Publications from the Yale/NHLBI Proteomics Center

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Publications from the Yale/NHLBI Proteomics Center

2006

N. Sun, R. Carroll, H. Zhao (2006)
Bayesian Error Analysis Model (BEAM) for reconstructing transcriptional regulatory networks.
Proceedings of the National Academy of Sciences, in press.
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, in press.
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.
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, in press.
B. Wu, Z. Guan, H. Zhao (2006)
Parametric and nonparametric FDR estimation revisited.
Biometrics, in press.
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. In press.
S. Wang, S. Huang, L. Zheng, H. Zhao (2006)
Mapping quantitative trait loci in non-inbred mosquito crosses.
Genetics, in press.
N. Liu, I. Beerman, R. Lifton, H. Zhao (2006)
Haplotype analysis in the presence of informatively missing genotype data.
Genetic Epidemiology, in press.
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.
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, in press.

2005

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.
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
L. Chen, H. Zhao (2005)
Negative correlation between compositional symmetries and local recombination rates
Bioinformatics, 21: 3951-3958. PDF
T. Huang, B. Wu, P. Lizardi, H. Zhao (2005)
Detection of DNA copy number alterations using penalized least squares regression
Bioinformatics, in press. PDF
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
Y. Liu, N. Sun, J. Liu, L. Chen, M. McIntosh, L. Zheng, H. Zhao (2005)
Identifying stage-specific genes by combining information from two different types of oligonucleotide arrays
CAMDA 2004 Proceedings, in press. PDF
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
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
Y. Liu, N. Liu, H. Zhao (2005)
Inferring protein-protein interactions through high-throughput interaction data from diverse organisms
Bioinformatics, 21: 3279-3285. PDF
N. Lin, H. Zhao (2005)
Are scale-free networks robust to measurement errors?
BMC Bioinformatics, 6:119. PDF
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
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
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
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
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
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
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
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
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
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
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
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, in press.
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.
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
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
W. Yu, B. Wu, T. Huang, X. Li, K. Williams, H. Zhao (2005)
Statistical methods in proteomics
Springer Handbook of Enginerring Statistics PDF
M. Holford, N. Li, P. Nadkarni, H. Zhao (2005)
VitaPad: visualization tools for the analysis of pathway data
Bioinformatics, 21: 1596-1602. PDF
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
G. Zou, H. Zhao (2005)
Family-based association tests for different family structures using pooled DNA
Annals of Human Genetics, 69: 429-442. PDF
L. Chen, H. Zhao (2005)
Integrating mRNA decay information into co-regulation study
Journal of Computer Science and Technology, 20: 434-438. PDF
Z. Guan, H. Zhao (2005)
A semiparametric approach for marker gene selection based on gene expression data
Bioinformatics, 21: 529-536. PDF
K. Zhang, F. Sun, H. Zhao. (2005)
HAPLORE: A program for haplotype reconstruction in general pedigrees without recombination.
Bioinformatics, 21: 90-103. PDF

2004

Y. Liu, H. Zhao (2004)
A computational approach for ordering signal transduction pathway components from genomics and proteomics data
BMC Bioinformatics, 5, 158 PDF
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
N. Lin, B. Wu, R. Jansen, M. Gerstein, H. Zhao (2004)
Information assessment on predicting protein-protein interactions
BMC Bioinformatics, 5, 154. PDF
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
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
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
Y. Lai, B. Wu, L. Chen, H. Zhao (2004)
Statistical method for identifying differential gene-gene coexpression patterns
Bioinformatics, 20: 3146-3155. PDF
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
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
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
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
G. Zou, H. Zhao. (2004)
The estimation of sibling genetic risk parameters revisited.
Genetic Epidemiology, 26: 286-293. PDF
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
N. Sun, H. Zhao. (2004)
Genomic approaches in dissecting complex biological pathways.
Pharmacogenomics, 5: 163-179. PDF
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
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
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
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
G. Zou, H. Zhao. (2004)
The impacts of errors in individual genotyping and DNA pooling on association studies.
Genetic Epidemiology, 26: 1-10. PDF

