger, Riccardo Calandrelli, Christine Disteche, David M Gilbert, Thomas Gregor, Anders S Hansen, Bo Huang, Danwei Huangfu, Reza Kalhor, Christina Leslie, Wenbo Li, Yun Li, Jian Ma, William S Noble, Peter J Park, Jennifer E Phillips-Cremins, Katherine S Pollard, Susanne Rafelski, Bing Ren, Yijun Ruan, Yaron Shav-Tal, Yin Shen, Jay Shendure, Xiaokun Shu, Caterina Strambio-De-Castillia, Anastassiia Vertii, Huaiying Zhang, Sheng Zhong. "Spatial and temporal organization of the genome: current state and future aims of the 4D Nucleome Project." Molecular Cell. 83(15):2624-2640, 2023.

Jacob Schreiber, Carles Boix, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins-Hooker, Bernhard Schölkopf, Gabriele Schweikert, Mateo Rojas Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, Mark James Carman, Pietro Pinoli, Chenyang Hong, Kevin Y. Yip, Jeffrey P. Spence, Sanjit Singh Batra, Yun S. Song, Shaun Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi, Jessika Adrian, Richard Sandstrom, Nina Farrell, Jessica Halow, Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles Epstein, J. Seth Strattan, Michael Snyder, Manolis Kellis, William Stafford Noble, Anshul Kundaje, ENCODE Imputation Challenge Participants. "The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles." Genome Biology. 24(9), 2023.

Kris G. Alavattam, Katie A. Mitzelfelt, Giancarlo Bonora, Paul A. Fields, Xiulan Yang, Han S. Chiu, Lil Pabon, Alessandro Bertero, Nicholas J. Palpant, William Stafford Noble, Charles E. Murry. "Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation." Stem Cell Reports. 18(1):159-174, 2023.

Syamand Hasam, Kristen Emery, William Stafford Noble, Uri Keich. "A pipeline for peptide detection using multiple decoys." Methods in Molecular Biology. 2426:25-34, 2023.

Nelle Varoquaux, William Stafford Noble, Jean-Phillipe Vert. "Inference of genome 3D architecture by modeling overdispersion of Hi-C data." Bioinformatics. 39(1):btac838, 2023.
PASTIS

Andy Lin, Brooke L. Deatherage Kaiser, Janine R. Hutchison, Jeffrey A. Bilmes, William Stafford Noble. "MS1Connect: a mass spectrometry run similarity measure". Bioinformatics. 39(2):btad058, 2023.
MS1Connect

William Stafford Noble. "Ten simple rules for defining a computational biology project." PLOS Computational Biology. 19(1):e1010786, 2023.

Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bimani, Jimmy K. Eng, William E. Fondrie, Charles E. Grant, Michael Hoopmann, Andy Lin, Yang Y. Lu, Robert L. Moritz, Michael J. MacCoss, William Stafford Noble. "The Crux toolkit for analysis of bottom-up tandem mass spectrometry proteomics data." Journal of Proteome Research. 22(2):561-569, 2023.
Crux

Frank Lawrence Nii Adoquaye Acquaye, Attila Kertesz-Farkas, William Stafford Noble. "Efficient indexing of peptides for database search using Tide." Journal of Proteome Research. 22(2):577-584, 2023.
Crux

2022

Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble. "Multimodal single-cell translation and alignment with semi-supervised learning." Journal of Computational Biology. 29(11):1198-1212, 2022.
Polarbear

Andy Lin, Temana Short, William Stafford Noble, Uri Keich. "Improving peptide-level mass spectrometry analysis via double competition" Journal of Proteome Research. 21(10):2412-2420, 2022.

Borislav Hristov, Jeffrey A. Bilmes, William Stafford Noble. "Linking cells across single-cell modalities by synergistic matching of neighborhood structure." Bioinformatics (Proceedings of the European Conference on Computational Biology). 8(Suppl_2):ii148-ii154, 2022.
Synmatch

Kayvon Mazooji, Sreeram Kannan, William Stafford Noble, Ilan Shomorony. "Fundamental limits of multi-sample flow graph decomposition." Proceedings of the IEEE International Symposium on Information Theory. 2403-2408, 2022.

Jack Freestone, Temana Short, William Stafford Noble, Uri Keich. "Group-walk, a rigorous approach to separate FDR analysis by TDC." Bioinformatics (Proceedings of the European Conference on Computational Biology). 38(Supplement_2):ii82-ii88, 2022.

Lilian R. Heil, William E. Fondrie, Christopher D. McGann, Alexander J. Federation, William Stafford Noble, Michael J. MacCoss, Uri Keich. "A flexible workflow for building spectral libraries from narrow window data independent acquisition mass spectrometry data." Journal of Proteome Research. 21(6):1382-1391, 2022.

Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble. "Semi-supervised single-cell cross-modality translation using Polarbear." Proceedings of the International Conference on Research in Computational Biology (RECOMB).
Polarbear

Melih Yilmaz, William Fondrie, Wout Bittremieux, Sewoong Oh, William Stafford Noble. "De novo mass spectrometry peptide sequencing with a transformer model." Proceedings of the International Conference on Machine Learning. 162:25514-25522, 2022.
Casanovo
Talk

Wout Bittremieux, William Stafford Noble. "A neural network for large-scale clustering of peptide mass spectra." Nature Methods. 19(6):658-659, 2022.
GLEAMS

Wout Bittremieux, Damon H. May, Jeff Bilmes, and William Stafford Noble. "A learned embedding for efficient joint analysis of millions of mass spectra." Nature Methods. 19(6):675-678, 2022.
GLEAMS

Ayse Berceste Dincer, Yang Lu, Devin Schweppe, Sewoong Oh, William Stafford Noble. "Reducing peptide sequence bias in quantitative mass spectrometry data with machine learning." Journal of Proteome Research. 21(7):1771-1782, 2022.
Pepper

Aakash Sur, William Stafford Noble, Peter J. Myler. "A benchmark of Hi-C scaffolders using reference genomes and de novo assemblies." bioRxiv, 2022.

Aakash Sur, William Stafford Noble, Shawn Sullivan, Peter Myler. "Edison: measuring scaffolding accuracy with edit distance." bioRxiv, 2022.
Edison

William S. Phipps, Kelly D. Smith, Han-Yin Yang, Clark M. Henderson, Hannah Pflaum, Melissa L. Lerch, William E. Fondrie, Michelle Emrick, Michael J. MacCoss, William Stafford Noble, Andy N. Hoofnagle. "Tandem mass spectrometry-based amyloid typing using manual microdissection and open-source data processing." American Journal of Clinical Pathology. 157(5):748-757, 2022.

Chengxiang Qiu, Junyue Cao, Tony Li, Sanjay Srivatsan, Xingfan Huang, Diego Calderon, William Stafford Noble, Christine M. Disteche, Malte Spielmann, Cecilia B. Moens, Cole Trapnell, Jay Shendure. "Systematic reconstruction of the cellular trajectories of mammalian embryogenesis." Nature Genetics. 54:328-341, 2022.

Magnus Palmblad, Sebastian Boecker, Sven Degroeve, Oliver Kohlbacher, Lukas Käll, William Stafford Noble, Matthias Wilhelm. "Interpretation of the DOME recommendations for machine learning in proteomics and metabolomics." Journal of Proteome Research. 21(4):1204-1207, 2022.

Sean Whalen, Jacob Schreiber^*, William Stafford Noble, Katherine Pollard. "Navigating the pitfalls of applying machine learning in genomics." Nature Reviews Genetics. 23(3):169-181, 2022. (featured article)
talk

Pilar Demetci, R Santorella, Brian Sandstede, William Stafford Noble, Ritambhara Singh. "SCOT: single-cell multi-omics alignment with optimal transport." Journal of Computational Biology. 29(1):3-18, 2022.
SCOT

Pilar Demetci, R Santorella, Brian Sandstede, William Stafford Noble, Ritambhara Singh. "Single-Cell Multiomics Integration by SCOT." Journal of Computational Biology. 29(1):19-22, 2022.
SCOT

2021

Timothy J. Durham, Riza M. Daza, Lou Gevirtzman, Darren A. Cusanovich, William Stafford Noble, Jay Shendure, Robert H. Waterston. "Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes." Genome Research. 31:1952-1969, 2021.

Dejun Lin, Justin Sanders, William Stafford Noble. "HiCRep.py: Fast comparison of Hi-C contact matrices in Python." Bioinformatics. 37(18):2996-2997, 2021.
HiCrep.py

Sarah G. Swygert, Dejun Lin, Stephanie Portillo-Ledesma, Po-Yen Lin, Dakota R. Hunt, Cheng-Fu Kao, Tamar Schlick, William Stafford Noble, Toshio Tsukiyama. "Chromatin fiber folding represses transcription and loop extrusion in quiescent cells." eLife. e72062, 2021.

Wout Bittremieux, Kris Laukens, William Stafford Noble, Pieter C. Dorrestein. "Large-scale tandem mass spectrum clustering using fast nearest neighbor searching." Rapid Communications in Mass Spectrometry. e9153, 2021.
falcon

Yang Young Lu, Jeff Bilmes, Ricard A. Rodriguez-Mias, Judit Villen, William Stafford Noble. "DIAmeter: Matching peptides to data-independent acquisition mass spectrometry data". Bioinformatics (Proceedings of the ISMB). 37(Supplement_1):i434-i442, 2021.
DIAmeter

Yang Young Lu, Timothy C. Yu, Giancarlo Bonora, William Stafford Noble. "ACE: Explaining cluster from an adversarial perspective." Proceedings of the International Conference on Machine Learning (ICML). 139:7156-7167, 2021.
ACE
Supplement

Yang Y. Lu, Wenbo Guo, Xinyu Xing, William Stafford Noble. "DANCE: Enhancing saliency maps using decoys." Proceedings of the International Conference on Machine Learning (ICML). 139:7124-7133, 2021.

Andy Lin, Deanna Plubell, Uri Keich, William Stafford Noble. "Accurately assigning peptides to spectra when only a subset of peptides are relevant." Journal of Proteome Research. 20(8):4153-4164, 2021.
Subset neighbor search

Giancarlo Bonora, Vijay Ramani, Ritambhara Singh, He Fang, D Jackson, Sanjay Srivatsan, Ruolan Qiu, Choli Lee, Cole Trapnell, Jay Shendure, Zhijun Duan, Xinxian Deng, William Stafford Noble, Christine M. Disteche. "Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation." Genome Biology. 22:279, 2021.
Supplement Data

Yang Young Lu, William Stafford Noble. "A wider field of view to predict expression." Nature Methods. 18:1155-1160, 2021

William E. Fondrie, Wout Bittremieux, William Stafford Noble. "ppx: Programmatic access to proteomics data repositories." Journal of Proteome Research. 20(9):4621-4624, 2021.
ppx

William E. Fondrie, William Stafford Noble. mokapot: Fast and flexible semi-supervised learning for peptide detection." Journal of Proteome Research. 20(4):1966-1971, 2021.
mokapot

Jacob Schreiber, Jeff Bilmes, William Stafford Noble. "Prioritizing transcriptomic and epigenomic experiments by using an optimization strategy that leverages imputed data." Bioinformatics, 37(4):439-447, 2021.

