Oguzhan Begik

Declines in mRNA synthesis set the rate of organismal aging

The paper shows that declining mRNA synthesis capacity during aging reduces mRNA abundance, driving organismal aging, and that manipulating this decline affects healthspan and lifespan.

FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling

FIRST-seq uses nanopore cDNA sequencing to profile RNA modifications and structures by analyzing RT errors, achieving single-nucleotide resolution without PCR or second-strand synthesis.

Nano3P-seq: charting the coding and non-coding transcriptome at single molecule resolution

The paper introduces Nano3P-seq, a nanopore-based method to analyze RNA polyA tail composition and length at single-molecule resolution, along with software PolyTailor for accurate estimation of transcript abundances and tail dynamics.

Unbiased functional genetic screens reveal essential RNA modifications in human cancer and drug resistance

The paper identifies essential RNA modifications in cancer using CRISPR screens and finds that mitochondrial metabolic plasticity influences drug resistance through specific RNA modifications.

Enhanced detection of RNA modifications and mappability with high-accuracy nanopore RNA basecalling models

This paper shows that using high-accuracy nanopore RNA basecalling models improves detection of RNA modifications, read mappability, and basecalling accuracy.

Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing

Nano3P-seq quantifies RNA abundance, tail composition, and tail length dynamics at single-read resolution without PCR or adapters.

Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

The paper introduces a method to quantify RNA modifications using nanopore sequencing, revealing novel modification sites and dynamics in yeast under environmental stress.

Barcoding and demultiplexing Oxford Nanopore native RNA sequencing reads with deep residual learning

This paper introduces a deep learning method for barcoding and demultiplexing direct RNA sequencing reads without base-calling or additional library steps, achieving high specificity and read demultiplexing rates.

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

The paper identifies tissue- and cancer-specific RNA modification machinery (RMP) expression patterns and dysregulation across 32 tissues, 10 species, and 13,358 tumor-normal samples.

Accurate detection of m6A RNA modifications in native RNA sequences

This paper demonstrates the detection of m6A RNA modifications in native RNA sequences using Oxford Nanopore Technologies with high accuracy.