Gregory M. Cooper

The paper identifies cell type-specific regulatory elements in nine mammals and shows their conservation and association with neuropsychiatric and neurodegenerative disease risks.

StarPhase diplotypes 21 pharmacogenes using long-read sequencing with high accuracy, updating 26.2% of existing diplotypes and highlighting gaps in pharmacogenomic databases.

This study shows that long-read genome sequencing improves diagnostic yield for neurodevelopmental disorders by identifying variants missed by short-read sequencing.

The paper identifies DNA variants with allele bias in TF binding across human brain regions, linking them to eQTLs and providing insights into gene regulation effects of common and rare variation.

The paper generates a multi-omic resource of TF binding maps in human brain tissues and links TF activities to neuropsychiatric disorder risk variants.

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 processes single-nuclei multi-omics data from 388 human brains to identify regulatory elements and build cell-type networks, revealing changes in aging and neuropsychiatric disorders.

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 evaluates the pathogenicity of intronic and synonymous variants using splicing prediction algorithms and in vitro assays, identifying potentially disease-causing variants previously classified as benign.

DegCre associates differential gene expression with regulatory regions using probabilistic correlation analysis across perturbation data.

The paper identifies clinically relevant variants in poison exons (PEs) that improve diagnostic yield for neurodevelopmental disorders by uncovering variants previously overlooked in standard analyses.

The paper identifies ZMYM3 variants in 22 individuals with neurodevelopmental delay, showing recurrent mutations, phenotypic overlap, and functional effects, supporting ZMYM3 as a novel NDD gene.

This study evaluates genome sequencing in hospitalized newborns, finding it more effective than standard care in identifying genetic diagnoses, especially in those with specific phenotypes.

The paper shows that MPRA data exhibit strand asymmetry favoring naturally transcribed strands, suggesting biological functions driving this effect across gene bodies and Alu elements.

This paper uses long-read genome sequencing to identify pathogenic variants in neurodevelopmental disorders, finding clinically relevant structural variants in two of six probands.

This study identifies a non-coding variant in SCN1A that causes aberrant inclusion of a poison exon, leading to reduced Nav1.1 expression and Dravet syndrome in a mouse model.

The paper evaluates genomic screening in Alabama, finding 51% of identified variants were false positives, with higher rates in African-Americans due to alternative alleles.

The paper identifies rare variants in TET2 associated with early-onset Alzheimer's disease and frontotemporal dementia, highlighting both coding and non-coding variants as risk factors.

Genome sequencing for early-onset dementia identified genetic variants in 50% of patients, including pathogenic variants and moderate penetrance alleles, supporting an oligogenic model.

The paper identifies degron variants in AFF3 causing a multi-system disorder with specific clinical features and demonstrates phenotypic overlap with AFF4-related syndromes.

The paper identifies de novo mutations in RALA, a RAS-like GTPase, as a cause of intellectual disability and developmental delay, showing their functional impact on GTP binding and effector interactions.

The paper reports secondary findings in parents of children with developmental delay through genomic sequencing, identifying clinically relevant variants in 9% of participants.

The paper presents a genome-wide interactome of DNA-associated proteins in human liver tissue, revealing binding patterns more consistent with liver biology than cell lines and highlighting non-coding variation impacts.

This study analyzes genomic data from 371 children with intellectual disability or developmental delay to identify pathogenic variants and assess diagnostic utility.