Publications

[163] H. Pang, H. Zhao (2008)
Building pathway clusters from Random Forests classification using class votes.
BMC Bioinformatics, in press.

[162] R. A. Price, W.-D. Li, H. Zhao (2008)
FTO gene associated with extreme obesity in cases, controls and extremely discordant sister pairs.
BMC Medical Genetics, in press.

[161] Y. Liu, I. Kim, H. Zhao (2008)
Protein interaction predictions from diverse sources.
Drug Discovery Today, in press.

[160] J. Liu, H. Zhao, J. Tan, D. Luo, W. Yu, E. J. Harner (2008)
Is subcellular localization informative for modeling protein-protein interaction signal?
Research Letters in Signal Processing, in press.

[159] T. Tong, H. Zhao (2008)
Practical guidelines for assessing power and false discovery rate for a fixed sample size in microarray experiments.
Statistics in Medicine, in press.

[158] J. Liu, W. Yu, B. Wu, H. Zhao (2008)
Bayesian mass spectra peak alignment from mass charge ratios.
Cancer Informatics, in press.

[157] W. Yu, Z. He, J. Liu, H. Zhao (2008)
Improving mass spectrometry peak detection using multiple peak alignment results.
Journal of Proteome Research, in press.

[156] W. Yu, R. Z. Qi, J. Liu, H. Zhao (2008)
Mass spectrometry based quantitative proteomics data analysis methods: A Review.
In press.

[155] H. Pang, I. Kim, H. Zhao (2008)
Pathway-based methods for analyzing microarray data.

[154] S. Budel, S-O Shim, Z. Feng, H. Zhao, F. Hisama, S. M. Strittmatter (2008)
No association between schizophrenia and polymorphisms of the PlexinA2 gene in Chinese Han Trios.
/Schizophrenia Research, in press.

[153] Y. Zuo, G. Zou, J. Wang, H. Zhao, H. Liang (2008)
Optimal two-stage design for case-control association analysis incorporating genotyping errors.
Annals of Human Genetics, in press.

[152] N. Liu, K. Zhang, H. Zhao (2008)
Haplotype Association Analysis.
In Genetic Dissection of Complex Traits, edited by DC Rao, in press.

[151] D. Datta, H. Zhao (2008)
Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae.
Bioinformatics, in press.

[150] J. Wang, G. Zou, H. Zhao (2007)
DNA pooling: Methods and applications in association studies.
In Current Topics in Human Genetics, Studies in Human Diseases edited by HW Deng, H. Shen, Y-J Liu, H. Hu, in press.

[149] S. Huang, D. Ballard, Z. Wu, H. Zhao (2007)
Expression quantitative trait loci mapping.
In Current Topics in Human Genetics, Studies in Human Diseases edited by HW Deng, H. Shen, Y-J Liu, H. Hu, in press.

[148] Z. Feng, N. Liu, H. Zhao (2007)
Haplotype inference and association analysis in unrelated samples.
In Current Topics in Human Genetics, Studies in Human Diseases edited by HW Deng, H. Shen, Y-J Liu, H. Hu, in press.

[147] S. Huang, D. Ballard, H. Zhao (2007)
The role of heritability in mapping expression quantitative trait loci.
BMC Proceedings, 1: S86.

[146] B. Z. Yang, H. R. Kranzler, H. Zhao, J. R. Gruen, X. Luo, J. Gelernter (2007)
Association of haplotypic variants in DRD2, ANKK1, TTC12 and NCAM1 to alcohol dependence in independent case-control and family samples.
Hum Mol Genet. 16: 2844-2853.

[145] V. Dinu, H. Zhao, P. Miller (2007)
Integrating domain knowledge with statistical and data mining methods for high density genomic SNP disease association analysis.
Journal of Biomedical Informatics, 40: 750-760.

[144] W. Yu, J. Liu, C. Colangelo, E. Gulcicek, H. Zhao (2007)
A new protocol of analyzing isotope coded affinity tag data from high resolution LC-MS spectrometry.
Computational Biology and Chemistry, 31: 215-221.

[143] S. Wang, H. Zhao (2007)
Sample size needed to detect gene-gene interactions using linkage analysis.
Annals of Human Genetics, 71: 828-842.

[142] J. Lee, K. He, V. Stolc, H. Lee, P. Figueroa, Y. Gao, W. Tongprasit, H. Zhao, I. Lee, X. W. Deng (2007)
Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development.
Plant Cell, 19: 731-749.

[141] T-S Lee, S. Mane, T. Eid, H. Zhao, A. Lin, Z. Guan, J. H. Kim, J. Schweitzer, D. King-Stevens, P. Weber, S. S. Spencer, D. D. Spencer, N. C. De Lanerolle. (2007)
Gene expression in temporal lobe epilepsy is consistent with increased release of glutamate by astrocytes.
Molecular Medicine 13: 1-13.

