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For: Bayzid MS, Warnow T. Gene tree parsimony for incomplete gene trees: addressing true biological loss. Algorithms Mol Biol 2018;13:1. [PMID: 29387142 PMCID: PMC5774205 DOI: 10.1186/s13015-017-0120-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 12/27/2017] [Indexed: 11/10/2022]  Open
Number Cited by Other Article(s)
1
Hakim SA, Ratul MRZ, Bayzid MS. wQFM-DISCO: DISCO-enabled wQFM improves phylogenomic analyses despite the presence of paralogs. BIOINFORMATICS ADVANCES 2024;4:vbae189. [PMID: 39664861 PMCID: PMC11634537 DOI: 10.1093/bioadv/vbae189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 10/18/2024] [Accepted: 11/24/2024] [Indexed: 12/13/2024]
2
Habib M, Roy K, Hasan S, Rahman AH, Bayzid MS. Terraces in species tree inference from gene trees. BMC Ecol Evol 2024;24:135. [PMID: 39497030 PMCID: PMC11533290 DOI: 10.1186/s12862-024-02309-z] [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: 11/12/2023] [Accepted: 09/16/2024] [Indexed: 11/06/2024]  Open
3
Schrago CG, Mello B. Challenges in Assembling the Dated Tree of Life. Genome Biol Evol 2024;16:evae229. [PMID: 39475308 PMCID: PMC11523137 DOI: 10.1093/gbe/evae229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2024] [Indexed: 11/02/2024]  Open
4
Schmidt S, Toivonen S, Medvedev P, Tomescu AI. Applying the Safe-And-Complete Framework to Practical Genome Assembly. LIPICS : LEIBNIZ INTERNATIONAL PROCEEDINGS IN INFORMATICS 2024;312:8. [PMID: 40297742 PMCID: PMC12037172 DOI: 10.4230/lipics.wabi.2024.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
5
Dai J, Rubel T, Han Y, Molloy EK. Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem. Algorithms Mol Biol 2024;19:2. [PMID: 38191515 PMCID: PMC10775561 DOI: 10.1186/s13015-023-00249-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024]  Open
6
Schmidt S, Khan S, Alanko JN, Pibiri GE, Tomescu AI. Matchtigs: minimum plain text representation of k-mer sets. Genome Biol 2023;24:136. [PMID: 37296461 PMCID: PMC10251615 DOI: 10.1186/s13059-023-02968-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: 12/16/2021] [Accepted: 05/10/2023] [Indexed: 06/12/2023]  Open
7
Bayzid MS. Inferring Optimal Species Trees in the Presence of Gene Duplication and Loss: Beyond Rooted Gene Trees. J Comput Biol 2023;30:161-175. [PMID: 36251762 DOI: 10.1089/cmb.2021.0522] [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: 11/05/2022]  Open
8
Mahbub S, Sawmya S, Saha A, Reaz R, Rahman MS, Bayzid MS. Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data. JOURNAL OF COMPUTATIONAL BIOLOGY : A JOURNAL OF COMPUTATIONAL MOLECULAR CELL BIOLOGY 2022;29:1156-1172. [PMID: 36048555 DOI: 10.1089/cmb.2022.0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
9
Cerón-Romero MA, Fonseca MM, de Oliveira Martins L, Posada D, Katz LA. Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages. Genome Biol Evol 2022;14:evac119. [PMID: 35880421 PMCID: PMC9366629 DOI: 10.1093/gbe/evac119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2022] [Indexed: 12/02/2022]  Open
10
Pinheiro D, Santander-Jimenéz S, Ilic A. PhyloMissForest: a random forest framework to construct phylogenetic trees with missing data. BMC Genomics 2022;23:377. [PMID: 35585494 PMCID: PMC9116704 DOI: 10.1186/s12864-022-08540-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/01/2022] [Indexed: 11/10/2022]  Open
11
Farah IT, Islam MM, Zinat KT, Rahman AH, Bayzid MS. Species tree estimation from gene trees by minimizing deep coalescence and maximizing quartet consistency: a comparative study and the presence of pseudo species tree terraces. Syst Biol 2021;70:1213-1231. [PMID: 33844023 DOI: 10.1093/sysbio/syab026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 11/14/2022]  Open
12
New Approaches for Inferring Phylogenies in the Presence of Paralogs. Trends Genet 2021;37:174-187. [DOI: 10.1016/j.tig.2020.08.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 12/18/2022]
13
Biological computation and computational biology: survey, challenges, and discussion. Artif Intell Rev 2021. [DOI: 10.1007/s10462-020-09951-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
14
Molloy EK, Warnow T. FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models. Bioinformatics 2020;36:i57-i65. [PMID: 32657396 PMCID: PMC7355287 DOI: 10.1093/bioinformatics/btaa444] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
15
Islam M, Sarker K, Das T, Reaz R, Bayzid MS. STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency. BMC Genomics 2020;21:136. [PMID: 32039704 PMCID: PMC7011378 DOI: 10.1186/s12864-020-6519-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 01/20/2020] [Indexed: 12/14/2022]  Open
16
Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. LECTURE NOTES IN COMPUTER SCIENCE 2020. [DOI: 10.1007/978-3-030-45257-5_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
17
Molloy EK, Warnow T. TreeMerge: a new method for improving the scalability of species tree estimation methods. Bioinformatics 2019;35:i417-i426. [PMID: 31510668 PMCID: PMC6612878 DOI: 10.1093/bioinformatics/btz344] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
18
Soto Gomez M, Pokorny L, Kantar MB, Forest F, Leitch IJ, Gravendeel B, Wilkin P, Graham SW, Viruel J. A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae). APPLICATIONS IN PLANT SCIENCES 2019;7:e11254. [PMID: 31236313 PMCID: PMC6580989 DOI: 10.1002/aps3.11254] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/01/2019] [Indexed: 05/14/2023]
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