Fengzhu Sun

发表

Research in Computational Molecular Biology

Xuegong Zhang, Minghua Deng, Rui Jiang, 2013, Lecture Notes in Computer Science.

Efficient statistical significance approximation for local similarity analysis of high-throughput time series data

Dongmei Ai, Fengzhu Sun, Li Charlie Xia, 2013, Bioinform..

Debojyoti Dutta, Fengzhu Sun, Jed A. Fuhrman, 2006, Bioinform..

MARD: a new method to detect differential gene expression in treatment-control time courses

Fengzhu Sun, Chao Cheng, Xiaotu Ma, 2006, Bioinform..

Identifying viruses from metagenomic data using deep learning

Chao Deng, Kai Song, Yi Li, 2020, Quantitative Biology.

Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks

Ting Chen, Fengzhu Sun, Xiaotu Ma, 2014, Briefings Bioinform..

Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships

Fengzhu Sun, Wangshu Zhang, Marcelo P. Coba, 2016, BMC Systems Biology.

Computational Methods for Predicting DomainDomain Interactions

Ting Chen, Fengzhu Sun, Hyunju Lee, 2010 .

Mapping gene ontology to proteins based on protein-protein interaction data

Ting Chen, Minghua Deng, Fengzhu Sun, 2004, Bioinform..

Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended Abstract

Kai Song, Jie Ren, Minghua Deng, 2012, RECOMB.

Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data

Fengzhu Sun, Jie Ren, Lin Wan, 2020, Quantitative Biology.

An integrative approach for causal gene identification and gene regulatory pathway inference

Li Wang, Ting Chen, Fengzhu Sun, 2006, ISMB.

Assessing Study Reproducibility through M2RI: A Novel Approach for Large-scale High-throughput Association Studies

Jianfeng Feng, Chao Xie, Zeyu Jiao, 2020, bioRxiv.

An Efficient Algorithm for Deciphering Regulatory Motifs

Minping Qian, Minghua Deng, Fengzhu Sun, 2007 .

An Integrated Probabilistic Model for Functional Prediction of Proteins

Ting Chen, Minghua Deng, Fengzhu Sun, 2004, J. Comput. Biol..

SolidBin: improving metagenome binning with semi-supervised normalized cut

Zhengyang Wang, Shanfeng Zhu, Fengzhu Sun, 2019, Bioinform..

Estimation of the Mutation Rate During Error-prone Polymerase Chain Reaction

Cheng Zhao, Fengzhu Sun, Dai Wang, 2000, J. Comput. Biol..

Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands

Martin Vingron, Sven Rahmann, Fengzhu Sun, 2008, J. Comput. Biol..

Predicting kinase functional sites using hierarchical stochastic language modelling

Minping Qian, Xiangzhong Fang, Luhua Lai, 2010 .

Assessment of the reliability of protein-protein interactions and protein function prediction

Ting Chen, Minghua Deng, Fengzhu Sun, 2002, Pacific Symposium on Biocomputing.

CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data

Li Wang, Fengzhu Sun, Xiaotu Ma, 2007, Bioinform..

Sequence Alignment as Hypothesis Testing

Xuegong Zhang, Lu Meng, Fengzhu Sun, 2011, J. Comput. Biol..

Inferring activity changes of transcription factors by binding association with sorted expression profiles

Fengzhu Sun, Chao Cheng, Xiting Yan, 2007, BMC Bioinform..

Statistical significance approximation for local similarity analysis of dependent time series data

Fengzhu Sun, Fang Zhang, Yihui Luan, 2019, BMC Bioinformatics.

Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy

Hua Yang, Rui Jiang, Ting Chen, 2006, BMC Bioinformatics.

Prediction of protein function using protein-protein interaction data

Kui Zhang, Ting Chen, Minghua Deng, 2002, Proceedings. IEEE Computer Society Bioinformatics Conference.

Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists

Quan Chen, Fengzhu Sun, Xianghong Jasmine Zhou, 2015, J. Comput. Biol..

A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium Measure

Kui Zhang, Fengzhu Sun, Sung K. Kim, 2004, Pacific Symposium on Biocomputing.

The Mutation Process of Microsatellites During the Polymerase Chain Reaction

Fengzhu Sun, Yinglei Lai, Norman Arnheim, 2003, J. Comput. Biol..

The effects of protein interactions, gene essentiality and regulatory regions on expression variation

Linqi Zhou, Fengzhu Sun, Xiaotu Ma, 2008, BMC Systems Biology.

