William Stafford Noble - Publications

Affiliations: 
1999-2002 Computer Science Columbia University, New York, NY 
 2002- Genome Sciences University of Washington, Seattle, Seattle, WA 
Area:
modeling biological processes at the molecular level
Website:
http://www.gs.washington.edu/faculty/noble.htm

182 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Bai W, Noble WS, Bilmes JA. Submodular Maximization via Gradient Ascent: The Case of Deep Submodular Functions. Advances in Neural Information Processing Systems. 2018: 7989-7999. PMID 30705579  0.56
2017 Liu J, Halloran JT, Bilmes JA, Daza RM, Lee C, Mahen EM, Prunkard D, Song C, Blau S, Dorschner MO, Gadi VK, Shendure J, Blau CA, Noble WS. Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies. Scientific Reports. 7: 16943. PMID 29208983 DOI: 10.1038/s41598-017-16813-4  0.56
2017 Sakano H, Zorio DAR, Wang X, Ting YS, Noble WS, MacCoss MJ, Rubel EW, Wang Y. Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein. The Journal of Comparative Neurology. PMID 28685837 DOI: 10.1002/cne.24281  0.36
2016 The M, MacCoss MJ, Noble WS, Käll L. Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0. Journal of the American Society For Mass Spectrometry. PMID 27572102 DOI: 10.1007/s13361-016-1460-7  0.36
2016 Halloran JT, Bilmes JA, Noble WS. A dynamic Bayesian network for accurate detection of peptides from tandem mass spectra. Journal of Proteome Research. PMID 27397138 DOI: 10.1021/acs.jproteome.6b00290  0.56
2016 Wang S, Halloran JT, Bilmes JA, Noble WS. Faster and more accurate graphical model identification of tandem mass spectra using trellises. Bioinformatics (Oxford, England). 32: i322-i331. PMID 27307634 DOI: 10.1093/bioinformatics/btw269  1
2016 Smith OK, Kim R, Fu H, Martin MM, Lin CM, Utani K, Zhang Y, Marks AB, Lalande M, Chamberlain S, Libbrecht MW, Bouhassira EE, Ryan MC, Noble WS, Aladjem MI. Distinct epigenetic features of differentiation-regulated replication origins. Epigenetics & Chromatin. 9: 18. PMID 27168766 DOI: 10.1186/s13072-016-0067-3  1
2015 Yardımcı GG, Noble WS. Predictive model of 3D domain formation via CTCF-mediated extrusion. Proceedings of the National Academy of Sciences of the United States of America. 112: 14404-5. PMID 26567152 DOI: 10.1073/pnas.1519849112  1
2015 Ay F, Noble WS. Analysis methods for studying the 3D architecture of the genome. Genome Biology. 16: 183. PMID 26328929 DOI: 10.1186/s13059-015-0745-7  1
2015 Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Käll L, Aebersold RH, Smith RD, Noble WS, MacCoss MJ. Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data. Molecular & Cellular Proteomics : McP. PMID 26217018 DOI: 10.1074/mcp.O114.047035  1
2015 Keich U, Kertesz-Farkas A, Noble WS. Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics. Journal of Proteome Research. 14: 3148-61. PMID 26152888 DOI: 10.1021/acs.jproteome.5b00081  1
2015 Riffle M, Merrihew GE, Jaschob D, Sharma V, Davis TN, Noble WS, MacCoss MJ. Visualization and Dissemination of Multidimensional Proteomics Data Comparing Protein Abundance During Caenorhabditis elegans Development. Journal of the American Society For Mass Spectrometry. PMID 26133526 DOI: 10.1007/s13361-015-1193-z  1
2015 Noble WS. Mass spectrometrists should search only for peptides they care about. Nature Methods. 12: 605-8. PMID 26125591 DOI: 10.1038/nmeth.3450  1
2015 Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ. A Deeper Look into Comet-Implementation and Features. Journal of the American Society For Mass Spectrometry. PMID 26115965 DOI: 10.1007/s13361-015-1179-x  1
2015 Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins DR, Akey JM. Comprehensive identification and analysis of human accelerated regulatory DNA. Genome Research. PMID 26104583 DOI: 10.1101/gr.192591.115  1
2015 Kertesz-Farkas A, Keich U, Noble WS. Tandem mass spectrum identification via cascaded search. Journal of Proteome Research. PMID 26084232 DOI: 10.1021/pr501173s  1
2015 Dileep V, Ay F, Sima J, Vera DL, Noble WS, Gilbert DM. Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program. Genome Research. PMID 25995270 DOI: 10.1101/gr.183699.114  1
2015 Bailey TL, Johnson J, Grant CE, Noble WS. The MEME Suite. Nucleic Acids Research. PMID 25953851 DOI: 10.1093/nar/gkv416  1
2015 Libbrecht MW, Noble WS. Machine learning applications in genetics and genomics. Nature Reviews. Genetics. 16: 321-32. PMID 25948244 DOI: 10.1038/nrg3920  1
2015 Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS. Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic Acids Research. 43: 5331-9. PMID 25940625 DOI: 10.1093/nar/gkv424  1
