• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4833559)   Today's Articles (5707)
For: Smith ML, Hahn MW. Phylogenetic inference using generative adversarial networks. Bioinformatics 2023;39:btad543. [PMID: 37669126 PMCID: PMC10500083 DOI: 10.1093/bioinformatics/btad543] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023]  Open
Number Cited by Other Article(s)
1
Salles MMA, Domingos FMCB. Towards the next generation of species delimitation methods: an overview of machine learning applications. Mol Phylogenet Evol 2025;210:108368. [PMID: 40348350 DOI: 10.1016/j.ympev.2025.108368] [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: 12/21/2023] [Revised: 02/25/2025] [Accepted: 05/04/2025] [Indexed: 05/14/2025]
2
Zhu Y, Li Y, Li C, Shen XX, Zhou X. A critical evaluation of deep-learning based phylogenetic inference programs using simulated datasets. J Genet Genomics 2025;52:714-717. [PMID: 39824436 DOI: 10.1016/j.jgg.2025.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2024] [Revised: 01/08/2025] [Accepted: 01/09/2025] [Indexed: 01/20/2025]
3
Nesterenko L, Blassel L, Veber P, Boussau B, Jacob L. Phyloformer: Fast, Accurate, and Versatile Phylogenetic Reconstruction with Deep Neural Networks. Mol Biol Evol 2025;42:msaf051. [PMID: 40066802 PMCID: PMC11965795 DOI: 10.1093/molbev/msaf051] [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: 07/23/2024] [Revised: 01/16/2025] [Accepted: 01/27/2025] [Indexed: 04/04/2025]  Open
4
Landis MJ, Thompson A. phyddle: software for exploring phylogenetic models with deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.08.06.606717. [PMID: 39149349 PMCID: PMC11326143 DOI: 10.1101/2024.08.06.606717] [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] [Indexed: 08/17/2024]
5
Roa Lozano J, Duncan M, McKenna DD, Castoe TA, DeGiorgio M, Adams R. TraitTrainR: accelerating large-scale simulation under models of continuous trait evolution. BIOINFORMATICS ADVANCES 2024;5:vbae196. [PMID: 39758830 PMCID: PMC11696700 DOI: 10.1093/bioadv/vbae196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 11/08/2024] [Accepted: 12/05/2024] [Indexed: 01/07/2025]
6
Silvestro D, Latrille T, Salamin N. Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation. Syst Biol 2024;73:789-806. [PMID: 38916476 PMCID: PMC11639169 DOI: 10.1093/sysbio/syae029] [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: 09/12/2023] [Revised: 05/21/2024] [Accepted: 06/24/2024] [Indexed: 06/26/2024]  Open
7
Bernardini G, van Iersel L, Julien E, Stougie L. Inferring phylogenetic networks from multifurcating trees via cherry picking and machine learning. Mol Phylogenet Evol 2024;199:108137. [PMID: 39029549 DOI: 10.1016/j.ympev.2024.108137] [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: 11/18/2023] [Revised: 02/19/2024] [Accepted: 06/29/2024] [Indexed: 07/21/2024]
8
Li Z, Hu Y, Song Y, Li D, Yang X, Zhang L, Li T, Wang H. Diversity, Distribution and Structural Prediction of the Pathogenic Bacterial Effectors EspN and EspS. Genes (Basel) 2024;15:1250. [PMID: 39457374 PMCID: PMC11507257 DOI: 10.3390/genes15101250] [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: 08/09/2024] [Revised: 09/20/2024] [Accepted: 09/23/2024] [Indexed: 10/28/2024]  Open
9
Li X, Zhou T, Feng X, Yau ST, Yau SST. Exploring geometry of genome space via Grassmann manifolds. Innovation (N Y) 2024;5:100677. [PMID: 39206218 PMCID: PMC11350263 DOI: 10.1016/j.xinn.2024.100677] [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] [Received: 02/06/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024]  Open
10
Mello B, Schrago CG. Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock. Genome Biol Evol 2024;16:evae199. [PMID: 39332907 PMCID: PMC11430275 DOI: 10.1093/gbe/evae199] [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] [Accepted: 09/08/2024] [Indexed: 09/29/2024]  Open
11
Mo YK, Hahn MW, Smith ML. Applications of machine learning in phylogenetics. Mol Phylogenet Evol 2024;196:108066. [PMID: 38565358 DOI: 10.1016/j.ympev.2024.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/16/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
12
Leuchtenberger AF, von Haeseler A. Learning From an Artificial Neural Network in Phylogenetics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:278-288. [PMID: 38198267 DOI: 10.1109/tcbb.2024.3352268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
PrevPage 1 of 1 1Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA