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For: Kolekar P, Kale M, Kulkarni-Kale U. Alignment-free distance measure based on return time distribution for sequence analysis: applications to clustering, molecular phylogeny and subtyping. Mol Phylogenet Evol 2012;65:510-22. [PMID: 22820020 DOI: 10.1016/j.ympev.2012.07.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 07/08/2012] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
van Zyl DJ, Dunaiski M, Tegally H, Baxter C, de Oliveira T, Xavier JS. Alignment-Free Viral Sequence Classification at Scale. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.10.627186. [PMID: 39713356 PMCID: PMC11661207 DOI: 10.1101/2024.12.10.627186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
2
Wang T, Yu ZG, Li J. CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model. Front Microbiol 2024;15:1339156. [PMID: 38572227 PMCID: PMC10987876 DOI: 10.3389/fmicb.2024.1339156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/23/2024] [Indexed: 04/05/2024]  Open
3
Limaye S, Shelke A, Kale MM, Kulkarni-Kale U, Kuchipudi SV. IDV Typer: An Automated Tool for Lineage Typing of Influenza D Viruses Based on Return Time Distribution. Viruses 2024;16:373. [PMID: 38543738 PMCID: PMC10976072 DOI: 10.3390/v16030373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/24/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024]  Open
4
Dey S, Ghosh P, Das S. Positional difference and Frequency (PdF) based alignment-free technique for genome sequence comparison. J Biomol Struct Dyn 2023;42:12660-12688. [PMID: 37885236 DOI: 10.1080/07391102.2023.2272748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023]
5
Andino R, Kirkegaard K, Macadam A, Racaniello VR, Rosenfeld AB. The Picornaviridae Family: Knowledge Gaps, Animal Models, Countermeasures, and Prototype Pathogens. J Infect Dis 2023;228:S427-S445. [PMID: 37849401 DOI: 10.1093/infdis/jiac426] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]  Open
6
Tang R, Yu Z, Li J. KINN: An alignment-free accurate phylogeny reconstruction method based on inner distance distributions of k-mer pairs in biological sequences. Mol Phylogenet Evol 2023;179:107662. [PMID: 36375789 DOI: 10.1016/j.ympev.2022.107662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/10/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
7
Bohnsack KS, Kaden M, Abel J, Villmann T. Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:119-135. [PMID: 34990369 DOI: 10.1109/tcbb.2022.3140873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
8
Gwak HJ, Rho M. ViBE: a hierarchical BERT model to identify eukaryotic viruses using metagenome sequencing data. Brief Bioinform 2022;23:6603436. [PMID: 35667011 DOI: 10.1093/bib/bbac204] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022]  Open
9
Hufsky F, Abecasis A, Agudelo-Romero P, Bletsa M, Brown K, Claus C, Deinhardt-Emmer S, Deng L, Friedel CC, Gismondi MI, Kostaki EG, Kühnert D, Kulkarni-Kale U, Metzner KJ, Meyer IM, Miozzi L, Nishimura L, Paraskevopoulou S, Pérez-Cataluña A, Rahlff J, Thomson E, Tumescheit C, van der Hoek L, Van Espen L, Vandamme AM, Zaheri M, Zuckerman N, Marz M. Women in the European Virus Bioinformatics Center. Viruses 2022;14:1522. [PMID: 35891501 PMCID: PMC9319252 DOI: 10.3390/v14071522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023]  Open
10
Mane A, Limaye S, Patil L, Kulkarni-Kale U. Genetic variability in minor capsid protein (L2 gene) of human papillomavirus type 16 among Indian women. Med Microbiol Immunol 2022;211:153-160. [PMID: 35552511 PMCID: PMC9101989 DOI: 10.1007/s00430-022-00739-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/21/2022] [Indexed: 11/17/2022]
11
Mane A, Limaye S, Patil L, Kulkarni-Kale U. Genetic variations in the long control region of human papillomavirus type 16 isolates from India: implications for cervical carcinogenesis. J Med Microbiol 2022;71. [PMID: 35040427 DOI: 10.1099/jmm.0.001475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
