Fengzhu Sun - Publications

University of Southern California, Los Angeles, CA, United States 

76 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Ai D, Chen L, Xie J, Cheng L, Zhang F, Luan Y, Li Y, Hou S, Sun F, Xia LC. Identifying local associations in biological time series: algorithms, statistical significance, and applications. Briefings in Bioinformatics. 24. PMID 37930023 DOI: 10.1093/bib/bbad390  0.684
2022 Tang T, Hou S, Fuhrman JA, Sun F. Phage-bacterial contig association prediction with a convolutional neural network. Bioinformatics (Oxford, England). 38: i45-i52. PMID 35758806 DOI: 10.1093/bioinformatics/btac239  0.683
2022 Pevzner P, Vingron M, Reidys C, Sun F, Istrail S. Michael Waterman's Contributions to Computational Biology and Bioinformatics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 35727100 DOI: 10.1089/cmb.2022.29066.pp  0.524
2022 Istrail S, Pevzner P, Sun F, Vingron M. Special Issue: Professor Michael Waterman's 80th Birthday, Part 1. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 35704861 DOI: 10.1089/cmb.2022.29065.si  0.384
2020 Wang Y, Chen Q, Deng C, Zheng Y, Sun F. KmerGO: A Tool to Identify Group-Specific Sequences With -mers. Frontiers in Microbiology. 11: 2067. PMID 32983048 DOI: 10.3389/Fmicb.2020.02067  0.381
2020 Lu YY, Bai J, Wang Y, Wang Y, Sun F. CRAFT: Compact genome Representation towards large-scale Alignment-Free daTabase. Bioinformatics (Oxford, England). PMID 32766810 DOI: 10.1093/Bioinformatics/Btaa699  0.369
2020 Wang Z, Wang Y, Fuhrman JA, Sun F, Zhu S. Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Briefings in Bioinformatics. PMID 32379299 DOI: 10.1093/Bib/Bbaa085  0.343
2019 Song K, Ren J, Sun F. Reads Binning Improves Alignment-Free Metagenome Comparison. Frontiers in Genetics. 10: 1156. PMID 31824565 DOI: 10.3389/Fgene.2019.01156  0.414
2019 Tang K, Ren J, Sun F. Afann: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression. Genome Biology. 20: 266. PMID 31801606 DOI: 10.1186/S13059-019-1872-3  0.419
2019 Zielezinski A, Girgis HZ, Bernard G, Leimeister CA, Tang K, Dencker T, Lau AK, Röhling S, Choi JJ, Waterman MS, Comin M, Kim SH, Vinga S, Almeida JS, Chan CX, ... ... Sun F, et al. Benchmarking of alignment-free sequence comparison methods. Genome Biology. 20: 144. PMID 31345254 DOI: 10.1186/S13059-019-1755-7  0.598
2019 You R, Yao S, Xiong Y, Huang X, Sun F, Mamitsuka H, Zhu S. NetGO: improving large-scale protein function prediction with massive network information. Nucleic Acids Research. PMID 31106361 DOI: 10.1093/Nar/Gkz388  0.313
2019 Chen S, Chen Y, Sun F, Waterman MS, Zhang X. A new statistic for efficient detection of repetitive sequences. Bioinformatics (Oxford, England). PMID 30993316 DOI: 10.1093/Bioinformatics/Btz262  0.613
2019 Wang Z, Wang Z, Lu YY, Sun F, Zhu S. SolidBin: Improving Metagenome Binning with Semi-supervised Normalized Cut. Bioinformatics (Oxford, England). PMID 30977806 DOI: 10.1093/Bioinformatics/Btz253  0.329
2019 Wang Z, Wang Y, Fuhrman JA, Sun F, Zhu S. Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Briefings in Bioinformatics. PMID 30860572 DOI: 10.1093/Bib/Bbz025  0.386
2019 Zhang F, Sun F, Luan Y. Statistical significance approximation for local similarity analysis of dependent time series data. Bmc Bioinformatics. 20: 53. PMID 30691412 DOI: 10.1186/S12859-019-2595-X  0.302
2018 Ren J, Bai X, Lu YY, Tang K, Wang Y, Reinert G, Sun F. Alignment-Free Sequence Analysis and Applications. Annual Review of Biomedical Data Science. 1: 93-114. PMID 31828235 DOI: 10.1146/annurev-biodatasci-080917-013431  0.338
2018 Tang K, Ren J, Cronn R, Erickson DL, Milligan BG, Parker-Forney M, Spouge JL, Sun F. Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA. Bmc Genomics. 19: 896. PMID 30526482 DOI: 10.1186/S12864-018-5253-1  0.356
2018 Li H, Sun F. Comparative studies of alignment, alignment-free and SVM based approaches for predicting the hosts of viruses based on viral sequences. Scientific Reports. 8: 10032. PMID 29968780 DOI: 10.1038/S41598-018-28308-X  0.354
