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Publications

Journal papers

  1. Joint principal trend analysis for longitudinal high-dimensional data
    Zhang Y, Ouyang Z
    Biometrics. 2017, Accepted.

  2. Dissecting pathway disturbances using network topology and multi-platform genomics data
    Zhang Y, Linder MH, Shojaie A, Ouyang Z, Shen R, Baggerly KA, Baladandayuthapani V, Zhao H
    Statistics in Biosciences. First Online: 04 May 2017. doi:10.1007/s12561-017-9193-0.

    [web]

  3. Genome-wide DNA methylation profiling reveals cancer-associated changes within early colonic neoplasia
    Hanley MP, Hahn MA, Li AX, Wu X, Lin J, Wang J, Choi AH, Ouyang Z, Fong Y, Pfeifer GP, Devers TJ, Rosenberg DW
    Oncogene. 2017, advance online publication 1 May 2017; doi: 10.1038/onc.2017.130.
    [web]
  1. A statistical framework for data integration through graphical models with application to cancer genomics
    Zhang Y, Ouyang Z, Zhao H
    Annals of Applied Statistics. 2017, no. 1, 161-184.

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  2. HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
    Zou C, Zhang Y, Ouyang Z
    Genome Biology. 2016 Mar 2; 17:40.
    [web]
    [software]
  1. Genome-wide probing of RNA structures in vitro using nucleases and deep sequencing
    Wan Y, Qu K, Ouyang Z, Chang HY
    Methods Mol Biol. 2016;1361:141-60.
    [web]
  1. Joint modeling of RNase footprint sequencing profiles for genome-wide inference of RNA structure
    Zou C, Ouyang Z
    Nucleic Acids Res. 2015 Oct 30;43(19):9187-97. Epub 2015 Sep 22.
    [web]
  1. Predicting quantitative outcomes of patients using longitudinal gene expression
    Zhang Y, Ouyang Z
    Sri Lankan Journal of Applied Statistics Special Issue: “Modern Statistical Methodologies in the Cutting Edge of Science”, 2014, 5:117-126.
    [web]
  1. Landscape and variation of RNA secondary structure across the human transcriptome
    Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY
    Nature, 2014, 505:706-9.
    [web]
  1. STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B cell lymphoma
    Hardee J, Ouyang Z, Zhang Y, Kundaje A, Lacroute P, Snyder MP
    G3: Genes, Genomes, Genetics. 2013, 3:2173-85.
    [web]

  2. Genome-wide mapping of RNA structure using nuclease digestion and high throughput sequencing
    Wan Y, Qu K, Ouyang Z, Chang HY
    Nature Protocols, 2013, 8:849-869.
    [web]

  3. SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
    Ouyang Z, Snyder MP, Chang HY
    Genome Research, 2013, 23:377-387. Published in Advance October 11, 2012.
    [web] [software]
  1. Genome-wide measurement of RNA folding energies
    Wan Y, Qu K, Ouyang Z, Kertesz M, Li J, Tibshirani R, Nutter RC, Segal E, Chang HY
    Molecular Cell, 2012, 48:1-13.
    [web]

  2. Architecture of the human regulatory network derived from ENCODE data
    Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M
    Nature, 2012, 489:91-100.
    [web]

  3. An integrated encyclopedia of DNA elements in the human genome
    ENCODE Project Consortium
    Nature, 2012, 489:57-74.
    [web]

  4. Correlation of global micro RNA expression with basal cell carcinoma subtype
    Heffelfinger C, Ouyang Z, Engberg A, Leffell DJ, Hanlon AM, Gordon PB, Zheng W, Zhao H, Snyder M, Bale AE
    G3: Genes, Genomes, Genetics, 2012, 2:279-86.
    [web]
  1. A new FACS approach isolates hESC derived endoderm using transcription factors
    Pan Y, Ouyang Z, Wong WH, Baker JC
    PLoS One, 2011, 6, e17536.
    [web]
  1. Noncoding RNA landmarks of pluripotency and reprogramming
    Ouyang Z, Zheng GX, Chang HY
    Cell Stem Cell, 2010, 7:649-50.
    [web]

  2. Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis
    Lee EY, Ji H, Ouyang Z, Zhou B, Ma W, Vokes SA, McMahon AP, Wong WH, Scott MP
    Proc. Natl Acad. Sci. USA, 2010, 107, 9736.
    [web]
  1. ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells
    Ouyang Z, Zhou Q, Wong WH
    Proc. Natl Acad. Sci. USA, 2009, 106:21521-21526.
    [web]
  1. Assessing the conservation of mammalian gene expression using high-density exon arrays
    Xing Y, Ouyang Z, Kapur K, Scott MP, Wong WH
    Molecular Biology and Evolution, 2007, 24:1283-1285.
    [web]

  2. Exon arrays provide accurate assessments of gene expression
    Kapur K, Xing Y, Ouyang Z, Wong WH
    Genome Biology, 2007, 8:R82.
    [web]
  1. Hierarchical structure analysis describing abnormal base composition of genomes
    Ouyang Z, Liu JK, She ZS
    Physical Review E, 2005, 72, 041915.
    [web]
  1. Scaling and hierarchical structures in DNA sequences
    Ouyang Z, Wang C, She ZS
    Physical Review Letters, 2004, 93, 078103.

    [web]

  2. Accuracy improvement for identifying translation initiation sites in microbial genomes
    Zhu H, Hu G, Ouyang Z, Wang J, She ZS
    Bioinformatics, 2004, 20, 3308-3317.
    [web]

  3. Multivariate entropy distance method for prokaryotic gene identification
    Ouyang Z, Zhu H, Wang J, She ZS
    Journal of Bioinformatics and Computational Biology, 2004, 2, 353-373.
    [web]
  1. A preliminary study to the origin and evolution of SARS-CoV
    She ZS, Yang Z, Ouyang Z, Zhu H, Wang C, Yin J
    Acta Scientiarum Naturalium Universitatis Pekinensis, 2003, 39, 809-814.
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Peer-reviewed conference papers

  1. Multi-track modeling for genome-scale reconstruction of 3D chromatin structure from Hi-C data
    Zou C, Zhang Y, Ouyang Z
    20th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2016).
    [web]

  2. Parallel implementation of SEMPHY-a structural EM algorithm for phylogenetic reconstruction
    Li E, Ouyang Z, Deng X, Zhang Y, Chen W
    Parallel Computing: Current & Future Issues of High-End Computing, Proceedings of the International Conference ParCo 2005, 33:631-638.
    [web]