Miranda Mudge, Brook L. Nunn, Erin Firth, Marcela Ewert, Kianna Hales, William E. Fondrie, William Stafford Noble, Jonathan Toner, Bonnie Light, Karen A. Junge. "Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments." Environmental Microbiology. 23(7):3840-3866, 2021.

2020

He Fang,^* Giancarlo Bonora,^*, JP Lewandowski, J Thakur, Galina N Filippova, Steve Henikoff, Jay Shendure, Zhijun Duan, Jonathan L. Rinn, Xinxian Deng, William Stafford Noble, Christime M. Disteche. "Trans- and cis-acting effects of the lncRNA Firre on epigenetic and structural features of the inactive X chromosome." Nature Communications. 11(1):6053, 2020.

Jacob Schreiber, Deepthi Hegde, William Stafford Noble. "Zero-shot imputations across species are enabled through joint modeling of human and mouse epigenomics." BCB '20: Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, article 39, pages 1-9, 2020.
Best paper award

Jacob Schreiber, Yang Y. Lu, William Stafford Noble. "Ledidi: Designing genomic edits that induce functional activity." bioRxiv, 2020.
Ledidi

Ritambhara Singh, Pilar Demetci, Giancarlo Bonora, Vijay Ramani, Choli Lee, He Fang, Zhijun Duan, Xinxian Deng, Jay Shendure, Christine Disteche, William Stafford Noble. "Unsupervised manifold alignment for single-cell multi-omics data." BCB '20: Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, article 40, pages 1-10, 2020.
MMD-MA
Talk

Wei Yang, Jeff Bilmes, William Stafford Noble. "Submodular sketches of single-cell RNA-seq measurements". BCB '20: Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, article 61, pages 1-6, 2020.
Talk

Hyeon-Jin Kim, Galip Gurkan Yardimci, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B. Ware, Jay Shendure, Zhijun Duan and William Stafford Noble. "Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data." PLOS Computational Biology, 16(9):e1008173, 2020.
Data
schic-topic-model

Jacob Schreiber, Ritambhara Singh, Jeff Bilmes, William Stafford Noble. "A pitfall for machine learning methods aiming to predict across cell types." Genome Biology. 21(1):282, 2020.

ENCODE Consortium. "Expanded encyclopedias of DNA elements in the human and mouse genomes." Nature. 583(7818):699-710, 2020.

Ariel Erijman, Lukasz Kozlowski, Salma Sohrabi-Jahromi, James Fishburn, Linda Warfield, Jacob Schreiber, William Stafford Noble, Johannes Soeding, Steven Hahn. "A high-throughput screen for transcription activation domains reveals their sequence characteristics and permits reliable prediction by deep learning." Molecular Cell. 78(5):P890-P892, 2020.

Jacob Schreiber, Jeff Bilmes, William Stafford Noble. "apricot: Submodular selection for data summarization in Python." Journal of Machine Learning Research, 21(161):1-6, 2020.
apricot

Kristen Emery, S Hasan, Uri Keich and William Stafford Noble. "Multiple competition based FDR control and peptide detection." Proceedings of the International on Research in Computational Biology (RECOMB). 24:54-71, 2020.
Supplement Talk

Jacob Schreiber, Timothy J. Durham, Jeff Bilmes, William Stafford Noble. "Multi-scale deep tensor factorization learns a latent representation of the human epigenome". Genome Biology. 81:21, 2020.
Avocado
Supplement
GenomeWeb

Jacob Schreiber, Jeff Bilmes, and William Stafford Noble. "Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples." Genome Biology. 81:22, 2020.

Sheng Pan, Meredith A. J. Hullar, Lisa A. Lai, Hong Peng, Damon May, William Stafford Noble, Daniel Raftery, Sandi L. Navarro, Marina L. Neuhouser, Paul D. Lampe, Joanna W. Lampe, Ru Chen. "Gut microbial protein expression in response to dietary patterns in a controlled feeding study: a metaproteomic approach." Microorganisms. 8(3):379, 2020.

Kate Cook, Borislav Hristov, Karine Le Roch, Jean-Philippe Vert, William Stafford Noble. "Measuring significant changes in chromatin conformation with ACCOST." Nucleic Acids Research. 48(5):2303-2311, 2020.
ACCOST

Brook Nunn, Molly Mikan, H. Harvey, Emma Timmins-Schiffman, Michael Riffle, Damon May, William Stafford Noble, and Ian Salter. "Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in Western Arctic Ocean microbiomes." The ISME Journal. 14:39-52, 2020.

Lindsay Pino, Brian C. Searle, Han-Yin Yang, Andrew N. Hoofnagle, William Stafford Noble, Michael J. MacCoss. "Matrix-matched calibration curves for assessing analytical figures of merit in quantitative proteomics." Journal of Proteome Research. 19(3):1147-1153, 2020.

Will Fondrie, William Stafford Noble. "A machine learning strategy that leverages large datasets to boost statistical power in small-scale experiments." Journal of Proteome Research, 19(3):1267-1274, 2020.
Percolator
GenomeWeb

Vijay Ramani, Xinxian Deng, Ruolan Qiu, Christine Disteche, William Stafford Noble, Jay Shendure, Zhijun Duan. "Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large numbers of single cells." Methods. 170:61-68, 2020.

2019

Alessandro Bertero, Paul A. Fields, AST Smith, A Leonard, K Beussman, NJ Sniadecki, D-H Kim, HF Tse, Lil Pabon, Jay Shendure, William Stafford Noble, Charles E. Murry. "Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy." Journal of Cell Biology. 218(9):2919-2944, 2019.
data

Yi Yin, Yue Jian, Kwan-Wood G. Lam, Joel B. Berletch, Christine M. Disteche, William Stafford Noble, Frank J. J Steemers, R. Daniel Camerini-Otero, Andrew C. Adey, Jay Shendure. "High-throughput single cell genome sequencing reveals cell-autonomous equational segregation in meiosis I." Molecular Cell. 76(4):676-690, 2019.

David F. Read, Kate Cook, Yang Y. Lu, Karine Le Roch, and William Stafford Noble. "Predicting gene expression in the human malaria parasite Plasmodium falciparum." PLOS Computational Biology. 15(9):e1007329, 2019.
Supplement

Wei Chen, Aaron McKenna, Jacob Schreiber, Maximilian Haeussler, Yi Yin, Vikram Agarwal, William Stafford Noble, Jay Shendure. "Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair." Nucleic Acids Research. 47(15):7989-8003, 2019.
Lindel

Jung-Sik Kim, Xiaoyuan He, Jie Liu, Zhijun Duan, Taeyeon Kim, Julia Gerard, Brian Kim, William S. Lane, William S. Noble, Bogdan Budnik, Todd Waldman. "Cohesin interacts with a panoply of splicing factors required for cell cycle progression and genomic organization". Journal of Biological Chemistry. 294(22):8760-8772, 2019.

John T. Halloran, Hantian Zhang, Kaan Kara, Cedric Renggli, Matthew The, Ce Zhang, David M. Rocke, Lukas Käll, William Stafford Noble. "Speeding up Percolator." Journal of Proteome Research. 18(9):3353-3359, 2019.

Wout Bittremieux, Kris Laukens, William Stafford Noble. "Extremely fast and accurate open modification spectral library searching of high-resolution mass spectra using feature hashing and graphics processing units". Journal of Proteome Research, 18(10):3972-3799, 2019.
ANN-SoLo

Alice Cheng, Charles E. Grant, William Stafford Noble, and Timothy L. Bailey. "MoMo: Discovery of statistically significant post-translational modification motifs." Bioinformatics. 35(16):2774-2782, 2019.
MEME Suite

Wenruo Bai, Jeff Bilmes, William Stafford Noble. "Submodular generalized matching for peptide identification in tandem mass spectrometry." IEEE Transactions in Computational Biology and Bioinformatics. 16(4):1168-1181, 2019.

Maxwell W. Libbrecht, Oscar Rodriguez, Zhiping Weng, Jeff A. Bilmes, Michael M. Hoffman, William Stafford Noble. "A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types." Genome Biology. 20:180, 2019.
Encyclopedia Segway SAGA interpretation

Gesine Cauer, Gurkan Yardimci, Jean-Philippe Vert, Nelle Varoquaux, William Stafford Noble. "Inferring diploid 3D chromatin structures from Hi-C data." 19th International Workshop on Algorithms in Bioinformatics (WABI 2019), 143(11):1-13, 2019.
PASTIS

Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, William Stafford Noble. "Jointly embedding multiple single-cell omics measurements." 19th International Workshop on Algorithms in Bioinformatics (WABI 2019), 143(10):1-13, 2019.
Supplement, Source code

Damon May, Kaipo Tamura, William Stafford Noble. "Detecting modifications in proteomics experiments with Param-Medic". Journal of Proteome Research. 18(4):1902-1906, 2019.
Param-medic Crux

Alessandro Bertero, Paul A. Fields, Vijay Ramani, Giancarlo Bonora, Gurkan Yardimci, Hans Reinecke, Lil Pabon, William Stafford Noble, Jay Shendure, Charles E. Murry. "Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory." Nature Communications. 10(1):1538, 2019.
data

Molly Gasperini, Andrew J. Hill, Jose L. McFaline-Figueroa, Beth Martin, Seungsoo Kim, M. D. Kim, Dana Jackson, Anh Leith, Jacob Schreiber, William S. Noble, Cole Trapnell, Nadav Ahituv, Jay Shendure. "A genome-wide framework for mapping gene regulation via cellular genetic screens." Cell. 176(1-2):377-390, 2019.

Gurkan Galip Yardimci, Hakan Ozadam, Michael E. G. Sauria, Oana Ursu, Koon-Kiu Yan, Tao Yang, Abhijit Chakraborty, Arya Kaul, Bryan R Lajoie, Fan Song, Ye Zhan, Ferhat Ay, Mark Gerstein, Anshul Kundaje, Qunhua Li, James Taylor, Feng Yue, Job Dekker, William S Noble. "Measuring the reproducibility and quality of Hi-C data." Genome Biology, 20(1):57, 2019.
3D Chromatin ReplicateQC

Uri Keich, Kaipo Tamura, and William Stafford Noble. "Averaging strategy to reduce variability in target-decoy estimates of false discovery rate." Journal of Proteome Research, 18(2):585-593, 2019.
Protocol

Alex Hu, Yang Lu, Jeff A. Bilmes, William Stafford Noble. "Joint precursor elution profile inference via regression for peptide detection in data-independent acquisition mass spectra." Journal of Proteome Research, 18(1):86-94, 2019.
Siren

Dejun Lin, Giancarlo Bonora, Gurkam Yardimci, and William Stafford Noble. "Computational methods for analyzing and modeling genome structure and organization." WIREs Systems Biology. 11(1):e1435, 2019.

