🏆 Finalist — NIH Data Sharing Index (“S-Index”) Challenge

William Stafford Noble

University of Washington

ORCID: 0000-0001-7283-4715

Also affiliated with Seattle University

Biochemistry, Genetics and Molecular BiologyChemistry

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile
36.0Author DataRank

Indexed papers

14in pilot corpus
datarank_citation_only_1hop_v6· scope data_onlyMethodology
Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 14 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

Top data-sharing exemplar

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Nature(2007)10.1038/nature05874
Top 1%
12.9DataRank
Top 1%5277 citations

J Stamatoyannopoulos, Simon G. Gregory, T Gingeras, Eoghan Harrington, Zhiping Weng +286 more

Papers

Driven by 107 papers — median percentile 82. Top paper: “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project”.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Nature(2007)10.1038/nature05874
Top 1%
12.9DataRank
Top 1%5277 citations

J Stamatoyannopoulos, Simon G. Gregory, T Gingeras, Eoghan Harrington, Zhiping Weng +286 more

Integrative annotation of chromatin elements from ENCODE data

Nucleic Acids Research(2012)10.1093/nar/gks1284
Top 2%
7.9DataRank
Top 2%628 citations

Jason Ernst, Steven P. Wilder, Anshul Kundaje, Robert S. Harris, Max Libbrecht +10 more

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Nature(2020)10.1038/s41586-020-2493-4
Top 3%
6.4DataRank
Top 3%2615 citations

Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian, Veena Afzal +501 more

Epigenetic priors for identifying active transcription factor binding sites

Bioinformatics(2011)10.1093/bioinformatics/btr614
N/A
5.9DataRank · unranked
134 citations

Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, Timothy L. Bailey +1 more

Widely distributed noncoding purifying selection in the human genome

Proceedings of the National Academy of Sciences(2007)10.1073/pnas.0705140104
N/A
4.5DataRank · unranked
97 citations

William S. Noble, Charles E. Grant, Shamil R. Sunyaev, John A. Stamatoyannopoulos, William Stafford Noble +3 more

Predicting Co-Complexed Protein Pairs from Heterogeneous Data

PLoS Computational Biology(2008)10.1371/journal.pcbi.1000054
N/A
4.0DataRank · unranked
72 citations

William Stafford Noble, Jian Qiu

Systematic reconstruction of cellular trajectories across mouse embryogenesis

Nature Genetics(2022)10.1038/s41588-022-01018-x
Top 6%
3.8DataRank
Top 6%212 citations

Junyue Cao, Beth Martin, Tony Li, Ian Welsh, Sanjay Srivatsan +10 more

A single-cell time-lapse of mouse prenatal development from gastrula to birth

Nature(2024)10.1038/s41586-024-07069-w
N/A
3.2DataRank · unranked
181 citations

Beth Martin, Ian Welsh, Riza M. Daza, Truc-Mai Le, Xingfan Huang +20 more

A pitfall for machine learning methods aiming to predict across cell types

Genome biology(2020)10.1186/s13059-020-02177-y
N/A
1.8DataRank · unranked
57 citations

Ritambhara Singh, Jeffrey A. Bilmes, William Stafford Noble, Jacob Matthew Schreiber

Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

Molecular Cell(2023)10.1016/j.molcel.2023.06.018
N/A
1.7DataRank · unranked
97 citations

Frank Alber, Sarah Aufmkolk, Brian J. Beliveau, Benoit G. Bruneau, Andrew S. Belmont +30 more

Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples

Genome biology(2020)10.1186/s13059-020-01978-5
Top 13%
1.6DataRank
Top 13%48 citations

Jeffrey A. Bilmes, William Stafford Noble, Jacob Matthew Schreiber

Protein Interaction Networks: Protein Domain Interaction and Protein Function Prediction

Handbook of Statistical Bioinformatics(2011)10.1007/978-3-642-16345-6_21
N/A
1.6DataRank · unranked
12 citations

