William Stafford Noble

ORCID

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 39

Top Venues

Publications

Jack Freestone, Lukas Käll, William Stafford Noble, Uri Keich
Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis. RECOMB (2024)
Andy Lin, Brooke L. Deatherage Kaiser, Janine R. Hutchison, Jeffrey A. Bilmes, William Stafford Noble
MS1Connect: a mass spectrometry run similarity measure. Bioinform. 39 (2) (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS Comput. Biol. 19 (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 Comput. Biol. 19 (5) (2023)
Brittany Baur, Junha Shin, Jacob Schreiber, Shilu Zhang, Yi Zhang, Mohith Manjunath, Jun S. Song, William Stafford Noble, Sushmita Roy
Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation. PLoS Comput. Biol. 19 (7) (2023)
Winston Chen, William Stafford Noble, Yang Young Lu
DeepROCK: Error-controlled interaction detection in deep neural networks. CoRR (2023)
Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble
Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning. J. Comput. Biol. 29 (11) (2022)
Kayvon Mazooji, Sreeram Kannan, William Stafford Noble, Ilan Shomorony
Fundamental Limits of Multi-Sample Flow Graph Decomposition. ISIT (2022)
Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh
Single-Cell Multiomics Integration by SCOT. J. Comput. Biol. 29 (1) (2022)
Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh
SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport. J. Comput. Biol. 29 (1) (2022)
Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble
Semi-supervised Single-Cell Cross-modality Translation Using Polarbear. RECOMB (2022)
Jacob M. Schreiber, Jeffrey A. Bilmes, William Stafford Noble
Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data. Bioinform. 37 (4) (2021)
Yang Young Lu, Timothy C. Yu, Giancarlo Bonora, William Stafford Noble
ACE: Explaining cluster from an adversarial perspective. ICML (2021)
Yang Young Lu, Jeff A. Bilmes, Ricard A. Rodriguez-Mias, Judit Villén, William Stafford Noble
DIAmeter: matching peptides to data-independent acquisition mass spectrometry data. Bioinform. 37 (Supplement) (2021)
Dejun Lin, Justin Sanders, William Stafford Noble
HiCRep.py: fast comparison of Hi-C contact matrices in Python. Bioinform. 37 (18) (2021)
Yang Young Lu, Wenbo Guo, Xinyu Xing, William Stafford Noble
DANCE: Enhancing saliency maps using decoys. ICML (2021)
Hyeon-Jin Kim, Galip Gürkan Yardimci, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B. Ware, Jay Shendure, Zhi-jun Duan, William Stafford Noble
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. PLoS Comput. Biol. 16 (9) (2020)
Jacob M. Schreiber, Jeffrey A. Bilmes, William Stafford Noble
apricot: Submodular selection for data summarization in Python. J. Mach. Learn. Res. 21 (2020)
Yang Lu, Wenbo Guo, Xinyu Xing, William Stafford Noble
Robust saliency maps with decoy-enhanced saliency score. CoRR (2020)
Wei Yang, Jeffrey A. Bilmes, William Stafford Noble
Submodular sketches of single-cell RNA-seq measurements. BCB (2020)
Kristen Emery, Syamand Hasam, William Stafford Noble, Uri Keich
Multiple Competition-Based FDR Control and Its Application to Peptide Detection. RECOMB (2020)
Ritambhara Singh, Pinar Demetci, Giancarlo Bonora, Vijay Ramani, Choli Lee, He Fang, Zhi-jun Duan, Xinxian Deng, Jay Shendure, Christine Disteche, William Stafford Noble
Unsupervised manifold alignment for single-cell multi-omics data. BCB (2020)
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 Comput. Biol. 15 (9) (2019)
Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, William Stafford Noble
Jointly Embedding Multiple Single-Cell Omics Measurements. WABI (2019)
Musa Nur Gabere, William Stafford Noble
Response to comments on 'Empirical comparison of web-based antimicrobial peptide prediction tools'. Bioinform. 35 (15) (2019)
Jacob M. Schreiber, Jeffrey A. Bilmes, William Stafford Noble