2018

Lindsay Pino, Brian Searle, E Huang, William Stafford Noble, Andy Hoofnagle, Michael J. MacCoss. "Calibration using a single-point external reference material harmonizes quantitative mass spectrometry proteomics data between platforms and laboratories." Analytical Chemistry. 90(21):13112-13117, 2018.

Yang Lu, Yinging Fan, Jinchi Lv, and William Stafford Noble. "DeepPINK: reproducible feature selection in deep neural networks." Advances in Neural Information Processing Systems. 31:8690-8700, 2018.
DeepPINK Supplement

Andy Lin, J. Jeffry Howbert, William Stafford Noble. "Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2 data". Journal of Proteome Research. 17(11):3644-3656, 2018.
Crux

Wenruo Bai, William Stafford Noble, Jeffrey A. Bilmes. "Submodular maximization via gradient ascent: The case of deep submodular functions." Advances in Neural Information Processing Systems. 31:7989-7999, 2018.

Wenxiu Ma, Giancarlo Bonora, J. B. Berletch, Xinxian Deng, William Stafford Noble, Christine M. Disteche. "X-chromosome inactivation and escape from X inactivation in mouse." Methods in Molecular Biology. 1861:205-219, 2018.

Jesse Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song, Victoria T. Le, Galip Gurkan Yardimci, Abhijit Chakraborty, Darrin V. Bann, Yanli Wang, Royden Clark, Lijun Zhang, Hongbo Yang, Tingting Liu, Sriranga Iyyanki, Lin An, Christopher Pool, Takayo Sasaki, Juan Carlos Rivera Mulia, Hakan Ozadam, Bryan R. Lajoie, Rajinder Kaul, Michael Buckley, Kristen Lee, Morgan Diegel, Dubravka Pezic, Christina Ernst, Suzana Hadjur, Duncan T. Odom, John A. Stamatoyannopoulos, James R. Broach, Ross Hardison, Ferhat Ay, William Stafford Noble, Job Dekker, David M Gilbert, Feng Yue. "Integrative detection and analysis of structural variation in cancer genomes." Nature Genetics. 50(10):1388-1398, 2018.

Wout Bittremieux, Pieter Meysman, William Stafford Noble, Kris Laukens. "Fast open modification spectral library searching through approximate nearest neighbor indexing". Journal of Proteome Research. 17(10):3463-3474, 2018.
ANN-SoLo

Giancarlo Bonora, Xinxian Deng, He Fang, Vijay Ramani, Ruolan Qiu, Joel Berletch, Gala N. Filippova, ZhiJun Duan, Jay Schendure, William S. Noble, Christine M. Disteche. "Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome." Nature Communications. 9(1):1445, 2018.
data

Maxwell W. Libbrecht, Jeffrey A. Bilmes and William Stafford Noble. "Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization." Proteins. 86(4):454-466, 2018
Source code

Wenxiu Ma, Ferhat Ay, Cholie Lee, G Gulsoy, Xinxian Deng, S Cook, J Hesson, C Cavanaugh, Carol B. Ware, Anton Krumm, Jay Shendure, C. Anthony Blau, Christin M. Disteche, William Stafford Noble, Zhijun Duan. "Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution." Methods. 142:59-73, 2018.

Timothy J. Durham, Maxwell W. Libbrecht, J. Jeffry Howbert, Jeff Bilmes and William Stafford Noble. "PREDICTD: PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition". Nature Communications. 9(1):1402, 2018
PREDICTD

Evelien M. Bunnik, Kate B. Cook, Nelle Varoquaux, Gayani Batugedara, Jacques Prudhomme, A. Cort, Lirong Shi, Chiara Andolina, Leila S. Ross, Declan Brady, David A. Fidock, Francois Nosten, Rita Tewari, Photini Sinnis, Ferhat Ay, Jean-Philippe Vert, William Stafford Noble, Karine G. Le Roch "Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages." Nature Communications, 9(1):1910, 2018.
Web Supplement

Jie Liu, Dejun Lin, Gurkan Yardimci and William Stafford Noble. "Unsupervised embedding of single-cell Hi-C data". Bioinformatics (Proceedings of the ISMB). 34(13):i96-i104, 2018.

Oana Ursu, Nathan Boley, M Taranova, Y X. R. Wang, Gurkan Yardimci, William Stafford Noble, and Anshul Kundaje. "GenomeDISCO: A concordance score for chromosome conformation capture experiments using random walks on contact map graphs." Bioinformatics, 34(16):2701-2707, 2018.
GenomeDISCO

Uri Keich and William Stafford Noble. "Controlling the FDR in imperfect matches to an incomplete database." Journal of the American Statistical Association. 113(523):973-982, 2018.

Rachel C. W. Chan, Maxwell W. Libbrecht, Eric G. Roberts, Jeffrey A. Bilmes, William Stafford Noble, and Michael M. Hoffman. "Segway 2.0: Gaussian mixture models and minibatch training." Bioinformatics. 34(4):669-671, 2018.
Segway

2017

Z. E. Sychev, Alex Hu, T. DiMaio, Anthony Gitter, N. D. Camp, William Stafford Noble, Alejandro Wolf-Yadlin, M. Lagunoff. "Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism." PLOS Pathogens. 13(3):e1006256, 2017.

Mike Riffle, Damon H. May, Emma Timmins-Schiffman, M. P. Mikan, Daniel Jaschob, William Stafford Noble, and Brook L Nunn. MetaGOmics: A web-based tool for peptide-centric functional and taxonomic analysis of metaproteomics data." Proteomes. 6(1), 2017.

Jacob Schreiber, Maxwell W. Libbrecht, Jeff Bilmes, William Stafford Noble. "Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architecture" bioRxiv, 2017
Rambutan

Tao Yang, Feiping Zhang, G. Gurkan Yardimci, F. Song, Ross C. Hardison, William Stafford Noble, Feng Yue, and Qunhua Li. "HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient." Genome Research, 27(11):1939-1949, 2017.
HiCRep

Umut Eser, Devon Chandler-Brown, Ferha Ay, Aaron F. Straight, Zhijun Duan, William Stafford Noble, Jan M. Skotheim. "Form and function of topologically associating genomic domains in budding yeast". Proceedings of the National Academy of Science. 114(15):E3061-E3070, 2017.

Jie Liu, John T. Halloran, Jeffrey A. Bilmes, Riza M. Daza, Choli Lee, Elisabeth M. Mahen, Donna Prunkard, Chaozhong Song, Sibel Blau, Michael O. Dorschner, Vijayakrishna K. Gadi, Jay Shendure, C. Anthony Blau, and William S. Noble. "Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies". Scientific Reports. 7(1):16943, 2017
THEMIS

Giancarlo Bonora and Christine M. Disteche. "Structural aspects of the inactive X chromosome." Philosophical Transactions of the Royal Society B., 372(1733), 2017.

William Stafford Noble. "Ten simple rules for writing a response to reviewers." PLOS Computational Biology. 13(10):e1005730, 2017.

Jacob Schreiber and William Stafford Noble. "Finding the optimal Bayesian network given a constraint graph." PeerJ Computer Science. 3:e122, 2017.

Wenxiu Ma, Lin Yang, Remo Rohs and William Stafford Noble. "DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding." Bioinformatics. 33(19):3003-3010, 2017.

Koon-Kiu Yan, Gurkan Yardimci, C. Yan, William Stafford Noble, and Mark Gerstein. "HiC-Spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps." Bioinformatics. 33(14):2199-2201, 2017.
HiC-Spector

Hitomi Sakano, DAR Zorio, X. Wang, Ying Sonia Ting, William Stafford Noble, Michael J. MacCoss, Edwin W. Rubel, Y Wang. "Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein." Journal of Comparative Neurology. 525(15):3341-3359, 2017.

Shengjie Wang, Haoran Cai, Jeff Bilmes, William Stafford Noble. "Training compressed fully-connected networks with a density-diversity penalty". Proceedings of the 5th International Conference on Learning Representations.

Seungsoo Kim, Ivan Liachko, DG Brickner, Kate Cook, William Stafford Noble, JH Brickner, Jay Shendure, and Maitreya J. Dunham. "The dynamic three-dimensional organization of the diploid yeast genome." eLife. 6:e23623, 2017.

Uri Keich and William Stafford Noble. "Progressive calibration and averaging for tandem mass spectrometry statistical confidence estimation: Why settle for a single decoy?" Proceedings of the International on Research in Computational Biology (RECOMB). 10229:99-116, 2017.

William Stafford Noble and Uri Keich. Response to 'Mass spectrometrists should search for all peptides, but assess only the ones they care about.'" Nature Methods. 14(7):644, 2017.

Musa N. Gabere and William Stafford Noble. "Empirical comparison of web-based antimicrobial peptide prediction tools." Bioinformatics. 33(13):1921-1929, 2017.

Damon H. May, Kaipo Tamura, William Stafford Noble. "Param-Medic: A tool for improving MS/MS database search yield by optimizing parameter settings." Journal of Proteome Research. 16(4):1817-1824, 2017. Supporting Information
Param-Medic, Crux

Job Dekker, Andrew S. Belmont, Mitchell Guttman, Victor O. Leshyk, John T. Lis, Stavros Lomvardas, Leonid A. Mirny, Clodagh C. O'Shea, Peter J. Park, Bing Ren, Joan C. Ritland Politz, Jay Shendure, Sheng Zhong and the 4D Nucleome Network. "The 4D nucleome project". Nature 549(7671):219-226, 2017.

Ying Sonia Ting, Jarrett D. Egertson, James Bollinger, Brian C. Searle, SH Payne, William Stafford Noble and Michael J MacCoss. "PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data." Nature Methods. 14(9):903-908, 2017.
PECAN

Vijay Ramani, Xinxian Deng, Ruolan Qiu, KL Gunderson, FJ Steemers, Christine M. Disteche, William Stafford Noble, Zhijun Duan, Jay Shendure. "Massively multiplex single-cell Hi-C." Nature Methods. 14(3):263-266, 2017.

Gurkan Yardimci and William Stafford Noble. "Software tools for visualizing Hi-C data." Genome Biology, 18(1):26, 2017.

Emma Timmins-Schiffman, Damon H. May, Molly Mikan, Michael Riffle, C. Frazar, H. R. Harvey, William Stafford Noble, Brook L. Nunn. "Critical decisions in metaproteomics: Achieving high confidence protein annotations in a sea of unknowns." The ISME Journal. 11(2):309-314, 2017.

2016

Alex Hu, William S. Noble, Alejandro Wolf-Yadlin. "Technical advances in proteomics: new developments in data-independent acquisition." F1000Research. 5(F1000 Faculty Rev):419, 2016.

