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Nancy R. Zhang, Ph.D. - Publications

Affiliations: 
2005 Stanford University, Palo Alto, CA 
Area:
Statistics, Biostatistics Biology
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49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Zhou Z, Xu B, Minn A, Zhang NR. DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing. Genome Biology. 21: 10. PMID 31937348 DOI: 10.1186/S13059-019-1922-X  0.335
2020 Agarwal D, Wang J, Zhang NR. Data Denoising and Post-Denoising Corrections in Single Cell RNA Sequencing Statistical Science. 35: 112-128. DOI: 10.1214/19-Sts7560  0.36
2019 Agarwal D, Zhang NR. Semblance: An empirical similarity kernel on probability spaces. Science Advances. 5: eaau9630. PMID 31840051 DOI: 10.1126/Sciadv.Aau9630  0.303
2018 Jiang Y, Wang R, Urrutia E, Anastopoulos IN, Nathanson KL, Zhang NR. CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing. Genome Biology. 19: 202. PMID 30477554 DOI: 10.1186/S13059-018-1578-Y  0.387
2018 Zhou Z, Wang W, Wang LS, Zhang NR. Integrative DNA copy number detection and genotyping from sequencing and array-based platforms. Bioinformatics (Oxford, England). 34: 2349-2355. PMID 29992253 DOI: 10.1093/Bioinformatics/Bty104  0.372
2018 Xia LC, Ai D, Lee H, Andor N, Li C, Zhang NR, Ji HP. SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution. Gigascience. PMID 29982625 DOI: 10.1093/Gigascience/Giy081  0.324
2018 Wang J, Huang M, Torre E, Dueck H, Shaffer S, Murray J, Raj A, Li M, Zhang NR. Gene expression distribution deconvolution in single-cell RNA sequencing. Proceedings of the National Academy of Sciences of the United States of America. PMID 29946020 DOI: 10.1073/Pnas.1721085115  0.317
2018 Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR. SAVER: gene expression recovery for single-cell RNA sequencing. Nature Methods. PMID 29941873 DOI: 10.1038/S41592-018-0033-Z  0.31
2018 Urrutia E, Chen H, Zhou Z, Zhang NR, Jiang Y. Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny. Bioinformatics (Oxford, England). PMID 29415173 DOI: 10.1093/Bioinformatics/Bty057  0.4
2017 Xia LC, Bell JM, Wood-Bouwens C, Chen JJ, Zhang NR, Ji HP. Identification of large rearrangements in cancer genomes with barcode linked reads. Nucleic Acids Research. PMID 29186506 DOI: 10.1093/Nar/Gkx1193  0.395
2017 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, ... ... Zhang NR, et al. Genetic and Genomic Characterization of 462 Melanoma Patient-Derived Xenografts, Tumor Biopsies, and Cell Lines. Cell Reports. 21: 1936-1952. PMID 29141224 DOI: 10.1016/J.Celrep.2017.10.052  0.326
2017 Jia C, Hu Y, Kelly D, Kim J, Li M, Zhang NR. Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data. Nucleic Acids Research. PMID 29036714 DOI: 10.1093/Nar/Gkx754  0.318
2017 Chen H, Jiang Y, Maxwell KN, Nathanson KL, Zhang N. ALLELE-SPECIFIC COPY NUMBER ESTIMATION BY WHOLE EXOME SEQUENCING. The Annals of Applied Statistics. 11: 1169-1192. PMID 28989557 DOI: 10.1214/17-Aoas1043  0.375
2017 Jiang Y, Zhang NR, Li M. SCALE: modeling allele-specific gene expression by single-cell RNA sequencing. Genome Biology. 18: 74. PMID 28446220 DOI: 10.1186/S13059-017-1200-8  0.313
2017 Wang X, Chen H, Zhang NR. DNA copy number profiling using single-cell sequencing. Briefings in Bioinformatics. PMID 28159966 DOI: 10.1093/Bib/Bbx004  0.376
2016 Jiang Y, Qiu Y, Minn AJ, Zhang NR. Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing. Proceedings of the National Academy of Sciences of the United States of America. PMID 27573852 DOI: 10.1073/Pnas.1522203113  0.361
