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2020 – today
- 2024
[j79]Dallace Francis, Fengzhu Sun:
A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data. BMC Bioinform. 25(1): 266 (2024)- [j78]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): 100969 (2024) - [c12]Yuxuan Du, Wenxuan Zuo, Fengzhu Sun:
ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation. RECOMB 2024: 99-114 - [i1]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 abs/2404.04317 (2024) - 2023
- [j77]Yilin Gao, Fengzhu Sun:
Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies. PLoS Comput. Biol. 19(10) (2023) - 2022
- [j76]Yuxuan Du, Fengzhu Sun:
HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs. Bioinform. 38(11): 2973-2979 (2022) - [j75]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): 106-120 (2022) - [j74]Sorin Istrail, Pavel A. Pevzner, Fengzhu Sun, Martin Vingron:
Special Issue: Professor Michael Waterman's 80th Birthday, Part 1. J. Comput. Biol. 29(7): 599-600 (2022) - [j73]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): 601-615 (2022) - [j72]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): 839-856 (2022) - [j71]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: 119166 (2022) - [j70]Yu Wang, Fengzhu Sun, Wei Lin, Shuqin Zhang:
AC-PCoA: Adjustment for confounding factors using principal coordinate analysis. PLoS Comput. Biol. 18(7) (2022) - 2021
- [j69]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): 611 (2021) - [j68]Yang Young Lu, Jiaxing Bai, Yiwen Wang, Ying Wang, Fengzhu Sun:
CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase. Bioinform. 37(2): 155-161 (2021) - [j67]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): 759-766 (2021) - 2020
- [j66]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): 777-790 (2020) - [j65]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): 64-77 (2020) - [j64]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): 143-154 (2020) - [j63]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): 177-186 (2020)
2010 – 2019
- 2019
- [j62]Ziye Wang, Zhengyang Wang, Yang Young Lu, Fengzhu Sun, Shanfeng Zhu:
SolidBin: improving metagenome binning with semi-supervised normalized cut. Bioinform. 35(21): 4229-4238 (2019) - [j61]Sijie Chen, Yixin Chen, Fengzhu Sun, Michael S. Waterman, Xuegong Zhang:
A new statistic for efficient detection of repetitive sequences. Bioinform. 35(22): 4596-4606 (2019) - [j60]Fang Zhang, Fengzhu Sun, Yihui Luan:
Statistical significance approximation for local similarity analysis of dependent time series data. BMC Bioinform. 20(1): 53 (2019) - [j59]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): W379-W387 (2019) - 2018
- [j58]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): 2465-2473 (2018) - 2017
- [j57]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): 39:1-39:12 (2017) - [j56]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): 791-798 (2017) - [j55]Ying Wang, Kun Wang, Yang Young Lu, Fengzhu Sun:
Improving contig binning of metagenomic data using (d2S) oligonucleotide frequency dissimilarity. BMC Bioinform. 18(1): 425:1-425:14 (2017) - [j54]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): 143-154 (2017) - [j53]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): W554-W559 (2017) - 2016
- [j52]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): 993-1000 (2016) - [j51]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): 4 (2016) - 2015
- [j50]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): 1067-1074 (2015) - [j49]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: 301:1-301:14 (2015) - [j48]Wenhui Wang, Xianghong Jasmine Zhou, Zhenqiu Liu, Fengzhu Sun:
Network tuned multiple rank aggregation and applications to gene ranking. BMC Bioinform. 16(S-1): S6 (2015) - [j47]Quan Chen, Xianghong Jasmine Zhou, Fengzhu Sun:
Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists. J. Comput. Biol. 22(2): 111-123 (2015) - 2014
- [j46]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): 343-353 (2014) - [j45]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): 685-698 (2014) - [j44]Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun, Charlotte M. Deane:
Alignment-free protein interaction network comparison. Bioinform. 30(17): 430-437 (2014) - [j43]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): 137-146 (2014) - 2013
- [j42]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): 230-237 (2013) - [j41]Jie Ren, Kai Song, Fengzhu Sun, Minghua Deng, Gesine Reinert:
Multiple alignment-free sequence comparison. Bioinform. 29(21): 2690-2698 (2013) - [j40]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): S1 (2013) - [j39]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): 64-79 (2013) - [j38]Fengzhu Sun:
Preface: Research in Computational Molecular Biology (RECOMB 2013). J. Comput. Biol. 20(10): 713 (2013) - [j37]Xuegong Zhang, Fengzhu Sun:
Meeting report on RECOMB 2013 (the 17th Annual International Conference on Research in Computational Molecular Biology). Quant. Biol. 1(2): 175-181 (2013) - [e1]Minghua Deng, Rui Jiang, Fengzhu Sun, Xuegong Zhang:
Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Proceedings. Lecture Notes in Computer Science 7821, Springer 2013, ISBN 978-3-642-37194-3 [contents] - 2012
- [j36]Ting Chen, Paul Marjoram, Fengzhu Sun, Xianghong Jasmine Zhou:
