Fumitaka Inoue

The paper identifies regulatory effects of Neanderthal and Denisovan introgression in immune-related genes using a massively parallel reporter assay across different cell types.

Rosalind, a DNA foundation model, predicts variant-gene regulatory relationships without proximity bias, identifying distal genes as more impactful in osteoporosis.

The paper introduces e2MPRA, a method that simultaneously measures regulatory activity and epigenomic features of CREs using lentivirus-based MPRA and targeted Cut&Tag or ATAC-seq.

This paper introduces ccMPRA, a method that combines Capture-C and MPRA to study promoter interactions and regulatory activity, identifying enhancers and silencers.

The paper identifies functional cis-regulatory elements in three human cell types using lentiMPRAs and develops predictive models for CRE function.

The paper constructs enhancer-promoter interaction networks during neural differentiation and identifies their temporal dynamics and disease-associated variant enrichment using computational and experimental methods.

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

The paper generates a molecular neuroanatomical map of the human prefrontal cortex using spatial transcriptomics and single nucleus RNA-sequencing, revealing novel spatial domains and cell-cell interactions linked to psychiatric disorders.

The paper uses MPRA in forebrain organoids to validate enhancer activity in early human neurodevelopment, identifying over 2,300 enhancers with temporal-specific activity.

This paper evaluates sequence design strategies for perturbation MPRA using a computational framework and finds that random nucleotide shuffling outperforms other methods.

The paper refines the annotation of endogenous retrovirus LTRs in primates by identifying new subfamilies and their regulatory roles through phylogenetic analysis and functional validation.

The paper uses perturbation assays to study how regulatory elements guide neural differentiation over time, identifying sequence-driven activity and environmental effects on transcription.

This study evaluates how experimental design, orientation, and sequence context affect MPRA results, finding significant differences in regulatory activity measurements.

The paper maps genomic and epigenomic features of leptin-responsive hypothalamic neurons and identifies regulatory elements overlapping obesity-associated SNPs.

The paper performs saturation mutagenesis on disease-associated regulatory elements to assess the functional effects of mutations, revealing variability in transcription factor binding site density and predictive power of conservation scores.