Tal Pupko

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 43

Top Topics

Acute Lymphoblastic Leukemia

Machine Learning

Top Venues

Bioinformatics (Oxford, England)

Molecular biology and evolution

Protein science : a publication of the Protein Society

Genome biology and evolution

This page only lists publications with an associated author ORCID identifier.

Publications

Michelle M Pena, Rishi Bhandari, Robert M Bowers, Kylie Weis, Eric Newberry, Naama Wagner, Tal Pupko, Jeffrey B Jones, Tanja Woyke, Boris A Vinatzer, Marie-Agnès Jacques, Neha Potnis
Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas. Genome biology and evolution 16 (4) (2024)
Elya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose, Tal Pupko
Statistical framework to determine indel-length distribution. Bioinformatics (Oxford, England) 40 (2) (2024)
Elya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose, Tal Pupko
Statistical framework to determine indel-length distribution. Bioinformatics (Oxford, England) 40 (2) (2024)
Dana Azouri, Oz Granit, Michael Alburquerque, Yishay Mansour, Tal Pupko, Itay Mayrose
The Tree Reconstruction Game: Phylogenetic Reconstruction Using Reinforcement Learning. Molecular biology and evolution 41 (6) (2024)
Dana Azouri, Oz Granit, Michael Alburquerque, Yishay Mansour, Tal Pupko, Itay Mayrose
The Tree Reconstruction Game: Phylogenetic Reconstruction Using Reinforcement Learning. Molecular biology and evolution 41 (6) (2024)
Elya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose, Tal Pupko
Statistical framework to determine indel-length distribution. Bioinformatics (Oxford, England) 40 (2) (2024)
Edo Dotan, Gal Jaschek, Tal Pupko, Yonatan Belinkov
Effect of tokenization on transformers for biological sequences. Bioinformatics (Oxford, England) 40 (4) (2024)
Dana Azouri, Oz Granit, Michael Alburquerque, Yishay Mansour, Tal Pupko, Itay Mayrose
The Tree Reconstruction Game: Phylogenetic Reconstruction Using Reinforcement Learning. Molecular biology and evolution 41 (6) (2024)
Elya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose, Tal Pupko
Statistical framework to determine indel-length distribution. Bioinformatics (Oxford, England) 40 (2) (2024)
Michelle M Pena, Rishi Bhandari, Robert M Bowers, Kylie Weis, Eric Newberry, Naama Wagner, Tal Pupko, Jeffrey B Jones, Tanja Woyke, Boris A Vinatzer, Marie-Agnès Jacques, Neha Potnis
Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas. Genome biology and evolution 16 (4) (2024)
Edo Dotan, Gal Jaschek, Tal Pupko, Yonatan Belinkov
Effect of tokenization on transformers for biological sequences. Bioinformatics (Oxford, England) 40 (4) (2024)
Edo Dotan, Gal Jaschek, Tal Pupko, Yonatan Belinkov
Effect of tokenization on transformers for biological sequences. Bioinformatics (Oxford, England) 40 (4) (2024)
Dana Azouri, Oz Granit, Michael Alburquerque, Yishay Mansour, Tal Pupko, Itay Mayrose
The Tree Reconstruction Game: Phylogenetic Reconstruction Using Reinforcement Learning. Molecular biology and evolution 41 (6) (2024)
Noa Ecker, Dorothée Huchon, Yishay Mansour, Itay Mayrose, Tal Pupko
A machine-learning-based alternative to phylogenetic bootstrap. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Dana Azouri, Oz Granit, Michael Alburquerque, Yishay Mansour, Tal Pupko, Itay Mayrose
The tree reconstruction game: phylogenetic reconstruction using reinforcement learning. Molecular biology and evolution (2024)
Yael Klirs, Maria Novosolov, Carmela Gissi, Rade Garic, Tal Pupko, Thomas Stach, Dorothée Huchon
Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss. Genome biology and evolution (2024)
Michelle M Pena, Rishi Bhandari, Robert M Bowers, Kylie Weis, Eric Newberry, Naama Wagner, Tal Pupko, Jeffrey B Jones, Tanja Woyke, Boris A Vinatzer, Marie-Agnès Jacques, Neha Potnis
Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas. Genome biology and evolution 16 (4) (2024)
Dana Azouri, Oz Granit, Michael Alburquerque, Yishay Mansour, Tal Pupko, Itay Mayrose
The Tree Reconstruction Game: Phylogenetic Reconstruction Using Reinforcement Learning. Molecular biology and evolution 41 (6) (2024)
Elya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose, Tal Pupko
Statistical framework to determine indel-length distribution. Bioinformatics (Oxford, England) 40 (2) (2024)
Benjamin D Redelings, Ian H Holmes, Gerton Lunter, Tal Pupko, Maria Anisimova
Indels: computational methods, evolutionary dynamics, and biological applications. Molecular biology and evolution (2024)
Noa Ecker, Dorothée Huchon, Yishay Mansour, Itay Mayrose, Tal Pupko
A machine-learning-based alternative to phylogenetic bootstrap. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Noa Ecker, Dorothée Huchon, Yishay Mansour, Itay Mayrose, Tal Pupko
A machine-learning-based alternative to phylogenetic bootstrap. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Barak Yariv, Elon Yariv, Amit Kessel, Gal Masrati, Adi Ben Chorin, Eric Martz, Itay Mayrose, Tal Pupko, Nir Ben-Tal