William Stafford Noble, Yanjun Qi

MEME SUITE: tools for motif discovery and searching

Nucleic Acids Research(2009)10.1093/nar/gkp335
N/A
1.4DataRank · unranked
11359 citations

L. Clementi, J. Ren, W. W. Li, Timothy L. Bailey, Mikael Bodén +7 more

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Cell(2023)10.1016/j.cell.2023.02.018
Top 15%
1.4DataRank
Top 15%82 citations

Jiahao Gao, Beatrice Borsari, Yucheng T. Yang, Timur R. Galeev, Gamze Gürsoy +95 more

Quantifying similarity between motifs

Genome Biology(2007)10.1186/gb-2007-8-2-r24
N/A
1.2DataRank · unranked
2280 citations

John A Stamatoyannopoulos, Timothy L Bailey, William Stafford Noble, Shobhit Gupta

Machine learning applications in genetics and genomics

Nature Reviews Genetics(2015)10.1038/nrg3920
N/A
1.1DataRank · unranked
1991 citations

William Stafford Noble, Maxwell W. Libbrecht

Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when adjacent sequences do not

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.03.462599
N/A
1.1DataRank · unranked
29 citations

Hannah L. Harris, Moshe Olshansky, Yossi Eliaz, Akshay Krishna, Achyuth Kalluchi +20 more

DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools

Genome Research(2024)10.1101/gr.279095.124
N/A
0.986DataRank · unranked
49 citations

Stephanie C. Bohaczuk, Yizi Mao, Jane Ranchalis, Benjamin J. Mallory, Alan Min +10 more

A statistical framework for genomic data fusion

Bioinformatics(2004)10.1093/bioinformatics/bth294
N/A
0.978DataRank · unranked
677 citations

Tijl De Bie, Nello Cristianini, Michael I. Jordan, William Stafford Noble, Gert R. G. Lanckriet

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Nature Methods(2012)10.1038/nmeth.1937
N/A
0.972DataRank · unranked
651 citations

Orion J. Buske, Jie Wang, Zhiping Weng, Jeff A Bilmes, William Stafford Noble +2 more

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

Nature Methods(2009)10.1038/nmeth.1313
N/A
0.956DataRank · unranked
584 citations

Xiaoyu Chen, Zhihong Zhang, Peter J. Sabo, Richard Sandstrom, Alex P. Reynolds +10 more

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

Genome biology(2021)10.1186/s13059-021-02432-w
Top 22%
0.925DataRank
Top 22%27 citations

Vijay Ramani, Ritambhara Singh, He Fang, Dana L. Jackson, Sanjay Srivatsan +9 more

Comparative analysis of metazoan chromatin organization

Nature(2014)10.1038/nature13415
N/A
0.910DataRank · unranked
429 citations

Youngsook L. Jung, Tao Liu, Burak H. Alver, Soohyun Lee, Kohta Ikegami +83 more

Systematic reconstruction of the cellular trajectories of mammalian embryogenesis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.08.447626
N/A
0.871DataRank · unranked
5 citations

Junyue Cao, Tony Li, Sanjay Srivatsan, Xingfan Huang, Diego Calderon +7 more

Chromatin alternates between A and B compartments at kilobase scale for subgenic organization

Nature Communications(2023)10.1038/s41467-023-38429-1
N/A
0.759DataRank · unranked
157 citations

Huiya Gu, Moshe Olshansky, Ailun Wang, Irene Farabella, Yossi Eliaz +25 more

Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome

Genome biology(2020)10.1186/s13059-020-01977-6
N/A
0.736DataRank · unranked
134 citations

Timothy Durham, Jeffrey A. Bilmes, William Stafford Noble, Jacob Matthew Schreiber

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data

PLoS Computational Biology(2020)10.1371/journal.pcbi.1008173
N/A
0.705DataRank · unranked
109 citations

Galip Gürkan Yardımcı, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu +7 more

