M. Ryan Corces

Comprehensive adjudication identifies 111 high-confidence loci for Alzheimer's disease and related dementias

The paper systematically adjudicates genetic evidence for Alzheimer's disease and related dementias, identifying 111 high-confidence loci through a tiered framework applied to large-scale genome-wide studies.

Tau reduction counteracts transcriptomic and behavioral abnormalities in an Alzheimer amyloid model

This study shows that reducing tau mitigates transcriptomic and behavioral issues in an Alzheimer's model without affecting amyloid levels.

APOE4 Drives Uniquely Dysfunctional Human Microglial States in Alzheimer's Disease

This study identifies APOE4/4-driven dysfunctional microglial states in Alzheimer's disease through multiomic analysis, revealing shifts toward terminal states with metabolic disruption and inflammatory signaling.

Massive-scale single-nucleus multi-omics identifies novel rare noncoding drivers of Parkinson's disease

The paper identifies rare noncoding variants associated with Parkinson's disease using multi-omic data from over 3.3 million nuclei.

Epiregulon: Inference of single-cell transcription factor activity to predict drug response and drivers of cell state

Epiregulon infers single-cell TF activity using ATAC-seq and RNA-seq to predict drug response and identify drivers of cell state.

CHOIR improves significance-based detection of cell types and states from single-cell data

CHOIR improves cell type and state detection in single-cell data by using statistical inference to assess clustering results, outperforming existing methods across multiple data types.

Systematic Identification of Post-Transcriptional Regulatory Modules

The paper systematically identifies post-transcriptional regulatory modules by integrating multimodal data on RBP interactions and functions.

Single-cell Spatial Proteomic Imaging for Human Neuropathology

This study uses spatial proteomics to analyze human brain tissues and identifies proteopathies and cell interactions in Alzheimer's disease.

Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation

The paper investigates how Polycomb-mediated genome architecture facilitates long-range H3K27 methylation spreading in ESCs and iPSCs, revealing RNA-dependent DNA looping and developmental gene roles in chromatin organization.

PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

PEPATAC is an ATAC-seq analysis pipeline that improves speed and accuracy through serial mitochondrial genome alignment, providing standardized outputs for downstream analysis.

Complement factor C1q mediates chronic neuron loss and inflammation post-brain injury

This study shows that C1q mediates chronic neuron loss and inflammation after brain injury by targeting the corticothalamic circuit in mice.

Clonal inactivation of telomerase promotes accelerated stem cell differentiation

This study shows that TERT inactivation accelerates stem cell differentiation and disrupts clone formation, independent of telomere elongation, and links TERT to MYC activity.

ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis

ArchR, an HDF5-backed R suite for end-to-end scATAC-seq analysis, outpaces SnapATAC and Signac and processes over 1.2 million simulated cells within 8 h on a laptop.

Recruitment of CTCF to an Fto enhancer is responsible for transgenerational inheritance of obesity

This study shows that BPA exposure in pregnant mice leads to transgenerational obesity via CTCF binding at Fto enhancers, which affects neural stem cells and AgRP/NPY neurons.

Single-cell epigenomic identification of inherited risk loci in Alzheimer's and Parkinson's disease

The paper uses single-cell epigenomic data to identify functional SNPs associated with Alzheimer's and Parkinson's disease, revealing novel gene-disease associations and regulatory mechanisms.

A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis

This study identifies a primed chromatin state in oligodendroglia that facilitates rapid activation of immune gene programs in multiple sclerosis.

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

The paper uses scATAC-seq to analyze chromatin accessibility in immune cell development and tumor microenvironments, identifying regulatory elements and trajectories associated with cell differentiation and therapy response.

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA

EMBLEM uses mitochondrial DNA mutations in ATAC-seq data to track cell lineage with high sensitivity and specificity in acute myeloid leukemia.

Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements

This paper uses HiChIP to map enhancer-promoter interactions in primary human cells, linking disease-associated DNA variants to their target genes.

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

Omni-ATAC improves ATAC-seq by reducing background noise and enabling analysis of frozen tissues, revealing disease-associated DNA element activities in human brain structures.

Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation

The paper uses single-cell chromatin accessibility to map the continuous regulatory variation in human hematopoietic differentiation and identifies epigenomic heterogeneity within cell populations.