World's Best Scientists 2026 revealed!

D-Index & Metrics

Genetics

D-Index
62
Citations
24204
World Ranking
2945
National Ranking
24

Overview

Tal Pupko is affiliated with Tel Aviv University in Israel and has made contributions primarily in the fields of Biochemistry, Genetics, and Molecular Biology. Their research spans several subfields, including Molecular Biology, Genetics, Plant Science, Artificial Intelligence, and Paleontology.

Their work covers a variety of main topics, notably Genomics and Phylogenetic Studies, RNA and protein synthesis mechanisms, Plant Pathogenic Bacteria Studies, Genetic diversity and population structure, Machine Learning in Bioinformatics, Bacterial Genetics and Biotechnology, and Evolution and Paleontology Studies.

Frequent co-authors collaborating with Tal Pupko include:

  • Oren Avram
  • Itay Mayrose
  • Naama Wagner
  • Gil Loewenthal
  • Noa Ecker

Tal Pupko has published in multiple venues, with a notable number of papers appearing in:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Bioinformatics
  • Molecular Biology and Evolution
  • Journal of Molecular Biology
  • Frontiers in Plant Science

Recent papers authored or co-authored by Tal Pupko include:

  • Using evolutionary data to make sense of macromolecules with a "face-lifted" ConSurf, 2023, Protein Science
  • Type III secretion system effectors form robust and flexible intracellular virulence networks, 2021, Science
  • Harnessing machine learning to guide phylogenetic-tree search algorithms, 2021, Nature Communications
  • ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning, 2020, Molecular Biology and Evolution
  • COVID-19 pandemic-related lockdown: response time is more important than its strictness, 2020, EMBO Molecular Medicine

Best Publications

  • ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.

    Haim Ashkenazy;Shiran Abadi;Eric Martz;Ofer Chay

  • ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

    Haim Ashkenazy;Elana Erez;Eric Martz;Tal Pupko

  • ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

    Meytal Landau;Itay Mayrose;Yossi Rosenberg;Fabian Glaser

  • ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information

    Fabian Glaser;Tal Pupko;Inbal Paz;Rachel E. Bell

  • GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

    Itamar Sela;Haim Ashkenazy;Kazutaka Katoh;Tal Pupko

  • Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues

    Tal Pupko;Rachel E. Bell;Itay Mayrose;Fabian Glaser

  • GUIDANCE: a web server for assessing alignment confidence scores

    Osnat Penn;Eyal Privman;Haim Ashkenazy;Giddy Landan

  • ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function

    Gershon Celniker;Guy Nimrod;Haim Ashkenazy;Fabian Glaser

  • ConSeq: the identification of functionally and structurally important residues in protein sequences

    Carine Berezin;Fabian Glaser;Josef Rosenberg;Inbal Paz

  • Comparison of Site-Specific Rate-Inference Methods for Protein Sequences: Empirical Bayesian Methods Are Superior

    Itay Mayrose;Dan Graur;Nir Ben-Tal;Tal Pupko

  • A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences

    Tal Pupko;Itsik Pe;Ron Shamir;Dan Graur

  • An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

    Osnat Penn;Eyal Privman;Giddy Landan;Dan Graur

  • FastML: a web server for probabilistic reconstruction of ancestral sequences

    Haim Ashkenazy;Osnat Penn;Adi Doron-Faigenboim;Ofir Cohen

  • Comparative Analysis Identifies Exonic Splicing Regulatory Sequences—The Complex Definition of Enhancers and Silencers

    Amir Goren;Oren Ram;Maayan Amit;Hadas Keren

  • Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach

    Adi Stern;Adi Doron-Faigenboim;Elana Erez;Eric Martz

  • Differential GC content between exons and introns establishes distinct strategies of splice-site recognition.

    Maayan Amit;Maya Donyo;Dror Hollander;Amir Goren

  • Rodent phylogeny revised: Analysis of six nuclear genes from all major rodent clades

    Shani Blanga-Kanfi;Hector Miranda;Hector Miranda;Osnat Penn;Tal Pupko

  • Model selection may not be a mandatory step for phylogeny reconstruction

    Shiran Abadi;Dana Azouri;Tal Pupko;Itay Mayrose

  • Genome-scale identification of Legionella pneumophila effectors using a machine learning approach.

    David Burstein;Tal Zusman;Elena Degtyar;Ram Viner

  • Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires

    David Burstein;Francisco Amaro;Tal Zusman;Ziv Lifshitz

Frequent Co-Authors

David E. Burstein
David E. Burstein Tel Aviv University
Nir Ben-Tal
Nir Ben-Tal Tel Aviv University
Dan Graur
Dan Graur University of Houston
Gil Ast
Gil Ast Tel Aviv University
Nir Friedman
Nir Friedman Weizmann Institute of Science
Uri Gophna
Uri Gophna Tel Aviv University
Itsik Pe'er
Itsik Pe'er Columbia University
Roded Sharan
Roded Sharan Tel Aviv University
Ron Shamir
Ron Shamir Tel Aviv University
Guido Sessa
Guido Sessa Tel Aviv University

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