Fengzhu Sun

发表

A dynamic programming algorithm for haplotype block partitioning

M. Waterman, Kui Zhang, Minghua Deng, 2002, Proceedings of the National Academy of Sciences of the United States of America.

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

Michael I. Jordan, William Stafford Noble, Gert R. G. Lanckriet, 2008, Genome Biology.

Inferring Domain–Domain Interactions From Protein–Protein Interactions

Minghua Deng, Ting Chen, Fengzhu Sun, 2002 .

Association of brain age with smoking, alcohol consumption, and genetic variants

A. Toga, Fengzhu Sun, Kaida Ning, 2018 .

An integrated probabilistic model for functional prediction of proteins

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

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

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

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

Sophie J. Weiss, J. Raes, L. Ursell, 2016, The ISME Journal.

An Efficient Algorithm for Deciphering Regulatory Motifs

Minping Qian, Minghua Deng, Fengzhu Sun, 2007 .

Conservation and implications of eukaryote transcriptional regulatory regions across multiple species

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

Further understanding human disease genes by comparing with housekeeping genes and other genes

Ting Chen, Fengzhu Sun, Zhidong Tu, 2006, BMC Genomics.

Comparative studies of alignment, alignment-free and SVM based approaches for predicting the hosts of viruses based on viral sequences

Fengzhu Sun, Han Li, 2018, Scientific Reports.

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.

Identifying viruses from metagenomic data by deep learning.

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

Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures

Ting Chen, Fengzhu Sun, Zhaoxia Yu, 2018, Front. Microbiol..

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains

Fengzhu Sun, Ying Wang, Weinan Liao, 2016, Scientific reports.

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

D. Caron, Fengzhu Sun, I. Hewson, 2011, The ISME Journal.

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

Yang Young Lu, Fengzhu Sun, J. Fuhrman, 2017, Microbiome.

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 metagenomic samples using sequence signatures

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

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.

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.

Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads

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

Benchmarking of alignment-free sequence comparison methods

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

A network-based integrated framework for predicting virus–prokaryote interactions

Fengzhu Sun, J. Fuhrman, J. Braun, 2020, NAR genomics and bioinformatics.

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

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

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 .

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

Fengzhu Sun, Hiroshi Mamitsuka, Xiaodi Huang, 2019, Nucleic acids research.

Network motif identification in stochastic networks.

Ting Chen, Fengzhu Sun, Zhidong Tu, 2006, Proceedings of the National Academy of Sciences of the United States of America.

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.

Association of relative brain age with tobacco smoking, alcohol consumption, and genetic variants

A. Toga, Fengzhu Sun, Kaida Ning, 2020, Scientific Reports.

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

Ying Wang, Shanfeng Zhu, Ziye Wang, 2020, Briefings Bioinform..

Improving brain age estimates with deep learning leads to identification of novel genetic factors associated with brain aging

A. Toga, Fengzhu Sun, Kaida Ning, 2020, Neurobiology of Aging.

The Polymerase Chain Reaction and Branching Processes

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

Stochastic Modeling of Polymerase Chain Reaction and Related Biotechnologies

Fengzhu Sun, 2001 .

Whole Genome Amplification and Branching Processes

M. Waterman, Fengzhu Sun, 1997, Advances in Applied Probability.

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.

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.

Afann: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression

Fengzhu Sun, Jie Ren, Kujin Tang, 2019, Genome Biology.

Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer

Yang Young Lu, Fengzhu Sun, Kujin Tang, 2018, Front. Microbiol..

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

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

Computational methods for the analysis of tag sequences in metagenomics studies.

Ting Chen, Fengzhu Sun, J. Fuhrman, 2012, Frontiers in bioscience.

Next-generation sequencing revealed divergence in deletions of the preS region in the HBV genome between different HBV-related liver diseases.

Fengzhu Sun, Shanfeng Zhu, Chunfang Gao, 2017, The Journal of general virology.

Michael Waterman's Contributions to Computational Biology and Bioinformatics

P. Pevzner, Fengzhu Sun, C. Reidys, 2022, J. Comput. Biol..

Towards enhanced and interpretable clustering/classification in integrative genomics

Yang Young Lu, Fengzhu Sun, Jinchi Lv, 2017, Nucleic acids research.