2016 Xia LC, Sakshuwong S, Hopmans ES, Bell JM, Grimes SM, Siegmund DO, Ji HP, Zhang NR. A genome-wide approach for detecting novel insertion-deletion variants of mid-range size. Nucleic Acids Research. PMID 27325742 DOI: 10.1093/Nar/Gkw481  0.657
2016 Zhang NR, Yakir B, Xia LC, Siegmund D. Scan statistics on Poisson random fields with applications in genomics The Annals of Applied Statistics. 10: 726-755. DOI: 10.1214/15-Aoas892  0.621
2016 Jiang Y, Qiu Y, Minn AJ, Zhang NR. Abstract 2373: Assessing intra-tumor heterogeneity and tracking longitudinal and spatial clonal evolution by next-generation sequencing Cancer Research. 76: 2373-2373. DOI: 10.1158/1538-7445.Am2016-2373  0.39
2015 Wang X, Chen M, Yu X, Pornputtapong N, Chen H, Zhang N, Powers RS, Krauthammer M. Global copy number profiling of cancer genomes. Bioinformatics (Oxford, England). PMID 26576652 DOI: 10.1093/Bioinformatics/Btv676  0.364
2015 Jiang Y, Oldridge DA, Diskin SJ, Zhang NR. CODEX: a normalization and copy number variation detection method for whole exome sequencing. Nucleic Acids Research. 43: e39. PMID 25618849 DOI: 10.1093/Nar/Gku1363  0.414
2015 Chen H, Bell JM, Zavala NA, Ji HP, Zhang NR. Allele-specific copy number profiling by next-generation DNA sequencing. Nucleic Acids Research. 43: e23. PMID 25477383 DOI: 10.1093/Nar/Gku1252  0.393
2015 Xia LC, Bell J, Chen J, Zhang NR, Ji HP. Abstract 4871: A new multiple feature approach for rapid and highly accurate somatic structural variation discovery from whole cancer genome sequencing Cancer Research. 75: 4871-4871. DOI: 10.1158/1538-7445.Am2015-4871  0.4
2015 Jiang Y, Oldridge DA, Diskin SJ, Zhang NR. Abstract 4868: CODEX: a normalization and copy number variation detection method for whole-exome sequencing Cancer Research. 75: 4868-4868. DOI: 10.1158/1538-7445.Am2015-4868  0.422
2013 Natsoulis G, Zhang N, Welch K, Bell J, Ji HP. Identification of Insertion Deletion Mutations from Deep Targeted Resequencing. Journal of Data Mining in Genomics & Proteomics. 4. PMID 24511426 DOI: 10.4172/2153-0602.1000132  0.34
2012 Levinson DF, Shi J, Wang K, Oh S, Riley B, Pulver AE, Wildenauer DB, Laurent C, Mowry BJ, Gejman PV, Owen MJ, Kendler KS, Nestadt G, Schwab SG, Mallet J, ... ... Zhang N, et al. Genome-wide association study of multiplex schizophrenia pedigrees. The American Journal of Psychiatry. 169: 963-73. PMID 22885689 DOI: 10.1176/Appi.Ajp.2012.11091423  0.486
2012 Zhang NR, Siegmund DO. Model selection for high-dimensional, multi-sequence change-point problems Statistica Sinica. 22: 1507-1538. DOI: 10.5705/Ss.2010.257  0.652
2012 Muralidharan O, Natsoulis G, Bell J, Ji H, Zhang NR. Detecting mutations in mixed sample sequencing data using empirical Bayes The Annals of Applied Statistics. 6: 1047-1067. DOI: 10.1214/12-Aoas538  0.386
2012 Shen JJ, Zhang NR. Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing The Annals of Applied Statistics. 6: 476-496. DOI: 10.1214/11-Aoas517  0.356
2011 Muralidharan O, Natsoulis G, Bell J, Newburger D, Xu H, Kela I, Ji H, Zhang N. A cross-sample statistical model for SNP detection in short-read sequencing data. Nucleic Acids Research. 40: e5. PMID 22064853 DOI: 10.1093/Nar/Gkr851  0.346
2011 Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, Bell J, Brown S, Holodniy M, Zhang N, Ji HP. Ultrasensitive detection of rare mutations using next-generation targeted resequencing. Nucleic Acids Research. 40: e2. PMID 22013163 DOI: 10.1093/Nar/Gkr861  0.333
2011 Natsoulis G, Bell JM, Xu H, Buenrostro JD, Ordonez H, Grimes S, Newburger D, Jensen M, Zahn JM, Zhang N, Ji HP. A flexible approach for highly multiplexed candidate gene targeted resequencing. Plos One. 6: e21088. PMID 21738606 DOI: 10.1371/Journal.Pone.0021088  0.328
