| Year |
Citation |
Score |
| 2023 |
Harris L, Fondrie WE, Oh S, Noble WS. Evaluating Proteomics Imputation Methods with Improved Criteria. Journal of Proteome Research. 22: 3427-3438. PMID 37861703 DOI: 10.1021/acs.jproteome.3c00205 |
0.768 |
|
| 2023 |
Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, ... ... Noble WS, et al. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. PMID 37419111 DOI: 10.1016/j.molcel.2023.06.018 |
0.517 |
|
| 2023 |
Nii Adoquaye Acquaye FL, Kertesz-Farkas A, Noble WS. Efficient Indexing of Peptides for Database Search Using Tide. Journal of Proteome Research. 22: 577-584. PMID 36633229 DOI: 10.1021/acs.jproteome.2c00617 |
0.302 |
|
| 2023 |
Kertesz-Farkas A, Nii Adoquaye Acquaye FL, Bhimani K, Eng JK, Fondrie WE, Grant C, Hoopmann MR, Lin A, Lu YY, Moritz RL, MacCoss MJ, Noble WS. The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data. Journal of Proteome Research. PMID 36598107 DOI: 10.1021/acs.jproteome.2c00615 |
0.765 |
|
| 2022 |
Dincer AB, Lu Y, Schweppe DK, Oh S, Noble WS. Reducing Peptide Sequence Bias in Quantitative Mass Spectrometry Data with Machine Learning. Journal of Proteome Research. PMID 35696663 DOI: 10.1021/acs.jproteome.2c00211 |
0.351 |
|
| 2022 |
Heil LR, Fondrie WE, McGann CD, Federation AJ, Noble WS, MacCoss MJ, Keich U. Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data. Journal of Proteome Research. 21: 1382-1391. PMID 35549345 DOI: 10.1021/acs.jproteome.1c00895 |
0.782 |
|
| 2022 |
Phipps WS, Smith KD, Yang HY, Henderson CM, Pflaum H, Lerch ML, Fondrie WE, Emrick MA, Wu CC, MacCoss MJ, Noble WS, Hoofnagle AN. Tandem Mass Spectrometry-Based Amyloid Typing Using Manual Microdissection and Open-Source Data Processing. American Journal of Clinical Pathology. 157: 748-757. PMID 35512256 DOI: 10.1093/ajcp/aqab185 |
0.741 |
|
| 2022 |
Demetci P, Santorella R, Sandstede B, Noble WS, Singh R. SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 29: 3-18. PMID 35050714 DOI: 10.1089/cmb.2021.0446 |
0.783 |
|
| 2022 |
Demetci P, Santorella R, Sandstede B, Noble WS, Singh R. Single-Cell Multiomics Integration by SCOT. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 34985990 DOI: 10.1089/cmb.2021.0477 |
0.782 |
|
| 2021 |
Whalen S, Schreiber J, Noble WS, Pollard KS. Navigating the pitfalls of applying machine learning in genomics. Nature Reviews. Genetics. PMID 34837041 DOI: 10.1038/s41576-021-00434-9 |
0.517 |
|
| 2021 |
Bonora G, Ramani V, Singh R, Fang H, Jackson DL, Srivatsan S, Qiu R, Lee C, Trapnell C, Shendure J, Duan Z, Deng X, Noble WS, Disteche CM. Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. Genome Biology. 22: 279. PMID 34579774 DOI: 10.1186/s13059-021-02432-w |
0.682 |
|
| 2021 |
Fondrie WE, Bittremieux W, Noble WS. ppx: Programmatic Access to Proteomics Data Repositories. Journal of Proteome Research. PMID 34342226 DOI: 10.1021/acs.jproteome.1c00454 |
0.758 |
|
| 2021 |
Mudge MC, Nunn BL, Firth E, Ewert M, Hales K, Fondrie WE, Noble WS, Toner J, Light B, Junge KA. Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments. Environmental Microbiology. PMID 33760340 DOI: 10.1111/1462-2920.15485 |
0.715 |
|
| 2021 |
Fondrie WE, Noble WS. mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection. Journal of Proteome Research. PMID 33596079 DOI: 10.1021/acs.jproteome.0c01010 |
0.764 |
|
| 2020 |
Singh R, Demetci P, Bonora G, Ramani V, Lee C, Fang H, Duan Z, Deng X, Shendure J, Disteche C, Noble WS. Unsupervised manifold alignment for single-cell multi-omics data. Acm-Bcb ... ... : the ... Acm Conference On Bioinformatics, Computational Biology and Biomedicine. Acm Conference On Bioinformatics, Computational Biology and Biomedicine. 2020: 1-10. PMID 33954299 DOI: 10.1145/3388440.3412410 |
0.78 |
|
| 2020 |
Schreiber J, Singh R, Bilmes J, Noble WS. A pitfall for machine learning methods aiming to predict across cell types. Genome Biology. 21: 282. PMID 33213499 DOI: 10.1186/s13059-020-02177-y |
0.705 |
|
| 2020 |
Kim HJ, Yardımcı GG, Bonora G, Ramani V, Liu J, Qiu R, Lee C, Hesson J, Ware CB, Shendure J, Duan Z, Noble WS. Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. Plos Computational Biology. 16: e1008173. PMID 32946435 DOI: 10.1371/Journal.Pcbi.1008173 |
