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For: Shrivastava S, Reddy CVSK, Mande SS. INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms. J Biosci 2011;35:351-64. [PMID: 20826944 DOI: 10.1007/s12038-010-0040-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Number Cited by Other Article(s)
1
Wijaya AJ, Anžel A, Richard H, Hattab G. Current state and future prospects of Horizontal Gene Transfer detection. NAR Genom Bioinform 2025;7:lqaf005. [PMID: 39935761 PMCID: PMC11811736 DOI: 10.1093/nargab/lqaf005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 12/26/2024] [Accepted: 02/04/2025] [Indexed: 02/13/2025]  Open
2
Chakraborty J, Roy RP, Chatterjee R, Chaudhuri P. Performance assessment of genomic island prediction tools with an improved version of Design-Island. Comput Biol Chem 2022;98:107698. [PMID: 35597186 DOI: 10.1016/j.compbiolchem.2022.107698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 04/01/2022] [Accepted: 05/11/2022] [Indexed: 11/03/2022]
3
Genomic Island Prediction via Chi-Square Test and Random Forest Algorithm. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021;2021:9969751. [PMID: 34122622 PMCID: PMC8169257 DOI: 10.1155/2021/9969751] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/14/2021] [Indexed: 12/02/2022]
4
Genomic islands and the evolution of livestock-associated Staphylococcus aureus genomes. Biosci Rep 2021;40:226941. [PMID: 33185245 PMCID: PMC7689654 DOI: 10.1042/bsr20202287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/23/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022]  Open
5
Bertelli C, Tilley KE, Brinkman FSL. Microbial genomic island discovery, visualization and analysis. Brief Bioinform 2020;20:1685-1698. [PMID: 29868902 PMCID: PMC6917214 DOI: 10.1093/bib/bby042] [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: 02/23/2018] [Revised: 04/30/2018] [Indexed: 12/27/2022]  Open
6
Mageeney CM, Lau BY, Wagner JM, Hudson CM, Schoeniger JS, Krishnakumar R, Williams KP. New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements. Nucleic Acids Res 2020;48:4052-4065. [PMID: 32182341 PMCID: PMC7192596 DOI: 10.1093/nar/gkaa156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/12/2022]  Open
7
2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome. BMC Bioinformatics 2020;21:159. [PMID: 32349677 PMCID: PMC7191778 DOI: 10.1186/s12859-020-3501-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/16/2020] [Indexed: 11/10/2022]  Open
8
Dai Q, Bao C, Hai Y, Ma S, Zhou T, Wang C, Wang Y, Huo W, Liu X, Yao Y, Xuan Z, Chen M, Zhang MQ. MTGIpick allows robust identification of genomic islands from a single genome. Brief Bioinform 2019;19:361-373. [PMID: 28025178 DOI: 10.1093/bib/bbw118] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
9
Tao J, Liu X, Yang S, Bao C, He P, Dai Q. An efficient genomic signature ranking method for genomic island prediction from a single genome. J Theor Biol 2019;467:142-149. [PMID: 30768974 DOI: 10.1016/j.jtbi.2019.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 01/13/2023]
10
da Silva Filho AC, Raittz RT, Guizelini D, De Pierri CR, Augusto DW, Dos Santos-Weiss ICR, Marchaukoski JN. Comparative Analysis of Genomic Island Prediction Tools. Front Genet 2018;9:619. [PMID: 30631340 PMCID: PMC6315130 DOI: 10.3389/fgene.2018.00619] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022]  Open
11
Bush EC, Clark AE, DeRanek CA, Eng A, Forman J, Heath K, Lee AB, Stoebel DM, Wang Z, Wilber M, Wu H. xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria. BMC Bioinformatics 2018;19:32. [PMID: 29402213 PMCID: PMC5799925 DOI: 10.1186/s12859-018-2038-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022]  Open
12
Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F. Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC Genomics 2018;19:54. [PMID: 29338683 PMCID: PMC5771137 DOI: 10.1186/s12864-017-4429-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/29/2017] [Indexed: 12/15/2022]  Open
13
Insights into horizontal acquisition patterns of dormancy and reactivation regulon genes in mycobacterial species using a partitioning-based framework. J Biosci 2016;41:475-85. [DOI: 10.1007/s12038-016-9622-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
14
Lu B, Leong HW. Computational methods for predicting genomic islands in microbial genomes. Comput Struct Biotechnol J 2016;14:200-6. [PMID: 27293536 PMCID: PMC4887561 DOI: 10.1016/j.csbj.2016.05.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 05/01/2016] [Accepted: 05/03/2016] [Indexed: 11/02/2022]  Open
15
Zhu Q, Kosoy M, Dittmar K. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. BMC Genomics 2014;15:717. [PMID: 25159222 PMCID: PMC4155097 DOI: 10.1186/1471-2164-15-717] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 08/20/2014] [Indexed: 11/23/2022]  Open
16
Identifying pathogenicity islands in bacterial pathogenomics using computational approaches. Pathogens 2014;3:36-56. [PMID: 25437607 PMCID: PMC4235732 DOI: 10.3390/pathogens3010036] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 12/30/2013] [Accepted: 01/07/2014] [Indexed: 12/22/2022]  Open
17
Jaron KS, Moravec JC, Martínková N. SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes. Bioinformatics 2013;30:1081-1086. [PMID: 24371153 DOI: 10.1093/bioinformatics/btt727] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/09/2013] [Indexed: 12/15/2022]  Open
18
Hasan MS, Liu Q, Wang H, Fazekas J, Chen B, Che D. GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences. Bioinformation 2012;8:203-5. [PMID: 22419842 PMCID: PMC3302003 DOI: 10.6026/97320630008203] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 11/24/2022]  Open
19
Das C, Ghosh TS, Mande SS. Computational analysis of the ESX-1 region of Mycobacterium tuberculosis: insights into the mechanism of type VII secretion system. PLoS One 2011;6:e27980. [PMID: 22140496 PMCID: PMC3227618 DOI: 10.1371/journal.pone.0027980] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 10/28/2011] [Indexed: 01/17/2023]  Open
20
Che D, Hasan MS, Wang H, Fazekas J, Huang J, Liu Q. EGID: an ensemble algorithm for improved genomic island detection in genomic sequences. Bioinformation 2011;7:311-4. [PMID: 22355228 PMCID: PMC3280502 DOI: 10.6026/007/97320630007311] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 11/17/2011] [Indexed: 11/23/2022]  Open
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