Carsten O. Daub

Impact of single-cell RNA reference selection for the deconvolution of breast cancer spatial transcriptomics datasets

This study evaluates how reference selection affects deconvolution accuracy in breast cancer spatial transcriptomics datasets, finding that small references can be effective and that perfect reference-ST matching improves results.

The DoGA Consortium Atlas of Canine Enhancers and Promoters Across Tissues and Development

The paper creates a transcription-based atlas of canine regulatory elements across tissues and development, identifying promoters and enhancers and their activity patterns.

Benchmarking tissue- and cell type-of-origin deconvolution in cell-free transcriptomics

This study benchmarks deconvolution methods for inferring tissue and cell type-of-origin from plasma cfRNA, showing method and reference variability impact performance.

Oxygen level alters energy metabolism in bovine preimplantation embryos

This study shows that hypoxia (6% O2) improves blastocyst formation in bovine embryos compared to normoxia (20% O2) and ultrahypoxia (2% O2), with normoxia altering energy metabolism and reducing blastocyst rates.

Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics

This study uses fractional factorial design to screen environmental factors on neural progenitors, identifying pathway-level changes linked to autism risk.

Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish

The paper creates a central repository for zebrafish developmental genomics data, identifies new cis-regulatory elements, and compares regulatory elements between zebrafish and mouse.

Sequence determinants of human gene regulatory elements

The paper identifies sequence determinants of human gene regulatory elements by analyzing transcriptional activity of long DNA sequences in three cell types, revealing distinct enhancer types and TF subtypes based on motif content and activity patterns.

Dog color patterns explained by modular promoters of ancient canid origin

The paper identifies regulatory modules controlling dog color patterns and shows their evolutionary origin in extinct canids.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

The paper identifies shared expression patterns of genetic variants across tissues and cell types, enabling fine mapping of disease-associated variants and revealing key cell types involved in disease pathogenesis.