Vijay Ramani, Darren A. Cusanovich, R. J. Hause, Wenxiu Ma, Xinxian Deng, C. Anthony Blau, C. Disteche, William Stafford Noble, Jay Shendure, and Zhijun Duan. "Mapping 3D genome architecture through in situ DNase Hi-C." Nature Protocols. 11(11):2014-2121, 2016.

Nao Hiranuma, Jie Liu, Chaozhong Song, Jacob Goldsmith, Michael Dorschner, Colin Pritchard, Kimberly Burton, Elisabeth Mahen, Sibel Blau, Francis Senecal, Wayne Monsky, Stephanie Parker, Stephen Schmechel, Stephen Allison, VK Gadi, Sofie Salama, Amie Radenbaugh, Mary Goldman, Jill Johnsen, Shelly Heimfeld, Vitalina Komashko, Marissa LaMadrid-Hermannsfeldt, Zhijun Duan, Steven Benz, Patrick Soon-Shiong, David Haussler, Jingchun Zhu, Walter Ruzzo, William Noble, and C. Anthony Blau. "Cis-compound mutations are prevalent in triple negative breast cancer and can drive tumor progression." bioRxiv, 2016.

Arjan van der Velde, Michael Purcaro, William Stafford Noble, and Zhiping Weng. "LR-DNase: Predicting TF binding prediction from DNase-seq data." bioRxiv, 2016.

Wenruo Bai, Jeff Bilmes and William Stafford Noble. "Bipartite matching generalizations for peptide identification in tandem mass spectrometry." ACM Conference on Bioinformatics, Computational Biology, and Health Informatics.
Best paper award

Kai Wei, Maxwell W. Libbrecht, Jeffry A. Bilmes and William Stafford Noble. "Choosing panels of genomics assays using submodular optimization." Genome Biology. 17(1):229, 2016.
Talk Web server

Matthew The, Michael J. MacCoss, William Stafford Noble and Lukas Käll. "Fast and accurate protein false discovery rates on large-scale proteomics data sets with Percolator 3.0." Journal of the American Society of Mass Spectrometry. 27:1719, 2016.
Percolator

Shengjie Wang, John Halloran, Jeff A. Bilmes and William Stafford Noble. "Faster and more accurate graphical model identification of tandem mass spectra using trellises." Bioinformatics (Proceedings of the ISMB). 32(12):i322-i331, 2016.

O. K. Smith, R. Kim, H. Fu, M. M. Martin, K. Utani, Y. Zhang, A. B. Marks, M. Lalande, S. Chamberlain, M. W. Libbrecht, E. E. Bouhassira, M. C. Ryan, W. S. Noble and M. I. Aladjem. "Distinct epigenetic features of differentiation-regulated replication origins." Epigenetics and Chromatin. 9(1):18, 2016.
Data

John Halloran, Jeff A. Bilmes and William Stafford Noble. "Dynamic Bayesian network for accurate detection of peptides from tandem mass spectra." Journal of Proteome Research. 15(8):2749-2759, 2016.
DRIP

Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. R. Harvery, Elhanan Borenstein, Brook L. Nunn and William Stafford Noble. "An alignment-free 'metapeptide' strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing." Journal of Proteome Research. 15(8):2697-2705, 2016.
Sixgill, Supplement

2015

Joel B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William Stafford Noble, and Christine M. Disteche. "Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model." Data in Brief. 5:761-769, 2015.

Charles E. Grant, James Johnson, Timothy L. Bailey, and William Stafford Noble. "MCAST: Scanning for cis-regulatory motif clusters." Bioinformatics. 2015
MCAST

Ferhat Ay, William Stafford Noble. "Analysis methods for studying the 3D architecture of the genome." Genome Biology. 16:183, 2015.

Xinxian Deng, Wenxiu Ma, Vijay Ramani, Andrew Hill, Fan Yang, Ferhat Ay, Joel Berletch, Carl Blau, Jay Shendure, Zhijun Duan, William Noble, Christine Disteche "Bipartite structure of the inactive mouse X chromosome." Genome Biology. 16:152, 2015.
Supplement
data

Ying Sonia Ting, Jarrett D. Eggertson, Sam H. Payne, Sangtae Kim, Brendan MacLean, Lukas Käll, Ruedi Aebersold, Richard D. Smith, William Stafford Noble, and Michael J. MacCoss. "Peptide-centric proteome analysis: an alternative strategy for the analysis of tandem mass spectrometry data." Molecular and Cellular Proteomics. 14(9):2301-2307, 2015.

Attila Kertesz-Farkas, Uri Keich and William Stafford Noble. "Tandem mass spectrum identification via cascade search." Journal of Proteome Research. 14(8):3027-3038, 2015.
Crux

Uri Keich, Attila Kertesz-Farkas and William Stafford Noble. "Improved false discovery rate estimation procedure for shotgun proteomics." Journal of Proteome Research. 14(8):3148-3161, 2015. (Correction)
Supplement, Crux

William Stafford Noble. "Mass spectrometrists should search only for peptides they care about." Nature Methods. 12(7):605-608, 2015.
Supplement

Timothy L. Bailey, James Johnson, Charles E. Grant and William Stafford Noble. "The MEME Suite." Nucleic Acids Resesearch. 43(W1):W39-49, 2015.
MEME

Rachel M. Gittelman, Enna Hun, Ferhat Ay, Jennifer Madeoy, Len Pennacchio, William Stafford Noble, David R. Hawkins and Joshua M. Akey. "Comprehensive identification and analysis of human accelerated regulatory DNA." Genome Research, 2015.

Vishnu Dileep, Ferhat Ay, Jiao Sima, Daniel L Vera, William Stafford Noble, and David M Gilbert. "Topologically-associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication timing program." Genome Research, 2015.

Maxwell Libbrecht and William Stafford Noble. "Machine learning applications in genetics and genomics". Nature Reviews Genetics. 16(6):321-332, 2015.

Nelle Varoquaux, Ivan Liachko, Ferhat Ay, Josh Burton, Jay Shendure, Maitreya Dunham, Jean-Philippe Vert and William Stafford Noble. "Accurate identification of centromere locations in yeast genomes using Hi-C." Nucleic Acids Research. 43(11):5331-5339, 2015.
Centurion, Biotechniques article

Maxwell Libbrecht, Michael Hoffman, Jeff Bilmes and William Stafford Noble. "Entropic graph-based posterior regularization." Proceedings of the International Conference on Machine Learning, 2015.
Source code Extended version

J. B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William Stafford Noble, Christine M. Disteche, Xinxian Deng. "Escape from X inactivation varies in mouse tissues." PLOS Genetics. 18(3):e1005079, 2015.

Fan Yang, Xinxian Deng, Wenxiu Ma, Joel B. Berletch, N Rabaia, J. M. Moore, G. N. Filippova, Y. Liu, William Stafford Noble, Jay Shendure and Christine M. Disteche. "The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation." Genome Biology. 16(1):52, 2015.

Ferhat Ay, Thanh H Vu, Michael J. Zeitz, Nelle Varoquaux, Jan E. Carette, Jean-Philippe Vert, Andrew R. Hoffman and William Stafford Noble. "Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C." BMC Genomics. 16:121, 2015.

Zafer Aydin, David Baker and William Stafford Noble. "Constructing structural profiles for protein torsion angle prediction." Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS-2015). Lisbon, Portugal, pp. 26-35, 2015.

Uri Keich and William Stafford Noble. "On the importance of well calibrated scores for identifying shotgun proteomics spectra." Journal of Proteome Research. 14(2):1147-1160, 2015. (Correction)
Supplementary data

Maxwell Libbrecht, Ferhat Ay, Michael Hoffman, David M. Gilbert, Jeff Bilmes and William Stafford Noble. "Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression." Genome Research. 25(2):544-557, 2015.
Source code

Wenxiu Ma, Ferhat Ay, Cholie Lee, Gunhan Gulsoy, Xinxian Deng, Savannah Cook, Jennifer Hesson, Christopher Cavanagh, Carol B. Ware, Anton Krumm, Jay Shendure, C. Anthony Blau, Christine Disteche, William Stafford Noble, Zhijun Duan. "Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of lincRNA genes in human cells." Nature Methods. 12(1):71-78, 2015.
Supplementary data

Jimmy K. Eng, Michael R. Hoopmann, T. A. Jahan, Jarrett D. Egertson, William Stafford Noble, and Michael J. MacCoss. "A deeper look into Comet — implementation and features." Journal of Proteome Research. 26(11):1865-1874, 2015.

Michael Riffle, Gennifer E. Merrihew, D. Jaschob, Vagisha Sharma, Trisah N. Davis, William Stafford Noble, and Michael J. MacCoss. "Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development." Journal of the American Society for Mass Spectrometry. 26(11):1827-1836, 2015.

2014

Ferhat Ay, Evelien M. Bunnik, Nelle Varoquaux, Jean-Philippe Vert, William Stafford Noble and Karine G. Le Roch. "Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum." Bioessays. Early online, 2014.
Supplement

Sean McIlwain, Kaipo Tamura, Attila Kertesz-Farkas, Charles E. Grant, Benjamin Diament, Barbara Frewen, J. Jeffry Howbert, Michael R. Hoopmann, Lukas Käll, Jimmy K. Eng, Michael J. MacCoss and William Stafford Noble. "Crux: rapid open source protein tandem mass spectrometry analysis." Journal of Proteome Research. 13(10):4488-4491, 2014.
Supplementary data

J. Jeffry Howbert and William Stafford Noble. "Computing exact p-values for a cross-correlation shotgun proteomics scoring function." Molecular and Cellular Proteomics. 13(9):2467-2479, 2014.
Supplementary data Blog post

P Park, J Ho, Y Jung, T Liu, B Alver, S Lee, K Ikegami, K Sohn, A Minoda, M Tolstorukov, A Appert, S Parker, T Gu, A Kundaje, N Riddle, E Bishop, T Egelhofer, S Hu, A Alekseyenko, Y Schwartz, D Asker, J Belsky, S Bowman, Q Chen, R Chen, D Day, Y Dong, X Duan, C Epstein, S Ercan, E Feingold, F Ferrari, J Garrigues, N Gehlenborg, P Good, P Haseley, D He, M Herrmann, M Hoffman, T Jeffers, P Kharchenko, P Kolasinska-Zwierz, C Kotwaliwale, N Kumar, S Langley, E Larschan, I Latorre, M Libbrecht, X Lin, R Park, M Pazin, H Pham, A Plachetka, B Qin, N Shoresh, P Stempor, A Vielle, C Wang, C Whittle, H Xue, R Kingston, JH Kim, B Bernstein, A Dernburg, V Pirrotta, M Kuroda, WS Noble, T Tullius, M Kellis, D MacAlpine, S Strome, S Elgin, XS Liu, J Lieb, J Ahringer, G Karpen, A Rechtsteiner and A Dose. "Comparative analysis of metazoan chromatin organization." Nature. 512:449-452, 2014.

