William Stafford Noble

According to our database1, William Stafford Noble authored at least 129 papers between 1996 and 2019.

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Bibliography

2019
Submodular Generalized Matching for Peptide Identification in Tandem Mass Spectrometry.
IEEE/ACM Trans. Comput. Biology Bioinform., 2019

Response to comments on 'Empirical comparison of web-based antimicrobial peptide prediction tools'.
Bioinformatics, 2019

2018
GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs.
Bioinformatics, 2018

Unsupervised embedding of single-cell Hi-C data.
Bioinformatics, 2018

Segway 2.0: Gaussian mixture models and minibatch training.
Bioinformatics, 2018

DeepPINK: reproducible feature selection in deep neural networks.
Proceedings of the Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, 2018

Submodular Maximization via Gradient Ascent: The Case of Deep Submodular Functions.
Proceedings of the Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, 2018

Choosing Non-redundant Representative Subsets Of Protein Sequence Data Sets Using Submodular Optimization.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

Unveiling Elements of Genomic Architecture with Genome Wide Chromatin Conformation Capture.
Proceedings of the AMIA 2018, 2018

2017
Learning Models of Biological Sequences.
Proceedings of the Encyclopedia of Machine Learning and Data Mining, 2017

Ten simple rules for writing a response to reviewers.
PLoS Computational Biology, 2017

Finding the optimal bayesian network given a constraint graph.
PeerJ PrePrints, 2017

Finding the optimal Bayesian network given a constraint graph.
PeerJ Computer Science, 2017

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.
Bioinformatics, 2017

DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.
Bioinformatics, 2017

Empirical comparison of web-based antimicrobial peptide prediction tools.
Bioinformatics, 2017

Progressive Calibration and Averaging for Tandem Mass Spectrometry Statistical Confidence Estimation: Why Settle for a Single Decoy?
Proceedings of the Research in Computational Molecular Biology, 2017

Training Compressed Fully-Connected Networks with a Density-Diversity Penalty.
Proceedings of the 5th International Conference on Learning Representations, 2017

2016
Faster and more accurate graphical model identification of tandem mass spectra using trellises.
Bioinformatics, 2016

MCAST: scanning for cis-regulatory motif clusters.
Bioinformatics, 2016

Bipartite matching generalizations for peptide identification in tandem mass spectrometry.
Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2015
Predictive model of 3D domain formation via CTCF-mediated extrusion.
Proc. Natl. Acad. Sci. U.S.A., 2015

The MEME Suite.
Nucleic Acids Research, 2015

Entropic Graph-based Posterior Regularization.
Proceedings of the 32nd International Conference on Machine Learning, 2015

Template Scoring Methods for Protein Torsion Angle Prediction.
Proceedings of the Biomedical Engineering Systems and Technologies, 2015

Constructing Structural Profiles for Protein Torsion Angle Prediction.
Proceedings of the BIOINFORMATICS 2015, 2015

2014
Inferring Clonal Composition from Multiple Sections of a Breast Cancer.
PLoS Computational Biology, 2014

Comparative analysis of metazoan chromatin organization Open.
Nature, 2014

A statistical approach for inferring the 3D structure of the genome.
Bioinformatics, 2014

Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry.
Proceedings of the Thirtieth Conference on Uncertainty in Artificial Intelligence, 2014

2013
Session Introduction.
Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Unsupervised pattern discovery in human chromatin structure through genomic segmentation.
Proceedings of the ACM Conference on Bioinformatics, 2013

2012
Faster Mass Spectrometry-Based Protein Inference: Junction Trees Are More Efficient than Sampling and Marginalization by Enumeration.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

Computational and Statistical Analysis of Protein Mass Spectrometry Data.
PLoS Computational Biology, 2012

Estimating relative abundances of proteins from shotgun proteomics data.
BMC Bioinformatics, 2012

A cross-validation scheme for machine learning algorithms in shotgun proteomics.
BMC Bioinformatics, 2012

Epigenetic priors for identifying active transcription factor binding sites.
Bioinformatics, 2012

Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra.
Proceedings of the Twenty-Eighth Conference on Uncertainty in Artificial Intelligence, 2012