Using evolutionary data to make sense of macromolecules with a "face-lifted" ConSurf. Protein science : a publication of the Protein Society 32 (3) (2023)
Barak Yariv, Elon Yariv, Amit Kessel, Gal Masrati, Adi Ben Chorin, Eric Martz, Itay Mayrose, Tal Pupko, Nir Ben-Tal
Using evolutionary data to make sense of macromolecules with a 'face-lifted' ConSurf. Protein science : a publication of the Protein Society (2023)
Barak Yariv, Elon Yariv, Amit Kessel, Gal Masrati, Adi Ben Chorin, Eric Martz, Itay Mayrose, Tal Pupko, Nir Ben-Tal
Using evolutionary data to make sense of macromolecules with a 'face-lifted' ConSurf. Protein science : a publication of the Protein Society (2023)
Barak Yariv, Elon Yariv, Amit Kessel, Gal Masrati, Adi Ben Chorin, Eric Martz, Itay Mayrose, Tal Pupko, Nir Ben-Tal
Using evolutionary data to make sense of macromolecules with a "face-lifted" ConSurf. Protein science : a publication of the Protein Society 32 (3) (2023)
Barak Yariv, Elon Yariv, Amit Kessel, Gal Masrati, Adi Ben Chorin, Eric Martz, Itay Mayrose, Tal Pupko, Nir Ben-Tal
Using evolutionary data to make sense of macromolecules with a 'face-lifted' ConSurf. Protein science : a publication of the Protein Society (2023)
Edo Dotan, Michael Alburquerque, Elya Wygoda, Dorothée Huchon, Tal Pupko
GenomeFLTR: filtering reads made easy. Nucleic acids research (2023)
Ksenia Polonsky, Tal Pupko, Natalia T Freund
Evaluation of the Ability of AlphaFold to Predict the Three-Dimensional Structures of Antibodies and Epitopes. Journal of immunology (Baltimore, Md. : 1950) (2023)
Gil Loewenthal, Elya Wygoda, Natan Nagar, Lior Glick, Itay Mayrose, Tal Pupko
The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns. Open biology 12 (12) (2022)
Gil Loewenthal, Elya Wygoda, Natan Nagar, Lior Glick, Itay Mayrose, Tal Pupko
The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns. Open biology 12 (12) (2022)
Gil Loewenthal, Elya Wygoda, Natan Nagar, Lior Glick, Itay Mayrose, Tal Pupko
The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns. Open biology 12 (12) (2022)
Gil Loewenthal, Dana Rapoport, Oren Avram, Asher Moshe, Elya Wygoda, Alon Itzkovitch, Omer Israeli, Dana Azouri, Reed A Cartwright, Itay Mayrose, Tal Pupko
A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions. Molecular biology and evolution 38 (12) (2022)
Asher Moshe, Elya Wygoda, Noa Ecker, Gil Loewenthal, Oren Avram, Omer Israeli, Einat Hazkani-Covo, Itsik Pe'er, Tal Pupko
An Approximate Bayesian Computation Approach for Modeling Genome Rearrangements. Molecular biology and evolution 39 (11) (2022)
Gil Loewenthal, Elya Wygoda, Natan Nagar, Lior Glick, Itay Mayrose, Tal Pupko
The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns. Open biology 12 (12) (2022)
Sapir Labes, Doron Stupp, Naama Wagner, Idit Bloch, Michal Lotem, Ephrat L Lahad, Paz Polak, Tal Pupko, Yuval Tabach
Machine-learning of complex evolutionary signals improves classification of SNVs. NAR genomics and bioinformatics 4 (2) (2022)
Noa Ecker, Dana Azouri, Ben Bettisworth, Alexandros Stamatakis, Yishay Mansour, Itay Mayrose, Tal Pupko
A LASSO-based approach to sample sites for phylogenetic tree search. Bioinformatics (Oxford, England) 38 (Suppl 1) (2022)
Tridib Mahata, Shahar Molshanski-Mor, Moran G Goren, Biswanath Jana, Miriam Kohen-Manor, Ido Yosef, Oren Avram, Tal Pupko, Dor Salomon, Qimron Udi
A phage mechanism for selective nicking of dUMP-containing DNA. Proceedings of the National Academy of Sciences of the United States of America 118 (23) (2021)
Natan Nagar, Noa Ecker, Gil Loewenthal, Oren Avram, Daniella Ben-Meir, Dvora Biran, Eliora Ron, Tal Pupko
Harnessing Machine Learning To Unravel Protein Degradation in Escherichia coli. mSystems 6 (1) (2021)
Dana Azouri, Shiran Abadi, Yishay Mansour, Itay Mayrose, Tal Pupko
Harnessing machine learning to guide phylogenetic-tree search algorithms. Nature communications 12 (1) (2021)
Oren Avram, Aya Kigel, Anna Vaisman-Mentesh, Sharon Kligsberg, Shai Rosenstein, Yael Dror, Tal Pupko, Yariv Wine
PASA: Proteomic analysis of serum antibodies web server. PLoS computational biology 17 (1) (2021)
David Ruano-Gallego, Julia Sanchez-Garrido, Zuzanna Kozik, Elena Núñez-Berrueco, Massiel Cepeda-Molero, Caroline Mullineaux-Sanders, Jasmine Naemi-Baghshomali Clark, Sabrina L Slater, Naama Wagner, Izabela Glegola-Madejska, Theodoros I Roumeliotis, Tal Pupko, Luis Ángel Fernández, Alfonso Rodríguez-Patón, Jyoti S Choudhary, Gad Frankel
Type III secretion system effectors form robust and flexible intracellular virulence networks. Science (New York, N.Y.) 371 (6534) (2021)
Gil Loewenthal, Shiran Abadi, Oren Avram, Keren Halabi, Noa Ecker, Natan Nagar, Itay Mayrose, Tal Pupko
COVID-19 pandemic-related lockdown: response time is more important than its strictness. EMBO molecular medicine 12 (11) (2020)