Habil Zare, Junfeng Wang, Alex Hu, Kris Weber, Josh Smith, Debbie Nickerson, ChaoZhong Song, Daniela Witten, C. Anthony Blau and William Stafford Noble. "Inferring clonal composition from multiple sections of a breast cancer." PLOS Computational Biology. 10(7):e1003703, 2014.
Supplementary data Clomial Biomedical Computation Review

John Halloran, Jeff Bilmes and William Stafford Noble. "Learning peptide-spectrum alignment models for tandem mass spectrometry." Thirtieth Conference on Uncertainty in Artificial Intelligence (UAI 2014). Ed. Nevin Zhang and Jin Tian. AUAI Press, Corvallis, OR. pp. 320-329, 2014
Supplementary data

Nelle Varoquaux, Ferhat Ay, William Stafford Noble and Jean-Philippe Vert. "A statistical approach for inferring the 3D structure of the genome." Bioinformatics (Proceedings of the ISMB). 30(12):i26-i33, 2014.
PASTIS

Wenxiu Ma, William Stafford Noble and Timothy L. Bailey. "Motif-based analysis of large nucleotide datasets using MEME-ChIP." Nature Protocols. 9(6):1428-1450, 2014.
Supplementary data

Ferhat Ay, Evelien M. Bunnik, Nelle Varoquaux, Sebastian M. Bol, Jacques Prudhomme, Jean-Philippe Vert, William Stafford Noble and Karine G. Le Roch. "Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression." Genome Research. 24(6):974-988, 2014.
Supplementary data, Press coverage

Ferhat Ay, Timothy L. Bailey and William Stafford Noble. "Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts." Genome Research. 24(6):999-1011, 2014.
Fit-Hi-C software and supplementary data

2013

Michael J. Zeitz, Paula L. Lerner, Ferhat Ay, Eric Van Nostrand, Juilia D. Heidmann, William Stafford Noble and Andrew R. Hoffman. "Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome." Nucleus. 4(6):487-493, 2013.

Michael J. Zeitz, Ferhat Ay, Julia D. Heidmann, Paula L. Lerner, William Stafford Noble, Brandon N. Steelman and Andrew R. Hoffman. "Genomic interaction profiles in breast cancer reveal altered chromatin architecture." PLoS One. 8(9):e73974, 2013.

Brittany S. Sexton, Denis Avey, Brooke R. Druliner, Justin A. Fincher, Daniel L. Vera, Daniel J. Grau, Mark L. Borowsky, Shobhit Gupta, Senthil Girimurugan, Eric Chicken, Jinfeng Zhang, William S. Noble, Fanxiu Zhu, Robert E. Kingston, and Jonathan Hancock Dennis. "The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed." Genome Research. 24(2):251-259, 2013.

Daniel A. Skelly, Gennifer E. Merrihew, Michael Riffle, Caitlin F. Connelly, Emily O. Kerr, Marnie Johansson, Daniel Jaschob, Beth Graczyk, Nicholas J. Shulman, Jon Wakefield, Sara J. Cooper, Stanley Fields, William S. Noble, Eric G. D. Muller, Trisha N. Davis, Maitreya J. Dunham, Michael J. MacCoss, and Joshua M Akey. "Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast." Genome Research. 23(9):1496-1504, 2013.

Xianxin Deng, Joel B. Berletch, Wenxiu Ma, Di K. Nguyen, Joseph B. Hiatt, William Stafford Noble, Jay Shendure and Christine M. Disteche. "Mammalian X upregulation is associated with enhanced transcription initiation, RNA half-life, and MOF-mediated H4K16 acetylation." Developmental Cell. 25(1):55-68, 2013.

Michael Hoffman, Jason Ernst, Steve P Wilder, Anshul Kundaje, Robert S. Harris, Max Libbrecht, Belinda Giardine, Paul Ellenbogen, Jeff A. Bilmes, Ewan Birney, Ross C. Hardison, Ian Dunham, Manolis Kellis and William Stafford Noble. "Integrative annotation of chromatin elements from ENCODE data." Nucleic Acids Research. 41(2):827-841, 2013.

MT Weirauch, A Cote, R Norel, M Annala, Y Zhao, S Talukder, A Vedenko, DREAM5 consortium, QD Morris, ML Bulyk, G Stolovitzky and TR Hughes. "An evaluation of methods for the modeling of transcription factor sequence specificity." Nature Biotechnology. 31(2):126-34, 2013.

2012

Viktor Granholm, William Stafford Noble and Lukas Käll. "Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics." Journal of Proteomics. 80:123-131, 2012.

Zhi-jun Duan, Mirela Andronescu, Kevin Schutz, C Lee, Jay Shendure, Stanley Fields, William Stafford Noble and C. Anthony Blau. "A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes." Methods. 58(3):277-288, 2012.

Viktor Granholm, William Stafford Noble and Lukas Käll. "A cross-validation scheme for machine learning algorithms in shotgun proteomics." BMC Bioinformatics. 13(Suppl 16):S3, 2012.

Sean McIlwain, Michael Mathews, Michael Bereman, Edwin W. Rubel, Michael J. MacCoss and William Stafford Noble. "Estimating relative abundances of proteins from shotgun proteomics data." BMC Bioinformatics. 13:308, 2012.
Supplement

Sara C. Di Rienzi, Kim C. Lindstrom, Tobias Mann, William Stafford Noble, MK Raghuraman and Bonita J. Brewer. "Maintaining replication origins in the face of genomic change." Genome Research. 22(10):1940-1952, 2012.

Ajit P. Singh, John Halloran, Jeff Bilmes and William Stafford Noble. "Spectrum identification using a dynamic Bayesian network model of tandem mass spectra." Uncertainty in Artificial Intelligence: Proceedings of the Twenty-Eighth Conference. Aug. 15-17, 2012. pp. 775-784.

Soyoung Ryu, David R. Goodlett, William Stafford Noble and Vladimir N. Minin. "A statistical approach to peptide identification from clustered tandem mass spectrometry data." Proceedings of the International Workshop on Computational Proteomics, IEEE BIBM.

Zafer Aydin, James Thompson, Jeff Bilmes, David Baker and William Stafford Noble. "Protein torsion angle class prediction by a hybrid architecture of Bayesian and neural networks." Proceedings of the 13th International Conference on Bioinformatics and Computational Biology. pp. 2012-2018.

Mariana Fioramonte, Aline Mara dos Santos, Sean McIlwain, William Stafford Noble, Kleber Gomes Franchini and Fabio Cesar Gozzo. "Analysis of secondary structure in proteins by chemical cross-linking coupled to mass spectrometry." Proteomics. 12(17):2746-52, 2012.

Marina Spivak, Michael S. Berriman, Michael J. MacCoss and William Stafford Noble. "Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments." Journal of Proteome Research. 11(9):4499-508, 2012.

The ENCODE Project Consortium. "An integrated encylopedia of DNA elements in the human genome." Nature. 489(7414):57-74, 2012.

Jie Wang, Jiali Zhuang, Sowmya Iyer, XinYing Lin, Troy W. Whitfield, Melissa Greven, Xianjun Dong, Anshul Kundaje, Yong Cheng, Ewan Birney, Richard M. Myers, William S. Noble, Michael Snyder and Zhiping Weng. "Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors." Genome Research. 22(9):1798-812, 2012.

Aaron Arvey, Phaedra Agius, William Stafford Noble and Christina Leslie. "Sequence and chromatin determinants of cell-type specific transcription factor binding." Genome Research. 22(9):1723-34, 2012.

Oliver Serang and William Stafford Noble. "Faster mass spectrometry-based protein inference: junction trees are more efficient than sampling and marginalization by enumeration." IEEE Transactions on Computational Biology and Bioinformatics. 9(3):809-817, 2012.
Fido

Daniela M. Witten and William Stafford Noble. "On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements." Nucleic Acids Research. 40(9):3849-3855, 2012.
Code

Benjamin J. Diament, Michael J. MacCoss, William Stafford Noble. "On the feasibility and utility of exploiting real time database search to improve adaptive peak selection." arXiv:1207.5848v1.

Yanjun Qi, Merja Oja, Jason Weston and William Stafford Noble. "A unified multitask architecture for predicting local protein properties." PLoS One. 7(3):e32235, 2012.
Supplementary data

Michael M. Hoffman, Orion J. Buske, Zhiping Weng, Jeff A. Bilmes and William Stafford Noble. "Unsupervised pattern discovery in human chromatin structure through genomic segmentation." Nature Methods. 9(5):473-476, 2012.
The Scientist

Marina Spivak, Jason Weston, Michael J. MacCoss and William Stafford Noble. "Direct maximization of protein identifications from tandem mass spectra." Molecular and Cellular Proteomics. 11(2):M111.012161, 2012.
Supplement

William Stafford Noble, C. Anthony Blau, Job Dekker, Zhi-jun Duan and Yi Mao. "The structure and function of chromatin and chromosomes." Proceedings of the Pacific Symposium on Biocomputing. 17:434-440, 2012.

William Stafford Noble and Michael J. MacCoss. "Computational and statistical analysis of protein mass spectrometry data." PLoS Computational Biology. 8(1):e1002296, 2012.

Oliver Serang and William Stafford Noble. "A review of statistical methods for protein identification using tandem mass spectrometry." Statistics and its Interface. 5:3-20, 2012.

Gabriel Cuellar-Partida, Fabian A. Buske, R C. McLeay, Tom Whitington, William Stafford Noble and Timothy L. Bailey. "Epigenetic priors for identifying active transcription factor binding sites." Bioinformatics. 28:56-62, 2012.
Supplementary data

2011

Orion J. Buske, Michael M. Hoffman, Nadia Ponts, Karine Le Roch and William Stafford Noble. "Exploratory analysis of genomic segmentations with Segtools." BMC Bioinformatics. 12:415, 2011.

Benjamin J. Diament and William Stafford Noble. "Faster SEQUEST searching for peptide identification from tandem mass spectra." Journal of Proteome Research. 10(9):3871-9, 2011.

Yanjun Qi and William Stafford Noble. "Protein interaction networks: protein domain interaction and protein function prediction." In Handbook of Statistical Bioinformatics. Ed. by HH Lu, B Schoelkopf and H. Zhao. Springer Verlag, 2011.

Emily Tanaka, Timothy L. Bailey, Charles E. Grant, William Stafford Noble and Uri Keich. "Improved similarity scores for comparing motifs." Bioinformatics. 27(12):1603-1609, 2011.

Viktor Granholm, William Stafford Noble and Lukas Käll. "On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics." Journal of Proteome Research. 10(5):2671-2678, 2011.

The ENCODE Project Consortium. "A user's guide to the Encylopedia of DNA Elements (ENCODE)." PLoS Biology. 9(4):e1001046, 2011.

