Eli Levy Karin
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View article: Metagenomic-scale analysis of the predicted protein structure universe
Metagenomic-scale analysis of the predicted protein structure universe Open
Protein structure prediction breakthroughs, notably AlphaFold2 and ESMfold, have led to an unprecedented influx of computationally derived structures. The AlphaFold Protein Structure Database now provides over 200 million models, while the…
View article: Cutting-edge deep-learning based tools for metagenomic research
Cutting-edge deep-learning based tools for metagenomic research Open
Recent years have seen incredible progress in the development of deep-learning (DL) tools for the analysis of biological data, with the most prominent example being AlphaFold2 for accurate protein structure prediction. DL-based tools are e…
View article: Rapid and sensitive protein complex alignment with Foldseek-Multimer
Rapid and sensitive protein complex alignment with Foldseek-Multimer Open
Advances in computational structure prediction will vastly augment the hundreds of thousands of currently available protein complex structures. Translating these into discoveries requires aligning them, which is computationally prohibitive…
View article: BFVD—a large repository of predicted viral protein structures
BFVD—a large repository of predicted viral protein structures Open
The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted structures with taxonomic labels. Despite providing predictions for over 214 million UniProt entries, the AFDB does not cover viral sequences…
View article: BFVD - a large repository of predicted viral protein structures
BFVD - a large repository of predicted viral protein structures Open
The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted structures with taxonomic labels. Despite providing predictions for over 214 million UniProt entries, the AFDB does not cover viral sequences…
View article: Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer
Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer Open
Advances in computational structure prediction will vastly augment the hundreds of thousands of currently-available protein complex structures. Translating these into discoveries requires aligning them, which is computationally prohibitive…
View article: Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer
Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer Open
Advances in computational structure prediction will vastly augment the hundreds of thousands of currently-available protein complex structures. Translating these into discoveries requires aligning them, which is computationally prohibitive…
View article: Easy and accurate protein structure prediction using ColabFold
Easy and accurate protein structure prediction using ColabFold Open
Since its public release in 2021, AlphaFold2 (AF2) has made investigating biological questions, using predicted protein structures of single monomers or full complexes, a common practice. ColabFold-AF2 is an open-source Jupyter Notebook in…
View article: Petascale Homology Search for Structure Prediction
Petascale Homology Search for Structure Prediction Open
The recent CASP15 competition highlighted the critical role of multiple sequence alignments (MSAs) in protein structure prediction, as demonstrated by the success of the top AlphaFold2-based prediction methods. To push the boundaries of MS…
View article: Identification of selective sweeps in bacteria
Identification of selective sweeps in bacteria Open
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…
View article: RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton
RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton Open
Zooplankton are important eukaryotic constituents of marine ecosystems characterized by limited motility in the water. These metazoans predominantly occupy intermediate trophic levels and energetically link primary producers to higher trop…
View article: SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts Open
Summary SpacePHARER (CRISPR Spacer Phage–Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage–host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER …
View article: Fast and sensitive taxonomic assignment to metagenomic contigs
Fast and sensitive taxonomic assignment to metagenomic contigs Open
Summary MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with rob…
View article: soedinglab/MMseqs2: MMseqs2 Release 13-45111
soedinglab/MMseqs2: MMseqs2 Release 13-45111 Open
New Taxonomy Workflow (new feature and breaking change) We introduce a new taxonomy workflow for assigning taxonomic labels to nucleotide sequences by searching against protein reference databases. For details see: Mirdita M, Steinegger M,…
View article: Fast and sensitive taxonomic assignment to metagenomic contigs
Fast and sensitive taxonomic assignment to metagenomic contigs Open
Summary MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with rob…
View article: A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution
A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution Open
Detecting the signature of selection in coding sequences and associating it with shifts in phenotypic states can unveil genes underlying complex traits. Of the various signatures of selection exhibited at the molecular level, changes in th…
View article: SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts
SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts Open
Summary SpacePHARER (CRISPR Spacer Phage-Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage-host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER …
View article: MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics
MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics Open
Background Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without …
View article: A codon model for associating phenotypic traits with altered selective patterns of sequence evolution
A codon model for associating phenotypic traits with altered selective patterns of sequence evolution Open
Changes in complex phenotypes, such as pathogenicity levels, trophic lifestyle, and habitat shifts are brought on by multiple genomic changes: sub- and neofunctionalization, loss of function, and levels of gene expression. Thus, detecting …
View article: SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts
SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts Open
Summary: SpacePHARER (CRISPR Spacer Phage-Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage-host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER…
View article: MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Open
Background Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without …
View article: MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Open
Background: Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without…
View article: Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction
Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction Open
The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is reconstructed assuming the MSA is correct. Yet, inferred MSAs wer…
View article: The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria
The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria Open
Perfect short inverted repeats (IRs) are known to be enriched in a variety of bacterial and eukaryotic genomes. Currently, it is unclear whether perfect IRs are conserved over evolutionary time scales. In this study, we aimed to characteri…
View article: TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites
TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites Open
Understanding species adaptation at the molecular level has been a central goal of evolutionary biology and genomics research. This important task becomes increasingly relevant with the constant rise in both genotypic and phenotypic data a…
View article: Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation
Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation Open
The most common evolutionary events at the molecular level are single-base substitutions, as well as insertions and deletions (indels) of short DNA segments. A large body of research has been devoted to develop probabilistic substitution m…
View article: SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm
SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm Open
Many analyses for the detection of biological phenomena rely on a multiple sequence alignment as input. The results of such analyses are often further studied through parametric bootstrap procedures, using sequence simulators. One of the p…
View article: An Integrated Model of Phenotypic Trait Changes and Site-Specific Sequence Evolution
An Integrated Model of Phenotypic Trait Changes and Site-Specific Sequence Evolution Open
Recent years have seen a constant rise in the availability of trait data, including morphological features, ecological preferences, and life history characteristics. These phenotypic data provide means to associate genomic regions with phe…