Fengzhu Sun

Li C. Xia, Dongmei Ai, Jacob Cram, Jed A. Fuhrman, Fengzhu Sun: Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. Bioinformatics 29(2): 230-237 (2013)

Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun: Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads. Journal of Computational Biology 20(2): 64-79 (2013)

Minghua Deng, Rui Jiang, Fengzhu Sun, Xuegong Zhang (Eds.): Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Proceedings. Lecture Notes in Computer Science 7821, Springer 2013, isbn 978-3-642-37194-3

Ting Chen, Paul Marjoram, Fengzhu Sun, Jasmine Xianghong Zhou: Preface: Special Issue. Journal of Computational Biology 19(6): 575-576 (2012)

Zhiyuan Zhai, Gesine Reinert, Kai Song, Michael S. Waterman, Yihui Luan, Fengzhu Sun: Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads. Journal of Computational Biology 19(6): 839-854 (2012)

Lin Wan, Fengzhu Sun: CEDER: Accurate Detection of Differentially Expressed Genes by Combining Significance of Exons Using RNA-Seq. IEEE/ACM Trans. Comput. Biology Bioinform. 9(5): 1281-1292 (2012)

Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun: Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended Abstract. RECOMB 2012: 272-285

Qin Chang, Yihui Luan, Fengzhu Sun: Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny. BMC Bioinformatics 12: 118 (2011)

Wangshu Zhang, Fengzhu Sun, Rui Jiang: Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. BMC Bioinformatics 12(S-1): S11 (2011)

Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman: Sequence Alignment as Hypothesis Testing. Journal of Computational Biology 18(5): 677-691 (2011)

Zhidong Tu, Jun Zhu, Fengzhu Sun: Inferring Signaling and Gene Regulatory Network from Genetic and Genomic Information. Handbook of Statistical Bioinformatics 2011: 479-500

Zhiyuan Zhai, Shih-Yen Ku, Yihui Luan, Gesine Reinert, Michael S. Waterman, Fengzhu Sun: The Power of Detecting Enriched Patterns: An HMM Approach. Journal of Computational Biology 17(4): 581-592 (2010)

Lin Wan, Gesine Reinert, Fengzhu Sun, Michael S. Waterman: Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics. Journal of Computational Biology 17(11): 1467-1490 (2010)

Wenhui Wang, Juan Nunez-Iglesias, Yihui Luan, Fengzhu Sun: 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 (2009)

Gesine Reinert, David Chew, Fengzhu Sun, Michael S. Waterman: Alignment-Free Sequence Comparison (I): Statistics and Power. Journal of Computational Biology 16(12): 1615-1634 (2009)

Xiting Yan, Fengzhu Sun: Testing gene set enrichment for subset of genes: Sub-GSE. BMC Bioinformatics 9 (2008)

Utz J. Pape, Sven Rahmann, Fengzhu Sun, Martin Vingron: Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands. Journal of Computational Biology 15(6): 547-564 (2008)

Xiaotu Ma, Hyunju Lee, Li Wang, Fengzhu Sun: CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data. Bioinformatics 23(2): 215-221 (2007)

Chao Cheng, Xiting Yan, Fengzhu Sun, Lei M. Li: Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinformatics 8 (2007)

Quansong Ruan, Joshua A. Steele, Michael S. Schwalbach, Jed A. Fuhrman, Fengzhu Sun: A dynamic programming algorithm for binning microbial community profiles. Bioinformatics 22(12): 1508-1514 (2006)

Quansong Ruan, Debojyoti Dutta, Michael S. Schwalbach, Joshua A. Steele, Jed A. Fuhrman, Fengzhu Sun: Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics 22(20): 2532-2538 (2006)

Chao Cheng, Xiaotu Ma, Xiting Yan, Fengzhu Sun, Lei M. Li: MARD: a new method to detect differential gene expression in treatment-control time courses. Bioinformatics 22(21): 2650-2657 (2006)

Hyunju Lee, Minghua Deng, Fengzhu Sun, Ting Chen: An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics 7: 269 (2006)

Pierre Nicolas, Fengzhu Sun, Lei M. Li: A model-based approach to selection of tag SNPs. BMC Bioinformatics 7: 303 (2006)

Rui Jiang, Hua Yang, Fengzhu Sun, Ting Chen: Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. BMC Bioinformatics 7: 417 (2006)

Zhidong Tu, Li Wang, Michelle N. Arbeitman, Ting Chen, Fengzhu Sun: An integrative approach for causal gene identification and gene regulatory pathway inference. ISMB (Supplement of Bioinformatics) 2006: 489-496

Kui Zhang, Fengzhu Sun, Hongyu Zhao: HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics 21(1): 90-103 (2005)

Kui Zhang, Zhaohui S. Qin, Ting Chen, Jun S. Liu, Michael S. Waterman, Fengzhu Sun: HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics 21(1): 131-134 (2005)

Minghua Deng, Zhidong Tu, Fengzhu Sun, Ting Chen: Mapping gene ontology to proteins based on protein-protein interaction data. Bioinformatics 20(6): 895-902 (2004)

Wentian Li, Fengzhu Sun, Ivo Grosse: Extreme Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression. Journal of Computational Biology 11(2/3): 215-226 (2004)

Minghua Deng, Ting Chen, Fengzhu Sun: An Integrated Probabilistic Model for Functional Prediction of Proteins. Journal of Computational Biology 11(2/3): 463-475 (2004)

Sung K. Kim, Kui Zhang, Fengzhu Sun: A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium Measure. Pacific Symposium on Biocomputing 2004: 128-139

Yinglei Lai, Deepali Shinde, Norman Arnheim, Fengzhu Sun: The Mutation Process of Microsatellites During the Polymerase Chain Reaction. Journal of Computational Biology 10(2): 143-155 (2003)

Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun: Prediction of Protein Function Using Protein-Protein Interaction Data. Journal of Computational Biology 10(6): 947-960 (2003)

Minghua Deng, Fengzhu Sun, Ting Chen: Assessment of the reliability of protein-protein interactions and protein function prediction. Pacific Symposium on Biocomputing 2003: 140-151

Minghua Deng, Ting Chen, Fengzhu Sun: An integrated probabilistic model for functional prediction of proteins. RECOMB 2003: 95-103

Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen: Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data. RECOMB 2003: 332-340

Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun: Prediction of Protein Function Using Protein-Protein Interaction Data. CSB 2002: 197-206

Kui Zhang, Ting Chen, Michael S. Waterman, Zhaohui S. Qin, Jun S. Liu, Fengzhu Sun: Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data. Computational Methods for SNPs and Haplotype Inference 2002: 96-112

Minghua Deng, Shipra Mehta, Fengzhu Sun, Ting Chen: Inferring domain-domain interactions from protein-protein interactions. RECOMB 2002: 117-126

Dai Wang, Cheng Zhao, Rong Cheng, Fengzhu Sun: Estimation of the Mutation Rate During Error-prone Polymerase Chain Reaction. Journal of Computational Biology 7(1-2): 143-158 (2000)

Fengzhu Sun: Modeling DNA Shuffling. Journal of Computational Biology 6(1): 77-90 (1999)

Fengzhu Sun: Modeling DNA shuffling. RECOMB 1998: 251-257

Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman: Pooling Strategies for Establishing Physical Genome Maps Using FISH. Journal of Computational Biology 4(4): 467-486 (1997)

Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman: Pooling strategies for establishing physical genome maps using FISH. RECOMB 1997: 294-299

Fengzhu Sun: The Polymerase Chain Reaction and Branching Processes. Journal of Computational Biology 2(1): 63-86 (1995)