[140] V. Dinu, P. Miller, H. Zhao. (2007)
Evidence for association between multiple complement pathway genes and AMD.
Genetic Epidemiology, 31: 224-237.

[139] I. Kim, Y. Liu, H. Zhao. (2007)
Bayesian methods for predicting interacting protein pairs using domain information.
Biometrics, 63: 824-833.

[138] Z. Guan, B. Wu, H. Zhao. (2007)
Nonparametric estimator of false discovery rate based on Bernstein polynomials.
Statistica Sinica, in press.

[137] Y. Liu, N. Sun, J. Liu, L. Chen, M. McIntosh, L. Zheng, H. Zhao (2007)
Identifying stage-specific genes by combining information from two different types of oligonucleotide arrays.
Methods of Microarray Data Analysis V, edited by P. McConnell, S. Lin and P. Hurban, 59-74.

[136] S. P. Wu, L. Leng, Z. Feng, N. Liu, H. Zhao, C. McDonald, A. Lee, F. C. Arnett, P. K. Gregersen, M. D. Mayes, R. Bucala R (2006)
Macrophage migration inhibitory factor promoter polymorphisms and the clinical expression of scleroderma.
Arthritis & Rheumatism 54: 3661-3669.

[135] S. S. Zhang, X. Xu, M. G. Liu, H. Zhao, M. B. Soares, C. J. Barnstable, X. Y. Fu (2006)
A biphasic pattern of gene expression during mouse retina development
BMC Developmental Biology, 6: 48.

[134] H. Pang, A. Lin, M. Holford, B. E. Enerson, B. Lu, M. P. Lawton, E. Floyd, H. Zhao (2006)
Pathway analysis using random forests classification and regression
Bioinformatics, 22: 2028-2036.

[133] B. Wu, N. Liu, H. Zhao (2006)
PSMIX: an R package for population stratification inference via maximum likelihood method
BMC Bioinformatics, 7: 317

[132] N. Liu, H. Zhao (2006)
A nonparametric approach for population structure inference using multilocus genotypes
Human Genomics, 2: 353-364

[131] X. You, M. Pan, W. Gao, H. S. Shiah, J. Tao, D. Zhang, F. Koumpouras, S. Wang, H. Zhao, J. A. Madri, D. Baker, Y. C. Cheng, Z. Yin (2006)
Effects of a novel tylophorine analog on collagen-induced arthritis through inhibition of the innate immune response
Arthritis & Rheumatism, 54: 877-886

[130] T. Tsubouchi, H. Zhao, G. S. Roeder (2006)
Crossover distribution by promoting synaptonemal complex formation together with Zip2
Developmental Cell, 10: 809-819.

[129] Y. Zuo, G. Zou, H. Zhao (2006)
Two-stage designs in case-control association analysis
Genetics, 173: 1747-1760.

[128] W. Yu, B. Wu, T. Huang, X. Li, K. Williams, H. Zhao (2005)
Statistical methods in proteomics
Springer Handbook of Engineering Statistics, 623-638 PDF

[127] B. Wu, T. Abbott, D. Fishman, W. McMurray, G. Mor, K. Stone, D. Ward, K. Williams, H. Zhao (2005)
Ovarian cancer classification based on mass spectrometry analysis of sera
Cancer Informatics, in press. PDF   Supplemental Materials

[126] W. Yu, B. Wu, J. Liu, X. Li, K. Stone, K. Williams, H. Zhao (2005)
MALDI-MS data analysis for disease biomarker discovery
New and Emerging Proteomics Techniques. Humana Press, 328: 199-216.

[125] N. Sun, R. Carroll, H. Zhao (2006)
Bayesian Error Analysis Model (BEAM) for reconstructing transcriptional regulatory networks.
Proceedings of the National Academy of Sciences, 103: 7988-7993.

[124] K. Zhang, H. Zhao (2006)
A comparison of several methods for haplotype frequency estimation and haplotype reconstruction for tightly linked markers from general pedigrees.
Genetic Epidemiology, 30: 423-437.

[123] B. E. Enerson, A. Lin, B. Lu, H. Zhao, M. P. Lawton, E. Floyd (2006)
Acute drug-induced vascular injury in beagle dogs: pathology and correlating genomic expression.
Toxicology Pathology 34: 27-32.

[122] J. Gelernter, C. Panhuysen, M. Wilcox, V. Hesselbrock, B. Rounsaville, J. Poling, R. Weiss, S. Sonne, H. Zhao, L. Farrer, H. R. Kranzler (2006)
Genomewide linkage scan for opioid dependence and related traits.
American Journal of Human Genetics, 78: 759-769.

[121] B. Wu, Z. Guan, H. Zhao (2006)
Parametric and nonparametric FDR estimation revisited.
Biometrics, in press.

