Publications

1996		2012

Click on the links below to see abstracts and PDFs.

2013
• Daniel A. Skelly, Gennifer E. Merrihew, Michael Riffle, Caitlin F. Connelly, Emily O. Kerr, Marnie Johansson, Daniel Jaschob, Beth Graczyk, Nicholas J. Shulman, Jon Wakefield, Sara J. Cooper, Stanley Fields, William S. Noble, Eric G.D. Muller, Trisha N. Davis, Maitreya J. Dunham, Michael J. MacCoss, and Joshua M Akey. ``Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast.'' Genome Research.
• Xianxin Deng, Joel B. Berletch, Wenxiu Ma, Di K. Nguyen, Joseph B. Hiatt, William Stafford Noble, Jay Shendure and Christine M. Disteche. "Mammalian X upregulation is associated with enhanced transcription initiation, RNA half-life, and MOF-mediated H4K16 acetylation." Developmental Cell. 25(1):55-68, 2013.
2012
• Viktor Granholm, William Stafford Noble and Lukas Käll. "Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics." Journal of Proteomics. 80:123-131, 2012.
• MT Weirauch, A Cote, R Norel, M Annala, Y Zhao, S Talukder, A Vedenko, DREAM5 consortium, QD Morris, ML Bulyk, G Stolovitzky and TR Hughes. "An evaluation of methods for the modeling of transcription factor sequence specificity." Nature Biotechnology. 31(2):126-34, 2013.
• Zhi-jun Duan, Mirela Andronescu, Kevin Schutz, C Lee, Jay Shendure, Stanley Fields, William Stafford Noble and C. Anthony Blau. "A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes." Methods. 58(3):277-288, 2012.
• Viktor Granholm, William Stafford Noble and Lukas Käll. "A cross-validation scheme for machine learning algorithms in shotgun proteomics." BMC Bioinformatics. 13(Suppl 16):S3, 2012.
• Michael Hoffman, Jason Ernst, Steve P Wilder, Anshul Kundaje, Robert S. Harris, Max Libbrecht, Belinda Giardine, Paul Ellenbogen, Jeff A. Bilmes, Ewan Birney, Ross C. Hardison, Ian Dunham, Manolis Kellis and William Stafford Noble. "Integrative annotation of chromatin elements from ENCODE data." Nucleic Acids Research.
• Sean McIlwain, Michael Mathews, Michael Bereman, Edwin W. Rubel, Michael J. MacCoss and William Stafford Noble. "Estimating relative abundances of proteins from shotgun proteomics data." BMC Bioinformatics. 13:308, 2012.
• Sara C. Di Rienzi, Kim C. Lindstrom, Tobias Mann, William Stafford Noble, MK Raghuraman and Bonita J. Brewer. "Maintaining replication origins in the face of genomic change." Genome Research. 22(10):1940-1952, 2012.
• Ajit P. Singh, John Halloran, Jeff Bilmes and William Stafford Noble. "Spectrum identification using a dynamic Bayesian network model of tandem mass spectra." Uncertainty in Artificial Intelligence: Proceedings of the Twenty-Eighth Conference. Aug. 15-17, 2012. pp. 775-784.
• Soyoung Ryu, David R. Goodlett, William Stafford Noble and Vladimir N. Minin. "A statistical approach to peptide identification from clustered tandem mass spectrometry data." Proceedings of the International Workshop on Computational Proteomics, IEEE BIBM.
• Zafer Aydin, James Thompson, Jeff Bilmes, David Baker and William Stafford Noble. "Protein torsion angle class prediction by a hybrid architecture of Bayesian and neural networks." Proceedings of the 13th International Conference on Bioinformatics and Computational Biology. pp. 2012-2018.
• Mariana Fioramonte, Aline Mara dos Santos, Sean McIlwain, William Stafford Noble, Kleber Gomes Franchini and Fabio Cesar Gozzo. "Analysis of secondary structure in proteins by chemical cross-linking coupled to mass spectrometry." Proteomics. 12(17):2746-52, 2012.
• Marina Spivak, Michael S. Berriman, Michael J. MacCoss and William Stafford Noble. "Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments." Journal of Proteome Research. 11(9):4499-508, 2012.
• The ENCODE Project Consortium. "An integrated encylopedia of DNA elements in the human genome." Nature. 489(7414):57-74, 2012.
• Jie Wang, Jiali Zhuang, Sowmya Iyer, XinYing Lin, Troy W. Whitfield, Melissa Greven, Xianjun Dong, Anshul Kundaje, Yong Cheng, Ewan Birney, Richard M. Myers, William S. Noble, Michael Snyder and Zhiping Weng. "Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors." Genome Research. 22(9):1798-812, 2012.
• Aaron Arvey, Phaedra Agius, William Stafford Noble and Christina Leslie. "Sequence and chromatin determinants of cell-type specific transcription factor binding." Genome Research. 22(9):1723-34, 2012.
• Oliver Serang and William Stafford Noble. "Faster mass spectrometry-based protein inference: junction trees are more efficient than sampling and marginalization by enumeration." IEEE Transactions on Computational Biology and Bioinformatics. 9(3):809-817, 2012.
