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Measuring the reproducibility and quality of Hi-C data.

Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS.

Genome Biol. 2019 Mar 19;20(1):57. doi: 10.1186/s13059-019-1658-7.


A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.

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.

Cell. 2019 Mar 7;176(6):1516. doi: 10.1016/j.cell.2019.02.027. No abstract available.


Detecting Modifications in Proteomics Experiments with Param-Medic.

May DH, Tamura K, Noble WS.

J Proteome Res. 2019 Mar 5. doi: 10.1021/acs.jproteome.8b00954. [Epub ahead of print]


Submodular Maximization via Gradient Ascent: The Case of Deep Submodular Functions.

Bai W, Noble WS, Bilmes JA.

Adv Neural Inf Process Syst. 2018 Dec;2018:7989-7999.


A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.

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.

Cell. 2019 Jan 10;176(1-2):377-390.e19. doi: 10.1016/j.cell.2018.11.029. Epub 2019 Jan 3. Erratum in: Cell. 2019 Mar 7;176(6):1516.


MoMo: Discovery of statistically significant post-translational modification motifs.

Cheng A, Grant CE, Noble WS, Bailey TL.

Bioinformatics. 2018 Dec 31. doi: 10.1093/bioinformatics/bty1058. [Epub ahead of print]


Response to comments on "Empirical comparison of web-based antimicrobial peptide prediction tools".

Gabere MN, Noble WS.

Bioinformatics. 2018 Dec 18. doi: 10.1093/bioinformatics/bty1024. [Epub ahead of print] No abstract available.


Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate.

Keich U, Tamura K, Noble WS.

J Proteome Res. 2019 Feb 1;18(2):585-593. doi: 10.1021/acs.jproteome.8b00802. Epub 2019 Jan 3.


Controlling the FDR in imperfect matches to an incomplete database.

Keich U, Noble WS.

J Am Stat Assoc. 2018;113(523):973-982. doi: 10.1080/01621459.2017.1375931. Epub 2018 Jun 28.


Joint Precursor Elution Profile Inference via Regression for Peptide Detection in Data-Independent Acquisition Mass Spectra.

Hu A, Lu YY, Bilmes J, Noble WS.

J Proteome Res. 2018 Oct 26. doi: 10.1021/acs.jproteome.8b00365. [Epub ahead of print]


Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories.

Pino LK, Searle BC, Huang EL, Noble WS, Hoofnagle AN, MacCoss MJ.

Anal Chem. 2018 Nov 6;90(21):13112-13117. doi: 10.1021/acs.analchem.8b04581. Epub 2018 Oct 23.


Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data.

Lin A, Howbert JJ, Noble WS.

J Proteome Res. 2018 Nov 2;17(11):3644-3656. doi: 10.1021/acs.jproteome.8b00206. Epub 2018 Oct 18.


X-Chromosome Inactivation and Escape from X Inactivation in Mouse.

Ma W, Bonora G, Berletch JB, Deng X, Noble WS, Disteche CM.

Methods Mol Biol. 2018;1861:205-219. doi: 10.1007/978-1-4939-8766-5_15.


Integrative detection and analysis of structural variation in cancer genomes.

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, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F.

Nat Genet. 2018 Oct;50(10):1388-1398. doi: 10.1038/s41588-018-0195-8. Epub 2018 Sep 10.


Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing.

Bittremieux W, Meysman P, Noble WS, Laukens K.

J Proteome Res. 2018 Oct 5;17(10):3463-3474. doi: 10.1021/acs.jproteome.8b00359. Epub 2018 Sep 13.


Computational methods for analyzing and modeling genome structure and organization.

Lin D, Bonora G, Yardımcı GG, Noble WS.

Wiley Interdiscip Rev Syst Biol Med. 2019 Jan;11(1):e1435. doi: 10.1002/wsbm.1435. Epub 2018 Jul 18. Review.


Submodular generalized matching for peptide identification in tandem mass spectrometry.

Bai W, Bilmes J, Noble WS.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Apr 2. doi: 10.1109/TCBB.2018.2822280. [Epub ahead of print]


Unsupervised embedding of single-cell Hi-C data.