HapBlock – A Suite of Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Based on Haplotype and Genotype Data

Jun S. Liu, Ting Chen, Fengzhu Sun, 2007 .

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

Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu, 2017, bioRxiv.

––In Honor of Professor Minping Qian’s 80th Birthday

Minghua Deng, Fengzhu Sun, Jianfeng Feng, 2019 .

A New Context Tree Inference Algorithm for Variable Length Markov Chain Model with Applications to Biological Sequence Analyses.

Fengzhu Sun, J. Ren, Shaokun An, 2022, Journal of computational biology : a journal of computational molecular cell biology.

Reduced fecal short‐chain fatty acids in hispanic children with ulcerative colitis

O. Fiehn, Fengzhu Sun, Y. Luan, 2021, Physiological reports.

Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC

Fengzhu Sun, Jianfeng Feng, Shanfeng Zhu, 2018, PLoS genetics.

A dynamic programming algorithm for binning microbial community proﬁles

Fengzhu Sun, J. Fuhrman, J. Steele, 2006 .

Chromatin Regulation and Gene Centrality Are Essential for Controlling Fitness Pleiotropy in Yeast

Fengzhu Sun, M. Arbeitman, Xiaotu Ma, 2009, PloS one.

Rapid diagnosis and comprehensive bacteria profiling of sepsis based on cell-free DNA

Fengzhu Sun, Wenyuan Li, X. Zhou, 2020, Journal of Translational Medicine.

Batch Normalization Followed by Merging Is Powerful for Phenotype Prediction Integrating Multiple Heterogeneous Studies

Fengzhu Sun, Yilin Gao, 2022, bioRxiv.

MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

Fengzhu Sun, Jie Ren, S. Michail, 2019, Genome Biology.

The Machine-Learning-Mediated Interface of Microbiome and Genetic Risk Stratification in Neuroblastoma Reveals Molecular Pathways Related to Patient Survival

Jiang F Zhong, Fengzhu Sun, H. Fletcher, 2022, Cancers.

Phage–bacterial contig association prediction with a convolutional neural network

Fengzhu Sun, J. Fuhrman, Shengwei Hou, 2022, Bioinformatics.

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

Fengzhu Sun, Jie Ren, Fengzhu Sun, 2018 .

Exploring the genome and protein space of viruses

Fengzhu Sun, Yousong Peng, Aiping Wu, 2022, bioRxiv.

Marine Bacterial, Archaeal, and Protistan Association Networks

Fengzhu Sun, J. Fuhrman, Jacob A. Cram, 2014 .

MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities

Fengzhu Sun, Shanfeng Zhu, R. You, 2021, bioRxiv.

SolidBin: improving metagenome binning with semi-supervised normalized cut

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

Sequence Alignment as Hypothesis Testing

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

Prediction of protein function using protein-protein interaction data

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

Alignment-Free Sequence Analysis and Applications.

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

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

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

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..

Inferring Signaling and Gene Regulatory Network from Genetic and Genomic Information

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

Research in Computational Molecular Biology

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

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

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

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

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

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

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

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..

A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank

Fengzhu Sun, Jianfeng Feng, Xing-Ming Zhao, 2021, Genome medicine.

Association of Genetic Variation in the Mitochondrial Genome with Blood Pressure and Metabolic Traits Study Participants Bp Phenotypes Metabolic Phenotypes Association Analyses and Permutation Tests Liu Et Al Mtdna Association with Bp 3 Characteristics of the Study Participants Association Analyses

Andrew D. Johnson, D. Levy, Fengzhu Sun, 2022 .

Metabolic Traits Association of Genetic Variation in the Mitochondrial Genome With Blood Pressure and

Andrew D. Johnson, D. Levy, Fengzhu Sun, 2012 .

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.