The Structure and Function of Chromatin and Chromosomes.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

A statistical approach to peptide identification from clustered tandem mass spectrometry data.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

2011
Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding.
PLoS Computational Biology, 2011

Exploratory analysis of genomic segmentations with Segtools.
BMC Bioinformatics, 2011

Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure.
BMC Bioinformatics, 2011

Improved similarity scores for comparing motifs.
Bioinformatics, 2011

FIMO: scanning for occurrences of a given motif.
Bioinformatics, 2011

A Three-Dimensional Model of the Yeast Genome.
Proceedings of the Research in Computational Molecular Biology, 2011

Protein Interaction Networks: Protein Domain Interaction and Protein Function Prediction.
Proceedings of the Handbook of Statistical Bioinformatics., 2011

2010
Learning Models of Biological Sequences.
Proceedings of the Encyclopedia of Machine Learning, 2010

Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens.
PLoS Computational Biology, 2010

High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions.
PLoS Computational Biology, 2010

Large-scale prediction of protein-protein interactions from structures.
BMC Bioinformatics, 2010

Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo.
BMC Bioinformatics, 2010

The Genomedata format for storing large-scale functional genomics data.
Bioinformatics, 2010

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data.
Bioinformatics [ISMB], 2010

Predicting Nucleosome Positioning Using Multiple Evidence Tracks.
Proceedings of the Research in Computational Molecular Biology, 2010

2009
A Quick Guide to Organizing Computational Biology Projects.
PLoS Computational Biology, 2009

MEME SUITE: tools for motif discovery and searching.
Nucleic Acids Research, 2009

RANKPROP: a web server for protein remote homology detection.
Bioinformatics, 2009

QVALITY: non-parametric estimation of q-values and posterior error probabilities.
Bioinformatics, 2009

Assessing phylogenetic motif models for predicting transcription factor binding sites.
Bioinformatics, 2009

On the Relationship between DNA Periodicity and Local Chromatin Structure.
Proceedings of the Research in Computational Molecular Biology, 2009

2008
Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks.
PLoS Computational Biology, 2008

Predicting Co-Complexed Protein Pairs from Heterogeneous Data.
PLoS Computational Biology, 2008

Predicting Human Nucleosome Occupancy from Primary Sequence.
PLoS Computational Biology, 2008

Combining classifiers for improved classification of proteins from sequence or structure.
BMC Bioinformatics, 2008

Automated mapping of large-scale chromatin structure in ENCODE.
Bioinformatics, 2008

Multi-Scale Correlations in Continuous Genomic Data.
Proceedings of the Biocomputing 2008, 2008

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Improved network-based identification of protein orthologs.
Proceedings of the ECCB'08 Proceedings, 2008

Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry.
Proceedings of the ECCB'08 Proceedings, 2008

2007
Multi-class Protein Classification Using Adaptive Codes.
J. Mach. Learn. Res., 2007

A new pairwise kernel for biological network inference with support vector machines.
BMC Bioinformatics, 2007

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.
BMC Bioinformatics, 2007

NIPS workshop on New Problems and Methods in Computational Biology.
BMC Bioinformatics, 2007

A structural alignment kernel for protein structures.
Bioinformatics, 2007

Unsupervised segmentation of continuous genomic data.
Bioinformatics, 2007

Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions.
Proceedings of the Research in Computational Molecular Biology, 2007

2006
Automated Validation of Polymerase Chain Reaction Amplicon Melting Curves.
J. Bioinformatics and Computational Biology, 2006

Protein Ranking by Semi-Supervised Network Propagation.
BMC Bioinformatics, 2006

Choosing negative examples for the prediction of protein-protein interactions.
BMC Bioinformatics, 2006

Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure.
Bioinformatics, 2006

Efficient identification of DNA hybridization partners in a sequence database.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

Nonstationary kernel combination.
Proceedings of the Machine Learning, 2006

Semi-Supervised Protein Classification Using Cluster Kernels.
Proceedings of the Semi-Supervised Learning, 2006

