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Items: 1 to 20 of 116


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.


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.


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.


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.


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.


Distinct epigenetic features of differentiation-regulated replication origins.

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.

Epigenetics Chromatin. 2016 May 10;9:18. doi: 10.1186/s13072-016-0067-3. eCollection 2016.


Technical advances in proteomics: new developments in data-independent acquisition.

Hu A, Noble WS, Wolf-Yadlin A.

F1000Res. 2016 Mar 31;5. pii: F1000 Faculty Rev-419. doi: 10.12688/f1000research.7042.1. eCollection 2016. Review.


MCAST: scanning for cis-regulatory motif clusters.

Grant CE, Johnson J, Bailey TL, Noble WS.

Bioinformatics. 2016 Apr 15;32(8):1217-9. doi: 10.1093/bioinformatics/btv750. Epub 2015 Dec 24.


Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model.

Berletch JB, Ma W, Yang F, Shendure J, Noble WS, Disteche CM, Deng X.

Data Brief. 2015 Nov 3;5:761-9. doi: 10.1016/j.dib.2015.10.033. eCollection 2015 Dec.


Predictive model of 3D domain formation via CTCF-mediated extrusion.

Yardımcı GG, Noble WS.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14404-5. doi: 10.1073/pnas.1519849112. Epub 2015 Nov 13. No abstract available.


Analysis methods for studying the 3D architecture of the genome.

Ay F, Noble WS.

Genome Biol. 2015 Sep 2;16:183. doi: 10.1186/s13059-015-0745-7. Review.


Bipartite structure of the inactive mouse X chromosome.

Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM.

Genome Biol. 2015 Aug 7;16:152. doi: 10.1186/s13059-015-0728-8.


Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data.

Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Käll L, Aebersold R, Smith RD, Noble WS, MacCoss MJ.

Mol Cell Proteomics. 2015 Sep;14(9):2301-7. doi: 10.1074/mcp.O114.047035. Epub 2015 Jul 27.


Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics.

Keich U, Kertesz-Farkas A, Noble WS.

J Proteome Res. 2015 Aug 7;14(8):3148-61. doi: 10.1021/acs.jproteome.5b00081. Epub 2015 Jul 27.


Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development.

Riffle M, Merrihew GE, Jaschob D, Sharma V, Davis TN, Noble WS, MacCoss MJ.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1827-36. doi: 10.1007/s13361-015-1193-z. Epub 2015 Jul 2.


Mass spectrometrists should search only for peptides they care about.

Noble WS.

Nat Methods. 2015 Jul;12(7):605-8. doi: 10.1038/nmeth.3450.


A deeper look into Comet--implementation and features.

Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1865-74. doi: 10.1007/s13361-015-1179-x. Epub 2015 Jun 27.


Comprehensive identification and analysis of human accelerated regulatory DNA.

Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM.

Genome Res. 2015 Sep;25(9):1245-55. doi: 10.1101/gr.192591.115. Epub 2015 Jun 23.


Tandem Mass Spectrum Identification via Cascaded Search.

Kertesz-Farkas A, Keich U, Noble WS.

J Proteome Res. 2015 Aug 7;14(8):3027-38. doi: 10.1021/pr501173s. Epub 2015 Jun 30.

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