[120] N. Sun, H. Zhao (2006)
A misclassification model for inferring transcriptional regulatory networks.
Bayesian Inference for Gene Expression and Proteomics. Editors: Kim-Anh Do, Peter Mueller, Marina Vannucci. 347-365.

[119] S. Wang, S. Huang, L. Zheng, H. Zhao (2006)
Mapping quantitative trait loci in non-inbred mosquito crosses.
Genetics, 172: 2293-2308.

[118] N. Liu, I. Beerman, R. Lifton, H. Zhao (2006)
Haplotype analysis in the presence of informatively missing genotype data.
Genetic Epidemiology, 30: 290-200.

[117] W. Yu, B. Wu, N. Lin, K. Stone, K. Williams, H. Zhao (2006)
Detecting and aligning peaks in mass spectrometry data with applications to MALDI.
Computational Biology and Chemistry, 30: 27-38.

[116] W. Yu, X. Li, J. Liu, B. Wu, K. Williams, H. Zhao (2006)
Multiple peak alignment in sequential data analysis: A scale-space based approach.
IEEE/ACM Trans. Computational Biology and Bioinformatics, 3: 208-219.

[115] L. A. Cupples, J. Bailey, K. C. Cartier, C. T. Falk, K. Y. Liu, Y. Ye, R. Yu, H. Zhang, Zhao H (2005)
Data mining.
Genetic Epidemiology 29 Suppl 1:S103-9.

[114] B-Z Yang, H. Zhao, H. R. Kranzler, J. Gelernter (2005)
Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment.
BMC Genetics, 6:50. PDF

[113] L. Chen, H. Zhao (2005)
Negative correlation between compositional symmetries and local recombination rates
Bioinformatics, 21: 3951-3958. PDF

[112] T. Huang, B. Wu, P. Lizardi, H. Zhao (2005)
Detection of DNA copy number alterations using penalized least squares regression
Bioinformatics, in press. PDF

[111] L. Ma, C. Chen, X. Liu, Y. Jiao, N. Su, L. Li, X. Wang, M. Cao, N. Sun, X. Zhang, J. Bao, J. Li, S. Pedersen, L. Bolund, H. Zhao, L. Yuan, G. K-S Wong, J. Wang, X. W. Deng, J. Wang (2005)
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
Genome Research, 15: 1274-1283. PDF

[110] F. W. Lohoff, T. N. Ferraro, T. Sander, H. Zhao, J. P. Dahl, W. H. Berrettini, R. J. Buono (2005)
No association between common variations in the human alpha 2 subunit gene (ATP1A2) of the sodium-potassium-transporting ATPase and idiopathic generalized epilepsy
Neuroscience Letters, 382: 33-38. PDF

[109] L. Ma, N. Sun, X. Liu, Y. Jiao, H. Zhao, X. W. Deng (2005)
Organ-specific expression of Arabidopsis genome during development
Plant Physiology, 138: 80-91. PDF

[108] Y. Liu, N. Liu, H. Zhao (2005)
Inferring protein-protein interactions through high-throughput interaction data from diverse organisms
Bioinformatics, 21: 3279-3285. PDF

[107] N. Lin, H. Zhao (2005)
Are scale-free networks robust to measurement errors?
BMC Bioinformatics, 6:119. PDF

[106] Y. Jiao, P. Jia, X. Wang, N. Su, S. Yu, D. Zhang, L. Ma, Q. Feng, Z. Jin, L. Li, Y. Xue, Z. Cheng, H. Zhao, B. Han, X. W. Deng XW (2005)
A tiling microarray expression analysis of Rice chromosome 4 suggests a chromosome-level regulation of transcription
Plant Cell, 17: 1641-1657. PDF

[105] G. Mor, I. Visintin, Y. Lai , H. Zhao, P. Schwartz, T. Rutherford, L. Yue, P. Bray-Ward, D. Ward (2005)
Serum protein markers for early detection of ovarian cancer
Proceedings of the National Academy of Sciences, 102: 7677-7682. PDF

[104] S. Wang, S. Huang, N. Liu, L. Chen, C. Oh, H. Zhao (2005)
Whole-genome linkage analysis in mapping alcoholism genes using single nucleotide polymorphisms and microsatellites
BMC Genetics 2005, 6(Suppl 1):S28. PDF

[103] C. Oh, S. Wang, N. Liu, L. Chen, H. Zhao (2005)
A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method
BMC Genetics 2005, 6(Suppl 1):S116. PDF

[102] N. Liu, L. Chen, S. Wang, C. Oh, H. Zhao (2005)
Comparison of single nucleotide polymorphisms and microsatellites in inference of population structure
BMC Genetics 2005, 6(Suppl 1):S26. PDF

[101] S. Huang, S. Wang, N. Liu, L. Chen, C. Oh, H. Zhao (2005)
Whole-genome association analysis to identify markers associated with recombination rates using single nucleotide polymorphisms and microsatellites
BMC Genetics 2005, 6(Suppl 1):S51. PDF

