Fengzhu Sun

Publication Activity (10 Years)

Years Active: 1995-2024
Publications (10 Years): 35

Top Topics

Computational Biology

Protein Function Prediction

Top Venues

J. Comput. Biol.

Briefings Bioinform.

Publications

Wenxuan Zuo, Zifan Zhu, Yuxuan Du, Yi-Chun Yeh, Jed A. Fuhrman, Jinchi Lv, Yingying Fan, Fengzhu Sun
DeepLINK-T: deep learning inference for time series data using knockoffs and LSTM. CoRR (2024)
Dallace Francis, Fengzhu Sun
A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data. BMC Bioinform. 25 (1) (2024)
Jiawei Huang, Yuxuan Du, Andres Stucky, Kevin R. Kelly, Jiang F. Zhong, Fengzhu Sun
DeepDecon accurately estimates cancer cell fractions in bulk RNA-seq data. Patterns 5 (6) (2024)
Yuxuan Du, Wenxuan Zuo, Fengzhu Sun
ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation. RECOMB (2024)
Yilin Gao, Fengzhu Sun
Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies. PLoS Comput. Biol. 19 (10) (2023)
Yuxuan Du, Sarah M. Laperriere, Jed A. Fuhrman, Fengzhu Sun
Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression. J. Comput. Biol. 29 (2) (2022)
Zeyu Jiao, Yinglei Lai, Jujiao Kang, Weikang Gong, Liang Ma, Tianye Jia, Chao Xie, Shitong Xiang, Wei Cheng, Andreas Heinz, Sylvane Desrivières, Gunter Schumann, Fengzhu Sun, Jianfeng Feng
A model-based approach to assess reproducibility for large-scale high-throughput MRI-based studies. NeuroImage 255 (2022)
Sorin Istrail, Pavel A. Pevzner, Fengzhu Sun, Martin Vingron
Special Issue: Professor Michael Waterman's 80th Birthday, Part 1. J. Comput. Biol. 29 (7) (2022)
Pavel A. Pevzner, Martin Vingron, Christian M. Reidys, Fengzhu Sun, Sorin Istrail
Michael Waterman's Contributions to Computational Biology and Bioinformatics. J. Comput. Biol. 29 (7) (2022)
Yuxuan Du, Fengzhu Sun
HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs. Bioinform. 38 (11) (2022)
Shaokun An, Jie Ren, Fengzhu Sun, Lin Wan
A New Context Tree Inference Algorithm for Variable Length Markov Chain Model with Applications to Biological Sequence Analyses. J. Comput. Biol. 29 (8) (2022)
Yu Wang, Fengzhu Sun, Wei Lin, Shuqin Zhang
AC-PCoA: Adjustment for confounding factors using principal coordinate analysis. PLoS Comput. Biol. 18 (7) (2022)
Yang Young Lu, Jiaxing Bai, Yiwen Wang, Ying Wang, Fengzhu Sun
CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase. Bioinform. 37 (2) (2021)
Ziye Wang, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, Shanfeng Zhu
Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Briefings Bioinform. 22 (1) (2021)
Xin Bai, Jie Ren, Yingying Fan, Fengzhu Sun
KIMI: Knockoff Inference for Motif Identification from molecular sequences with controlled false discovery rate. Bioinform. 37 (6) (2021)
Ziye Wang, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, Shanfeng Zhu
Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Briefings Bioinform. 21 (3) (2020)
Minghua Deng, Jianfeng Feng, Hong Qian, Lin Wan, Fengzhu Sun
International Workshop on Applications of Probability and Statistics to Biology, July 11-13, 2019. Quant. Biol. 8 (2) (2020)
Jie Ren, Kai Song, Chao Deng, Nathan A. Ahlgren, Jed A. Fuhrman, Yi Li, Xiaohui Xie, Ryan Poplin, Fengzhu Sun
Identifying viruses from metagenomic data using deep learning. Quant. Biol. 8 (1) (2020)
Lin Wan, Xin Kang, Jie Ren, Fengzhu Sun
Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data. Quant. Biol. 8 (2) (2020)
Fang Zhang, Fengzhu Sun, Yihui Luan
Statistical significance approximation for local similarity analysis of dependent time series data. BMC Bioinform. 20 (1) (2019)
Sijie Chen, Yixin Chen, Fengzhu Sun, Michael S. Waterman, Xuegong Zhang
A new statistic for efficient detection of repetitive sequences. Bioinform. 35 (22) (2019)
Ronghui You, Shuwei Yao, Yi Xiong, Xiaodi Huang, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
NetGO: improving large-scale protein function prediction with massive network information. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Ziye Wang, Zhengyang Wang, Yang Young Lu, Fengzhu Sun, Shanfeng Zhu
SolidBin: improving metagenome binning with semi-supervised normalized cut. Bioinform. 35 (21) (2019)
Ronghui You, Zihan Zhang, Yi Xiong, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank. Bioinform. 34 (14) (2018)
Yang Young Lu, Ting Chen, Jed A. Fuhrman, Fengzhu Sun
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge. Bioinform. 33 (6) (2017)