Zafer Aydin, Ajit Singh, Jeff Bilmes and William Stafford Noble. "Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure." BMC Bioinformatics. 12:154, 2011.

Charles E. Grant, Timothy L. Bailey and William Stafford Noble. "FIMO: Scanning for occurrences of a given motif." Bioinformatics. 27(7):1017-1018, 2011.

Iain Melvin, Jason Weston, William Stafford Noble and Christina Leslie. "Detecting remote evolutionary relationships among proteins by large-scale semantic embedding." PLoS Computational Biology. 7(1):e1001047, 2011
Supplement

William Stafford Noble and Christina Leslie. "Learning models of biological sequences." In Encyclopedia of Machine Learning. Ed. by C Sammut and GI Webb. Springer Verlag, 2011.

Emmet Hirsch, Courtney Lim, Debra Dobrez, MG Adams and William Stafford Noble. "Meteorological factors and the timing of the initiating event of parturition." International Journal of Biometeorology. 55(2):265, 2011.

2010

Vagisha Sharma, Jimmy K. Eng, Sergey Feldman, Priska von Haller, Michael J. MacCoss and William Stafford Noble. "Precursor charge state prediction for electron transfer dissociation tandem mass spectra." Journal of Proteome Research. 9(10):5438-5444, 2010.

Oliver Serang, Michael J. MacCoss and William Stafford Noble. "Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data." Journal of Proteome Research. 9(10):5346-5357, 2010.

Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble and Christina Leslie. "High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions." PLoS Computational Biology. 6(9):e10000916, 2010.

Sheila Moore Reynolds, Jeffrey A. Bilmes and William Stafford Noble. "Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens". PLoS Computational Biology. 6(7):e10000834, 2010.

Sheila Reynolds, Zhiping Weng, Jeffrey Bilmes and William Stafford Noble. "Predicting nucleosome positioning using multiple evidence tracks." Proceedings of the International Conference on Research in Computational Biology (RECOMB). Lecture Notes in Computer Science, 2010, Volume 6044/2010, pp. 441-455.

Zhijun Duan, Mirela Andronescu, Kevin Schutz, Sean McIlwain, Yoo Jung Kim, Choli Lee, Jay Shendure, Stanley Fields, C. Anthony Blau and William S. Noble. "A three-dimensional model of the yeast genome". Nature. 465:363-367, 2010.
Supplementary materials
"Genome Blossoms" in The Scientist

Xiaoyu Chen, Michael Hoffman, Jeffrey A. Bilmes, Jay R. Hesselberth and William Stafford Noble. "A dynamic Bayesian network for identifying protein binding footprints from single molecule based sequencing data." Bioinformatics (Proceedings of the ISMB). 26(12):i334-i342, 2010.

Michael M. Hoffman, Orion J. Buske and William Stafford Noble. "The Genomedata format for storing large-scale functional genomics data." Bioinformatics. 26(11):1458-1459, 2010.

Sean McIlwain, Paul Draghicescu, Pragya Singh, Dave R. Goodlett and William Stafford Noble. "Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs." Journal of Proteome Research. 9(5):2488-2495, 2010.
Supplement

Nir Yosef, Jens Gramm, Qian-fei Wang, William Stafford Noble, Richard M. Karp and Roded Sharan. "Prediction of phenotype information from genotype data." Communications in Information and Systems. 10(2):99-114, 2010.

Martial Hue, Michael Riffle, Jean-Philippe Vert and William Stafford Noble. "Large-scale prediction of protein-protein interactions from structures." BMC Bioinformatics. 11:144, 2010.

Zafer Aydin, John I. Murray, Robert H. Waterston and 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." BMC Bioinformatics. 11(1):84, 2010.

2009

William Stafford Noble. "How does multiple testing correction work?" Nature Biotechnology. 27(12):1135-1137, 2009.

William Stafford Noble. "A quick guide to organizing computational biology experiments." PLoS Computational Biology. 5(7):e1000424, 2009.
Software Carpentry slides on Data Management by Orion Buske, based in part on ideas from this article.

Tobias Mann, Rich Humbert, Michael Dorschner, John A. Stamatoyannopoulos and William Stafford Noble. "A thermodynamic approach to PCR primer design." Nucleic Acids Research. 25(12):i339-347, 2009.
Pythia

John Hawkins, Charles E. Grant, William Stafford Noble and Timothy L. Bailey. "Assessing phylogenetic motif models for predicting transcription factor binding sites." Bioinformatics (Proceedings of the ISMB). 25(12):i339-347, 2009.

Timothy L. Bailey, Michael Boden, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jane Ren, Wilfred W. Li and William Stafford Noble. "MEME Suite: tools for motif discovery and searching." Nucleic Acids Research. 37(Web server issue):W202-208, 2009.
MEME

Marina Spivak, Jason Weston, Leon Bottou, Lukas Käll and William Stafford Noble. "Improvements to the Percolator algorithm for peptide identification from shotgun proteomics data sets." Journal of Proteome Research. 8(7):3737-3745, 2009.

Sheila Reynolds, Jeffrey A. Bilmes and William Stafford Noble. "On the relationship between DNA periodicity and local chromatin structure." Proceedings of the International Conference on Research in Computational Biology (RECOMB). May 18-21, 2009. pp. 434-450.

Aaron A. Klammer, Christopher Y. Park and William Stafford Noble. "Statistical calibration of the SEQUEST XCorr function." Journal of Proteome Research. 8(4):2106-2113, 2009.

Jay Hesselberth, Xiaoyu Chen, Zhihong Zhang, Pete J. Sabo, Richard Sandstrom, Alex P. Reynolds, Robert E. Thurman, Shane Neph, Michael S. Kuehn, William Stafford Noble, Stanley Fields and John A. Stamatoyannopoulos. "Global mapping of protein-DNA interactions in vivo by digital genomic footprinting." Nature Methods. 6(4):283-289, 2009.
Supplementary data

Lukas Käll, John D. Storey and William Stafford Noble. "QVALITY: Nonparametric estimation of q values and posterior error probabilities." Bioinformatics. 25(7):964-966, 2009.
Qvality software and web server

Iian Melvin, Jason Weston, Christina Leslie and William Stafford Noble. "Rankprop: a web server for protein remote homology detection." Bioinformatics. 25(1):121-122, 2009.
Web server

2008

Sheila M. Reynolds, Lukas Käll, Jeff A. Bilmes and William Stafford Noble. "Transmembrane topology and signal peptide prediction using dynamic Bayesian networks." PLoS Computational Biology. 4(11):e1000213, 2008.

Gennifer E. Merrihew, Colleen Davis, Brent Ewing, Gary Williams, Lukas Käll, Barbara E. Frewen, William Stafford Noble, Phil Green, James H. Thomas, Michael J. MacCoss. "Use of shotgun proteomics for the identification, confirmation and correction of C. elegans gene annotations." Genome Research. 18(10):1660-1669, 2008.

Iain Melvin, Jason Weston, Christina Leslie and William Stafford Noble. Combining classifiers for improved classification of proteins from sequence or structure BMC Bioinformatics. 9:389, 2008.
Supplement

Heng Lian, William Thompson, Robert E. Thurman, John A. Stamatoyannpoulos, William Stafford Noble and Charles Lawrence. "Automated mapping of large-scale chromatin structure in ENCODE." Bioinformatics. 24(17):1911-1916, 2008.
Supplementary data
Source code

Shobhit Gupta, Jonathan Dennis, Robert E. Thurman, Robert Kingston, John A. Stamatoyannopoulos and William Stafford Noble. "Predicting human nucleosome occupancy from primary sequence." PLoS Computational Biology. 4(8):e10000134, 2008.
Supplement

Nir Yosef, Roded Sharan and William Stafford Noble. "Improved network-based identification of protein orthologs." Bioinformatics (Proceedings of the ECCB). 24(16):i200-i206, 2008.

Lukas Käll, John Storey and William Stafford Noble. "Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry." Bioinformatics (Proceedings of the ECCB). 24(16):i42-i48, 2008.
Qvality software, web server and supplement

Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. MacCoss and William Stafford Noble. "Rapid and accurate peptide identification from tandem mass spectra." Journal of Proteome Research. 7(7):3022-3027, 2008.
Crux

Aaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael J. MacCoss and William Stafford Noble. "Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification." Bioinformatics (Proceedings of the ISMB). 24(13):i345-i356, 2008.

L Pena-Castillo, M Tasan, CL Myers, H Lee, T Joshi, C Zhang, Y Guan, M Leone, A Pagnani, WK Kim, C Krumpelman, W Tian, G Obozinski, Y Qi, S Mostafavi, GN Lin, G Berriz, F Gibbons, G Lanckriet, J Qiu, C Grant, Z Barutcuoglu, DP Hill, D Warde-Farely, C Grouios, D Ray, JA Blake, M Deng, M Jordan, WS Noble, Q Morris, J Klein-Seetharaman, Z Bar-Joseph, T Chen, F Sun, OG Troyanskaya, EM Marcotte, D Xu, TR Hughes and FP Roth. "A critical assessment of M. musculus gene function prediction using integrated genomic evidence." Genome Biology. 9(Suppl 1):S2, 2008.

Guillaume Obozinski, Gert Lanckriet, Charles E. Grant, Michael I. Jordan and William Stafford Noble. "Consistent probabilistic outputs for protein function prediction." Genome Biology. 9(Suppl 1):S6, 2008.

Jian Qiu and William Stafford Noble. "Predicting co-complexed protein pairs from heterogeneous data." PLoS Computational Biology. 4(4):e1000054, 2008.

Robert E. Thurman, William Stafford Noble and John A. Stamatoyannopoulos. "Multi-scale correlations in continuous genomic data." Proceedings of the Pacific Symposium on Biocomputing. January 4-8, 2008. pp. 201-215.

Lukas Käll, John D. Storey, Michael J. MacCoss and William Stafford Noble. "Assigning significance to peptides identified by tandem mass spectrometry using decoy databases." Journal of Proteome Research. 7(1):29-34, 2008

Lukas Käll, John D. Storey, Michael J. MacCoss and William Stafford Noble. "Posterior error probabilities and false discovery rates: two sides of the same coin." Journal of Proteome Research. 7(1):40-44, 2008.

2007

Jean-Philippe Vert, Jian Qiu and William Stafford Noble. "A new pairwise kernel for biological network inference with support vector machines." BMC Bioinformatics. 8(Suppl. 10):S8, 2007.

Jian Qiu, Will Sheffler, David Baker and William Stafford Noble. "Ranking predicted protein structures with support vector regression." Proteins: Structure, Function, and Bioinformatics. 71(3):1175-1182, 2007.

Lukas Käll, Jesse Canterbury, Jason Weston, William Stafford Noble and Michael J. MacCoss. "Semi-supervised learning for peptide identification from shotgun proteomics datasets." Nature Methods. 4(11):923-925, 2007.
Supplement Percolator

Jason Weston, Gokhan Bakir, Olivier Bousquet, Tobias Mann, William Stafford Noble and Bernhard Scholkopf. "Joint kernel maps." In Predicting Structured Data. Ed. by Gokhan Bakir, Thomas Hofmann, Bernhard Scholkopf, Alex J. Smola, Ben Taskar and V. S. N. Vishwanathan. MIT Press, 2007.

