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Figure and Ground: How the Visual Cortex Integrates Local Cues for Global Organization.

von der Heydt R, Zhang NR.

J Neurophysiol. 2018 Jul 25. doi: 10.1152/jn.00125.2018. [Epub ahead of print]


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 Mar 31. doi: 10.1111/biom.12873. [Epub ahead of print]


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. 2017 Feb 4. doi: 10.1093/bib/bbx004. [Epub ahead of print]


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.

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