Thomas Manke

The paper introduces ATACofthesnake, a scalable framework for analyzing multifactorial and time course chromatin accessibility data, providing a structured workflow to handle such data reproducibly.

This study investigates the role of DOT1L in astrogenesis, identifying its role in maintaining astrocyte states and revealing multiple origins and state conversions of cortical astrocytes.

This paper improves scATAC-seq by introducing fixation, cryopreservation, and multiplexing to enable reliable analysis of preserved cells.

The paper uses multi-omics data to show FOXG1 regulates transcription and epigenetic processes in mouse hippocampal neurons, working with NEUROD1 to control synaptogenesis.

AutoRELACS automates the RELACS ChIP-seq protocol, enabling high-throughput data generation and analysis with quality comparable to manual methods.

This study investigates how DOT1L methyltransferase activity affects chromatin states and gene expression during neuronal differentiation of mouse embryonic stem cells.

CRUP predicts condition-specific regulatory units by analyzing histone modification ChIP-seq data and linking enhancers to target genes in rheumatoid arthritis.

snakePipes provides a flexible, scalable pipeline for integrative epigenomic analysis across multiple assays, simplifying reproducibility and extending existing studies.

The paper integrates single cell RNA-seq with bulk epigenomic data to identify distinct regulatory states in bidirectional promoters and their associations with structural features and TF binding.

The paper identifies partially methylated domains (PMDs) as widespread epigenomic features across human and mouse cells, showing cell-type specificity and links to gene expression, replication timing, and proliferation.

Parkour is a web-based software package for managing next generation sequencing sample preparation workflows, improving efficiency and quality through automated tracking and staff assignment.

The paper presents a community-driven framework for interactive data analytics training in life sciences, enabling researchers to learn through web-based computation without software installation.

This paper introduces a method for ultra-parallelized ChIP-seq using barcoded intact nuclei, enabling high-throughput analysis of chromatin-associated proteins.

The paper identifies DNA motifs at TAD boundaries in flies and shows they encode 3D genome architecture, with an online database for exploration.

normR normalizes ChIP-seq data to improve enrichment calling in different histone modification regimes.