2015 Ay F, Vu TH, Zeitz MJ, Varoquaux N, Carette JE, Vert JP, Hoffman AR, Noble WS. Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C. Bmc Genomics. 16: 121. PMID 25887659 DOI: 10.1186/s12864-015-1236-7  1
2015 Yang F, Deng X, Ma W, Berletch JB, Rabaia N, Wei G, Moore JM, Filippova GN, Xu J, Liu Y, Noble WS, Shendure J, Disteche CM. The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation. Genome Biology. 16: 52. PMID 25887447 DOI: 10.1186/s13059-015-0618-0  1
2015 Berletch JB, Ma W, Yang F, Shendure J, Noble WS, Disteche CM, Deng X. Escape from X inactivation varies in mouse tissues. Plos Genetics. 11: e1005079. PMID 25785854 DOI: 10.1371/journal.pgen.1005079  1
2015 Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS. Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression. Genome Research. 25: 544-57. PMID 25677182 DOI: 10.1101/gr.184341.114  1
2015 Keich U, Noble WS. On the importance of well-calibrated scores for identifying shotgun proteomics spectra. Journal of Proteome Research. 14: 1147-60. PMID 25482958 DOI: 10.1021/pr5010983  1
2015 Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nature Methods. 12: 71-8. PMID 25437436 DOI: 10.1038/nmeth.3205  1
2015 Ay F, Bunnik EM, Varoquaux N, Vert JP, Noble WS, Le Roch KG. Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 37: 182-94. PMID 25394267 DOI: 10.1002/bies.201400145  1
2015 Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM. Bipartite structure of the inactive mouse X chromosome Genome Biology. 16. DOI: 10.1186/s13059-015-0728-8  1
2015 Berletch JB, Ma W, Yang F, Shendure J, Noble WS, Disteche CM, Deng X. Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model Data in Brief. 5: 761-769. DOI: 10.1016/j.dib.2015.10.033  1
2015 Aydin Z, Baker D, Noble WS. Template scoring methods for protein torsion angle prediction Communications in Computer and Information Science. 574: 206-223. DOI: 10.1007/978-3-319-27707-3_13  1
2015 Aydin Z, Baker D, Noble WS. Constructing structural profiles for protein torsion angle prediction Bioinformatics 2015 - 6th International Conference On Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference On Biomedical Engineering Systems and Technologies, Biostec 2015. 26-35.  1
2014 Halloran JT, Bilmes JA, Noble WS. Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry. Uncertainty in Artificial Intelligence : Proceedings of the ... Conference. Conference On Uncertainty in Artificial Intelligence. 30: 320-329. PMID 25298752  1
2014 McIlwain S, Tamura K, Kertesz-Farkas A, Grant CE, Diament B, Frewen B, Howbert JJ, Hoopmann MR, Käll L, Eng JK, MacCoss MJ, Noble WS. Crux: rapid open source protein tandem mass spectrometry analysis. Journal of Proteome Research. 13: 4488-91. PMID 25182276 DOI: 10.1021/pr500741y  1
2014 Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, ... ... Noble WS, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/nature13415  0.68
2014 Zare H, Wang J, Hu A, Weber K, Smith J, Nickerson D, Song C, Witten D, Blau CA, Noble WS. Inferring clonal composition from multiple sections of a breast cancer. Plos Computational Biology. 10: e1003703. PMID 25010360 DOI: 10.1371/journal.pcbi.1003703  1
2014 Varoquaux N, Ay F, Noble WS, Vert JP. A statistical approach for inferring the 3D structure of the genome. Bioinformatics (Oxford, England). 30: i26-33. PMID 24931992 DOI: 10.1093/bioinformatics/btu268  1
2014 Howbert JJ, Noble WS. Computing exact p-values for a cross-correlation shotgun proteomics score function. Molecular & Cellular Proteomics : McP. 13: 2467-79. PMID 24895379 DOI: 10.1074/mcp.O113.036327  1
2014 Ma W, Noble WS, Bailey TL. Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nature Protocols. 9: 1428-50. PMID 24853928 DOI: 10.1038/nprot.2014.083  1
2014 Ay F, Bunnik EM, Varoquaux N, Bol SM, Prudhomme J, Vert JP, Noble WS, Le Roch KG. Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression. Genome Research. 24: 974-88. PMID 24671853 DOI: 10.1101/gr.169417.113  1
2014 Ay F, Bailey TL, Noble WS. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Research. 24: 999-1011. PMID 24501021 DOI: 10.1101/gr.160374.113  1
2014 Sexton BS, Avey D, Druliner BR, Fincher JA, Vera DL, Grau DJ, Borowsky ML, Gupta S, Girimurugan SB, Chicken E, Zhang J, Noble WS, Zhu F, Kingston RE, Dennis JH. The spring-loaded genome: nucleosome redistributions are widespread, transient, and DNA-directed. Genome Research. 24: 251-9. PMID 24310001 DOI: 10.1101/gr.160150.113  1
