Fengzhu Sun (Publications since 1995)


Statistical Genetics

29. Kui Zhang, Fengzhu Sun, Hongyu Zhao (2004)  "HAPLORE: A Program for Haplotype Reconstruction in General Pedigrees without Recombination." In press. Bioinformatics.
28. Schulze TG, Zhang K, Chen YS, Akula N, Sun FZ, McMahon FJ (2004) "Defining haplotype blocks and tag SNPs in the human genome." Human Molecular Genetics 13 335-342
27. Zhang K, Qin ZHS, Liu JS, Chen T, Waterman MS, Sun FZ (2004) Haplotype  Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies. Genome Research 14:908-916
26. Sung Kim, Kui Zhang, Fengzhu Sun (2003) "Detecting Susceptibility Genes in Case-Control Studies Using Set Association Analysis."  BMC Genetics 2003, 4(Suppl 1):S9
25. Zhang K, Sun FZ, Waterman MS and Chen T (2003) "Dynamic programming algorithms for  partitioning sequence variation in human chromosomes." HERMIS, 4:15-26
24. Kim SK, Zhang K, Sun FZ (2004) A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium Measure .  Pacific Symposium on Biocomputing 2004:128-139
23. Sun, FZ, Cui, J, Gavras, H, Schwartz, F (2003) A novel class of tests for the detection of mitochondrial DNA–mutation involvement in diseases. Am J Hum Genet 72:1515-1526
22. Zhang K, Chen T, Waterman MS,  Sun FZ (2003) "A set of dynamic algorithms for haplotype block partition and tag SNP selection via haplotype data and genotype data,"  Proceedings of DIMACS workshop on SNP
21. Zhang K, Sun FZ, Waterman MS,  Chen T (2003) "Haplotype block partitioning with limited resources and applications to human chromosome 21 haplotype data (PROGRAM)," Am J Hum Genet 73 63-73
20. Zhang K, Calabrese P, Nordborg M, and Sun FZ (2002) "Haplotype Block Structure and Its Applications to Association Studies: Power and Study Designs," Am J Hum Genet 71 1386-1394
19. Zhang K, Deng MH, Chen T, Waterman MS, Sun FZ (2002) "A dynamic programming algorithm for haplotype block partitioning (PROGRAM)," Proc Natl Acad Sci USA 99 7335-7339
18. Zhang SL,  Zhang K, Li JM, Sun FZ, Zhao HY (2001) "Test of linkage and association for quantitative traits in general pedigrees: the quantitative pedigree disequilibrium test," Genet Epidemiol 21 S370-S375
17 Li JM, D Wang, JP Dong, RF Jiang, K Zhang, SL Zhang, HY Zhao, FZ Sun (2001) "The Power of Transmission Disequilibrium Tests for Quantitative Traits," Genet Epidemiol 21 S632-S637
16. Jiang R, Dong J, Wang D, Sun FZ (2001), "Fine-scale mapping using Hardy-Weinberg Disequilibrium,"Ann Hum Genet, 65 207-219
15. Flanders WD, Sun FZ,  Yang QH (2001), "A new estimator of the genotype risk ratio for use in case parental-control studies,"Am J Epidemol 154 259-263
14. Sun FZ,  Yang QH, Zhao HY, Flanders WD (2000), "Transmission/disequilibrium tests for quantitative traits,"Ann Hum Genet, 64 555-565
13. Zhao HY, Zhang SL, Merikangas KR, Widenauer DB, Sun FZ, Kidd KK. (2000), "Transmission/disequilibrium tests using multiple tightly linked markers,"Am J Hum Genet, 67 936-946
12. Yang QH, Khoury MJ, Coughlin SS, Sun FZ, Flanders WD (2000), "On the use of population-based registries in the clinical validation of genetic testing for disease susceptibility,"Genetics in Medicine, 2 186-192
11. Wang D, Sun FZ (2000), "Sample sizes for the transmission/disequilibrium tests: The TDT, S-TDT and 1-TDT,"Commun Stat-Theory M, 29 1129-1142 
10. Sun FZ, Cheng R, Flanders WD, Yang QH, Khoury MJ (1999), "Whole genome association studies for genes affecting alcohol dependence,"Genet Epidemiol, 17 S337-342 
9. Yang QH, Khoury MJ, Atkinson M, Sun FZ, Cheng R, Flanders WD (1999), "Using case-control designs for genome wide screening for associations between genetic markers and disease susceptibility loci,"Genet Epidemiol, 17 S779-784 
8. Sun FZ (1999), "Biological and statistical studies for diseases involving mtDNA mutations,In: Halloran ME, Geisser S (eds)"Statistics in Genetics, 133-146. Springer, New York 
7. Yang QH, Khoury MJ, Atkinson M, Sun FZ, Flanders WD (1999), "Case-only design to measure gene-gene interactions,"Epidemiology, 10 167-170 
6. Sun FZ, Flanders WD, Yang QH, Khoury MJ (1999), "Transmission disequilibrium test (TDT) when only one parent is available: The 1-TDT,"Am J Epidemol, 150 97-104 
5. Sun FZ, Flanders WD, Yang QH, Khoury MJ (1998), "A new method for estimating the risk ratio in studies using case-parental control design,"Am J Epidemol, 148 902-909 
4. Sun FZ, Ashley AE, Durham LK, Feingold E, Halloran ME, Manatunga AK, Sherman SL (1998), "Testing for contributions of mitochondrial DNA mutations to complex diseases,"Genet Epidemiol, 15 451-469 
3. Savage-Austin A, Sun FZ, Crawford DC, Ashley AE, Yang QH, Sherman SL (1997), "Sequential sibpair and association studies to detect genes in quantitative traits,"Genet Epidemiol, 14 885-890 
2. Yang QH, Atkinson M, Sun FZ, Sherman SL, Khoury MJ (1997), "The method of sib-pair linkage analysis in the context of case-control design,"Genet Epidemiol, 14 939-944 
1. Brown MD, Sun FZ, Wallace DC (1997) "Clustering of Leber hereditary optic neuropathy patients on a Caucasian mitochondrial lineage,"Am J Hum Genet , 60 381-387 


