Peter Florian Stadler

REvolutionH-tl: A Fast and Robust Tool for Decoding Evolutionary Gene Histories

REvolutionH-tl automates evolutionary gene history analysis from sequence data, outperforming existing tools in speed and accuracy with integrated visualization.

Partial Fitch Graphs: Characterization, Satisfiability and Complexity

The paper characterizes partial Fitch graphs, shows their satisfiability, and proves NP-hardness of recovering full Fitch graphs from partial data.

Anchors for Homology-Based Scaffolding

This paper introduces an anchor-based scaffolding framework for homology-based ordering of contigs, achieving accuracy comparable to state-of-the-art methods, especially in multi-reference settings.

A little feat in translation: miniaturized tRNAs in nematode and arachnid mitochondria

The paper analyzes and characterizes mitochondrial tRNAs in nematodes and arachnids, revealing structural deviations and editing events not captured by genome-based predictions.

Octopamine receptors at a glance: from expression and anatomical maps to their role in development and behavior in the Drosophila melanogaster larva

The paper compiles and analyzes a complete set of octopamine receptor mutant lines in Drosophila melanogaster to study their expression, function, and role in development and behavior.

BioAutoML-FAST: an automated machine-learning platform for reusable and benchmarked biological sequence models

BioAutoML-FAST provides an automated ML platform for biological sequence analysis, offering reusable models and benchmarking across genomic, transcriptomic, and proteomic tasks.

A sequential, RNA-derived, modified adenosine pathway safeguards cellular metabolism

The paper shows that modified adenosines from RNA catabolism are sequentially metabolized to prevent toxicity and maintain metabolic balance.

Recently evolved, stage-specific genes are enriched at life stage transitions in flies

The paper identifies recently evolved, stage-specific genes enriched at life stage transitions in dipteran species, suggesting ongoing evolutionary processes shaping developmental transitions.

Telomerase RNA gene duplications drive telomeric repeatdiversity and evolution in Andrena bees

The paper identifies multiple TR gene copies in Andrena bees that generate diverse telomeric repeats, showing TR gene duplication drives telomere sequence diversity in insects.

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.

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

The paper analyzes the genome and population genomics of Coffea arabica to reveal its diversification history and breeding-related genetic changes.

Evolutionary conservation of secondary structures in the lncRNAs of plants

The paper identifies conserved structural motifs in lncRNAs across 16 Brassicaceae species, highlighting their potential functional significance.

Salt corrections for RNA secondary structures in the ViennaRNA package

The paper updates the ViennaRNA package to include salt corrections for RNA secondary structure prediction, improving accuracy under varying ion concentrations.

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

The paper benchmarks 16 circRNA detection tools across three human cell types, finding large differences in sensitivity but consistent precision, and recommends tool combinations for improved detection.

Tailored machine learning models for functional RNA detection in genome-wide screens

The paper introduces a software framework for training and evaluating machine learning models to detect functional RNA in genome-wide screens, demonstrating its use in Drosophila melanogaster.

Mitochondrial genomes in Perkinsus decode conserved frameshifts in all genes

The paper sequences four Perkinsus mitochondrial genomes, identifies conserved frameshifts in all genes, and proposes a decoding mechanism involving unused codons.

Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional Bayesian approaches

This paper presents a computational method to improve variant calling from bisulfite sequencing data using conventional software by manipulating base quality scores.

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

MuDoGeR simplifies genome recovery from metagenomes for non-experts, demonstrating effectiveness across various sample sizes.

OrtSuite - from genomes to prediction of microbial interactions within targeted ecosystem processes

OrtSuite predicts microbial interactions based on genomic content for specific ecosystem processes using ortholog clustering and user-defined functions.

PredicTF: a tool to predict bacterial transcription factors in complex microbial communities.

PredicTF predicts bacterial transcription factors in microbial communities using genomic and metagenomic data from environmental isolates and anammox bioreactors.

Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis

This paper benchmarks nine tools for mapping whole genome bisulfite data, finding BWA-meth and BSMAP perform best in alignment and methylation analysis.

Beyond Plug and Pray: Context Sensitivity and in silico Design of Artificial Neomycin Riboswitches

The paper designs synthetic neomycin-responsive riboswitches and shows that their function depends on sequence context, introducing in silico methods to improve design.

Supervised and Unsupervised Classification of lncRNA Subtypes

The paper investigates whether host gene function or mechanisms correlate with payload type in lncRNAs, finding no significant association beyond payload type.

Splicing conservation signals in plant long non-coding RNAs

The paper identifies splicing conservation in lncRNAs across Brassicaceae species, finding 17.9% of intergenic lncRNAs show conservation, supporting stabilizing selection.

Identification of RNA 3' ends and termination sites in Haloferax volcanii

This study identifies RNA 3' termini and termination sites in Haloferax volcanii using a novel algorithm and RNAseq data, revealing distinct motifs for intergenic and coding regions.

Economic Genome Assembly from Low Coverage Illumina and Nanopore Data

LazyBastard improves genome assembly accuracy for yeast and fruit fly using low-coverage Illumina and Nanopore data with reduced computational effort.

Assessing the Quality of Cotranscriptional Folding Simulations

The paper introduces BarMap-QA, a pipeline for assessing the quality of cotranscriptional folding simulations of RNA elements.

flowEMMi: An automated model-based clustering tool for microbial cytometric data

flowEMMi automates clustering of microbial cytometric data using Gaussian mixture models, improving speed and accuracy over manual and existing methods.

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes

TerrestrialMetagenomeDB curates and standardizes metadata for terrestrial metagenomes to facilitate comparison and meta-analysis across datasets.

Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure

The paper introduces bi-alignments to model incongruent evolution of RNA sequence and structure, showing they are a special case of 4-way alignments and finding such incongruence is not rare in the Rfam database.