Aaron A. Klammer, Xianhua Yi, Michael J. MacCoss and William Stafford Noble. "Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions." Analytical Chemistry. 79(16):6111-6118, 2007.

Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, William Stafford Noble and Christina Leslie. "SVM-fold: a tool for discriminative multi-class protein fold and superfamily recognition." BMC Bioinformatics. 8(Suppl 4):S2, 2007.

Iain Melvin, Eugene Ie, Jason Weston, William Stafford Noble and Christina Leslie. "Multi-class protein classification using adaptive codes." Journal of Machine Learning Research. 8(Jul):1557-1581, 2007

Heather E. Peckham, Robert E. Thurman, Yutao Fu, John A. Stamatoyannopoulos, William Stafford Noble, Kevin Struhl and Zhiping Weng. "Nucleosome positioning signals in genomic DNA." Genome Research. 17(8):1170-1177, 2007.
Supplement

Saurabh Asthana, William Stafford Noble, Grigory Kryukov, Charles E. Grant, Shamil Sunyaev and John A. Stamatoyannopoulos. "Widely distributed non-coding selection in the human genome." Proceedings of the National Academy of Science. 104(30):12410-12415, 2007.

The ENCODE Project Consortium. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE project." Nature. 447:779-816, 2007.

Robert E. Thurman, Nathan Day, William Stafford Noble and John A. Stamatoyannopoulos. "Identification of higher-order functional domains in the human ENCODE regions." Genome Research. 17(6):917-927, 2007.

Nathan Day, Andrew Hemmaplardh, Robert E. Thurman, John A. Stamatoyannopoulos and William Stafford Noble. "Unsupervised segmentation of continuous genomic data." Bioinformatics. 23(11):1424-1426, 2007

Jonathan H. Dennis, Hua-Ying Fan, Sheila R. Reynolds, Guocheng Yuan, Jim Meldrim, Daniel J. Richter, Daniel G. Peterson, Oliver J. Rando, William Stafford Noble and Robert E. Kingston. "Independent and complementary methods for large-scale structural analysis of mammalian chromatin." Genome Research. 17(6):928-939, 2007.

Jian Qiu, Martial Hue, Asa Ben-Hur, Jean-Philippe Vert and William Stafford Noble. "A structural alignment kernel for protein structures." Bioinformatics. 23(9):1090-1098, 2007.
Aaron Klammer, Xianhua Yi, Michael J. MacCoss and William Stafford Noble. "Peptide retention time prediction yields improved tandem mass spectrum identification for diverse chromatography conditions." Proceedings of the International Conference on Research in Computational Biology (RECOMB). April 21-25, 2007. pp. 459-472.
ChargeCzar

Shobhit Gupta, John A. Stamatoyannopoulos, Timothy L. Bailey and William Stafford Noble. "Quantifying similarity between motifs." Genome Biology. 8:R24, 2007.
Supplement

William Stafford Noble and Asa Ben-Hur. "Integrating information for protein function prediction." In Bioinformatics - From Genomes to Therapies. T. Lenguaer, ed. Vol. 3. pp. 1297-1314.

2006

William Stafford Noble. "What is a support vector machine?" Nature Biotechnology. 24(12):1565-1567, 2006.
Extended version

Darrin P. Lewis, Tony Jebara and William Stafford Noble. "Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure." Bioinformatics. 22(22):2753-2760, 2006.
Supplement

Barbara E. Frewen, Gennifer E. Merrihew, William Stafford Noble and Michael J. MacCoss. "Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries." Analytical Chemistry. 78(16):5678-5684, 2006.

Tata Pramila, Wei Wu, William Stafford Noble and Linda L. Breeden. "The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S phase gap in the transcriptional circuitry of the cell cycle." Genes and Development. 20(16):2266-2278, 2006.

Jean-Philippe Vert, Robert Thurman and William Stafford Noble. "Kernels for gene regulatory regions." Advances in Neural Information Processing Systems 18, 2006.

Tobias Mann and William Stafford Noble. "Efficient identification of DNA binding partners in a sequence database." Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference). 22:e350-e358, 2006.

Tobias Mann, Richard Humbert, John Stamatoyannopoulos and William Stafford Noble. "Automated validation of polymerase chain reactions using amplicon melting curves." Journal of Bioinformatics and Computational Biology. 22(14):350-358, 2006.

PJ Sabo, MS Kuehn, R Thurman, B Johnson, EM Johnson, H Cao, M Yu, J Goldy, E Rosenzweigh, J Goldy, A Haydock, M Weaver, A Shafer, K Lee, F Neri, R Humbert, MA Singer, TA Richmond, MO Dorschner, M McArthur, M Hawrylycz, RD Green, PA Navas, WS Noble and JA Stamatoyannopoulos. "Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays." Nature Methods. 3(7):511-518, 2006.

Darrin P. Lewis, Tony Jebara and William Stafford Noble. "Nonstationary kernel combination." Proceedings of the International Conference on Machine Learning, June 25-29, 2006, Pittsburgh, PA.

Asa Ben-Hur and William Stafford Noble. "Choosing negative examples for the prediction of protein-protein interactions." BMC Bioinformatics. 7(Suppl 1):S2, 2006.

Jason Weston, Rui Kuang, Christina Leslie, William Stafford Noble. "Protein ranking by semi-supervised network propagation." BMC Bioinformatics. 7(Suppl 1):S10, 2006.

2005

Jason Weston, Christina Leslie, Eugene Ie and William Stafford Noble. "Semi-supervised protein classification using cluster kernels." Semi-supervised Learning. O Chapelle, B Schoelkopf and A Zien, ed. MIT Press, 2005. pp. 321-338.
Supplement

William Stafford Noble, Rui Kuang, Christina Leslie and Jason Weston. "Identifying remote protein homologs by network propagation." FEBS Journal. 272(20):5119-5128, 2005.

Rui Kuang, Jason Weston, William Stafford Noble and Christina Leslie. "Motif-based protein ranking by network propagation." Bioinformatics. 21(19):3711-3718, 2005.

Eugene Ie, Jason Weston, William Stafford Noble and Christina Leslie. "Adaptive codes for multi-class protein classification." Proceedings of the International Conference on Machine Learning, August 7-11, 2005, Bonn, Germany.

Aaron Klammer, Christine C. Wu, Michael J. MacCoss, William Stafford Noble. "Peptide charge state determination for low-resolution tandem mass spectra." Proceedings of the Computational Systems Bioinformatics Conference, August 8-11, 2005, Stanford, CA. pp. 175-185.

Tobias Mann, Richard Humbert, John Stamatoyannopoulos and William Stafford Noble. "Automated validation of polymerase chain reactions using amplicon melting curves." Proceedings of the Computational Systems Bioinformatics Conference, August 8-11, 2005, Stanford, CA. pp. 377-385.

Will Sheffler, Eli Upfal, John Sedivy and William Stafford Noble. "A learned comparative expression measure for Affymetrix GeneChip DNA microarrays." Proceedings of the Computational Systems Bioinformatics Conference, August 8-11, 2005, Stanford, CA. pp. 144-154.

John P. Miller, Russel S. Lo, Asa Ben-Hur, Cynthia Desmarais, Igor Stagljar, William Stafford Noble and Stanley Fields. "Large-scale identification of yeast integral membrane protein interactions." Proceedings of the National Academy of Science. 102(34):12123-12128, 2005.

Jason Weston, Christina Leslie, Eugene Ie, Dengyong Zhou, Andre Eliseeff and William Stafford Noble. "Semi-supervised protein classification using cluster kernels." Bioinformatics. 21(15):3241-3247, 2005.
Supplement

Asa Ben-Hur and William Stafford Noble. "Kernel methods for predicting protein-protein interactions." Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference). 21(Suppl 1):i38-i46, 2005.

William Stafford Noble, Scott Kuehn, Robert Thurman, Richard Humbert, James C. Wallace, Man Yu, Michael Hawrylycz and John Stamatoyannopoulos. "Predicting the in vivo signature of human gene regulatory sequences." Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference). 21(Suppl 1):i338-i343, 2005.
Supplement

M Tompa, N Li, TL Bailey, GM Church, B De Moor, E Eskin, AV Favorov, MC Frith, Y Fu, WJ Kent, VJ Makeev, AA Mironov, WS Noble, G Pavesi, G Pesole, M Regnier, N Simonis, S Sinha, G Thijs, J van Helden, M Vandenbogaert, Z Weng, C Workman, C Ye and Z Zhu. "Assessing computational tools for the discovery of transcription factor binding sites." Nature Biotechnology. 23(1):137-144, 2005.

2004

E Feingold, PJ Good, ..., WS Noble, ..., FS Collins. "The ENCODE (Encyclopedia of DNA Elements) Project." Science. 306:636-640, 2004.

Lanckriet, Gert R. G., Tijl De Bie, Nello Cristianini, Michael I. Jordan and William Stafford Noble. "A statistical framework for genomic data fusion." Bioinformatics. 20(16):2626-2635, 2004.

Noble, William Stafford. "Data hoarding is harming proteomics." Nature Biotechnology. 22(10):1209.

Noble, William Stafford. "Support vector machine applications in computational biology." Kernel Methods in Computational Biology. B. Schoelkopf, K. Tsuda and J.-P. Vert, ed. MIT Press, 2004. pp. 71-92.

Weston, Jason, Christina Leslie, Denyong Zhou and William Stafford Noble. "Semi-supervised protein classification using cluster kernels." Advances in Neural Information Processing Systems 16, 2004. pp. 595-602.

Tsuda, Koji and William Stafford Noble. "Learning kernels from biological networks by maximizing entropy." Bioinformatics (Proceedings of the ISMB/ECCB). 20(Suppl. 1):i326-i333, 2004.

Lu, Henry, Weiqun Li, William Stafford Noble, Donald Payan and D. C. Anderson. "Riboproteomics of the hepatitis C virus internal ribosomal entry site." Journal of Proteome Research Web Release Date: 17-Jul-2004; (Article) DOI: 10.1021/pr0499592

Wu, Wei and William Stafford Noble. "Genomic data visualization on the web." Bioinformatics. 20(11):1804-1805, 2004.

Weston, Jason, Andre Eliseeff, Dengyong Zhou, Christina Leslie and William Stafford Noble. "Protein ranking: from local to global structure in the protein similarity network." Proceedings of the National Academy of Science. 101(17):6559-6563, 2004.
Supplement

Leslie, Christina, Eleazar Eskin, Adiel Cohen, Jason Weston and William Stafford Noble. "Mismatch string kernels for discriminative protein classification." Bioinformatics. 20(4):467-476, 2004.
String kernel software

Pavlidis, Paul, Ilan Wapinski and WS Noble. "Support vector machine classification on the web." Bioinformatics. 20(4):586-587, 2004.