Massively parallel characterization of transcriptional regulatory elements

Nature(2025)10.1038/s41586-024-08430-9
N/A
0.689DataRank · unranked
98 citations

Fumitaka Inoue, Max Schubach, Dmitry Penzar, Beth Martin, Pyaree Mohan Dash +12 more

Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.10.544439
N/A
0.624DataRank · unranked
63 citations

Kristine A. Tsantilas, Jea Park, Deanna L. Plubell, Justin Sanders, Previn Naicker +14 more

Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome

Nature Communications(2025)10.1038/s41467-025-60595-7
N/A
0.606DataRank · unranked
56 citations

Kristine A. Tsantilas, Jea Park, Deanna L. Plubell, Justin Sanders, Previn Naicker +14 more

Epiphany: predicting Hi-C contact maps from 1D epigenomic signals

Genome biology(2023)10.1186/s13059-023-02934-9
N/A
0.601DataRank · unranked
54 citations

Arnav Das, Vianne R. Gao, Alireza Karbalayghareh, William Stafford Noble, Jeffrey A. Bilmes +2 more

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

Nature Communications(2024)10.1038/s41467-024-53628-0
N/A
0.579DataRank · unranked
23 citations

Rui Yang, Arnav Das, Renhe Luo, Hanzhi Luo, Dylan McNally +19 more

Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes

Nature Communications(2024)10.1038/s41467-024-45519-1
N/A
0.493DataRank · unranked
14 citations

Steven Abel, Charles A.S. Banks, Borislav H. Hristov, Jacques Prudhomme, Kianna Hales +4 more

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.05.535726
N/A
0.470DataRank · unranked
22 citations

Beth Martin, Ian Welsh, Riza M. Daza, Truc-Mai Le, Xingfan Huang +20 more

Biological databases in the age of generative artificial intelligence

Bioinformatics Advances(2024)10.1093/bioadv/vbaf044
N/A
0.418DataRank · unranked
8 citations

Teresa K. Attwood, Judith A. Blake, Philip E. Bourne, Ana Conesa, Terry Gaasterland +17 more

Harmful algal blooms are preceded by a predictable and quantifiable shift in the oceanic microbiome

Nature Communications(2025)10.1038/s41467-025-59250-y
N/A
0.406DataRank · unranked
14 citations

Michael Riffle, Gabriella Chebli, Deanna L. Plubell, Tatiana A. Rynearson, William Stafford Noble +4 more

Submodular sketches of single-cell RNA-seq measurements

(2020)10.1145/3388440.3412409
Top 49%
0.365DataRank
Top 49%4 citations

Jeffrey A. Bilmes, William Stafford Noble, Wei Yang

Proteome-wide identification of amino acid substitutions deleterious for protein function

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.06.487405
N/A
0.360DataRank · unranked
7 citations

Kyle Hess, Bianca Y. Ruiz, Ian R. Smith, Anthony S. Barente, Stephanie M. Zimmerman +5 more

Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation

Stem Cell Reports(2022)10.1016/j.stemcr.2022.11.003
N/A
0.312DataRank · unranked
7 citations

Katie A. Mitzelfelt, Giancarlo Bonora, Paul Fields, Xiulan Yang, Han Sheng Chiu +6 more

Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days

Scientific Data(2024)10.1038/s41597-024-04013-5
Top 54%
0.312DataRank
Top 54%7 citations

Emma Timmins‐Schiffman, Miranda C. Mudge, Deanna L. Plubell, Gabriella Chebli, Julia Kubanek +21 more

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.27.550836
N/A
0.269DataRank · unranked
5 citations

Rui Yang, Arnav Das, Renhe Luo, Hanzhi Luo, Dylan McNally +19 more

Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation

PLoS Computational Biology(2023)10.1371/journal.pcbi.1011286
N/A
0.253DataRank · unranked
4 citations