[100] L. Chen, N. Liu, S. Wang, C. Oh, N. J. Carriero, H. Zhao (2005)
Whole genome association studies on alcoholism comparing different phenotypes using single nucleotide polymorphisms and microsatellites
BMC Genetics 2005, 6(Suppl 1):S130. PDF

[99] B. Z. Yang, H. Zhao, H. R. Kranzler, J. Gelernter (2005)
Practical population group assignment with selected informative markers: Characteristics and properties of Bayesian clustering via STRUCTURE
Genet Epidemiology, 28: 302-312. PDF

[98] S. S. Zhang, X. Xu, J. Li, M. G. Liu, H. Zhao, M. B. Soares, C. J. Barnstable, X. Y. Fu (2005)
Comprehensive in silico functional specification of mouse retina transcripts
BMC Genomics, 6: 40. PDF

[97] L. Chen, H. Zhao (2005)
Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains
BMC Genomics, 6: 44. PDF

[96] E. Gulcicek, C. Colangelo, W. McMurray, K. Stone, B. Wu, T. Wu, H. Spratt, A. Kurosky, H. Zhao, K. Williams (2005)
Proteomics and the analysis of proteomic data
Current Protocols in Bioinformatics (Davison, D., Page, R., Petsko, G., Stormo, G., and Stein, L. eds) John Wiley and Sons, Indianapolis, IN, in press.

[95] N. Carriero, M. V. Osier, K-H Cheung, P. L. Miller, M. Gerstein, H. Zhao, B. Wu, S. Rifkin, J. Chang, H. Zhang, K. White, K. Williams, M. Schultz (2005)
A 'High Productivity/Low Maintenance' approach to high performance computation for biomedicine: four case studies
Journal of American Medical Informatics Association, 12: 90-98. PDF

[94] Y. Lai, H. Zhao (2005)
A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data
Computational Biology and Chemistry, 29: 47-54. PDF

[93] M. Holford, N. Li, P. Nadkarni, H. Zhao (2005)
VitaPad: visualization tools for the analysis of pathway data
Bioinformatics, 21: 1596-1602. PDF

[92] B. S. Kennedy, S. V. Kasl, J. Lichtman, H. Zhao (2005)
Predicting readmission stroke type among blacks and whites in California
Journal of Stroke and Cerebrovascular Disease, in press. PDF

[91] G. Zou, H. Zhao (2005)
Family-based association tests for different family structures using pooled DNA
Annals of Human Genetics, 69: 429-442. PDF

[90] L. Chen, H. Zhao (2005)
Integrating mRNA decay information into co-regulation study
Journal of Computer Science and Technology, 20: 434-438. PDF

[89] Z. Guan, H. Zhao (2005)
A semiparametric approach for marker gene selection based on gene expression data
Bioinformatics, 21: 529-536. PDF

[88] K. Zhang, F. Sun, H. Zhao. (2005)
HAPLORE: A program for haplotype reconstruction in general pedigrees without recombination.
Bioinformatics, 21: 90-103. PDF

[87] Y. Liu, H. Zhao (2004)
A computational approach for ordering signal transduction pathway components from genomics and proteomics data
BMC Bioinformatics, 5, 158 PDF

[86] F. H. Wilson, A. Hariri, A. Farhi, H. Zhao, K. F. Petersen, H. R. Toka, C. Nelson-Williams, K. M. Raja, M. Kashgarian, G. I. Shulman, S. J. Scheinman, R. P. Lifton (2004)
A cluster of metabolic defects caused by mutation in a mitochondrial tRNA
Science, 306: 1190-1194. PDF

[85] N. Lin, B. Wu, R. Jansen, M. Gerstein, H. Zhao (2004)
Information assessment on predicting protein-protein interactions
BMC Bioinformatics, 5, 154. PDF

[84] Y. Gao, J. Li, E. Strickland, S. Hua, H. Zhao, Z. Chen, L. Qu, X. W. Deng (2004)
An Arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in Vitro
Plant Molecular Biology 54: 683-699. PDF

[83] M. V. Osier, H. Zhao, K-H Cheung (2004)
Handling multiple testing while interpreting microarrays with the gene ontology database
BMC Bioinformatics, 5, 124. PDF

[82] N. Liu, S. L. Sawyer, N. Mukherjee, A. J. Pakstis, J. R. Kidd, K. K. Kidd, A. J.Brookes, H. Zhao (2004)
Haplotype block structures show significant variation among populations
Genetic Epidemiology, 27: 385-400. PDF

[81] Y. Lai, B. Wu, L. Chen, H. Zhao (2004)
Statistical method for identifying differential gene-gene coexpression patterns
Bioinformatics, 20: 3146-3155. PDF