Lanckriet, Gert R. G., Minghua Deng, Nello Cristianini, Michael I. Jordan and William Stafford Noble. "Kernel-based data fusion and its application to protein function prediction in yeast." Proceedings of the Pacific Symposium on Biocomputing, January 3-8, 2004. pp. 300-311.

2003

Liao, Li and William Stafford Noble. "Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships." Journal of Computational Biology. 10(6):857-868, 2003.

Qin, Jie, Darrin Lewis and William Stafford Noble. "Kernel hierarchical clustering of microarray gene expression data." Bioinformatics. 19(16):2097-2104, 2003.

Eskin, Eleazar, William Stafford Noble and Yoram Singer. "Protein family classification using sparse Markov transducers." Journal of Computational Biology. 10(2):187-213, 2003.

Gomez, Shawn M., William Stafford Noble and Andrey Rzhetsky. "Learning to predict protein-protein interactions from protein sequences." Bioinformatics (Proceedings of the Georgia Tech International Conference on Bioinformatics). 19:1875-1881, 2003.

Leslie, Christina, Eleazar Eskin, Jason Weston and William Stafford Noble. "Mismatch string kernels for SVM protein classification." Neural Information Processing Systems 15, 2003. pp. 1441-1448.
String kernel oftware

Bailey, Timothy and William Stafford Noble. "Searching for statistically significant regulatory modules" Bioinformatics (Proceedings of the European Conference on Computational Biology). 19(Suppl. 2):ii16-ii25, 2003.

Pavlidis, Paul, Qinghong Li and William Stafford Noble. "The effect of replication on gene expression microarray experiments." Bioinformatics. 19(13):1620-1627, 2003.

Gururaja, Tarikere, Weiqun Li, William Stafford Noble, Donald G. Payan and D. C. Anderson. "Multiple functional categories of proteins identified in an in vitro cellular ubiquitin affinity extract using shotgun peptide sequencing." Journal of Proteome Research. 2:394-404, 2003.

Segal, Neil H., Paul Pavlidis, Cristina R. Antonescu, Robert G. Maki, William Stafford Noble, James M. Woodruff, Jonathan J. Lewis, Murray F. Brennan, Alan N. Houghton and Carlos Cordon-Cardo. "Classification and subtype prediction of soft tissue sarcoma by functional genomics and support vector machine analysis." American Journal of Pathology. 169:691-700, 2003.

Neil H. Segal, Paul Pavlidis, William Stafford Noble, Cristina R. Antonescu, Agnes Viale, Umadevi V. Wesley, Klaus Busam, Humilidad Gallardo, Dianne DeSantis, Murray F. Brennan, Carlos Cordon-Cardo, Jedd D. Wolchok and Alan N. Houghton. "Classification of clear cell sarcoma as melanoma of soft parts by genomic profiling." Journal of Clinical Oncology. 21:1775-1781, 2003.

Pavlidis, Paul and William Stafford Noble. "Matrix2png: A utility for visualizing matrix data." Bioinformatics. 19(2):295-296, 2003.

Anderson, David C., Weiqun Li, Donald G. Payan and William Stafford Noble. "A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores." Journal of Proteome Research. 2(2):137-146, 2003.

2002

Eleazar Eskin, William Stafford Noble and Yoram Singer. "Using substitution matrices to estimate probability distributions for biological sequences." Journal of Computational Biology. 9(6):775-91, 2002.

Bernhard Schoelkopf, Jason Weston, Eleazar Eskin, Christina Leslie and William Stafford Noble. "A kernel approach for learning from almost orthogonal patterns." Proceedings of the 13th European Conference on Machine Learning, August 19-23, 2002. pp. 511-528.

Bernhard Scholkopf, Jason Weston, Eleazar Eskin, Christina Leslie and William Stafford Noble. "Dealing with large diagonals in kernel matrices." Annals of the Institute on Statistical Mathematics, 55(2):391-408, 2003.

Liao, Li and William Stafford Noble. "Combining pairwise sequence similarity and support vector machines for remote protein homology detection". Proceedings of the Sixth Annual International Conference on Research in Computational Molecular Biology, April 18-21, 2002. pp. 225-232.

Pavlidis, Paul, Jason Weston, Jinsong Cai and William Stafford Noble. "Learning gene functional classifications from multiple data types." Journal of Computational Biology. 9(2):401-411, 2002.

Pavlidis, Paul, Darrin P. Lewis and William Stafford Noble. "Exploring gene expression data with class scores." Proceedings of the Pacific Symposium on Biocomputing, January 2-7, 2002. pp. 474-485.

Leslie, Christina, Eleazar Eskin and William Stafford Noble. "The spectrum kernel: A string kernel for SVM protein classification." Proceedings of the Pacific Symposium on Biocomputing, January 2-7, 2002. pp. 564-575.
String kernel software

2001

Pavlidis, Paul and William Stafford Noble. "Analysis of strain and regional variation in gene expression in mouse brain." Genome Biology. 2(10): research0042.1-0042.15, 2001.

Pavlidis, Paul, Christopher Tang and William Stafford Noble. "Classification of genes using probabilistic models of microarray expression profiles." Proceedings of BIOKDD 2001: Workshop on Data Mining in Bioinformatics.

Muhle, Rebecca A., Paul Pavlidis, William Noble Grundy and Emmet Hirsch. "A high throughput study of gene expression in preterm labor using a subtractive microarray approach." American Journal of Obstetrics and Gynecology, 185(3):716-24, 2001.

Eskin, Eleazar, William Noble Grundy and Yoram Singer. "Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences." Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology. July 21-25, 2001. pp. 65-73.

Pavlidis, Paul, Jason Weston, Jinsong Cai and William Noble Grundy. "Gene functional classification from heterogeneous data" Proceedings of the Fifth International Conference on Computational Molecular Biology, April 21-24, 2001. pp. 242-248.
Supplement

Pavlidis, Paul, Terrence S. Furey, Muriel Liberto, David Haussler and William Noble Grundy. "Promoter region-based classification of genes." Proceedings of the Pacific Symposium on Biocomputing, January 3-7, 2001. pp. 151-163.

2000

Eskin, Eleazar, William Noble Grundy and Yoram Singer. "Protein family classification using sparse Markov transducers." Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology. August 20-23, 2000. pp. 134-145.

Brown, Michael P. S., William Noble Grundy, David Lin, Nello Cristianini, Charles Sugnet, Terrence S. Furey, Manuel Ares, Jr., and David Haussler. "Knowledge-based analysis of microarray gene expression data using support vector machines." Proceedings of the National Academy of Science. 97(1):262-267, 2000.

1999

Grundy, William Noble and Gavin J. P. Naylor. "Phylogenetic Inference from Conserved Sites Alignments". The Journal of Experimental Zoology: Molecular and Developmental Evolution. 285(2):128-139, 1999.

Grundy, William Noble and Timothy L. Bailey. "Family Pairwise Search with embedded motif models". Bioinformatics. 15(6):463-470, 1999.

Baker, Michael, William N. Grundy and Charles P. Elkan. "A common ancestor for a subunit in the mitochondrial proton-translocating NADH:ubiquinone oxidoreductase (complex I) and short-chain dehydrogenases/reductases". Cellular and Molecular Life Sciences. 55(3):450-455, 1999.

Bailey, Timothy L. and William Noble Grundy. "Classifying proteins by family using the product of correlated p-values". Proceedings of the Third International Conference on Computational Molecular Biology (RECOMB99), April 11-14, 1999. pp. 10-14.

Bailey, Timothy L., Michael E. Baker, Charles P. Elkan and William N. Grundy. "MEME, MAST, and Meta-MEME: New Tools for Motif Discovery in Protein Sequences" in Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications. J. Wang, B. Shapiro and D. Shasha, editors. Oxford UP, 1999.

1998

Grundy, William Noble. A Bayesian Approach to Motif-based Protein Modeling. Ph.D. dissertation. University of California, San Diego. June, 1998.

Grundy, William Noble. "Homology Detection via Family Pairwise Search". Journal of Computational Biology, 5(3):479-492, 1998.

Baker, Michael E., William N. Grundy and Charles P. Elkan. "Spinach CSP41, an mRNA-binding protein and ribonuclease, is homologous to nucleotide-sugar epimerases and hydroxysteroid dehydrogenases" Biochemical and Biophysical Research Communications, 248(2):250-254, 1998.

Grundy, William Noble. "Family-based Homology Detection via Pairwise Sequence Comparison". Proceedings of the Second Annual International Conference on Computational Molecular Biology, March 22-25, 1998. pp. 94-100.

1997

Grundy, William N., Timothy L. Bailey, Charles P. Elkan and Michael E. Baker. "Meta-MEME: Motif-based Hidden Markov Models of Protein Families". Computer Applications in the Biosciences. 13(4):397-406, 1997.

Grundy, William Noble. "Modeling Biological Sequences Using HTK" Technical report prepared for Entropic Research Laboratory, Inc. March, 1997.

Grundy, William N., Timothy L. Bailey, Charles P. Elkan and Michael E. Baker. "Hidden Markov Model Analysis of Motifs in Steroid Dehydrogenases and their Homologs." Biochemical and Biophysical Research Communications. 231(3):760-766, 1997.

before 1997

Batali, John and William Noble Grundy. "Modeling the Evolution of Motivation". Evolutionary Computation. 4(3):235-270, 1996.

Grundy, William N., Timothy L. Bailey and Charles P. Elkan. "ParaMEME: A Parallel Implementation and a Web Interface for a DNA and Protein Motif Discovery Tool" (with corrections). Computer Applications in the Biosciences. 12(4):303-310, 1996.

Grundy, William Noble. "Solar Cookers and Social Classes in Southern Africa." Techné: Journal of Technology Studies. Gray Norton, ed. Vol. V, Winter 1995. pp. 3-7.

Grundy, William. "Building a Simple Recognition System Using HTK." Entropic Research Laboratory, Washington, DC. August, 1994.

Bernstein, Jared, et al. The Latino40 Speech Database. Entropic Research Laboratory, Washington, DC. 1994.

Grundy, William and Roy Grundy "Diffusion of Innovation: Solar Oven Use in Lesotho (Africa)." Advances in Solar Cooking: Proceedings of the 2nd International Conference on Solar Cooker Use and Technology. Shyam S. Nandwani, ed. July 12-15, 1994. pp. 240-247.

Grundy, Bill. Making a Thinking Robot. Senior Honors Thesis, Symbolic Systems Program, Stanford University, 1991. Advisor: Fred Dretske.

Stanford Fleet Street Singers. curious... Bill Grundy, Producer. 1990.
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Grundy, Bill. "The Coinage of Sicyon." The Numismatist. November, 1986. pp. 2307-8.