Zhenqiu Liu, Fengzhu Sun, Dermot P. B. McGovern
Sparse generalized linear model with L 0 approximation for feature selection and prediction with big omics data. BioData Min. 10 (1) (2017)
Yang Young Lu, Kujin Tang, Jie Ren, Jed A. Fuhrman, Michael S. Waterman, Fengzhu Sun
CAFE: aCcelerated Alignment-FrEe sequence analysis. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Ying Wang, Kun Wang, Yang Young Lu, Fengzhu Sun
) oligonucleotide frequency dissimilarity. BMC Bioinform. 18 (1) (2017)
Mengge Zhang, Lianping Yang, Jie Ren, Nathan A. Ahlgren, Jed A. Fuhrman, Fengzhu Sun
Prediction of virus-host infectious association by supervised learning methods. BMC Bioinform. 18 (S-3) (2017)
Wangshu Zhang, Marcelo P. Coba, Fengzhu Sun
Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships. BMC Syst. Biol. 10 (S-1) (2016)
Jie Ren, Kai Song, Minghua Deng, Gesine Reinert, Charles H. Cannon, Fengzhu Sun
Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics. Bioinform. 32 (7) (2016)
Li C. Xia, Dongmei Ai, Jacob A. Cram, Xiaoyi Liang, Jed A. Fuhrman, Fengzhu Sun
Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains. BMC Bioinform. 16 (2015)
Quan Chen, Xianghong Jasmine Zhou, Fengzhu Sun
Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists. J. Comput. Biol. 22 (2) (2015)
Zhenqiu Liu, Fengzhu Sun, Jonathan Braun, Dermot P. B. McGovern, Steven T. Piantadosi
Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data. Bioinform. 31 (7) (2015)
Wenhui Wang, Xianghong Jasmine Zhou, Zhenqiu Liu, Fengzhu Sun
Network tuned multiple rank aggregation and applications to gene ranking. BMC Bioinform. 16 (S-1) (2015)
Xiaotu Ma, Ting Chen, Fengzhu Sun
Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. Briefings Bioinform. 15 (5) (2014)
Kai Song, Jie Ren, Gesine Reinert, Minghua Deng, Michael S. Waterman, Fengzhu Sun
New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. Briefings Bioinform. 15 (3) (2014)
Chun-Chi Liu, Yu-Ting Tseng, Wenyuan Li, Chia-Yu Wu, Ilya Mayzus, Andrey Rzhetsky, Fengzhu Sun, Michael S. Waterman, Jeremy J. W. Chen, Preet M. Chaudhary, Joseph Loscalzo, Edward Crandall, Xianghong Jasmine Zhou
DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun, Charlotte M. Deane
Alignment-free protein interaction network comparison. Bioinform. 30 (17) (2014)
Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun
Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads. J. Comput. Biol. 20 (2) (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 Genom. 14 (S-1) (2013)
Jie Ren, Kai Song, Fengzhu Sun, Minghua Deng, Gesine Reinert
Multiple alignment-free sequence comparison. Bioinform. 29 (21) (2013)
Xuegong Zhang, Fengzhu Sun
Meeting report on RECOMB 2013 (the 17th Annual International Conference on Research in Computational Molecular Biology). Quant. Biol. 1 (2) (2013)
Fengzhu Sun
Preface: Research in Computational Molecular Biology (RECOMB 2013). J. Comput. Biol. 20 (10) (2013)
Li C. Xia, Dongmei Ai, Jacob A. Cram, Jed A. Fuhrman, Fengzhu Sun
Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. Bioinform. 29 (2) (2013)
Ting Chen, Paul Marjoram, Fengzhu Sun, Xianghong Jasmine Zhou
Preface: Special Issue. J. Comput. Biol. 19 (6) (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. J. Comput. Biol. 19 (6) (2012)
Lin Wan, Fengzhu Sun
CEDER: Accurate Detection of Differentially Expressed Genes by Combining Significance of Exons Using RNA-Seq. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (5) (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)
Qin Chang, Yihui Luan, Fengzhu Sun
Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny. BMC Bioinform. 12 (2011)
Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman
Sequence Alignment as Hypothesis Testing. J. Comput. Biol. 18 (5) (2011)
Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. BMC Syst. Biol. 5 (2011)
Li C. Xia, Joshua A. Steele, Jacob A. Cram, Zoe G. Cardon, Sheri L. Simmons, Joseph J. Vallino, Jed A. Fuhrman, Fengzhu Sun
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Syst. Biol. 5 (S-2) (2011)
Wangshu Zhang, Fengzhu Sun, Rui Jiang
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. BMC Bioinform. 12 (S-1) (2011)
Zhiyuan Zhai, Shih-Yen Ku, Yihui Luan, Gesine Reinert, Michael S. Waterman, Fengzhu Sun
The Power of Detecting Enriched Patterns: An HMM Approach. J. Comput. Biol. 17 (4) (2010)
