Publications by authors named "William Noble"

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Proteomics Data Imputation With a Deep Model That Learns From Many Datasets.
Lincoln Harris, William S Noble

Mol Cell Proteomics· December 2025

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An integrated view of the structure and function of the human 4D nucleome.
Job Dekker, Betul Akgol Oksuz, Yang Zhang, Ye Wang, Miriam K Minsk, William S Noble

Nature· December 2025

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Improvements to Casanovo, a Deep Learning Peptide Sequencer.
Gwenneth Straub, Varun Ananth, William E Fondrie, Chris Hsu, Daniela Klaproth-Andrade, William Stafford Noble

J Proteome Res· December 2025

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Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics.
Bo Wen, Chris Hsu, David Shteynberg, Wen-Feng Zeng, Michael Riffle, William S Noble

Nat Commun· November 2025

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Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases.
Maria Chernigovskaya, Khang Lê Quý, Maria Stensland, Sachin Singh, Rowan Nelson, William S Noble

Cell Syst· November 2025

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Multicondition and multimodal temporal profile inference during mouse embryonic development.
Ran Zhang, Chengxiang Qiu, Galina N Filippova, Gang Li, Jay Shendure, William Stafford Noble

Genome Res· October 2025

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HypoAD: volumetric and single-cell analysis reveals changes in the human hypothalamus in aging and Alzheimer's disease.
Doudou Yu, Jürgen Germann, Ghulam Murtaza, Kaitlyn H Hajdarovic, Kelsey R Babcock, William Stafford Noble

bioRxiv· October 2025

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Improved Detection of Differentially Abundant Proteins through FDR-Control of Peptide-Identity-Propagation.
Alexander J Solivais, Hannah Boekweg, Lloyd M Smith, William S Noble, Michael R Shortreed

J Proteome Res· September 2025

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Fast and Memory-Efficient Searching of Large-Scale Mass Spectrometry Data Using Tide.
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Vladislav Ostapenko, Rufino Haroldo Locon, Yang Lu, William Stafford Noble

J Proteome Res· September 2025

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Error-controlled non-additive interaction discovery in machine learning models.
Winston Chen, Yifan Jiang, William Stafford Noble, Yang Young Lu

Nat Mach Intell· September 2025

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Predicting chromatin conformation contact maps.
Alan Min, Jacob Schreiber, Anshul Kundaje, William S Noble

PLoS One· September 2025

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Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment.
Bo Wen, Jack Freestone, Michael Riffle, Michael J MacCoss, William S Noble

Nat Methods· July 2025

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Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome.
Christine C Wu, Kristine A Tsantilas, Jea Park, Deanna Plubell, Justin A Sanders, William S Noble

Nat Commun· July 2025

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A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data.
Justin Sanders, Bo Wen, Paul A Rudnick, Richard S Johnson, Christine C Wu, William Stafford Noble

Nat Methods· July 2025

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Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.
Sriram Pendyala, Katie Partington, Nicholas Bradley, Abbye E McEwen, Gwenneth Straub, William S Noble

bioRxiv· July 2025

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Sceptic: pseudotime analysis for time-series single-cell sequencing and imaging data.
Gang Li, Hyeon-Jin Kim, Sriram Pendyala, Ran Zhang, Jean-Philippe Vert, William Stafford Noble

Genome Biol· July 2025

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Predicting cell cycle stage from 3D single-cell nuclear-stained images.
Gang Li, Eva K Nichols, Valentino E Browning, Nicolas J Longhi, Madison Sanchez-Forman, William Stafford Noble

Life Sci Alliance· June 2025

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A haplotype-resolved view of human gene regulation.
Mitchell R Vollger, Elliott G Swanson, Shane J Neph, Jane Ranchalis, Katherine M Munson, William S Noble

bioRxiv· June 2025

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How to Train a Postprocessor for Tandem Mass Spectrometry Proteomics Database Search While Maintaining Control of the False Discovery Rate.
Jack Freestone, Lukas Käll, William Stafford Noble, Uri Keich

J Proteome Res· May 2025

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Open-Source and FAIR Research Software for Proteomics.
Yasset Perez-Riverol, Wout Bittremieux, William S Noble, Lennart Martens, Aivett Bilbao

J Proteome Res· May 2025

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Self-supervised learning from small-molecule mass spectrometry data.
Wout Bittremieux, William Stafford Noble

Nat Biotechnol· May 2025

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Improved quantitative accuracy in data-independent acquisition proteomics via retention time boundary imputation.
Lincoln Harris, Michael Riffle, William Stafford Noble, Michael J MacCoss

bioRxiv· May 2025

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Harmful algal blooms are preceded by a predictable and quantifiable shift in the oceanic microbiome.
Miranda C Mudge, Michael Riffle, Gabriella Chebli, Deanna L Plubell, Tatiana A Rynearson, William S Noble

Nat Commun· April 2025

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CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation.
He Fang, Ana R Tronco, Giancarlo Bonora, Truong Nguyen, Jitendra Thakur, William S Noble

BMC Biol· March 2025

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Biological databases in the age of generative artificial intelligence.
Mihai Pop, Teresa K Attwood, Judith A Blake, Philip E Bourne, Ana Conesa, William S Noble

Bioinform Adv· March 2025

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