Nikolay E. Shirokikh

T2G converts transcriptome-aligned BAM files to genome coordinates, improving specificity and splice junction accuracy across RNA sequencing technologies.

The paper integrates multi-omic data from yeast to identify translational programs during glucose starvation, revealing convergent cis-regulatory mechanisms in repressed genes.

The paper updates a yeast reference transcriptome using direct RNA sequencing to improve UTR annotation and provides a reusable pipeline for future updates.

SWARM improves detection of RNA modifications by reducing false positives and reveals new splicing-related pseudouridylation patterns.

VX provides a genome and transcriptome viewer with an embedded API and analysis framework enabling script and AI agent interaction.

dirCLIP uses nanopore sequencing to profile variant-specific RNA-protein interactions, revealing isoform-selective binding and co-occurring sites with high concordance to short-read data.

FracFixR estimates original RNA fraction proportions from fractionated sequencing data, correcting biases and enabling accurate differential expression analysis.

The paper introduces DTI, a new RNA integrity metric based on nanopore sequencing, and the INDEGRA package to correct biases and enable accurate transcriptome comparisons.

The paper presents a long-read RNA sequencing atlas across mammals, revealing conserved transcript complexity and m6A modifications, and their evolutionary roles.

R2Dtool integrates and visualizes isoform-resolved RNA features using transcript and genome annotations to enable comprehensive analysis of RNA modifications and structures.

RISER enables real-time RNA class enrichment or depletion during direct RNA sequencing, improving detection of low-abundance RNAs by reducing dominant RNA reads.

This paper introduces a language-informed basecalling method for Nanopore direct RNA sequencing, showing that incorporating mRNA sequence biases improves basecalling accuracy.

CHEUI predicts m6A and m5C modifications at single-molecule resolution, revealing co-occurrence of these modifications in mRNAs across cell lines and tissues.

The paper introduces a method to quantify protein synthesis rates by analyzing ribosome co-localization dynamics on mRNA.

The paper introduces Sel-TCP-seq to study initiation factor dynamics, revealing staged initiation and co-translational assembly of initiation complexes in yeast and human cells.