[80] R. Marathe, Z. Guan, R. Anandalakshmi, H. Zhao, S. Dinesh-Kumar (2004)
Study of Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray
Plant Molecular Biology, 55: 501-520. PDF

[79] Hoek, K., Rimm, D.L., Williams, K.R., Zhao, H., Ariyan, S., Lin, A., Kluger, H.M., Berger, A.J., Cheng, E., Trombetta, E.S.,Wu, T., Niinobe, M., Yoshikawa, K., Hannigan, G.E., Halaban, R. (2004)
Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas.
Cancer Research, 64: 5270-5282.PDF

[78] Y. Xia, H. Yu, R. Jansen, M. Seringhaus, S. Baxter, D. Greenbaum, H. Zhao, M. Gerstein. (2004)
Analyzing cellular biochemistry in terms of molecular networks.
Annual Review of Biochemistry, 73: 1051-1087. PDF

[77] R. J. Buono , F. W. Lohoff, T. Sander, M. R. Sperling, M. J. O'Connor, D. J. Dlugos, S. G. Ryan, G. T. Golden, H. Zhao, T. M. Scattergood, W. H. Berrettini, T. N. Ferraro. (2004)
Association between variation in the human KCNJ10 potassium ion channel gene and seizure susceptibility.
Epilepsy Reserach, 58: 175-183. PDF

[76] G. Zou, H. Zhao. (2004)
The estimation of sibling genetic risk parameters revisited.
Genetic Epidemiology, 26: 286-293. PDF

[75] X. Sun, J. C. Stephens, H. Zhao. (2004)
The impact of sample size and marker selection on the study of haplotype structures.
Human Genomics, 1: 179-193. PDF

[74] N. Sun, H. Zhao. (2004)
Genomic approaches in dissecting complex biological pathways.
Pharmacogenomics, 5: 163-179. PDF

[73] C.-S. Goh, N. Lan, S. Douglas, B. Wu, N. Echols, A. Smith, D. Milburn, G. T. Montelione, H. Zhao, M. Gerstein. (2004)
Mining the structural genomics pipeline: Identification of protein properties that affect high-throughput experimental analysis.
Journal of Molecular Biology, 336: 115-130.  PDF

[72] W. D. Li, C. Dong, D. Li, H. Zhao, R. A. Price. (2004)
An obesity-related locus in chromosome region 12q23-24.
Diabetes 53: 812-820.PDF

[71] T. N. Ferraro, G. T. Golden, G. G. Smith, J. F. Martin, F. W. Lohoff, T. A. Gieringer, D. Zamboni, C. L. Schwebel1, D. M. Press, S. O. Kratzer, H. Zhao, W. H. Berrettini, R. J. Buono. (2004)
Fine mapping of a seizure susceptibility locus on mouse chromosome 1: Nomination of Kcnj10 as a causative gene.
Mammalian Genome, 15: 239-251. PDF

[70] W. Zhao, J. Wang, X. He, X. Huang, Y. Jiao, M. Dai, S. Wei, J. Fu, Y. Chen, X. Ren, Y. Zhang, P. Ni, J. Zhang, S. Li, J. Wang, G. Wong, H. Zhao, J. Yu, H. Yang, J. Wang. (2004)
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.
Nucleic Acid Research, 32, D377-382.  PDF

[69] G. Zou, H. Zhao. (2004)
The impacts of errors in individual genotyping and DNA pooling on association studies.
Genetic Epidemiology, 26: 1-10.  PDF

[68] N. Sun, L. Ma, D. Pan, H. Zhao, X-W Deng. (2003)
Evaluation of regulatory potential of Calvin cycle pathway steps based on large-scale gene expression profiling data.
Plant Molecular Biology, 53: 467-478. PDF

[67] D. Pan, N. Sun, K-H Cheung, Z. Guan, L. Ma, M. Holford, X-W Deng, H. Zhao (2003)
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis.
BMC Bioinformatics, 4, 56.  PDF

[66] L. Zheng, S. Wang, P. Romans, H. Zhao, C. Luna, M. Q. Benedict (2003)
Quantitative trait loci in Anopheles gambiae controlling the encapsulation response against Plasmodium cynomolgi Ceylon.
BMC Genetics 2003, 4, 16  PDF

[65] Y. Jiao, H. Yang, L. Ma, N. Sun, H. Yu, T. Liu, Y. Gao, H. Gu, Z. Chen, M. Wada, M. Gerstein, H. Zhao, L. Qu, X. W. Deng. (2003)
A genome wide analysis of blue light regulation of Arabidopsis transcription factor gene expression during seedling development.
Plant Physiology, 133: 1480-1493.  PDF

[64] G. Garcia-Rostan, H. Zhao, M. Pollan, A. Herrero, R. L. Camp, J. Pardo, R. Wu, J. Costa, M. L. Carcangiu, G. Tallini. (2003)
Ras mutations are associated with aggressive tumor phenotypes and poor prognosis in thyroid cancer.
Journal of Clinical Oncology, 21: 3226-3235.  PDF

