Sven Rahmann

High-performance xenograft read-sorting for DNA methylation analysis

The paper improves a tool for sorting DNA reads in xenograft models, enhancing efficiency for epigenetic analysis.

DivQuant: Estimation of Species Richness and Entropy from Small Samples

DivQuant estimates species richness and entropy from small samples, achieving accurate confidence intervals and outperforming existing methods across multiple datasets.

Integrated flexible DNA methylation-chromatin segmentation modeling enhances epigenomic state annotation

ESMM improves epigenomic state annotation by integrating DNA methylation and chromatin marks, enhancing the detection of heterochromatic regions and regulatory element boundaries.

PanXpress: Gene expression quantification with a pan-transcriptomic gapped k-mer index

PanXpress quantifies bacterial gene expression using a pan-transcriptomic gapped k-mer index, achieving high recall and precision in mixed strain samples.

Error Correction Algorithms for Efficient Gene ExpressionQuantification in Single Cell Transcriptomics

This paper introduces an algorithm for error correction in scRNA-seq data, improving gene expression quantification efficiency and accuracy.

Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index

Cleanifier removes human contamination from microbial sequences using a pangenome index and spaced seeds, achieving speed and accuracy comparable to existing tools.

A complex osteoporotic milieu is associated with arterial stiffening and PDGF-BB-mediated calcification of human smooth muscle cells

This study identifies a complex osteoporotic systemic milieu linked to arterial stiffening and PDGF-BB-mediated vascular calcification in human smooth muscle cells.

Activation of NF-κB signaling by optogenetic clustering of IKKα and β

The paper develops optogenetic tools to cluster eGFP-tagged proteins and uses them to activate NF-κB signaling by clustering IKKα and IKKβ.

A Comprehensive Review and Evaluation of Species Richness Estimation

The paper reviews and evaluates species richness estimation methods on real and simulated data, finding that different methods perform best under varying population compositions and sample sizes.

EpiSegMix: A Flexible Distribution Hidden Markov Model with Duration Modeling for Chromatin State Discovery

EpiSegMix improves chromatin state segmentation by using a flexible hidden Markov model with duration modeling, outperforming existing tools in predicting gene expression.

Design of Worst-Case-Optimal Spaced Seeds

The paper designs spaced seeds that are optimal for worst-case scenarios, enabling robust read mapping even with many sequence differences.

Rapid T cell receptor interaction grouping with ting

The paper introduces an efficient algorithm for clustering T cell receptor sequences, outperforming GLIPH in speed and accuracy on real datasets.

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data

GAMIBHEAR reconstructs haplotypes from Genome Architecture Mapping data to enable allele-specific chromatin conformation analysis.

Fast lightweight accurate xenograft sorting

The paper introduces a fast and lightweight alignment-free method for xenograft sorting that outperforms existing approaches in speed while maintaining accuracy.

Detecting High Scoring Local Alignments in Pangenome Graphs

The paper introduces a heuristic method for finding high-scoring local alignments of DNA queries to pangenome graphs and demonstrates its scalability and effectiveness.

wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data

wg-blimp is an end-to-end pipeline for whole genome bisulfite sequencing data analysis that improves upon existing tools by offering a comprehensive workflow and interactive interface, validated on public datasets.

Modeling and simulating networks of interdependent protein interactions

The paper introduces a model to simulate protein complex formation with interaction dependencies, showing that dependencies limit complex sizes and affect perturbation propagation.

TaxMapper: An Analysis Tool, Reference Database and Workflow for Metatranscriptome Analysis of Eukaryotic Microorganisms

TaxMapper improves metatranscriptome analysis of eukaryotic microorganisms by providing a reference database, a mapping tool, and an automated workflow for taxonomic and functional annotation.