12
Bohnsack KS, Kaden M, Abel J, Saralajew S, Villmann T. The Resolved Mutual Information Function as a Structural Fingerprint of Biomolecular Sequences for Interpretable Machine Learning Classifiers. ENTROPY (BASEL, SWITZERLAND) 2021;23:1357. [PMID: 34682081 PMCID: PMC8534762 DOI: 10.3390/e23101357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022]
13
Qi Z, Wen X. Novel Protein Sequence Comparison Method Based on Transition Probability Graph and Information Entropy. Comb Chem High Throughput Screen 2020;25:392-400. [PMID: 32875978 DOI: 10.2174/1386207323666200901103001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 11/22/2022]
14
ProtPCV: A Fixed Dimensional Numerical Representation of Protein Sequence to Significantly Reduce Sequence Search Time. Interdiscip Sci 2020;12:276-287. [PMID: 32524529 DOI: 10.1007/s12539-020-00380-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 05/19/2020] [Accepted: 06/02/2020] [Indexed: 10/24/2022]
15
Mitra U, Bhattacharyya B, Mukhopadhyay T. PEER: A direct method for biosequence pattern mining through waits of optimal k-mers. Inf Sci (N Y) 2020. [DOI: 10.1016/j.ins.2019.12.072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
16
Mane A, Patil L, Limaye S, Nirmalkar A, Kulkarni‐Kale U. Characterization of major capsid protein (L1) variants of Human papillomavirus type 16 by cervical neoplastic status in Indian women: Phylogenetic and functional analysis. J Med Virol 2020;92:1303-1308. [DOI: 10.1002/jmv.25675] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/10/2020] [Indexed: 11/10/2022]
17
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, James BT, Sun F, Morgenstern B, Karlowski WM. Benchmarking of alignment-free sequence comparison methods. Genome Biol 2019;20:144. [PMID: 31345254 PMCID: PMC6659240 DOI: 10.1186/s13059-019-1755-7] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/03/2019] [Indexed: 11/22/2022]  Open
18
Genetic diversity and evolutionary dynamics of dengue isolates from India. Virusdisease 2019;30:354-359. [PMID: 31803801 DOI: 10.1007/s13337-019-00538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022]  Open
19
Criscuolo A. A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies. RESEARCH IDEAS AND OUTCOMES 2019. [DOI: 10.3897/rio.5.e36178] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
20
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
21
Saw AK, Raj G, Das M, Talukdar NC, Tripathy BC, Nandi S. Alignment-free method for DNA sequence clustering using Fuzzy integral similarity. Sci Rep 2019;9:3753. [PMID: 30842590 PMCID: PMC6403383 DOI: 10.1038/s41598-019-40452-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/28/2019] [Indexed: 12/28/2022]  Open
22
An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes. PLoS One 2018;13:e0206409. [PMID: 30427878 PMCID: PMC6235296 DOI: 10.1371/journal.pone.0206409] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/14/2018] [Indexed: 01/11/2023]  Open
23
Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes. Biosystems 2018;167:33-46. [DOI: 10.1016/j.biosystems.2018.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/18/2018] [Accepted: 03/19/2018] [Indexed: 12/11/2022]
24
A novel fast vector method for genetic sequence comparison. Sci Rep 2017;7:12226. [PMID: 28939913 PMCID: PMC5610321 DOI: 10.1038/s41598-017-12493-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/07/2017] [Indexed: 11/08/2022]  Open
25
Waman VP, Kale MM, Kulkarni-Kale U. Genetic diversity and evolution of dengue virus serotype 3: A comparative genomics study. INFECTION GENETICS AND EVOLUTION 2017;49:234-240. [PMID: 28126562 DOI: 10.1016/j.meegid.2017.01.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/14/2017] [Accepted: 01/21/2017] [Indexed: 11/29/2022]