Liu J, Lin D, Yardimci GG, Noble WS.

Bioinformatics. 2018 Jul 1;34(13):i96-i104. doi: 10.1093/bioinformatics/bty285.


Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages.

Bunnik EM, Cook KB, Varoquaux N, Batugedara G, Prudhomme J, Cort A, Shi L, Andolina C, Ross LS, Brady D, Fidock DA, Nosten F, Tewari R, Sinnis P, Ay F, Vert JP, Noble WS, Le Roch KG.

Nat Commun. 2018 May 15;9(1):1910. doi: 10.1038/s41467-018-04295-5.


Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome.

Bonora G, Deng X, Fang H, Ramani V, Qiu R, Berletch JB, Filippova GN, Duan Z, Shendure J, Noble WS, Disteche CM.

Nat Commun. 2018 Apr 13;9(1):1445. doi: 10.1038/s41467-018-03694-y.


PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition.

Durham TJ, Libbrecht MW, Howbert JJ, Bilmes J, Noble WS.

Nat Commun. 2018 Apr 11;9(1):1402. doi: 10.1038/s41467-018-03635-9.


Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.

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.

Methods. 2018 Jun 1;142:59-73. doi: 10.1016/j.ymeth.2018.01.014. Epub 2018 Jan 31.


Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization.

Libbrecht MW, Bilmes JA, Noble WS.

Proteins. 2018 Apr;86(4):454-466. doi: 10.1002/prot.25461. Epub 2018 Feb 1.


Progressive calibration and averaging for tandem mass spectrometry statistical confidence estimation: Why settle for a single decoy?

Keich U, Noble WS.

Res Comput Mol Biol. 2017 May;10229:99-116. doi: 10.1007/978-3-319-56970-3_7. Epub 2017 Apr 12.


MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data.

Riffle M, May DH, Timmins-Schiffman E, Mikan MP, Jaschob D, Noble WS, Nunn BL.

Proteomes. 2017 Dec 27;6(1). pii: E2. doi: 10.3390/proteomes6010002.


Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies.

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.

Sci Rep. 2017 Dec 5;7(1):16943. doi: 10.1038/s41598-017-16813-4.


Segway 2.0: Gaussian mixture models and minibatch training.

Chan RCW, Libbrecht MW, Roberts EG, Bilmes JA, Noble WS, Hoffman MM.

Bioinformatics. 2018 Feb 15;34(4):669-671. doi: 10.1093/bioinformatics/btx603.


Ten simple rules for writing a response to reviewers.

Noble WS.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005730. doi: 10.1371/journal.pcbi.1005730. eCollection 2017 Oct. No abstract available.


HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.

Yang T, Zhang F, Yardımcı GG, Song F, Hardison RC, Noble WS, Yue F, Li Q.

Genome Res. 2017 Nov;27(11):1939-1949. doi: 10.1101/gr.220640.117. Epub 2017 Aug 30.


PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data.

Ting YS, Egertson JD, Bollinger JG, Searle BC, Payne SH, Noble WS, MacCoss MJ.

Nat Methods. 2017 Sep;14(9):903-908. doi: 10.1038/nmeth.4390. Epub 2017 Aug 7.


Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein.

Sakano H, Zorio DAR, Wang X, Ting YS, Noble WS, MacCoss MJ, Rubel EW, Wang Y.

J Comp Neurol. 2017 Oct 15;525(15):3341-3359. doi: 10.1002/cne.24281. Epub 2017 Jul 24.


Response to "Mass spectrometrists should search for all peptides, but assess only the ones they care about".

Noble WS, Keich U.

Nat Methods. 2017 Jun 29;14(7):644. doi: 10.1038/nmeth.4339. No abstract available.


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

Ma W, Yang L, Rohs R, Noble WS.

Bioinformatics. 2017 Oct 1;33(19):3003-3010. doi: 10.1093/bioinformatics/btx336.


The dynamic three-dimensional organization of the diploid yeast genome.

Kim S, Liachko I, Brickner DG, Cook K, Noble WS, Brickner JH, Shendure J, Dunham MJ.