[63] G. Zou, H. Zhao. (2003)
Haplotype frequency estimation in the presence of genotyping errors.
Human Heredity, 56: 131-138.  PDF

[62] L. V. Sun, L. Chen, F. Greil, N. Negre, T.-R. Li, G. Cavalli, H. Zhao, B. Van Steensel, K. P. White (2003)
Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila.
Proceedings of the National Academy of Sciences, 100: 9428-9433.  PDF

[61] X. Luo, H. R. Kranzler, H. Zhao, J. Gelernter. (2003)
Haplotypes at the OPRM1 locus are associated with susceptibility to substance dependence in European-Americans.
American Journal of Medical Genetics 120B: 97-108.  PDF

[60a] X. Luo, J. Gelernter, H. Zhao, H. R. Kranzler (2005)
Response to Dr. Kopke's comments on haplotypes at the OPRM1 locus
American Journal of Medical Genetics 135B: 102. PDF

[60] N. M. Wikonkal, E. Remenyik, D. Knezevic, W. Zhang, M. Liu, H. Zhao, T. R. Berton, D. G. Johnson, D. E. Brash. (2003)
Inactivating E2f1 reverts apoptosis resistance and cancer sensitivity in Trp53-deficient mice.
Nature Cell Biology 5: 655-660.  PDF

[59] W-D Li, D. Li, S. Wang, S. Zhang, H. Zhao, R. A. Price. (2003)
Linkage and linkage disequilibrium mapping of genes influencing human obesity in chromosome region 7q22.1-7q35.
Diabetes, 52: 1557-1561.  PDF

[58] S. Wang, H. Zhao. (2003)
Sample size needed to detect gene-gene interactions using association designs.
American Journal of Epidemiology, 158: 899-914.  PDF

[57] B. Wu, T. Abbott, D. Fishman, W. McMurray, G. Mor, K. Stone, D. Ward, K. Williams, H. Zhao. (2003)
Comparison of statistical methods for classification of ovarian cancer using a proteomics dataset.
Bioinformatics, 19: 1636-1643.  PDF   Supplemental Materials

[56] H. Zhao, R. Pfiffer, M. H. Gail. (2003)
Haplotype analysis in population genetics and association studies.
Pharmacogenomics, 4: 171-178.  PDF

[55] G. Zou, D. Pan, H. Zhao. (2003)
Genotyping error detection through tightly linked markers.
Genetics, 164: 1161-1173.  PDF

[54] H-S Chen, X. Zhu, H. Zhao, S. Zhang. (2003)
Qualitative semi-parametric test to detect genetic association in case-control design under structured population.
Annals of Human Genetics, 67: 250-264. PDF

[53] H. Zhao, B. Wu, N. Sun. (2003)
DNA-protein binding and gene expression patterns In: Goldstein DR(ed).
Science and Statistics: A Festschrift for Terry Speed. IMS Lecture Notes-Monograph Series, Vol. 40, pp 259-274.  PDF

[52] L. Ma, H. Zhao, X-W Deng. (2003)
Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development.
Development, 130: 969-981.  PDF

[51] S. Wang, K. K. Kidd, H. Zhao. (2003)
On the use of DNA pooling to estimate haplotype frequencies.
Genetic Epidemiology, 24: 74-82.  PDF

[50] S. Zhang, X. Zhu, H. Zhao. (2003)
On a semi-parametric test to detect associations between quantitative traits and candidate genes using unrelated individuals.
Genetic Epidemiology, 24: 44-56.  PDF

[49] C. Dong, S. Wang, W-D Li, H. Zhao R. A. Price. (2003)
Interacting genetic loci in chromosome regions 20q and 10q influence extreme human obesity.
American Journal of Human Genetics, 72: 115-124.  PDF

[48] H. Wang, L. Ma, J. Haboshi, J. Li, H. Zhao X-W Deng. (2002)
Analysis of far-red light regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis .
Plant Journal, 32: 723-733.  PDF

[47] L. Ma, Y. Gao, L. Qu, Z. Chen, J. Li, H. Zhao X-W Deng. (2002)
Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis.
Plant Cell, 14: 2383-2398.  PDF

[46] G. Wu, X. Tian, S. Nishimura, G. S. Markowitz, V. D'Agati, J. H. Park, L. Yao, L. Li, L. Geng, H. Zhao W. Edelmann, S. Somlo. (2002)
Trans-heterozygous Pkd1 and Pkd2 mutations modify expression of polycystic kidney disease.
Human Molecular Genetics, 16: 1845-1854.  PDF

[45] K. H. Cheung, K. White, J. Hager, M. Gerstein, V. Reinke, K. Nelson, P. Masiar, R. Srivastava, Y. Li, J. Li, J. M. Li, H. Zhao D. B. Allison, M. Snyder, P. Miller, K. Williams. (2002)
YMD: A microarray Database for Large-scale Gene Expression Analysis.
Proceedings of AMIA Symposium 140-144.PDF

