|
|
|
95. |
Zhai ZY, Reinert G, Song K, Waterman MS, Luan YH, Sun FZ (2012) Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads. In Press, Journal of Computational Biology |
|
94. |
Song K, Ren J, Zhai ZY, Liu XM, Deng MH, Sun FZ (2012) Alignment-free sequence comparison based on NGS reads: extended abstract. Accepted, RECOMB2012 Proceedings |
|
93. |
Chang
Q, Luan YH, Chen T, Fuhrman JA, Sun FZ (2012) Computational methods
for the analysis of tag sequences in metagenomics
studies. In press, Frontiers in Bioscience, S4, 1333-1343, June 1. |
|
92. |
Wan
L, Yan XT, Chen T, Sun FZ (2012)
Modeling RNA degradation for RNA-Seq with applications(Program). Biostatistics, published online Feb. 21, 2012 |
|
91. |
Wan
L, Sun FZ (2012) CEDER: Accurate detection of differentially expressed genes by
combining significance of exons using RNA-Seq. To appear, IEEE/ACM
Transactions on Computational Biology and Bioinformatics (APBC2012), 9(1),
JANUARY/FEBRUARY 2012 |
|
90. |
Xia
L, Cram JA, Chen T, Fuhrman JA, Sun FZ (2011) Accurate genome relative abundance
estimation based on shotgun metagenomic reads (Program). PLoS One 6(12): e27992 |
|
89. |
Xia
L, Steele JA, Cram JA, Cardon ZG, Simmons SL, Vallino JL, Fuhrman JA, Sun FZ (2011) Extended local
similarity analysis (eLSA) of microbial community
and other time series data with replicates (Program). BMC Systems
Biology (GIW2012)5(Suppl 2):S15 |
|
83. |
Meng L,
Sun FZ, Zhang XG, Waterman MS (2011) Sequence
alignment as hypothesis testing. Journal of Computational Biology
18(5):677-691. |
|
82. |
Zhang WS, Sun FZ, Jiang R (2011) Integrating multiple
protein-protein interaction networks to prioritize disease genes: A Bayesian
regression approach. BMC Bioinformatics (APBC2011) 12(Suppl 1):S11. |
|
81. |
Yu H, Pei GJ, Ge P, Fang XZ, Sun FZ, Lai
LH, Qian MP, Deng MH (2010) Predicting kinase
functional sites using hierarchical stochastic language modeling. Statistics
and its Interface 3:523-532. |
|
80. |
Zhai
ZY, Ku SY, Luan YH, Reinert G, Waterman MS, Sun FZ
(2010) The Power of
Detecting Enriched Patterns: An HMM Approach. Journal of Computational Biology
17(4):581-592. PMID: 20426691(software) |
|
79. |
Wan L, Reinert G, Sun FZ, Waterman MS
(2010) Alignment free
sequence comparison (II): theoretical power of comparison statistics. Journal
of Computational Biology 17(11): 1349-1372. PMID: 20973742 (software) |
|
78. |
Reinert
G, Chew D, Sun FZ, Waterman MS (2009)
Alignment free sequence comparison (I): statistics and power. Journal of
Computational Biology 16(12): 1615-1634 (software) |
|
77. |
Zhou LQ, Ma XT, Arbeitman MN, Sun FZ (2009)
Chromatin regulation and gene centrality are essential for controlling
fitness pleiotropy in Yeast. PLoS ONE 4(11): e8086 |
|
76. |
Sanders LE, Lebo MS, Dalton JE, Sun FZ, Arbeitman
MN (2009) Ecdysone receptor mediates courtship behaviors in Drosophila
by acting in the fruitless circuit in an isoform-specific manner. Current
Biology 19:1447-1452 |
|
75. |
Wang L, Tu Z, Sun FZ (2009) A network-based
integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila (ISMB 2010 highlight track). BMC
Genomics 10:220 (software) |
|
74. |
Jiang R, Chen T, Sun FZ (2009) Bayesian models and Gibbs
sampling strategies for local graph alignment and network motif
identification in stochastic biological networks. Communications in
Systems and Information 9(4):347-370 |
|
73. |
Lebo MS, Sanders LE , Sun FZ, Arbeitman MN(2009) Somatic, Germline and Sex Hierarchy Regulated Gene Expression
During Drosophila Metamorphosis. BMC Genomics 10:80 |
|
72. |
Wang WH, Nunez-Iglesias J, Luan YH, Sun FZ (2009)
Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in
biological networks under a pseudo-likelihood parameter estimation approach. BMC Bioinformatics 10:277 |
|
71. |
Wang L, Sun FZ, Chen T (2008) Prioritizing functional
modules mediating genetic perturbations and their phenotypic effects: a
global strategy (ISMB 2009 highlight track). Genome Biology 9:R174 |
|
70. |
Wan L, Li DY, Zhang DL, Liu X, Fu WJ, Zhu LH, Deng MH, Sun FZ, Qian MP (2008) Conservation
and implications of eukaryote transcriptional regulatory regions across
multiple species. BMC Genomics 9:623 |
|
69. |
Yan XT, Sun FZ (2008) Testing
gene set enrichment for subset of genes:Sub-GSE.