0.337 |
|
| 2020 |
Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, ... ... Noble WS, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4 |
0.364 |
|
| 2020 |
Schreiber J, Bilmes J, Noble WS. Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples. Genome Biology. 21: 82. PMID 32228713 DOI: 10.1186/S13059-020-01978-5 |
0.341 |
|
| 2020 |
Schreiber J, Durham T, Bilmes J, Noble WS. Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome. Genome Biology. 21: 81. PMID 32228704 DOI: 10.1186/S13059-020-01977-6 |
0.356 |
|
| 2020 |
Pino LK, Searle BC, Yang HY, Hoofnagle AN, Noble WS, MacCoss MJ. Matrix-matched calibration curves for assessing analytical figures of merit in quantitative proteomics. Journal of Proteome Research. PMID 32037841 DOI: 10.1021/Acs.Jproteome.9B00666 |
0.809 |
|
| 2020 |
Cook KB, Hristov BH, Le Roch KG, Vert JP, Noble WS. Measuring significant changes in chromatin conformation with ACCOST. Nucleic Acids Research. PMID 32034421 DOI: 10.1093/nar/gkaa069 |
0.329 |
|
| 2020 |
Fondrie WE, Noble WS. A machine learning strategy that leverages large datasets to boost statistical power in small-scale experiments. Journal of Proteome Research. PMID 32009418 DOI: 10.1021/Acs.Jproteome.9B00780 |
0.757 |
|
| 2019 |
Liu J, Huang Y, Singh R, Vert JP, Noble WS. Jointly Embedding Multiple Single-Cell Omics Measurements. Algorithms in Bioinformatics : ... International Workshop, Wabi ..., Proceedings. Wabi (Workshop). 143. PMID 34632462 DOI: 10.4230/LIPIcs.WABI.2019.10 |
0.722 |
|
| 2019 |
Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z. Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells. Methods (San Diego, Calif.). PMID 31536770 DOI: 10.1016/J.Ymeth.2019.09.012 |
0.317 |
|
| 2019 |
Read DF, Cook K, Lu YY, Le Roch KG, Noble WS. Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features. Plos Computational Biology. 15: e1007329. PMID 31509524 DOI: 10.1371/journal.pcbi.1007329 |
0.31 |
|
| 2019 |
Yin Y, Jiang Y, Lam KG, Berletch JB, Disteche CM, Noble WS, Steemers FJ, Camerini-Otero RD, Adey AC, Shendure J. High-Throughput Single-Cell Sequencing with Linear Amplification. Molecular Cell. PMID 31495564 DOI: 10.1016/J.Molcel.2019.08.002 |
0.309 |
|
| 2019 |
Libbrecht MW, Rodriguez OL, Weng Z, Bilmes JA, Hoffman MM, Noble WS. A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types. Genome Biology. 20: 180. PMID 31462275 DOI: 10.1186/S13059-019-1784-2 |
0.667 |
|
| 2019 |
Bittremieux W, Laukens K, Noble WS. Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units. Journal of Proteome Research. PMID 31448616 DOI: 10.1021/acs.jproteome.9b00291 |
0.436 |
|
| 2019 |
Halloran JT, Zhang H, Kara K, Renggli C, The M, Zhang C, Rocke DM, Käll L, Noble WS. Speeding up Percolator. Journal of Proteome Research. PMID 31407580 DOI: 10.1021/acs.jproteome.9b00288 |
0.436 |
|
| 2019 |
Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure J. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. Nucleic Acids Research. PMID 31165867 DOI: 10.1093/Nar/Gkz487 |
0.308 |
|
| 2019 |
Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE. Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. Nature Communications. 10: 1538. PMID 30948719 DOI: 10.1038/S41467-019-09483-5 |
0.318 |
|
| 2019 |
May DH, Tamura K, Noble WS. Detecting modifications in proteomics experiments with Param-Medic. Journal of Proteome Research. PMID 30714740 DOI: 10.1021/Acs.Jproteome.8B00954 |
0.437 |
|
| 2019 |
Keich U, Tamura K, Noble WS. Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate. Journal of Proteome Research. 18: 585-593. PMID 30560673 DOI: 10.1021/acs.jproteome.8b00802 |
0.348 |
|
| 2018 |
Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell. PMID 30612741 DOI: 10.1016/J.Cell.2018.11.029 |
0.333 |
|
| 2018 |
Cheng A, Grant CE, Noble WS, Bailey TL. MoMo: Discovery of statistically significant post-translational modification motifs. Bioinformatics (Oxford, England). PMID 30596994 DOI: 10.1093/Bioinformatics/Bty1058 |
0.394 |