26
Waman VP, Kolekar P, Ramtirthkar MR, Kale MM, Kulkarni-Kale U. Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes. PeerJ 2016;4:e2326. [PMID: 27635316 PMCID: PMC5012332 DOI: 10.7717/peerj.2326] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/14/2016] [Indexed: 01/09/2023]  Open
27
Waman VP, Kasibhatla SM, Kale MM, Kulkarni-Kale U. Population genomics of dengue virus serotype 4: insights into genetic structure and evolution. Arch Virol 2016;161:2133-48. [DOI: 10.1007/s00705-016-2886-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 05/02/2016] [Indexed: 12/30/2022]
28
Kolekar PS, Waman VP, Kale MM, Kulkarni-Kale U. RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach. PLoS One 2016;11:e0149350. [PMID: 26870949 PMCID: PMC4752186 DOI: 10.1371/journal.pone.0149350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/29/2016] [Indexed: 11/24/2022]  Open
29
PCV: An Alignment Free Method for Finding Homologous Nucleotide Sequences and its Application in Phylogenetic Study. Interdiscip Sci 2016;9:173-183. [PMID: 26825665 DOI: 10.1007/s12539-015-0136-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 11/03/2015] [Accepted: 12/15/2015] [Indexed: 10/22/2022]
30
Progressive alignment of genomic signals by multiple dynamic time warping. J Theor Biol 2015;385:20-30. [PMID: 26300069 DOI: 10.1016/j.jtbi.2015.08.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 07/21/2015] [Accepted: 08/03/2015] [Indexed: 11/22/2022]
31
Sedlar K, Skutkova H, Vitek M, Provaznik I. Set of rules for genomic signal downsampling. Comput Biol Med 2015;69:308-14. [PMID: 26078051 DOI: 10.1016/j.compbiomed.2015.05.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 05/25/2015] [Accepted: 05/26/2015] [Indexed: 12/14/2022]
32
Kubicova V, Provaznik I. Use of whole genome DNA spectrograms in bacterial classification. Comput Biol Med 2015;69:298-307. [PMID: 26004007 DOI: 10.1016/j.compbiomed.2015.04.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 04/03/2015] [Accepted: 04/29/2015] [Indexed: 12/16/2022]
33
Xie XH, Yu ZG, Han GS, Yang WF, Anh V. Whole-proteome based phylogenetic tree construction with inter-amino-acid distances and the conditional geometric distribution profiles. Mol Phylogenet Evol 2015;89:37-45. [PMID: 25882834 DOI: 10.1016/j.ympev.2015.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 03/29/2015] [Accepted: 04/06/2015] [Indexed: 11/18/2022]
34
A novel k-word relative measure for sequence comparison. Comput Biol Chem 2014;53PB:331-338. [PMID: 25462340 DOI: 10.1016/j.compbiolchem.2014.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 08/10/2014] [Accepted: 10/25/2014] [Indexed: 12/28/2022]
35
Gupta S, Chavan S, Deobagkar DN, Deobagkar DD. Bio/chemoinformatics in India: an outlook. Brief Bioinform 2014;16:710-31. [PMID: 25159593 DOI: 10.1093/bib/bbu028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/28/2014] [Indexed: 12/25/2022]  Open
36
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]
37
Kolekar P, Hake N, Kale M, Kulkarni-Kale U. WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution. J Virol Methods 2014;198:41-55. [PMID: 24388930 DOI: 10.1016/j.jviromet.2013.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 11/27/2013] [Accepted: 12/17/2013] [Indexed: 01/20/2023]
38
Cheng J, Cao F, Liu Z. AGP: a multimethods web server for alignment-free genome phylogeny. Mol Biol Evol 2013;30:1032-7. [PMID: 23389766 PMCID: PMC7574599 DOI: 10.1093/molbev/mst021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
39
Tretyakov K, Goldberg T, Jin VX, Horton P. Summary of talks and papers at ISCB-Asia/SCCG 2012. BMC Genomics 2013. [PMCID: PMC3639071 DOI: 10.1186/1471-2164-14-s2-i1] [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] [Indexed: 11/10/2022]  Open
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