Jesse A Gillis

The paper maps DNA damage response states in aging mouse brains, revealing opposing neuronal and vascular spatial patterns linked to genome maintenance.

The paper identifies a Pax6 interneuron subclass in mice through cross-species transcriptomic analysis and highlights primate-specific divergence in the Sncg subclass.

The paper evaluates doublet detection methods for identifying segmentation errors in spatial transcriptomics by simulating molecular admixture between neighboring cells.

This paper evaluates single-cell foundation models using an unsupervised framework that assesses their robustness to nuisance perturbations, revealing significant differences in structural stability between models ranked similarly by standard benchmarks.

This study identifies two distinct subgroups of 16p11.2 deletion mice with different seizure susceptibility, circuit activity, brain structure, and gene expression profiles.

Reprocessing nine human brain datasets (2,157,582 cells, 156 donors, GW6 to adulthood) under one marker-based taxonomy yields 35 replicable cell types with cell type-specific timing of adult-like maturation.

The paper evaluates cluster replicability across two mouse brain atlases using single-cell and single-nucleus RNA sequencing, identifying 2009 reciprocally matched clusters with consistent spatial and gene expression patterns.

This paper reports on the fourth CAFA challenge, showing improvements in Gene Ontology term prediction but highlighting challenges in new evaluation settings.

The paper shows transcriptomic individuality in genetically identical armadillo quadruplets is driven by monocyte lineage expansion and stable gene expression differences.

The paper compiles a large transcriptomic dataset of neocortical development and uses joint matrix decomposition to identify conserved transcriptome dynamics across mammals and developmental stages.

The paper shows a neofunctionalized gene in Solanaceae plants became a flowering antagonist, influencing adaptation across species and environments.

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

XC-ID identifies the active X chromosome in single-cell RNA-seq data with high accuracy, revealing dosage-compensation patterns.

This study uses single-cell RNA-seq to identify stem cell regulators in maize and Arabidopsis, revealing genes linked to yield traits and shoot development.

The paper evaluates computational methods for predicting cell type-specific enhancers in the mouse cortex using in vivo validation data and finds that open chromatin and sequence models improve prediction accuracy.

The paper develops a cell type-agnostic model to predict developmental age from transcriptomes, achieving high accuracy across human brain datasets and organoids.

The paper identifies NEUROG2's role in regulating a human-specific gene regulatory program in neural progenitor cells through transcriptomic analysis of knock-in organoids.

The paper introduces CellREADR, an RNA-based technology for targeting and manipulating animal cells by coupling RNA sensing with effector protein translation, and provides a detailed experimental protocol for its implementation.

The paper identifies coordinated gene expression between spatially adjacent cells across multiple brain datasets, revealing biological processes and potential therapeutic targets.

The paper uses pan-genomics and genome editing in Solanum to show that paralog diversification hinders genotype-phenotype predictability in crop domestication.

The paper investigates convergent evolution of plant prickles, finding that mutations in a cytokinin gene repeatedly cause prickle loss across species.

Dune improves replicability of cell type discovery in scRNA-Seq by optimizing the trade-off between cluster resolution and cross-dataset consistency.

Longitudinal gene expression in identical armadillo quadruplets reveals a major role for developmental stochasticity.

The paper measures XCI ratios across 9 mammalian species and finds stochasticity, not genetics, primarily explains XCI variability.

This study uses single nucleus transcriptomics to compare human and non-human primate cortical tissues, identifying human-specific gene expression patterns and their potential functional roles.

The paper quantifies how well neural organoids preserve primary tissue co-expression, showing they can achieve high fidelity in recapitulating fetal brain development.

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

The paper shows Rad53 binds to gene promoters under replication stress, influencing gene expression and coordinating replication with transcription.

The paper benchmarks neuronal cell-type annotation in scATAC-seq data using marker genes and introduces a deep learning model to predict chromatin accessibility from DNA sequence.

The paper creates a high-density chromatin interaction network across species by integrating 3C experiments, showing improved prediction of coexpression and eQTL for long-range and trans chromatin contacts.