Hongyu Zhao

Can Yang, Lin Wang, Shuqin Zhang, Hongyu Zhao: Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping. Bioinformatics 29(8): 1026-1034 (2013)

Lisa M. Chung, John P. Ferguson, Wei Zheng, Feng Qian, Vincent Bruno, Ruth R. Montgomery, Hongyu Zhao: Differential expression analysis for paired RNA-seq data. BMC Bioinformatics 14: 110 (2013)

Xin Qi, Ruiyan Luo, Hongyu Zhao: Sparse principal component analysis by choice of norm. J. Multivariate Analysis 114: 127-160 (2013)

Gengxin Li, Joel Gelernter, Henry R. Kranzler, Hongyu Zhao: M³: an improved SNP calling algorithm for Illumina BeadArray data. Bioinformatics 28(3): 358-365 (2012)

Tiejun Tong, Liang Chen, Hongyu Zhao: Improved mean estimation and its application to diagonal discriminant analysis. Bioinformatics 28(4): 531-537 (2012)

Haisu Ma, Hongyu Zhao: iFad: an integrative factor analysis model for drug-pathway association inference^†. Bioinformatics 28(14): 1911-1918 (2012)

Haisu Ma, Hongyu Zhao: FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment. Bioinformatics 28(20): 2662-2670 (2012)

Sunghee Oh, Hongyu Zhao, James Noonan: Time Course RNA-seq: A Potential Avenue with Somewhat Different Approach in Tandem of Differential Analysis. CISIS 2012: 580-587

Liyou Yang, Hongyu Zhao, Yongqiang Wang: Application of TDMI in Government Informatization. ICPCA/SWS 2012: 697-710

Henry Horng-Shing Lu, Bernhard Schölkopf, Hongyu Zhao (Eds.): Handbook of Statistical Bioinformatics. Springer Handbooks of Computational Statistics, Springer 2011, isbn 978-3-642-16344-9

Haisu Ma, Eric E. Schadt, Lee M. Kaplan, Hongyu Zhao: COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. Bioinformatics 27(9): 1290-1298 (2011)

Wei Zheng, Lisa M. Chung, Hongyu Zhao: Bias Detection and Correction in RNA-Sequencing Data. BMC Bioinformatics 12: 290 (2011)

Zengyou He, Hongyu Zhao, Weichuan Yu: Score regularization for peptide identification. BMC Bioinformatics 12(S-1): S2 (2011)

Xin Qi, Hongyu Zhao: Some theoretical properties of Silverman's method for Smoothed functional principal component analysis. J. Multivariate Analysis 102(4): 741-767 (2011)

Hyonho Chun, Jia Kang, Xianghua Zhang, Minghua Deng, Haisu Ma, Hongyu Zhao: Reverse Engineering of Gene Regulation Networks with an Application to the DREAM4 in silico Network Challenge. Handbook of Statistical Bioinformatics 2011: 461-477

Hongyu Zhao, Xiaomei Zhang: The Training of Agricultural Extension Workers of Heilongjiang Province. CSISE (3) 2011: 235-239

Herbert Pang, Debayan Datta, Hongyu Zhao: Pathway analysis using random forests with bivariate node-split for survival outcomes. Bioinformatics 26(2): 250-258 (2010)

Hongyu Zhao, Pingzhi Fan, Vahid Tarokh: On the equivalence of interleavers for turbo codes using quadratic permutation polynomials over integer rings. IEEE Communications Letters 14(3): 236-238 (2010)

Zhelong Wang, Ming Jiang, Hongyu Zhao, Hongyi Li, Yuechao Wang: A Pilot Study on Evaluating Recovery of the Post-Operative Based on Acceleration and sEMG. BSN 2010: 3-8

Chuan Dai, Zhelong Wang, Hongyu Zhao: A Medical Tracking System for Contrast Media. LSMS/ICSEE 2010: 525-531

