Author

Elya Wygoda

Tel Aviv University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 5

Signature Assays, Organisms & Methods

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Approach:deep learning· 3 Assay:protein sequence· 3 Approach:transformer / foundation model· 3 Approach:statistical model· 2 Assay:DNA methylation· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Research Focus:phylogenetics / evolution· 1

Frequent Co-Authors

Tal PupkoiD· 5 shared Edo DotaniD· 3 shared Yonatan BelinkoviD· 3 shared Asaf Schers· 2 shared Gil LoewenthaliD· 2 shared Itay MayroseiD· 2 shared Oren AvramiD· 2 shared Alon ItzkovitchiD· 1 shared

Activity by Year

2021-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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5 shared papersBioinformatics

Tal PupkoORCID

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Author profile →

5 papers

Recent·Most cited

Phylogenetic tree inference using generative models

Edo Dotan, Asaf Schers, Elya Wygoda, Tal Pupko, Yonatan Belinkov

This paper introduces BetaInfer, a generative model for phylogenetic tree inference that maps unaligned sequences to trees, achieving competitive performance compared to traditional methods.

bioRxiv · Jun 16, 2026 · PreprintBioinformatics

Ancestral sequence reconstruction using generative models

Edo Dotan, Elya Wygoda, Asaf Schers, Iris Lyubman, Yonatan Belinkov, Tal Pupko

This paper introduces BetaReconstruct, a generative model for ancestral sequence reconstruction that outperforms traditional methods without requiring multiple sequence alignments or phylogenetic trees.

bioRxiv · Jan 21, 2026 · PreprintBioinformatics

BetaAlign: a deep learning approach for multiple sequence alignment

Edo Dotan, Elya Wygoda, Noa Ecker, Michael Alburquerque, Oren Avram, Yonatan Belinkov, Tal Pupko

BetaAlign uses deep learning to align biological sequences, achieving accuracy comparable to or better than existing tools.

Bioinformatics · Dec 26, 2024Peer-reviewedBioinformatics

The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns

Gil Loewenthal, Elya Wygoda, Natan Nagar, Lior Glick, Itay Mayrose, Tal Pupko

The paper develops a model of indel dynamics incorporating border-induced selection and applies it to human intron length distribution to explain long neutral sequences.

Open Biology · Dec 1, 2022Peer-reviewedBioinformatics

A probabilistic model for indel evolution: differentiating insertions from deletions

Gil Loewenthal, Dana Rapoport, Oren Avram, Asher Moshe, Elya Wygoda, Alon Itzkovitch, Omer Israeli, Dana Azouri, Reed A. Cartwright, Itay Mayrose, Tal Pupko

This paper introduces a probabilistic model for indel evolution that distinguishes insertions from deletions, showing higher deletion rates and negative correlation with population size in empirical data.

Molecular Biology and Evolution · Sep 1, 2021Peer-reviewedBioinformatics