• Daniela M. Witten and William Stafford Noble. "On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements." Nucleic Acids Research. 40(9):3849-3855, 2012.
• Benjamin J. Diament, Michael J. MacCoss, William Stafford Noble. "On the feasibility and utility of exploiting real time database search to improve adaptive peak selection." arXiv:1207.5848v1.
• Yanjun Qi, Merja Oja, Jason Weston and William Stafford Noble. "A unified multitask architecture for predicting local protein properties." PLoS One. 7(3):e32235, 2012.
• Michael M. Hoffman, Orion J. Buske, Zhiping Weng, Jeff A. Bilmes and William Stafford Noble. "Unsupervised pattern discovery in human chromatin structure through genomic segmentation." Nature Methods. 9(5):473-476, 2012.
• Marina Spivak, Jason Weston, Michael J. MacCoss and William Stafford Noble. "Direct maximization of protein identifications from tandem mass spectra." Molecular and Cellular Proteomics. 11(2):M111.012161, 2012.
• William Stafford Noble, C. Anthony Blau, Job Dekker, Zhi-jun Duan and Yi Mao. "The structure and function of chromatin and chromosomes." Proceedings of the Pacific Symposium on Biocomputing. 17:434-440, 2012.
• William Stafford Noble and Michael J. MacCoss. "Computational and statistical analysis of protein mass spectrometry data." PLoS Computational Biology. 8(1):e1002296, 2012.
• Oliver Serang and William Stafford Noble. "A review of statistical methods for protein identification using tandem mass spectrometry." Statistics and its Interface. 5:3-20, 2012.
2011
• Gabriel Cuellar-Partida, Fabian A. Buske, R C. McLeay, Tom Whitington, William Stafford Noble and Timothy L. Bailey. "Epigenetic priors for identifying active transcription factor binding sites." Bioinformatics.28:56-62, 2011.
• Orion J. Buske, Michael M. Hoffman, Nadia Ponts, Karine Le Roch and William Stafford Noble. "Exploratory analysis of genomic segmentations with Segtools." BMC Bioinformatics. 12:415, 2011.
• Benjamin J. Diament and William Stafford Noble. "Faster SEQUEST searching for peptide identification from tandem mass spectra." Journal of Proteome Research. 10(9):3871-9, 2011.
• Yanjun Qi and William Stafford Noble. "Protein interaction networks: protein domain interaction and protein function prediction." In Handbook of Statistical Bioinformatics. Ed. by HH Lu, B Schoelkopf and H. Zhao. Springer Verlag, 2011.
• Emily Tanaka, Timothy L. Bailey, Charles E. Grant, William Stafford Noble and Uri Keich. "Improved similarity scores for comparing motifs." Bioinformatics. 27(12):1603-1609, 2011.
• Viktor Granholm, William Stafford Noble and 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. 10(5):2671-2678, 2011.
• The ENCODE Project Consortium. "A user's guide to the Encylopedia of DNA Elements (ENCODE)." PLoS Biology. 9(4):e1001046, 2011.
• Zafer Aydin, Ajit Singh, Jeff Bilmes and William Stafford Noble. "Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure." BMC Bioinformatics. 12:154, 2011.
• Charles E. Grant, Timothy L. Bailey and William Stafford Noble. "FIMO: Scanning for occurrences of a given motif." Bioinformatics. 27(7):1017-1018, 2011.
• Iain Melvin, Jason Weston, William Stafford Noble and Christina Leslie. "Detecting remote evolutionary relationships among proteins by large-scale semantic embedding." PLoS Computational Biology. 7(1):e1001047, 2011
• William Stafford Noble and Christina Leslie. "Learning models of biological sequences." In Encyclopedia of Machine Learning. Ed. by C Sammut and GI Webb. Springer Verlag, 2011.
• Emmet Hirsch, Courtney Lim, Debra Dobrez, MG Adams and William Stafford Noble. "Meteorological factors and the timing of the initiating event of parturition." International Journal of Biometeorology. 55(2):265, 2011.
2010
• Vagisha Sharma, Jimmy K. Eng, Sergey Feldman, Priska von Haller, Michael J. MacCoss and William Stafford Noble. "Precursor charge state prediction for electron transfer dissociation tandem mass spectra." Journal of Proteome Research. 9(10):5438-5444, 2010.
• Oliver Serang, Michael J. MacCoss and William Stafford Noble. "Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data." Journal of Proteome Research. 9(10):5346-5357, 2010.
• Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble and Christina Leslie. "High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions." PLoS Computational Biology. 6(9):e10000916, 2010.
• Sheila Moore Reynolds, Jeffrey A. Bilmes and 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. 6(7):e10000834, 2010.
• Sheila Reynolds, Zhiping Weng, Jeffrey Bilmes and William Stafford Noble. "Predicting nucleosome positioning using multiple evidence tracks." Proceedings of the International Conference on Research in Computational Biology (RECOMB). Lecture Notes in Computer Science, 2010, Volume 6044/2010, pp. 441-455.
