William Stafford Noble

143 papers A* 7A 3B 10C 5Misc 6Journal 89Unranked 19

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Foundation model for mass spectrometry proteomics. CoRR Justin Sanders, Melih Yilmaz, Jacob H. Russell, Wout Bittremieux, William Fondrie, Nicholas M. Riley, Sewoong Oh, William Stafford Noble
2024	J	`jnl`	A BLAST from the past: revisiting blastp's Bioinform. Yang Young Lu, William Stafford Noble, Uri Keich
2024	J	`jnl`	A learned score function improves the power of mass spectrometry database search. Bioinform. Varun Ananth, Justin Sanders, Melih Yilmaz, Bo Wen, Sewoong Oh, William Stafford Noble
2024	J	`jnl`	Error-controlled non-additive interaction discovery in machine learning models. CoRR Winston Chen, Yifan Jiang, William Stafford Noble, Yang Young Lu
2024	B	`conf`	Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis. RECOMB Jack Freestone, Lukas Käll, William Stafford Noble, Uri Keich
2023	J	`jnl`	DeepROCK: Error-controlled interaction detection in deep neural networks. CoRR Winston Chen, William Stafford Noble, Yang Young Lu
2023	J	`jnl`	LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis. Bioinform. Laetitia Meng-Papaxanthos, Ran Zhang, Gang Li, Marco Cuturi, William Stafford Noble, Jean-Philippe Vert
2023	J	`jnl`	Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation. PLoS Comput. Biol. Brittany Baur, Junha Shin, Jacob Schreiber, Shilu Zhang, Yi Zhang, Mohith Manjunath, Jun S. Song, William Stafford Noble, Sushmita Roy
2023	J	`jnl`	MS1Connect: a mass spectrometry run similarity measure. Bioinform. Andy Lin, Brooke L. Deatherage Kaiser, Janine R. Hutchison, Jeffrey A. Bilmes, William Stafford Noble
2023	J	`jnl`	Matrix prior for data transfer between single cell data types in latent Dirichlet allocation. PLoS Comput. Biol. Alan Min, Timothy Durham, Louis Gevirtzman, William Stafford Noble
2023	J	`jnl`	Ten simple rules for defining a computational biology project. PLoS Comput. Biol. William Stafford Noble
2022	B	`conf`	Fundamental Limits of Multi-Sample Flow Graph Decomposition. ISIT Kayvon Mazooji, Sreeram Kannan, William Stafford Noble, Ilan Shomorony
2022	J	`jnl`	Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition. Bioinform. Jack Freestone, Temana Short, William Stafford Noble, Uri Keich
2022	J	`jnl`	Linking cells across single-cell modalities by synergistic matching of neighborhood structure. Bioinform. Borislav H. Hristov, Jeff A. Bilmes, William Stafford Noble
2022	J	`jnl`	Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning. J. Comput. Biol. Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble
2022	J	`jnl`	SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport. J. Comput. Biol. Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh
2022	B	`conf`	Semi-supervised Single-Cell Cross-modality Translation Using Polarbear. RECOMB Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble
2022	J	`jnl`	Single-Cell Multiomics Integration by SCOT. J. Comput. Biol. Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh
2021	A*	`conf`	ACE: Explaining cluster from an adversarial perspective. ICML Yang Young Lu, Timothy C. Yu, Giancarlo Bonora, William Stafford Noble
2021	A*	`conf`	DANCE: Enhancing saliency maps using decoys. ICML Yang Young Lu, Wenbo Guo, Xinyu Xing, William Stafford Noble
2021	J	`jnl`	DIAmeter: matching peptides to data-independent acquisition mass spectrometry data. Bioinform. Yang Young Lu, Jeff A. Bilmes, Ricard A. Rodriguez-Mias, Judit Villén, William Stafford Noble
2021	J	`jnl`	HiCRep.py: fast comparison of Hi-C contact matrices in Python. Bioinform. Dejun Lin, Justin Sanders, William Stafford Noble
2021	J	`jnl`	Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data. Bioinform. Jacob M. Schreiber, Jeffrey A. Bilmes, William Stafford Noble
2020	J	`jnl`	Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. PLoS Comput. Biol. 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
2020	B	`conf`	Multiple Competition-Based FDR Control and Its Application to Peptide Detection. RECOMB Kristen Emery, Syamand Hasam, William Stafford Noble, Uri Keich
2020	J	`jnl`	Robust saliency maps with decoy-enhanced saliency score. CoRR Yang Lu, Wenbo Guo, Xinyu Xing, William Stafford Noble
2020	—	`conf`	Submodular sketches of single-cell RNA-seq measurements. BCB Wei Yang, Jeffrey A. Bilmes, William Stafford Noble
2020	—	`conf`	Unsupervised manifold alignment for single-cell multi-omics data. BCB Ritambhara Singh, Pinar Demetci, Giancarlo Bonora, Vijay Ramani, Choli Lee, He Fang, Zhi-jun Duan, Xinxian Deng, Jay Shendure, Christine Disteche, William Stafford Noble
2020	J	`jnl`	apricot: Submodular selection for data summarization in Python. J. Mach. Learn. Res. Jacob M. Schreiber, Jeffrey A. Bilmes, William Stafford Noble
2019	C	`conf`	Inferring Diploid 3D Chromatin Structures from Hi-C Data. WABI Alexandra Gesine Cauer, Gürkan Yardimci, Jean-Philippe Vert, Nelle Varoquaux, William Stafford Noble
2019	C	`conf`	Jointly Embedding Multiple Single-Cell Omics Measurements. WABI Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, William Stafford Noble
2019	J	`jnl`	Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features. PLoS Comput. Biol. David F. Read, Kate Cook, Yang Young Lu, Karine G. Le Roch, William Stafford Noble
2019	J	`jnl`	Response to comments on 'Empirical comparison of web-based antimicrobial peptide prediction tools'. Bioinform. Musa Nur Gabere, William Stafford Noble
2019	J	`jnl`	apricot: Submodular selection for data summarization in Python. CoRR Jacob M. Schreiber, Jeffrey A. Bilmes, William Stafford Noble
2018	—	`conf`	Choosing Non-redundant Representative Subsets Of Protein Sequence Data Sets Using Submodular Optimization. BCB Maxwell W. Libbrecht, Jeffrey A. Bilmes, William Stafford Noble
2018	A*	`conf`	DeepPINK: reproducible feature selection in deep neural networks. NeurIPS Yang Young Lu, Yingying Fan, Jinchi Lv, William Stafford Noble
2018	J	`jnl`	DeepPINK: reproducible feature selection in deep neural networks. CoRR Yang Young Lu, Yingying Fan, Jinchi Lv, William Stafford Noble
2018	J	`jnl`	GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs. Bioinform. Oana Ursu, Nathan Boley, Maryna Taranova, Y. X. Rachel Wang, Galip Gürkan Yardimci, William Stafford Noble, Anshul Kundaje
2018	J	`jnl`	Segway 2.0: Gaussian mixture models and minibatch training. Bioinform. Rachel C. W. Chan, Maxwell W. Libbrecht, Eric G. Roberts, Jeffrey A. Bilmes, William Stafford Noble, Michael M. Hoffman
2018	A*	`conf`	Submodular Maximization via Gradient Ascent: The Case of Deep Submodular Functions. NeurIPS Wenruo Bai, William Stafford Noble, Jeff A. Bilmes
2018	J	`jnl`	Unsupervised embedding of single-cell Hi-C data. Bioinform. Jie Liu, Dejun Lin, Galip Gürkan Yardimci, William Stafford Noble
2017	J	`jnl`	DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding. Bioinform. Wenxiu Ma, Lin Yang, Remo Rohs, William Stafford Noble
2017	J	`jnl`	Empirical comparison of web-based antimicrobial peptide prediction tools. Bioinform. Musa Nur Gabere, William Stafford Noble
2017	—	`ch.`	Learning Models of Biological Sequences. Encyclopedia of Machine Learning and Data Mining William Stafford Noble, Christina S. Leslie
2017	B	`conf`	Progressive Calibration and Averaging for Tandem Mass Spectrometry Statistical Confidence Estimation: Why Settle for a Single Decoy? RECOMB Uri Keich, William Stafford Noble
2017	J	`jnl`	Ten simple rules for writing a response to reviewers. PLoS Comput. Biol. William Stafford Noble
2016	J	`jnl`	MCAST: scanning for Bioinform. Charles E. Grant, James Johnson, Timothy L. Bailey, William Stafford Noble
2015	—	`conf`	Constructing Structural Profiles for Protein Torsion Angle Prediction. BIOINFORMATICS Zafer Aydin, David Baker, William Stafford Noble
2015	A*	`conf`	Entropic Graph-based Posterior Regularization. ICML Maxwell W. Libbrecht, Michael M. Hoffman, Jeff A. Bilmes, William Stafford Noble
2015	J	`jnl`	Predictive model of 3D domain formation via CTCF-mediated extrusion. Proc. Natl. Acad. Sci. USA Galip Gürkan Yardimci, William Stafford Noble
2015	—	`conf`	Template Scoring Methods for Protein Torsion Angle Prediction. BIOSTEC (Selected Papers) Zafer Aydin, David Baker, William Stafford Noble
2014	J	`jnl`	A statistical approach for inferring the 3D structure of the genome. Bioinform. Nelle Varoquaux, Ferhat Ay, William Stafford Noble, Jean-Philippe Vert
2014	J	`jnl`	Inferring Clonal Composition from Multiple Sections of a Breast Cancer. PLoS Comput. Biol. 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
2014	A	`conf`	Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry. UAI John T. Halloran, Jeff A. Bilmes, William Stafford Noble
2013	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng
2013	—	`conf`	Unsupervised pattern discovery in human chromatin structure through genomic segmentation. BCB Michael M. Hoffman, Orion J. Buske, Jie Wang, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble
2012	J	`jnl`	A cross-validation scheme for machine learning algorithms in shotgun proteomics. BMC Bioinform. Viktor Granholm, William Stafford Noble, Lukas Käll
2012	J	`jnl`	Computational and Statistical Analysis of Protein Mass Spectrometry Data. PLoS Comput. Biol. William Stafford Noble, Michael J. MacCoss
2012	J	`jnl`	Epigenetic priors for identifying active transcription factor binding sites. Bioinform. Gabriel Cuéllar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, Timothy L. Bailey
2012	J	`jnl`	Estimating relative abundances of proteins from shotgun proteomics data. BMC Bioinform. Sean McIlwain, Michael Mathews, Michael Bereman, Edwin W. Rubel, Michael J. MacCoss, William Stafford Noble
2012	J	`jnl`	Faster Mass Spectrometry-Based Protein Inference: Junction Trees Are More Efficient than Sampling and Marginalization by Enumeration. IEEE ACM Trans. Comput. Biol. Bioinform. Oliver Serang, William Stafford Noble
2012	J	`jnl`	Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra CoRR Ajit P. Singh, John T. Halloran, Jeff A. Bilmes, Katrin Kirchhoff, William Stafford Noble
2012	A	`conf`	Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra. UAI Ajit P. Singh, John T. Halloran, Jeff A. Bilmes, Katrin Kirchhoff, William Stafford Noble
2012	Misc	`conf`	The Structure and Function of Chromatin and Chromosomes. Pacific Symposium on Biocomputing William Stafford Noble, C. Anthony Blau, Job Dekker, Zhi-jun Duan, Yi Mao
2011	B	`conf`	A Three-Dimensional Model of the Yeast Genome. RECOMB William Stafford Noble, Zhi-jun Duan, Mirela Andronescu, Kevin Schutz, Sean McIlwain, Yoo Jung Kim, Choli Lee, Jay Shendure, Stanley Fields, C. Anthony Blau
2011	J	`jnl`	Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding. PLoS Comput. Biol. Iain Melvin, Jason Weston, William Stafford Noble, Christina S. Leslie
2011	J	`jnl`	Exploratory analysis of genomic segmentations with Segtools. BMC Bioinform. Orion J. Buske, Michael M. Hoffman, Nadia Ponts, Karine G. Le Roch, William Stafford Noble
2011	J	`jnl`	FIMO: scanning for occurrences of a given motif. Bioinform. Charles E. Grant, Timothy L. Bailey, William Stafford Noble
2011	J	`jnl`	Improved similarity scores for comparing motifs. Bioinform. Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William Stafford Noble, Uri Keich
2011	J	`jnl`	Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure. BMC Bioinform. Zafer Aydin, Ajit P. Singh, Jeff A. Bilmes, William Stafford Noble
