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For: Maiolo M, Zhang X, Gil M, Anisimova M. Progressive multiple sequence alignment with indel evolution. BMC Bioinformatics 2018;19:331. [PMID: 30241460 PMCID: PMC6151001 DOI: 10.1186/s12859-018-2357-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/03/2018] [Indexed: 12/30/2022]  Open
Number Cited by Other Article(s)
1
Redelings BD, Holmes I, Lunter G, Pupko T, Anisimova M. Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications. Mol Biol Evol 2024;41:msae177. [PMID: 39172750 PMCID: PMC11385596 DOI: 10.1093/molbev/msae177] [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: 04/10/2024] [Revised: 07/02/2024] [Accepted: 07/09/2024] [Indexed: 08/24/2024]  Open
2
Chen YR, Harel I, Singh PP, Ziv I, Moses E, Goshtchevsky U, Machado BE, Brunet A, Jarosz DF. Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate. Dev Cell 2024;59:1892-1911.e13. [PMID: 38810654 PMCID: PMC11265985 DOI: 10.1016/j.devcel.2024.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/13/2024] [Accepted: 04/15/2024] [Indexed: 05/31/2024]
3
Wygoda E, Loewenthal G, Moshe A, Alburquerque M, Mayrose I, Pupko T. Statistical framework to determine indel-length distribution. Bioinformatics 2024;40:btae043. [PMID: 38269647 PMCID: PMC10868340 DOI: 10.1093/bioinformatics/btae043] [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: 06/21/2023] [Revised: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 01/26/2024]  Open
4
Hajihassan Z, Afsharian NP, Ansari-Pour N. In silico engineering a CD80 variant with increased affinity to CTLA-4 and decreased affinity to CD28 for optimized cancer immunotherapy. J Immunol Methods 2023;513:113425. [PMID: 36638881 DOI: 10.1016/j.jim.2023.113425] [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: 06/25/2022] [Revised: 11/20/2022] [Accepted: 01/08/2023] [Indexed: 01/11/2023]
5
Zhang Y, Zhang Q, Liu Y, Lin M, Ding C. Multiple Sequence Alignment based on deep Q Network with negative feedback policy. Comput Biol Chem 2022;101:107780. [DOI: 10.1016/j.compbiolchem.2022.107780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/27/2022] [Accepted: 10/18/2022] [Indexed: 11/28/2022]
6
Jowkar G, Pečerska J, Maiolo M, Gil M, Anisimova M. ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process. Syst Biol 2022:6648472. [PMID: 35866991 DOI: 10.1093/sysbio/syac050] [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: 11/04/2021] [Accepted: 07/06/2022] [Indexed: 11/12/2022]  Open
7
Chao J, Tang F, Xu L. Developments in Algorithms for Sequence Alignment: A Review. Biomolecules 2022;12:biom12040546. [PMID: 35454135 PMCID: PMC9024764 DOI: 10.3390/biom12040546] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 01/27/2023]  Open
8
Maiolo M, Gatti L, Frei D, Leidi T, Gil M, Anisimova M. ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process. BMC Bioinformatics 2021;22:518. [PMID: 34689750 PMCID: PMC8543915 DOI: 10.1186/s12859-021-04442-8] [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: 09/29/2020] [Accepted: 10/13/2021] [Indexed: 11/10/2022]  Open
9
Redelings BD. BAli-Phy version 3: model-based co-estimation of alignment and phylogeny. Bioinformatics 2021;37:3032-3034. [PMID: 33677478 DOI: 10.1093/bioinformatics/btab129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 02/10/2021] [Accepted: 02/26/2021] [Indexed: 02/02/2023]  Open
10
Metaheuristics for multiple sequence alignment: A systematic review. Comput Biol Chem 2021;94:107563. [PMID: 34425495 DOI: 10.1016/j.compbiolchem.2021.107563] [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: 12/07/2020] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 11/21/2022]
11
Delucchi M, Näf P, Bliven S, Anisimova M. TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner. FRONTIERS IN BIOINFORMATICS 2021;1:691865. [PMID: 36303789 PMCID: PMC9581039 DOI: 10.3389/fbinf.2021.691865] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022]  Open
12
Kaden M, Bohnsack KS, Weber M, Kudła M, Gutowska K, Blazewicz J, Villmann T. Learning vector quantization as an interpretable classifier for the detection of SARS-CoV-2 types based on their RNA sequences. Neural Comput Appl 2021;34:67-78. [PMID: 33935376 PMCID: PMC8076884 DOI: 10.1007/s00521-021-06018-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 04/07/2021] [Indexed: 02/06/2023]
13
Scossa F, Fernie AR. Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants? Comput Struct Biotechnol J 2021;19:1579-1594. [PMID: 33868595 PMCID: PMC8039532 DOI: 10.1016/j.csbj.2021.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023]  Open
14
Maiolo M, Ulzega S, Gil M, Anisimova M. Accelerating phylogeny-aware alignment with indel evolution using short time Fourier transform. NAR Genom Bioinform 2021;2:lqaa092. [PMID: 33575636 PMCID: PMC7671320 DOI: 10.1093/nargab/lqaa092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 11/14/2022]  Open
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