Alexander Mitrofanov

CRISCross: Integration of Epigenetic Information for Deep-Learning-Based Prediction of CRISPR-Cas9 Off-Targets Across Cell Types

CRISCross improves CRISPR-Cas9 off-target prediction by integrating epigenetic features with sequence data across cell types, showing better performance than sequence-only models.

Biological Foundation Models Enable CRISPR Array Detection Without Metagenomic Assembly

This paper introduces a foundation model for CRISPR array detection that works without metagenomic assembly, achieving high accuracy on both short and long sequences.

The complexity of multiple CRISPR arrays in strains with (co-occurring) CRISPR systems

The paper analyzes CRISPR systems in prokaryotes, finding that multiple CRISPR arrays co-occur with Cas loci, vary in structure, and may function independently or collaboratively.

Comprehensive Analysis of CRISPR Array Repeat Mutations Reveals Subtype-Specific Patterns and Links to Spacer Dynamics

The paper analyzes CRISPR array repeat mutations across prokaryotic genomes, revealing subtype-specific patterns and a link between repeat mutations and spacer dynamics.

An evolutionary approach to predict the orientation of CRISPR arrays

CRISPR-evOr predicts CRISPR array orientation by analyzing evolutionary patterns, improving accuracy for arrays other tools cannot confidently resolve.

Analysis of tracrRNAs reveals subgroup V2 of type V-K CAST systems

The paper identifies a new subgroup of type V-K CAST systems in cyanobacteria through phylogenetic analysis and characterizes its unique features.

SpacerPlacer: Ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions

SpacerPlacer reconstructs ancestral CRISPR array evolution, revealing frequent spacer deletions and a decrease in deletion frequency towards both ends of arrays.

CRISPRIdentify: Identification of CRISPR arrays using machine learning approach

CRISPRIdentify uses machine learning to detect CRISPR arrays with reduced false positives and provides certainty scores for identified regions.