Explanipedia

The role of plant polyploidy in the structure of plant-pollinator communities Open

Keren Halabi, Noa Ecker, Nathália Susin Streher, Tal Pupko, Tia‐Lynn Ashman , et al. · 2025

Polyploidization is a major macromutation, bearing notable genomic and ecological consequences. While the impact of polyploidy on plant abiotic niches is well studied, our understanding of its consequences on biotic interactions, and parti…

M1CR0B1AL1Z3R 2.0: an enhanced web server for comparative analysis of bacterial genomes at scale Open

Yair Shimony, Edo Dotan, Elya Wygoda, Naama Wagner, Iris Lyubman , et al. · 2025

Large-scale analyses of bacterial genomic datasets contribute to the comprehensive characterization of complex microbial dynamics among different strains and species. Such analyses often include open reading frame extraction, orthogroup in…

Effectidor II: a pan-genomic AI-based algorithm for the prediction of type III secretion system effectors Open

Naama Wagner, Ella Baumer, Iris Lyubman, Yair Shimony, Noam Bracha , et al. · 2025

Motivation Type III secretion systems are used by many Gram-negative bacteria to inject type 3 effectors (T3Es) directly into eukaryotic cells, promoting disease or provoking immune response. Because of these opposing evolutionary forces, …

BetaAlign: a deep learning approach for multiple sequence alignment Open

Edo Dotan, Elya Wygoda, Noa Ecker, Michael Alburquerque, Oren Avram , et al. · 2024

Motivation Multiple sequence alignments (MSAs) are extensively used in biology, from phylogenetic reconstruction to structure and function prediction. Here, we suggest an out-of-the-box approach for the inference of MSAs, which relies on a…

Protein2Text: Providing Rich Descriptions for Protein Sequences Open

Edo Dotan, Iris Lyubman, Eran Bacharach, Tal Pupko, Yonatan Belinkov · 2024

Understanding the functionality of proteins has been a focal point of biological research due to their critical roles in various biological processes. Unraveling protein functions is essential for advancements in medicine, agriculture, and…

Phylogenetic Analysis of 590 Species Reveals Distinct Evolutionary Patterns of Intron–Exon Gene Structures Across Eukaryotic Lineages Open

Lior Glick, Silvia Castiglione, Gil Loewenthal, Pasquale Raia, Tal Pupko , et al. · 2024

Introns are highly prevalent in most eukaryotic genomes. Despite the accumulating evidence for benefits conferred by the possession of introns, their specific roles and functions, as well as the processes shaping their evolution, are still…

Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications Open

Benjamin D. Redelings, Ian Holmes, Gerton Lunter, Tal Pupko, Maria Anisimova · 2024

Insertions and deletions constitute the second most important source of natural genomic variation. Insertions and deletions make up to 25% of genomic variants in humans and are involved in complex evolutionary processes including genomic r…

Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica : Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss Open

Yael Klirs, Maria Novosolov, Carmela Gissi, Rade Garić, Tal Pupko , et al. · 2024

Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation …

A machine-learning-based alternative to phylogenetic bootstrap Open

Noa Ecker, Dorothée Huchon, Yishay Mansour, Itay Mayrose, Tal Pupko · 2024

Motivation Currently used methods for estimating branch support in phylogenetic analyses often rely on the classic Felsenstein’s bootstrap, parametric tests, or their approximations. As these branch support scores are widely used in phylog…

The Tree Reconstruction Game: Phylogenetic Reconstruction Using Reinforcement Learning Open

Dana Azouri, Oz Granit, Michael Alburquerque, Yishay Mansour, Tal Pupko , et al. · 2024

The computational search for the maximum-likelihood phylogenetic tree is an NP-hard problem. As such, current tree search algorithms might result in a tree that is the local optima, not the global one. Here, we introduce a paradigm shift f…

Evolutionary Insights from the Mitochondrial Genome ofOikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss Open

Yael Klirs, Maria Novosolov, Carmela Gissi, Rade Garić, Tal Pupko , et al. · 2024

Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation …

Evolution of myxozoan mitochondrial genomes: insights from myxobolids Open

Tatiana Orli Milkewitz Sandberg, Dayana Yahalomi, Noam Bracha, Michal Haddas‐Sasson, Tal Pupko , et al. · 2024

Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas Open

Michelle M. Pena, Rishi Bhandari, Robert M. Bowers, Kylie Weis, Eric A. Newberry , et al. · 2024

The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue-specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, s…

Effect of tokenization on transformers for biological sequences Open

Edo Dotan, Gal Jaschek, Tal Pupko, Yonatan Belinkov · 2024

Motivation Deep-learning models are transforming biological research, including many bioinformatics and comparative genomics algorithms, such as sequence alignments, phylogenetic tree inference, and automatic classification of protein func…

BetaAlign: a deep learning approach for multiple sequence alignment Open

Edo Dotan, Elya Wygoda, Noa Ecker, Michael Alburquerque, Oren Avram , et al. · 2024

The multiple sequence alignment (MSA) problem is a fundamental pillar in bioinformatics, comparative genomics, and phylogenetics. Here we characterize and improve BetaAlign, the first deep learning aligner, which substantially deviates fro…