2018 Wang Y, Fu L, Ren J, Yu Z, Chen T, Sun F. Identifying Sequences for Microbial Communities Using Long -mer Sequence Signatures. Frontiers in Microbiology. 9: 872. PMID 29774017 DOI: 10.3389/Fmicb.2018.00872  0.404
2018 Tang K, Lu YY, Sun F. Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer. Frontiers in Microbiology. 9: 711. PMID 29713314 DOI: 10.3389/Fmicb.2018.00711  0.398
2017 Bai X, Tang K, Ren J, Waterman M, Sun F. Optimal choice of word length when comparing two Markov sequences using a χ (2)-statistic. Bmc Genomics. 18: 732. PMID 28984181 DOI: 10.1186/S12864-017-4020-Z  0.616
2017 Lu YY, Lv J, Fuhrman JA, Sun F. Towards enhanced and interpretable clustering/classification in integrative genomics. Nucleic Acids Research. PMID 28977511 DOI: 10.1093/Nar/Gkx767  0.312
2017 Wang Y, Wang K, Lu YY, Sun F. Improving contig binning of metagenomic data using [Formula: see text] oligonucleotide frequency dissimilarity. Bmc Bioinformatics. 18: 425. PMID 28931373 DOI: 10.1186/S12859-017-1835-1  0.322
2017 Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome. 5: 69. PMID 28683828 DOI: 10.1186/S40168-017-0283-5  0.36
2017 Lu YY, Tang K, Ren J, Fuhrman JA, Waterman MS, Sun F. CAFE: aCcelerated Alignment-FrEe sequence analysis. Nucleic Acids Research. PMID 28472388 DOI: 10.1093/Nar/Gkx351  0.62
2016 Ahlgren NA, Ren J, Lu YY, Fuhrman JA, Sun F. Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences. Nucleic Acids Research. PMID 27899557 DOI: 10.1093/Nar/Gkw1002  0.324
2016 Liao W, Ren J, Wang K, Wang S, Zeng F, Wang Y, Sun F. Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains. Scientific Reports. 6: 37243. PMID 27876823 DOI: 10.1038/Srep37243  0.397
2016 Lu YY, Chen T, Fuhrman JA, Sun F. COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge. Bioinformatics (Oxford, England). PMID 27256312 DOI: 10.1093/Bioinformatics/Btw290  0.411
2016 Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. The Isme Journal. PMID 26905627 DOI: 10.1038/Ismej.2015.235  0.334
2015 Xia LC, Ai D, Cram JA, Liang X, Fuhrman JA, Sun F. Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains. Bmc Bioinformatics. 16: 301. PMID 26390921 DOI: 10.1186/S12859-015-0732-8  0.321
2015 Ren J, Song K, Deng M, Reinert G, Cannon CH, Sun F. Inference of Markovian Properties of Molecular Sequences from NGS Data and Applications to Comparative Genomics. Bioinformatics (Oxford, England). PMID 26130573 DOI: 10.1093/Bioinformatics/Btv395  0.432
2015 Wang W, Zhou X, Liu Z, Sun F. Network tuned multiple rank aggregation and applications to gene ranking. Bmc Bioinformatics. 16: S6. PMID 25708095 DOI: 10.1186/1471-2105-16-S1-S6  0.309
2014 Liu CC, Tseng YT, Li W, Wu CY, Mayzus I, Rzhetsky A, Sun F, Waterman M, Chen JJ, Chaudhary PM, Loscalzo J, Crandall E, Zhou XJ. DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. Nucleic Acids Research. 42: W137-46. PMID 24895436 DOI: 10.1093/Nar/Gku412  0.549
2014 Wang Y, Liu L, Chen L, Chen T, Sun F. Comparison of metatranscriptomic samples based on k-tuple frequencies. Plos One. 9: e84348. PMID 24392128 DOI: 10.1371/Journal.Pone.0084348  0.401
2014 Song K, Ren J, Reinert G, Deng M, Waterman MS, Sun F. New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. Briefings in Bioinformatics. 15: 343-53. PMID 24064230 DOI: 10.1093/Bib/Bbt067  0.635
2013 Ren J, Song K, Sun F, Deng M, Reinert G. Multiple alignment-free sequence comparison. Bioinformatics (Oxford, England). 29: 2690-8. PMID 23990418 DOI: 10.1093/Bioinformatics/Btt462  0.381
2013 Ma X, Chen T, Sun F. Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. Briefings in Bioinformatics. 15: 685-98. PMID 23788799 DOI: 10.1093/Bib/Bbt041  0.32
2013 Song K, Ren J, Zhai Z, Liu X, Deng M, Sun F. Alignment-free sequence comparison based on next-generation sequencing reads. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 64-79. PMID 23383994 DOI: 10.1089/Cmb.2012.0228  0.383
