Ali Mortazavi

LEUTX mediates amplification of DUX4 signaling and aberrant myotube differentiation in facioscapulohumeral muscular dystrophy

This study identifies LEUTX as a key amplifier of DUX4 signaling in FSHD, showing its role in disrupting myotube differentiation and promoting aberrant gene expression.

Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation

The paper uses hybrid crosses to analyze regulatory variation in mouse tissues, finding cell-type-specific trans-acting effects and highlighting the limitations of bulk tissue analysis.

Single-Cell Genomics Decontamination with CellSweep

CellSweep removes technical contamination from single-cell genomics data, improving accuracy in downstream analysis.

Dogme: A nextflow pipeline for reprocessing nanopore RNA and DNA modifications

Dogme is a Nextflow pipeline that automates reprocessing of ONT data for modification detection and transcript quantification, showing reproducible results across biological replicates.

Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains captures global and local expression variation

The paper characterizes transcriptomes across 8 tissues in 8 mouse strains to identify expression variation linked to genetic differences and phenotypic traits.

Genome-wide analysis of FSHD cell lines using Nanopore sequencing reveals allele-specific differences at DUX4 target genes and complex repeats

Long-read sequencing transcriptome quantification with lr-kallisto

The paper develops lr-kallisto, a tool for accurate long-read transcriptome quantification using ONT data, showing improved results with exome capture.

Determining gene specificity from multivariate single-cell RNA sequencing data

The paper introduces ember, an entropy-based framework to assess gene specificity in single-cell RNA sequencing data, revealing unexpected patterns in gene expression across tissues and mouse strains.

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states

The paper identifies regulatory programs in postnatal mouse development using single-nucleus data, revealing cell-type-specific and common regulatory topics across multiple tissues.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

Within-subject changes in DNA-methylome profile identify individual signatures of early-life adversity, with a potential to predict neuropsychiatric outcome.

This paper identifies DNA methylation changes in children linked to early-life adversity and shows their correlation with later executive function, with sex-dependent effects.

Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD

The paper introduces Topyfic, a reproducible LDA method, to identify cellular programs in single-cell data and shows sex-specific differences in microglial activation in Alzheimer's disease mouse models.

C5aR1 antagonism suppresses inflammatory glial gene expression and alters cellular signaling in an aggressive Alzheimer's model

Pharmacologic inhibition of C5aR1 suppresses disease-enhancing processes and promotes disease mitigating pathways in an aggressive model of Alzheimer's disease.

L-GIREMI uncovers RNA editing sites in long-read RNA-seq

L-GIREMI detects RNA editing sites in long-read RNA-seq with high accuracy by addressing sequencing errors and biases.

PyWGCNA: A Python package for weighted gene co-expression network analysis

PyWGCNA is a Python package for weighted gene co-expression network analysis, enabling module identification and comparison in RNA-seq data.

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

The ENCODE Uniform Analysis Pipelines

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

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.

A Trem2*R47H mouse model without cryptic splicing drives age- and disease-dependent tissue damage and synaptic loss in response to plaques

Analysis of alternative polyadenylation from long-read or short-read RNA-seq with LAPA

LAPA analyzes alternative polyadenylation from long-read and short-read RNA-seq data, showing improved detection and revealing gene expression links to polyadenylation changes.

Engineered SMCHD1 and D4Z4 mutations reveal roles of D4Z4 heterochromatin disruption and feedforward DUX4 network activation in FSHD

The paper uses engineered human myoblasts to show that D4Z4 heterochromatin disruption and DUX4 network activation are key in FSHD.

C5aR1 antagonism alters microglial polarization and mitigates disease progression in a mouse model of Alzheimers disease

The paper shows that C5aR1 antagonism reduces amyloid load and dystrophic neurites in a mouse model of Alzheimer's disease, shifting microglial polarization toward a neuroprotective phenotype.

Modulation of C5a-C5aR1 signaling alters the dynamics of AD progression

This study shows that modulating C5a-C5aR1 signaling in Alzheimer's disease models affects cognitive decline and gene expression related to inflammation and astrocyte activation.

Integrative analysis of Hydra head regeneration reveals actions of conserved signaling pathways and transposable elements

This study uses multi-omics data to identify signaling pathways and transposable elements involved in Hydra head regeneration.

Uncovering the mesendoderm gene regulatory network through multi-omic data integration

The paper builds a genome-scale gene regulatory network for vertebrate mesendoderm development using multi-omic data integration and validates novel transcription factor interactions.

A catalog of transcription start sites across 115 human tissue and cell types

The paper generates a catalog of experimentally validated transcription start sites (TSSs) across 115 human tissues and cell types, updating TSS annotations for 20% of GENCODE genes and identifying new GWAS candidate genes.

Systematic phenotyping and characterization of the 3xTg-AD mouse model of Alzheimer's Disease

This paper characterizes the 3xTg-AD mouse model of Alzheimer's Disease across its lifespan and compares it with the 5xFAD model to assess pathology and model drift.

Single-Cell transcriptional changes in hypothalamic CRH-expressing neurons after early-life adversity inform enduring alterations in responses to stress

This study uses single-cell RNA sequencing to identify lasting transcriptional changes in hypothalamic CRH-expressing neurons after early-life adversity, linking these changes to long-term stress responses.

Systematic Phenotyping and Characterization of the 5xFAD mouse model of Alzheimer's Disease

The paper performs a comprehensive phenotypic analysis of the 5xFAD mouse model across its lifespan, identifying novel age-related pathological features.