William Stafford Noble (William S Noble, Galip Gürkan Yardımcı, W S Noble)

Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2016-2023
Publications (10 Years): 74

Top Topics

Mass Spectrometry

Machine Learning

Top Venues

Journal of proteome research

PLoS computational biology

Nature communications

bioRxiv : the preprint server for biology

This page only lists publications with an associated author ORCID identifier.

Publications

Lincoln Harris, William E Fondrie, Sewoong Oh, William Stafford Noble
Evaluating Proteomics Imputation Methods with Improved Criteria. Journal of proteome research (2023)
Alan Min, Timothy Durham, Louis Gevirtzman, William Stafford Noble
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation. PLoS computational biology 19 (5) (2023)
Ran Zhang, Mu Yang, Jacob Schreiber, Diana R O'Day, James M A Turner, Jay Shendure, Christine M Disteche, Xinxian Deng, William Stafford Noble
Cross-species imputation and comparison of single-cell transcriptomic profiles. bioRxiv : the preprint server for biology (2023)
Frank Lawrence Nii Adoquaye Acquaye, Attila Kertesz-Farkas, William Stafford Noble
Efficient Indexing of Peptides for Database Search Using Tide. Journal of proteome research (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
Vikram Agarwal, Fumitaka Inoue, Max Schubach, Beth K Martin, Pyaree Mohan Dash, Zicong Zhang, Ajuni Sohota, William Stafford Noble, Galip Gürkan Yardimci, Martin Kircher, Jay Shendure, Nadav Ahituv
Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types. bioRxiv : the preprint server for biology (2023)
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) (2023)
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie, Charles Grant, Michael R 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) (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
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. bioRxiv : the preprint server for biology (2023)
Nelle Varoquaux, William Stafford Noble, Jean-Philippe Vert
Inference of 3D genome architecture by modeling overdispersion of Hi-C data. Bioinformatics (Oxford, England) 39 (1) (2023)
Alan Min, Timothy Durham, Louis Gevirtzman, William Stafford Noble
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation. PLoS computational biology 19 (5) (2023)
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie, Charles Grant, Michael R 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) (2023)
Hannah L Harris, Huiya Gu, Moshe Olshansky, Ailun Wang, Irene Farabella, Yossi Eliaz, Achyuth Kalluchi, Akshay Krishna, Mozes Jacobs, Gesine Cauer, Melanie Pham, Suhas S P Rao, Olga Dudchenko, Arina Omer, Kiana Mohajeri, Sungjae Kim, Michael H Nichols, Eric S Davis, Dimos Gkountaroulis, Devika Udupa, Aviva Presser Aiden, Victor G Corces, Douglas H Phanstiel, William Stafford Noble, Guy Nir, Michele Di Pierro, 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 (1) (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie, Charles Grant, Michael R 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 (2023)
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) (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
Andy Lin, Brooke L Deatherage Kaiser, Janine R Hutchison, Jeffrey A Bilmes, William Stafford Noble
MS1Connect: a mass spectrometry run similarity measure. Bioinformatics (Oxford, England) 39 (2) (2023)
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) (2023)
Arya Ebadi, Jack Freestone, William Stafford Noble, Uri Keich
Bridging the False Discovery Gap. Journal of proteome research (2023)
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. bioRxiv : the preprint server for biology (2023)
Andy Lin, Brooke L Deatherage Kaiser, Janine R Hutchison, Jeffrey A Bilmes, William Stafford Noble
MS1Connect: a mass spectrometry run similarity measure. Bioinformatics (Oxford, England) 39 (2) (2023)
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie, Charles Grant, Michael R 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) (2023)
Alan Min, Timothy Durham, Louis Gevirtzman, William Stafford Noble
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation. PLoS computational biology 19 (5) (2023)
