Kevin Lamkiewicz

Reducing haystacks to needles - ViralClust: A Nextflow pipeline to cluster viral sequences

ViralClust reduces large viral sequence datasets by clustering, preserving genetic diversity and reducing computational burden.

RNA-Protein Interaction Prediction without High-Throughput Data: An Overview and Benchmark of in silico Tools

This paper reviews RPI prediction tools that do not require high-throughput data and evaluates their performance across species and output types.

Comprehensive Survey of Conserved RNA Secondary Structures in Full-Genome Alignment of Hepatitis C Virus

The paper identifies conserved RNA secondary structures in HCV genomes through full-genome alignment and analysis, showing conservation in specific regions like core, NS5A, and NS5B.

Pangenome calculation beyond the species level using RIBAP: A comprehensive bacterial core genome annotation pipeline based on Roary and pairwise ILPs

RIBAP improves pangenome analysis by using ILP to refine gene clusters, outperforming existing tools in identifying core genes across diverse bacterial genomes.

Extensive genomic divergence among 61 strains of Chlamydia psittaci

The paper analyzes 61 Chlamydia psittaci genomes to identify genomic features correlated with host tropism and phylogeny.

A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes

The paper annotates and analyzes non-coding RNAs in 16 bat genomes, revealing new expression patterns and providing a resource for studying bat biology and host-virus interactions.

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

This study uses direct RNA nanopore sequencing to analyze full-length coronavirus genomes, identifying structural variants and methylation sites in viral RNAs.

Identification of potential microRNAs associated with Herpesvirus family based on bioinformatic analysis

This study identifies potential miRNAs in Herpesvirus family members using a bioinformatic pipeline, finding novel candidates in Epstein-Barr virus and Human Herpesvirus 7.