2013 Chen Q, Sun F. A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms. Bmc Genomics. 14: S1. PMID 23369070 DOI: 10.1186/1471-2164-14-S1-S1  0.397
2012 Jiang B, Song K, Ren J, Deng M, Sun F, Zhang X. Comparison of metagenomic samples using sequence signatures. Bmc Genomics. 13: 730. PMID 23268604 DOI: 10.1186/1471-2164-13-730  0.426
2012 Zhai Z, Reinert G, Song K, Waterman MS, Luan Y, Sun F. Normal and compound poisson approximations for pattern occurrences in NGS reads. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 839-54. PMID 22697250 DOI: 10.1089/Cmb.2012.0029  0.635
2012 Chang Q, Luan Y, Chen T, Fuhrman JA, Sun F. Computational methods for the analysis of tag sequences in metagenomics studies. Frontiers in Bioscience (Scholar Edition). 4: 1333-43. PMID 22652875 DOI: 10.2741/S335  0.415
2011 Xia LC, Steele JA, Cram JA, Cardon ZG, Simmons SL, Vallino JJ, Fuhrman JA, Sun F. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. Bmc Systems Biology. 5: S15. PMID 22784572 DOI: 10.1186/1752-0509-5-S2-S15  0.314
2011 Xia LC, Cram JA, Chen T, Fuhrman JA, Sun F. Accurate genome relative abundance estimation based on shotgun metagenomic reads. Plos One. 6: e27992. PMID 22162995 DOI: 10.1371/Journal.Pone.0027992  0.382
2011 Liu X, Wan L, Li J, Reinert G, Waterman MS, Sun F. New powerful statistics for alignment-free sequence comparison under a pattern transfer model. Journal of Theoretical Biology. 284: 106-16. PMID 21723298 DOI: 10.1016/J.Jtbi.2011.06.020  0.605
2011 Meng L, Sun F, Zhang X, Waterman MS. Sequence alignment as hypothesis testing. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 677-91. PMID 21554016 DOI: 10.1089/Cmb.2010.0328  0.588
2011 Zhang W, Chen Y, Sun F, Jiang R. DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. Bmc Systems Biology. 5: 55. PMID 21504591 DOI: 10.1186/1752-0509-5-55  0.392
2011 Zhang W, Sun F, Jiang R. Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. Bmc Bioinformatics. 12: S11. PMID 21342540 DOI: 10.1186/1471-2105-12-S1-S11  0.448
2010 Wan L, Reinert G, Sun F, Waterman MS. Alignment-free sequence comparison (II): theoretical power of comparison statistics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 1467-90. PMID 20973742 DOI: 10.1089/Cmb.2010.0056  0.59
2010 Zhai Z, Ku SY, Luan Y, Reinert G, Waterman MS, Sun F. The power of detecting enriched patterns: an HMM approach. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 581-92. PMID 20426691 DOI: 10.1089/Cmb.2009.0218  0.591
2009 Reinert G, Chew D, Sun F, Waterman MS. Alignment-free sequence comparison (I): statistics and power. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1615-34. PMID 20001252 DOI: 10.1089/Cmb.2009.0198  0.597
2009 Wang L, Tu Z, Sun F. A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila. Bmc Genomics. 10: 220. PMID 19435510 DOI: 10.1186/1471-2164-10-220  0.319
2009 Chen T, Jiang R, Sun F. Bayesian Models and Gibbs Sampling Strategies for Local Graph Alignment and Motif Identification in Stochastic Biological Networks Communications in Information and Systems. 9: 347-370. DOI: 10.4310/Cis.2009.V9.N4.A3  0.311
2008 Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, ... ... Sun F, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology. 9: S2. PMID 18613946 DOI: 10.1186/Gb-2008-9-S1-S2  0.377
2007 Jiang R, Yang H, Zhou L, Kuo CC, Sun F, Chen T. Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations. American Journal of Human Genetics. 81: 346-60. PMID 17668383 DOI: 10.1086/519747  0.448
2007 Ma X, Lee H, Wang L, Sun F. CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data. Bioinformatics (Oxford, England). 23: 215-21. PMID 17098772 DOI: 10.1093/Bioinformatics/Btl569  0.318
2006 Jiang R, Yang H, Sun F, Chen T. Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. Bmc Bioinformatics. 7: 417. PMID 16984653 DOI: 10.1186/1471-2105-7-417  0.44