2013 Zeitz MJ, Lerner PP, Ay F, Van Nostrand E, Heidmann JD, Noble WS, Hoffman AR. Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome. Nucleus (Austin, Tex.). 4: 487-93. PMID 24448439 DOI: 10.4161/nucl.27364  1
2013 Zeitz MJ, Ay F, Heidmann JD, Lerner PL, Noble WS, Steelman BN, Hoffman AR. Genomic interaction profiles in breast cancer reveal altered chromatin architecture. Plos One. 8: e73974. PMID 24019942 DOI: 10.1371/journal.pone.0073974  1
2013 Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M, Jaschob D, Graczyk B, Shulman NJ, Wakefield J, Cooper SJ, Fields S, Noble WS, Muller EG, Davis TN, et al. Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome Research. 23: 1496-504. PMID 23720455 DOI: 10.1101/gr.155762.113  1
2013 Deng X, Berletch JB, Ma W, Nguyen DK, Hiatt JB, Noble WS, Shendure J, Disteche CM. Mammalian X upregulation is associated with enhanced transcription initiation, RNA half-life, and MOF-mediated H4K16 acetylation. Developmental Cell. 25: 55-68. PMID 23523075 DOI: 10.1016/j.devcel.2013.01.028  1
2013 Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, et al. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 31: 126-34. PMID 23354101 DOI: 10.1038/nbt.2486  1
2013 Granholm V, Navarro JF, Noble WS, Käll L. Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics. Journal of Proteomics. 80: 123-31. PMID 23268117 DOI: 10.1016/j.jprot.2012.12.007  1
2013 Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Research. 41: 827-41. PMID 23221638 DOI: 10.1093/nar/gks1284  1
2012 Singh AP, Halloran J, Bilmes JA, Kirchoff K, Noble WS. Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra. Uncertainty in Artificial Intelligence : Proceedings of the ... Conference. Conference On Uncertainty in Artificial Intelligence. 28: 775-785. PMID 25383048  1
2012 Ryu S, Goodlett DR, Noble WS, Minin VN. A statistical approach to peptide identification from clustered tandem mass spectrometry data. Proceedings. Ieee International Conference On Bioinformatics and Biomedicine. 648-653. PMID 23828149 DOI: 10.1109/BIBMW.2012.6470214  1
2012 Granholm V, Noble WS, Käll L. A cross-validation scheme for machine learning algorithms in shotgun proteomics. Bmc Bioinformatics. 13: S3. PMID 23176259 DOI: 10.1186/1471-2105-13-S16-S3  1
2012 McIlwain S, Mathews M, Bereman MS, Rubel EW, MacCoss MJ, Noble WS. Estimating relative abundances of proteins from shotgun proteomics data. Bmc Bioinformatics. 13: 308. PMID 23164367 DOI: 10.1186/1471-2105-13-308  1
2012 Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Research. 22: 1798-812. PMID 22955990 DOI: 10.1101/gr.139105.112  1
2012 Arvey A, Agius P, Noble WS, Leslie C. Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Research. 22: 1723-34. PMID 22955984 DOI: 10.1101/gr.127712.111  1
2012 Spivak M, Bereman MS, Maccoss MJ, Noble WS. Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments. Journal of Proteome Research. 11: 4499-508. PMID 22866926 DOI: 10.1021/pr300234m  1
2012 Fioramonte M, dos Santos AM, McIlwain S, Noble WS, Franchini KG, Gozzo FC. Analysis of secondary structure in proteins by chemical cross-linking coupled to MS. Proteomics. 12: 2746-52. PMID 22778071 DOI: 10.1002/pmic.201200040  1
2012 Duan Z, Andronescu M, Schutz K, Lee C, Shendure J, Fields S, Noble WS, Anthony Blau C. A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes. Methods (San Diego, Calif.). 58: 277-88. PMID 22776363 DOI: 10.1016/j.ymeth.2012.06.018  1
2012 Di Rienzi SC, Lindstrom KC, Mann T, Noble WS, Raghuraman MK, Brewer BJ. Maintaining replication origins in the face of genomic change. Genome Research. 22: 1940-52. PMID 22665441 DOI: 10.1101/gr.138248.112  1
2012 Qi Y, Oja M, Weston J, Noble WS. A unified multitask architecture for predicting local protein properties. Plos One. 7: e32235. PMID 22461885 DOI: 10.1371/journal.pone.0032235  1
2012 Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nature Methods. 9: 473-6. PMID 22426492 DOI: 10.1038/nmeth.1937  1
2012 Serang O, Noble WS. 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. 9: 809-17. PMID 22331862 DOI: 10.1109/TCBB.2012.26  1
2012 Noble WS, MacCoss MJ. Computational and statistical analysis of protein mass spectrometry data. Plos Computational Biology. 8: e1002296. PMID 22291580 DOI: 10.1371/journal.pcbi.1002296  1
2012 Witten DM, Noble WS. On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements. Nucleic Acids Research. 40: 3849-55. PMID 22266657 DOI: 10.1093/nar/gks012  1
2012 Noble WS, Blau CA, Dekker J, Duan ZJ, Mao Y. The structure and function of chromatin and chromosomes. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 434-40. PMID 22174298  1
