Fei Chen

eScreen: a deep learning framework for functionally decoding the regulatory genome at single-nucleotide resolution

The paper introduces eScreen, a deep learning model that decodes regulatory genome function at single-nucleotide resolution using CRISPR screen data, achieving high accuracy and mechanistic interpretation.

Super-CUT&Tag: A Sensitive, Spatially Resolved Approach for Epigenomic Profiling in Tissue Sections

Super-CUT&Tag improves spatial epigenomic profiling by increasing sensitivity and resolution, revealing active-chromatin heterogeneity in mouse embryonic tissues.

The Genetic Basis of Bacterial Adaptation to Hosts

This study identifies host-associated bacterial genes and functions using comparative genomics, revealing new roles in host-microbe interactions and microbial evolution.

ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cells

ChemPert provides a database of transcriptional responses in non-cancer cells to improve drug response predictions for non-cancer diseases.

Klf4 methylated by Prmt1 is required for lineage segregation of epiblast and primitive endoderm

This study identifies Prmt1-mediated Klf4 methylation as critical for lineage segregation between epiblast and primitive endoderm in mouse embryos.

High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope

The paper develops a new method to map nuclear pore-chromatin interactions and finds NPCs are associated with super-enhancers and form transcriptional condensates.

Precision mapping of the mouse brain metabolome

This study maps the mouse brain metabolome using targeted metabolomics, creating detailed maps of 79 metabolites at high resolution.

Reduction of neuronal activity mediated by blood-vessel regression in the brain

This study shows that blood vessel regression in the brain reduces neuronal activity by impairing mitochondrial metabolism and glutamate production.