|
| 2018 |
Gabere MN, Noble WS. Response to comments on "Empirical comparison of web-based antimicrobial peptide prediction tools". Bioinformatics (Oxford, England). PMID 30561528 DOI: 10.1093/bioinformatics/bty1024 |
0.344 |
|
| 2018 |
Keich U, Noble WS. Controlling the FDR in imperfect matches to an incomplete database. Journal of the American Statistical Association. 113: 973-982. PMID 30546175 DOI: 10.1080/01621459.2017.1375931 |
0.324 |
|
| 2018 |
Hu A, Lu YY, Bilmes J, Noble WS. Joint Precursor Elution Profile Inference via Regression for Peptide Detection in Data-Independent Acquisition Mass Spectra. Journal of Proteome Research. PMID 30362768 DOI: 10.1021/Acs.Jproteome.8B00365 |
0.416 |
|
| 2018 |
Pino LK, Searle BC, Huang E, Noble WS, Hoofnagle AN, MacCoss MJ. Calibration using a single-point external reference material harmonizes quantitative mass spectrometry proteomics data between platforms and laboratories. Analytical Chemistry. PMID 30350613 DOI: 10.1021/acs.analchem.8b04581 |
0.79 |
|
| 2018 |
Lin A, Howbert JJ, Noble WS. Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2 data. Journal of Proteome Research. PMID 30221945 DOI: 10.1021/acs.jproteome.8b00206 |
0.398 |
|
| 2018 |
Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, ... ... Noble WS, et al. Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics. PMID 30202056 DOI: 10.1038/S41588-018-0195-8 |
0.336 |
|
| 2018 |
Bittremieux W, Meysman P, Noble WS, Laukens K. Fast open modification spectral library searching through approximate nearest neighbor indexing. Journal of Proteome Research. PMID 30184435 DOI: 10.1021/acs.jproteome.8b00359 |
0.41 |
|
| 2018 |
Lin D, Bonora G, Yardımcı GG, Noble WS. Computational methods for analyzing and modeling genome structure and organization. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. e1435. PMID 30022617 DOI: 10.1002/Wsbm.1435 |
0.35 |
|
| 2018 |
Bai W, Bilmes J, Noble WS. Submodular generalized matching for peptide identification in tandem mass spectrometry. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 29993658 DOI: 10.1109/Tcbb.2018.2822280 |
0.461 |
|
| 2018 |
Durham TJ, Libbrecht MW, Howbert JJ, Bilmes J, Noble WS. PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition. Nature Communications. 9: 1402. PMID 29643364 DOI: 10.1038/S41467-018-03635-9 |
0.395 |
|
| 2018 |
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. Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. Methods (San Diego, Calif.). PMID 29382556 DOI: 10.1016/J.Ymeth.2018.01.014 |
0.318 |
|
| 2018 |
Libbrecht MW, Bilmes JA, Noble WS. Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization. Proteins. PMID 29345009 DOI: 10.1002/Prot.25461 |
0.346 |
|
| 2017 |
Riffle M, May DH, Timmins-Schiffman E, Mikan MP, Jaschob D, Noble WS, Nunn BL. MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data. Proteomes. 6. PMID 29280960 DOI: 10.3390/Proteomes6010002 |
0.398 |
|
| 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 |
0.303 |
|
| 2017 |
Chan RCW, Libbrecht MW, Roberts EG, Bilmes JA, Noble WS, Hoffman MM. Segway 2.0: Gaussian mixture models and minibatch training. Bioinformatics (Oxford, England). PMID 29028889 DOI: 10.1093/Bioinformatics/Btx603 |
0.649 |
|
| 2017 |
Yang T, Zhang F, Yardimci GG, Song F, Hardison RC, Noble WS, Yue F, Li Q. HiCRep: assessing the reproducibility of Hi-C data using a stratum- adjusted correlation coefficient. Genome Research. PMID 28855260 DOI: 10.1101/Gr.220640.117 |
0.334 |
|
| 2017 |
Ting YS, Egertson JD, Bollinger JG, Searle BC, Payne SH, Noble WS, MacCoss MJ. PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data. Nature Methods. PMID 28783153 DOI: 10.1038/Nmeth.4390 |
0.623 |
|
| 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 |
0.548 |
|
| 2017 |
Noble WS, Keich U. Response to "Mass spectrometrists should search for all peptides, but assess only the ones they care about". Nature Methods. 14: 644. PMID 28661496 DOI: 10.1038/nmeth.4339 |
0.316 |
|
| 2017 |
