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2017

  • Zhang Y. (2016) On the use of p-values in genome wide disease association mapping. J Biom Biostat, 7:3.

  • Zhang Y, An L, Yue F, Hardison RC (2016). Jointly characterizing epigenetic dynamics across multiple human cell types. Nucleic Acids Res, 44(14):6721-31.

2016

  • Chen KB, Hardison RC, Zhang Y. (2014) dCaP: detecting differential binding events in multiple conditions and proteins. BMC Genomics, 15(Suppl 9):S12.

  • Zhang Y, Ghosh S, Hakondarson H. (2014) Dynamic Bayesian testing of sets of variants in complex diseases. Genetics, 98(3):867-78.

  • Lee Y, Ghosh D, Zhang Y. (2014) Regression hidden Markov modeling reveals heterogeneous gene expression regulation: a case study in mouse embryonic stem cells. , 15:360  doi:10.1186/1471-2164-15-360

  • Lee Y, Ghosh D, Hardison RC, Zhang Y. (2014) MRHMMs: Multivariate Regression Hidden Markov Models and the variantS. , 30(12):1755-6.

2014

  • Ding Y, Tang Y, Kwok CT, Zhang Y, Bevilacqua PC, Assmann SM (2013) In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. . doi:10.1038/nature12756

  • Lee Y, Ghosh D, Zhang Y. (2013) Association testing to detect gene–gene interactions on sex chromosomes in trio data. 13 November 2013, 4:239

  • Zhang Y. (2013) De novo inference of stratification and local admixture in sequencing studies. BMC Bioinfomatics, 14(Suppl 5): S17. PMCID: PMC3622634.

  • Zhang Y. (2013) A dynamic Bayesian Markov model for phasing and characterizing haplotypes in next generation sequencing. Bioinformatics, 29(7):878-85 PMID: 23407359

  • Zhang Y. (2013) Detecting interacting mutation clusters in HIV-1 drug resistance. Proceedings of BIOINFORMATICS 2013 – International Conference on Bioinformatics Models, Methods and Algorithms.

2013

  • Song G, Riemer C, Dickins B, Kim HL, Zhang L, Zhang Y, Hsu CH, Hardison RC, NISC Comparative Sequencing Program, Green ED, Miller W (2012) Revealing Mammalian Evolutionary Relationships by Comparative Analysis of Gene Clusters. Genome Bio Evol, 4:586-601.

  • Xu J, Zhang Y. (2012) A Generalized Linear Model for Peak Calling in ChIP-Seq Data. . 19:826-838

  • Zhang Y. (2012) A Novel Bayesian Graphical Model for Genome-Wide Multi-SNP Association Mapping. Genet Epi, 36:36-37. PMID: 22127647

2012

  • Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M,Crawford GE, Furey TS, Kellis M, Miller W, Taylor J, Schuster SC, Zhang Y, Chiaromonte F, Blobel GA, Weiss MJ, Hardison RC (2011) Dynamics of the Epigenetic Landscape During Erythroid Differentiation after GATA1 Restoration. Genome Res. 21:1659–1671.

  • Zhang Y, Zhang J, Liu JS (2011) Block-Based Bayesian Epistasis Association Mapping with Application to WTCCC Type 1 Diabetes Data. Ann Appl Stat. 5:2052-2077.

  • Zhang Y and Liu JS (2011) Fast and Accurate Approximation to Significance Tests in Genome-Wide Association Studies. J Am Stat Assoc, 106:846-857.

  • Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, Hardie RA, Woodbridge P, Tindall EA, Bertelsen MF, Dixon D, Pyecroft S, Helgen KM, Lesk AM, Pringle TH, Patterson N, Zhang Y, Kreiss A, Woods GM, Jones ME, Schuster SC. (2011) Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil), Proc Natl Acad Sci. 108:12348-53

  • Song G, Hsu CH, Riemer C, Zhang Y, Kim HL, Hoffmann F, Zhang L, Hardison R, NISC Comparative Sequencing Program, Green E, Miller W (2011). Conversion Events in Gene Cluster. . 11:226

  • Zhang Y, Jiang B, Zhu J, and Liu JS (2011) Bayesian Models for Detecting Epistatic Interactions from Genetic Data. Ann Hum Genet. 75:183-193.

  • Zhang Y. (2011) Bayesian Epistasis Association Mapping via SNP Imputation. Biostatistics, 12:211-222.

