Matthias Zytnicki

Complete pangenome graph annotation with GrAnnoT and GrAPEx

The paper introduces GrAnnoT and GrAPEx to fully annotate pangenome graphs, integrating annotations from multiple genomes and annotating non-annotated regions, reducing reference bias.

A novel class of tiny box C/D-like RNAs reveals hidden complexity in the mouse box C/D RNA repertoire

The paper identifies a new class of short box C/D-like RNAs in mice, expanding the known repertoire of SNORDs and raising questions about their function and evolution.

SPA-C: an hybrid tool to accurately scaffold genomes using Hi-C and Deep-Learning

SPA-C improves genome scaffolding by combining Hi-C data with a CNN and graph-solving algorithm, outperforming existing methods on benchmark genomes.

GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph

GrAnnoT transfers annotations to pangenome graphs, improving their utility for genomic analysis across species.

HiCDOC: chromatin compartment prediction and differential analysis from Hi-C data with replicates

HiCDOC predicts and differentially analyzes chromatin compartments from Hi-C data with replicates, identifying biologically relevant compartment changes supported by transcriptional differences.

Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs

The paper introduces a method to measure differences between pangenome graphs using pairwise graph edit distance and applies it to yeast and human datasets.

Benchmarking long-read genome assemblers for three sequencing protocols and three agricultural species

This study benchmarks long-read genome assemblers across three agricultural species and three sequencing protocols to evaluate their performance and provide insights into optimal tool and technology combinations.

Assessing genome conservation on pangenome graphs with PanSel

PanSel computes conservation scores for genomic segments in pangenome graphs and identifies significantly conserved or divergent regions.

srnaMapper: an optimal mapping tool for sRNA-Seq reads

srnaMapper is a tool designed to map short RNA-Seq reads efficiently, handling errors and redundancy, and outperforms existing tools on benchmark datasets.

Finding differentially expressed sRNA-Seq regions with srnadiff

srnadiff is a new method for detecting differentially expressed sRNAs without external annotations, outperforming existing approaches on multiple datasets.

Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species.

The paper annotates transcriptomes and chromatin structures in liver and T cells from four livestock species using RNA-seq, ATAC-seq, and Hi-C, revealing conserved regulatory elements and genome organization patterns.