2011	—	`ch.`	Protein Interaction Networks: Protein Domain Interaction and Protein Function Prediction. Handbook of Statistical Bioinformatics Yanjun Qi, William Stafford Noble
2010	J	`jnl`	A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinform. Xiaoyu Chen, Michael M. Hoffman, Jeff A. Bilmes, Jay R. Hesselberth, William Stafford Noble
2010	J	`jnl`	High Resolution Models of Transcription Factor-DNA Affinities Improve PLoS Comput. Biol. Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble, Christina S. Leslie
2010	J	`jnl`	Large-scale prediction of protein-protein interactions from structures. BMC Bioinform. Martial Hue, Michael Riffle, Jean-Philippe Vert, William Stafford Noble
2010	—	`ch.`	Learning Models of Biological Sequences. Encyclopedia of Machine Learning William Stafford Noble, Christina S. Leslie
2010	J	`jnl`	Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in PLoS Comput. Biol. Sheila M. Reynolds, Jeff A. Bilmes, William Stafford Noble
2010	B	`conf`	Predicting Nucleosome Positioning Using Multiple Evidence Tracks. RECOMB Sheila M. Reynolds, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble
2010	J	`jnl`	The Genomedata format for storing large-scale functional genomics data. Bioinform. Michael M. Hoffman, Orion J. Buske, William Stafford Noble
2010	J	`jnl`	Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing BMC Bioinform. Zafer Aydin, John I. Murray, Robert H. Waterston, William Stafford Noble
2009	J	`jnl`	A Quick Guide to Organizing Computational Biology Projects. PLoS Comput. Biol. William Stafford Noble
2009	J	`jnl`	Assessing phylogenetic motif models for predicting transcription factor binding sites. Bioinform. John Hawkins, Charles E. Grant, William Stafford Noble, Timothy L. Bailey
2009	J	`jnl`	MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin C. Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William Stafford Noble
2009	B	`conf`	On the Relationship between DNA Periodicity and Local Chromatin Structure. RECOMB Sheila M. Reynolds, Jeff A. Bilmes, William Stafford Noble
2009	J	`jnl`	QVALITY: non-parametric estimation of Bioinform. Lukas Käll, John D. Storey, William Stafford Noble
2009	J	`jnl`	RANKPROP: a web server for protein remote homology detection. Bioinform. Iain Melvin, Jason Weston, Christina S. Leslie, William Stafford Noble
2008	J	`jnl`	Automated mapping of large-scale chromatin structure in ENCODE. Bioinform. Heng Lian, William A. Thompson, Robert E. Thurman, John A. Stamatoyannopoulos, William Stafford Noble, Charles E. Lawrence
2008	J	`jnl`	Combining classifiers for improved classification of proteins from sequence or structure. BMC Bioinform. Iain Melvin, Jason Weston, Christina S. Leslie, William Stafford Noble
2008	C	`conf`	Improved network-based identification of protein orthologs. ECCB Nir Yosef, Roded Sharan, William Stafford Noble
2008	A	`conf`	Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. ISMB Aaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael J. MacCoss, William Stafford Noble
2008	Misc	`conf`	Multi-Scale Correlations in Continuous Genomic Data. Pacific Symposium on Biocomputing Robert E. Thurman, William Stafford Noble, John A. Stamatoyannopoulos
2008	C	`conf`	Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. ECCB Lukas Käll, John D. Storey, William Stafford Noble
2008	J	`jnl`	Predicting Co-Complexed Protein Pairs from Heterogeneous Data. PLoS Comput. Biol. Jian Qiu, William Stafford Noble
2008	J	`jnl`	Predicting Human Nucleosome Occupancy from Primary Sequence. PLoS Comput. Biol. Shobhit Gupta, Jonathan H. Dennis, Robert E. Thurman, Robert E. Kingston, John A. Stamatoyannopoulos, William Stafford Noble
2008	J	`jnl`	Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks. PLoS Comput. Biol. Sheila M. Reynolds, Lukas Käll, Michael Riffle, Jeff A. Bilmes, William Stafford Noble