Zhelong Wang, Chuan Dai, Hongyu Zhao: A real time object tracking system for contrast media injection. SMC 2010: 3749-3753

Kun He, Xueyong Li, Junli Zhou, Xingwang Deng, Hongyu Zhao, Jingchu Luo: NTAP: for NimbleGen tiling array ChIP-chip data analysis. Bioinformatics 25(14): 1838-1840 (2009)

Debayan Datta, Hongyu Zhao: Effect of false positive and false negative rates on inference of binding target conservation across different conditions and species from ChIP-chip data. BMC Bioinformatics 10 (2009)

Joshua N. Sampson, Hongyu Zhao: Genotyping and inflated type I error rate in genome-wide association case/control studies. BMC Bioinformatics 10 (2009)

Hongyu Zhao, Pingzhi Fan, P. Takis Mathiopoulos, Stylianos Papaharalabos: On SNR Estimation Techniques for Turbo Decoding Over Uncorrelated Rayleigh Fading Channels With Unknown Fading Parameters. IEEE T. Vehicular Technology 58(9): 4955-4961 (2009)

Debayan Datta, Hongyu Zhao: Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. Bioinformatics 24(4): 545-552 (2008)

Jiguo Cao, Hongyu Zhao: Estimating dynamic models for gene regulation networks. Bioinformatics 24(14): 1619-1624 (2008)

Liang Chen, Tiejun Tong, Hongyu Zhao: Considering dependence among genes and markers for false discovery control in eQTL mapping. Bioinformatics 24(18): 2015-2022 (2008)

Herbert Pang, Hongyu Zhao: Building pathway clusters from Random Forests classification using class votes. BMC Bioinformatics 9 (2008)

Hongqi Gong, Lihua Li, Hongyu Zhao: Automatic Labeling System of Words in Text Materials for College English Tests. ISIP 2008: 209-213

Weichuan Yu, Junfeng Liu, Chris Colangelo, Erol Gulcicek, Hongyu Zhao: A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC-MS spectrometry. Computational Biology and Chemistry 31(3): 215-221 (2007)

Hongyu Zhao, Pingzhi Fan: A note on "a simple coefficient test for cubic permutation polynomials over integer rings". IEEE Communications Letters 11(12): 991 (2007)

Valentin Dinu, Hongyu Zhao, Perry L. Miller: Integrating domain knowledge with statistical and data mining methods for high-density genomic SNP disease association analysis. Journal of Biomedical Informatics 40(6): 750-760 (2007)

Herbert Pang, Aiping Lin, Matthew Holford, Bradley E. Enerson, Bin Lu, Michael P. Lawton, Eugenia Floyd, Hongyu Zhao: Pathway analysis using random forests classification and regression. Bioinformatics 22(16): 2028-2036 (2006)

Baolin Wu, Nianjun Liu, Hongyu Zhao: PSMIX: an R package for population structure inference via maximum likelihood method. BMC Bioinformatics 7: 317 (2006)

Weichuan Yu, Baolin Wu, Ning Lin, Kathy Stone, Kenneth Williams, Hongyu Zhao: Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Computational Biology and Chemistry 30(1): 27-38 (2006)

Weichuan Yu, Xiaoye Li, Junfeng Liu, Baolin Wu, Kenneth R. Williams, Hongyu Zhao: Multiple Peak Alignment in Sequential Data Analysis: A Scale-Space-Based Approach. IEEE/ACM Trans. Comput. Biology Bioinform. 3(3): 208-219 (2006)

Kui Zhang, Fengzhu Sun, Hongyu Zhao: HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics 21(1): 90-103 (2005)

Zhong Guan, Hongyu Zhao: A semiparametric approach for marker gene selection based on gene expression data. Bioinformatics 21(4): 529-536 (2005)

Matthew Holford, Naixin Li, Prakash M. Nadkarni, Hongyu Zhao: VitaPad: visualization tools for the analysis of pathway data. Bioinformatics 21(8): 1596-1602 (2005)

