Panos Roussos

Fast Probabilistic Whitening Transformation for Ultra-High Dimensional Genetic Data

The paper introduces a probabilistic whitening transformation for high-dimensional genetic data, showing it is faster and more accurate than existing methods for imputing z-statistics and identifying genetic regulatory signals.

Human Choroid Plexus Organoids Progress to Postnatal-like Maturation and Reveal a Closing Window of Developmental Plasticity

This study uses single-cell RNA sequencing to track the maturation of human choroid plexus organoids and identifies a stage-dependent window of developmental plasticity.

Cross-source proteogenomic profiling of human microglia reveals a conserved core membrane protein and HERV signature

This study compares transcriptome and proteome profiles of three microglia sources, identifying shared surface markers and HERV expression patterns, suggesting MDMi as a practical model for functional studies.

GROMTools: scalable individual-level GReX imputation for mega-biobank-scale cohorts

GROMTools, a sparse-weight C++/R engine streaming PLINK2 genotypes, reproduces PrediXcan and PLINK2 GReX imputations with about 100-fold less CPU time and 33-fold less peak memory.

Fast, flexible analysis of differences in cellular composition with crumblr

Crumblr is a statistical method for analyzing changes in cell type composition across studies, showing increased power over existing methods in simulations and applied to multiple single-cell RNA-seq datasets.

Efficient differential expression analysis of large-scale single cell transcriptomics data using dreamlet

The paper introduces dreamlet, an R package for efficient differential expression analysis of large-scale single-cell transcriptomics data, showing improved speed and memory usage compared to existing methods.

Single-nucleus transcriptome-wide association study of human brain disorders

This study performs a single-nucleus transcriptome-wide association study to identify gene-trait associations in brain disorders, revealing cell-type-specific genetic regulation and ancestry-specific patterns.

Single-Nucleus Atlas of Cell-Type Specific Genetic Regulation in the Human Brain

The paper constructs a single-nucleus atlas of genetic regulation in the human brain, identifying cell-type-specific regulatory effects and disease-associated genes.

Plasticity of Human Microglia and Brain Perivascular Macrophages in Aging and Alzheimer's Disease

The paper profiles human myeloid cells across aging and Alzheimer's disease, identifies AD-associated changes, and links GPNMB to neuroprotection via TREM2.

Spatialproteomics - an interoperable toolbox for analyzing highly multiplexed fluorescence image data

The paper introduces spatialproteomics, a Python toolbox for analyzing highly multiplexed fluorescence images, demonstrating its use on lymph node and lymphoma data.

Gene regulatory programs of cognitive resilience and pathogenesis in Alzheimer's disease

The paper identifies three gene regulatory states associated with cognitive resilience and pathogenesis in Alzheimer's disease using single-cell data from the dorsolateral prefrontal cortex.

Combinatorial effects of gene dosage, polygenic background and environment on complex traits

The paper examines how gene dosage, polygenic background, and environment influence complex traits like height and BMI using large-scale data from multiple cohorts.

Early microglial priming in Alzheimer's disease revealed by ME-seq

The paper introduces ME-seq, a technology that profiles DNA methylation, gene expression, and chromatin accessibility in single nuclei, revealing early microglial priming in Alzheimer's disease.

Single-cell atlas of transcriptomic vulnerability across multiple neurodegenerative and neuropsychiatric diseases

The paper constructs a single-cell transcriptomic atlas of the human dorsolateral prefrontal cortex across neurodegenerative and neuropsychiatric diseases, revealing shared and distinct molecular mechanisms.

Cell-type-resolved NRXN1 isoforms across human brain tissues and hiPSC cortical organoids

The paper develops an integrative sequencing strategy to catalog NRXN1 isoforms across human brain tissues and hiPSC organoids, revealing cell-type-specific splicing patterns and therapeutic potential of ASO targeting.