apricot: Submodular selection for data summarization in Python. CoRR (2019)
Alexandra Gesine Cauer, Gürkan Yardimci, Jean-Philippe Vert, Nelle Varoquaux, William Stafford Noble
Inferring Diploid 3D Chromatin Structures from Hi-C Data. WABI (2019)
Yang Young Lu, Yingying Fan, Jinchi Lv, William Stafford Noble
DeepPINK: reproducible feature selection in deep neural networks. NeurIPS (2018)
Oana Ursu, Nathan Boley, Maryna Taranova, Y. X. Rachel Wang, Galip Gürkan Yardimci, William Stafford Noble, Anshul Kundaje
GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs. Bioinform. 34 (16) (2018)
Rachel C. W. Chan, Maxwell W. Libbrecht, Eric G. Roberts, Jeffrey A. Bilmes, William Stafford Noble, Michael M. Hoffman
Segway 2.0: Gaussian mixture models and minibatch training. Bioinform. 34 (4) (2018)
Maxwell W. Libbrecht, Jeffrey A. Bilmes, William Stafford Noble
Choosing Non-redundant Representative Subsets Of Protein Sequence Data Sets Using Submodular Optimization. BCB (2018)
Yang Young Lu, Yingying Fan, Jinchi Lv, William Stafford Noble
DeepPINK: reproducible feature selection in deep neural networks. CoRR (2018)
Jie Liu, Dejun Lin, Galip Gürkan Yardimci, William Stafford Noble
Unsupervised embedding of single-cell Hi-C data. Bioinform. 34 (13) (2018)
Wenruo Bai, William Stafford Noble, Jeff A. Bilmes
Submodular Maximization via Gradient Ascent: The Case of Deep Submodular Functions. NeurIPS (2018)
Musa Nur Gabere, William Stafford Noble
Empirical comparison of web-based antimicrobial peptide prediction tools. Bioinform. 33 (13) (2017)
William Stafford Noble
Ten simple rules for writing a response to reviewers. PLoS Comput. Biol. 13 (10) (2017)
Uri Keich, William Stafford Noble
Progressive Calibration and Averaging for Tandem Mass Spectrometry Statistical Confidence Estimation: Why Settle for a Single Decoy? RECOMB (2017)
Wenxiu Ma, Lin Yang, Remo Rohs, William Stafford Noble
DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding. Bioinform. 33 (19) (2017)
Charles E. Grant, James Johnson, Timothy L. Bailey, William Stafford Noble
-regulatory motif clusters. Bioinform. 32 (8) (2016)
Galip Gürkan Yardimci, William Stafford Noble
Predictive model of 3D domain formation via CTCF-mediated extrusion. Proc. Natl. Acad. Sci. USA 112 (47) (2015)
Zafer Aydin, David Baker, William Stafford Noble
Template Scoring Methods for Protein Torsion Angle Prediction. BIOSTEC (Selected Papers) (2015)
Zafer Aydin, David Baker, William Stafford Noble
Constructing Structural Profiles for Protein Torsion Angle Prediction. BIOINFORMATICS (2015)
Maxwell W. Libbrecht, Michael M. Hoffman, Jeff A. Bilmes, William Stafford Noble
Entropic Graph-based Posterior Regularization. ICML (2015)
Habil Zare, Junfeng Wang, Alex Hu, Kris Weber, Joshua D. Smith, Deborah A. Nickerson, ChaoZhong Song, Daniela M. Witten, C. Anthony Blau, William Stafford Noble
Inferring Clonal Composition from Multiple Sections of a Breast Cancer. PLoS Comput. Biol. 10 (7) (2014)
John T. Halloran, Jeff A. Bilmes, William Stafford Noble
Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry. UAI (2014)
Nelle Varoquaux, Ferhat Ay, William Stafford Noble, Jean-Philippe Vert
A statistical approach for inferring the 3D structure of the genome. Bioinform. 30 (12) (2014)
Michael M. Hoffman, Orion J. Buske, Jie Wang, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. BCB (2013)
Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng
Session Introduction. Pacific Symposium on Biocomputing (2013)
Viktor Granholm, William Stafford Noble, Lukas Käll
A cross-validation scheme for machine learning algorithms in shotgun proteomics. BMC Bioinform. 13 (S-16) (2012)
Gabriel Cuéllar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, Timothy L. Bailey
Epigenetic priors for identifying active transcription factor binding sites. Bioinform. 28 (1) (2012)
William Stafford Noble, C. Anthony Blau, Job Dekker, Zhi-jun Duan, Yi Mao