2011

  • Zhang Y, Book chapter: False Positive Control for Genome-Wide ChIP-Chip Tiling Arrays. (2010) Frontiers in Computational and System Biology. Feng J., Fu W, Sun F (eds.), Springer.

  • Chen KB, Zhang Y. (2010) A Varying Threshold Method for ChIP Peak-Calling Using Multiple Sources of Information. , 26:i504-i510.

  • Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Wang Q, Nazareth LV, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Taliwal V, Hubisz MJ, Danko CG, Teo WS, Buboltz A, Zhang Z, Oosthuysen A, Steenkamp A, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova K, Nekrutenko A, Mardis ER, Patterson N, Pringle T, Chiaromonte F, Mullikin J, Eichler EE, Hardison RC, Gibbs RA, Siepel A, Harkins TT, Hayes VM (2010) Complete Khoisan and Bantu Genomes from Southern Africa. , 463: 943-947

  • Hsu CH, Zhang Y, Hardison RC, NICS Comparative Sequencing Program, Green ED, and Miller W (2010) An Effective Method for Detecting Gene Conversion Events in Whole Genomes, . 17:1281-1297.

  • Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller WC (2010) Calling SNPs without a Reference Sequence. , 11:130

  • Miller WC, Wright S, Zhang Y, Schuster SC, Hayes VM. (2010) Optimization Methods for Selecting Founder Individuals for Captive Breeding or Reintroduction of Endangered Species. Pac. Symp. Biocomput, 15:43–53

  • Hsu CH, Zhang Y, Hardison R, Miller W (2009) Whole-Genome Analysis of Gene Conversion Events. RECOMB-CG, 181-192

  • Y, Wu W,  Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, Blobel GA, Weiss MJ and Hardison RC (2009) Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications and mRNA expression. Genome Res. 19: 2172-2184.

  • Zhang Y, Song GT, Vinar T, Green ED, Siepel A, Miller W (2009) Evolutionary History Reconstruction for Mammalian Complex Gene Clusters. J Comp Biol, 16:1051-1070.

  • Zhang Y, Song GT, Hsu CH, Miller W (2009) Simultaneous History Reconstruction for Complex Gene Clusters in Multiple Species. Pac. Symp. Biocomput 14:162-173.

  • Zhang Y, Niu T (2009) Handbook on Analyzing Human Genetics Data – Computational Approaches and Software. Chapter2: Haplotype Structure. Edited by Lin SL and Zhao HY, Springer.

  • Zhang Y. (2008) Poisson Approximation for Significance in Genome-wide ChIP-chip Tiling Arrays.Bioinformatics, 24(24):2825-2831.

  • Zhang Y. (2008) Tree-guided Bayesian inference of population structures. Bioinformatics, 24:965-971.

  • Zhang Y, Song GT, Vinar T, Green ED, Siepel A, Miller W (2008) Reconstructing the evolutionary history of complex human gene clusters. Proceedings of RECOMB 2008, 29-49.

  • Zhang Y, Liu J (2007) Bayesian inference of epistatic interactions in case-control studies. Nat Genet. 39:1167-1173.

  • Zhang Y, Niu T, Liu J (2006) A coalescence-guided hierarchical Bayesian method for haplotype inference. Am J Hum Genet, 79(2):313-322.

  • Valouev A*, Zhang Y*, Schwartz DC, Waterman MS (2006) Refinement of optical map assemblies. . 22:1217-1224. (*equal contribution)

  • Valouev A, Li L, Liu Y, Schwartz DC, Yang Y, Zhang Y, Waterman MC (2006) Alignment of optical maps. 13(2):442-462.

  • Zhang Y, Waterman MS (2005) An Eulerian path approach to local multiple alignment for DNA sequences. Proc Natl Acad Sci. 102(5):1285-1290.

  • Zhang Y, Waterman MS (2003) An Eulerian path approach to global multiple alignment for DNA sequences. J. Comp. Biol., 10(6): 803-819.

  • Zhang Y, Waterman MS (2003) DNA sequence assembly and multiple DNA sequence alignment by an Eulerian path approach. Cold Spring Harb Symp Quant Biol., 68:205-212.

  • Waterman MS, Zhang Y. (2003) Eulerian path methods for multiple sequence alignment. . Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003, IEEE Computer Society, Order Number PR02000, Aug 11-14.

2010 AND BEFORE

PUBLICATIONS

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