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William Stafford Noble

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TOP 3
Michael M Hoffman; Manolis Kellis; Anshul Kundaje; Max Libbrecht; Steven P Wilder; Jeffrey A Bilmes; Ewan Birney; Ian Dunham; Paul M Ellenbogen; Jason Ernst; Belinda Giardine; Ross C Hardison; Robert S Harris; William Stafford Noble
Integrative annotation of chromatin elements from ENCODE data.
Marina Spivak; Michael S Bereman; Michael J Maccoss; William Stafford Noble
Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments.
Aaron Arvey; Phaedra Agius; William Stafford Noble; Christina Leslie
Sequence and chromatin determinants of cell-type-specific transcription factor binding.

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All Publications

2013: Michael M Hoffman; Manolis Kellis; Anshul Kundaje; Max Libbrecht; Steven P Wilder; Jeffrey A Bilmes; Ewan Birney; Ian Dunham; Paul M Ellenbogen; Jason Ernst; Belinda Giardine; Ross C Hardison; Robert S Harris; William Stafford Noble
Integrative annotation of chromatin elements from ENCODE data.
Nucleic acids research 2013;41(2):827-41.
2012: Marina Spivak; Michael S Bereman; Michael J Maccoss; William Stafford Noble
Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments.
Journal of proteome research 2012;11(9):4499-508.
2012: Aaron Arvey; Phaedra Agius; William Stafford Noble; Christina Leslie
Sequence and chromatin determinants of cell-type-specific transcription factor binding.
Genome research 2012;22(9):1723-34.
2012: Michael M Hoffman; Jeff A Bilmes; Orion J Buske; Jie Wang; Zhiping Weng; William Stafford Noble
Unsupervised pattern discovery in human chromatin structure through genomic segmentation.
Nature methods 2012;9(5):473-6.
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 transactions on computational biology and bioinformatics / IEEE, ACM 2012;9(3):809-17.
2012: Daniela M Witten; William Stafford Noble
On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements.
Nucleic acids research 2012;40(9):3849-55.
2012: Marina Spivak; Daniela Tomazela; Jason Weston; Michael J MacCoss; William Stafford Noble
Direct maximization of protein identifications from tandem mass spectra.
Molecular & cellular proteomics : MCP 2012;11(2):M111.012161.
2012: Viktor Granholm; William Stafford Noble; Lukas Käll
A cross-validation scheme for machine learning algorithms in shotgun proteomics.
BMC bioinformatics 2012;13 Suppl 16():S3.
2012: Sean McIlwain; Michael S Bereman; Michael J MacCoss; Michael Mathews; Edwin W Rubel; William Stafford Noble
Estimating relative abundances of proteins from shotgun proteomics data.
BMC bioinformatics 2012;13():308.
2012: Yanjun Qi; Jason Weston; Merja Oja; William Stafford Noble
A unified multitask architecture for predicting local protein properties.
PloS one 2012;7(3):e32235.
2012: William Stafford Noble; Michael J MacCoss
Computational and statistical analysis of protein mass spectrometry data.
PLoS computational biology 2012;8(1):e1002296.
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. Pacific Symposium on Biocomputing 2012;():434-40.
2011: Benjamin J Diament; William Stafford Noble
Faster SEQUEST searching for peptide identification from tandem mass spectra.
Journal of proteome research 2011;10(9):3871-9.
2011: Emi Tanaka; Timothy Bailey; Charles E Grant; William Stafford Noble; Uri Keich
Improved similarity scores for comparing motifs.
Bioinformatics (Oxford, England) 2011;27(12):1603-9.
2011: Viktor Granholm; William Stafford Noble; Lukas Käll
On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics.
Journal of proteome research 2011;10(5):2671-8.
2011: Charles E Grant; Timothy Lawrence Bailey; William Stafford Noble
FIMO: scanning for occurrences of a given motif.
Bioinformatics (Oxford, England) 2011;27(7):1017-8.
2011: Orion J Buske; Michael M Hoffman; Karine G Le Roch; Nadia Ponts; William Stafford Noble
Exploratory analysis of genomic segmentations with Segtools.
BMC bioinformatics 2011;12():415.
2011: Zafer Aydin; Jeff Bilmes; Ajit Singh; William Stafford Noble
Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure.
BMC bioinformatics 2011;12():154.
2011: Iain Melvin; Jason Weston; William Stafford Noble; Christina Leslie
Detecting remote evolutionary relationships among proteins by large-scale semantic embedding.
PLoS computational biology 2011;7(1):e1001047.
2010: Oliver Serang; Michael J MacCoss; William Stafford Noble
Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data.
Journal of proteome research 2010;9(10):5346-57.
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.
Bioinformatics (Oxford, England) 2010;26(12):i334-42.
2010: Michael M Hoffman; Orion J Buske; William Stafford Noble
The Genomedata format for storing large-scale functional genomics data.
Bioinformatics (Oxford, England) 2010;26(11):1458-9.
2010: Sean McIlwain; Paul Draghicescu; Pragya Singh; David R Goodlett; William Stafford Noble
Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs.
Journal of proteome research 2010;9(5):2488-95.
2010: Phaedra Agius; Aaron Arvey; William Chang; William Stafford Noble; Christina Leslie
High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.
PLoS computational biology 2010;6(9):.
2010: Sheila M Reynolds; Jeff A Bilmes; William Stafford Noble
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;6(7):e1000834.
2010: Martial Hue; Michael Riffle; Jean-Philippe Vert; William Stafford Noble
Large-scale prediction of protein-protein interactions from structures.
BMC bioinformatics 2010;11():144.
2010: Zafer Aydin; John I Murray; Robert H Waterston; William Stafford Noble
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;11():84.
2009: William Stafford Noble
How does multiple testing correction work?
Nature biotechnology 2009;27(12):1135-7.
2009: William Stafford Noble
A quick guide to organizing computational biology projects.
PLoS computational biology 2009;5(7):e1000424.
2009: Tobias Mann; Richard Humbert; Michael O Dorschner; John A Stamatoyannopoulos; William Stafford Noble
A thermodynamic approach to PCR primer design.
Nucleic acids research 2009;37(13):e95.
2009: Marina Spivak; Jason Weston; Léon Bottou; Lukas Käll; William Stafford Noble
Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets.
Journal of proteome research 2009;8(7):3737-45.
2009: John Hawkins; Charles Grant; William Stafford Noble; Timothy Lawrence Bailey
Assessing phylogenetic motif models for predicting transcription factor binding sites.
Bioinformatics (Oxford, England) 2009;25(12):i339-47.
2009: Aaron A Klammer; Christopher Y Park; William Stafford Noble
Statistical calibration of the SEQUEST XCorr function.
Journal of proteome research 2009;8(4):2106-13.
2009: Lukas Käll; John D Storey; William Stafford Noble
QVALITY: non-parametric estimation of q-values and posterior error probabilities.
Bioinformatics (Oxford, England) 2009;25(7):964-6.
2009: Iain Melvin; Jason Weston; Christina Leslie; William Stafford Noble
RANKPROP: a web server for protein remote homology detection.
Bioinformatics (Oxford, England) 2009;25(1):121-2.
2008: Sheila M Reynolds; Lukas Käll; Michael E Riffle; Jeff A Bilmes; William Stafford Noble
Transmembrane topology and signal peptide prediction using dynamic bayesian networks.
PLoS computational biology 2008;4(11):e1000213.
2008: Gennifer E Merrihew; Colleen Davis; Brent Ewing; Gary Williams; Lukas Käll; Barbara E Frewen; William Stafford Noble; Phil Green; James H Thomas; Michael J MacCoss
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations.
Genome research 2008;18(10):1660-9.
2008: Heng Lian; William A Thompson; Robert Thurman; John A Stamatoyannopoulos; William Stafford Noble; Charles E Lawrence
Automated mapping of large-scale chromatin structure in ENCODE.
Bioinformatics (Oxford, England) 2008;24(17):1911-6.
2008: Lukas Käll; John D Storey; William Stafford Noble
Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry.
Bioinformatics (Oxford, England) 2008;24(16):i42-8.
2008: Nir Yosef; Roded Sharan; William Stafford Noble
Improved network-based identification of protein orthologs.
Bioinformatics (Oxford, England) 2008;24(16):i200-6.
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.
Bioinformatics (Oxford, England) 2008;24(13):i348-56.
2008: Jian Qiu; Will Sheffler; David Baker; William Stafford Noble
Ranking predicted protein structures with support vector regression.
Proteins 2008;71(3):1175-82.