2012 Cuellar-Partida G, Buske FA, McLeay RC, Whitington T, Noble WS, Bailey TL. Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics (Oxford, England). 28: 56-62. PMID 22072382 DOI: 10.1093/bioinformatics/btr614  1
2012 Spivak M, Weston J, Tomazela D, MacCoss MJ, Noble WS. Direct maximization of protein identifications from tandem mass spectra. Molecular & Cellular Proteomics : McP. 11: M111.012161. PMID 22052992 DOI: 10.1074/mcp.M111.012161  1
2012 Serang O, Noble W. A review of statistical methods for protein identification using tandem mass spectrometry Statistics and Its Interface. 5: 3-20.  1
2011 Buske OJ, Hoffman MM, Ponts N, Le Roch KG, Noble WS. Exploratory analysis of genomic segmentations with Segtools. Bmc Bioinformatics. 12: 415. PMID 22029426 DOI: 10.1186/1471-2105-12-415  1
2011 Diament BJ, Noble WS. Faster SEQUEST searching for peptide identification from tandem mass spectra. Journal of Proteome Research. 10: 3871-9. PMID 21761931 DOI: 10.1021/pr101196n  1
2011 Aydin Z, Singh A, Bilmes J, Noble WS. Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure. Bmc Bioinformatics. 12: 154. PMID 21569525 DOI: 10.1186/1471-2105-12-154  1
2011 Tanaka E, Bailey T, Grant CE, Noble WS, Keich U. Improved similarity scores for comparing motifs. Bioinformatics (Oxford, England). 27: 1603-9. PMID 21543443 DOI: 10.1093/bioinformatics/btr257  1
2011 Granholm V, Noble WS, Käll L. 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: 2671-8. PMID 21391616 DOI: 10.1021/pr1012619  1
2011 Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics (Oxford, England). 27: 1017-8. PMID 21330290 DOI: 10.1093/bioinformatics/btr064  1
2011 Melvin I, Weston J, Noble WS, Leslie C. Detecting remote evolutionary relationships among proteins by large-scale semantic embedding. Plos Computational Biology. 7: e1001047. PMID 21298082 DOI: 10.1371/journal.pcbi.1001047  1
2011 Hirsch E, Lim C, Dobrez D, Adams MG, Noble W. Meteorological factors and timing of the initiating event of human parturition. International Journal of Biometeorology. 55: 265-72. PMID 20526783 DOI: 10.1007/s00484-010-0332-2  1
2010 Agius P, Arvey A, Chang W, Noble WS, Leslie C. High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions. Plos Computational Biology. 6. PMID 20838582 DOI: 10.1371/journal.pcbi.1000916  1
2010 Sharma V, Eng JK, Feldman S, von Haller PD, MacCoss MJ, Noble WS. Precursor charge state prediction for electron transfer dissociation tandem mass spectra. Journal of Proteome Research. 9: 5438-44. PMID 20731383 DOI: 10.1021/pr1006685  1
2010 Serang O, MacCoss MJ, Noble WS. Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data. Journal of Proteome Research. 9: 5346-57. PMID 20712337 DOI: 10.1021/pr100594k  1
2010 Reynolds SM, Bilmes JA, Noble WS. 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: e1000834. PMID 20628623 DOI: 10.1371/journal.pcbi.1000834  1
2010 Chen X, Hoffman MM, Bilmes JA, Hesselberth JR, Noble WS. A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinformatics (Oxford, England). 26: i334-42. PMID 20529925 DOI: 10.1093/bioinformatics/btq175  1
2010 Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS. A three-dimensional model of the yeast genome. Nature. 465: 363-7. PMID 20436457 DOI: 10.1038/nature08973  1
2010 Hoffman MM, Buske OJ, Noble WS. The Genomedata format for storing large-scale functional genomics data. Bioinformatics (Oxford, England). 26: 1458-9. PMID 20435580 DOI: 10.1093/bioinformatics/btq164  1
2010 McIlwain S, Draghicescu P, Singh P, Goodlett DR, Noble WS. Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs. Journal of Proteome Research. 9: 2488-95. PMID 20349954 DOI: 10.1021/pr901163d  1
2010 Hue M, Riffle M, Vert JP, Noble WS. Large-scale prediction of protein-protein interactions from structures. Bmc Bioinformatics. 11: 144. PMID 20298601 DOI: 10.1186/1471-2105-11-144  1
2010 Aydin Z, Murray JI, Waterston RH, Noble WS. 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: 84. PMID 20146825 DOI: 10.1186/1471-2105-11-84  1
2010 Reynolds SM, Weng Z, Bilmes JA, Noble WS. Predicting nucleosome positioning using multiple evidence tracks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6044: 441-455. DOI: 10.1007/978-3-642-12683-3_29  1
2009 Noble WS. How does multiple testing correction work? Nature Biotechnology. 27: 1135-7. PMID 20010596 DOI: 10.1038/nbt1209-1135  1
2009 Noble WS. A quick guide to organizing computational biology projects. Plos Computational Biology. 5: e1000424. PMID 19649301 DOI: 10.1371/journal.pcbi.1000424  1