Eser U, Chandler-Brown D, Ay F, Straight AF, Duan Z, Noble WS, Skotheim JM. Form and function of topologically associating genomic domains in budding yeast. Proceedings of the National Academy of Sciences of the United States of America. PMID 28348222 DOI: 10.1073/Pnas.1612256114 |
0.341 |
|
| 2017 |
May DH, Tamura K, Noble WS. Param-Medic: a Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings. Journal of Proteome Research. PMID 28263070 DOI: 10.1021/Acs.Jproteome.7B00028 |
0.419 |
|
| 2017 |
Gabere MN, Noble WS. Empirical comparison of web-based antimicrobial peptide prediction tools. Bioinformatics (Oxford, England). PMID 28203715 DOI: 10.1093/bioinformatics/btx081 |
0.37 |
|
| 2017 |
Yardımcı GG, Noble WS. Software tools for visualizing Hi-C data. Genome Biology. 18: 26. PMID 28159004 DOI: 10.1186/S13059-017-1161-Y |
0.313 |
|
| 2017 |
Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J. Massively multiplex single-cell Hi-C. Nature Methods. PMID 28135255 DOI: 10.1038/Nmeth.4155 |
0.314 |
|
| 2016 |
Wei K, Libbrecht MW, Bilmes JA, Noble WS. Choosing panels of genomics assays using submodular optimization. Genome Biology. 17: 229. PMID 27846892 DOI: 10.1186/S13059-016-1089-7 |
0.331 |
|
| 2016 |
Keich U, Noble WS. Correction to "On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra". Journal of Proteome Research. PMID 27767322 DOI: 10.1021/acs.jproteome.6b00843 |
0.327 |
|
| 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 |
0.643 |
|
| 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 |
0.44 |
|
| 2016 |
May DH, Timmins-Schiffman E, Mikan MP, Harvey HR, Borenstein E, Nunn BL, Noble WS. An alignment-free 'metapeptide' strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research. PMID 27396978 DOI: 10.1021/Acs.Jproteome.6B00239 |
0.416 |
|
| 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 |
0.441 |
|
| 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 |
0.327 |
|
| 2016 |
Hu A, Noble WS, Wolf-Yadlin A. Technical advances in proteomics: new developments in data-independent acquisition. F1000research. 5. PMID 27092249 DOI: 10.12688/f1000research.7042.1 |
0.438 |
|
| 2015 |
Grant CE, Johnson J, Bailey TL, Noble WS. MCAST: Scanning for cis-regulatory motif clusters. Bioinformatics (Oxford, England). PMID 26704599 DOI: 10.1093/Bioinformatics/Btv750 |
0.309 |
|
| 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 |
0.355 |
|
| 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 |
0.633 |
|
| 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 |
0.325 |
|
| 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 |
0.606 |
|
| 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 |
0.4 |
|
| 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 |
0.553 |
|
| 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 |
0.327 |
|
| 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 |
0.424 |
|
| 2015 |
Bailey TL, Johnson J, Grant CE, Noble WS. The MEME Suite. Nucleic Acids Research. PMID 25953851 DOI: 10.1093/Nar/Gkv416 |
0.36 |
|
| 2015 |
Libbrecht MW, Noble WS. Machine learning applications in genetics and genomics. Nature Reviews. Genetics. 16: 321-32. PMID 25948244 DOI: 10.1038/nrg3920 |
0.363 |
|
| 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 |
0.345 |
|
| 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 |
0.352 |
|
| 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 |
0.656 |
|
| 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 |
0.324 |
|
| 2015 |
Blau CA, Pritchard C, Dorschner MO, Blau S, Mecham B, Mahen E, Gadi V, Monsky W, Burton K, Ramirez A, Stilwell J, Kladjian E, Collins C, McCune JS, Noble WS, et al. Abstract P4-08-01: Assessing the safety and feasibility of efficient hypothesis testing in patients with metastatic triple negative breast cancer Cancer Research. 75. DOI: 10.1158/1538-7445.Sabcs14-P4-08-01 |
0.476 |
|
| 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 |
0.786 |
|
| 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 |
0.643 |
|
| 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 |
0.365 |
|
| 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 |
0.409 |
|
| 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 |
0.371 |
|
| 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 |