2008: Jian Qiu; William Stafford Noble
Predicting co-complexed protein pairs from heterogeneous data.
PLoS computational biology 2008;4(4):e1000054.
2008: Shobhit Gupta; Jonathan H. Dennis; Robert E Thurman; Robert Kingston; John A Stamatoyannopoulos; William Stafford Noble
Predicting human nucleosome occupancy from primary sequence.
PLoS computational biology 2008;4(8):e1000134.
2008: Guillaume Obozinski; Gert Lanckriet; Charles Grant; Michael I Jordan; William Stafford Noble
Consistent probabilistic outputs for protein function prediction.
Genome biology 2008;9 Suppl 1():S6.
2008: Robert E Thurman; William Stafford Noble; John A Stamatoyannopoulos
Multi-scale correlations in continuous genomic data.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2008;():201-15.
2008: Lukas Käll; John D Storey; Michael J MacCoss; William Stafford Noble
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases.
Journal of proteome research 2008;7(1):29-34.
2008: Lukas Käll; John D Storey; Michael J MacCoss; William Stafford Noble
Posterior error probabilities and false discovery rates: two sides of the same coin.
Journal of proteome research 2008;7(1):40-4.
2007: Lukas Käll; Jesse D Canterbury; Jason Weston; William Stafford Noble; Michael J MacCoss
Semi-supervised learning for peptide identification from shotgun proteomics datasets.
Nature methods 2007;4(11):923-5.
2007: Aaron A Klammer; Xianhua Yi; Michael J MacCoss; William Stafford Noble
Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions.
Analytical chemistry 2007;79(16):6111-8.
2007: Heather E Peckham; Robert E Thurman; Yutao Fu; John A Stamatoyannopoulos; William Stafford Noble; Kevin Struhl; Zhiping Weng
Nucleosome positioning signals in genomic DNA.
Genome research 2007;17(8):1170-7.
2007: Saurabh Asthana; William Stafford Noble; Gregory V Kryukov; Charles E Grant; Shamil Sunyaev; John A Stamatoyannopoulos
Widely distributed noncoding purifying selection in the human genome.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(30):12410-5.
2007: Robert E Thurman; Nathan Day; William Stafford Noble; John A Stamatoyannopoulos
Identification of higher-order functional domains in the human ENCODE regions.
Genome research 2007;17(6):917-27.
2007: Nathan Day; Andrew Hemmaplardh; Robert E Thurman; John A Stamatoyannopoulos; William Stafford Noble
Unsupervised segmentation of continuous genomic data.
Bioinformatics (Oxford, England) 2007;23(11):1424-6.
2007: Jian Qiu; Martial Hue; Asa Ben-Hur; Jean-Philippe Vert; William Stafford Noble
A structural alignment kernel for protein structures.
Bioinformatics (Oxford, England) 2007;23(9):1090-8.
2007: Jean-Philippe Vert; Jian Qiu; William Stafford Noble
A new pairwise kernel for biological network inference with support vector machines.
BMC bioinformatics 2007;8 Suppl 10():S8.
2007: Shobhit Gupta; John A Stamatoyannopoulos; Timothy Lawrence Bailey; William Stafford Noble
Quantifying similarity between motifs.
Genome biology 2007;8(2):R24.
2006: William Stafford Noble
What is a support vector machine?
Nature biotechnology 2006;24(12):1565-7.
2006: Darrin P Lewis; Tony Jebara; William Stafford Noble
Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure.
Bioinformatics (Oxford, England) 2006;22(22):2753-60.
2006: Tata Pramila; Wei Wu; Shawna Miles; William Stafford Noble; Linda L Breeden
The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle.
Genes & development 2006;20(16):2266-78.
2006: Barbara E Frewen; Gennifer E Merrihew; Christine C Wu; William Stafford Noble; Michael J MacCoss
Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries.
Analytical chemistry 2006;78(16):5678-84.
2006: Tobias P Mann; William Stafford Noble
Efficient identification of DNA hybridization partners in a sequence database.
Bioinformatics (Oxford, England) 2006;22(14):e350-8.