[44] A. Mani, S. M. Meraji, R. Houshyar, J. Radhakrishnan, A. Mani, M. Ahangar, T. M. Rezaie, M. A. Taghavinejad, B. Broumand, H. Zhao, C. Nelson-Williams, R. P. Lifton. (2002)
Finding genetic contributions to sporadic disease: A recessive locus at 12q24 commonly contributes to patent ductus arteriosus.
PNAS 99 : 15054-15059.  PDF

[43] X. Zhu, S. Zhang, H. Zhao R. S. Cooper. (2002)
Association mapping using a mixture model for complex traits.
Genetic Epidemiology, 23: 181-196.  PDF

[42] S. Zhang, K. Zhang, J. Li, and H. Zhao. (2002)
On a family-based haplotype pattern mining method for linkage disequilirbium mapping.
Pacific Symposium on Biocomputing, 100-111.  PDF

[41] S. Zhang and H. Zhao. (2002)
Linkage disequilibrium mapping with genotype data.
Genetic Epidemiology, 22: 66-77.  PDF  related program

[40] S. Zhang, K. K. Kidd, and H. Zhao. (2002)
Detecting genetic association in case-control studies using similarity-based association tests.
Statistica Sinica, 12: 337-359.  PDF

[39] J. Li, S. Sherman, N. Lamb, and H. Zhao. (2001)
Multipoint genetic mapping with trisomy data.
American Journal of Human Genetics, 69:1255-1265.  PDF

[38] H. Wang, L. Ma, J. Li, H. Zhao, and X-W Deng. (2001)
Direct interaction of Arabidopsis cryptochromes  with COP1 in light control development.
Science, 294: 154-158.  PDF

[37] L. Ma, J. Li, J. Hager, L. Qu, Z. Chen, H. Zhao, and X-W Deng. (2001)
Light control of Arabidopsis development entails co-ordinated regulation of genome expression and cellular pathways.
Plant Cell, 13: 2589-2607.  PDF

[36] S. Zhang, A. J. Pakstis, K. K. Kidd, and H. Zhao. (2001)
Comparisons of two methods for haplotype reconstruction and haplotype frequency estimates from population data.
American Journal of Human Genetics, 69: 906-912.  PDF

[35] S. Zhang and H. Zhao. (2001)
Quantitative similarity-based association test using population samples.
American Journal of Human Genetics, 69: 601-614.  PDF   related program.

[34] H. Zhao, J. Li, and W. P. Robinson. (2001)
Statistical analysis of uniparental disomy data using hidden Markov models.
Biometrics, 57:1074-1079.  PDF  related program

[33] H. Zhao and F. Liang. (2001)
On relationship inference using continuous gamete identity by descent data.
Journal of Computational Biology, 8: 191-200.  PDF

[32] J. Li, D. Wang,  J. Dong, R. Jiang, K. Zhang, S. Zhang, H. Zhao, and F. Sun. (2001)
The power of transmission disequilibrium tests for quantitative traits.
Genetic Epidemiology, 21: S632-S637.  PDF

[31] S. Zhang, K. Zhang, J. Li, F. Sun, and H. Zhao. (2001)
Test of association for quantitative traits in general pedigrees: the quantitative pedigree disequilibrium test.
Genetic Epidemiology, 21: S370-S375.  PDF

[30] A. Kamina, R. W. Makuch, and H. Zhao. (2001)
Stochastic modeling of early HIV-1 population dynamics.
Mathematical Biosciences, 170: 187-198.  PDF

[29] T. P. Speed and H. Zhao. (2001)
Chromosome maps.
Handbook of Statistical Genetics, 3-39.  PDF

[28] H. Zhao, K. R. Merikangas, and K. K. Kidd. (2000)
Reply to Kong and Nicolae.
American Journal of Human Genetics, 67: 1355-1356.   PDF

[27] H. Zhao , S. Zhang, K. R. Merikangas, M. Trixler, D. B. Wildenauer, F. Sun, and K. K. Kidd. (2000)
Transmission/disequilibrium tests using multiple tightly linked markers.
American Journal of Human Genetics, 67:936-946.  PDF   related program.

