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Data denoising with transfer learning in single-cell transcriptomics.

Wang J, Agarwal D, Huang M, Hu G, Zhou Z, Ye C, Zhang NR.

Nat Methods. 2019 Sep;16(9):875-878. doi: 10.1038/s41592-019-0537-1. Epub 2019 Aug 30.


Opposing Functions of Interferon Coordinate Adaptive and Innate Immune Responses to Cancer Immune Checkpoint Blockade.

Benci JL, Johnson LR, Choa R, Xu Y, Qiu J, Zhou Z, Xu B, Ye D, Nathanson KL, June CH, Wherry EJ, Zhang NR, Ishwaran H, Hellmann MD, Wolchok JD, Kambayashi T, Minn AJ.

Cell. 2019 Aug 8;178(4):933-948.e14. doi: 10.1016/j.cell.2019.07.019.


Use of a Bile Salt Export Pump Knockdown Rat Susceptibility Model to Interrogate Mechanism of Drug-Induced Liver Toxicity.

Li Y, Evers R, Hafey MJ, Cheon K, Duong H, Lynch D, LaFranco-Scheuch L, Pacchione S, Tamburino AM, Tanis KQ, Geddes K, Holder D, Zhang NR, Kang W, Gonzalez RJ, Galijatovic-Idrizbegovic A, Pearson KM, Lebron JA, Glaab WE, Sistare FD.

Toxicol Sci. 2019 Jul 1;170(1):180-198. doi: 10.1093/toxsci/kfz079.


Regular transient limb ischemia prevents atherosclerosis progression in hypercholesterolemic rabbits.

Zhou Y, Zhang NR, Zheng ZN, Yang Y, Lyu BF, Wang HL, Jin SQ.

Chin Med J (Engl). 2019 May 5;132(9):1079-1086. doi: 10.1097/CM9.0000000000000204.


Bulk tissue cell type deconvolution with multi-subject single-cell expression reference.

Wang X, Park J, Susztak K, Zhang NR, Li M.

Nat Commun. 2019 Jan 22;10(1):380. doi: 10.1038/s41467-018-08023-x.


CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing.

Jiang Y, Wang R, Urrutia E, Anastopoulos IN, Nathanson KL, Zhang NR.

Genome Biol. 2018 Nov 26;19(1):202. doi: 10.1186/s13059-018-1578-y.


Figure and ground: how the visual cortex integrates local cues for global organization.

von der Heydt R, Zhang NR.

J Neurophysiol. 2018 Dec 1;120(6):3085-3098. doi: 10.1152/jn.00125.2018. Epub 2018 Jul 25.


Integrative DNA copy number detection and genotyping from sequencing and array-based platforms.

Zhou Z, Wang W, Wang LS, Zhang NR.

Bioinformatics. 2018 Jul 15;34(14):2349-2355. doi: 10.1093/bioinformatics/bty104.


SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.

Xia LC, Ai D, Lee H, Andor N, Li C, Zhang NR, Ji HP.

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy081.


Gene expression distribution deconvolution in single-cell RNA sequencing.

Wang J, Huang M, Torre E, Dueck H, Shaffer S, Murray J, Raj A, Li M, Zhang NR.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):E6437-E6446. doi: 10.1073/pnas.1721085115. Epub 2018 Jun 26.


SAVER: gene expression recovery for single-cell RNA sequencing.

Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR.

Nat Methods. 2018 Jul;15(7):539-542. doi: 10.1038/s41592-018-0033-z. Epub 2018 Jun 25.


First Giant Steps Toward a Cell Atlas of Atherosclerosis.

Zhang H, Zhang NR, Li M, Reilly MP.

Circ Res. 2018 Jun 8;122(12):1632-1634. doi: 10.1161/CIRCRESAHA.118.313076. No abstract available.


Sensitivity analysis and power for instrumental variable studies.

Wang X, Jiang Y, Zhang NR, Small DS.

Biometrics. 2018 Dec;74(4):1150-1160. doi: 10.1111/biom.12873. Epub 2018 Mar 31.


Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny.

Urrutia E, Chen H, Zhou Z, Zhang NR, Jiang Y.