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

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

The Mutation Process of Microsatellites During the Polymerase Chain Reaction

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

Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders

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

Maternal influence on blood pressure suggests involvement of mitochondrial DNA in the pathogenesis of hypertension: the Framingham Heart Study

D. Levy, Fengzhu Sun, R. Vasan, 2007, Journal of hypertension.

Identifying viruses from metagenomic data using deep learning

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

Alignment-free protein interaction network comparison

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

A new statistic for efficient detection of repetitive sequences

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

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

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

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..

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

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

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

Fengzhu Sun, Shuli Kang, Wenyuan Li, 2017, Genome Biology.

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

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

DeepLINK: Deep learning inference using knockoffs with applications to genomics

Fengzhu Sun, Jinchi Lv, Yingying Fan, 2021, Proceedings of the National Academy of Sciences.

Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis

Matthew S. Lebo, Fengzhu Sun, M. Arbeitman, 2009, BMC Genomics.

KIMI: Knockoff Inference for Motif Identification from molecular sequences with controlled false discovery rate

Yingying Fan, Xin Bai, Fengzhu Sun, 2020, Bioinform..

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

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

Modeling RNA degradation for RNA-Seq with applications.

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

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

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

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

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

Multiple alignment-free sequence comparison

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

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

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

Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists

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

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.

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.

CAFE: aCcelerated Alignment-FrEe sequence analysis

Jed A. Fuhrman, Jie Ren, Yang Young Lu, 2017, Nucleic Acids Res..

Increasing prediction performance of colorectal cancer disease status using random forests classification based on metagenomic shotgun sequencing data

Fengzhu Sun, Zifan Zhu, Yilin Gao, 2022, Synthetic and systems biotechnology.

DeepMicrobeFinder Sorts Metagenomes into Prokaryotes, Eukaryotes and Viruses, with Marine Applications

Ting Chen, Fengzhu Sun, J. Fuhrman, 2021 .

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

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

Reads Binning Improves Alignment-Free Metagenome Comparison

Jie Ren, Kai Song, Fengzhu Sun, 2019, Front. Genet..

MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

Fengzhu Sun, Jie Ren, S. Michail, 2019, Genome Biology.

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

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

Benchmarking of alignment-free sequence comparison methods

Jonas S. Almeida, Hani Z. Girgis, M. Waterman, 2019, bioRxiv.

Prediction of virus-host infectious association by supervised learning methods

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

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

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

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.

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..

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

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

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

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

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

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

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

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

Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients.

O. Fiehn, Fengzhu Sun, K. Whiteson, 2018, FEMS microbiology ecology.

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

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

Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA

David L. Erickson, Fengzhu Sun, J. Spouge, 2018, BMC Genomics.

Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer

C. Lajonchere, Fengzhu Sun, S. Dry, 2022, Nature Communications.

Prediction of protein function using protein-protein interaction data.

Kui Zhang, Minghua Deng, Ting Chen, 2003, Journal of computational biology : a journal of computational molecular cell biology.

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

Fengzhu Sun, Yuxuan Du, 2021, bioRxiv.

HiCzin: Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression

Fengzhu Sun, J. Fuhrman, Yuxuan Du, 2021, bioRxiv.

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.

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..

A Mathematical Analysis ofin VitroMolecular Selection – Amplification

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

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

ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network

Fengzhu Sun, X. Zhou, Shanfeng Zhu, 2021, NAR genomics and bioinformatics.

A dynamic programming algorithm for binning microbial community profiles

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

Inferring domain-domain interactions from protein-protein interactions

Minghua Deng, Ting Chen, Fengzhu Sun, 2002, RECOMB '02.

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.

Afann: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression

Fengzhu Sun, Kujin Tang, Jie Jessie Ren, 2019, Genome Biology.

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

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

Ecdysone Receptor Acts in fruitless- Expressing Neurons to Mediate Drosophila Courtship Behaviors

Matthew S. Lebo, Fengzhu Sun, M. Arbeitman, 2009, Current Biology.

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

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

Assessing the power of tag SNPs in the mapping of quantitative trait loci (QTL) with extremal and random samples

Fengzhu Sun, Kui Zhang, 2005, BMC Genetics.

Detecting susceptibility genes in case-control studies using set association

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

Parity is associated with cognitive function and brain age in both females and males

A. Toga, Fengzhu Sun, Kaida Ning, 2020, Scientific Reports.

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.

