Ilya J. Finkelstein

This study reveals the structural basis for Cas13d's target discrimination and activation through cryo-EM structures and kinetic analysis of matched and mismatched RNA targets.

The paper identifies a phage-encoded factor that activates the Hna anti-phage defense system by overcoming its auto-inhibition.

The paper develops CATNAP, a single-reaction method combining isothermal DNA amplification and Cas12a detection for sensitive HPV detection in low-resource settings.

This paper discovers and engineers retron-based gene editors for precise genome editing in mammalian cells and vertebrates, achieving high efficiency with novel reverse transcriptases and delivery strategies.

The paper identifies distinct epigenetic subdomains in subtelomeric heterochromatin of S. pombe, showing position-specific silencing and the role of structural variants in epigenetic stability.

This study identifies distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons, showing they use CRISPR RNAs and alternative unguided mechanisms for gene transfer.

The paper introduces RNA-CHAMP, a platform to measure RNA binding specificity of CRISPR-Cas13d, revealing structural and sequence determinants of target recognition and enabling SNP detection in SARS-CoV-2 variants.

This study shows that CTCF orientation and R-loops regulate cohesin-mediated DNA looping and 3D genome structure.

The paper identifies new CRISPR-associated transposons (CASTs) by analyzing metagenomic databases, revealing novel architectures and systems that co-opt different CRISPR-Cas effectors.

The paper identifies SARS-CoV-2 neutralizing antibodies from convalescent patients and describes a novel quaternary binding mechanism using high-throughput methods.

The paper sequences 320 SARS-CoV-2 genomes from Houston to study early pandemic spread, finding diverse origins and no evidence of more virulent strains.

The paper profiles cleavage specificity and kinetics of CRISPR nucleases using NucleaSeq and CHAMP, finding engineered Cas9s show improved specificity while wtCas12a has similar specificity to wtCas9 in vitro.

This study shows DNA-PK promotes MRN and phosphorylated CtIP for efficient DNA end processing, facilitating the transition from non-homologous end joining to homologous recombination.

The paper systematically identifies endogenous human ribonucleoprotein complexes using a proteomics method and provides a resource for studying RNA-associated protein complexes.

The paper uses quantitative kinetics to analyze DNA target specificity of CRISPR-Cas12a, revealing that R-loop propagation is rate-limiting and mismatches are discriminated during this process.

The paper develops a high-throughput single-molecule assay to study ssDNA-binding protein interactions and their effects on ssDNA length.

The paper shows that RNAi-induced heterochromatin spread is stochastic, while a memory element called REIII provides deterministic, high-fidelity spreading in fission yeast.

The paper introduces and validates FREE barcodes, which correct DNA synthesis and sequencing errors, including insertions and deletions, improving accuracy and efficiency in high-throughput sequencing.

This study uses a microfluidic platform to show that fission yeast cells can divide for over 75 generations without showing signs of aging, and their lifespan can be extended by genetic or drug interventions.