Bioinformatics. 2018 Jun 15;34(12):2126-2128. doi: 10.1093/bioinformatics/bty057.


Learning-dependent chromatin remodeling highlights noncoding regulatory regions linked to autism.

Koberstein JN, Poplawski SG, Wimmer ME, Porcari G, Kao C, Gomes B, Risso D, Hakonarson H, Zhang NR, Schultz RT, Abel T, Peixoto L.

Sci Signal. 2018 Jan 16;11(513). pii: eaan6500. doi: 10.1126/scisignal.aan6500.


MicroRNA‑138 promotes proliferation and suppresses mitochondrial depolarization in human pulmonary artery smooth muscle cells through targeting TASK‑1.

Liu JJ, Zhang H, Xing F, Tang B, Wu SL, Xuan L, Kang PF, Xu Q, Wang HJ, Zhang NR, Wang XJ.

Mol Med Rep. 2018 Feb;17(2):3021-3027. doi: 10.3892/mmr.2017.8200. Epub 2017 Dec 6.


MTHFR C677T gene polymorphism and the severity of coronary lesions in acute coronary syndrome.

Li MN, Wang HJ, Zhang NR, Xuan L, Shi XJ, Zhou T, Chen B, Zhang J, Li H.

Medicine (Baltimore). 2017 Dec;96(49):e9044. doi: 10.1097/MD.0000000000009044.


Identification of large rearrangements in cancer genomes with barcode linked reads.

Xia LC, Bell JM, Wood-Bouwens C, Chen JJ, Zhang NR, Ji HP.

Nucleic Acids Res. 2018 Feb 28;46(4):e19. doi: 10.1093/nar/gkx1193.


Functional germline variants as potential co-oncogenes.

Agarwal D, Nowak C, Zhang NR, Pusztai L, Hatzis C.

NPJ Breast Cancer. 2017 Nov 22;3:46. doi: 10.1038/s41523-017-0051-5. eCollection 2017. Review.


Genetic and Genomic Characterization of 462 Melanoma Patient-Derived Xenografts, Tumor Biopsies, and Cell Lines.

Garman B, Anastopoulos IN, Krepler C, Brafford P, Sproesser K, Jiang Y, Wubbenhorst B, Amaravadi R, Bennett J, Beqiri M, Elder D, Flaherty KT, Frederick DT, Gangadhar TC, Guarino M, Hoon D, Karakousis G, Liu Q, Mitra N, Petrelli NJ, Schuchter L, Shannan B, Shields CL, Wargo J, Wenz B, Wilson MA, Xiao M, Xu W, Xu X, Yin X, Zhang NR, Davies MA, Herlyn M, Nathanson KL.

Cell Rep. 2017 Nov 14;21(7):1936-1952. doi: 10.1016/j.celrep.2017.10.052.


Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data.

Jia C, Hu Y, Kelly D, Kim J, Li M, Zhang NR.

Nucleic Acids Res. 2017 Nov 2;45(19):10978-10988. doi: 10.1093/nar/gkx754.


BRCA locus-specific loss of heterozygosity in germline BRCA1 and BRCA2 carriers.

Maxwell KN, Wubbenhorst B, Wenz BM, De Sloover D, Pluta J, Emery L, Barrett A, Kraya AA, Anastopoulos IN, Yu S, Jiang Y, Chen H, Zhang NR, Hackman N, D'Andrea K, Daber R, Morrissette JJD, Mitra N, Feldman M, Domchek SM, Nathanson KL.

Nat Commun. 2017 Aug 22;8(1):319. doi: 10.1038/s41467-017-00388-9.


Corrigendum: Allelic variation contributes to bacterial host specificity.

Yue M, Han X, De Masi L, Zhu C, Ma X, Zhang J, Wu R, Schmieder R, Kaushik RS, Fraser GP, Zhao S, McDermott PF, Weill FX, Mainil JG, Arze C, Fricke WF, Edwards RA, Brisson D, Zhang NR, Rankin SC, Schifferli DM.

Nat Commun. 2017 Aug 8;8:15229. doi: 10.1038/ncomms15229.


SCALE: modeling allele-specific gene expression by single-cell RNA sequencing.