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie, Charles Grant, Michael R 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) (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
Borislav Hrisimirov Hristov, William Stafford Noble, Alessandro Bertero
Systematic identification of inter-chromosomal interaction networks supports the existence of RNA factories. bioRxiv : the preprint server for biology (2023)
Alan Min, Timothy Durham, Louis Gevirtzman, William Stafford Noble
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation. PLoS computational biology 19 (5) (2023)
Gayani Batugedara, Xueqing M Lu, Borislav Hristov, Steven Abel, Zeinab Chahine, Thomas Hollin, Desiree Williams, Tina Wang, Anthony Cort, Todd Lenz, Trevor A Thompson, Jacques Prudhomme, Abhai K Tripathi, Guoyue Xu, Juliana Cudini, Sunil Dogga, Mara N K Lawniczak, William Stafford Noble, Photini Sinnis, Karine Le Roch
Novel insights into the role of long non-coding RNA in the human malaria parasite, Plasmodium falciparum. Nature communications 14 (1) (2023)
Andy Lin, Temana Short, William Stafford Noble, Uri Keich
Improving Peptide-Level Mass Spectrometry Analysis via Double Competition. Journal of proteome research 21 (10) (2022)
Chengxiang Qiu, Junyue Cao, Beth K Martin, Tony Li, Ian C Welsh, Sanjay Srivatsan, Xingfan Huang, Diego Calderon, William Stafford Noble, Christine M Disteche, Stephen A Murray, Malte Spielmann, Cecilia B Moens, Cole Trapnell, Jay Shendure
Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nature genetics 54 (3) (2022)
Ayse B Dincer, Yang Lu, Devin K Schweppe, Sewoong Oh, William Stafford Noble
Reducing Peptide Sequence Bias in Quantitative Mass Spectrometry Data with Machine Learning. Journal of proteome research 21 (7) (2022)
Wout Bittremieux, Damon H May, Jeffrey Bilmes, William Stafford Noble
A learned embedding for efficient joint analysis of millions of mass spectra. Nature methods 19 (6) (2022)
Magnus Palmblad, Sebastian Böcker, Sven Degroeve, Oliver Kohlbacher, Lukas Käll, William Stafford Noble, Mathias Wilhelm
Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics. Journal of proteome research 21 (4) (2022)
Sean Whalen, Jacob Schreiber, William Stafford Noble, Katherine S Pollard
Navigating the pitfalls of applying machine learning in genomics. Nature reviews. Genetics (2021)
Jacob Schreiber, Jeffrey Bilmes, William Stafford Noble
Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data. Bioinformatics (Oxford, England) 37 (4) (2021)
Yang Young Lu, William Stafford Noble
A wider field of view to predict expression. Nature methods 18 (10) (2021)
William E Fondrie, Wout Bittremieux, William Stafford Noble
ppx: Programmatic Access to Proteomics Data Repositories. Journal of proteome research 20 (9) (2021)
Timothy J Durham, Riza M Daza, Louis Gevirtzman, Darren A Cusanovich, Olubusayo Bolonduro, William Stafford Noble, Jay Shendure, Robert H Waterston
Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes. Genome research 31 (10) (2021)
Andy Lin, Deanna L 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) (2021)
William E Fondrie, William Stafford Noble
mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection. Journal of proteome research 20 (4) (2021)
He Fang, Giancarlo Bonora, Jordan P Lewandowski, Jitendra Thakur, Galina N Filippova, Steven Henikoff, Jay Shendure, Zhijun Duan, John L Rinn, Xinxian Deng, William Stafford Noble, Christine M Disteche
Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. Nature communications 11 (1) (2020)
Lindsay K 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) (2020)
Hyeon-Jin Kim, Galip Gürkan Yardimci, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B Ware, Jay Shendure, Zhijun Duan, William Stafford Noble
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. PLoS computational biology 16 (9) (2020)
William E Fondrie, William Stafford Noble
Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments. Journal of proteome research 19 (3) (2020)
Damon H May, Kaipo Tamura, William Stafford Noble
