Xian Adiconis

Single cell eQTL mapping reveals convergent glial-neuronal risk architecture in Parkinson's disease

The paper fine-maps PD GWAS signals across cell types, revealing convergent glial-neuronal risk genes and a shared vesiculopathy network.

Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data

This paper develops computational tools for allelic imbalance analysis using single-nucleus RNA-seq and demonstrates their application in a Parkinson's disease cohort.

The G-protein coupled receptor GPR34 maintains the homeostatic state of microglia and restrains the disease-associated microglial response in an Alzheimers disease model

This study shows that GPR34 maintains microglial homeostasis and limits disease-associated microglial responses in Alzheimer's disease models.

Human brain organoids record the passage of time over multiple years in culture

This study shows human brain organoids can mature over 5 years in culture, transcriptionally aging and retaining memory of time spent in vitro.

A foundational neuronal protein network model unifying multimodal genetic, transcriptional, and proteomic perturbations in schizophrenia.

The paper identifies three neuron-specific schizophrenia protein networks enriched for genetic and transcriptional perturbations and validates their disruption in 22q11.2 deletion carriers.

Systematic evaluation of single-cell multimodal data integration for comprehensive human reference atlas.

This paper benchmarks multimodal single-cell data integration methods to improve kidney reference atlas quality by identifying adaptive states and rare cell types.

Multi-donor human cortical Chimeroids reveal individual susceptibility to neurotoxic triggers

The paper introduces a multi-donor brain organoid model called Chimeroids to study individual genetic variation in neurotoxin susceptibility.

Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types

This study uses single-cell transcriptomics to show that heterochronic parabiosis alters aging signatures in multiple brain cell types, with endothelial cells showing significant transcriptional changes.

The effect of background noise and its removal on the analysis of single-cell expression data

This study evaluates background noise in single-cell RNA-seq data and assesses methods for its removal, finding that CellBender performs best for marker gene detection.

Cell-type specific developmental defects in PTEN-mutant cortical organoids converge on abnormal circuit activity

The paper investigates how PTEN heterozygous mutations affect different cell types in human cortical organoids and shows that these effects lead to abnormal circuit activity regardless of genetic background.

Single cell RNA-seq by mostly-natural sequencing by synthesis

The paper benchmarks a new low-cost sequencing by synthesis method for scRNA-seq, showing comparable results to existing technologies and enabling cost-effective large-scale applications.

Single-cell multiomics atlas of organoid development uncovers longitudinal molecular programs of cellular diversification of the human cerebral cortex

The paper presents a single-cell multiomics atlas of human cortical organoid development, revealing molecular programs of cellular diversification and identifying human-specific gene roles in lineage establishment.

Pluripotent stem cell derived models of neurological diseases reveal early transcriptional heterogeneity

The paper uses scRNA-seq to show increased transcriptional heterogeneity in neurodegenerative disease models, suggesting early regulatory imbalances.

A comprehensive fitness landscape model reveals the evolutionary history and future evolvability of eukaryotic cis-regulatory DNA sequences

The paper constructs a deep transformer model to predict gene expression from cis-regulatory DNA sequences in yeast, revealing evolutionary constraints and evolvability patterns.

Human brain organoids reveal accelerated development of cortical neuron classes as a shared feature of autism risk genes

This study uses human brain organoids to show that ASD risk genes cause accelerated development of specific cortical neuron classes.

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

This study benchmarks 13 scRNA-seq protocols to evaluate their effectiveness in characterizing cell types and states for cell atlas projects.

Single-cell profiles of retinal neurons differing in resilience to injury reveal neuroprotective genes

The paper identifies neuroprotective genes in retinal ganglion cells by analyzing their resilience to injury using single-cell RNA-seq and functional assays.

Single-cell transcriptomics of the aged mouse brain reveals convergent, divergent and unique aging signatures

This study uses single-cell transcriptomics to analyze aged mouse brains, identifying cell-type-specific aging signatures and highlighting molecular processes like ribosomal biogenesis.

Systematic comparative analysis of single cell RNA-sequencing methods

Seven single-cell and single-nucleus protocols run side by side on the same cell lines, PBMCs and mouse cortex, analysed through one pipeline: 10x Chromium led the high-throughput methods.

Comparative analysis highlights variable genome content of wheat rusts and divergence of the mating loci.

The paper compares the genomes of three wheat rust pathogens to identify gene content variation and divergence in mating loci, highlighting differences in genome size, heterozygosity, and effector expression.