Lin Wan, Gesine Reinert, Fengzhu Sun, Michael S. Waterman
Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics. J. Comput. Biol. 17 (11) (2010)
Ting Chen, Rui Jiang, Fengzhu Sun
Bayesian Models and Gibbs Sampling Strategies for Local Graph Alignment and Motif Identification in Stochastic Biological Networks. Commun. Inf. Syst. 9 (4) (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 Bioinform. 10 (2009)
Gesine Reinert, David Chew, Fengzhu Sun, Michael S. Waterman
Alignment-Free Sequence Comparison (I): Statistics and Power. J. Comput. Biol. 16 (12) (2009)
Linqi Zhou, Xiaotu Ma, Fengzhu Sun
The effects of protein interactions, gene essentiality and regulatory regions on expression variation. BMC Syst. Biol. 2 (2008)
Xiting Yan, Fengzhu Sun
Testing gene set enrichment for subset of genes: Sub-GSE. BMC Bioinform. 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. J. Comput. Biol. 15 (6) (2008)
Chao Cheng, Xiting Yan, Fengzhu Sun, Lei M. Li
Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinform. 8 (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. Bioinform. 23 (2) (2007)
Quansong Ruan, Joshua A. Steele, Michael S. Schwalbach, Jed A. Fuhrman, Fengzhu Sun
A dynamic programming algorithm for binning microbial community profiles. Bioinform. 22 (12) (2006)
Pierre Nicolas, Fengzhu Sun, Lei M. Li
A model-based approach to selection of tag SNPs. BMC Bioinform. 7 (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. Bioinform. 22 (21) (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)
Rui Jiang, Hua Yang, Fengzhu Sun, Ting Chen
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. BMC Bioinform. 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. Bioinform. 22 (20) (2006)
Hyunju Lee, Minghua Deng, Fengzhu Sun, Ting Chen
An integrated approach to the prediction of domain-domain interactions. BMC Bioinform. 7 (2006)
Kui Zhang, Fengzhu Sun, Hongyu Zhao
HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinform. 21 (1) (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. Bioinform. 21 (1) (2005)
Minghua Deng, Zhidong Tu, Fengzhu Sun, Ting Chen
Mapping gene ontology to proteins based on protein-protein interaction data. Bioinform. 20 (6) (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)
Minghua Deng, Ting Chen, Fengzhu Sun
An Integrated Probabilistic Model for Functional Prediction of Proteins. J. Comput. Biol. 11 (2/3) (2004)
Wentian Li, Fengzhu Sun, Ivo Grosse
Extreme Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression. J. Comput. Biol. 11 (2/3) (2004)
Minghua Deng, Ting Chen, Fengzhu Sun
An integrated probabilistic model for functional prediction of proteins. RECOMB (2003)
Minghua Deng, Fengzhu Sun, Ting Chen
Assessment of the reliability of protein-protein interactions and protein function prediction. Pacific Symposium on Biocomputing (2003)
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)
Yinglei Lai, Deepali Shinde, Norman Arnheim, Fengzhu Sun
The Mutation Process of Microsatellites During the Polymerase Chain Reaction. J. Comput. Biol. 10 (2) (2003)
Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun
Prediction of Protein Function Using Protein-Protein Interaction Data. J. Comput. Biol. 10 (6) (2003)
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)
Minghua Deng, Shipra Mehta, Fengzhu Sun, Ting Chen
Inferring domain-domain interactions from protein-protein interactions. RECOMB (2002)
Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun
Prediction of Protein Function Using Protein-Protein Interaction Data. CSB (2002)
Dai Wang, Cheng Zhao, Rong Cheng, Fengzhu Sun
Estimation of the Mutation Rate During Error-prone Polymerase Chain Reaction. J. Comput. Biol. 7 (1-2) (2000)
Fengzhu Sun
Modeling DNA Shuffling. J. Comput. Biol. 6 (1) (1999)
David C. Torney, Fengzhu Sun, William J. Bruno
Optimizing Nonadaptive Group Tests for Objects with Heterogeneous Priors. SIAM J. Appl. Math. 58 (4) (1998)
Fengzhu Sun
Modeling DNA shuffling. RECOMB (1998)
Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman
Pooling Strategies for Establishing Physical Genome Maps Using FISH. J. Comput. Biol. 4 (4) (1997)
Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman
Pooling strategies for establishing physical genome maps using FISH. RECOMB (1997)
Fengzhu Sun
The Polymerase Chain Reaction and Branching Processes. J. Comput. Biol. 2 (1) (1995)