• Zhijun Duan, Mirela Andronescu, Kevin Schutz, Sean McIlwain, Yoo Jung Kim, Choli Lee, Jay Shendure, Stanley Fields, C. Anthony Blau and William S. Noble. "A three-dimensional model of the yeast genome". Nature. 465:363-367, 2010.
• Xiaoyu Chen, Michael Hoffman, Jeffrey A. Bilmes, Jay R. Hesselberth and William Stafford Noble. "A dynamic Bayesian network for identifying protein binding footprints from single molecule based sequencing data." Bioinformatics (Proceedings of the ISMB). 26(12):i334-i342, 2010.
• Michael M. Hoffman, Orion J. Buske and William Stafford Noble. "The Genomedata format for storing large-scale functional genomics data." Bioinformatics. 26(11):1458-1459, 2010.
• Sean McIlwain, Paul Draghicescu, Pragya Singh, Dave R. Goodlett and William Stafford Noble. "Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs." Journal of Proteome Research. 9(5):2488-2495, 2010.
• Nir Yosef, Jens Gramm, Qian-fei Wang, William Stafford Noble, Richard M. Karp and Roded Sharan. "Prediction of phenotype information from genotype data." Communications in Information and Systems. 10(2):99-114, 2010.
• Martial Hue, Michael Riffle, Jean-Philippe Vert and William Stafford Noble. "Large-scale prediction of protein-protein interactions from structures." BMC Bioinformatics. 11:144, 2010.
• Zafer Aydin, John I. Murray, Robert H. Waterston and 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. 11(1):84, 2010.
2009
• William Stafford Noble. "How does multiple testing correction work?" Nature Biotechnology. 27(12):1135-1137, 2009.
• William Stafford Noble. "A quick guide to organizing computational biology experiments." PLoS Computational Biology. 5(7):e1000424, 2009
• Tobias Mann, Rich Humbert, Michael Dorschner, John A. Stamatoyannopoulos and William Stafford Noble. "A thermodynamic approach to PCR primer design." Nucleic Acids Research. 25(12):i339-347, 2009.
• John Hawkins, Charles E. Grant, William Stafford Noble and Timothy L. Bailey. "Assessing phylogenetic motif models for predicting transcription factor binding sites.". Bioinformatics (Proceedings of the ISMB). 25(12):i339-347, 2009.
• Timothy L. Bailey, Michael Boden, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jane Ren, Wilfred W. Li and William Stafford Noble. "MEME Suite: tools for motif discovery and searching." Nucleic Acids Research. 37(Web server issue):W202-208, 2009.
• Marina Spivak, Jason Weston, Leon Bottou, Lukas Käll and William Stafford Noble. "Improvements to the Percolator algorithm for peptide identification from shotgun proteomics data sets." Journal of Proteome Research. 8(7):3737-3745, 2009.
• Sheila Reynolds, Jeffrey A. Bilmes and William Stafford Noble. "On the relationship between DNA periodicity and local chromatin structure." Proceedings of the International Conference on Research in Computational Biology (RECOMB). May 18-21, 2009. pp. 434-450.
• Aaron A. Klammer, Christopher Y. Park and William Stafford Noble. "Statistical calibration of the SEQUEST XCorr function." Journal of Proteome Research. 8(4):2106-2113, 2009.
• Jay Hesselberth, Xiaoyu Chen, Zhihong Zhang, Pete J. Sabo, Richard Sandstrom, Alex P. Reynolds, Robert E. Thurman, Shane Neph, Michael S. Kuehn, William Stafford Noble, Stanley Fields and John A. Stamatoyannopoulos. "Global mapping of protein-DNA interactions in vivo by digital genomic footprinting." Nature Methods. 6(4):283-289, 2009.
• Lukas Käll, John D. Storey and William Stafford Noble. "QVALITY: Nonparametric estimation of q values and posterior error probabilities." Bioinformatics. 25(7):964-966, 2009.
• Iian Melvin, Jason Weston, Christina Leslie and William Stafford Noble. "Rankprop: a web server for protein remote homology detection." Bioinformatics. 25(1):121-122, 2009.
2008
• Sheila M. Reynolds, Lukas Käll, Jeff A. Bilmes and William Stafford Noble. "Transmembrane topology and signal peptide prediction using dynamic Bayesian networks." PLoS Computational Biology. 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. 18(10):1660-1669, 2008.
• Iain Melvin, Jason Weston, Christina Leslie and William Stafford Noble. "Combining classifiers for improved classification of proteins from sequence or structure." BMC Bioinformatics. 9:389, 2008.
• Heng Lian, William Thompson, Robert E. Thurman, John A. Stamatoyannpoulos, William Stafford Noble and Charles Lawrence. "Automated mapping of large-scale chromatin structure in ENCODE." Bioinformatics. 24(17):1911-1916, 2008.
• Shobhit Gupta, Jonathan Dennis, Robert E. Thurman, Robert Kingston, John A. Stamatoyannopoulos and William Stafford Noble. "Predicting human nucleosome occupancy from primary sequence." PLoS Computational Biology. 4(8):e10000134, 2008.
