Arndt von Haeseler

Phylo-Movies: Animating Phylogenetic Trees from Sliding-Window Analyses

Phylo-Movies animates phylogenetic tree changes across genomic windows to identify recombination breakpoints and rogue taxa in norovirus genomes.

Genomic GC bias correction improves species abundance estimation from metagenomic data

This paper introduces GuaCAMOLE, a method to correct GC bias in metagenomic data, improving species abundance estimation across 3435 colorectal cancer gut microbiomes.

Rethinking scRNA-seq Trajectories in Phylogenetic Paradigms: Overcoming Challenges of Missing Ancestral Information

CellREST reinterprets scRNA-seq trajectory reconstruction as a phylogenetic inference problem, uncovering circular processes and converging differentiation scenarios in simulated and experimental data.

GTestimate: Improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator

GTestimate improves scRNA-seq normalization by using the Good-Turing estimator to better estimate relative gene expression and cell-cell distances.

Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols

The paper evaluates four organoid protocols to recreate human brain cell diversity, identifies factors affecting variability, and introduces a scoring system to assess differentiation propensities.

Neutral competition explains the clonal composition of neural organoids

The paper explains the clonal composition of neural organoids using a neutral competition model that accounts for observed lineage size variability.

Liquid footprinting: A novel approach for DNA footprinting using short double-stranded cell-free DNA from plasma

This paper introduces a method to enrich short double-stranded cfDNA from plasma for genome-wide DNA footprinting, identifying disease-specific biomarkers in cancer and sepsis.

Gentrius: identifying equally scoring trees in phylogenomics with incomplete data

Gentrius generates all equally scoring phylogenetic trees from incomplete datasets, revealing the full set of compatible trees and their consensus.

Cellular stress in brain organoids is limited to a distinct and bioinformatically removable subpopulation.

The paper identifies a stress signature in brain organoid scRNA-seq data and introduces Gruffi to remove stressed cells, improving developmental accuracy.

SVhound: Detection of future Structural Variation hotspots

SVhound predicts regions likely to contain novel structural variations by analyzing population-level SV datasets, showing high correlation with full datasets and applicability across species.

TMT-Opsins differentially modulate medaka brain function in a context-dependent fashion

This paper investigates how TMT-opsins modulate medaka brain function differently in various contexts, revealing non-additive interactions and behavioral impacts.

Poly(ADP-ribose) glycohydrolase promotes formation and homology-directed repair of meiotic DNA double-strand breaks independent of its catalytic activity

This study identifies PARG's role in promoting meiotic DNA break formation and repair in C. elegans, independent of its catalytic activity.

Polymorphism-aware species trees with advanced mutation models, bootstrap and rate heterogeneity

This paper introduces PoMo, a polymorphism-aware phylogenetic model that improves species tree inference by accounting for polymorphisms and integrates advanced mutation models and rate heterogeneity.

Accurate detection of complex structural variations using single molecule sequencing

The paper introduces open-source tools for detecting structural variations using long-read sequencing, achieving high sensitivity and precision in complex regions and identifying novel variants in human genomes.

TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers

TRUmiCount corrects molecule counting biases in NGS by modeling PCR and sequencing processes, improving accuracy over existing UMI-based methods.

Thiol-linked alkylation for the metabolic sequencing of RNA

SLAM-seq enables RNA polymerase II-dependent gene expression dynamics analysis by detecting 4-thiouridine incorporation at single-nucleotide resolution in mouse embryonic stem cells.

Reversible Polymorphism-Aware Phylogenetic Models and their Application to Tree Inference

This paper introduces revPoMo, a polymorphism-aware phylogenetic model that improves species tree estimation accuracy without increasing runtime with larger sample sizes.

Teaser: Individualized benchmarking and optimization of read mapping results for NGS data

Teaser benchmarks and optimizes read mapping parameters for NGS data, showing how Bowtie2 can be tailored for different datasets.