Junha Shin, Jacob Matthew Schreiber, Shilu Zhang, Yi Zhang, Mohith Manjunath +4 more

Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.24.396713
N/A
0.241DataRank · unranked
4 citations

Dejun Lin, Stephanie Portillo‐Ledesma, Po‐Yen Lin, Dakota R. Hunt, Cheng-Fu Kao +4 more

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.20.390765
N/A
0.241DataRank · unranked
4 citations

Vijay Ramani, Ritambhara Singh, He Fang, Dana L. Jackson, Sanjay Srivatsan +9 more

Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.29.458098
N/A
0.234DataRank · unranked
3 citations

Jacob Matthew Schreiber, Junha Shin, Shilu Zhang, Yi Zhang, Mohith Manjunath +4 more

Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data

Bioinformatics(2020)10.1093/bioinformatics/btaa830
N/A
0.208DataRank · unranked
3 citations

Jeffrey A. Bilmes, William Stafford Noble, Jacob Matthew Schreiber

The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.30.502157
N/A
0.190DataRank · unranked
2 citations

Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang +40 more

Multicondition and multimodal temporal profile inference during mouse embryonic development

Genome Research(2025)10.1101/gr.279997.124
Top 70%
0.165DataRank
Top 70%2 citations

Chengxiang Qiu, Galina N. Filippova, Gang Li, Jay Shendure, Jean‐Philippe Vert +4 more

Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.27.614549
Top 70%
0.165DataRank
Top 70%2 citations

Emma Timmins‐Schiffman, Miranda C. Mudge, Deanna L. Plubell, Gabriella Chebli, Julia Kubanek +20 more

The Crux toolkit for analysis of bottom-up tandem mass spectrometry proteomics data

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.02.510538
N/A
0.165DataRank · unranked
2 citations

Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K. Eng, William E. Fondrie, Charles E. Grant +7 more

HiCRep.py: Fast comparison of Hi-C contact matrices in Python

10.1101/2020.10.27.357756
N/A
0.165DataRank · unranked
2 citations

Justin Sanders, William Stafford Noble, Dejun Lin

CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation

BMC Biology(2025)10.1186/s12915-025-02137-7
N/A
0DataRank · unranked
4 citations

Ana R. Tronco, Giancarlo Bonora, Truong N. Nguyen, Jitendra Thakur, Joel B. Berletch +8 more

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

Genome biology(2025)10.1186/s13059-025-03679-3
N/A
0DataRank · unranked
5 citations

Hyeonjin Kim, Sriram Pendyala, Ran Zhang, Jean‐Philippe Vert, Christine M. Distèche +4 more

Predicting cell cycle stage from 3D single-cell nuclear-stained images

Life Science Alliance(2025)10.26508/lsa.202403067
N/A
0DataRank · unranked
1 citations

Eva K. Nichols, Valentino E. Browning, Nicolas J Longhi, Madison Sanchez-Forman, Conor K. Camplisson +3 more

Improved quantitation in data-independent acquisition proteomics via retention time boundary imputation

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.27.656394
N/A
0DataRank · unranked
2 citations

Michael Riffle, Nicholas Shulman, William E. Fondrie, Christine C. Wu, Danielle P. Johnson Erickson +8 more

Predicting chromatin conformation contact maps

PLoS ONE(2025)10.1371/journal.pone.0331124
N/A
0DataRank · unranked
0 citations

Jacob Matthew Schreiber, Anshul Kundaje, William Stafford Noble, Alan Min

Predicting cell cycle stage from 3D single-cell nuclear-stained images

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.30.610553
N/A
0DataRank · unranked
0 citations

Eva K. Nichols, Valentino E. Browning, Nicolas J. Longhi, Conor K. Camplisson, Brian J. Beliveau +2 more

Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

Genome Biology(2025)10.1186/s13059-025-03494-w
N/A
0DataRank · unranked
0 citations

Carles B. Adsera, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang +45 more

