Fengzhu Sun - RankMe

100 papers B 8Misc 2Journal 86Unranked 3

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Correction: Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations. PLoS Comput. Biol. Fengzhu Sun, Yue Huang, Tianqi Tang, Xiaowu Dai
2025	J	`jnl`	DeepDeconUQ estimates malignant cell fraction prediction intervals in bulk RNA-seq tissue. PLoS Comput. Biol. Jiawei Huang, Yuxuan Du, Kevin R. Kelly, Jinchi Lv, Yingying Fan, Jiang F. Zhong, Fengzhu Sun
2025	J	`jnl`	Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations. PLoS Comput. Biol. Yue Huang, Tianqi Tang, Xiaowu Dai, Fengzhu Sun
2024	J	`jnl`	A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data. BMC Bioinform. Dallace Francis, Fengzhu Sun
2024	J	`jnl`	DeepDecon accurately estimates cancer cell fractions in bulk RNA-seq data. Patterns Jiawei Huang, Yuxuan Du, Andres Stucky, Kevin R. Kelly, Jiang F. Zhong, Fengzhu Sun
2024	J	`jnl`	DeepLINK-T: deep learning inference for time series data using knockoffs and LSTM. CoRR Wenxuan Zuo, Zifan Zhu, Yuxuan Du, Yi-Chun Yeh, Jed A. Fuhrman, Jinchi Lv, Yingying Fan, Fengzhu Sun
2024	B	`conf`	ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation. RECOMB Yuxuan Du, Wenxuan Zuo, Fengzhu Sun
2024	J	`jnl`	Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart. J. Comput. Biol. Yuxuan Du, Wenxuan Zuo, Fengzhu Sun
2023	J	`jnl`	Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies. PLoS Comput. Biol. Yilin Gao, Fengzhu Sun
2023	J	`jnl`	Identifying local associations in biological time series: algorithms, statistical significance, and applications. Briefings Bioinform. Dongmei Ai, Lulu Chen, Jiemin Xie, Longwei Cheng, Fang Zhang, Yihui Luan, Yang Li, Shengwei Hou, Fengzhu Sun, Li Charlie Xia
2022	J	`jnl`	A New Context Tree Inference Algorithm for Variable Length Markov Chain Model with Applications to Biological Sequence Analyses. J. Comput. Biol. Shaokun An, Jie Ren, Fengzhu Sun, Lin Wan
2022	J	`jnl`	A model-based approach to assess reproducibility for large-scale high-throughput MRI-based studies. NeuroImage 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
2022	J	`jnl`	AC-PCoA: Adjustment for confounding factors using principal coordinate analysis. PLoS Comput. Biol. Yu Wang, Fengzhu Sun, Wei Lin, Shuqin Zhang
2022	J	`jnl`	HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs. Bioinform. Yuxuan Du, Fengzhu Sun
2022	J	`jnl`	Michael Waterman's Contributions to Computational Biology and Bioinformatics. J. Comput. Biol. Pavel A. Pevzner, Martin Vingron, Christian M. Reidys, Fengzhu Sun, Sorin Istrail
2022	J	`jnl`	Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression. J. Comput. Biol. Yuxuan Du, Sarah M. Laperriere, Jed A. Fuhrman, Fengzhu Sun
2022	J	`jnl`	Phage-bacterial contig association prediction with a convolutional neural network. Bioinform. Tianqi Tang, Shengwei Hou, Jed A. Fuhrman, Fengzhu Sun
2022	J	`jnl`	Special Issue: Professor Michael Waterman's 80th Birthday, Part 1. J. Comput. Biol. Sorin Istrail, Pavel A. Pevzner, Fengzhu Sun, Martin Vingron
2021	J	`jnl`	CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase. Bioinform. Yang Young Lu, Jiaxing Bai, Yiwen Wang, Ying Wang, Fengzhu Sun
2021	J	`jnl`	Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Briefings Bioinform. Ziye Wang, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, Shanfeng Zhu
2021	J	`jnl`	KIMI: Knockoff Inference for Motif Identification from molecular sequences with controlled false discovery rate. Bioinform. Xin Bai, Jie Ren, Yingying Fan, Fengzhu Sun
2020	J	`jnl`	Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Briefings Bioinform. Ziye Wang, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, Shanfeng Zhu
2020	J	`jnl`	Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data. Quant. Biol. Lin Wan, Xin Kang, Jie Ren, Fengzhu Sun
