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Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features.

Read DF, Cook K, Lu YY, Le Roch KG, Noble WS.

PLoS Comput Biol. 2019 Sep 11;15(9):e1007329. doi: 10.1371/journal.pcbi.1007329. [Epub ahead of print]


High-Throughput Single-Cell Sequencing with Linear Amplification.

Yin Y, Jiang Y, Lam KG, Berletch JB, Disteche CM, Noble WS, Steemers FJ, Camerini-Otero RD, Adey AC, Shendure J.

Mol Cell. 2019 Aug 28. pii: S1097-2765(19)30618-5. doi: 10.1016/j.molcel.2019.08.002. [Epub ahead of print]


Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes.

Mikan MP, Harvey HR, Timmins-Schiffman E, Riffle M, May DH, Salter I, Noble WS, Nunn BL.

ISME J. 2019 Sep 6. doi: 10.1038/s41396-019-0503-z. [Epub ahead of print]


A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types.

Libbrecht MW, Rodriguez OL, Weng Z, Bilmes JA, Hoffman MM, Noble WS.

Genome Biol. 2019 Aug 28;20(1):180. doi: 10.1186/s13059-019-1784-2.


Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units.

Bittremieux W, Laukens K, Noble WS.

J Proteome Res. 2019 Aug 30. doi: 10.1021/acs.jproteome.9b00291. [Epub ahead of print]


Speeding Up Percolator.

Halloran JT, Zhang H, Kara K, Renggli C, The M, Zhang C, Rocke DM, Käll L, Noble WS.

J Proteome Res. 2019 Sep 6;18(9):3353-3359. doi: 10.1021/acs.jproteome.9b00288. Epub 2019 Aug 23.


Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy.

Bertero A, Fields PA, Smith AST, Leonard A, Beussman K, Sniadecki NJ, Kim DH, Tse HF, Pabon L, Shendure J, Noble WS, Murry CE.

J Cell Biol. 2019 Sep 2;218(9):2919-2944. doi: 10.1083/jcb.201902117. Epub 2019 Aug 8.


Tackling gaps in developing life-changing treatments for dementia.

Mauricio R, Benn C, Davis J, Dawson G, Dawson LA, Evans A, Fox N, Gallacher J, Hutton M, Isaac J, Jones DNC, Jones L, Lalli G, Libri V, Lovestone S, Moody C, Noble W, Perry H, Pickett J, Reynolds D, Ritchie C, Rohrer JD, Routledge C, Rowe J, Snyder H, Spires-Jones T, Swartz J, Truyen L, Whiting P; Therapeutics for Dementia Consortium.

Alzheimers Dement (N Y). 2019 Jun 24;5:241-253. doi: 10.1016/j.trci.2019.05.001. eCollection 2019. Review.


Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair.

Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure J.

Nucleic Acids Res. 2019 Sep 5;47(15):7989-8003. doi: 10.1093/nar/gkz487.


LMTK2 binds to kinesin light chains to mediate anterograde axonal transport of cdk5/p35 and LMTK2 levels are reduced in Alzheimer's disease brains.

Mórotz GM, Glennon EB, Gomez-Suaga P, Lau DHW, Robinson ED, Sedlák É, Vagnoni A, Noble W, Miller CCJ.

Acta Neuropathol Commun. 2019 May 8;7(1):73. doi: 10.1186/s40478-019-0715-5.


Building interventions when distress is under debate: a case study from Appalachia.

Snell-Rood C, Jenkins R, Hudson K, Frazier C, Noble W, Feltner F.

Transcult Psychiatry. 2019 Oct;56(5):918-946. doi: 10.1177/1363461519833580. Epub 2019 May 1.


Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression.

Kim JS, He X, Liu J, Duan Z, Kim T, Gerard J, Kim B, Pillai MM, Lane WS, Noble WS, Budnik B, Waldman T.

J Biol Chem. 2019 May 31;294(22):8760-8772. doi: 10.1074/jbc.RA119.007832. Epub 2019 Apr 22.


Rural Adult Perspectives on Impact of Hearing Loss and Barriers to Care.