2007	J	`jnl`	A new pairwise kernel for biological network inference with support vector machines. BMC Bioinform. Jean-Philippe Vert, Jian Qiu, William Stafford Noble
2007	J	`jnl`	A structural alignment kernel for protein structures. Bioinform. Jian Qiu, Martial Hue, Asa Ben-Hur, Jean-Philippe Vert, William Stafford Noble
2007	J	`jnl`	Multi-class Protein Classification Using Adaptive Codes. J. Mach. Learn. Res. Iain Melvin, Eugene Ie, Jason Weston, William Stafford Noble, Christina S. Leslie
2007	J	`jnl`	NIPS workshop on New Problems and Methods in Computational Biology. BMC Bioinform. Gal Chechik, Christina S. Leslie, William Stafford Noble, Gunnar Rätsch, Quaid Morris, Koji Tsuda
2007	B	`conf`	Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions. RECOMB Aaron A. Klammer, Xianhua Yi, Michael J. MacCoss, William Stafford Noble
2007	J	`jnl`	SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. BMC Bioinform. Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, William Stafford Noble, Christina S. Leslie
2007	J	`jnl`	Unsupervised segmentation of continuous genomic data. Bioinform. Nathan Day, Andrew Hemmaplardh, Robert E. Thurman, John A. Stamatoyannopoulos, William Stafford Noble
2006	J	`jnl`	Automated Validation of Polymerase Chain Reaction Amplicon Melting Curves. J. Bioinform. Comput. Biol. Tobias P. Mann, Richard Humbert, John A. Stamatoyannopoulos, William Stafford Noble
2006	J	`jnl`	Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinform. Asa Ben-Hur, William Stafford Noble
2006	—	`conf`	Efficient identification of DNA hybridization partners in a sequence database. ISMB (Supplement of Bioinformatics) Tobias P. Mann, William Stafford Noble
2006	J	`jnl`	Metric learning pairwise kernel for graph inference CoRR Jean-Philippe Vert, Jian Qiu, William Stafford Noble
2006	A*	`conf`	Nonstationary kernel combination. ICML Darrin P. Lewis, Tony Jebara, William Stafford Noble
2006	J	`jnl`	Protein Ranking by Semi-Supervised Network Propagation. BMC Bioinform. Jason Weston, Rui Kuang, Christina S. Leslie, William Stafford Noble
2006	—	`ch.`	Semi-Supervised Protein Classification Using Cluster Kernels. Semi-Supervised Learning Jason Weston, Christina S. Leslie, Eugene Ie, William Stafford Noble
2006	J	`jnl`	Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure. Bioinform. Darrin P. Lewis, Tony Jebara, William Stafford Noble
2005	—	`conf`	A Learned Comparative Expression Measure for Affymetrix GeneChip DNA Microarrays. CSB Will Sheffler, Eli Upfal, John Sedivy, William Stafford Noble
2005	—	`conf`	Automated Validation of Polymerase Chain Reactions Using Amplicon Melting Curves. CSB Tobias P. Mann, Richard Humbert, John A. Stamatoyannopoulos, William Stafford Noble
2005	J	`jnl`	Guest Editor's Introduction to the Special Issue: Machine Learning for Bioinformatics-Part 2. IEEE ACM Trans. Comput. Biol. Bioinform. Charles X. Ling, William Stafford Noble, Qiang Yang
2005	J	`jnl`	Guest Editors' Introduction to the Special Issue: Machine Learning for Bioinformatics - Part 1. IEEE ACM Trans. Comput. Biol. Bioinform. Charles X. Ling, William Stafford Noble, Qiang Yang
2005	—	`conf`	Kernel methods for predicting protein-protein interactions. ISMB (Supplement of Bioinformatics) Asa Ben-Hur, William Stafford Noble
2005	—	`conf`	Kernels for gene regulatory regions. NIPS Jean-Philippe Vert, Robert E. Thurman, William Stafford Noble
2005	J	`jnl`	Motif-based protein ranking by network propagation. Bioinform. Rui Kuang, Jason Weston, William Stafford Noble, Christina S. Leslie
2005	A*	`conf`	Multi-class protein fold recognition using adaptive codes. ICML Eugene Ie, Jason Weston, William Stafford Noble, Christina S. Leslie
2005	—	`conf`	Peptide Charge State Determination for Low-Resolution Tandem Mass Spectra. CSB Aaron A. Klammer, Christine C. Wu, Michael J. MacCoss, William Stafford Noble