2003

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
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
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
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
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
G. Zou, H. Zhao. (2003)
Haplotype frequency estimation in the presence of genotyping errors.
Human Heredity, 56: 131-138. PDF
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
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
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
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
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
S. Wang, H. Zhao. (2003)
Sample size needed to detect gene-gene interactions using association designs.
American Journal of Epidemiology, 158: 899-914. PDF
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
H. Zhao, R. Pfiffer, M. H. Gail. (2003)
Haplotype analysis in population genetics and association studies.
Pharmacogenomics, 4: 171-178. PDF
G. Zou, D. Pan, H. Zhao. (2003)
Genotyping error detection through tightly linked markers.
Genetics, 164: 1161-1173. PDF
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
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
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
S. Wang, K. K. Kidd, H. Zhao. (2003)
On the use of DNA pooling to estimate haplotype frequencies.
Genetic Epidemiology, 24: 74-82. PDF
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
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

Submitted Manuscripts

Mahajan, M.C., Narlikar, G.J., Boyapaty, G., Kingston, R.E., Weissman, S.M. (2005) A unique complex of hnRNP C1/C2, SWI/SNF and NurD/MeCP1 constitutes the chromatin opening activity of the locus control region. Molecular Cell (under revision).
Yu, W., Wu, B., Lin, N., Stone, K., Williams, K., and Zhao, H. (2005) Detecting and Aligning Peaks in Mass Spectrometry Data with Applications to MALDI. Applied Bioinformatics, submitted.
Shi, Y., Xiang, R., Horv�th, C., and Wilkins, J.A. (2005) Quantitative analysis of membrane proteins from breast cancer cell lines BT474 and MCF7 using multistep solid phase mass tagging and 2D LC/MS, J. Proteome Res., submitted.
Shi, Y., Hill, J., Xiang, R., Horvath, C., and Wilkins, J., (2005) Quantitative analysis of the Escherichia coli proteome using multistep solid phase mass tagging and 2D LC/MS, Applied and Environmental Microbiology, submitted
Yu, W., Li, X., Liu, J., Wu, B., Williams, K., and Zhao, H. (2005) Multiple Peak Alignment in Sequential Data Analysis: A Scale-Space Based Approach. IEEE Transactions on Computational Biology, submitted.

Published and Submitted Abstracts

Kluger, M.S., Manes, T. and Pober, J.S. (2004) ICAM-1 as a basis for vascular leak induced by cytokine-mediated endothelial cell activation. J. Invest. Dermatol. 122 (3):A4. (Also presented as a poster and workshop presentation at the 65th Annual Meeting of the Society for Investigative Dermatology in April, 2004).
Yu, W. and H. Zhao. (2004) Aligning Spectral Peaks in Mass Spectrometry Data with a Robust Point Matching Approach. 52nd ASMS Conference on Mass Spectrometry and Allied Topics, May 23 - 27, 2004.
Lam, T., McMurray, W., Stone, K., Gulcicek, E., Colangelo, C., Williams, K. (2005) Optimization of Multi-Dimensional Protein Identification Technologies (MudPIT) for Fourier Transform Ion Cyclotron Resonance (FT-ICR) Mass Spectrometry. 53rd ASMS Conference on Mass Spectrometry, June 5 - 9, 2005.
Berberich, M., Stone, K., LoPresti, M., Weissman, S., Williams, K., Colangelo, C. (2005) A Comprehensive Cellular Snapshot Using Multiple Protein Profiling Technologies. 53rd ASMS Conference on Mass Spectrometry, June 5 - 9, 2005.
Gulcicek, E., Berberich, M., Colangelo, C., Lam, TuKiet, McMurray, W., Stone, K., and Williams, K.R. (2005) Mass Spectrometric Integration of Robust Phosphoprotein Profiling Strategies. 53rd ASMS Conference on Mass Spectrometry, June 5 - 9, 2005.
Shifman, M., Sun, Kexin, Colangelo, Chris, Cheung, K., Miller, Perry, and Williams, Kenneth, �YPED: A Proteomics Database for Protein Expression Analysis� submitted to the Symposium of American Medical Informatics Association (AMIA), October 22-26, 2005, Washington, DC.


		Copyright © 2002, Yale University, New Haven, Connecticut, USA. All rights reserved. Comments or suggestions to Greg Blasko. Last modified: 27-Mar-2006 (GB)