• Nir Yosef, Roded Sharan and William Stafford Noble. "Improved network-based identification of protein orthologs." Bioinformatics (Proceedings of the ECCB). 24(16):i200-i206, 2008.
• Lukas Käll, John Storey and William Stafford Noble. "Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry." Bioinformatics (Proceedings of the ECCB). 24(16):i42-i48, 2008.
• Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. MacCoss and William Stafford Noble. "Rapid and accurate peptide identification from tandem mass spectra." Journal of Proteome Research. 7(7):3022-3027, 2008.
• Aaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael J. MacCoss and William Stafford Noble. "Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification." Bioinformatics (Proceedings of the ISMB). 24(13):i345-i356, 2008.
• L Pena-Castillo, M Tasan, CL Myers, H Lee, T Joshi, C Zhang, Y Guan, M Leone, A Pagnani, WK Kim, C Krumpelman, W Tian, G Obozinski, Y Qi, S Mostafavi, GN Lin, G Berriz, F Gibbons, G Lanckriet, J Qiu, C Grant, Z Barutcuoglu, DP Hill, D Warde-Farely, C Grouios, D Ray, JA Blake, M Deng, M Jordan, WS Noble, Q Morris, J Klein-Seetharaman, Z Bar-Joseph, T Chen, F Sun, OG Troyanskaya, EM Marcotte, D Xu, TR Hughes and FP Roth. "A critical assessment of M. musculus gene function prediction using integrated genomic evidence." Genome Biology. 9(Suppl 1):S2, 2008.
• Guillaume Obozinski, Gert Lanckriet, Charles E. Grant, Michael I. Jordan and William Stafford Noble. "Consistent probabilistic outputs for protein function prediction." Genome Biology. 9(Suppl 1):S6, 2008.
• Jian Qiu and William Stafford Noble. "Predicting co-complexed protein pairs from heterogeneous data." PLoS Computational Biology. 4(4):e1000054, 2008.
• Robert E. Thurman, William Stafford Noble and John A. Stamatoyannopoulos. "Multi-scale correlations in continuous genomic data." Proceedings of the Pacific Symposium on Biocomputing. January 4-8, 2008. pp. 201-215.
• Lukas Käll, John D. Storey, Michael J. MacCoss and William Stafford Noble. "Assigning significance to peptides identified by tandem mass spectrometry using decoy databases." Journal of Proteome Research. 7(1):29-34, 2008
• Lukas Käll, John D. Storey, Michael J. MacCoss and William Stafford Noble. "Posterior error probabilities and false discovery rates: two sides of the same coin." Journal of Proteome Research. 7(1):40-44, 2008.
2007
• Jean-Philippe Vert, Jian Qiu and William Stafford Noble. "A new pairwise kernel for biological network inference with support vector machines." BMC Bioinformatics. 8(Suppl. 10):S8, 2007.
• Jian Qiu, Will Sheffler, David Baker and William Stafford Noble. "Ranking predicted protein structures with support vector regression." Proteins: Structure, Function, and Bioinformatics. 71(3):1175-1182, 2007.
• Lukas Käll, Jesse Canterbury, Jason Weston, William Stafford Noble and Michael J. MacCoss. "Semi-supervised learning for peptide identification from shotgun proteomics datasets." Nature Methods. 4(11):923-925, 2007.
• Jason Weston, Gokhan Bakir, Olivier Bousquet, Tobias Mann, William Stafford Noble and Bernhard Scholkopf. "Joint kernel maps." In Predicting Structured Data. Ed. by Gokhan Bakir, Thomas Hofmann, Bernhard Scholkopf, Alex J. Smola, Ben Taskar and V. S. N. Vishwanathan. MIT Press, 2007.
• Aaron A. Klammer, Xianhua Yi, Michael J. MacCoss and William Stafford Noble. "Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions." Analytical Chemistry. 79(16):6111-6118, 2007.
• Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, William Stafford Noble and Christina Leslie. "SVM-fold: a tool for discriminative multi-class protein fold and superfamily recognition." BMC Bioinformatics. 8(Suppl 4):S2, 2007.
• Iain Melvin, Eugene Ie, Jason Weston, William Stafford Noble and Christina Leslie. "Multi-class protein classification using adaptive codes." Journal of Machine Learning Research. 8(Jul):1557-1581, 2007
• Heather E. Peckham, Robert E. Thurman, Yutao Fu, John A. Stamatoyannopoulos, William Stafford Noble, Kevin Struhl and Zhiping Weng. "Nucleosome positioning signals in genomic DNA." Genome Research. 17(8):1170-1177, 2007.
• Saurabh Asthana, William Stafford Noble, Grigory Kryukov, Charles E. Grant, Shamil Sunyaev and John A. Stamatoyannopoulos. "Widely distributed non-coding selection in the human genome." Proceedings of the National Academy of Science. 104(30):12410-12415, 2007.
• The ENCODE Project Consortium. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE project." Nature. 447:779-816, 2007.