CRAFT: Compact genome Representation towards large-scale Alignment-Free daTabase

Ying Wang, Yiwen Wang, Fengzhu Sun, 2020 .

A new statistic for efficient detection of repetitive sequences

Yixin Chen, Sijie Chen, Xuegong Zhang, 2019, Bioinform..

Proceedings of the 17th international conference on Research in Computational Molecular Biology

Rui Jiang, Minghua Deng, Fengzhu Sun, 2013 .

Modeling DNA shuffling

Fengzhu Sun, Fengzhu Sun, 1998, RECOMB '98.

Modeling DNA Shuffling

Fengzhu Sun, 1999, J. Comput. Biol..

An integrated probabilistic model for functional prediction of proteins

Ting Chen, Minghua Deng, Fengzhu Sun, 2003, RECOMB '03.

Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads

Kai Song, Gesine Reinert, Fengzhu Sun, 2012, J. Comput. Biol..

A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

Quan Chen, Fengzhu Sun, Fengzhu Sun, 2013, BMC Genomics.

Alignment-free protein interaction network comparison

Gesine Reinert, Charlotte M. Deane, Waqar Ali, 2014, Bioinform..

Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data

Kui Zhang, Ting Chen, Fengzhu Sun, 2003, RECOMB '03.

Prediction of virus-host infectious association by supervised learning methods

Jie Ren, Lianping Yang, Fengzhu Sun, 2017, BMC Bioinformatics.

The Power of Detecting Enriched Patterns: An HMM Approach

Gesine Reinert, Shih-Yen Ku, Fengzhu Sun, 2010, J. Comput. Biol..

Extreme Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression

Ivo Grosse, Wentian Li, Fengzhu Sun, 2004, J. Comput. Biol..

DiseaseConnect: a comprehensive web server for mechanism-based disease–disease connections

Andrey Rzhetsky, Chun-Chi Liu, Fengzhu Sun, 2014, Nucleic Acids Res..

Preface: Research in Computational Molecular Biology (RECOMB 2013)

Fengzhu Sun, 2013, J. Comput. Biol..

Alignment-Free Sequence Analysis and Applications.

Gesine Reinert, Fengzhu Sun, Jie Ren, 2018, Annual review of biomedical data science.

New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing

Kai Song, Gesine Reinert, Jie Ren, 2014, Briefings Bioinform..

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains

Dongmei Ai, Fengzhu Sun, Li Charlie Xia, 2015, BMC Bioinformatics.

DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases

Yong Chen, Rui Jiang, Fengzhu Sun, 2011, BMC Systems Biology.

Network tuned multiple rank aggregation and applications to gene ranking

Fengzhu Sun, Wenhui Wang, Zhenqiu Liu, 2015, BMC Bioinformatics.

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO‐alignment and paired‐end read LinkAge

Ting Chen, Fengzhu Sun, Jed A. Fuhrman, 2016, Bioinform..

Dynamic Programming Algorithms for Haplotype Block Partition and Applications to Association Studies

Fengzhu Sun, 2002, RECOMB 2002.

Hapblock: Haplotype Block Partitioning and Tag Snp Selection Software Using a Set of Dynamic Programming Algorithms

Kui Zhang, Ting Chen, Zhaohui S. Qin, 2022 .

A new statistic for efficient detection of repetitive sequences

Sijie Chen, Xuegong Zhang, Fengzhu Sun, 2018, bioRxiv.

Testing gene set enrichment for subset of genes: Sub-GSE

Fengzhu Sun, Xiting Yan, Fengzhu Sun, 2008, BMC Bioinformatics.

Inferring Signaling and Gene Regulatory Network from Genetic and Genomic Information

Jun Zhu, Fengzhu Sun, Zhidong Tu, 2011, Handbook of Statistical Bioinformatics.

GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank

Yi Xiong, Hiroshi Mamitsuka, Shanfeng Zhu, 2017, bioRxiv.

Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data

Kui Zhang, Ting Chen, Zhaohui S. Qin, 2002, Computational Methods for SNPs and Haplotype Inference.

The Polymerase Chain Reaction and Branching Processes

Fengzhu Sun, Fengzhu Sun, 1995, J. Comput. Biol..

Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences

Ying Wang, Shanfeng Zhu, Fengzhu Sun, 2019, Briefings Bioinform..

Alignment-Free Sequence Comparison (I): Statistics and Power

Gesine Reinert, Fengzhu Sun, Michael S. Waterman, 2009, J. Comput. Biol..

Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach

Rui Jiang, Fengzhu Sun, Wangshu Zhang, 2011, BMC Bioinformatics.

Diffusion kernel-based logistic regression models for protein function prediction.

Ting Chen, Minghua Deng, Fengzhu Sun, 2006, Omics : a journal of integrative biology.

A model-based approach to selection of tag SNPs

Fengzhu Sun, Pierre Nicolas, Lei M. Li, 2006, BMC Bioinformatics.

Pooling Strategies for Establishing Physical Genome Maps Using FISH

Fengzhu Sun, Norman Arnheim, Michael Waterman, 1997, J. Comput. Biol..

HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination

Hongyu Zhao, Kui Zhang, Fengzhu Sun, 2005, Bioinform..

CEDER: Accurate Detection of Differentially Expressed Genes by Combining Significance of Exons Using RNA-Seq

Lin Wan, Fengzhu Sun, Fengzhu Sun, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

International Workshop on Applications of Probability and Statistics to Biology, July 11–13, 2019

Jianfeng Feng, Lin Wan, Minghua Deng, 2019, Quantitative Biology.

Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics

Kai Song, Gesine Reinert, Jie Ren, 2015, Bioinform..

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates

Fengzhu Sun, Li Charlie Xia, Jacob Cram, 2011, BMC Systems Biology.

Improving contig binning of metagenomic data using \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S $$\end{doc

Ying Wang, Fengzhu Sun, Yang Young Lu, 2017, BMC Bioinformatics.

A dynamic programming algorithm for binning microbial community profiles

Fengzhu Sun, Jed A. Fuhrman, Quansong Ruan, 2006, Bioinform..

Pooling strategies for establishing physical genome maps using FISH

Gary Benson, Fengzhu Sun, Michael S. Waterman, 1997, RECOMB '97.

Bayesian Models and Gibbs Sampling Strategies for Local Graph Alignment and Motif Identification in Stochastic Biological Networks

Rui Jiang, Ting Chen, Fengzhu Sun, 2009, Commun. Inf. Syst..

Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics

Gesine Reinert, Lin Wan, Fengzhu Sun, 2010, J. Comput. Biol..

Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny

Fengzhu Sun, Qin Chang, Yihui Luan, 2011, BMC Bioinformatics.

Multiple alignment-free sequence comparison

Kai Song, Gesine Reinert, Jie Ren, 2013, Bioinform..

Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data

Steve Piantadosi, Fengzhu Sun, Zhenqiu Liu, 2015, Bioinform..

Meeting report on RECOMB 2013 (the 17th Annual International Conference on Research in Computational Molecular Biology)

Xuegong Zhang, Fengzhu Sun, 2013, Quantitative Biology.

Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads

Kai Song, Jie Ren, Minghua Deng, 2013, J. Comput. Biol..

CRAFT: Compact genome Representation towards large-scale Alignment-Free daTabase.

Ying Wang, Yiwen Wang, Fengzhu Sun, 2020, Bioinformatics.

An integrated approach to the prediction of domain-domain interactions

Ting Chen, Minghua Deng, Fengzhu Sun, 2006, BMC Bioinformatics.

Sparse generalized linear model with L0 approximation for feature selection and prediction with big omics data

Fengzhu Sun, Zhenqiu Liu, Dermot P. B. McGovern, 2017, BioData Mining.

Abstract 24: Multi-feature ensemble learning on cell-free dna for accurately detecting and locating cancer

Frank Alber, Fengzhu Sun, Xianghong Jasmine Zhou, 2021, Clinical Research (Excluding Clinical Trials).

Classifying Alzheimer's disease with brain imaging and genetic data using a neural network framework

Arthur W. Toga, Fengzhu Sun, Kaida Ning, 2018, Neurobiology of Aging.

NetGO: improving large-scale protein function prediction with massive network information

Hiroshi Mamitsuka, Shanfeng Zhu, Yi Xiong, 2018, bioRxiv.

A Mathematical Analysis ofin VitroMolecular Selection – Amplification

David J. Galas, Fengzhu Sun, Michael S. Waterman, 1996 .

Haplotype block structure and its applications to association studies: power and study designs.

Fengzhu Sun, Kui Zhang, Kui Zhang, 2002, American journal of human genetics.

Identifying viruses from metagenomic data by deep learning.

Fengzhu Sun, Jed A. Fuhrman, Nathan A. Ahlgren, 2018, 1806.07810.

