Michael R. Fiorini

Transcriptional pathways of definitive ALS genes implicate novel disease-associated target genes

The paper identifies novel disease-associated target genes by analyzing transcriptional pathways linked to definitive ALS genes using RNA sequencing and single-nuclei transcriptomics.

Microglia from Friedreich Ataxia patients are intrinsically primed for neuroinflammation

This study shows that microglia from Friedreich Ataxia patients have an intrinsic pro-inflammatory phenotype due to FXN deficiency, identifying potential therapeutic targets.

Transcriptome-based screening in TARDBP/TDP-43 knock-in motor neurons identifies the NEDD8-activating enzyme inhibitor MLN4924

The paper identifies MLN4924 as a compound that improves cell viability in TDP-43 mutant motor neurons by targeting NEDD8-activating enzyme.

Ensemblex: an accuracy-weighted ensemble genetic demultiplexing framework for population-scale scRNAseq sample pooling

Ensemblex improves accuracy in genetic demultiplexing of pooled scRNA-seq samples by combining four algorithms with accuracy weighting.

Segpy: a streamlined, user-friendly pipeline for variant segregation analysis

Segpy is a user-friendly pipeline for variant segregation analysis that supports single-family, multi-family, and population-based datasets to evaluate genetic variant co-segregation with disease.

Interpretable machine learning classifiers implicate GPC6 in Parkinson's disease from single-nuclei midbrain transcriptomes

The paper uses machine learning on single-nuclei RNA sequencing data to identify GPC6 as a genetic risk factor for Parkinson's disease.

ScRNAbox: Empowering Single-Cell RNA Sequencing on High Performance Computing Systems

scRNAbox provides an HPC-friendly scRNA-seq analysis pipeline with quality control, integration, clustering, annotation, and differential expression analysis.

Evaluating the utility of REVEL and CADD for interpreting variants in amyotrophic lateral sclerosis genes

This study evaluates REVEL and CADD in predicting pathogenic variants in ALS-associated genes, finding REVEL has a clear threshold while CADD lacks accuracy for variants of uncertain significance.

Sex-stratified RNA-seq analysis reveals traumatic brain injury-induced transcriptional changes in the female hippocampus conducive to dementia

This study performs sex-stratified RNA-seq analysis of TBI-affected brain regions and identifies female-specific gene modules linked to dementia in TBI donors.