Jiang Y, Zhang NR, Li M.

Genome Biol. 2017 Apr 26;18(1):74. doi: 10.1186/s13059-017-1200-8.


DNA copy number profiling using single-cell sequencing.

Wang X, Chen H, Zhang NR.

Brief Bioinform. 2018 Sep 28;19(5):731-736. doi: 10.1093/bib/bbx004.


Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing.

Jiang Y, Qiu Y, Minn AJ, Zhang NR.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):E5528-37. doi: 10.1073/pnas.1522203113. Epub 2016 Aug 29.


A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.

Xia LC, Sakshuwong S, Hopmans ES, Bell JM, Grimes SM, Siegmund DO, Ji HP, Zhang NR.

Nucleic Acids Res. 2016 Sep 6;44(15):e126. doi: 10.1093/nar/gkw481. Epub 2016 Jun 20.


Synthesis and optimization of N-heterocyclic pyridinones as catechol-O-methyltransferase (COMT) inhibitors.

Zhao Z, Harrison ST, Schubert JW, Sanders JM, Polsky-Fisher S, Zhang NR, McLoughlin D, Gibson CR, Robinson RG, Sachs NA, Kandebo M, Yao L, Smith SM, Hutson PH, Wolkenberg SE, Barrow JC.

Bioorg Med Chem Lett. 2016 Jun 15;26(12):2952-2956. doi: 10.1016/j.bmcl.2016.03.095. Epub 2016 Apr 7.


Global copy number profiling of cancer genomes.

Wang X, Chen M, Yu X, Pornputtapong N, Chen H, Zhang NR, Powers RS, Krauthammer M.

Bioinformatics. 2016 Mar 15;32(6):926-8. doi: 10.1093/bioinformatics/btv676. Epub 2015 Nov 16.


Emergence of Hemagglutinin Mutations During the Course of Influenza Infection.

Cushing A, Kamali A, Winters M, Hopmans ES, Bell JM, Grimes SM, Xia LC, Zhang NR, Moss RB, Holodniy M, Ji HP.

Sci Rep. 2015 Nov 5;5:16178. doi: 10.1038/srep16178.


Allelic variation contributes to bacterial host specificity.

Yue M, Han X, De Masi L, Zhu C, Ma X, Zhang J, Wu R, Schmieder R, Kaushik RS, Fraser GP, Zhao S, McDermott PF, Weill FX, Mainil JG, Arze C, Fricke WF, Edwards RA, Brisson D, Zhang NR, Rankin SC, Schifferli DM.

Nat Commun. 2015 Oct 30;6:8754. doi: 10.1038/ncomms9754. Erratum in: Nat Commun. 2017 Aug 08;8:15229.


Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression.

Peixoto LL, Wimmer ME, Poplawski SG, Tudor JC, Kenworthy CA, Liu S, Mizuno K, Garcia BA, Zhang NR, Giese K, Abel T.

BMC Genomics. 2015;16 Suppl 5:S5. doi: 10.1186/1471-2164-16-S5-S5. Epub 2015 May 26.


CODEX: a normalization and copy number variation detection method for whole exome sequencing.

Jiang Y, Oldridge DA, Diskin SJ, Zhang NR.

Nucleic Acids Res. 2015 Mar 31;43(6):e39. doi: 10.1093/nar/gku1363. Epub 2015 Jan 23.


Allele-specific copy number profiling by next-generation DNA sequencing.

Chen H, Bell JM, Zavala NA, Ji HP, Zhang NR.

Nucleic Acids Res. 2015 Feb 27;43(4):e23. doi: 10.1093/nar/gku1252. Epub 2014 Dec 3.


Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer.

Nadauld LD, Garcia S, Natsoulis G, Bell JM, Miotke L, Hopmans ES, Xu H, Pai RK, Palm C, Regan JF, Chen H, Flaherty P, Ootani A, Zhang NR, Ford JM, Kuo CJ, Ji HP.

Genome Biol. 2014 Aug 27;15(8):428. doi: 10.1186/s13059-014-0428-9.


Serine 363 is required for nociceptin/orphanin FQ opioid receptor (NOPR) desensitization, internalization, and arrestin signaling.

