Jennifer A. Akiyama

Functional architecture of cardiac TF regulatory landscapes in control of mammalian heart development

The paper identifies essential cardiac enhancer modules and regulatory mechanisms governing heart development, revealing resilience in cis-regulatory architectures and the role of Hand2 upstream regulatory intervals.

Uncovering Hidden Enhancers Through Unbiased In Vivo Testing

The paper identifies hidden enhancers in mouse embryos that are not detected by conventional chromatin profiling methods, highlighting a significant gap in enhancer discovery.

Mutagenesis Sensitivity Mapping of HumanEnhancers In Vivo

The paper maps the mutagenic sensitivity of human enhancers in vivo by systematically mutating enhancer sequences and using predictive modeling to identify critical nucleotides.

Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis

The paper identifies combinatorial TF-cRE interactions in mouse basal ganglia development, revealing modules that drive GABAergic neurogenesis and suppress other fates.

Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity

The paper combines massively parallel reporter assays and mouse transgenic assays to study the functional impact of non-coding variants on neuronal enhancer activity, finding strong correlations and additional pleiotropic effects.

Cell Type- and Tissue-specific Enhancers in Craniofacial Development

The paper identifies 14,000 human craniofacial enhancers across developmental stages and shows 56% are conserved in mice, providing cell type- and stage-specific activity profiles.

Genome-Wide Fetalization of Enhancer Architecture in Heart Disease

The paper identifies widespread epigenomic changes in idiopathic dilated cardiomyopathy, showing a shift toward fetal-like enhancer states and providing a data resource for further study.

De Novo Mutation in an Enhancer of EBF3 in simplex autism

Whole-genome sequencing in thousands of families reveals variants relevant to simplex autism in a brain enhancer of the well-established neurodevelopmental disorder gene EBF3.

A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

This study identifies a gene desert critical for Shox2 regulation and embryonic survival through enhancer networks in mouse development.

A cross-organism framework for supervised enhancer prediction with epigenetic pattern recognition and targeted validation

This paper develops a cross-organism framework for enhancer prediction using Drosophila STARR-seq data and supervised machine learning, validated in mouse and human with 153 enhancers.

Systematic mapping of chromatin state landscapes during mouse development

The paper systematically maps chromatin state landscapes during mouse development by profiling histone modifications across 72 tissue-stages, identifying dynamic enhancers and transcriptional regulators.

Parkinson-associated SNCA enhancer variants revealed by open chromatin in mouse dopamine neurons

The paper identifies Parkinson's risk variants in a SNCA enhancer by analyzing open chromatin in mouse dopamine neurons and validates their function in zebrafish and mice.