The Structure and Function of Chromatin and Chromosomes. Pacific Symposium on Biocomputing (2012)
William Stafford Noble, Michael J. MacCoss
Computational and Statistical Analysis of Protein Mass Spectrometry Data. PLoS Comput. Biol. 8 (1) (2012)
Sean McIlwain, Michael Mathews, Michael Bereman, Edwin W. Rubel, Michael J. MacCoss, William Stafford Noble
Estimating relative abundances of proteins from shotgun proteomics data. BMC Bioinform. 13 (2012)
Ajit P. Singh, John T. Halloran, Jeff A. Bilmes, Katrin Kirchhoff, William Stafford Noble
Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra. UAI (2012)
Oliver Serang, William Stafford Noble
Faster Mass Spectrometry-Based Protein Inference: Junction Trees Are More Efficient than Sampling and Marginalization by Enumeration. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (3) (2012)
Ajit P. Singh, John T. Halloran, Jeff A. Bilmes, Katrin Kirchhoff, William Stafford Noble
Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra CoRR (2012)
Iain Melvin, Jason Weston, William Stafford Noble, Christina S. Leslie
Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding. PLoS Comput. Biol. 7 (1) (2011)
Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William Stafford Noble, Uri Keich
Improved similarity scores for comparing motifs. Bioinform. 27 (12) (2011)
Zafer Aydin, Ajit P. Singh, Jeff A. Bilmes, William Stafford Noble
Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure. BMC Bioinform. 12 (2011)
Orion J. Buske, Michael M. Hoffman, Nadia Ponts, Karine G. Le Roch, William Stafford Noble
Exploratory analysis of genomic segmentations with Segtools. BMC Bioinform. 12 (2011)
William Stafford Noble, Zhi-jun Duan, Mirela Andronescu, Kevin Schutz, Sean McIlwain, Yoo Jung Kim, Choli Lee, Jay Shendure, Stanley Fields, C. Anthony Blau
A Three-Dimensional Model of the Yeast Genome. RECOMB (2011)
Charles E. Grant, Timothy L. Bailey, William Stafford Noble
FIMO: scanning for occurrences of a given motif. Bioinform. 27 (7) (2011)
Sheila M. Reynolds, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble
Predicting Nucleosome Positioning Using Multiple Evidence Tracks. RECOMB (2010)
Zafer Aydin, John I. Murray, Robert H. Waterston, William Stafford Noble
embryo. BMC Bioinform. 11 (2010)
Sheila M. Reynolds, Jeff A. Bilmes, William Stafford Noble
. PLoS Comput. Biol. 6 (7) (2010)
Michael M. Hoffman, Orion J. Buske, William Stafford Noble
The Genomedata format for storing large-scale functional genomics data. Bioinform. 26 (11) (2010)
Xiaoyu Chen, Michael M. Hoffman, Jeff A. Bilmes, Jay R. Hesselberth, William Stafford Noble
A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinform. 26 (12) (2010)
Martial Hue, Michael Riffle, Jean-Philippe Vert, William Stafford Noble
Large-scale prediction of protein-protein interactions from structures. BMC Bioinform. 11 (2010)
Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble, Christina S. Leslie
Binding Predictions. PLoS Comput. Biol. 6 (9) (2010)
Sheila M. Reynolds, Jeff A. Bilmes, William Stafford Noble
On the Relationship between DNA Periodicity and Local Chromatin Structure. RECOMB (2009)
Lukas Käll, John D. Storey, William Stafford Noble
-values and posterior error probabilities. Bioinform. 25 (7) (2009)
Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin C. Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William Stafford Noble
MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Iain Melvin, Jason Weston, Christina S. Leslie, William Stafford Noble
RANKPROP: a web server for protein remote homology detection. Bioinform. 25 (1) (2009)
William Stafford Noble
A Quick Guide to Organizing Computational Biology Projects. PLoS Comput. Biol. 5 (7) (2009)
John Hawkins, Charles E. Grant, William Stafford Noble, Timothy L. Bailey
Assessing phylogenetic motif models for predicting transcription factor binding sites. Bioinform. 25 (12) (2009)
Jian Qiu, William Stafford Noble
Predicting Co-Complexed Protein Pairs from Heterogeneous Data. PLoS Comput. Biol. 4 (4) (2008)