Zhang NR, Planer W, Siuda ER, Zhao HC, Stickler L, Chang SD, Baird MA, Cao YQ, Bruchas MR.

J Biol Chem. 2012 Dec 7;287(50):42019-30. doi: 10.1074/jbc.M112.405696. Epub 2012 Oct 19.


[A preliminary study on the relationship between HLA-Cw polymorphism and susceptibility to pulmonary tuberculosis].

Zhang NR, Fan G, Deng YF, Wang XF, Lu C, Zhang CZ, Dong ZF, Zhang J, Li L, Zhao SM, Lu ZM.

Zhonghua Jie He He Hu Xi Za Zhi. 2012 Feb;35(2):120-4. Chinese.


Emerging applications for high-resolution MS in discovery bioanalysis.

Emary WB, Zhang NR.

Bioanalysis. 2011 Nov;3(22):2485-9. doi: 10.4155/bio.11.245. No abstract available.


Antiviral efficacy upon administration of a HepDirect prodrug of 2'-C-methylcytidine to hepatitis C virus-infected chimpanzees.

Carroll SS, Koeplinger K, Vavrek M, Zhang NR, Handt L, MacCoss M, Olsen DB, Reddy KR, Sun Z, van Poelje PD, Fujitaki JM, Boyer SH, Linemeyer DL, Hecker SJ, Erion MD.

Antimicrob Agents Chemother. 2011 Aug;55(8):3854-60. doi: 10.1128/AAC.01152-10. Epub 2011 May 31.


Estimation of parent specific DNA copy number in tumors using high-density genotyping arrays.

Chen H, Xing H, Zhang NR.

PLoS Comput Biol. 2011 Jan 27;7(1):e1001060. doi: 10.1371/journal.pcbi.1001060.


Importance sampling of word patterns in DNA and protein sequences.

Chan HP, Zhang NR, Chen LH.

J Comput Biol. 2010 Dec;17(12):1697-709. doi: 10.1089/cmb.2008.0233.


Sustained viral response in a hepatitis C virus-infected chimpanzee via a combination of direct-acting antiviral agents.

Olsen DB, Davies ME, Handt L, Koeplinger K, Zhang NR, Ludmerer SW, Graham D, Liverton N, MacCoss M, Hazuda D, Carroll SS.

Antimicrob Agents Chemother. 2011 Feb;55(2):937-9. doi: 10.1128/AAC.00990-10. Epub 2010 Nov 29.


Detecting simultaneous changepoints in multiple sequences.

Zhang NR, Siegmund DO, Ji H, Li JZ.

Biometrika. 2010 Sep;97(3):631-645. Epub 2010 Jun 16.


Analysis of the context integration mechanisms underlying figure-ground organization in the visual cortex.

Zhang NR, von der Heydt R.

J Neurosci. 2010 May 12;30(19):6482-96. doi: 10.1523/JNEUROSCI.5168-09.2010.



Zhou YH, Chen J, Cheng Y, Zhang NR.

Acta Crystallogr Sect E Struct Rep Online. 2010 Dec 4;67(Pt 1):m15-6. doi: 10.1107/S1600536810049275.


Joint estimation of DNA copy number from multiple platforms.

Zhang NR, Senbabaoglu Y, Li JZ.

Bioinformatics. 2010 Jan 15;26(2):153-60. doi: 10.1093/bioinformatics/btp653. Epub 2009 Nov 20.


Quantitation of small molecules using high-resolution accurate mass spectrometers - a different approach for analysis of biological samples.

Zhang NR, Yu S, Tiller P, Yeh S, Mahan E, Emary WB.

Rapid Commun Mass Spectrom. 2009 Apr;23(7):1085-94. doi: 10.1002/rcm.3975.


Robust antiviral efficacy upon administration of a nucleoside analog to hepatitis C virus-infected chimpanzees.

Carroll SS, Ludmerer S, Handt L, Koeplinger K, Zhang NR, Graham D, Davies ME, MacCoss M, Hazuda D, Olsen DB.

Antimicrob Agents Chemother. 2009 Mar;53(3):926-34. doi: 10.1128/AAC.01032-08. Epub 2008 Dec 15.


Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, 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, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

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