0.324 |
|
| 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 |
0.336 |
|
| 2014 |
Viner C, Johnson J, Grant CE, Bailey TL, Noble WS, Hoffman MM. Transcription factor motif discovery and prediction in an expanded epigenetic alphabet Genome. 57: 378-379. DOI: 10.1139/Gen-2014-0153 |
0.6 |
|
| 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 |
0.526 |
|
| 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 |
0.402 |
|
| 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 |
0.724 |
|
| 2013 |
Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 813-814. DOI: 10.1145/2506583.2506701 |
0.65 |
|
| 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 |
0.565 |
|
| 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 |
0.387 |
|
| 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 |
0.603 |
|
| 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 |
0.552 |
|
| 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 |
0.324 |
|
| 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 |
0.636 |
|
| 2012 |
Serang O, Noble W. A review of statistical methods for protein identification using tandem mass spectrometry. Statistics and Its Interface. 5: 3-20. PMID 22833779 DOI: 10.4310/Sii.2012.V5.N1.A2 |
0.753 |
|
| 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 |
0.321 |
|
| 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 |
0.302 |
|
| 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 |
0.318 |
|
| 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 |
0.564 |
|
| 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 |
0.61 |
|
| 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 |
0.748 |
|
| 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 |
0.566 |
|
| 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 |
0.344 |
|
| 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 |
0.379 |
|
| 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 |
0.609 |
|
| 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 |
0.668 |
|
| 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 |
0.796 |
|
| 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 |
0.347 |
|
| 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 |
0.331 |
|
| 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 |
0.383 |
|
| 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 |
0.354 |
|
| 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 |
0.368 |
|
| 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 |
0.376 |
|
| 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 |
0.555 |
|
| 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 |
0.8 |
|
| 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 |
0.328 |
|
| 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 |
0.713 |
|
| 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 |
0.654 |
|
| 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 |
0.59 |
|
| 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 |
0.329 |
|
| 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 |
0.329 |
|
| 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 |
0.328 |
|
| 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 |
0.364 |
|
| 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 |
0.443 |
|
| 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 |
0.489 |
|
| 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 |
0.796 |
|
| 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 |
0.335 |
|
| 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 |
0.387 |
|
| 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 |
0.373 |
|
| 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 |
0.326 |
|
| 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 |
0.616 |
|
| 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 |
0.342 |
|
| 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 |
0.574 |
|
| 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 |
0.332 |
|
| 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 |
0.811 |
|
| 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 |
0.815 |
|
| 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 |
0.373 |
|
