Daniel Krizanc

Anticodon nucleotide modifications affect translational tuning by the ribosomal CAR surface

The paper investigates how anticodon nucleotide modifications affect translational tuning via interactions at the ribosomal CAR site.

Systems analysis of ribosomal CAR-site dynamics

The paper introduces an analysis pipeline using mdsa-tools to study ribosomal CAR-site dynamics through molecular dynamics simulations and unsupervised learning.

Interplay of the ribosome A and CAR sites

The paper uses molecular dynamics simulations to study the interaction between the ribosome's A site and CAR site, revealing sequence-dependent modulation of hydrogen bonding and π-stacking interactions.

StACKER, A TOOL FOR SYSTEMS LEVEL ANALYSIS OF BASE STACKING IN NUCLEOTIDE-RICH STRUCTURES

The paper introduces StACKER, a Python tool for analyzing base stacking in nucleic acid structures, and applies it to ribosome simulations to reveal conformational changes linked to translation phenotypes.

GNN codon adjacency regulates protein translation

The paper shows that adjacent GNN codons slow translation in yeast, likely due to ribosome interactions with the CAR surface during translocation.

GCN sensitive protein translation in yeast

The paper investigates GCN codon periodicity in yeast mRNA ramps and shows its impact on translation efficiency through experimental and computational analysis.

Ecotype Simulation 2: An improved algorithm for efficiently demarcating microbial species from large sequence datasets

Ecotype Simulation 2 improves the analysis of large sequence datasets to identify ecologically distinct microbial species more efficiently.