• Robert E. Thurman, Nathan Day, William Stafford Noble and John A. Stamatoyannopoulos. "Identification of higher-order functional domains in the human ENCODE regions." Genome Research. 17(6):917-927, 2007.
• Nathan Day, Andrew Hemmaplardh, Robert E. Thurman, John A. Stamatoyannopoulos and William Stafford Noble. "Unsupervised segmentation of continuous genomic data." Bioinformatics. 23(11):1424-1426, 2007
• Jonathan H. Dennis, Hua-Ying Fan, Sheila R. Reynolds, Guocheng Yuan, Jim Meldrim, Daniel J. Richter, Daniel G. Peterson, Oliver J. Rando, William Stafford Noble and Robert E. Kingston. "Independent and complementary methods for large-scale structural analysis of mammalian chromatin." Genome Research. 17(6):928-939, 2007.
• Jian Qiu, Martial Hue, Asa Ben-Hur, Jean-Philippe Vert and William Stafford Noble. "A structural alignment kernel for protein structures." Bioinformatics. 23(9):1090-1098, 2007.
• Aaron Klammer, Xianhua Yi, Michael J. MacCoss and William Stafford Noble. "Peptide retention time prediction yields improved tandem mass spectrum identification for diverse chromatography conditions." Proceedings of the International Conference on Research in Computational Biology (RECOMB). April 21-25, 2007. pp. 459-472.
• Shobhit Gupta, John A. Stamatoyannopoulos, Timothy L. Bailey and William Stafford Noble. "Quantifying similarity between motifs." Genome Biology. 8:R24, 2007.
• William Stafford Noble and Asa Ben-Hur. "Integrating information for protein function prediction." In Bioinformatics - From Genomes to Therapies. T. Lenguaer, ed. Vol. 3. pp. 1297-1314.
2006
• William Stafford Noble. "What is a support vector machine?" Nature Biotechnology. 24(12):1565-1567, 2006.
• Darrin P. Lewis, Tony Jebara and William Stafford Noble. "Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure." Bioinformatics. 22(22):2753-2760, 2006.
• Barbara E. Frewen, Gennifer E. Merrihew, William Stafford Noble and Michael J. MacCoss. "Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries." Analytical Chemistry. 78(16):5678-5684, 2006.
• Tata Pramila, Wei Wu, William Stafford Noble and 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 and Development. 20(16):2266-2278, 2006.
• Jean-Philippe Vert, Robert Thurman and William Stafford Noble. "Kernels for gene regulatory regions." Advances in Neural Information Processing Systems 18, 2006.
• Tobias Mann and William Stafford Noble. "Efficient identification of DNA binding partners in a sequence database." Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference). 22:e350-e358, 2006.
• Tobias Mann, Richard Humbert, John Stamatoyannopoulos and William Stafford Noble. "Automated validation of polymerase chain reactions using amplicon melting curves." Journal of Bioinformatics and Computational Biology. 22(14):350-358, 2006.
• PJ Sabo, MS Kuehn, R Thurman, B Johnson, EM Johnson, H Cao, M Yu, J Goldy, E Rosenzweigh, J Goldy, A Haydock, M Weaver, A Shafer, K Lee, F Neri, R Humbert, MA Singer, TA Richmond, MO Dorschner, M McArthur, M Hawrylycz, RD Green, PA Navas, WS Noble and JA Stamatoyannopoulos. "Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays." Nature Methods. 3(7):511-518, 2006.
• Darrin P. Lewis, Tony Jebara and William Stafford Noble. "Nonstationary kernel combination." Proceedings of the International Conference on Machine Learning, June 25-29, 2006, Pittsburgh, PA.
• Asa Ben-Hur and William Stafford Noble. "Choosing negative examples for the prediction of protein-protein interactions." BMC Bioinformatics. 7(Suppl 1):S2, 2006.
• Jason Weston, Rui Kuang, Christina Leslie, William Stafford Noble. "Protein ranking by semi-supervised network propagation." BMC Bioinformatics. 7(Suppl 1):S10, 2006.
2005
• Jason Weston, Christina Leslie, Eugene Ie and William Stafford Noble. "Semi-supervised protein classification using cluster kernels." Semi-supervised Learning. O Chapelle, B Schoelkopf and A Zien, ed. MIT Press, 2005. pp. 321-338.
• William Stafford Noble, Rui Kuang, Christina Leslie and Jason Weston. "Identifying remote protein homologs by network propagation." FEBS Journal. 272(20):5119-5128, 2005.
• Rui Kuang, Jason Weston, William Stafford Noble and Christina Leslie. "Motif-based protein ranking by network propagation." Bioinformatics. 21(19):3711-3718, 2005.
• Eugene Ie, Jason Weston, William Stafford Noble and Christina Leslie. "Adaptive codes for multi-class protein classification." Proceedings of the International Conference on Machine Learning, August 7-11, 2005, Bonn, Germany.
• Aaron Klammer, Christine C. Wu, Michael J. MacCoss, William Stafford Noble. "Peptide charge state determination for low-resolution tandem mass spectra." Proceedings of the Computational Systems Bioinformatics Conference, August 8-11, 2005, Stanford, CA. pp. 175-185.