2005	—	`conf`	Predicting the ISMB (Supplement of Bioinformatics) William Stafford Noble, Scott Kuehn, Robert E. Thurman, Man Yu, John A. Stamatoyannopoulos
2005	J	`jnl`	Semi-supervised protein classification using cluster kernels. Bioinform. Jason Weston, Christina S. Leslie, Eugene Ie, Dengyong Zhou, André Elisseeff, William Stafford Noble
2004	J	`jnl`	A statistical framework for genomic data fusion. Bioinform. Gert R. G. Lanckriet, Tijl De Bie, Nello Cristianini, Michael I. Jordan, William Stafford Noble
2004	J	`jnl`	Genomic data visualization on the Web. Bioinform. Wei Wu, William Stafford Noble
2004	Misc	`conf`	Kernel-Based Data Fusion and Its Application to Protein Function Prediction in Yeast. Pacific Symposium on Biocomputing Gert R. G. Lanckriet, Minghua Deng, Nello Cristianini, Michael I. Jordan, William Stafford Noble
2004	—	`conf`	Learning kernels from biological networks by maximizing entropy. ISMB/ECCB (Supplement of Bioinformatics) Koji Tsuda, William Stafford Noble
2004	J	`jnl`	Mismatch string kernels for discriminative protein classification. Bioinform. Christina S. Leslie, Eleazar Eskin, Adiel Cohen, Jason Weston, William Stafford Noble
2004	J	`jnl`	Support vector machine classification on the web. Bioinform. Paul Pavlidis, Ilan Wapinski, William Stafford Noble
2003	J	`jnl`	Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships. J. Comput. Biol. Li Liao, William Stafford Noble
2003	J	`jnl`	Kernel hierarchical gene clustering from microarray expression data. Bioinform. Jie Qin, Darrin P. Lewis, William Stafford Noble
2003	J	`jnl`	Learning to predict protein-protein interactions from protein sequences. Bioinform. Shawn M. Gomez, William Stafford Noble, Andrey Rzhetsky
2003	J	`jnl`	Matrix2png: a utility for visualizing matrix data. Bioinform. Paul Pavlidis, William Stafford Noble
2003	J	`jnl`	Protein Family Classification Using Sparse Markov Transducers. J. Comput. Biol. Eleazar Eskin, William Stafford Noble, Yoram Singer
2003	C	`conf`	Searching for statistically significant regulatory modules. ECCB Timothy L. Bailey, William Stafford Noble
2003	—	`conf`	Semi-supervised Protein Classification Using Cluster Kernels. NIPS Jason Weston, Christina S. Leslie, Dengyong Zhou, André Elisseeff, William Stafford Noble
2003	J	`jnl`	The effect of replication on gene expression microarray experiments. Bioinform. Paul Pavlidis, Qinghong Li, William Stafford Noble
2002	—	`conf`	A Kernel Approach for Learning from Almost Orthogonal Patterns. PKDD Bernhard Schölkopf, Jason Weston, Eleazar Eskin, Christina S. Leslie, William Stafford Noble
2002	—	`conf`	A Kernel Approach for Learning from almost Orthogonal Patterns. ECML Bernhard Schölkopf, Jason Weston, Eleazar Eskin, Christina S. Leslie, William Stafford Noble
2002	B	`conf`	Combining pairwise sequence similarity and support vector machines for remote protein homology detection. RECOMB Li Liao, William Stafford Noble
2002	Misc	`conf`	Exploring Gene Expression Data with Class Scores. Pacific Symposium on Biocomputing Paul Pavlidis, Darrin P. Lewis, William Stafford Noble
2002	J	`jnl`	Learning Gene Functional Classifications from Multiple Data Types. J. Comput. Biol. Paul Pavlidis, Jason Weston, Jinsong Cai, William Stafford Noble
2002	—	`conf`	Mismatch String Kernels for SVM Protein Classification. NIPS Christina S. Leslie, Eleazar Eskin, Jason Weston, William Stafford Noble
2002	Misc	`conf`	The Spectrum Kernel: A String Kernel for SVM Protein Classification. Pacific Symposium on Biocomputing Christina S. Leslie, Eleazar Eskin, William Stafford Noble
2002	J	`jnl`	Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences. J. Comput. Biol. Eleazar Eskin, William Stafford Noble, Yoram Singer
2001	—	`conf`	Classification of genes using probabilistic models of microarray expression profiles. BIOKDD Paul Pavlidis, Christopher Tang, William Stafford Noble