BMC Bioinformatics 9:362 (software) |
|
52. |
Zhidong Tu, Li Wang, Michelle Arbeitman, Ting Chen & Fengzhu Sun (2006) An integrative approach for causal gene identification and gene regulatory pathway inference (Program). Bioinformatics (ISMB 2006) 22:e489-e496 |
|
51. |
Zhidong Tu, Li Wang, Min Xu, Xianghong Zhou, Ting Chen & Fengzhu Sun (2006) Further understanding human disease genes by comparing with housekeeping genes and other genes. BMC Genomics 7:31 |
|
50. |
Kui Zhang, Fengzhu Sun (2005) Assessing the power of tag SNPs in the mapping of quantitative trait loci (QTL) with extremal and random samples. BMC Genetics 6:51 |
|
49. |
Kui Zhang, Zhaohui Qin, Ting Chen, Jun S. Liu, Michael S. Waterman, Fengzhu Sun (2005) HapBlock: Haplotype block partitioning and Tag SNP selection software using a set of dynamic programming algorithms (Program). Bioinformatics 21:131-134 |
|
48. |
Kui Zhang, Fengzhu Sun, Hongyu Zhao (2005) HAPLORE: A program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics 21:90-103 |
|
47. |
Faina Schwartz, Arvi Duka, Fengzhu Sun, Jing Cui, Athanasios Manolis and Haralambos Gavras (2004) Mitochondrial genome mutations in hypertensive individuals. Hypertension17:629-635 |
|
46. |
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 |
|
45. |
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 |
|
44. |
Deng MH, Tu ZD, Sun FZ, Chen T (2004) Mapping
gene ontology to proteins based on protein–protein interaction data.
Bioinformatics 20:895-902 |
|
43. |
Deng MH, Chen T, Sun FZ
(2004) Integrated
probabilistic model for functional prediction of proteins, RECOMB2003.
Also on Journal of Computational Biology, 11:463-476 |
|
42. |
Li WT, Sun FZ, Grosse I
(2004) Extreme-value
distribution based gene selection criteria for discriminant microarray data
analysis using logistic regression. RECOMB2003. Also on Journal
of Computational Biology 11:215-226 |
|
41. |
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 |
|
40. |
Kim SK, Zhang K, Sun FZ (2004) A comparison of different strategies for computing confidence intervals of the linkage disequilibrium measure D'. Pacific Symposium on Biocomputing 2004:128-139 |
|
39. |
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 |
|
38. |
Zhang K, Sun FZ, Waterman MS and Chen T (2003) Dynamic programming algorithms for partitioning sequence variation in human chromosomes. HERMIS, 4:15-26. Also “Computer Mathematics and Its Applications; Advances and Developments (1994-2005)?E.A. Lipitakis, Editor, LEA Publishers (2006), 431-442 |
|
37. |
Sun, FZ, Cui, J, Gavras, H, Schwartz, F (2003) A novel class of tests for the detection of mitochondrial DNAmutation involvement in diseases. Am J Hum Genet 72:1515-1526 |
|
30. |
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 |
|
29. |
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 |
|
28. |
Deng MH, Zhang K, Mehta S,
Chen T, Sun FZ (2002) Prediction
of protein function using protein-protein interaction data (supplement).