Elife. 2017 May 24;6. pii: e23623. doi: 10.7554/eLife.23623.


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

Yan KK, Yardimci GG, Yan C, Noble WS, Gerstein M.

Bioinformatics. 2017 Jul 15;33(14):2199-2201. doi: 10.1093/bioinformatics/btx152.


Form and function of topologically associating genomic domains in budding yeast.

Eser U, Chandler-Brown D, Ay F, Straight AF, Duan Z, Noble WS, Skotheim JM.

Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):E3061-E3070. doi: 10.1073/pnas.1612256114. Epub 2017 Mar 27. Erratum in: Proc Natl Acad Sci U S A. 2017 Oct 10;114(41):E8801.


Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings.

May DH, Tamura K, Noble WS.

J Proteome Res. 2017 Apr 7;16(4):1817-1824. doi: 10.1021/acs.jproteome.7b00028. Epub 2017 Mar 13.


Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism.

Sychev ZE, Hu A, DiMaio TA, Gitter A, Camp ND, Noble WS, Wolf-Yadlin A, Lagunoff M.

PLoS Pathog. 2017 Mar 3;13(3):e1006256. doi: 10.1371/journal.ppat.1006256. eCollection 2017 Mar.


Empirical comparison of web-based antimicrobial peptide prediction tools.

Gabere MN, Noble WS.

Bioinformatics. 2017 Jul 1;33(13):1921-1929. doi: 10.1093/bioinformatics/btx081.


Software tools for visualizing Hi-C data.

Yardımcı GG, Noble WS.

Genome Biol. 2017 Feb 3;18(1):26. doi: 10.1186/s13059-017-1161-y. Review.


Massively multiplex single-cell Hi-C.

Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J.

Nat Methods. 2017 Mar;14(3):263-266. doi: 10.1038/nmeth.4155. Epub 2017 Jan 30.


Choosing panels of genomics assays using submodular optimization.

Wei K, Libbrecht MW, Bilmes JA, Noble WS.

Genome Biol. 2016 Nov 15;17(1):229.


Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.

Timmins-Schiffman E, May DH, Mikan M, Riffle M, Frazar C, Harvey HR, Noble WS, Nunn BL.

ISME J. 2017 Feb;11(2):309-314. doi: 10.1038/ismej.2016.132. Epub 2016 Nov 8. No abstract available.


Correction to "On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra".

Keich U, Noble WS.

J Proteome Res. 2016 Dec 2;15(12):4770-4778. Epub 2016 Oct 21. No abstract available.


Correction to "Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics".

Keich U, Kertesz-Farkas A, Noble WS.

J Proteome Res. 2016 Dec 2;15(12):4779-4780. Epub 2016 Oct 21. No abstract available.


Mapping 3D genome architecture through in situ DNase Hi-C.

Ramani V, Cusanovich DA, Hause RJ, Ma W, Qiu R, Deng X, Blau CA, Disteche CM, Noble WS, Shendure J, Duan Z.

Nat Protoc. 2016 Nov;11(11):2104-21. doi: 10.1038/nprot.2016.126. Epub 2016 Sep 29.


Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0.

The M, MacCoss MJ, Noble WS, Käll L.

J Am Soc Mass Spectrom. 2016 Nov;27(11):1719-1727. Epub 2016 Aug 29.


Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.

Halloran JT, Bilmes JA, Noble WS.

J Proteome Res. 2016 Aug 5;15(8):2749-59. doi: 10.1021/acs.jproteome.6b00290. Epub 2016 Jul 22.


An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing.

May DH, Timmins-Schiffman E, Mikan MP, Harvey HR, Borenstein E, Nunn BL, Noble WS.

J Proteome Res. 2016 Aug 5;15(8):2697-705. doi: 10.1021/acs.jproteome.6b00239. Epub 2016 Jul 19.


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

Wang S, Halloran JT, Bilmes JA, Noble WS.

Bioinformatics. 2016 Jun 15;32(12):i322-i331. doi: 10.1093/bioinformatics/btw269.

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