2009 Mann T, Humbert R, Dorschner M, Stamatoyannopoulos J, Noble WS. A thermodynamic approach to PCR primer design. Nucleic Acids Research. 37: e95. PMID 19528077 DOI: 10.1093/nar/gkp443  1
2009 Hawkins J, Grant C, Noble WS, Bailey TL. Assessing phylogenetic motif models for predicting transcription factor binding sites. Bioinformatics (Oxford, England). 25: i339-47. PMID 19478008 DOI: 10.1093/bioinformatics/btp201  1
2009 Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research. 37: W202-8. PMID 19458158 DOI: 10.1093/nar/gkp335  1
2009 Spivak M, Weston J, Bottou L, Käll L, Noble WS. Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets. Journal of Proteome Research. 8: 3737-45. PMID 19385687 DOI: 10.1021/pr801109k  1
2009 Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nature Methods. 6: 283-9. PMID 19305407 DOI: 10.1038/nmeth.1313  1
2009 Klammer AA, Park CY, Noble WS. Statistical calibration of the SEQUEST XCorr function. Journal of Proteome Research. 8: 2106-13. PMID 19275164 DOI: 10.1021/pr8011107  1
2009 Käll L, Storey JD, Noble WS. QVALITY: non-parametric estimation of q-values and posterior error probabilities. Bioinformatics (Oxford, England). 25: 964-6. PMID 19193729 DOI: 10.1093/bioinformatics/btp021  1
2009 Melvin I, Weston J, Leslie C, Noble WS. RANKPROP: a web server for protein remote homology detection. Bioinformatics (Oxford, England). 25: 121-2. PMID 18990723 DOI: 10.1093/bioinformatics/btn567  1
2009 Reynolds SM, Bilmes JA, Noble WS. On the relationship between DNA periodicity and local chromatin structure Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5541: 434-450. DOI: 10.1007/978-3-642-02008-7_31  1
2008 Reynolds SM, Käll L, Riffle ME, Bilmes JA, Noble WS. Transmembrane topology and signal peptide prediction using dynamic bayesian networks. Plos Computational Biology. 4: e1000213. PMID 18989393 DOI: 10.1371/journal.pcbi.1000213  1
2008 Melvin I, Weston J, Leslie CS, Noble WS. Combining classifiers for improved classification of proteins from sequence or structure. Bmc Bioinformatics. 9: 389. PMID 18808707 DOI: 10.1186/1471-2105-9-389  1
2008 Gupta S, Dennis J, Thurman RE, Kingston R, Stamatoyannopoulos JA, Noble WS. Predicting human nucleosome occupancy from primary sequence. Plos Computational Biology. 4: e1000134. PMID 18725940 DOI: 10.1371/journal.pcbi.1000134  1
2008 Käll L, Storey JD, Noble WS. Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. Bioinformatics (Oxford, England). 24: i42-8. PMID 18689838 DOI: 10.1093/bioinformatics/btn294  1
2008 Yosef N, Sharan R, Noble WS. Improved network-based identification of protein orthologs. Bioinformatics (Oxford, England). 24: i200-6. PMID 18689825 DOI: 10.1093/bioinformatics/btn277  1
2008 Merrihew GE, Davis C, Ewing B, Williams G, Käll L, Frewen BE, Noble WS, Green P, Thomas JH, MacCoss MJ. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Research. 18: 1660-9. PMID 18653799 DOI: 10.1101/gr.077644.108  1
2008 Obozinski G, Lanckriet G, Grant C, Jordan MI, Noble WS. Consistent probabilistic outputs for protein function prediction. Genome Biology. 9: S6. PMID 18613950 DOI: 10.1186/gb-2008-9-s1-s6  1
2008 Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, ... ... Noble WS, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology. 9: S2. PMID 18613946 DOI: 10.1186/gb-2008-9-s1-s2  1
2008 Lian H, Thompson WA, Thurman R, Stamatoyannopoulos JA, Noble WS, Lawrence CE. Automated mapping of large-scale chromatin structure in ENCODE. Bioinformatics (Oxford, England). 24: 1911-6. PMID 18591192 DOI: 10.1093/bioinformatics/btn335  1
2008 Klammer AA, Reynolds SM, Bilmes JA, MacCoss MJ, Noble WS. Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. Bioinformatics (Oxford, England). 24: i348-56. PMID 18586734 DOI: 10.1093/bioinformatics/btn189  1
2008 Park CY, Klammer AA, Käll L, MacCoss MJ, Noble WS. Rapid and accurate peptide identification from tandem mass spectra. Journal of Proteome Research. 7: 3022-7. PMID 18505281 DOI: 10.1021/pr800127y  1
2008 Qiu J, Noble WS. Predicting co-complexed protein pairs from heterogeneous data. Plos Computational Biology. 4: e1000054. PMID 18421371 DOI: 10.1371/journal.pcbi.1000054  1
2008 Thurman RE, Noble WS, Stamatoyannopoulos JA. Multi-scale correlations in continuous genomic data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 201-15. PMID 18229687  1
2008 Käll L, Storey JD, MacCoss MJ, Noble WS. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. Journal of Proteome Research. 7: 29-34. PMID 18067246 DOI: 10.1021/pr700600n  1