2011 Chen H, Xing H, Zhang NR. Estimation of parent specific DNA copy number in tumors using high-density genotyping arrays. Plos Computational Biology. 7: e1001060. PMID 21298078 DOI: 10.1371/Journal.Pcbi.1001060  0.356
2011 Levinson DF, Duan J, Oh S, Wang K, Sanders AR, Shi J, Zhang N, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, Byerley WF, Black DW, et al. Copy number variants in schizophrenia: confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications. The American Journal of Psychiatry. 168: 302-16. PMID 21285140 DOI: 10.1176/Appi.Ajp.2010.10060876  0.462
2011 Siegmund D, Yakir B, Zhang NR. Detecting simultaneous variant intervals in aligned sequences The Annals of Applied Statistics. 5: 645-668. DOI: 10.1214/10-Aoas400  0.649
2011 Siegmund DO, Zhang NR, Yakir B. False discovery rate for scanning statistics Biometrika. 98: 979-985. DOI: 10.1093/Biomet/Asr057  0.6
2011 Efron B, Zhang NR. False discovery rates and copy number variation Biometrika. 98: 251-271. DOI: 10.1093/Biomet/Asr018  0.368
2010 Zhang NR, Siegmund DO, Ji H, Li JZ. Detecting simultaneous changepoints in multiple sequences. Biometrika. 97: 631-645. PMID 22822250 DOI: 10.1093/Biomet/Asq025  0.645
2010 Chan HP, Zhang NR, Chen LHY. Importance sampling of word patterns in DNA and protein sequences. Journal of Computational Biology. 17: 1697-1709. PMID 21128856 DOI: 10.1089/Cmb.2008.0233  0.308
2010 Zhang NR, Senbabaoglu Y, Li JZ. Joint estimation of DNA copy number from multiple platforms. Bioinformatics (Oxford, England). 26: 153-60. PMID 19933593 DOI: 10.1093/Bioinformatics/Btp653  0.364
2010 Bickel PJ, Boley N, Brown JB, Huang H, Zhang NR. Subsampling methods for genomic inference Annals of Applied Statistics. 4: 1660-1697. DOI: 10.1214/10-Aoas363  0.373
2010 Fan AC, Dermody JL, Kong C, Zhang N, Xu L, Renschler JP, Orban MW, Varasteh B, Sridhar K, Natkunam Y, Coutre SE, Greenberg P, Felsher DW. Nanoscale approaches to define biologic signatures and measure proteomic response to targeted therapies in hematologic and solid tumors Clinical Cancer Research. 16. DOI: 10.1158/Diag-10-Pr6  0.307
2010 Siegmund D, Yakir B, Zhang N. Tail Approximations for Maxima of Random Fields by Likelihood Ratio Transformations Sequential Analysis. 29: 245-262. DOI: 10.1080/07474946.2010.487428  0.603
2009 Schiffman JD, Wang Y, McPherson LA, Welch K, Zhang N, Davis R, Lacayo NJ, Dahl GV, Faham M, Ford JM, Ji HP. Molecular inversion probes reveal patterns of 9p21 deletion and copy number aberrations in childhood leukemia. Cancer Genetics and Cytogenetics. 193: 9-18. PMID 19602459 DOI: 10.1016/J.Cancergencyto.2009.03.005  0.343
2008 Lai TL, Xing H, Zhang N. Stochastic segmentation models for array-based comparative genomic hybridization data analysis. Biostatistics (Oxford, England). 9: 290-307. PMID 17855472 DOI: 10.1093/biostatistics/kxm031  0.528
2008 Zhang NR, Wildermuth MC, Speed TP. Transcription factor binding site prediction with multivariate gene expression data The Annals of Applied Statistics. 2: 332-365. DOI: 10.1214/10.1214/07-Aoas142  0.315
2007 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, ... ... Zhang NR, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.345
2007 Zhang NR, Siegmund DO. A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data. Biometrics. 63: 22-32. PMID 17447926 DOI: 10.1111/J.1541-0420.2006.00662.X  0.665
2007 Chan HP, Zhang NR. Scan Statistics With Weighted Observations Journal of the American Statistical Association. 102: 595-602. DOI: 10.1198/016214506000001392  0.376
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