Publications

  1. Kim W, Mirdita M, Levy Karin E, Gilchrist CL, Schweke H, Söding J, Levy E & Steinegger M. Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer. BioRxiv. 2024.
  2. Kim G^, Lee S^, Levy Karin E^, Kim H, Moriwaki Y, Ovchinnikov S, Steinegger M & Mirdita M. Easy and accurate protein structure prediction using ColabFold. Nature Protocols. 2024. s41596-024-01060-5. PDF
  3. Lee S, Kim G, Levy Karin E, Mirdita M, Park S, Chikhi R, Babaian A, Kryshtafovych A, & Steinegger M. Petabase-Scale Homology Search for Structure Prediction. Cold Spring Harbor Perspectives in Biology. 2024. a041465. PDF
  4. Raghavan V, Eichele G, Larink O, Levy Karin E, & Söding J. RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton. NAR Genomics and Bioinformatics. 2023. lqad007. PDF
  5. Mirdita M, Steinegger M, Breitwieser F, Soeding J^, & Levy Karin E^. Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinformatics. 2021; btab184. PDF
  6. Zhang R, Mirdita M, Levy Karin E, Norroy C, Galiez C, & Soeding J. SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts. Bioinformatics. 2021; btab222. PDF
  7. Halabi K, Levy Karin E^, Guéguen L, & Mayrose I^. TraitRELAX - A codon model for associating phenotypic traits with altered selective patterns of sequence evolution. Systematic Biology. 2020; syaa087. PDF
  8. Levy Karin E, Mirdita M, & Soeding J. MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics. Microbiome. 2020; 8:48. PDF
  9. Levy Karin E, Ashkenazy H, Hein J, & Pupko T. A simulation-based approach to statistical alignment. Systematic Biology. 2019; 2:252-266. PDF
  10. Ashkenazy H, Sela I, Levy Karin E, Landan G, & Pupko T. Multiple sequence alignment averaging improves phylogeny reconstruction. Systematic Biology. 2019; 1:117–130. PDF
  11. Lavi B, Levy Karin E, Pupko T, & Hazkani-Covo E. The prevalence and evolutionary conservation of inverted repeats in proteobacteria. Genome Biology and Evolution. 2018; 3:918–927. PDF
  12. Mushegian A, Levy Karin E, & Pupko T. Sequence analysis of malacoherpesvirus proteins: pan-herpesvirus capsid module and replication enzymes with an ancient connection to - “Megavirales”. Virology. 2018; 513: 114-128. PDF
  13. Levy Karin E^, Ashkenazy H^, Wicke S, Pupko T, & Mayrose I. TraitRateProp: a web server for the detection of associations between phenotypic trait changes and specific sequence sites. Nucleic Acids Research. 2017; 45:W260-W264. PDF
  14. Ashkenazy H^, Levy Karin E^, Mertens Z, Cartwright R, & Pupko T. SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm. Nucleic Acids Research. 2017; 45:W453-W457. PDF
  15. Levy Karin E, Wicke S, Pupko T, & Mayrose I. An integrated model of phenotypic trait changes and site-specific sequence evolution. Systematic Biology. 2017; 6:917–933. PDF
  16. Levy Karin E^, Shkedy D^, Ashkenazy H, Cartwright R, & Pupko T. Inferring rates and length-distributions of indels using approximate Bayesian computation. Genome Biology and Evolution. 2017; 9:1280-1294. PDF
  17. Preisner H, Levy Karin E, Poschmann G, Stühler K, Pupko T, & Gould S. The cytoskeleton of parabasalian parasites comprises proteins that share properties common to intermediate filament proteins. Protist. 2016; 167:526–543. PDF
  18. Levy Karin E^, Rabin A^, Ashkenazy H, Shkedy D, Avram O, Cartwright R, & Pupko T. Inferring indel parameters using a simulation-based approach. Genome Biology and Evolution. 2015; 7:3226-3238. PDF
  19. Levy Karin E, Susko E, & Pupko T. Alignment errors strongly impact likelihood-based tests for comparing topologies. Molecular Biology and Evolution. 2014; 31:3057-3067. PDF
  20. Cohen O, Ashkenazy H, Levy Karin E, Burstein D, & Pupko T. CoPAP: co-evolution of presence-absence patterns. Nucleic Acids Research. 2013; 41:W232-W237. PDF

Tools

MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. It combines fast and sensitive homology search capabilities with a dynamic programming procedure to recover optimal exons sets. It reduces redundancies in multiple discoveries of the same gene and resolves conflicting gene predictions.

MetaEuk in GitHub


TraitRateProp is a method for testing whether the rate of sequence evolution of a protein or genomic region is associated with changes in a binary phenotypic trait. It detects specific sequence sites whose evolutionary rate is most affected following trait transitions, suggesting a shift in functional/structural constraints.

      source
      webserver


SpartaABC is an Approximate Bayesian Computation (ABC) reject algorithm to infer insertion and deletion (indel) parameters from sequence data. SpartaABC infers the indel-to-substitution rate ratio (IR), the shape parameter (A) of the power law distribution controlling the indel length, and the root length parameter (RL).

  source
  webserver


SimBa-SAl is a simulation-based approach for statistical alignment inference. The SimBa-SAl simulator implements a stochastic evolutionary model of indel formation and generates a long true alignment. It tabulates the probabilities of chop-associated segments (Miklos et al. 2004) based on their frequencies in simulation. The SimBa-SAl inference program takes as input such tabulated chop probabilities and uses them for various statistical alignment computations.

   sim source
   inf source

Teaching

  • Perl programming for biology students (0455-3065)
    • Fall 2016-2017
    • Fall 2015-2016
    • Fall 2014-2015
    • Fall 2013-2014
    • Fall 2012-2013

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  • Math introductory course for biology students (8888-42002)
    • Summer 2015
    • Summer 2014
    • Summer 2013

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