2006: Peter J Sabo; Michael S Kuehn; Robert Thurman; Brett E Johnson; Ericka M Johnson; Hua Cao; Man Yu; Elizabeth Rosenzweig; Jeff Goldy; Andrew Haydock; Molly Weaver; Anthony Shafer; Kristin Lee; Fidencio Neri; Richard Humbert; Singer Michael; Richmond Todd; Michael O Dorschner; Michael McArthur; Michael Hawrylycz; Roland D Green; Patrick A Navas; William Stafford Noble; John A Stamatoyannopoulos
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays.
Nature methods 2006;3(7):511-8.
2006: Tobias P Mann; Richard Humbert; John A Stamatoyannopolous; William Stafford Noble
Automated validation of polymerase chain reaction amplicon melting curves.
Journal of bioinformatics and computational biology 2006;4(2):299-315.
2006: Asa Ben-Hur; William Stafford Noble
Choosing negative examples for the prediction of protein-protein interactions.
BMC bioinformatics 2006;7 Suppl 1():S2.
2006: Jason Weston; Rui Kuang; Christina Leslie; William Stafford Noble
Protein ranking by semi-supervised network propagation.
BMC bioinformatics 2006;7 Suppl 1():S10.
2005: William Stafford Noble; Rui Kuang; Christina Leslie; Jason Weston
Identifying remote protein homologs by network propagation.
The FEBS journal 2005;272(20):5119-28.
2005: Rui Kuang; Jason Weston; William Stafford Noble; Christina Leslie
Motif-based protein ranking by network propagation.
Bioinformatics (Oxford, England) 2005;21(19):3711-8.
2005: John P Miller; Russell S Lo; Asa Ben-Hur; Cynthia Desmarais; Igor Stagljar; William Stafford Noble; Stanley Fields
Large-scale identification of yeast integral membrane protein interactions.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(34):12123-8.
2005: Jason Weston; Christina Leslie; Eugene Ie; Dengyong Zhou; Andre Elisseeff; William Stafford Noble
Semi-supervised protein classification using cluster kernels.
Bioinformatics (Oxford, England) 2005;21(15):3241-7.
2005: Asa Ben-Hur; William Stafford Noble
Kernel methods for predicting protein-protein interactions.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i38-46.
2005: William Stafford Noble; Scott Kuehn; Robert Thurman; Man Yu; John A Stamatoyannopoulos
Predicting the in vivo signature of human gene regulatory sequences.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i338-43.
2005: Tobias P Mann; Richard Humbert; John A Stamatoyannopolous; William Stafford Noble
Automated validation of polymerase chain reactions using amplicon melting curves.
Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference 2005;():377-85.
2005: Aaron A Klammer; Christine C Wu; Michael J MacCoss; William Stafford Noble
Peptide charge state determination for low-resolution tandem mass spectra.
Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference 2005;():175-85.
2005: Will Sheffler; Eli Upfal; John Sedivy; William Stafford Noble
A learned comparative expression measure for affymetrix genechip DNA microarrays.
Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference 2005;():144-54.
2005: Martin Tompa; Nan Li; Timothy Lawrence Bailey; George M Church; Bart De Moor; Eleazar Eskin; Alexander Favorov; Martin C Frith; Yutao Fu; W James Kent; Vsevolod Makeev; Andrey A Mironov; William Stafford Noble; Giulio Pavesi; Graziano Pesole; Mireille Régnier; Nicolas Simonis; Saurabh sinha; Gert Thijs; Jacques Van Helden; Mathias Vandenbogaert; Zhiping Weng; Christopher Workman; Chun Ye; Zhou Zhu
Assessing computational tools for the discovery of transcription factor binding sites.
Nature biotechnology 2005;23(1):137-44.
2004: Gert R G Lanckriet; Tijl De Bie; Nello Cristianini; Michael I Jordan; William Stafford Noble
A statistical framework for genomic data fusion.
Bioinformatics (Oxford, England) 2004;20(16):2626-35.
2004: William Stafford Noble
Data hoarding is harming proteomics.
Nature biotechnology 2004;22(10):1209; discussion 1209.
2004: Henry Lu; Weiqun Li; William Stafford Noble; Donald G Payan; D C Anderson
Riboproteomics of the hepatitis C virus internal ribosomal entry site.
Journal of proteome research 2004;3(5):949-57.
2004: Koji Tsuda; William Stafford Noble
Learning kernels from biological networks by maximizing entropy.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i326-33.
2004: Wei Wu; William Stafford Noble
Genomic data visualization on the Web.
