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For: 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. J Theor Biol 2011;284:106-16. [PMID: 21723298 DOI: 10.1016/j.jtbi.2011.06.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 05/30/2011] [Accepted: 06/17/2011] [Indexed: 12/15/2022]
Number Cited by Other Article(s)
1
Pevzner P, Vingron M, Reidys C, Sun F, Istrail S. Michael Waterman's Contributions to Computational Biology and Bioinformatics. J Comput Biol 2022;29:601-615. [PMID: 35727100 DOI: 10.1089/cmb.2022.29066.pp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
2
Lajevardy SA, Kargari M. Developing new genetic algorithm based on integer programming for multiple sequence alignment. Soft comput 2022. [DOI: 10.1007/s00500-022-06790-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
3
Cattaneo G, Ferraro Petrillo U, Giancarlo R, Palini F, Romualdi C. The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis. Bioinformatics 2022;38:925-932. [PMID: 34718420 DOI: 10.1093/bioinformatics/btab747] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/07/2021] [Accepted: 10/26/2021] [Indexed: 02/03/2023]  Open
4
Sarkar BK, Sharma AR, Bhattacharya M, Sharma G, Lee SS, Chakraborty C. Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter. Sci Rep 2021;11:13701. [PMID: 34211040 PMCID: PMC8249421 DOI: 10.1038/s41598-021-93154-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]  Open
5
Luczak BB, James BT, Girgis HZ. A survey and evaluations of histogram-based statistics in alignment-free sequence comparison. Brief Bioinform 2020;20:1222-1237. [PMID: 29220512 PMCID: PMC6781583 DOI: 10.1093/bib/bbx161] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/13/2017] [Indexed: 11/29/2022]  Open
6
Huang GD, Liu XM, Huang TL, Xia LC. The statistical power of k-mer based aggregative statistics for alignment-free detection of horizontal gene transfer. Synth Syst Biotechnol 2019;4:150-156. [PMID: 31508512 PMCID: PMC6723412 DOI: 10.1016/j.synbio.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/14/2019] [Accepted: 08/05/2019] [Indexed: 12/21/2022]  Open
7
Lebatteux D, Remita AM, Diallo AB. Toward an Alignment-Free Method for Feature Extraction and Accurate Classification of Viral Sequences. J Comput Biol 2019;26:519-535. [PMID: 31050550 DOI: 10.1089/cmb.2018.0239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
8
Ren J, Bai X, Lu YY, Tang K, Wang Y, Reinert G, Sun F. Alignment-Free Sequence Analysis and Applications. Annu Rev Biomed Data Sci 2018;1:93-114. [PMID: 31828235 PMCID: PMC6905628 DOI: 10.1146/annurev-biodatasci-080917-013431] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
9
Zielezinski A, Vinga S, Almeida J, Karlowski WM. Alignment-free sequence comparison: benefits, applications, and tools. Genome Biol 2017;18:186. [PMID: 28974235 PMCID: PMC5627421 DOI: 10.1186/s13059-017-1319-7] [Citation(s) in RCA: 263] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
10
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 2016;32:993-1000. [PMID: 26130573 PMCID: PMC6169497 DOI: 10.1093/bioinformatics/btv395] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 03/11/2015] [Accepted: 06/25/2015] [Indexed: 11/13/2022]  Open
11
Comin M, Antonello M. On the comparison of regulatory sequences with multiple resolution Entropic Profiles. BMC Bioinformatics 2016;17:130. [PMID: 26987840 PMCID: PMC4797186 DOI: 10.1186/s12859-016-0980-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 03/06/2016] [Indexed: 11/28/2022]  Open
12
Galzitskaya OV, Lobanov MY. Phyloproteomic Analysis of 11780 Six-Residue-Long Motifs Occurrences. BIOMED RESEARCH INTERNATIONAL 2015;2015:208346. [PMID: 26114101 PMCID: PMC4465679 DOI: 10.1155/2015/208346] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 11/03/2014] [Indexed: 12/31/2022]
13
Bonham-Carter O, Steele J, Bastola D. Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. Brief Bioinform 2014;15:890-905. [PMID: 23904502 PMCID: PMC4296134 DOI: 10.1093/bib/bbt052] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 05/31/2013] [Indexed: 12/17/2022]  Open
14
Comin M, Schimd M. Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns. BMC Bioinformatics 2014;15 Suppl 9:S1. [PMID: 25252700 PMCID: PMC4168702 DOI: 10.1186/1471-2105-15-s9-s1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]  Open
15
Ali W, Rito T, Reinert G, Sun F, Deane CM. Alignment-free protein interaction network comparison. Bioinformatics 2014;30:i430-7. [PMID: 25161230 PMCID: PMC4147900 DOI: 10.1093/bioinformatics/btu447] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
16
Comin M, Verzotto D. Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014;11:628-637. [PMID: 26356333 DOI: 10.1109/tcbb.2014.2306830] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
17
Gunasinghe U, Alahakoon D, Bedingfield S. Extraction of high quality k-words for alignment-free sequence comparison. J Theor Biol 2014;358:31-51. [PMID: 24846728 DOI: 10.1016/j.jtbi.2014.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 05/04/2014] [Accepted: 05/07/2014] [Indexed: 10/25/2022]
18
Alignment free comparison: k word voting model and its applications. J Theor Biol 2013;335:276-82. [DOI: 10.1016/j.jtbi.2013.06.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 04/25/2013] [Accepted: 06/26/2013] [Indexed: 02/06/2023]
19
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. Brief Bioinform 2013;15:343-53. [PMID: 24064230 DOI: 10.1093/bib/bbt067] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
20
Ren J, Song K, Sun F, Deng M, Reinert G. Multiple alignment-free sequence comparison. Bioinformatics 2013;29:2690-8. [PMID: 23990418 DOI: 10.1093/bioinformatics/btt462] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
21
Song K, Ren J, Zhai Z, Liu X, Deng M, Sun F. Alignment-free sequence comparison based on next-generation sequencing reads. J Comput Biol 2013;20:64-79. [PMID: 23383994 DOI: 10.1089/cmb.2012.0228] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
22
Behnam E, Waterman MS, Smith AD. A geometric interpretation for local alignment-free sequence comparison. J Comput Biol 2013;20:471-85. [PMID: 23829649 PMCID: PMC3704055 DOI: 10.1089/cmb.2012.0280] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
23
Mahmud MP, Wiedenhoeft J, Schliep A. Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees. Bioinformatics 2013;28:i325-i332. [PMID: 22962448 PMCID: PMC3436807 DOI: 10.1093/bioinformatics/bts380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
24
Kelly S, Maini PK. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments. PLoS One 2013;8:e58537. [PMID: 23554899 PMCID: PMC3598851 DOI: 10.1371/journal.pone.0058537] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 02/07/2013] [Indexed: 01/03/2023]  Open
25
Warnow T. Large-Scale Multiple Sequence Alignment and Phylogeny Estimation. MODELS AND ALGORITHMS FOR GENOME EVOLUTION 2013. [DOI: 10.1007/978-1-4471-5298-9_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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