A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning

Molecular Cell(2020)10.1016/j.molcel.2020.04.020
N/A
0DataRank · unranked
141 citations

Lukasz P. Kozlowski, Salma Sohrabi-Jahromi, James Fishburn, Linda Warfield, Jacob Matthew Schreiber +4 more

Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome

Nature Communications(2020)10.1038/s41467-020-19879-3
N/A
0DataRank · unranked
64 citations

Giancarlo Bonora, Jordan P. Lewandowski, Jitendra Thakur, Galina N. Filippova, Steven Henikoff +7 more

Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach

Microorganisms(2020)10.3390/microorganisms8030379
N/A
0DataRank · unranked
24 citations

Meredith A.J. Hullar, Lisa A. Lai, Hong Peng, Damon May, William Stafford Noble +7 more

Measuring significant changes in chromatin conformation with ACCOST

Nucleic Acids Research(2020)10.1093/nar/gkaa069
N/A
0DataRank · unranked
29 citations

Borislav H. Hristov, Karine G. Le Roch, Jean‐Philippe Vert, William Stafford Noble, Kate B. Cook

Gromov-Wasserstein optimal transport to align single-cell multi-omics data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.28.066787
N/A
0DataRank · unranked
66 citations

Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh, Pınar Demetçi

Zero-shot imputations across species are enabled through joint modeling of human and mouse epigenomics

(2020)10.1145/3388440.3412412
N/A
0DataRank · unranked
6 citations

Deepthi Hegde, William Stafford Noble, Jacob Matthew Schreiber

mokapot: Fast and flexible semi-supervised learning for peptide detection

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.01.407270
N/A
0DataRank · unranked
4 citations

William Stafford Noble, William E. Fondrie

Improving power while controlling the false discovery rate when only a subset of peptides are relevant

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.20.347278
N/A
0DataRank · unranked
0 citations

Deanna L. Plubell, Uri Keich, William Stafford Noble, Andy Lin

mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection

Journal of Proteome Research(2021)10.1021/acs.jproteome.0c01010
N/A
0DataRank · unranked
75 citations

William Stafford Noble, William E. Fondrie

HiCRep.py: fast comparison of Hi-C contact matrices in Python

Bioinformatics(2021)10.1093/bioinformatics/btab097
N/A
0DataRank · unranked
43 citations

Justin J. Sanders, William Stafford Noble, Dejun Lin

Large‐scale tandem mass spectrum clustering using fast nearest neighbor searching

Rapid Communications in Mass Spectrometry(2021)10.1002/rcm.9153
N/A
0DataRank · unranked
31 citations

Kris Laukens, William Stafford Noble, Pieter C. Dorrestein, Wout Bittremieux

DIAmeter: matching peptides to data-independent acquisition mass spectrometry data

Bioinformatics(2021)10.1093/bioinformatics/btab284
N/A
0DataRank · unranked
29 citations

Jeff Bilmes, Ricard A. Rodríguez‐Mias, Judit Villén, William Stafford Noble, Yang Young Lu

ppx: Programmatic Access to Proteomics Data Repositories

Journal of Proteome Research(2021)10.1021/acs.jproteome.1c00454
N/A
0DataRank · unranked
12 citations

Wout Bittremieux, William Stafford Noble, William E. Fondrie

Tandem Mass Spectrometry–Based Amyloid Typing Using Manual Microdissection and Open-Source Data Processing

American Journal of Clinical Pathology(2021)10.1093/ajcp/aqab185
N/A
0DataRank · unranked
9 citations

Kelly D. Smith, Han-Yin Yang, Clark M. Henderson, Hannah Pflaum, Melissa Lerch +7 more

A wider field of view to predict expression

Nature Methods(2021)10.1038/s41592-021-01259-4
N/A
0DataRank · unranked
4 citations

