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[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