| 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 |
0.635 |
|
| 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 |
0.563 |
|
| 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 |
0.316 |
|
| 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 |
0.364 |
|
| 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 |
0.629 |
|
| 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 |
0.337 |
|
| 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 |
0.8 |
|
| 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 |
0.302 |
|
| 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 |
0.783 |
|
| 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 |
0.351 |
|
| 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 |
0.361 |
|
| 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 |
0.317 |
|
| 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 |
0.355 |
|
| 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 |
0.332 |
|
| 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 |
0.3 |
|
| 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. |
0.537 |
|
| 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 |
0.789 |
|
| 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 |
0.309 |
|
| 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 |
0.628 |
|
| 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 |
0.317 |
|
| 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 |
0.325 |
|
| 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 |
0.337 |
|
| 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 |
0.322 |
|
| 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 |
0.336 |
|
| 2006 |
Lewis DP, Jebara T, Noble WS. Nonstationary kernel combination Acm International Conference Proceeding Series. 148: 553-560. DOI: 10.1145/1143844.1143914 |
0.732 |
|
| 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 |
0.806 |
|
| 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 |
0.328 |
|
| 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 |
0.307 |
|
| 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 |
0.331 |
|
| 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 |
0.361 |
|
| 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 |
0.371 |
|
| 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 |
0.316 |
|
| 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 |
0.379 |
|
| 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 |
0.536 |
|
| 2004 |
Noble WS. Data hoarding is harming proteomics. Nature Biotechnology. 22: 1209; discussion 120. PMID 15470451 DOI: 10.1038/nbt1004-1209a |
0.334 |
|
| 2004 |
Lanckriet GR, De Bie T, Cristianini N, Jordan MI, Noble WS. A statistical framework for genomic data fusion. Bioinformatics (Oxford, England). 20: 2626-35. PMID 15130933 DOI: 10.1093/bioinformatics/bth294 |
0.334 |
|
| 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 |
0.32 |
|
| 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 |
0.304 |
|
| 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 |
0.371 |
|
| 2004 |
Wu W, Noble WS. Genomic data visualization on the Web. Bioinformatics (Oxford, England). 20: 1804-5. PMID 14988106 DOI: 10.1093/bioinformatics/bth154 |
0.335 |
|
| 2004 |
Noble WS. Reply to 'Data hoarding is harming proteomics' Nature Biotechnology. 22: 1209-1209. DOI: 10.1038/Nbt1004-1209B |
0.334 |
|
| 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 |
0.357 |
|
| 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 |
0.68 |
|
| 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 |
0.339 |
|
| 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 |
0.319 |
|
| 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 |
0.332 |
|
| 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 |
0.305 |
|
| 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 |
0.342 |
|
| 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 |
0.433 |
|
| 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 |
0.317 |
|
| 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 |
0.389 |
|
| 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 |
0.643 |
|
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