Manja Marz

This study uses genomic feature extraction and machine learning to identify environmental adaptations in prokaryotes, revealing gene and ncRNA associations with salinity, temperature, oxygen, and pH preferences.

The paper describes methods for automated viral ncRNA annotation and programmatic access to Rfam data via its API, enabling integration into bioinformatics workflows.

This paper provides an overview and analysis of nanopore sequencing, offering guidelines to address challenges and maximize information gain from the technology.

diffONT predicts methylation-specific PCR biomarkers from nanopore sequencing data, improving specificity for hypermethylated regions suitable for MSP primer design.

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

The paper provides the first full-genome multiple sequence alignment for all known pestivirus species and identifies conserved and novel RNA secondary structures.

AnchoRNA improves full-genome alignment of viral sequences by identifying conserved anchor regions, enhancing alignment accuracy and efficiency.

Rfam 15.0 expands coverage to 26,106 genomes, improves RNA family annotations with 3D structures, and synchronizes with miRBase, enhancing RNA research and machine learning applications.

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.

This study compares two Arabidopsis genotypes to show how immunity and bacterial recruitment interact to influence heat stress tolerance.

VIRify identifies and classifies viral contigs and prophages from metagenomic data with high accuracy across prokaryotic and eukaryotic viruses.

The paper assembles 35 European Mycoplasma bovis genomes using a hybrid approach, identifies clade-specific genes, and reveals geographic clustering in a phylogenetic tree.

The paper assembles repetitive TALomes in Xanthomonas using Oxford Nanopore sequencing and presents a correction pipeline to improve accuracy.

Magnipore identifies differential signal shifts between SARS-CoV-2 samples to detect mutations and potential modifications in Oxford Nanopore sequencing data.

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

BERTax uses deep learning to classify DNA sequences taxonomically without requiring known database relatives, outperforming existing methods for novel organisms and combining with databases to improve accuracy.

The paper shows that exosomes from aged mice can cross the blood-brain barrier and activate glial cells, as indicated by increased GFAP expression.

EpiDope uses a deep neural network to predict linear B-cell epitopes with higher accuracy than existing tools, reducing laboratory costs and time.

This paper introduces a deep learning method to predict viral hosts using only viral genome sequences, achieving high accuracy across three virus species.

PoSeiDon detects recombination events and positive selection in protein-coding sequences using a Nextflow pipeline with Docker support.

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.

The paper investigates miRNA expression changes in trophoblastic cell lines under LIF stimulation and identifies associated pathways.

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

The paper introduces nanotext, a novel representation of genome content for machine learning, and applies it to predict culture media and growth temperatures from metagenome assembled genomes.

This study examines alternative splicing changes during aging across species and tissues, finding that the overall transcriptomic landscape remains stable despite specific gene splicing variations.

SilentMutations (SIM) analyzes the effect of mutations on long-range RNA-RNA interactions in viral genomes, predicting disruptive and compensatory mutants.

The paper presents a comprehensive miRNA and ncRNA catalogue for the short-lived fish Nothobranchius furzeri and compares it to other fish species.