2008 Käll L, Storey JD, MacCoss MJ, Noble WS. Posterior error probabilities and false discovery rates: two sides of the same coin. Journal of Proteome Research. 7: 40-4. PMID 18052118 DOI: 10.1021/pr700739d  1
2008 Qiu J, Sheffler W, Baker D, Noble WS. Ranking predicted protein structures with support vector regression. Proteins. 71: 1175-82. PMID 18004754 DOI: 10.1002/prot.21809  1
2008 Noble WS, Ben-Hur A. Integrating Information for Protein Function Prediction Bioinformatics-From Genomes to Therapies. 3: 1297-1314. DOI: 10.1002/9783527619368.ch35  1
2007 Vert JP, Qiu J, Noble WS. A new pairwise kernel for biological network inference with support vector machines. Bmc Bioinformatics. 8: S8. PMID 18269702 DOI: 10.1186/1471-2105-8-S10-S8  1
2007 Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nature Methods. 4: 923-5. PMID 17952086 DOI: 10.1038/nmeth1113  1
2007 Asthana S, Noble WS, Kryukov G, Grant CE, Sunyaev S, Stamatoyannopoulos JA. Widely distributed noncoding purifying selection in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 104: 12410-5. PMID 17640883 DOI: 10.1073/pnas.0705140104  1
2007 Klammer AA, Yi X, MacCoss MJ, Noble WS. Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions. Analytical Chemistry. 79: 6111-8. PMID 17622186 DOI: 10.1021/ac070262k  1
2007 Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z. Nucleosome positioning signals in genomic DNA. Genome Research. 17: 1170-7. PMID 17620451 DOI: 10.1101/gr.6101007  1
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Noble WS, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/nature05874  1
2007 Melvin I, Ie E, Kuang R, Weston J, Noble WS, Leslie C. SVM-Fold: A tool for discriminative multi-class protein fold and superfamily recognition Bmc Bioinformatics. 8. PMID 17570145 DOI: 10.1186/1471-2105-8-S4-S2  1
2007 Dennis JH, Fan HY, Reynolds SM, Yuan G, Meldrim JC, Richter DJ, Peterson DG, Rando OJ, Noble WS, Kingston RE. Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Research. 17: 928-39. PMID 17568008 DOI: 10.1101/gr.5636607  1
2007 Thurman RE, Day N, Noble WS, Stamatoyannopoulos JA. Identification of higher-order functional domains in the human ENCODE regions. Genome Research. 17: 917-27. PMID 17568007 DOI: 10.1101/gr.6081407  1
2007 Day N, Hemmaplardh A, Thurman RE, Stamatoyannopoulos JA, Noble WS. Unsupervised segmentation of continuous genomic data. Bioinformatics (Oxford, England). 23: 1424-6. PMID 17384021 DOI: 10.1093/bioinformatics/btm096  1
2007 Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS. Quantifying similarity between motifs. Genome Biology. 8: R24. PMID 17324271 DOI: 10.1186/gb-2007-8-2-r24  1
2007 Qiu J, Hue M, Ben-Hur A, Vert JP, Noble WS. A structural alignment kernel for protein structures. Bioinformatics (Oxford, England). 23: 1090-8. PMID 17234638 DOI: 10.1093/bioinformatics/btl642  1
2007 Chechik G, Leslie C, Noble WS, Rätsch G, Morris Q, Tsuda K. NIPS workshop on new problems and methods in computational biology Bmc Bioinformatics. 8. DOI: 10.1186/1471-2105-8-S10-S1  1
2007 Klammer AA, Yi X, MacCoss MJ, Noble WS. Peptide retention time prediction yields improved tandem mass spectrum identification for diverse chromatography conditions Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4453: 459-472.  1
2007 Melvin I, Ie E, Weston J, Noble WS, Leslie C. Multi-class protein classification using adaptive codes Journal of Machine Learning Research. 8: 1557-1581.  1
2006 Noble WS. What is a support vector machine? Nature Biotechnology. 24: 1565-7. PMID 17160063 DOI: 10.1038/nbt1206-1565  1
2006 Lewis DP, Jebara T, Noble WS. Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure. Bioinformatics (Oxford, England). 22: 2753-60. PMID 16966363 DOI: 10.1093/bioinformatics/btl475  1
2006 Pramila T, Wu W, Miles S, Noble WS, Breeden LL. 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. 20: 2266-78. PMID 16912276 DOI: 10.1101/gad.1450606  1
2006 Frewen BE, Merrihew GE, Wu CC, Noble WS, MacCoss MJ. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Analytical Chemistry. 78: 5678-84. PMID 16906711 DOI: 10.1021/ac060279n  1
2006 Mann TP, Noble WS. Efficient identification of DNA hybridization partners in a sequence database. Bioinformatics (Oxford, England). 22: e350-8. PMID 16873493 DOI: 10.1093/bioinformatics/btl240  1
2006 Mann TP, Humbert R, Stamatoyannopolous JA, Noble WS. Automated validation of polymerase chain reaction amplicon melting curves. Journal of Bioinformatics and Computational Biology. 4: 299-315. PMID 16819785 DOI: 10.1142/S0219720006001989  1
2006 Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, ... ... Noble WS, et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature Methods. 3: 511-8. PMID 16791208 DOI: 10.1038/nmeth890  1
