| Year |
Citation |
Score |
| 2024 |
Hou S, Tang T, Cheng S, Liu Y, Xia T, Chen T, Fuhrman JA, Sun F. DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses. Nar Genomics and Bioinformatics. 6: lqae044. PMID 38711860 DOI: 10.1093/nargab/lqae044 |
0.699 |
|
| 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 |
0.669 |
|
| 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 |
0.672 |
|
| 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 |
0.527 |
|
| 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 |
0.382 |
|
| 2022 |
Bai X, Ren J, Sun F. MLR-OOD: a Markov chain based Likelihood Ratio method for Out-Of-Distribution detection of genomic sequences. Journal of Molecular Biology. 167586. PMID 35427634 DOI: 10.1016/j.jmb.2022.167586 |
0.308 |
|
| 2020 |
Ren J, Song K, Deng C, Ahlgren NA, Fuhrman JA, Li Y, Xie X, Poplin R, Sun F. Identifying viruses from metagenomic data using deep learning. Quantitative Biology (Beijing, China). 8: 64-77. PMID 34084563 DOI: 10.1007/s40484-019-0187-4 |
0.312 |
|
| 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 |
0.388 |
|
| 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 |
0.376 |
|
| 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 |
0.351 |
|
| 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 |
0.422 |
|
| 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 |
0.427 |
|
| 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 |
0.604 |
|
| 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 |
0.619 |
|
| 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 |
0.334 |
|
| 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 |
0.393 |
|
| 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 |
0.347 |
|
| 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 |
0.36 |
|
| 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 |
0.363 |
|
| 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 |
0.412 |
|
| 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 |
0.404 |
|
| 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 |
0.623 |
|
| 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 |
0.314 |
|
| 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 |
0.329 |
|
| 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 |
0.369 |
|
| 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 |
0.624 |
|
| 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 |
0.33 |
|
| 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 |
0.407 |
|
| 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 |
0.423 |
|
| 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 |
0.335 |
|
| 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 |
0.323 |
|
| 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 |
0.442 |
|
| 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 |
0.305 |
|
| 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 |
0.548 |
|
| 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 |
0.408 |
|
| 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 |
0.641 |
|
| 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 |
0.391 |
|
| 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 |
0.318 |
|
| 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 |
0.389 |
|
| 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 |
0.4 |
|
| 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 |
0.435 |
|
| 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 |
0.64 |
|
| 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 |
0.425 |
|
| 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 |
0.313 |
|
| 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 |
0.386 |
|
| 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 |
0.609 |
|
| 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 |
0.592 |
|
| 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 |
0.384 |
|
| 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 |
0.44 |
|
| 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 |
0.593 |
|
| 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 |
0.594 |
|
| 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 |
0.601 |
|
| 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 |
0.318 |
|
| 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 |
0.31 |
|
| 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 |
0.379 |
|
| 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 |
0.443 |
|
| 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 |
0.314 |
|
| 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 |
0.435 |
|
| 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 |
0.305 |
|
| 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 |
0.329 |
|
| 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 |
0.388 |
|
| 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 |
0.33 |
|
| 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 |
0.308 |
|
| 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 |
0.555 |
|
| 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 |
0.318 |
|
| 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 |
0.569 |
|
| 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 |
0.324 |
|
| 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 |
0.335 |
|
| 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 |
0.575 |
|
| 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 |
0.307 |
|
| 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 |
0.541 |
|
| 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 |
0.323 |
|
| 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 |
0.608 |
|
| 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 |
0.531 |
|
| 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 |
0.591 |
|
| 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 |
0.576 |
|
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