Preface: Special Issue. J. Comput. Biol. 19(6): 575-576 (2012) - [j35]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): 839-854 (2012) - [j34]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): 1281-1292 (2012) - [c11]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: 272-285 - 2011
- [j33]Qin Chang, Yihui Luan, Fengzhu Sun:
Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny. BMC Bioinform. 12: 118 (2011) - [j32]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): S11 (2011) - [j31]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: 55 (2011) - [j30]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): S15 (2011) - [j29]Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman:
Sequence Alignment as Hypothesis Testing. J. Comput. Biol. 18(5): 677-691 (2011) - [p1]Zhidong Tu, Jun Zhu, Fengzhu Sun:
Inferring Signaling and Gene Regulatory Network from Genetic and Genomic Information. Handbook of Statistical Bioinformatics 2011: 479-500 - 2010
- [j28]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): 581-592 (2010) - [j27]Lin Wan, Gesine Reinert, Fengzhu Sun, Michael S. Waterman:
Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics. J. Comput. Biol. 17(11): 1467-1490 (2010)
2000 – 2009
- 2009
- [j26]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: 277 (2009) - [j25]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): 347-370 (2009) - [j24]Gesine Reinert, David Chew, Fengzhu Sun, Michael S. Waterman:
Alignment-Free Sequence Comparison (I): Statistics and Power. J. Comput. Biol. 16(12): 1615-1634 (2009) - 2008
- [j23]Xiting Yan, Fengzhu Sun:
Testing gene set enrichment for subset of genes: Sub-GSE. BMC Bioinform. 9 (2008) - [j22]Linqi Zhou, Xiaotu Ma, Fengzhu Sun:
The effects of protein interactions, gene essentiality and regulatory regions on expression variation. BMC Syst. Biol. 2: 54 (2008) - [j21]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): 547-564 (2008) - 2007
- [j20]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): 215-221 (2007) - [j19]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) - 2006
- [j18]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): 1508-1514 (2006) - [j17]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): 2532-2538 (2006) - [j16]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): 2650-2657 (2006) - [j15]Hyunju Lee, Minghua Deng, Fengzhu Sun, Ting Chen:
An integrated approach to the prediction of domain-domain interactions. BMC Bioinform. 7: 269 (2006) - [j14]Pierre Nicolas, Fengzhu Sun, Lei M. Li:
A model-based approach to selection of tag SNPs. BMC Bioinform. 7: 303 (2006) - [j13]Rui Jiang, Hua Yang, Fengzhu Sun, Ting Chen:
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. BMC Bioinform. 7: 417 (2006) - [c10]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: 489-496 - 2005
- [j12]Kui Zhang, Fengzhu Sun, Hongyu Zhao:
HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinform. 21(1): 90-103 (2005) - [j11]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): 131-134 (2005) - 2004
- [j10]Minghua Deng, Zhidong Tu, Fengzhu Sun, Ting Chen:
Mapping gene ontology to proteins based on protein-protein interaction data. Bioinform. 20(6): 895-902 (2004) - [j9]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): 215-226 (2004) - [j8]Minghua Deng, Ting Chen, Fengzhu Sun:
An Integrated Probabilistic Model for Functional Prediction of Proteins. J. Comput. Biol. 11(2/3): 463-475 (2004) - [c9]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: 128-139 - 2003
- [j7]Yinglei Lai, Deepali Shinde, Norman Arnheim, Fengzhu Sun:
The Mutation Process of Microsatellites During the Polymerase Chain Reaction. J. Comput. Biol. 10(2): 143-155 (2003) - [j6]Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun:
Prediction of Protein Function Using Protein-Protein Interaction Data. J. Comput. Biol. 10(6): 947-960 (2003) - [c8]Minghua Deng, Fengzhu Sun, Ting Chen:
Assessment of the reliability of protein-protein interactions and protein function prediction. Pacific Symposium on Biocomputing 2003: 140-151 - [c7]Minghua Deng, Ting Chen, Fengzhu Sun:
An integrated probabilistic model for functional prediction of proteins. RECOMB 2003: 95-103 - [c6]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: 332-340 - 2002
- [c5]Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun:
Prediction of Protein Function Using Protein-Protein Interaction Data. CSB 2002: 197-206 - [c4]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: 96-112 - [c3]Minghua Deng, Shipra Mehta, Fengzhu Sun, Ting Chen:
Inferring domain-domain interactions from protein-protein interactions. RECOMB 2002: 117-126 - 2000
- [j5]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): 143-158 (2000)
1990 – 1999
- 1999
- [j4]Fengzhu Sun:
Modeling DNA Shuffling. J. Comput. Biol. 6(1): 77-90 (1999) - 1998
- [j3]David C. Torney, Fengzhu Sun, William J. Bruno:
Optimizing Nonadaptive Group Tests for Objects with Heterogeneous Priors. SIAM J. Appl. Math. 58(4): 1043-1059 (1998) - [c2]Fengzhu Sun:
Modeling DNA shuffling. RECOMB 1998: 251-257 - 1997
- [j2]Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman:
Pooling Strategies for Establishing Physical Genome Maps Using FISH. J. Comput. Biol. 4(4): 467-486 (1997) - [c1]Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman:
Pooling strategies for establishing physical genome maps using FISH. RECOMB 1997: 294-299 - 1995
- [j1]Fengzhu Sun:
The Polymerase Chain Reaction and Branching Processes. J. Comput. Biol. 2(1): 63-86 (1995)
Coauthor Index
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