The first IEEE Computer Society bioinformatics conference, CSB2002, 117-126.
Also on Journal of Computational Biology, 10:947-960 |
|
27. |
Deng MH, Mehta S, Sun FZ,
Chen T (2002) Inferring domain-domain
interactions from protein-protein interactions (supplement). RECOMB2002:117-126.
Also on Genome Research 12:1540-1548. |
|
26. |
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 |
|
25 |
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 |
|
24. |
Jiang R, Dong J, Wang D, Sun FZ (2001) Fine-scale mapping using Hardy-Weinberg Disequilibrium. Ann Hum Genet, 65 207-219 |
|
23. |
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 |
|
22. |
Sun FZ, Yang QH, Zhao HY, Flanders WD (2000) Transmission/disequilibrium tests for quantitative traits. Ann Hum Genet, 64 555-565 |
|
21. |
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 |
|
20. |
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 |
|
19. |
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 |
|
18. |
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 |
|
17. |
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 |
|
16. |
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 |
|
15. |
Yang QH, Khoury MJ, Atkinson M, Sun FZ, Flanders WD (1999) Case-only design to measure gene-gene interactions. Epidemiology, 10 167-170 |
|
14. |
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 |
|
13. |
Sun, FZ (1999) Modeling
DNA shuffling. J Comp Biol, 6
77-90 |
|
12. |
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 |
|
11. |
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 |
|
10. |
Bruno W, Sun FZ, Torney DC
(1998) Optimum
group testing designs for partially characterized objects. J Appl Math, 58 1043-1059 |
|
9. |
Savage-Austin A, Sun FZ, |
|
8. |
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 |
|
7. |
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. |
Sun FZ, Benson G, Arnheim N, Waterman MS (1997) Pooling strategies for establishing physical genome maps using FISH. J Comp Biol, 4 467-486 |
|
5. |
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 Biol, 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 Research, 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 Biol, 23 3034-3040. |
Book Chapters
9. Zhidong Tu, Jun Zhu, and Fengzhu Sun (2011) Inferring
signaling and gene regulatory network from genetic and genomic information.
Henry Horng-Shing Lu, Bernhard Scholkopf
and Hongyu Zhao (editors): Handbook of Computational
Statistics: Statistical Bioinformatics, Springer. Pp479-500.
8. Hyunju Lee, Ting Chen, Fengzhu Sun (2010) Domain-Domain
Interactions. Jianfeng Feng,
Wenjiang Fu, Fengzhu Sun (Editors): Frontiers in Computational
and Systems Biology. Springer. Pp. 157-173.
7. Fengzhu Sun, Ting Chen, Minghua Deng, Hyunju Lee, Zhidong Tu (2010) Data
integration for the study of protein interactions. In Darlene R . Goldstein and Rudy Guerra
(Editors): Meta-analysis and Combining Information in Genetics and Genomics, Pp
259-274 Chapman and Hall
6. Kui Zhang, Fengzhu Sun (2007). Tag
SNP Selection and Its Applications in Association Studies. Hongwen Deng, Hui Shen, Yongjun Liu, and Hai Hu (Editors): Current Topics in Human Genetics: Studies
in Complex Diseases. World Scientific Publishing. pp.
95-122.
5. Xiucheng
Feng, Lin Wan, Minghua
Deng, Fengzhu Sun and Minping
Qian (2007) An
Efficient Algorithm for Deciphering Regulatory Motifs. Jianfeng Feng, Jürgen Jost and Minping Qian (Editors):
Networks: From Biology to Theory, Part III.
4. 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
3. 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. Computational Methods for SNPs
and Haplotype Inference, Istrail S, Waterman M and
Clark A (eds), 96-112
2. 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.
1.
Sun FZ (1999) Biological
and statistical studies for diseases involving mtDNA
mutations. In: Halloran ME, Geisser S (eds) Statistics in Genetics.
Springer, New York, pp 133-146.
Books
Frontiers
in Computational and Systems Biology (2010) (in honor of Professor Minping Qian’s 70th
birthday), Jiangfeng Feng, Wenjian Fu, Fengzhu Sun
(editors), Springer
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