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Number Cited by Other Article(s)
1
Xu R, Li D, Yang W, Wang G, Li Y. Improving ncRNA family prediction using multi-modal contrastive learning of sequence and structure. Bioinformatics 2024;40:btae640. [PMID: 39460948 PMCID: PMC11639665 DOI: 10.1093/bioinformatics/btae640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 10/15/2024] [Accepted: 10/22/2024] [Indexed: 10/28/2024]  Open
2
Zhang Y, Wang J, Yu J. PSA: an effective method for predicting horizontal gene transfers through parsimonious phylogenetic networks. Cladistics 2024;40:443-455. [PMID: 38717786 DOI: 10.1111/cla.12578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 03/08/2024] [Accepted: 03/20/2024] [Indexed: 07/15/2024]  Open
3
Hong Y, Wang J. Frin: An Efficient Method for Representing Genome Evolutionary History. Front Genet 2019;10:1261. [PMID: 31867045 PMCID: PMC6909884 DOI: 10.3389/fgene.2019.01261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 11/14/2019] [Indexed: 11/13/2022]  Open
4
Jamil HM. Optimizing Phylogenetic Queries for Performance. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:1692-1705. [PMID: 28858810 DOI: 10.1109/tcbb.2017.2743706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
5
Wang J, Guo M. A review of metrics measuring dissimilarity for rooted phylogenetic networks. Brief Bioinform 2018;20:1972-1980. [DOI: 10.1093/bib/bby062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/20/2018] [Indexed: 11/14/2022]  Open
6
Zou Q, Wan S, Zeng X, Ma ZS. Reconstructing evolutionary trees in parallel for massive sequences. BMC SYSTEMS BIOLOGY 2017;11:100. [PMID: 29297337 PMCID: PMC5751538 DOI: 10.1186/s12918-017-0476-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
7
Chen X, Wang C, Tang S, Yu C, Zou Q. CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment. BMC Bioinformatics 2017. [PMID: 28646874 PMCID: PMC5483318 DOI: 10.1186/s12859-017-1725-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
8
Wang J, Guo M. A Metric on the Space of kth-order reduced Phylogenetic Networks. Sci Rep 2017;7:3189. [PMID: 28600511 DOI: 10.1038/s41598-017-03363-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 04/27/2017] [Indexed: 11/09/2022]  Open
9
Wang J. A Survey of Methods for Constructing Rooted Phylogenetic Networks. PLoS One 2016;11:e0165834. [PMID: 27806124 PMCID: PMC5091748 DOI: 10.1371/journal.pone.0165834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/18/2016] [Indexed: 11/18/2022]  Open
10
Constructing Phylogenetic Networks Based on the Isomorphism of Datasets. BIOMED RESEARCH INTERNATIONAL 2016;2016:4236858. [PMID: 27547759 PMCID: PMC4980496 DOI: 10.1155/2016/4236858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/30/2016] [Indexed: 11/18/2022]
11
Wang J. A Metric on the Space of Partly Reduced Phylogenetic Networks. BIOMED RESEARCH INTERNATIONAL 2016;2016:7534258. [PMID: 27419137 PMCID: PMC4935902 DOI: 10.1155/2016/7534258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/23/2016] [Indexed: 11/17/2022]
12
Zou Q, Hu Q, Guo M, Wang G. HAlign: Fast multiple similar DNA/RNA sequence alignment based on the centre star strategy. Bioinformatics 2015;31:2475-81. [DOI: 10.1093/bioinformatics/btv177] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/23/2015] [Indexed: 12/26/2022]  Open
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