James P. Noonan

This study shows that the human-specific HAR HACNS1 drives opposing heterochronic changes in craniofacial and limb development through altered gene regulatory networks.

This study identifies cell type-specific gene expression changes in Chd8 haploinsufficient mouse cortex during development, highlighting dysregulation in progenitors and neurons.

The paper maps chromatin interactions of Human Accelerated Regions (HARs) in human and chimpanzee neural stem cells to identify gene targets and their role in neurodevelopment.

The paper identifies human accelerated regions (HARs) that regulate gene networks involved in neural progenitor fate transitions, specifically affecting apical-to-basal polarity and cortical development.

The paper shows that turnover of CpG islands in enhancers is linked to changes in enhancer activity across mammals, including humans, and contributes to gene regulatory innovation.

The paper identifies accelerated evolution in conserved enhancer elements across mammals and links it to regulatory function turnover and developmental gene modifications.

The paper examines the role of the human-specific enhancer HACNS1 in human evolution by analyzing its effects on gene expression in humanized mice.

The paper identifies human-specific substitutions affecting enhancer activity in neurodevelopmental regions by testing their impact in human neural stem cells.

The paper disrupts enhancers and genes in human neural stem cells to study their effects on proliferation and identifies regulatory elements linked to neurodevelopmental disorders.

LESSeq identifies differential alternative splicing using RNA-Seq data by analyzing local splicing events and quantifying their significance across cellular conditions.

The paper identifies unique cortical enhancers that enable cell-type-specific genetic tools through Enhancer-Driven Gene Expression.

This paper introduces a statistical framework to identify risk genes from de novo mutations in whole-genome sequencing studies, finding new autism risk genes.

The paper creates an epigenomic atlas of early human craniofacial development, identifies novel enhancers, and links them to HOXA genes involved in craniofacial abnormalities.

The paper disrupts the major promoter-enhancer interaction for Pitx1 in mice and finds minimal phenotypic effects despite complete disruption of the topological interaction.