Powell W, Jacobs JA, Noble W, Bush ML, Snell-Rood C.

J Community Health. 2019 Aug;44(4):668-674. doi: 10.1007/s10900-019-00656-3.


Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory.

Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE.

Nat Commun. 2019 Apr 4;10(1):1538. doi: 10.1038/s41467-019-09483-5.


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.


The VAPB-PTPIP51 endoplasmic reticulum-mitochondria tethering proteins are present in neuronal synapses and regulate synaptic activity.

Gómez-Suaga P, Pérez-Nievas BG, Glennon EB, Lau DHW, Paillusson S, Mórotz GM, Calì T, Pizzo P, Noble W, Miller CCJ.

Acta Neuropathol Commun. 2019 Mar 6;7(1):35. doi: 10.1186/s40478-019-0688-4.


Sleep well to slow Alzheimer's progression?

Noble W, Spires-Jones TL.

Science. 2019 Feb 22;363(6429):813-814. doi: 10.1126/science.aaw5583. No abstract available.


Detecting Modifications in Proteomics Experiments with Param-Medic.

May DH, Tamura K, Noble WS.

J Proteome Res. 2019 Apr 5;18(4):1902-1906. doi: 10.1021/acs.jproteome.8b00954. Epub 2019 Mar 5.


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.


A pathogenic tau fragment compromises microtubules, disrupts insulin signaling and induces the unfolded protein response.

Guo T, Dakkak D, Rodriguez-Martin T, Noble W, Hanger DP.

Acta Neuropathol Commun. 2019 Jan 3;7(1):2. doi: 10.1186/s40478-018-0651-9.


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

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

Bioinformatics. 2019 Aug 15;35(16):2774-2782. doi: 10.1093/bioinformatics/bty1058.


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

Gabere MN, Noble WS.

Bioinformatics. 2019 Aug 1;35(15):2695-2696. doi: 10.1093/bioinformatics/bty1024. 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. 2019 Jan 4;18(1):86-94. doi: 10.1021/acs.jproteome.8b00365. Epub 2018 Oct 26.


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.


Characterisation of tau in the human and rodent enteric nervous system under physiological conditions and in tauopathy.

Lionnet A, Wade MA, Corbillé AG, Prigent A, Paillusson S, Tasselli M, Gonzales J, Durieu E, Rolli-Derkinderen M, Coron E, Duchalais E, Neunlist M, Perkinton MS, Hanger DP, Noble W, Derkinderen P.

Acta Neuropathol Commun. 2018 Jul 23;6(1):65. doi: 10.1186/s40478-018-0568-3.


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.


Preparation of organotypic brain slice cultures for the study of Alzheimer's disease.

Croft CL, Noble W.

Version 2. F1000Res. 2018 May 15 [revised 2018 Jan 1];7:592. doi: 10.12688/f1000research.14500.2. eCollection 2018.


Submodular Generalized Matching for Peptide Identification in Tandem Mass Spectrometry.

Bai W, Bilmes J, Noble WS.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1168-1181. doi: 10.1109/TCBB.2018.2822280. Epub 2018 Apr 2.


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.


Ammon's Horn 2 (CA2) of the Hippocampus: A Long-Known Region with a New Potential Role in Neurodegeneration.

Pang CC, Kiecker C, O'Brien JT, Noble W, Chang RC.

Neuroscientist. 2019 Apr;25(2):167-180. doi: 10.1177/1073858418778747. Epub 2018 Jun 5. Review.


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.


A new TAO kinase inhibitor reduces tau phosphorylation at sites associated with neurodegeneration in human tauopathies.

Giacomini C, Koo CY, Yankova N, Tavares IA, Wray S, Noble W, Hanger DP, Morris JDH.

Acta Neuropathol Commun. 2018 May 7;6(1):37. doi: 10.1186/s40478-018-0539-8.


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.


Protection From Dental Erosion: All Fluorides are Not Equal.

Faller RV, Noble WH.

Compend Contin Educ Dent. 2018 Mar;39(3):e13-e17.


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.

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