Decreased secondary faecal bile acids in children with ulcerative colitis and Clostridioides difficile infection

Fengzhu Sun, Y. Luan, C. Gayer, 2021, Alimentary pharmacology & therapeutics.

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

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

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

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

Mitochondrial genome mutations in hypertensive individuals.

Fengzhu Sun, H. Gavras, A. Manolis, 2004, American journal of hypertension.

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

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

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

Fengzhu Sun, Yuxuan Du, 2022, Genome Biology.

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.

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.

Comparison of Metatranscriptomic Samples Based on k-Tuple Frequencies

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

Rapid diagnosis and comprehensive bacteria profiling of sepsis based on cell-free DNA

Fengzhu Sun, Wenyuan Li, X. Zhou, 2020, Journal of Translational Medicine.

On the use of population-based registries in the clinical validation of genetic tests for disease susceptibility

Fengzhu Sun, M. Khoury, S. Coughlin, 1999, Genetics in Medicine.

A novel class of tests for the detection of mitochondrial DNA-mutation involvement in diseases.

Fengzhu Sun, H. Gavras, F. Schwartz, 2003, American journal of human genetics.

A model-based approach to selection of tag SNPs

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

Network tuned multiple rank aggregation and applications to gene ranking

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

A model-based approach to assess reproducibility for large-scale high-throughput MRI-based studies

Fengzhu Sun, W. Cheng, Jianfeng Feng, 2022, NeuroImage.

Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression

Fengzhu Sun, J. Fuhrman, S. Laperriere, 2022, J. Comput. Biol..

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

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

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

Fengzhu Sun, J. Fuhrman, L. C. Xia, 2015, BMC Bioinformatics.

Improving contig binning of metagenomic data using d2S$$ {d}_2^S $$ oligonucleotide frequency dissimilarity

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

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

M. Waterman, Fengzhu Sun, Jie Ren, 2017, BMC Genomics.

An integrated approach to the prediction of domain-domain interactions

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

Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads

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

Modeling DNA shuffling

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

The Power of Detecting Enriched Patterns: An HMM Approach

Gesine Reinert, Shih-Yen Ku, Fengzhu Sun, 2010, 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..

KmerGO: A Tool to Identify Group-Specific Sequences With k-mers

Ying Wang, Chao Deng, Fengzhu Sun, 2020, Frontiers in Microbiology.

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

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

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

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

Genomic mapping by end-characterized random clones: a mathematical analysis.

M S Waterman, M. Waterman, Fengzhu Sun, 1995, Genomics.

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.

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

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

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

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

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

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

Bioinformatics Original Paper Cgi: a New Approach for Prioritizing Genes by Combining Gene Expression and Protein–protein Interaction Data

Fengzhu Sun, Hyunju Lee, Xiaotu Ma, 2022 .

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms

Zhaohui S. Qin, M. Waterman, Ting Chen, 2005, Bioinform..

A model-based approach to selection of tag SNPs

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

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

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

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.

Alignment-Free Sequence Analysis and Applications.

Yang Young Lu, G. Reinert, Fengzhu Sun, 2018, Annual review of biomedical data science.

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms

Zhaohui S. Qin, M. Waterman, Ting Chen, 2005, Bioinform..

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..

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

M. Waterman, G. Reinert, Minghua Deng, 2014, Briefings Bioinform..

Parity is associated with cognitive function and brain age in both females and males

A. Toga, Fengzhu Sun, Kaida Ning, 2020, Scientific Reports.

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

Fengzhu Sun, M. Vingron, U. Pape, 2008, J. Comput. Biol..

Inferring domain-domain interactions from protein-protein interactions

Minghua Deng, Ting Chen, Fengzhu Sun, 2002, RECOMB '02.

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

Yang Young Lu, Fengzhu Sun, J. Fuhrman, 2017, Microbiome.

Further understanding human disease genes by comparing with housekeeping genes and other genes

Ting Chen, Fengzhu Sun, Zhidong Tu, 2006, BMC Genomics.

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

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

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

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

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

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