William Stafford Noble, Yang Young Lu

Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

Genome Research(2021)10.1101/gr.271791.120
N/A
0DataRank · unranked
26 citations

Riza M. Daza, Louis Gevirtzman, Darren A. Cusanovich, Olubusayo Bolonduro, William Stafford Noble +3 more

Large-scale tandem mass spectrum clustering using fast nearest neighbor searching

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.05.429957
N/A
0DataRank · unranked
5 citations

Kris Laukens, William Stafford Noble, Pieter C. Dorrestein, Wout Bittremieux

DIAmeter: Matching peptides to data-independent acquisition mass spectrometry data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.29.428872
N/A
0DataRank · unranked
5 citations

Jeff Bilmes, Ricard A. Rodríguez‐Mias, Judit Villén, William Stafford Noble, Yang Young Lu

Inference of genome 3D architecture by modeling overdispersion of Hi-C data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.04.429864
N/A
0DataRank · unranked
4 citations

William Stafford Noble, Jean‐Philippe Vert, Nelle Varoquaux

ppx: Programmatic access to proteomics data repositories

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.29.446304
N/A
0DataRank · unranked
0 citations

Wout Bittremieux, William Stafford Noble, William E. Fondrie

A flexible workflow for building spectral libraries from narrow window data independent acquisition mass spectrometry data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.22.469568
N/A
0DataRank · unranked
0 citations

William E. Fondrie, Christopher D. McGann, Alexander Federation, William Stafford Noble, Michael J. MacCoss +2 more

Improving Peptide-Level Mass Spectrometry Analysis via Double Competition

Journal of Proteome Research(2022)10.1021/acs.jproteome.2c00282
N/A
0DataRank · unranked
29 citations

Temana Short, William Stafford Noble, Uri Keich, Andy Lin

Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data

Journal of Proteome Research(2022)10.1021/acs.jproteome.1c00895
N/A
0DataRank · unranked
18 citations

William E. Fondrie, Christopher D. McGann, Alexander Federation, William Stafford Noble, Michael J. MacCoss +2 more

Linking cells across single-cell modalities by synergistic matching of neighborhood structure

Bioinformatics(2022)10.1093/bioinformatics/btac481
N/A
0DataRank · unranked
4 citations

Jeffrey A. Bilmes, William Stafford Noble, Borislav H. Hristov

Predicting A/B compartments from histone modifications using deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.19.488754
N/A
0DataRank · unranked
12 citations

Nitya Thakkar, Hannah L. Harris, Megan Zhang, Susanna Liu, Mark Gerstein +6 more

Improving peptide-level mass spectrometry analysis via double competition

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.11.491571
N/A
0DataRank · unranked
4 citations

Temana Short, William Stafford Noble, Uri Keich, Andy Lin

Deciphering the non-coding code of pathogenicity and sexual differentiation in the human malaria parasite

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.12.511630
N/A
0DataRank · unranked
3 citations

Xueqing Maggie Lu, Steven Abel, Zeinab Chahine, Borislav H. Hristov, Desiree Williams +15 more

Linking cells across single-cell modalities by synergistic matching of neighborhood structure

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.20.488794
N/A
0DataRank · unranked
0 citations

Jeffrey A. Bilmes, William Stafford Noble, Borislav H. Hristov

Novel insights into the role of long non-coding RNA in the human malaria parasite, Plasmodium falciparum

Nature Communications(2023)10.1038/s41467-023-40883-w
N/A
0DataRank · unranked
22 citations

Xueqing Maggie Lu, Borislav H. Hristov, Steven Abel, Zeinab Chahine, Thomas Hollin +15 more

The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data

Journal of Proteome Research(2023)10.1021/acs.jproteome.2c00615
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20 citations

Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K. Eng, William E. Fondrie, Charles E. Grant +7 more

Inference of 3D genome architecture by modeling overdispersion of Hi-C data

Bioinformatics(2023)10.1093/bioinformatics/btac838
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16 citations