2006 Ben-Hur A, Noble WS. Choosing negative examples for the prediction of protein-protein interactions. Bmc Bioinformatics. 7: S2. PMID 16723005 DOI: 10.1186/1471-2105-7-S1-S2  1
2006 Weston J, Kuang R, Leslie C, Noble WS. Protein ranking by semi-supervised network propagation. Bmc Bioinformatics. 7: S10. PMID 16723003 DOI: 10.1186/1471-2105-7-S1-S10  1
2006 Lewis DP, Jebara T, Noble WS. Nonstationary kernel combination Acm International Conference Proceeding Series. 148: 553-560. DOI: 10.1145/1143844.1143914  1
2005 Mann TP, Humbert R, Stamatoyannopolous JA, Noble WS. Automated validation of polymerase chain reactions using amplicon melting curves. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 377-85. PMID 16447995 DOI: 10.1109/CSB.2005.17  1
2005 Klammer AA, Wu CC, MacCoss MJ, Noble WS. Peptide charge state determination for low-resolution tandem mass spectra. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 175-85. PMID 16447975 DOI: 10.1109/CSB.2005.44  1
2005 Sheffler W, Upfal E, Sedivy J, Noble WS. A learned comparative expression measure for affymetrix genechip DNA microarrays. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 144-54. PMID 16447972 DOI: 10.1109/CSB.2005.5  1
2005 Noble WS, Kuang R, Leslie C, Weston J. Identifying remote protein homologs by network propagation. The Febs Journal. 272: 5119-28. PMID 16218946 DOI: 10.1111/j.1742-4658.2005.04947.x  1
2005 Miller JP, Lo RS, Ben-Hur A, Desmarais C, Stagljar I, Noble WS, Fields S. Large-scale identification of yeast integral membrane protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 102: 12123-8. PMID 16093310 DOI: 10.1073/pnas.0505482102  1
2005 Kuang R, Weston J, Noble WS, Leslie C. Motif-based protein ranking by network propagation. Bioinformatics (Oxford, England). 21: 3711-8. PMID 16076885 DOI: 10.1093/bioinformatics/bti608  1
2005 Ben-Hur A, Noble WS. Kernel methods for predicting protein-protein interactions. Bioinformatics (Oxford, England). 21: i38-46. PMID 15961482 DOI: 10.1093/bioinformatics/bti1016  1
2005 Noble WS, Kuehn S, Thurman R, Yu M, Stamatoyannopoulos J. Predicting the in vivo signature of human gene regulatory sequences. Bioinformatics (Oxford, England). 21: i338-43. PMID 15961476 DOI: 10.1093/bioinformatics/bti1047  1
2005 Weston J, Leslie C, Ie E, Zhou D, Elisseeff A, Noble WS. Semi-supervised protein classification using cluster kernels. Bioinformatics (Oxford, England). 21: 3241-7. PMID 15905279 DOI: 10.1093/bioinformatics/bti497  1
2005 Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, et al. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology. 23: 137-44. PMID 15637633 DOI: 10.1038/nbt1053  0.56
2005 Ie E, Weston J, Noble WS, Leslie C. Multi-class protein fold recognition using adaptive codes Icml 2005 - Proceedings of the 22nd International Conference On Machine Learning. 329-336. DOI: 10.1145/1102351.1102393  1
2005 Ling CX, Noble WS, Yang Q. Guest editor's introduction to the special issue: Machine learning for bioinformatics - Part 2 Ieee/Acm Transactions On Computational Biology and Bioinformatics. 2: 177. DOI: 10.1109/TCBB.2005.41  1
2005 Ling CX, Noble WS, Yang Q. Guest editors' introduction to the special issue: Machine learning for bioinformatics - Part 1 Ieee/Acm Transactions On Computational Biology and Bioinformatics. 2: 81-82. DOI: 10.1109/TCBB.2005.25  1
2005 Vert JP, Thurman R, Noble WS. Kernels for gene regulatory regions Advances in Neural Information Processing Systems. 1401-1408.  1
2004 Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Noble WS, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/science.1105136  1
2004 Lu H, Li W, Noble WS, Payan D, Anderson DC. Riboproteomics of the hepatitis C virus internal ribosomal entry site. Journal of Proteome Research. 3: 949-57. PMID 15473682 DOI: 10.1021/pr0499592  1
2004 Noble WS. Data hoarding is harming proteomics. Nature Biotechnology. 22: 1209; discussion 120. PMID 15470451 DOI: 10.1038/nbt1004-1209a  1
2004 Tsuda K, Noble WS. Learning kernels from biological networks by maximizing entropy. Bioinformatics (Oxford, England). 20: i326-33. PMID 15262816 DOI: 10.1093/bioinformatics/bth906  1
2004 Weston J, Elisseeff A, Zhou D, Leslie CS, Noble WS. 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. 101: 6559-63. PMID 15087500 DOI: 10.1073/pnas.0308067101  1
2004 Lanckriet GR, Deng M, Cristianini N, Jordan MI, Noble WS. Kernel-based data fusion and its application to protein function prediction in yeast. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 300-11. PMID 14992512  1