2020	J	`jnl`	Identifying viruses from metagenomic data using deep learning. Quant. Biol. Jie Ren, Kai Song, Chao Deng, Nathan A. Ahlgren, Jed A. Fuhrman, Yi Li, Xiaohui Xie, Ryan Poplin, Fengzhu Sun
2020	J	`jnl`	International Workshop on Applications of Probability and Statistics to Biology, July 11-13, 2019. Quant. Biol. Minghua Deng, Jianfeng Feng, Hong Qian, Lin Wan, Fengzhu Sun
2019	J	`jnl`	A new statistic for efficient detection of repetitive sequences. Bioinform. Sijie Chen, Yixin Chen, Fengzhu Sun, Michael S. Waterman, Xuegong Zhang
2019	J	`jnl`	NetGO: improving large-scale protein function prediction with massive network information. Nucleic Acids Res. Ronghui You, Shuwei Yao, Yi Xiong, Xiaodi Huang, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
2019	J	`jnl`	SolidBin: improving metagenome binning with semi-supervised normalized cut. Bioinform. Ziye Wang, Zhengyang Wang, Yang Young Lu, Fengzhu Sun, Shanfeng Zhu
2019	J	`jnl`	Statistical significance approximation for local similarity analysis of dependent time series data. BMC Bioinform. Fang Zhang, Fengzhu Sun, Yihui Luan
2018	J	`jnl`	GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank. Bioinform. Ronghui You, Zihan Zhang, Yi Xiong, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
2017	J	`jnl`	CAFE: aCcelerated Alignment-FrEe sequence analysis. Nucleic Acids Res. Yang Young Lu, Kujin Tang, Jie Ren, Jed A. Fuhrman, Michael S. Waterman, Fengzhu Sun
2017	J	`jnl`	COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge. Bioinform. Yang Young Lu, Ting Chen, Jed A. Fuhrman, Fengzhu Sun
2017	J	`jnl`	Improving contig binning of metagenomic data using (d BMC Bioinform. Ying Wang, Kun Wang, Yang Young Lu, Fengzhu Sun
2017	J	`jnl`	Prediction of virus-host infectious association by supervised learning methods. BMC Bioinform. Mengge Zhang, Lianping Yang, Jie Ren, Nathan A. Ahlgren, Jed A. Fuhrman, Fengzhu Sun
2017	J	`jnl`	Sparse generalized linear model with L 0 approximation for feature selection and prediction with big omics data. BioData Min. Zhenqiu Liu, Fengzhu Sun, Dermot P. B. McGovern
2016	J	`jnl`	Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics. Bioinform. Jie Ren, Kai Song, Minghua Deng, Gesine Reinert, Charles H. Cannon, Fengzhu Sun
2016	J	`jnl`	Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships. BMC Syst. Biol. Wangshu Zhang, Marcelo P. Coba, Fengzhu Sun
2015	J	`jnl`	Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists. J. Comput. Biol. Quan Chen, Xianghong Jasmine Zhou, Fengzhu Sun
2015	J	`jnl`	Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data. Bioinform. Zhenqiu Liu, Fengzhu Sun, Jonathan Braun, Dermot P. B. McGovern, Steven T. Piantadosi
2015	J	`jnl`	Network tuned multiple rank aggregation and applications to gene ranking. BMC Bioinform. Wenhui Wang, Xianghong Jasmine Zhou, Zhenqiu Liu, Fengzhu Sun
2015	J	`jnl`	Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains. BMC Bioinform. Li C. Xia, Dongmei Ai, Jacob A. Cram, Xiaoyi Liang, Jed A. Fuhrman, Fengzhu Sun
2014	J	`jnl`	Alignment-free protein interaction network comparison. Bioinform. Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun, Charlotte M. Deane
2014	J	`jnl`	DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. Nucleic Acids Res. 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
2014	J	`jnl`	Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. Briefings Bioinform. Xiaotu Ma, Ting Chen, Fengzhu Sun
2014	J	`jnl`	New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. Briefings Bioinform. Kai Song, Jie Ren, Gesine Reinert, Minghua Deng, Michael S. Waterman, Fengzhu Sun
2013	J	`jnl`	A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms. BMC Genom. Quan Chen, Fengzhu Sun
2013	J	`jnl`	Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads. J. Comput. Biol. Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun
2013	J	`jnl`	Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. Bioinform. Li C. Xia, Dongmei Ai, Jacob A. Cram, Jed A. Fuhrman, Fengzhu Sun
2013	J	`jnl`	Meeting report on RECOMB 2013 (the 17th Annual International Conference on Research in Computational Molecular Biology). Quant. Biol. Xuegong Zhang, Fengzhu Sun
2013	J	`jnl`	Multiple alignment-free sequence comparison. Bioinform. Jie Ren, Kai Song, Fengzhu Sun, Minghua Deng, Gesine Reinert
2013	J	`jnl`	Preface: Research in Computational Molecular Biology (RECOMB 2013). J. Comput. Biol. Fengzhu Sun
2013	B	`ed.`	Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Proceedings RECOMB Minghua Deng, Rui Jiang, Fengzhu Sun, Xuegong Zhang
2012	B	`conf`	Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended Abstract. RECOMB Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun
2012	J	`jnl`	CEDER: Accurate Detection of Differentially Expressed Genes by Combining Significance of Exons Using RNA-Seq. IEEE ACM Trans. Comput. Biol. Bioinform. Lin Wan, Fengzhu Sun
2012	J	`jnl`	Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads. J. Comput. Biol. Zhiyuan Zhai, Gesine Reinert, Kai Song, Michael S. Waterman, Yihui Luan, Fengzhu Sun
2012	J	`jnl`	Preface: Special Issue. J. Comput. Biol. Ting Chen, Paul Marjoram, Fengzhu Sun, Xianghong Jasmine Zhou
2011	J	`jnl`	DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. BMC Syst. Biol. Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang
2011	J	`jnl`	Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Syst. Biol. Li C. Xia, Joshua A. Steele, Jacob A. Cram, Zoe G. Cardon, Sheri L. Simmons, Joseph J. Vallino, Jed A. Fuhrman, Fengzhu Sun
2011	—	`ch.`	Inferring Signaling and Gene Regulatory Network from Genetic and Genomic Information. Handbook of Statistical Bioinformatics Zhidong Tu, Jun Zhu, Fengzhu Sun
2011	J	`jnl`	Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. BMC Bioinform. Wangshu Zhang, Fengzhu Sun, Rui Jiang
2011	J	`jnl`	Sequence Alignment as Hypothesis Testing. J. Comput. Biol. Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman
2011	J	`jnl`	Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny. BMC Bioinform. Qin Chang, Yihui Luan, Fengzhu Sun
2010	J	`jnl`	Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics. J. Comput. Biol. Lin Wan, Gesine Reinert, Fengzhu Sun, Michael S. Waterman
2010	J	`jnl`	The Power of Detecting Enriched Patterns: An HMM Approach. J. Comput. Biol. Zhiyuan Zhai, Shih-Yen Ku, Yihui Luan, Gesine Reinert, Michael S. Waterman, Fengzhu Sun
2009	J	`jnl`	Alignment-Free Sequence Comparison (I): Statistics and Power. J. Comput. Biol. Gesine Reinert, David Chew, Fengzhu Sun, Michael S. Waterman
2009	J	`jnl`	Bayesian Models and Gibbs Sampling Strategies for Local Graph Alignment and Motif Identification in Stochastic Biological Networks. Commun. Inf. Syst. Ting Chen, Rui Jiang, Fengzhu Sun
2009	J	`jnl`	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. Wenhui Wang, Juan Nunez-Iglesias, Yihui Luan, Fengzhu Sun
2008	J	`jnl`	Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands. J. Comput. Biol. Utz J. Pape, Sven Rahmann, Fengzhu Sun, Martin Vingron
2008	J	`jnl`	Testing gene set enrichment for subset of genes: Sub-GSE. BMC Bioinform. Xiting Yan, Fengzhu Sun
2008	J	`jnl`	The effects of protein interactions, gene essentiality and regulatory regions on expression variation. BMC Syst. Biol. Linqi Zhou, Xiaotu Ma, Fengzhu Sun
2007	J	`jnl`	CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data. Bioinform. Xiaotu Ma, Hyunju Lee, Li Wang, Fengzhu Sun
2007	J	`jnl`	Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinform. Chao Cheng, Xiting Yan, Fengzhu Sun, Lei M. Li
2006	J	`jnl`	A dynamic programming algorithm for binning microbial community profiles. Bioinform. Quansong Ruan, Joshua A. Steele, Michael S. Schwalbach, Jed A. Fuhrman, Fengzhu Sun
