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Items: 1 to 20 of 192


Computational methods for analyzing and modeling genome structure and organization.

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

Wiley Interdiscip Rev Syst Biol Med. 2018 Jul 18:e1435. doi: 10.1002/wsbm.1435. [Epub ahead of print] 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.

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