Robert E. Thurman, William Stafford Noble, John A. Stamatoyannopoulos
Multi-Scale Correlations in Continuous Genomic Data. Pacific Symposium on Biocomputing (2008)
Iain Melvin, Jason Weston, Christina S. Leslie, William Stafford Noble
Combining classifiers for improved classification of proteins from sequence or structure. BMC Bioinform. 9 (2008)
Aaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael J. MacCoss, William Stafford Noble
Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. ISMB (2008)
Lukas Käll, John D. Storey, William Stafford Noble
Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. ECCB (2008)
Nir Yosef, Roded Sharan, William Stafford Noble
Improved network-based identification of protein orthologs. ECCB (2008)
Heng Lian, William A. Thompson, Robert E. Thurman, John A. Stamatoyannopoulos, William Stafford Noble, Charles E. Lawrence
Automated mapping of large-scale chromatin structure in ENCODE. Bioinform. 24 (17) (2008)
Shobhit Gupta, Jonathan H. Dennis, Robert E. Thurman, Robert E. Kingston, John A. Stamatoyannopoulos, William Stafford Noble
Predicting Human Nucleosome Occupancy from Primary Sequence. PLoS Comput. Biol. 4 (8) (2008)
Sheila M. Reynolds, Lukas Käll, Michael Riffle, Jeff A. Bilmes, William Stafford Noble
Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks. PLoS Comput. Biol. 4 (11) (2008)
Jean-Philippe Vert, Jian Qiu, William Stafford Noble
A new pairwise kernel for biological network inference with support vector machines. BMC Bioinform. 8 (S-10) (2007)
Gal Chechik, Christina S. Leslie, William Stafford Noble, Gunnar Rätsch, Quaid Morris, Koji Tsuda
NIPS workshop on New Problems and Methods in Computational Biology. BMC Bioinform. 8 (S-10) (2007)
Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, William Stafford Noble, Christina S. Leslie
SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. BMC Bioinform. 8 (S-4) (2007)
Iain Melvin, Eugene Ie, Jason Weston, William Stafford Noble, Christina S. Leslie
Multi-class Protein Classification Using Adaptive Codes. J. Mach. Learn. Res. 8 (2007)
Jian Qiu, Martial Hue, Asa Ben-Hur, Jean-Philippe Vert, William Stafford Noble
A structural alignment kernel for protein structures. Bioinform. 23 (9) (2007)
Nathan Day, Andrew Hemmaplardh, Robert E. Thurman, John A. Stamatoyannopoulos, William Stafford Noble
Unsupervised segmentation of continuous genomic data. Bioinform. 23 (11) (2007)
Aaron A. Klammer, Xianhua Yi, Michael J. MacCoss, William Stafford Noble
Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions. RECOMB (2007)
Darrin P. Lewis, Tony Jebara, William Stafford Noble
Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure. Bioinform. 22 (22) (2006)
Darrin P. Lewis, Tony Jebara, William Stafford Noble
Nonstationary kernel combination. ICML (2006)
Tobias P. Mann, Richard Humbert, John A. Stamatoyannopoulos, William Stafford Noble
Automated Validation of Polymerase Chain Reaction Amplicon Melting Curves. J. Bioinform. Comput. Biol. 4 (2) (2006)
Jean-Philippe Vert, Jian Qiu, William Stafford Noble
Metric learning pairwise kernel for graph inference CoRR (2006)
Tobias P. Mann, William Stafford Noble
Efficient identification of DNA hybridization partners in a sequence database. ISMB (Supplement of Bioinformatics) (2006)
Jason Weston, Rui Kuang, Christina S. Leslie, William Stafford Noble
Protein Ranking by Semi-Supervised Network Propagation. BMC Bioinform. 7 (S-1) (2006)
Asa Ben-Hur, William Stafford Noble
Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinform. 7 (S-1) (2006)
Jean-Philippe Vert, Robert E. Thurman, William Stafford Noble
Kernels for gene regulatory regions. NIPS (2005)
Asa Ben-Hur, William Stafford Noble
Kernel methods for predicting protein-protein interactions. ISMB (Supplement of Bioinformatics) (2005)

William Stafford Noble.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

William Stafford Noble