2006 Ruan Q, Dutta D, Schwalbach MS, Steele JA, Fuhrman JA, Sun F. Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics (Oxford, England). 22: 2532-8. PMID 16882654 DOI: 10.1093/Bioinformatics/Btl417  0.304
2006 Tu Z, Wang L, Arbeitman MN, Chen T, Sun F. An integrative approach for causal gene identification and gene regulatory pathway inference. Bioinformatics (Oxford, England). 22: e489-96. PMID 16873511 DOI: 10.1093/Bioinformatics/Btl234  0.332
2006 Jiang R, Tu Z, Chen T, Sun F. Network motif identification in stochastic networks. Proceedings of the National Academy of Sciences of the United States of America. 103: 9404-9. PMID 16769903 DOI: 10.1073/Pnas.0507841103  0.396
2006 Ruan Q, Steele JA, Schwalbach MS, Fuhrman JA, Sun F. A dynamic programming algorithm for binning microbial community profiles. Bioinformatics (Oxford, England). 22: 1508-14. PMID 16567364 DOI: 10.1093/Bioinformatics/Btl114  0.328
2005 Zhang K, Sun F. Assessing the power of tag SNPs in the mapping of quantitative trait loci (QTL) with extremal and random samples. Bmc Genetics. 6: 51. PMID 16236175 DOI: 10.1186/1471-2156-6-51  0.311
2005 Zhang K, Qin Z, Chen T, Liu JS, Waterman MS, Sun F. HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics (Oxford, England). 21: 131-4. PMID 15333454 DOI: 10.1093/Bioinformatics/Bth482  0.557
2004 Schwartz F, Duka A, Sun F, Cui J, Manolis A, Gavras H. Mitochondrial genome mutations in hypertensive individuals. American Journal of Hypertension. 17: 629-35. PMID 15233983 DOI: 10.1016/J.Amjhyper.2004.02.020  0.317
2004 Zhang K, Qin ZS, Liu JS, Chen T, Waterman MS, Sun F. Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Research. 14: 908-16. PMID 15078859 DOI: 10.1101/Gr.1837404  0.571
2003 Kim S, Zhang K, Sun F. Detecting susceptibility genes in case-control studies using set association. Bmc Genetics. S9. PMID 14975077 DOI: 10.1186/1471-2156-4-S1-S9  0.329
2003 Schulze TG, Zhang K, Chen YS, Akula N, Sun F, McMahon FJ. Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome. Human Molecular Genetics. 13: 335-42. PMID 14681300 DOI: 10.1093/Hmg/Ddh035  0.338
2003 Zhang K, Sun F, Waterman MS, Chen T. Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. American Journal of Human Genetics. 73: 63-73. PMID 12802783 DOI: 10.1086/376437  0.577
2002 Zhang K, Calabrese P, Nordborg M, Sun F. Haplotype block structure and its applications to association studies: power and study designs. American Journal of Human Genetics. 71: 1386-94. PMID 12439824 DOI: 10.1086/344780  0.311
2002 Zhang K, Deng M, Chen T, Waterman MS, Sun F. A dynamic programming algorithm for haplotype block partitioning. Proceedings of the National Academy of Sciences of the United States of America. 99: 7335-9. PMID 12032283 DOI: 10.1073/Pnas.102186799  0.543
2000 Zhao H, Zhang S, Merikangas KR, Trixler M, Wildenauer DB, Sun F, Kidd KK. Transmission/disequilibrium tests using multiple tightly linked markers. American Journal of Human Genetics. 67: 936-46. PMID 10968775 DOI: 10.1086/303073  0.326
1997 Sun F, Benson G, Arnheim N, Waterman M. Pooling strategies for establishing physical genome maps using FISH Journal of Computational Biology. 4: 467-486. PMID 9385540 DOI: 10.1089/Cmb.1997.4.467  0.472
1997 Sun F, Waterman MS. Whole Genome Amplification And Branching Processes Advances in Applied Probability. 29: 629-668. DOI: 10.2307/1428080  0.603
1996 Sun F, Galas D, Waterman MS. A Mathematical Analysis ofin VitroMolecular Selection – Amplification Journal of Molecular Biology. 258: 650-660. PMID 8636999 DOI: 10.1006/Jmbi.1996.0276  0.53
1995 Port E, Sun F, Martin D, Waterman MS. Genomic mapping by end-characterized random clones: a mathematical analysis. Genomics. 26: 84-100. PMID 7782090 DOI: 10.1016/0888-7543(95)80086-2  0.587
1995 Sun F, Arnheim N, Waterman MS. Whole genome amplification of single cells: Mathematical analysis of PEP and tagged PCR Nucleic Acids Research. 23: 3034-3040. PMID 7659528 DOI: 10.1093/Nar/23.15.3034  0.574
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