[26] H. Zhao, J Li, and W. P. Robinson. (2000)
Multipoint genetic mapping with uniparental disomy data.
American Journal of Human Genetics, 67: 851-861.   PDF    related program

[25] F. Sun, W. D. Flanders, Q. Yang, and H. Zhao. (2000)
Transmission/disequilibrium tests for quantitative traits.
Annals of Human Genetics, 64: 555-565.   PDF

[24] H. Zhao(2000)
Family-based association studies.
Statistical Methods in Medical Research, 9: 563-587.  PDF

[23] K. Zhang and H. Zhao. (2000)
Assessing reliability of gene clusters from gene expression data.
Functional & Integrative Genomics, 1: 156-173.   PDF   related program

[22] S. Zhang and H. Zhao. (2000)
Linkage disequilibrium mapping in populations of variable size using the decay of haplotype sharing and a stepwise-mutation model.
Genetic Epidemiology 9(Supp1):S994105   PDF   related program

[21] J. R. Kidd, A. J. Pakstis, H. Zhao, R-B Lu, F. E. Okonofua, A. Odunsi, E. Grigorenko, B. Bonne-Tamir, J. Friedlaender, L. O. Schulz, J. Parnas, and K. K. Kidd. (2000)
Haplotypes and linkage disequilibrium at the phenylalanine hydroxylase locus, PAH, in a global representation of populations.
American Journal of Human Genetics, 66: 1882-1899.   PDF

[20] H. Zhao and T. P. Speed. (1999)
On a Markov model for chromatid interference.
Statistics in Molecular Biology (IMS Lecture Notes 33), 1-20.   PDF

[19] L. J. Sheffield, M. P. Knauert, A. J. Pakstis, H. Zhao, and K. K. Kidd. (1999)
Analyses of the COGA data set in one ethnic group with examinations of alternative definitions of alcoholism.
Genetic Epidemiology, 17, S319-S324.

[18] H. Zhao, L. J. Sheffield, A. J. Pakstis, M. P. Knauert, and K. K. Kidd. (1999)
A more powerful method to evaluate p-values in GENEHUNTER.
Genetic Epidemiology, 17: S415-S420.   PDF

[17] H. Zhao, K. R. Merikangas, and K. K. Kidd. (1999)
On a randomization test in linkage analysis.
American Journal of Human Genetics, 65: 1449-1456.   PDF

[16] H. Zhao, A. J. Pakstis, J. R. Kidd, K. K. Kidd. (1999)
Assessing linkage disequilibrium in a complex genetic system.
Annals of Human Genetics, 63: 167-179.   PDF

[15] H. Zhao (1999)
The interpretation of the parameters in the transmission/disequilibrium test.
American Journal of Human Genetics, 64: 326-328.   PDF

[14] H. Zhao and T. P. Speed. (1998)
Statistical analysis of half-tetrads.
Genetics, 150: 473-485.   PDF

[13] H. Zhao and T. P. Speed. (1998)
Statistical analysis of ordered tetrads.
Genetics, 150: 459-472.    PDF

[12] H. Zhao and T. P. Speed. (1998)
Stochastic modeling of the crossover process during meiosis.
Communications in Statistics, Theory and Methods, 27: 1557-1580.  PDF

[11] K. K. Kidd, B. Morar, C. M. Castiglione, H. Zhao, and others. (1998)
A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus.
Human Genetics, 103: 211-227.  PDF

[10] H. Zhao, H. Zhang, and J. I. Rotter. (1997)
Cost-effective sib-pair designs in the mapping quantitative-trait loci.
American Journal of Human Genetics, 60: 1211-1221. PDF

[9] H. Zhang, H. Zhao, and K. R. Merikangas. (1997)
Strategies to identify genes for complex diseases.
Annals of Medicine, 29: 493-498.

[8] K. Lange, H. Zhao, and T. P. Speed. (1997)
The Poisson-skip model of crossing-over.
Annals of Applied Probability, 7: 299-313.   PDF

[7] D. R. Goldstein, H. Zhao, and T. P. Speed. (1997)
The effects of genotyping errors and interference on estimation of genetic distance.
Human Heredity, 47: 86-100.

[6] J. D. Ohmen, H. Y. Yang, K. K. Yamamoto, H. Zhao, and others. (1996)
Susceptibility locus for inflammatory bowel disease on chromosome 16 has a role in Crohns disease, but not in Ulcerative Colotis.
Human Molecular Genetics, 5: 1679-1683.    PDF

[5] H. Zhao and T. P. Speed. (1996)
On genetic map functions.
Genetics, 142: 1369-1377. PDF

[4] H. Zhao, M. S. McPeek, and T. P. Speed. (1995)
Statistical analysis of crossover interference using the chi-square model.
Genetics, 139: 1045-1056.  PDF

[3] H. Zhao, M. S. McPeek, and T. P. Speed. (1995)
Statistical analysis of chromatid interference.
Genetics, 139: 1057-1065.  PDF

[2] D. R. Goldstein, H. Zhao, and T. P. Speed. (1995)
Relative efficiencies of X² models of recombination for exclusion mapping and gene ordering.
Genomics, 27: 265-273.  PDF

[1] K. Doksum, S. Blyth, E. Bradlow, X. L. Meng, and H. Zhao. (1994)
Correlation curves as local measures of variance explained by regression.
Journal of American Statistical Association, 89: 571-583. PDF