Jishou Ruan

Precise annotation of Drosophila mitochondrial genomes leads to insights into AT-rich regions

The paper precisely annotates Drosophila mitochondrial genomes, identifies conserved polyA motifs in control regions, and provides a high-quality D. simulans mt genome.

How the replication and transcription complex functions in jumping transcription of SARS-CoV-2

The paper proposes a two-route model for SARS-CoV-2 RTC function in jumping transcription, identifies a motif for METTL3 recognition, and reports TRS hairpins for NSP15 cleavage and RNA methylation.

Full-length Genome of a Ogataea polymorpha strain CBS4732 ura3Δ reveals large duplicated segments in subtelomeric regions

The paper reports the full-length genome of O. polymorpha HU-11/CBS4732, revealing large duplicated segments in subtelomeric regions and structural variations between CBS4732 and NCYC495.

The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-2019 pandemics

The paper identifies recombination regions and mutation sites in SARS-CoV-2, SARS-CoV, and SARS-like CoVs, linking specific genetic features to pandemic emergence.

A negative feedback model to explain regulation of SARS-CoV-2 replication and transcription

The paper proposes a negative feedback model explaining SARS-CoV-2 replication and transcription regulation through nsp15 cleavage of transcription regulatory sequences.

NormExpression: an R package to normalize gene expression data using evaluated methods

NormExpression evaluates normalization methods using AUCVC and mSCC metrics, showing consistency across bulk and scRNA-seq data, and provides an R package for method comparison.

Using pan RNA-seq analysis to reveal the ubiquitous existence of 5' and 3' end small RNAs

This study uses pan RNA-seq to show the widespread presence of 5' and 3' end small RNAs, which can annotate mitochondrial and nuclear non-coding genes and identify new steady-state RNAs, challenging classical theories.

Two novel lncRNAs discovered in human mitochondrial DNA using PacBio full-length transcriptome data

The paper uses PacBio full-length transcriptome data to discover two novel lncRNAs in human mitochondrial DNA and propose a new class of lncRNAs called ltiRNAs.