2006	J	`jnl`	A model-based approach to selection of tag SNPs. BMC Bioinform. Pierre Nicolas, Fengzhu Sun, Lei M. Li
2006	J	`jnl`	An integrated approach to the prediction of domain-domain interactions. BMC Bioinform. Hyunju Lee, Minghua Deng, Fengzhu Sun, Ting Chen
2006	—	`conf`	An integrative approach for causal gene identification and gene regulatory pathway inference. ISMB (Supplement of Bioinformatics) Zhidong Tu, Li Wang, Michelle N. Arbeitman, Ting Chen, Fengzhu Sun
2006	J	`jnl`	Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinform. Quansong Ruan, Debojyoti Dutta, Michael S. Schwalbach, Joshua A. Steele, Jed A. Fuhrman, Fengzhu Sun
2006	J	`jnl`	MARD: a new method to detect differential gene expression in treatment-control time courses. Bioinform. Chao Cheng, Xiaotu Ma, Xiting Yan, Fengzhu Sun, Lei M. Li
2006	J	`jnl`	Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. BMC Bioinform. Rui Jiang, Hua Yang, Fengzhu Sun, Ting Chen
2005	J	`jnl`	HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinform. Kui Zhang, Fengzhu Sun, Hongyu Zhao
2005	J	`jnl`	HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinform. Kui Zhang, Zhaohui S. Qin, Ting Chen, Jun S. Liu, Michael S. Waterman, Fengzhu Sun
2004	Misc	`conf`	A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium Measure. Pacific Symposium on Biocomputing Sung K. Kim, Kui Zhang, Fengzhu Sun
2004	J	`jnl`	An Integrated Probabilistic Model for Functional Prediction of Proteins. J. Comput. Biol. Minghua Deng, Ting Chen, Fengzhu Sun
2004	J	`jnl`	Extreme Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression. J. Comput. Biol. Wentian Li, Fengzhu Sun, Ivo Grosse
2004	J	`jnl`	Mapping gene ontology to proteins based on protein-protein interaction data. Bioinform. Minghua Deng, Zhidong Tu, Fengzhu Sun, Ting Chen
2003	B	`conf`	An integrated probabilistic model for functional prediction of proteins. RECOMB Minghua Deng, Ting Chen, Fengzhu Sun
2003	Misc	`conf`	Assessment of the reliability of protein-protein interactions and protein function prediction. Pacific Symposium on Biocomputing Minghua Deng, Fengzhu Sun, Ting Chen
2003	B	`conf`	Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data. RECOMB Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen
2003	J	`jnl`	Prediction of Protein Function Using Protein-Protein Interaction Data. J. Comput. Biol. Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun
2003	J	`jnl`	The Mutation Process of Microsatellites During the Polymerase Chain Reaction. J. Comput. Biol. Yinglei Lai, Deepali Shinde, Norman Arnheim, Fengzhu Sun
2002	—	`conf`	Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data. Computational Methods for SNPs and Haplotype Inference Kui Zhang, Ting Chen, Michael S. Waterman, Zhaohui S. Qin, Jun S. Liu, Fengzhu Sun
2002	B	`conf`	Inferring domain-domain interactions from protein-protein interactions. RECOMB Minghua Deng, Shipra Mehta, Fengzhu Sun, Ting Chen
2002	—	`conf`	Prediction of Protein Function Using Protein-Protein Interaction Data. CSB Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun
2000	J	`jnl`	Estimation of the Mutation Rate During Error-prone Polymerase Chain Reaction. J. Comput. Biol. Dai Wang, Cheng Zhao, Rong Cheng, Fengzhu Sun
1999	J	`jnl`	Modeling DNA Shuffling. J. Comput. Biol. Fengzhu Sun
1998	B	`conf`	Modeling DNA shuffling. RECOMB Fengzhu Sun
1998	J	`jnl`	Optimizing Nonadaptive Group Tests for Objects with Heterogeneous Priors. SIAM J. Appl. Math. David C. Torney, Fengzhu Sun, William J. Bruno
1997	J	`jnl`	Pooling Strategies for Establishing Physical Genome Maps Using FISH. J. Comput. Biol. Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman
1997	B	`conf`	Pooling strategies for establishing physical genome maps using FISH. RECOMB Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman
1995	J	`jnl`	The Polymerase Chain Reaction and Branching Processes. J. Comput. Biol. Fengzhu Sun