Statistical framework to determine indel-length distribution Open

Elya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose , et al. · 2024

Motivation Insertions and deletions (indels) of short DNA segments, along with substitutions, are the most frequent molecular evolutionary events. Indels were shown to affect numerous macro-evolutionary processes. Because indels may span m…

A machine-learning based alternative to phylogenetic bootstrap Open

Noa Ecker, Yishay Mansour, Itay Mayrose, Tal Pupko · 2024

A data-driven approach to estimate branch support values with a probabilistic interpretation

Effect of Tokenization on Transformers for Biological Sequences Open

Edo Dotan, Gal Jaschek, Tal Pupko, Yonatan Belinkov · 2023

Deep learning models are transforming biological research. Many bioinformatics and comparative genomics algorithms analyze genomic data, either DNA or protein sequences. Examples include sequence alignments, phylogenetic tree inference and…

Evaluation of the Ability of AlphaFold to Predict the Three-Dimensional Structures of Antibodies and Epitopes Open

Ksenia Polonsky, Tal Pupko, Natalia T. Freund · 2023

Being able to accurately predict the three-dimensional structure of an antibody can facilitate fast and precise antibody characterization and epitope prediction, with important diagnostic and clinical implications. In the current study, we…

Comparative sequence analysis of pPATH pathogenicity plasmids in Pantoea agglomerans gall-forming bacteria Open

Naama Geraffi, Priya Gupta, Naama Wagner, Isaac Barash, Tal Pupko , et al. · 2023

Acquisition of the pathogenicity plasmid pPATH that encodes a type III secretion system (T3SS) and effectors (T3Es) has likely led to the transition of a non-pathogenic bacterium into the tumorigenic pathogen Pantoea agglomerans . P. agglo…

Genetic and functional diversity help explain pathogenic, weakly pathogenic, and commensal lifestyles in the genusXanthomonas Open

Michelle M. Pena, Rishi Bhandari, Robert M. Bowers, Kylie Weis, Eric A. Newberry , et al. · 2023

The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, s…

Complete genome sequence of an Israeli isolate of Xanthomonas hortorum pv. pelargonii strain 305 and novel type III effectors identified in Xanthomonas Open

Naama Wagner, Daniella Ben‐Meir, Doron Teper, Tal Pupko · 2023

Xanthomonas hortorum pv. pelargonii is the causative agent of bacterial blight in geranium ornamental plants, the most threatening bacterial disease of this plant worldwide. Xanthomonas fragariae is the causative agent of angular leaf spot…

GenomeFLTR: filtering reads made easy Open

Edo Dotan, Michael Alburquerque, Elya Wygoda, Dorothée Huchon, Tal Pupko · 2023

In the last decade, advances in sequencing technology have led to an exponential increase in genomic data. These new data have dramatically changed our understanding of the evolution and function of genes and genomes. Despite improvements …

Identification of selective sweeps in bacteria Open

Oren Avram, Eli Levy Karin, Jukka Corander, Yaara Oren, Tal Pupko · 2023

Selective sweeps occur when a beneficial mutation spreads rapidly throughout the population due to natural selection. Searching for selective sweeps has proved to be one of the most fruitful ways to detect the footprints selection leaves o…

The tree reconstruction game: phylogenetic reconstruction using reinforcement learning Open

Dana Azouri, Oz Granit, Michael Alburquerque, Yishay Mansour, Tal Pupko , et al. · 2023

We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny reco…

Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf Open

Barak Yariv, Elon Yariv, Amit Kessel, Gal Masrati, Adi Ben Chorin , et al. · 2023

The ConSurf web‐sever for the analysis of proteins, RNA, and DNA provides a quick and accurate estimate of the per‐site evolutionary rate among homologues. The analysis reveals functionally important regions, such as catalytic and ligand‐b…

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

Gil Loewenthal, Elya Wygoda, Natan Nagar, Lior Glick, Itay Mayrose , et al. · 2022

Insertions and deletions (indels) of short DNA segments are common evolutionary events. Numerous studies showed that deletions occur more often than insertions in both prokaryotes and eukaryotes. It raises the question why neutral sequence…

Natural language processing approach to model the secretion signal of type III effectors Open

Naama Wagner, Michael Alburquerque, Noa Ecker, Edo Dotan, Ben Zerah , et al. · 2022

Type III effectors are proteins injected by Gram-negative bacteria into eukaryotic hosts. In many plant and animal pathogens, these effectors manipulate host cellular processes to the benefit of the bacteria. Type III effectors are secrete…

An Approximate Bayesian Computation Approach for Modeling Genome Rearrangements Open

Asher Moshe, Elya Wygoda, Noa Ecker, Gil Loewenthal, Oren Avram , et al. · 2022

The inference of genome rearrangement events has been extensively studied, as they play a major role in molecular evolution. However, probabilistic evolutionary models that explicitly imitate the evolutionary dynamics of such events, as we…

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

Gil Loewenthal, Elya Wygoda, Natan Nagar, Lior Glick, Itay Mayrose , et al. · 2022

Insertions and deletions (indels) of short DNA segments are common evolutionary events. Numerous studies showed that deletions occur more often than insertions in both prokaryotes and eukaryotes. It raises the question why neutral sequence…

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