Kynon JM Benjamin

IsoGraph resolves coordinated transcript choice and gene abundance in the aging human brain

IsoGraph identifies age-associated transcript-usage signals in human brain transcriptomes, distinguishing them from gene abundance and cellular composition effects.

Local SNP-explained methylation variation reveals genetically anchored and exposure-associated methylation architecture in the human brain

The paper uses SNP-based modeling to classify methylation variation in the human brain, revealing genetically anchored and exposure-associated patterns in an underrepresented population.

RFMix-reader: Accelerated reading and processing for local ancestry studies

RFMix-reader efficiently processes large RFMix output files for local ancestry studies, improving computational efficiency and memory usage.

Convergence of Angiotensin Signaling on Lung Pericyte and Stromal Behaviors

The paper identifies AGTR1 as a selective marker for lung pericytes and shows its role in regulating pericyte behaviors in the airspace microvasculature.

Lifespan analysis of repeat expression reveals age-dependent upregulation of HERV-K in the neurotypical human brain

The paper analyzes repeat expression across the human lifespan in the neurotypical brain, identifying age-dependent upregulation of HERV-K in older adults.

dRFEtools: Dynamic recursive feature elimination for omics

dRFEtools implements dynamic recursive feature elimination to improve prediction accuracy and reduce computational time in omics data analysis.

Genetic and environmental contributions to ancestry differences in gene expression in the human brain

The paper examines how genetic ancestry influences gene expression and DNA methylation in admixed African/Black Americans, showing environmental and genetic factors affect brain disease risk.

Transcriptional and genetic sex differences for schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus

The paper identifies sex differences in schizophrenia across three brain regions using RNA-seq and genotypes, finding sex-specific genes, eQTLs, and transcriptional features.

Variation in TAF1 expression in female carrier induced pluripotent stem cells and human brain ontogeny has implications for adult neostriatum vulnerability in X-linked Dystonia Parkinsonism

This study characterizes TAF1 expression variation in XDP female carriers and human brain ontogeny, identifying age- and region-specific patterns that may explain neostriatum vulnerability in XDP.

Ventral forebrain organoids derived from individuals with schizophrenia recapitulate perturbed striatal gene expression dynamics of the donor's brains

The paper uses ventral forebrain organoids from schizophrenia patients and controls to show accelerated maturation of inhibitory neurons and shared gene expression patterns with postmortem brain tissue.

A single cell trajectory of human archetypal pluripotent stem cell differentiation to trophoblast stem cells reveals induction of endogenous BMP5/7 and GATA3 without transitioning through a naive state

This paper shows that primed human pluripotent stem cells can differentiate to trophoblast stem cells without becoming naive, using specific signaling conditions and revealing a transcriptional network involving BMP5/7 and GATA3.