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For: Göke J, Schulz MH, Lasserre J, Vingron M. Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. ACTA ACUST UNITED AC 2012;28:656-63. [PMID: 22247280 PMCID: PMC3289921 DOI: 10.1093/bioinformatics/bts028] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
1
Oh JW, Beer MA. Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals. Nat Commun 2024;15:6464. [PMID: 39085231 PMCID: PMC11291912 DOI: 10.1038/s41467-024-50708-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 07/17/2024] [Indexed: 08/02/2024]  Open
2
Swain MT, Vickers M. Interpreting alignment-free sequence comparison: what makes a score a good score? NAR Genom Bioinform 2022;4:lqac062. [PMID: 36071721 PMCID: PMC9442500 DOI: 10.1093/nargab/lqac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/01/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022]  Open
3
Storato D, Comin M. K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:220-229. [PMID: 34606462 DOI: 10.1109/tcbb.2021.3117406] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
4
Qian Y, Zhang Y, Zhang J. Alignment-Free Sequence Comparison With Multiple k Values. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:1841-1849. [PMID: 31765317 DOI: 10.1109/tcbb.2019.2955081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
5
Zhang T, Wang R, Jiang Q, Wang Y. An Information Gain-based Method for Evaluating the Classification Power of Features Towards Identifying Enhancers. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191120141032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
6
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
7
Liu Z, Dong W, Luo W, Jiang W, Li Q, He Z. HLMethy: a machine learning-based model to identify the hidden labels of m6A candidates. PLANT MOLECULAR BIOLOGY 2019;101:575-584. [PMID: 31722090 DOI: 10.1007/s11103-019-00930-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
8
Bernard G, Chan CX, Chan YB, Chua XY, Cong Y, Hogan JM, Maetschke SR, Ragan MA. Alignment-free inference of hierarchical and reticulate phylogenomic relationships. Brief Bioinform 2019;20:426-435. [PMID: 28673025 PMCID: PMC6433738 DOI: 10.1093/bib/bbx067] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/04/2017] [Indexed: 11/22/2022]  Open
9
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]
10
Qian J, Marchiori D, Comin M. Fast and Sensitive Classification of Short Metagenomic Reads with SKraken. BIOMEDICAL ENGINEERING SYSTEMS AND TECHNOLOGIES 2018. [DOI: 10.1007/978-3-319-94806-5_12] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
11
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
12
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 2017;18:732. [PMID: 28984181 PMCID: PMC5629589 DOI: 10.1186/s12864-017-4020-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
13
Zhang M, Yang L, Ren J, Ahlgren NA, Fuhrman JA, Sun F. Prediction of virus-host infectious association by supervised learning methods. BMC Bioinformatics 2017;18:60. [PMID: 28361670 PMCID: PMC5374558 DOI: 10.1186/s12859-017-1473-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
14
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
15
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
16
Göke J, Lu X, Chan YS, Ng HH, Ly LH, Sachs F, Szczerbinska I. Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells. Cell Stem Cell 2015;16:135-41. [PMID: 25658370 DOI: 10.1016/j.stem.2015.01.005] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/20/2014] [Accepted: 01/14/2015] [Indexed: 12/11/2022]
17
Comin M, Leoni A, Schimd M. Clustering of reads with alignment-free measures and quality values. Algorithms Mol Biol 2015;10:4. [PMID: 25691913 PMCID: PMC4331138 DOI: 10.1186/s13015-014-0029-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 12/17/2014] [Indexed: 12/03/2022]  Open
18
Inferring phylogenies of evolving sequences without multiple sequence alignment. Sci Rep 2014;4:6504. [PMID: 25266120 PMCID: PMC4179140 DOI: 10.1038/srep06504] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 09/10/2014] [Indexed: 12/25/2022]  Open
19
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
20
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]
21
He B, Chen C, Teng L, Tan K. Global view of enhancer-promoter interactome in human cells. Proc Natl Acad Sci U S A 2014;111:E2191-9. [PMID: 24821768 PMCID: PMC4040567 DOI: 10.1073/pnas.1320308111] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
22
Leimeister CA, Boden M, Horwege S, Lindner S, Morgenstern B. Fast alignment-free sequence comparison using spaced-word frequencies. ACTA ACUST UNITED AC 2014;30:1991-9. [PMID: 24700317 PMCID: PMC4080745 DOI: 10.1093/bioinformatics/btu177] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
23
Schwaiger M, Schönauer A, Rendeiro AF, Pribitzer C, Schauer A, Gilles AF, Schinko JB, Renfer E, Fredman D, Technau U. Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res 2014;24:639-50. [PMID: 24642862 PMCID: PMC3975063 DOI: 10.1101/gr.162529.113] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
24
Burden CJ, Leopardi P, Forêt S. The distribution of word matches between Markovian sequences with periodic boundary conditions. J Comput Biol 2013;21:41-63. [PMID: 24160839 DOI: 10.1089/cmb.2012.0277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
25
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]
26
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
27
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
28
Ghandi M, Mohammad-Noori M, Beer MA. Robust k-mer frequency estimation using gapped k-mers. J Math Biol 2013;69:469-500. [PMID: 23861010 DOI: 10.1007/s00285-013-0705-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 06/09/2013] [Indexed: 10/26/2022]
29
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
30
Yu C, Hernandez T, Zheng H, Yau SC, Huang HH, He RL, Yang J, Yau SST. Real time classification of viruses in 12 dimensions. PLoS One 2013;8:e64328. [PMID: 23717598 PMCID: PMC3661469 DOI: 10.1371/journal.pone.0064328] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 04/12/2013] [Indexed: 11/18/2022]  Open
31
Protection against experimental melioidosis following immunization with live Burkholderia thailandensis expressing a manno-heptose capsule. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2013;20:1041-7. [PMID: 23677322 DOI: 10.1128/cvi.00113-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
32
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
33
Chan CX, Ragan MA. Next-generation phylogenomics. Biol Direct 2013;8:3. [PMID: 23339707 PMCID: PMC3564786 DOI: 10.1186/1745-6150-8-3] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/17/2013] [Indexed: 12/14/2022]  Open
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