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Fengzhu Sun

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TOP 3
Kai Song; Minghua Deng; Xuemei Liu; Jie Ren; Zhiyuan Zhai; Fengzhu Sun
Alignment-free sequence comparison based on next-generation sequencing reads.
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.
Quan Chen; Fengzhu Sun
A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms.

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All Publications

2013: Kai Song; Minghua Deng; Xuemei Liu; Jie Ren; Zhiyuan Zhai; Fengzhu Sun
Alignment-free sequence comparison based on next-generation sequencing reads.
Journal of computational biology : a journal of computational molecular cell biology 2013;20(2):64-79.
2013: 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 (Oxford, England) 2013;29(2):230-7.
2013: Quan Chen; Fengzhu Sun
A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms.
BMC genomics 2013;14 Suppl 1():S1.
2012: Chunyu Liu; Shih-Jen Hwang; Andrew D Johnson; Daniel Levy; Orian S Shirihai; Fengzhu Sun; Ramachandran S Vasan; Qiong Yang; Faina Schwartz
Association of genetic variation in the mitochondrial genome with blood pressure and metabolic traits.
Hypertension 2012;60(4):949-56.
2012: Lin Wan; Fengzhu Sun
CEDER: accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2012;9(5):1281-92.
2012: Lin Wan; Xiting Yan; Ting Chen; Fengzhu Sun
Modeling RNA degradation for RNA-Seq with applications.
Biostatistics (Oxford, England) 2012;13(4):734-47.
2012: Zhiyuan Zhai; Michael S Waterman; Yihui Luan; Gesine Reinert; Kai Song; Fengzhu Sun
Normal and compound poisson approximations for pattern occurrences in NGS reads.
Journal of computational biology : a journal of computational molecular cell biology 2012;19(6):839-54.
2012: Ting Chen; Paul Marjoram; Fengzhu Sun; Jasmine Xianghong Zhou
In this special issue of the Journal of Computational Biology, we take great pleasure in celebrating the landmark birthdays of two leaders in our field.
Journal of computational biology : a journal of computational molecular cell biology 2012;19(6):575-6.
2012: Bai Jiang; Jie Ren; Kai Song; Fengzhu Sun; Minghua Deng; Xuegong Zhang
Comparison of metagenomic samples using sequence signatures.
BMC genomics 2012;13():730.
2012: Qin Chang; Ting Chen; Jed A Fuhrman; Yihui Luan; Fengzhu Sun
Computational methods for the analysis of tag sequences in metagenomics studies.
Frontiers in bioscience (Scholar edition) 2012;4():1333-43.
2011: Li C Xia; Joseph J Vallino; Zoe G Cardon; Jacob A Cram; Jed A Fuhrman; Sheri L Simmons; Joshua A Steele; Fengzhu Sun
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates.
BMC systems biology 2011;5 Suppl 2():S15.
2011: Xuemei Liu; Gesine Reinert; Lin Wan; Michael S Waterman; Jing Li; Fengzhu Sun
New powerful statistics for alignment-free sequence comparison under a pattern transfer model.
Journal of theoretical biology 2011;284(1):106-16.
2011: Joshua A Steele; Fengzhu Sun; Patrick D Vigil; Li Xia; J Michael Beman; David A Caron; Cheryl-Emiliane T Chow; Peter D Countway; Ian Hewson; Adriane C Jones; Diane Y Kim; Anand Patel; Julie M Rose; Rohan Sachdeva; Michael S Schwalbach; Jed A Fuhrman
Marine bacterial, archaeal and protistan association networks reveal ecological linkages.
The ISME journal 2011;5(9):1414-25.
2011: Feng He; Yue-Qing Hu; Shili Lin; Fengzhu Sun; Jingyuan Yang; Ji-Yuan Zhou; Wing Kam Fung
Detection of parent-of-origin effects for quantitative traits in complete and incomplete nuclear families with multiple children.
American journal of epidemiology 2011;174(2):226-33.
2011: Lu Meng; Fengzhu Sun; Xuegong Zhang; Michael S Waterman
Sequence alignment as hypothesis testing.
Journal of computational biology : a journal of computational molecular cell biology 2011;18(5):677-91.
2011: Qin Chang; Yihui Luan; Fengzhu Sun
Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny.
BMC bioinformatics 2011;12():118.
2011: Wangshu Zhang; Fengzhu Sun; Yong Chen; Rui Jiang
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases.
BMC systems biology 2011;5():55.
2011: Wangshu Zhang; Fengzhu Sun; Rui Jiang
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach.
BMC bioinformatics 2011;12 Suppl 1():S11.
2010: Lin Wan; Gesine Reinert; Fengzhu Sun; Michael S Waterman
Alignment-free sequence comparison (II): theoretical power of comparison statistics.
