Tal Pupko

Tel Aviv University — Israel

Biochemistry, Genetics and Molecular Biology · Life Sciences

59h-index21.7kcitations181works8.22yr avg
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Research Topics

Genomics and Phylogenetic Studies(96), RNA and protein synthesis mechanisms(46), Genetic diversity and population structure(31), Machine Learning in Bioinformatics(20), Protein Structure and Dynamics(19)

Publications181 total

Efficient algorithms for simulating sequences along a phylogenetic tree
Bioinformatics·2025· 1 citedOpen Access
The role of plant polyploidy in the structure of plant-pollinator communities
2025Open Access
M1CR0B1AL1Z3R 2.0: an enhanced web server for comparative analysis of bacterial genomes at scale
Nucleic Acids Research·2025· 4 citedOpen Access
Effectidor II: a pan-genomic AI-based algorithm for the prediction of type III secretion system effectors
Bioinformatics·2025· 5 citedOpen Access
BetaAlign: a deep learning approach for multiple sequence alignment
Bioinformatics·2024· 5 citedOpen Access
Protein2Text: Providing Rich Descriptions for Protein Sequences
2024· 1 citedOpen Access
Phylogenetic Analysis of 590 Species Reveals Distinct Evolutionary Patterns of Intron–Exon Gene Structures Across Eukaryotic Lineages
Molecular Biology and Evolution·2024· 10 citedOpen Access
Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications
Molecular Biology and Evolution·2024· 26 citedOpen Access
Evolutionary Insights from the Mitochondrial Genome of <i>Oikopleura dioica</i> : Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss
Genome Biology and Evolution·2024· 5 citedOpen Access
A machine-learning-based alternative to phylogenetic bootstrap
Bioinformatics·2024· 4 citedOpen Access
The Tree Reconstruction Game: Phylogenetic Reconstruction Using Reinforcement Learning
Molecular Biology and Evolution·2024· 13 citedOpen Access
Evolutionary Insights from the Mitochondrial Genome of <i>Oikopleura dioica</i> : Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss
2024· 2 citedOpen Access
Evolution of myxozoan mitochondrial genomes: insights from myxobolids
BMC Genomics·2024· 10 citedOpen Access
Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus <i>Xanthomonas</i>
Genome Biology and Evolution·2024· 19 citedOpen Access
Effect of tokenization on transformers for biological sequences
Bioinformatics·2024· 33 citedOpen Access
BetaAlign: a deep learning approach for multiple sequence alignment
2024· 2 citedOpen Access
Statistical framework to determine indel-length distribution
Bioinformatics·2024· 9 citedOpen Access
A machine-learning based alternative to phylogenetic bootstrap
Figshare·2024Open Access
Evaluation of the Ability of AlphaFold to Predict the Three-Dimensional Structures of Antibodies and Epitopes
The Journal of Immunology·2023· 30 cited
Effect of Tokenization on Transformers for Biological Sequences
2023· 5 citedOpen Access
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Frequent Co-authors

Itay Mayrose(15), Eric Martz(9), Nir Ben‐Tal(9), Haim Ashkenazy(7), Fabian Glaser(6), Adi Doron‐Faigenboim(6), David Burstein(6), Nimrod D. Rubinstein(6), Ofir Cohen(5), Osnat Penn(5), Dan Graur(4), Gil Ast(4), Jonathan M. Gershoni(4), O.C.K.M. Penn(3), Eran Bacharach(3), Maayan Amit(3), Schraga Schwartz(3), Dorothée Huchon(3), Tal Zusman(3), Gil Segal(3)