• Tobias Mann, Richard Humbert, John Stamatoyannopoulos and William Stafford Noble. "Automated validation of polymerase chain reactions using amplicon melting curves." Proceedings of the Computational Systems Bioinformatics Conference, August 8-11, 2005, Stanford, CA. pp. 377-385.
• Will Sheffler, Eli Upfal, John Sedivy and William Stafford Noble. "A learned comparative expression measure for Affymetrix GeneChip DNA microarrays." Proceedings of the Computational Systems Bioinformatics Conference, August 8-11, 2005, Stanford, CA. pp. 144-154.
• John P. Miller, Russel S. Lo, Asa Ben-Hur, Cynthia Desmarais, Igor Stagljar, William Stafford Noble and Stanley Fields. "Large-scale identification of yeast integral membrane protein interactions." Proceedings of the National Academy of Science. 102(34):12123-12128, 2005.
• Jason Weston, Christina Leslie, Eugene Ie, Dengyong Zhou, Andre Eliseeff and William Stafford Noble. "Semi-supervised protein classification using cluster kernels." Bioinformatics. 21(15):3241-3247, 2005.
• Asa Ben-Hur and William Stafford Noble. "Kernel methods for predicting protein-protein interactions." Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference). 21(Suppl 1):i38-i46, 2005.
• William Stafford Noble, Scott Kuehn, Robert Thurman, Richard Humbert, James C. Wallace, Man Yu, Michael Hawrylycz and John Stamatoyannopoulos. "Predicting the in vivo signature of human gene regulatory sequences." Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference). 21(Suppl 1):i338-i343, 2005.
• M Tompa, N Li, TL Bailey, GM Church, B De Moor, E Eskin, AV Favorov, MC Frith, Y Fu, WJ Kent, VJ Makeev, AA Mironov, WS Noble, G Pavesi, G Pesole, M Regnier, N Simonis, S Sinha, G Thijs, J van Helden, M Vandenbogaert, Z Weng, C Workman, C Ye and Z Zhu. "Assessing computational tools for the discovery of transcription factor binding sites." Nature Biotechnology. 23(1):137-144, 2005.
2004
• Lanckriet, Gert R. G., Tijl De Bie, Nello Cristianini, Michael I. Jordan and William Stafford Noble. "A statistical framework for genomic data fusion." Bioinformatics. 20(16):2626-2635, 2004.
• Noble, William Stafford. "Data hoarding is harming proteomics." Nature Biotechnology. 22(10):1209.
• Noble, William Stafford. "Support vector machine applications in computational biology." Kernel Methods in Computational Biology. B. Schoelkopf, K. Tsuda and J.-P. Vert, ed. MIT Press, 2004. pp. 71-92.
• Weston, Jason, Christina Leslie, Denyong Zhou and William Stafford Noble. "Semi-supervised protein classification using cluster kernels." Advances in Neural Information Processing Systems 16, 2004. pp. 595-602.
• Tsuda, Koji and William Stafford Noble. "Learning kernels from biological networks by maximizing entropy." Bioinformatics (Proceedings of the ISMB/ECCB). 20(Suppl. 1):i326-i333, 2004.
• Lu, Henry, Weiqun Li, William Stafford Noble, Donald Payan and D. C. Anderson. "Riboproteomics of the hepatitis C virus internal ribosomal entry site." Journal of Proteome Research Web Release Date: 17-Jul-2004; (Article) DOI: 10.1021/pr0499592
• Wu, Wei and William Stafford Noble. "Genomic data visualization on the web." Bioinformatics. 20(11):1804-1805, 2004.
• Weston, Jason, Andre Eliseeff, Dengyong Zhou, Christina Leslie and William Stafford Noble. "Protein ranking: from local to global structure in the protein similarity network." Proceedings of the National Academy of Science. 101(17):6559-6563, 2004.
• Leslie, Christina, Eleazar Eskin, Adiel Cohen, Jason Weston and William Stafford Noble. "Mismatch string kernels for discriminative protein classification." Bioinformatics. 20(4):467-476, 2004.
• Pavlidis, Paul, Ilan Wapinski and WS Noble. "Support vector machine classification on the web." Bioinformatics. 20(4):586-587, 2004.
• Lanckriet, Gert R. G., Minghua Deng, Nello Cristianini, Michael I. Jordan and William Stafford Noble. "Kernel-based data fusion and its application to protein function prediction in yeast." Proceedings of the Pacific Symposium on Biocomputing, January 3-8, 2004. pp. 300-311.
2003
• Liao, Li and William Stafford Noble. "Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships." Journal of Computational Biology. 10(6):857-868, 2003.
• Qin, Jie, Darrin Lewis and William Stafford Noble. "Kernel hierarchical clustering of microarray gene expression data." Bioinformatics. 19(16):2097-2104, 2003.
• Eskin, Eleazar, William Stafford Noble and Yoram Singer. "Protein family classification using sparse Markov transducers." Journal of Computational Biology. 10(2):187-213, 2003.
• Gomez, Shawn M., William Stafford Noble and Andrey Rzhetsky. "Learning to predict protein-protein interactions from protein sequences." Bioinformatics (Proceedings of the Georgia Tech International Conference on Bioinformatics). 19:1875-1881, 2003.
• Leslie, Christina, Eleazar Eskin, Jason Weston and William Stafford Noble. "Mismatch string kernels for SVM protein classification." Neural Information Processing Systems 15, 2003. pp. 1441-1448.
• Bailey, Timothy and William Stafford Noble. "Searching for statistically significant regulatory modules" Bioinformatics (Proceedings of the European Conference on Computational Biology). 19(Suppl. 2):ii16-ii25, 2003.
• Pavlidis, Paul, Qinghong Li and William Stafford Noble. "The effect of replication on gene expression microarray experiments." Bioinformatics. 19(13):1620-1627, 2003.
• Gururaja, Tarikere, Weiqun Li, William Stafford Noble, Donald G. Payan and D. C. Anderson. "Multiple functional categories of proteins identified in an in vitro cellular ubiquitin affinity extract using shotgun peptide sequencing." Journal of Proteome Research. 2:394-404, 2003.
• Segal, Neil H., Paul Pavlidis, Cristina R. Antonescu, Robert G. Maki, William Stafford Noble, James M. Woodruff, Jonathan J. Lewis, Murray F. Brennan, Alan N. Houghton and Carlos Cordon-Cardo. "Classification and subtype prediction of soft tissue sarcoma by functional genomics and support vector machine analysis." American Journal of Pathology. 169:691-700, 2003.
• Neil H. Segal, Paul Pavlidis, William Stafford Noble, Cristina R. Antonescu, Agnes Viale, Umadevi V. Wesley, Klaus Busam, Humilidad Gallardo, Dianne DeSantis, Murray F. Brennan, Carlos Cordon-Cardo, Jedd D. Wolchok and Alan N. Houghton. "Classification of clear cell sarcoma as melanoma of soft parts by genomic profiling." Journal of Clinical Oncology. 21:1775-1781, 2003.
• Pavlidis, Paul and William Stafford Noble. "Matrix2png: A utility for visualizing matrix data." Bioinformatics. 19(2):295-296, 2003.
• Anderson, David C., Weiqun Li, Donald G. Payan and 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. 2(2):137-146, 2003.
2002
• Eleazar Eskin, William Stafford Noble and Yoram Singer. "Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences." Journal of Computational Biology. 9(6):775-91, 2002.
• Weston, Jason, Bernhard Schoelkopf, Eleazar Eskin, Christina Leslie and William Stafford Noble. "Dealing with large diagonals in kernel matrices." Principles of Data Mining and Knowledge Discovery. Springer Lecture Notes in Computer Science 243.
• Schoelkopf, Bernhard, Jason Weston, Eleazar Eskin, Christina Leslie and William Stafford Noble. "A kernel approach for learning from almost orthogonal patterns." Proceedings of the 13th European Conference on Machine Learning, August 19-23, 2002. pp. 511-528.
• Liao, Li and William Stafford Noble. "Combining pairwise sequence similarity and support vector machines for remote protein homology detection". Proceedings of the Sixth Annual International Conference on Research in Computational Molecular Biology, April 18-21, 2002. pp. 225-232.
• Pavlidis, Paul, Jason Weston, Jinsong Cai and William Stafford Noble. "Learning gene functional classifications from multiple data types." Journal of Computational Biology. 9(2):401-411, 2002.
• Pavlidis, Paul, Darrin P. Lewis and William Stafford Noble. "Exploring gene expression data with class scores." Proceedings of the Pacific Symposium on Biocomputing, January 2-7, 2002. pp. 474-485.
• Leslie, Christina, Eleazar Eskin and William Stafford Noble. "The spectrum kernel: A string kernel for SVM protein classification." Proceedings of the Pacific Symposium on Biocomputing, January 2-7, 2002. pp. 564-575.
2001
• Pavlidis, Paul and William Stafford Noble. "Analysis of strain and regional variation in gene expression in mouse brain." Genome Biology. 2(10): research0042.1-0042.15, 2001.
• Pavlidis, Paul, Christopher Tang and William Stafford Noble. "Classification of genes using probabilistic models of microarray expression profiles." Proceedings of BIOKDD 2001: Workshop on Data Mining in Bioinformatics.
• Muhle, Rebecca A., Paul Pavlidis, William Noble Grundy and Emmet Hirsch. "A high throughput study of gene expression in preterm labor using a subtractive microarray approach." American Journal of Obstetrics and Gynecology, 185(3):716-24, 2001.
• Eskin, Eleazar, William Noble Grundy and Yoram Singer. "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. July 21-25, 2001. pp. 65-73.
• Pavlidis, Paul, Jason Weston, Jinsong Cai and William Noble Grundy. "Gene functional classification from heterogeneous data" Proceedings of the Fifth International Conference on Computational Molecular Biology, April 21-24, 2001. pp. 242-248.