2004 Pavlidis P, Wapinski I, Noble WS. Support vector machine classification on the web. Bioinformatics (Oxford, England). 20: 586-7. PMID 14990457 DOI: 10.1093/bioinformatics/btg461  1
2004 Leslie CS, Eskin E, Cohen A, Weston J, Noble WS. Mismatch string kernels for discriminative protein classification. Bioinformatics (Oxford, England). 20: 467-76. PMID 14990442 DOI: 10.1093/bioinformatics/btg431  1
2004 Wu W, Noble WS. Genomic data visualization on the Web. Bioinformatics (Oxford, England). 20: 1804-5. PMID 14988106 DOI: 10.1093/bioinformatics/bth154  1
2003 Liao L, Noble WS. 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. 10: 857-68. PMID 14980014 DOI: 10.1089/106652703322756113  1
2003 Qin J, Lewis DP, Noble WS. Kernel hierarchical gene clustering from microarray expression data. Bioinformatics (Oxford, England). 19: 2097-104. PMID 14594715 DOI: 10.1093/bioinformatics/btg288  1
2003 Gomez SM, Noble WS, Rzhetsky A. Learning to predict protein-protein interactions from protein sequences. Bioinformatics (Oxford, England). 19: 1875-81. PMID 14555619 DOI: 10.1093/bioinformatics/btg352  1
2003 Bailey TL, Noble WS. Searching for statistically significant regulatory modules. Bioinformatics (Oxford, England). 19: ii16-25. PMID 14534166 DOI: 10.1093/bioinformatics/btg1054  1
2003 Pavlidis P, Li Q, Noble WS. The effect of replication on gene expression microarray experiments. Bioinformatics (Oxford, England). 19: 1620-7. PMID 12967957 DOI: 10.1093/bioinformatics/btg227  1
2003 Gururaja T, Li W, Noble WS, Payan DG, Anderson DC. 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. PMID 12938929 DOI: 10.1021/pr034019n  1
2003 Segal NH, Pavlidis P, Antonescu CR, Maki RG, Noble WS, DeSantis D, Woodruff JM, Lewis JJ, Brennan MF, Houghton AN, Cordon-Cardo C. Classification and subtype prediction of adult soft tissue sarcoma by functional genomics. The American Journal of Pathology. 163: 691-700. PMID 12875988 DOI: 10.1016/S0002-9440(10)63696-6  1
2003 Eskin E, Noble WS, Singer Y. Protein family classification using sparse markov transducers. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 187-213. PMID 12804091 DOI: 10.1089/106652703321825964  1
2003 Segal NH, Pavlidis P, Noble WS, Antonescu CR, Viale A, Wesley UV, Busam K, Gallardo H, DeSantis D, Brennan MF, Cordon-Cardo C, Wolchok JD, Houghton AN. 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. 21: 1775-81. PMID 12721254 DOI: 10.1200/JCO.2003.10.108  1
2003 Anderson DC, Li W, Payan DG, Noble WS. 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: 137-46. PMID 12716127 DOI: 10.1021/pr0255654  1
2003 Pavlidis P, Noble WS. Matrix2png: a utility for visualizing matrix data. Bioinformatics (Oxford, England). 19: 295-6. PMID 12538257 DOI: 10.1093/bioinformatics/19.2.295  0.44
2003 Weston J, Schölkopf B, Eskin E, Leslie C, Noble WS. Dealing with large diagonals in kernel matrices Annals of the Institute of Statistical Mathematics. 55: 391-408. DOI: 10.1023/A:1026338322729  1
2003 Leslie C, Eskin E, Weston J, Noble WS. Mismatch string kernels for SVM protein classification Advances in Neural Information Processing Systems 1
2002 Eskin E, Noble WS, Singer Y. Using substitution matrices to estimate probability distributions for biological sequences. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 775-91. PMID 12614546 DOI: 10.1089/10665270260518263  1
2002 Pavlidis P, Weston J, Cai J, Noble WS. Learning gene functional classifications from multiple data types. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 401-11. PMID 12015889 DOI: 10.1089/10665270252935539  1
2002 Leslie C, Eskin E, Noble WS. The spectrum kernel: a string kernel for SVM protein classification. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 564-75. PMID 11928508  1
2002 Pavlidis P, Lewis DP, Noble WS. Exploring gene expression data with class scores. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 474-85. PMID 11928500  1
2002 Schölkopf B, Weston J, Eskin E, Leslie C, Noble WS. A kernel approach for learning from almost orthogonal patterns Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2431: 494-511.  1
2002 Liao L, Noble WS. Combining pairwise sequence similarity and support vector machines for remote protein homology detection Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 225-232.  1
2001 Pavlidis P, Noble WS. Analysis of strain and regional variation in gene expression in mouse brain. Genome Biology. 2: RESEARCH0042. PMID 11597334  1
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