Optimal choice of word length when comparing two Markov sequences using a χ2-statistic

Jie Ren, Fengzhu Sun, Kujin Tang, 2017, BMC Genomics.

Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy

Ting Chen, Fengzhu Sun, Li Wang, 2008, Genome Biology.

CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA

Wei Wang, Frank Alber, Min Yu, 2017, Genome Biology.

Modeling RNA degradation for RNA-Seq with applications.

Ting Chen, Fengzhu Sun, Xiting Yan, 2012, Biostatistics.

Metagenomic unmapped reads provide important insights into human microbiota and disease associations

Fengzhu Sun, Jie Ren, Fengzhu Sun, 2018 .

Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome.

Kui Zhang, Fengzhu Sun, Thomas G Schulze, 2004, Human molecular genetics.

A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila

Fengzhu Sun, Li Wang, Zhidong Tu, 2009, BMC Genomics.

Sampling distribution for microsatellites amplified by PCR: mean field approximation and its applications to genotyping.

Fengzhu Sun, Fengzhu Sun, Yinglei Lai, 2004, Journal of theoretical biology.

Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations.

C.-C. Jay Kuo, C-C Jay Kuo, Ting Chen, 2007, American journal of human genetics.

New powerful statistics for alignment-free sequence comparison under a pattern transfer model.

Gesine Reinert, Jing Li, Fengzhu Sun, 2011, Journal of theoretical biology.

Conservation and implications of eukaryote transcriptional regulatory regions across multiple species

Minping Qian, Wenjiang J. Fu, Minghua Deng, 2008, BMC Genomics.

Benchmarking of alignment-free sequence comparison methods

Matteo Comin, Jonas S. Almeida, Burkhard Morgenstern, 2019, Genome Biology.

A Set of Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection via Haplotype Data or Genotype Data

Ting Chen, Fengzhu Sun, Michael S. Waterman, 2003 .

CAFE : aCcelerated Alignment-FrEe sequence analysis : Supplementary Material

Fengzhu Sun, Jed A. Fuhrman, Michael S. Waterman, 2017 .

Detecting susceptibility genes in case-control studies using set association

Kui Zhang, Fengzhu Sun, Fengzhu Sun, 2003, BMC Genetics.

Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data.

Ting Chen, Fengzhu Sun, Michael S Waterman, 2003, American journal of human genetics.

Data integration for the study of protein interactions

Minghua Deng, Fengzhu Sun, Hyunju Lee, 2009 .

Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads

Li C. Xia, Ting Chen, Fengzhu Sun, 2011, PloS one.

Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies.

Ting Chen, Zhaohui S. Qin, Fengzhu Sun, 2004, Genome research.

A network-based integrated framework for predicting virus-host interactions

Jie Ren, Fengzhu Sun, Jed A. Fuhrman, 2018, bioRxiv.

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes

Fengzhu Sun, Jed A Fuhrman, Fengzhu Sun, 2015, The ISME Journal.

Alignment-free \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$d_2^*$\end{document} oligonucleotide frequency dissi

Jie Ren, Fengzhu Sun, Yang Young Lu, 2016, Nucleic acids research.

The relationship between microsatellite slippage mutation rate and the number of repeat units.

Fengzhu Sun, Fengzhu Sun, Yinglei Lai, 2003, Molecular biology and evolution.

Comparison of Metatranscriptomic Samples Based on k-Tuple Frequencies

Ying Wang, Ting Chen, Fengzhu Sun, 2014, PloS one.

Microsatellite mutations during the polymerase chain reaction: mean field approximations and their applications.

Fengzhu Sun, Fengzhu Sun, Yinglei Lai, 2003, Journal of theoretical biology.

Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites.

Fengzhu Sun, Norman Arnheim, Deepali Shinde, 2003, Nucleic acids research.

Test of Association for Quantitative Traits in General Pedigrees: The Quantitative Pedigree Disequilibrium Test

Hongyu Zhao, Fengzhu Sun, Kui Zhang, 2001, Genetic epidemiology.

Comparison of metagenomic samples using sequence signatures

Minghua Deng, Fengzhu Sun, Xuegong Zhang, 2012, BMC Genomics.

Frontiers in Computational and Systems Biology

Wenjiang J. Fu, Fengzhu Sun, Jianfeng Feng, 2010 .

Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders

Fengzhu Sun, Hui Yang, Giulio Genovese, 2017, Nature Neuroscience.