Journal of computational biology : a journal of computational molecular cell biology 2010;17(11):1467-90.
2010: 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 : a journal of computational molecular cell biology 2010;17(4):581-92.
2009: Gesine Reinert; David Chew; Fengzhu Sun; Michael S Waterman
Alignment-free sequence comparison (I): statistics and power.
Journal of computational biology : a journal of computational molecular cell biology 2009;16(12):1615-34.
2009: Justin E Dalton; Matthew S Lebo; Laura E Sanders; Fengzhu Sun; Michelle N Arbeitman
Ecdysone receptor acts in fruitless- expressing neurons to mediate drosophila courtship behaviors.
Current biology : CB 2009;19(17):1447-52.
2009: Linqi Zhou; Xiaotu Ma; Michelle N Arbeitman; Fengzhu Sun
Chromatin regulation and gene centrality are essential for controlling fitness pleiotropy in yeast.
PloS one 2009;4(11):e8086.
2009: 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 2009;10():277.
2009: Li Wang; Zhidong Tu; Fengzhu Sun
A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila.
BMC genomics 2009;10():220.
2009: Matthew S Lebo; Laura E Sanders; Fengzhu Sun; Michelle N Arbeitman
Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis.
BMC genomics 2009;10():80.
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 : a journal of computational molecular cell biology 2008;15(6):547-64.
2008: Lin Wan; Dayong Li; Donglei Zhang; Xue Liu; Wenjiang J Fu; Lihuang Zhu; Minghua Deng; Fengzhu Sun; Minping Qian
Conservation and implications of eukaryote transcriptional regulatory regions across multiple species.
BMC genomics 2008;9():623.
2008: Li Wang; Fengzhu Sun; Ting Chen
Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy.
Genome biology 2008;9(12):R174.
2008: Xiting Yan; Fengzhu Sun
Testing gene set enrichment for subset of genes: Sub-GSE.
BMC bioinformatics 2008;9():362.
2008: Linqi Zhou; Xiaotu Ma; Fengzhu Sun
The effects of protein interactions, gene essentiality and regulatory regions on expression variation.
BMC systems biology 2008;2():54.
2007: Qiong Yang; Sung K Kim; Fengzhu Sun; Jing Cui; Martin G Larson; Ramachandran S Vasan; Daniel Levy; Faina Schwartz
Maternal influence on blood pressure suggests involvement of mitochondrial DNA in the pathogenesis of hypertension: the Framingham Heart Study.
Journal of hypertension 2007;25(10):2067-73.
2007: Rui Jiang; Hua Yang; Linqi Zhou; C-C Jay Kuo; Fengzhu Sun; Ting Chen
Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations.
American journal of human genetics 2007;81(2):346-60.
2007: Yue-Qing Hu; Ji-Yuan Zhou; Fengzhu Sun; Wing K Fung
The transmission disequilibrium test and imprinting effects test based on case-parent pairs.
Genetic epidemiology 2007;31(4):273-87.
2007: 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 (Oxford, England) 2007;23(2):215-21.
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 2007;8():452.
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 (Oxford, England) 2006;22(21):2650-7.
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 (Oxford, England) 2006;22(20):2532-8.
2006: Zhidong Tu; Li Wang; Michelle N Arbeitman; Ting Chen; Fengzhu Sun
An integrative approach for causal gene identification and gene regulatory pathway inference.
Bioinformatics (Oxford, England) 2006;22(14):e489-96.
2006: Rui Jiang; Zhidong Tu; Ting Chen; Fengzhu Sun
Network motif identification in stochastic networks.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(25):9404-9.
2006: Quansong Ruan; Joshua A Steele; Michael S Schwalbach; Jed A Fuhrman; Fengzhu Sun
A dynamic programming algorithm for binning microbial community profiles.
Bioinformatics (Oxford, England) 2006;22(12):1508-14.
2006: Rui Jiang; Hua Yang; Fengzhu Sun; Ting Chen
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy.
BMC bioinformatics 2006;7():417.
2006: Pierre Nicolas; Fengzhu Sun; Lei M Li
A model-based approach to selection of tag SNPs.
BMC bioinformatics 2006;7():303.
2006: Hyunju Lee; Minghua Deng; Fengzhu Sun; Ting Chen
An integrated approach to the prediction of domain-domain interactions.
BMC bioinformatics 2006;7():269.
2006: Hyunju Lee; Zhidong Tu; Minghua Deng; Fengzhu Sun; Ting Chen
Diffusion kernel-based logistic regression models for protein function prediction.
Omics : a journal of integrative biology 2006;10(1):40-55.
2006: Zhidong Tu; Li Wang; Min Xu; Xianghong Zhou; Ting Chen; Fengzhu Sun
Further understanding human disease genes by comparing with housekeeping genes and other genes.