Bioinformatics (Oxford, England) 2004;20(11):1804-5.
2004: Jason Weston; Andre Elisseeff; Dengyong Zhou; Christina Leslie; William Stafford Noble
Protein ranking: from local to global structure in the protein similarity network.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(17):6559-63.
2004: Paul Pavlidis; Ilan Wapinski; William Stafford Noble
Support vector machine classification on the web.
Bioinformatics (Oxford, England) 2004;20(4):586-7.
2004: Christina Leslie; Eleazar Eskin; Adiel Cohen; Jason Weston; William Stafford Noble
Mismatch string kernels for discriminative protein classification.
Bioinformatics (Oxford, England) 2004;20(4):467-76.
2004: Gert R G Lanckriet; M Deng; Nello Cristianini; Michael I Jordan; William Stafford Noble
Kernel-based data fusion and its application to protein function prediction in yeast.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():300-11.
2003: Jie Qin; Darrin P Lewis; William Stafford Noble
Kernel hierarchical gene clustering from microarray expression data.
Bioinformatics (Oxford, England) 2003;19(16):2097-104.
2003: Shawn Gomez; William Stafford Noble; Andrey Rzhetsky
Learning to predict protein-protein interactions from protein sequences.
Bioinformatics (Oxford, England) 2003;19(15):1875-81.
2003: Timothy Lawrence Bailey; William Stafford Noble
Searching for statistically significant regulatory modules.
Bioinformatics (Oxford, England) 2003;19 Suppl 2():ii16-25.
2003: Paul Pavlidis; Qinghong Li; William Stafford Noble
The effect of replication on gene expression microarray experiments.
Bioinformatics (Oxford, England) 2003;19(13):1620-7.
2003: Neil H Segal; Paul Pavlidis; Cristina R Antonescu; ROBERT G MAKI; William Stafford Noble; Diann DeSantis; James M Woodruff; Jonathan J Lewis; Murray F Brennan; Alan N Houghton; Carlos Cordon-Cardo
Classification and subtype prediction of adult soft tissue sarcoma by functional genomics.
The American journal of pathology 2003;163(2):691-700.
2003: Tarikere L Gururaja; Weiqun Li; William Stafford Noble; Donald G Payan; Dave C Anderson
Multiple functional categories of proteins identified in an in vitro cellular ubiquitin affinity extract using shotgun peptide sequencing.
Journal of proteome research 2003;2(4):394-404.
2003: Neil H Segal; Paul Pavlidis; William Stafford Noble; Cristina R Antonescu; Agnes Viale; Umadevi V Wesley; Klaus J Busam; Humilidad F Gallardo; Diann DeSantis; Murray F Brennan; Carlos Cordon-Cardo; Jedd D Wolchok; Alan N Houghton
Classification of clear-cell sarcoma as a subtype of melanoma by genomic profiling.
Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2003;21(9):1775-81.
2003: D C Anderson; Weiqun Li; Donald G Payan; William Stafford Noble
A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores.
Journal of proteome research 2003;2(2):137-46.
2003: Paul Pavlidis; William Stafford Noble
Matrix2png: a utility for visualizing matrix data.
Bioinformatics (Oxford, England) 2003;19(2):295-6.
2003: Li Liao; William Stafford Noble
Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(6):857-68.
2003: Eleazar Eskin; William Stafford Noble; Yoram Singer
Protein family classification using sparse markov transducers.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(2):187-213.
2002: Eleazar Eskin; William Stafford Noble; Yoram Singer
Using substitution matrices to estimate probability distributions for biological sequences.
Journal of computational biology : a journal of computational molecular cell biology 2002;9(6):775-91.
2002: Paul Pavlidis; Jason Weston; Jinsong Cai; William Stafford Noble
Learning gene functional classifications from multiple data types.
Journal of computational biology : a journal of computational molecular cell biology 2002;9(2):401-11.
2002: Christina Leslie; Eleazar Eskin; William Stafford Noble
The spectrum kernel: a string kernel for SVM protein classification.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():564-75.
2002: Paul Pavlidis; Darrin P Lewis; William Stafford Noble
Exploring gene expression data with class scores.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():474-85.
2001: Paul Pavlidis; William Stafford Noble
Analysis of strain and regional variation in gene expression in mouse brain.
Genome biology 2001;2(10):RESEARCH0042.