Akanksha Srivastava

SWARM resolves nanopore signal interference between RNA modification types and reveals splicing-shaped pseudouridylation

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

Charge reversal at the Lhcb2 N-terminus impairs phosphorylation and PSI-LHCII complex formation

This study shows that a negative charge at the Lhcb2 N-terminus impairs phosphorylation and PSI-LHCII complex formation in Arabidopsis, while a downstream charge has no effect.

RATTLE: Reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing

RATTLE reconstructs and quantifies transcripts from Nanopore sequencing without a reference genome, showing accuracy and scalability across simulated and experimental data.

Prediction of m6A and m5C at single-molecule resolution reveals a cooccurrence of RNA modifications across the transcriptome

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

Systematic benchmarking of tools for CpG methylation detection from Nanopore sequencing

The paper benchmarks CpG methylation detection tools from Nanopore sequencing, finding tradeoffs in accuracy and introducing a consensus method, METEORE, to improve results.

ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning

ReorientExpress is a reference-free tool that uses deep learning to orient nanopore cDNA reads, improving transcriptome analysis without requiring a genome or transcriptome reference.

HOME: A histogram based machine learning approach for effective identification of differentially methylated regions

HOME identifies differentially methylated regions with higher accuracy and broader applicability across organisms and contexts.

DNA Methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity

The paper examines DNA methylation variation in Brachypodium distachyon, showing correlations with genetic diversity and transposable element polymorphisms.