Yin Liu, Nianjun Liu, Hongyu Zhao: Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics 21(15): 3279-3285 (2005)

Tao Huang, Baolin Wu, Paul Lizardi, Hongyu Zhao: Detection of DNA copy number alterations using penalized least squares regression. Bioinformatics 21(20): 3811-3817 (2005)

Liang Chen, Hongyu Zhao: Negative correlation between compositional symmetries and local recombination rates. Bioinformatics 21(21): 3951-3958 (2005)

Nan Lin, Hongyu Zhao: Are scale-free networks robust to measurement errors? BMC Bioinformatics 6: 119 (2005)

Yinglei Lai, Hongyu Zhao: A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data. Computational Biology and Chemistry 29(1): 47-54 (2005)

Yinglei Lai, Hongyu Zhao: Erratum to "A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data": [Comput. Biol. Chem. 29(2005) 47-54]. Computational Biology and Chemistry 29(3): 258 (2005)

Nicholas Carriero, Michael V. Osier, Kei-Hoi Cheung, Perry L. Miller, Mark Gerstein, Hongyu Zhao, Baolin Wu, Scott Rifkin, Joseph T. Chang, Heping Zhang, Kevin White, Kenneth Williams, Martin H. Schultz: Case Report: A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies. JAMIA 12(1): 90-98 (2005)

Liang Chen, Hongyu Zhao: Integrating mRNA Decay Information into Co-Regulation Study. J. Comput. Sci. Technol. 20(4): 434-438 (2005)

Weichuan Yu, Xiaoye Li, Hongyu Zhao: Aligning Peaks Across Multiple Mass Spectrometry Data Sets Using A Scale-Space Based Approach. CSB Workshops 2005: 126-127

Yinglei Lai, Baolin Wu, Liang Chen, Hongyu Zhao: A statistical method for identifying differential gene-gene co-expression patterns. Bioinformatics 20(17): 3146-3155 (2004)

Michael V. Osier, Hongyu Zhao, Kei-Hoi Cheung: Handling multiple testing while interpreting microarrays with the Gene Ontology Database. BMC Bioinformatics 5: 124 (2004)

Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao: Information assessment on predicting protein-protein interactions. BMC Bioinformatics 5: 154 (2004)

Yin Liu, Hongyu Zhao: A computational approach for ordering signal transduction pathway components from genomics and proteomics Data. BMC Bioinformatics 5: 158 (2004)

Wenming Zhao, Jing Wang, Ximiao He, Xiaobing Huang, Yongzhi Jiao, Mingtao Dai, Shulin Wei, Jian Fu, Ye Chen, Xiaoyu Ren, Yong Zhang, Peixiang Ni, Jianguo Zhang, Songgang Li, Jian Wang, Gane Ka-Shu Wong, Hongyu Zhao, Jun Yu, Huanming Yang, Jun Wang: BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Research 32(Database-Issue): 377-382 (2004)

Baolin Wu, Tom Abbott, David Fishman, Walter McMurray, Gil Mor, Kathryn Stone, David Ward, Kenneth Williams, Hongyu Zhao: Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics 19(13): 1636-1643 (2003)

Deyun Pan, Ning Sun, Kei-Hoi Cheung, Zhong Guan, Ligeng Ma, Matthew Holford, Xingwang Deng, Hongyu Zhao: PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. BMC Bioinformatics 4: 56 (2003)

Shuanglin Zhang, Kui Zhang, Jinming Li, Hongyu Zhao: On a Family-Based Haplotype Pattern Mining Method for Linkage Disequilibrium Mapping. Pacific Symposium on Biocomputing 2002: 100-111

Hongyu Zhao, Feng Liang: On Relationship Inference Using Gamete Identity by Descent Data. Journal of Computational Biology 8(2): 191-200 (2001)