2005
Guest Editor's Introduction to the Special Issue: Machine Learning for Bioinformatics-Part 2.
IEEE/ACM Trans. Comput. Biology Bioinform., 2005

Guest Editors' Introduction to the Special Issue: Machine Learning for Bioinformatics - Part 1.
IEEE/ACM Trans. Comput. Biology Bioinform., 2005

Semi-supervised protein classification using cluster kernels.
Bioinformatics, 2005

Motif-based protein ranking by network propagation.
Bioinformatics, 2005

Kernels for gene regulatory regions.
Proceedings of the Advances in Neural Information Processing Systems 18 [Neural Information Processing Systems, 2005

Predicting the in vivo signature of human gene regulatory sequence.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

Kernel methods for predicting protein-protein interactions.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

Multi-class protein fold recognition using adaptive codes.
Proceedings of the Machine Learning, 2005

A Learned Comparative Expression Measure for Affymetrix GeneChip DNA Microarrays.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005

Automated Validation of Polymerase Chain Reactions Using Amplicon Melting Curves.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005

Peptide Charge State Determination for Low-Resolution Tandem Mass Spectra.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005

2004
Genomic data visualization on the Web.
Bioinformatics, 2004

Support vector machine classification on the web.
Bioinformatics, 2004

Mismatch string kernels for discriminative protein classification.
Bioinformatics, 2004

A statistical framework for genomic data fusion.
Bioinformatics, 2004

Kernel-Based Data Fusion and Its Application to Protein Function Prediction in Yeast.
Proceedings of the Biocomputing 2004, 2004

Learning kernels from biological networks by maximizing entropy.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2003
Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships.
Journal of Computational Biology, 2003

Kernel hierarchical gene clustering from microarray expression data.
Bioinformatics, 2003

Matrix2png: a utility for visualizing matrix data.
Bioinformatics, 2003

The effect of replication on gene expression microarray experiments.
Bioinformatics, 2003

Learning to predict protein-protein interactions from protein sequences.
Bioinformatics, 2003

Semi-supervised Protein Classification Using Cluster Kernels.
Proceedings of the Advances in Neural Information Processing Systems 16 [Neural Information Processing Systems, 2003

Searching for statistically significant regulatory modules.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

2002
Learning Gene Functional Classifications from Multiple Data Types.
Journal of Computational Biology, 2002

Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences.
Journal of Computational Biology, 2002

Combining pairwise sequence similarity and support vector machines for remote protein homology detection.
Proceedings of the Sixth Annual International Conference on Computational Biology, 2002

Exploring Gene Expression Data with Class Scores.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

The Spectrum Kernel: A String Kernel for SVM Protein Classification.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

A Kernel Approach for Learning from Almost Orthogonal Patterns.
Proceedings of the Principles of Data Mining and Knowledge Discovery, 2002

Mismatch String Kernels for SVM Protein Classification.
Proceedings of the Advances in Neural Information Processing Systems 15 [Neural Information Processing Systems, 2002

A Kernel Approach for Learning from almost Orthogonal Patterns.
Proceedings of the Machine Learning: ECML 2002, 2002

2001
Gene functional classification from heterogeneous data.
Proceedings of the Fifth Annual International Conference on Computational Biology, 2001

Promoter Region-Based Classification of Genes.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

Classification of genes using probabilistic models of microarray expression profiles.
Proceedings of the ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2001), 2001

Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

2000
Protein Family Classification Using Sparse Markov Transducers.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

1999
Family pairwise search with embedded motif models.
Bioinformatics, 1999

Classifying proteins by family using the product of correlated p-values.
Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

MEME, MAST, and Meta-MEME: New Tools for Motif Discovery in Protein Sequences.
Proceedings of the Pattern Discovery in Biomolecular Data: Tools, 1999

1998
Homology Detection via Family Pairwise Search.
Journal of Computational Biology, 1998

Family-based homology detection via pairwise sequence comparison.
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998

1997
Meta-MEME: motif-based hidden Markov models of protein families.
Computer Applications in the Biosciences, 1997

1996
Modeling the Evolution of Motivation.
Evolutionary Computation, 1996

ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool.
Computer Applications in the Biosciences, 1996


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