Detecting Modifications in Proteomics Experiments with Param-Medic. Journal of proteome research 18 (4) (2019)
Maxwell W Libbrecht, Oscar L Rodriguez, Zhiping Weng, Jeffrey 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 (1) (2019)
David F Read, Kate Cook, Yang Young Lu, Karine G Le Roch, William Stafford Noble
Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features. PLoS computational biology 15 (9) (2019)
Galip Gürkan Yardımcı, 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 Stafford Noble
Measuring the reproducibility and quality of Hi-C data. Genome biology 20 (1) (2019)
John T Halloran, Hantian Zhang, Kaan Kara, Cédric Renggli, Matthew The, Ce Zhang, David M Rocke, Lukas Käll, William Stafford Noble
Speeding Up Percolator. Journal of proteome research 18 (9) (2019)
Alessandro Bertero, Paul A Fields, Vijay Ramani, Giancarlo Bonora, Galip G 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) (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) (2019)
Molly P Mikan, H Rodger Harvey, Emma B Timmins-Schiffman, Michael Riffle, Damon H May, Ian Salter, William Stafford Noble, Brook L Nunn
Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes. The ISME journal 14 (1) (2019)
William Stafford Noble, Uri Keich
Response to "Mass spectrometrists should search for all peptides, but assess only the ones they care about". Nature methods 14 (7) (2019)
Uri Keich, Kaipo Tamura, William Stafford Noble
Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate. Journal of proteome research 18 (2) (2019)
Giancarlo Bonora, X Deng, H Fang, V Ramani, R Qiu, J B Berletch, G N Filippova, Zhijun Duan, J Shendure, William Stafford Noble, Christine M Disteche
Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. Nature communications 9 (1) (2018)
Evelien M Bunnik, Kate B Cook, Nelle Varoquaux, Gayani Batugedara, Jacques Prudhomme, Anthony Cort, Lirong Shi, Chiara Andolina, Leila S Ross, Declan Brady, David A Fidock, Francois H 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) (2018)
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) (2018)
Lindsay K Pino, Brian C Searle, Eric L Huang, William Stafford Noble, Andrew N 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) (2018)
Timothy J Durham, Maxwell W Libbrecht, J Jeffry Howbert, Jeff Bilmes, William Stafford Noble
PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition. Nature communications 9 (1) (2018)
Jesse R Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song, Victoria T Le, Galip Gürkan Yardımcı, 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 C 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) (2018)
Alex Hu, Yang Young Lu, Jeff 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) (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) (2018)
Vijay Ramani, Xinxian Deng, Ruolan Qiu, Kevin L Gunderson, Frank J Steemers, Christine M Disteche, William Stafford Noble, Zhijun Duan, Jay Shendure
Massively multiplex single-cell Hi-C. Nature methods 14 (3) (2017)
Ying Sonia Ting, Jarrett D Egertson, James G Bollinger, Brian C Searle, Samuel H Payne, William Stafford Noble, Michael J MacCoss
PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data. Nature methods 14 (9) (2017)
William Stafford Noble, William Stafford Noble
Software tools for visualizing Hi-C data. Genome biology 18 (1) (2017)
William Stafford Noble
Ten simple rules for writing a response to reviewers. PLoS computational biology 13 (10) (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, William Stafford Noble
Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies. Scientific reports 7 (1) (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) (2017)
Zoi E Sychev, Alex Hu, Terri A DiMaio, Anthony Gitter, Nathan D Camp, William Stafford Noble, Alejandro Wolf-Yadlin, Michael Lagunoff
Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. PLoS pathogens 13 (3) (2017)
Emma Timmins-Schiffman, Damon H May, Molly Mikan, Michael Riffle, Chris 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) (2016)
Kai Wei, Maxwell W Libbrecht, Jeffrey A Bilmes, William Stafford Noble
Choosing panels of genomics assays using submodular optimization. Genome biology 17 (1) (2016)