William Stafford Noble, Jean‐Philippe Vert, Nelle Varoquaux

A High-Throughput PIXUL–Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes

Laboratory Investigation(2023)10.1016/j.labinv.2023.100282
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8 citations

Ilona M. Babenko, Ran Zhang, William Stafford Noble, Oleg Denisenko, Tomáš Vaisar +2 more

LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis

Bioinformatics(2023)10.1093/bioinformatics/btad420
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3 citations

Ran Zhang, Gang Li, Marco Cuturi, William Stafford Noble, Jean‐Philippe Vert +1 more

MS1Connect: a mass spectrometry run similarity measure

Bioinformatics(2023)10.1093/bioinformatics/btad058
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1 citations

Brooke L. Deatherage Kaiser, Janine R. Hutchison, Jeffrey A. Bilmes, William Stafford Noble, Andy Lin

Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.05.531189
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53 citations

Fumitaka Inoue, Max Schubach, Beth Martin, Pyaree Mohan Dash, Zicong Zhang +7 more

DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.20.537673
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14 citations

Stephanie C. Bohaczuk, Yizi Mao, Jane Ranchalis, Benjamin J. Mallory, Alan Min +10 more

CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.04.539469
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6 citations

Ana R. Tronco, Giancarlo Bonora, Truong N. Nguyen, Jitendra Thakur, Joel B. Berletch +7 more

Systematic identification of inter-chromosomal interaction networks supports the existence of RNA factories

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.21.558852
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2 citations

William Stafford Noble, Alessandro Bertero, Borislav H. Hristov

Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.06.530899
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0DataRank · unranked
0 citations

Conor K. Camplisson, Qiaoyi Lin, Karen H. Miga, William Stafford Noble, Brian J. Beliveau +1 more

Pseudotime analysis for time-series single-cell sequencing and imaging data

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.03.565575
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0DataRank · unranked
0 citations

Hyeonjin Kim, Sriram Pendyala, Ran Zhang, Christine M. Distèche, Jean‐Philippe Vert +4 more

PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition

Harvard Dataverse(2023)10.7910/dvn/hnuusj
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0DataRank
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Maxwell W. Libbrecht, James Jeffry Howbert, Jeff Bilmes, William Stafford Noble, Timothy Durham

Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes

Nature Communications(2024)10.1038/s41467-024-45385-x
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12 citations

Conor K. Camplisson, Qiaoyi Lin, Karen H. Miga, William Stafford Noble, Brian J. Beliveau +1 more

Predicting A/B compartments from histone modifications using deep learning

iScience(2024)10.1016/j.isci.2024.109570
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12 citations

Nitya Thakkar, Hannah L. Harris, Susanna Liu, Megan Zhang, Mark Gerstein +6 more

Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model

Bioinformatics(2024)10.1093/bioinformatics/btae211
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6 citations

Yifeng Liu, Addie Woicik, Minsi Lu, Anupama Jha, Xiao Wang +7 more

Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.01.596967
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19 citations

Jack Freestone, Michael Riffle, Michael J. MacCoss, William Stafford Noble, Uri Keich +1 more

Nascent transcript O-MAP reveals the molecular architecture of a single-locus subnuclear compartment built by RBM20 and the TTN RNA

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.05.622011
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6 citations

Aidan M. Fenix, Daphnée M. Marciniak, Qiaoyi Lin, Sara Bianchi, Borislav H. Hristov +11 more

Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories

Genome Research(2024)10.1101/gr.278327.123
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1 citations

William Stafford Noble, Alessandro Bertero, Borislav H. Hristov

Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment

Nature Methods(2025)10.1038/s41592-025-02719-x
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39 citations

Jack Freestone, Michael Riffle, Michael J. MacCoss, William Stafford Noble, Uri Keich +1 more

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics

Nature Communications(2025)10.1038/s41467-025-64928-4
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0DataRank · unranked
12 citations

Chris Hsu, David Shteynberg, Wen-Feng Zeng, Michael Riffle, Alexis Chang +8 more