A Transcriptomic Roadmap of Parkinson's Disease Progression at Single Cell Resolution

This study creates a single-nucleus transcriptomic atlas of Parkinson's disease progression, identifying cell-type-specific gene expression changes and linking them to genetic risk factors and disease stages.

ZBTB7A regulates MDD-specific chromatin signatures and astrocyte-mediated stress vulnerability in orbitofrontal cortex

The paper identifies ZBTB7A as a key regulator of MDD-specific chromatin signatures and astrocyte-mediated stress vulnerability in the orbitofrontal cortex.

Dopaminoceptive D1 and D2 neurons in ventral hippocampus arbitrate approach and avoidance in anxiety

This study identifies D1 and D2 dopamine receptor-expressing neurons in the mouse ventral hippocampus and shows they mediate opposing approach/avoidance behaviors during anxiety-related tasks.

Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing

The paper presents a long-read RNA-seq atlas of microglia isoforms, identifying novel isoforms and their associations with genetic risk loci in Alzheimer's and Parkinson's disease.

Cholesterol Dysregulation in APOE4 Astrocytes Promotes α-Synuclein Pathology in miBrains, a Human Brain Tissue Model

This study develops a human brain tissue model (miBrain) to show that APOE4 astrocytes with cholesterol dysregulation promote α-synuclein pathology through endolysosomal dysfunction.

Modeling diagnostic code dropout of schizophrenia in electronic health records improves phenotypic data quality and cross-ancestry transferability of polygenic scores

This paper models diagnostic code dropout in EHR data to improve phenotyping for schizophrenia, enhancing polygenic score transferability across ancestries.

A genetically based computational drug repurposing framework for rapid identification of candidate compounds: application to COVID-19

This paper presents a computational drug repurposing framework that identifies FDA-approved drugs for COVID-19 by integrating genetic expression data and EMR data, finding four compounds with protective effects in validation.

Integrating GWAS and Transcriptomic Data Using PrediXcan and Multimodal Deep Learning Reveals Genetic Basis and Drug Repositioning Opportunities for Alzheimer's Disease

This paper integrates GWAS and transcriptomic data using PrediXcan and a deep learning model to identify genetic factors and drug candidates for Alzheimer's disease.

Comprehensive profiling of small RNAs and their changes and linkages to mRNAs in schizophrenia and bipolar disorder

This study profiles small RNAs in schizophrenia and bipolar disorder, finding altered sncRNA abundance and links to accelerated aging and key biological processes.

Transcriptome and chromatin accessibility landscapes across 25 distinct human brain regions expand the susceptibility gene set for neuropsychiatric disorders

The paper maps transcriptomic and chromatin accessibility profiles across 25 human brain regions and identifies genes linked to neuropsychiatric disorder risk.

A lifespan transcriptomic atlas of the human prefrontal cortex at single-cell resolution

This study creates a single-nucleus transcriptomic atlas of the human DLPFC across the lifespan, revealing three transcriptomic phases and ten age-related trajectories linked to neurodevelopmental and neurodegenerative disease risk.

Transcriptomic signatures of nine high-risk neuropsychiatric copy number variants in human brain cells

The paper analyzes transcriptomic differences in human brain cells with nine high-risk neuropsychiatric CNVs compared to non-carriers, finding widespread gene expression disruptions and shared functional pathways.

A conserved cell-type gradient across the human mediodorsal and paraventricular thalamus

The paper identifies a conserved excitatory neuron gradient in human mediodorsal thalamus using single-nucleus and spatial transcriptomics, linking it to psychiatric disorder risk.

Diversity and Scale: Genetic Architecture of 2,068 Traits in the VA Million Veteran Program

Population-stratified GWAS of 2,068 traits in 635,969 Million Veteran Program participants, 29% genetically non-European, yields 98,485 associations and 57,601 fine-mapped signals with largely shared cross-population architecture.

A public resource of single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease

The paper provides a public resource of single nucleus RNA sequencing data and multiscale networks from Alzheimer's disease and non-disease individuals, linking genetic variants to molecular features and revealing novel disease biology.