6. Deng MH, Tu ZD, Sun FZ, Chen T (2004) "Mapping gene ontology to proteins based on protein–protein interaction data." Bioinformatics 20:895-902
5. Li WT, Sun FZ, Grosse I (2004) "Extreme-Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression." RECOMB2003
4. Deng MH, Chen T, Sun FZ (2003) "Integrated Probabilistic Model for Functional Prediction of Proteins," RECOMB2003
3. Deng, MH, Sun FZ, Chen, T (2003) "Assessment of the reliability of protein-protein interactions and protein function prediction (PROGRAM),"  Pacific Symposium on Biocomputing, PSB2003, 8:140-151
2. Deng MH, Zhang K, Mehta S, Chen T, Sun FZ (2002) "Prediction of protein function using protein-protein interaction data (PROGRAM)," J Comp Bio, In press. See also The first IEEE Computer Society bioinformatics conference, CSB2002, 117-126
1. Deng MH, Mehta S, Sun FZ, Chen T (2002) "Inferring domain-domain interactions from protein-protein interactions (PROGRAM)," Genome Research 12 1540-1548. See also RECOMB2002:117-126

Theoretical studies of PCR related biotechnologies

16. Lai YL, Sun FZ (2004) "Sampling Distribution for Microsatellites Amplified by PCR: Mean Field Approximation and its Application to Genotyping." J Theor Biol, 228:185-194
15. Lai YL, Sun FZ (2004) "Understanding the mutation mechanisms during polymerase chain reaction (extended abstract)" In M. Huebner and M. Sorensen (eds) Workshop on Dynamical Stochastic Modeling in Biology, pages 59-68
14. Lai YL, Sun FZ (2003) "The relationship between microsatellite slippage mutation rate and the number of repeat units," Mol Bio Evol 20: 2123-2131
13. Lai YL, Sun FZ (2003) "Microsatellite mutations during the polymerase chian reaction: mean field approximations and their applications," J Theor Biol, 224:127-137
12. Lai YL, Shinde D, Sun FZ, Arnheim N (2003) "The mutation process of microsatellites during the polymerase chain reaction," J Comp Biol, 10:143-155
11. Shinde D, Lai YL, Sun FZ, Arnheim N (2003) "Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites," Nucl Acids Res, 31 974-980
10. Sun FZ (2001) "Stochastic modeling of polymerase chain reaction and related biotechnologies," Bulletin of the International Statistical Institute, 53rd session proceedings, book 1: 393-396
9. Wang D, Zhao C, Cheng R, Sun FZ (2000) "Estimating the mutation rate during error-prone polymerase chain reaction,"J Comp Biol, 7 143-158 
8. Sun, FZ (1999), "Modeling DNA shuffling,(figure)" J Comp Biol, 6 77-90
7. Bruno W, Sun FZ, Torney DC (1998), "Optimum group testing designs for partially characterized objects," SIAM J Appl Math, 58 1043-1059
6. Sun FZ, Benson G, Arnheim N, Waterman MS (1997) , "Pooling strategies for establishing physical genome maps using FISH," J Comp Biol, 4 467-486
Sun FZ, Waterman MS (1997) , "Whole genome amplification and branching processes," Adv Appl Prob, 29 629-684
4. Sun FZ, Galas D, Waterman MS (1996), "A mathematical analysis of in vitro selection amplification," J Mol Bio, 258 650-660
3. Sun FZ, Arnheim N, Waterman MS (1995), "Whole genome amplification of single cells: mathematical analysis of PEP and tagged PCR," Nucleic Acids Rsearch, 23 3034-3040. 
2. Port E, Sun FZ, Martin D, Waterman MS (1995), "Genomic mapping by end characterized random clones: A mathematical analysis,"Genomics, 26 84-100 
1. Sun FZ (1995), "The polymerase chain reaction and branching processes," J Comp Bio, 23 3034-3040.



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