• Pavlidis, Paul, Terrence S. Furey, Muriel Liberto, David Haussler and William Noble Grundy. "Promoter region-based classification of genes." Proceedings of the Pacific Symposium on Biocomputing, January 3-7, 2001. pp. 151-163.
2000
• Eskin, Eleazar, William Noble Grundy and Yoram Singer. "Protein family classification using sparse Markov transducers." Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology. August 20-23, 2000. pp. 134-145.
• Brown, Michael P. S., William Noble Grundy, David Lin, Nello Cristianini, Charles Sugnet, Terrence S. Furey, Manuel Ares, Jr., and David Haussler. "Knowledge-based analysis of microarray gene expression data using support vector machines." Proceedings of the National Academy of Science. 97(1):262-267, 2000.
1999
• Grundy, William Noble and Gavin J. P. Naylor. "Phylogenetic Inference from Conserved Sites Alignments". The Journal of Experimental Zoology: Molecular and Developmental Evolution. 285(2):128-139, 1999.
• Grundy, William Noble and Timothy L. Bailey. "Family Pairwise Search with embedded motif models". Bioinformatics. 15(6):463-470, 1999.
• Baker, Michael, William N. Grundy and Charles P. Elkan. "A common ancestor for a subunit in the mitochondrial proton-translocating NADH:ubiquinone oxidoreductase (complex I) and short-chain dehydrogenases/reductases". Cellular and Molecular Life Sciences. 55(3):450-455, 1999.
• Bailey, Timothy L. and William Noble Grundy. "Classifying proteins by family using the product of correlated p-values". Proceedings of the Third International Conference on Computational Molecular Biology (RECOMB99), April 11-14, 1999. pp. 10-14.
• Bailey, Timothy L., Michael E. Baker, Charles P. Elkan and William N. Grundy. "MEME, MAST, and Meta-MEME: New Tools for Motif Discovery in Protein Sequences" in Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications. J. Wang, B. Shapiro and D. Shasha, editors. Oxford UP, 1999.
1998
• Grundy, William Noble. A Bayesian Approach to Motif-based Protein Modeling. Ph.D. dissertation. University of California, San Diego. June, 1998.
• Grundy, William Noble. "Homology Detection via Family Pairwise Search". Journal of Computational Biology, 5(3):479-492, 1998.
• Baker, Michael E., William N. Grundy and Charles P. Elkan. "Spinach CSP41, an mRNA-binding protein and ribonuclease, is homologous to nucleotide-sugar epimerases and hydroxysteroid dehydrogenases" Biochemical and Biophysical Research Communications, 248(2):250-254, 1998.
• Grundy, William Noble. "Family-based Homology Detection via Pairwise Sequence Comparison". Proceedings of the Second Annual International Conference on Computational Molecular Biology, March 22-25, 1998. pp. 94-100.
1997
• Grundy, William N., Timothy L. Bailey, Charles P. Elkan and Michael E. Baker. "Meta-MEME: Motif-based Hidden Markov Models of Protein Families". Computer Applications in the Biosciences. 13(4):397-406, 1997.
• Grundy, William Noble. "Modeling Biological Sequences Using HTK" Technical report prepared for Entropic Research Laboratory, Inc. March, 1997.
• Grundy, William N., Timothy L. Bailey, Charles P. Elkan and Michael E. Baker. "Hidden Markov Model Analysis of Motifs in Steroid Dehydrogenases and their Homologs." Biochemical and Biophysical Research Communications. 231(3):760-766, 1997.
before 1997
• Batali, John and William Noble Grundy. "Modeling the Evolution of Motivation". Evolutionary Computation. 4(3):235-270, 1996.
• Grundy, William N., Timothy L. Bailey and Charles P. Elkan. "ParaMEME: A Parallel Implementation and a Web Interface for a DNA and Protein Motif Discovery Tool" (with corrections). Computer Applications in the Biosciences. 12(4):303-310, 1996.
• Grundy, William Noble. "Solar Cookers and Social Classes in Southern Africa." Techné: Journal of Technology Studies. Gray Norton, ed. Vol. V, Winter 1995. pp. 3-7.
• Grundy, William. "Building a Simple Recognition System Using HTK." Entropic Research Laboratory, Washington, DC. August, 1994.
• Bernstein, Jared, et al. The Latino40 Speech Database. Entropic Research Laboratory, Washington, DC. 1994.
• Grundy, William and Roy Grundy "Diffusion of Innovation: Solar Oven Use in Lesotho (Africa)." Advances in Solar Cooking: Proceedings of the 2nd International Conference on Solar Cooker Use and Technology. Shyam S. Nandwani, ed. July 12-15, 1994. pp. 240-247.
• Grundy, Bill. Making a Thinking Robot. Senior Honors Thesis, Symbolic Systems Program, Stanford University, 1991. Advisor: Fred Dretske.
• Stanford Fleet Street Singers. curious... Bill Grundy, Producer. 1990.
• Grundy, Bill. "The Coinage of Sicyon." The Numismatist. November, 1986. pp. 2307-8.