BMC genomics 2006;7():31.
2005: Kui Zhang; Fengzhu Sun
Assessing the power of tag SNPs in the mapping of quantitative trait loci (QTL) with extremal and random samples.
BMC genetics 2005;6():51.
2005: Kui Zhang; Zhaohui Qin; Ting Chen; Jun Liu; Michael S Waterman; Fengzhu Sun
HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms.
Bioinformatics (Oxford, England) 2005;21(1):131-4.
2005: Kui Zhang; Fengzhu Sun; Hongyu Zhao
HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination.
Bioinformatics (Oxford, England) 2005;21(1):90-103.
2004: Faina Schwartz; Arvi Duka; Fengzhu Sun; Jing Cui; Athanasios Manolis; Haralambos Gavras
Mitochondrial genome mutations in hypertensive individuals.
American journal of hypertension 2004;17(7):629-35.
2004: Yinglei Lai; Fengzhu Sun
Sampling distribution for microsatellites amplified by PCR: mean field approximation and its applications to genotyping.
Journal of theoretical biology 2004;228(2):185-94.
2004: Kui Zhang; Zhaohui S Qin; Jun Liu; Ting Chen; Michael S Waterman; Fengzhu Sun
Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies.
Genome research 2004;14(5):908-16.
2004: Minghua Deng; Zhidong Tu; Fengzhu Sun; Ting Chen
Mapping Gene Ontology to proteins based on protein-protein interaction data.
Bioinformatics (Oxford, England) 2004;20(6):895-902.
2004: Thomas G. Schulze; Kui Zhang; Yu-Sheng Chen; Nirmala Akula; Fengzhu Sun; Francis McMajon
Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome.
Human molecular genetics 2004;13(3):335-42.
2004: Minghua Deng; Ting Chen; Fengzhu Sun
An integrated probabilistic model for functional prediction of proteins.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(2-3):463-75.
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 : a journal of computational molecular cell biology 2004;11(2-3):215-26.
2004: S K Kim; Kui Zhang; Fengzhu Sun
A comparison of different strategies for computing confidence intervals of the linkage disequilibrium measure D'.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():128-39.
2003: Yinglei Lai; Fengzhu Sun
The relationship between microsatellite slippage mutation rate and the number of repeat units.
Molecular biology and evolution 2003;20(12):2123-31.
2003: Yinglei Lai; Fengzhu Sun
Microsatellite mutations during the polymerase chain reaction: mean field approximations and their applications.
Journal of theoretical biology 2003;224(1):127-37.
2003: Kui Zhang; Fengzhu Sun; Michael S Waterman; Ting Chen
Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data.
American journal of human genetics 2003;73(1):63-73.
2003: Fengzhu Sun; Jing Cui; Haralambos Gavras; Faina Schwartz
A novel class of tests for the detection of mitochondrial DNA-mutation involvement in diseases.
American journal of human genetics 2003;72(6):1515-26.
2003: Deepali Shinde; Yinglei Lai; Fengzhu Sun; Norman Arnheim
Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites.
Nucleic acids research 2003;31(3):974-80.
2003: Minghua Deng; Kui Zhang; Shipra Mehta; Ting Chen; Fengzhu Sun
Prediction of protein function using protein-protein interaction data.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(6):947-60.
2003: Sung Kim; Kui Zhang; Fengzhu Sun
Detecting susceptibility genes in case-control studies using set association.
BMC genetics 2003;4 Suppl 1():S9.
2003: Yinglei Lai; Deepali Shinde; Norman Arnheim; Fengzhu Sun
The mutation process of microsatellites during the polymerase chain reaction.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(2):143-55.
2003: Minghua Deng; Fengzhu Sun; Ting Chen
Assessment of the reliability of protein-protein interactions and protein function prediction.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2003;():140-51.
2002: Kui Zhang; Peter Calabrese; Magnus Nordborg; Fengzhu Sun
Haplotype block structure and its applications to association studies: power and study designs.
American journal of human genetics 2002;71(6):1386-94.
2002: Minghua Deng; Shipra Mehta; Fengzhu Sun; Ting Chen
Inferring domain-domain interactions from protein-protein interactions.
Genome research 2002;12(10):1540-8.
2002: Kui Zhang; Minghua Deng; Ting Chen; Michael S Waterman; Fengzhu Sun
A dynamic programming algorithm for haplotype block partitioning.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(11):7335-9.
2002: Minghua Deng; Kui Zhang; Shipra Mehta; Ting Chen; Fengzhu Sun
Prediction of protein function using protein-protein interaction data.
Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference 2002;1():197-206.
2000: D Wang; C Zhao; R Cheng; Fengzhu Sun
Estimation of the mutation rate during error-prone polymerase chain reaction.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):143-58.