Stephen A. Murray

Svep1 orchestrates distal airway patterning and alveolar differentiation in murine lung development

This study shows that Svep1 is essential for proper lung development by regulating airway branching and alveolar differentiation in mice.

Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes

The paper develops STEAM, an evolution-augmented deep learning model, to predict mammalian enhancer landscapes across species using comparative genomics and single-cell data.

Splicing of ultraconserved poison exons controls mitotic fidelity and stem cell viability

This study shows that ultraconserved poison exons regulate mitotic splicing fidelity and stem cell viability by controlling SR protein levels and splicing networks.

Novel mouse reporter models for the detection of genome editing events in vivo

The paper develops new mouse reporter models to detect genome editing events in vivo, including gene repair and CRISPR indels, and A-base editor activity.

Data-driven prioritization of mouse strains for improved preclinical modeling of rare and common disease

This paper introduces a genomic framework to prioritize mouse strains for preclinical disease modeling, showing high sensitivity in predicting strain vulnerability to diseases.

Modeling patient variants of Cnot1 and Cdc42bpb results in distinct forms of congenital diaphragmatic hernia in mice

The paper validates two genes, Cnot1 and Cdc42bpb, as causes of congenital diaphragmatic hernia in mice using patient-specific variants and shows distinct hernia phenotypes.

Zfp750 prevents oral adhesions and promotes temporary epithelial fusions

The paper investigates the role of Zfp750 in periderm development and orofacial cleft risk by analyzing genetic variants and mouse models.

Efficient in vivo mammalian neuron editing using peptide-mediated CRISPR enzyme delivery

This study develops Neuro-PERC, a peptide-mediated CRISPR delivery method, enabling efficient in vivo neuronal editing in mice and pigs, and extending survival in a Huntington's disease model.

Generation and Characterization of a Knockout Mouse of an Enhancer of EBF3

The paper generates a mouse model with a deletion in an enhancer of EBF3, showing reduced Ebf3 expression and sex-specific behavioral and phenotypic differences.

Caspase-11 drives macrophage hyperinflammation in models of Polg-related mitochondrial disease

This study identifies caspase-11 as a driver of macrophage hyperinflammation in Polg-related mitochondrial disease models, linking IFN-I signaling to exacerbated infection outcomes.

The contribution of de novo coding mutations to meningomyelocele

The paper identifies de novo mutations contributing to meningomyelocele risk by analyzing trios and finding damaging mutations in 22.3% of cases.

The spectrum of gene intolerance to variation: Insights from a rare disease cohort

The paper analyzes gene intolerance to loss-of-function variation in a rare disease cohort to identify patterns in gene expression, sequence features, and disease associations across FUSIL categories.

A Comprehensive Atlas of AAV Tropism in the Mouse

This paper maps the tissue tropism of ten AAV serotypes in mice after systemic delivery, identifying liver preference and unexpected transduction in adrenals, testes, and ovaries.

The ClinGen Syndromic Disorders Gene Curation Expert Panel: Assessing the Clinical Validity of 111 Gene-Disease Relationships

The paper curates 111 gene-disease relationships for syndromic disorders, classifying their clinical validity and identifying gaps in knowledge.

Alternating hemiplegia of childhood associated mutations in Atp1a3 reveal diverse neurological alterations in mice.

This study investigates the effects of two common Atp1a3 mutations in mice, revealing distinct neurological phenotypes and potential therapeutic avenues for alternating hemiplegia of childhood.

A frameshift mutation in the murine Prkra gene causes dystonia and exhibits abnormal cerebellar development and reduced eIF2α phosphorylation.

This study investigates the effects of a Prkra frameshift mutation in mice, showing reduced eIF2 phosphorylation and cerebellar abnormalities linked to dystonia.

Lethal phenotypes in Mendelian disorders

This paper curates human essential genes based on lethality in Mendelian disorders and explores their relationships with constraint metrics and viability data.

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

12.4 million single-nucleus transcriptomes from 83 staged mouse embryos (E8 to P0) yield 190 cell types, a zygote-to-pup cell-type tree, and rapid postnatal transcriptional shifts.

DISCOVERY AND VALIDATION OF GENES DRIVING DRUG-INTAKE AND RELATED BEHAVIORAL TRAITS IN MICE

This study identifies and validates 22 genes that drive drug intake and related behavioral traits in mice through knockout screening and behavioral assays.

Whole genome analysis for 163 guide RNAs in Cas9 edited mice reveals minimal off-target activity

The paper analyzes whole-genome sequencing data from Cas9-edited mice to assess off-target mutagenesis, finding minimal off-target activity across 163 guide RNAs.

Spatial transcriptome profiling uncovers metabolic regulation of left-right patterning

The paper identifies metabolic regulation in left-right patterning using spatial transcriptome data, linking glycolysis and Bmp7 to heart and gut looping.

Mendelian gene identification through mouse embryo viability screening

The paper identifies novel Mendelian genes by analyzing mouse embryo lethality and linking them to human disease phenotypes and genetic variants.

Efficient in vivo neuronal genome editing in the mouse brain using nanocapsules containing CRISPR-Cas9 ribonucleoproteins

This study develops non-viral nanocapsules for in vivo CRISPR-Cas9 delivery to edit neuronal DNA in mice, achieving efficient and safe genome editing in specific neuron types.

MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses

MusMorph provides standardized mouse morphology data for meta-analyses, including craniofacial and brain structures across developmental stages and genotypes.

Shapes and Genescapes: Mapping Multivariate Phenotype-Biological Process Associations for Craniofacial Shape

The paper develops a process-centered multivariate genotype-phenotype approach to analyze craniofacial shape variation in mice, linking gene sets to shape axes and predicting phenotypic effects beyond shape.

Facial shape and allometry quantitative trait locus intervals in the Diversity Outbred mouse are enriched for known skeletal and facial development genes

This study identifies 37 QTL for facial shape in DO mice, finding enrichment for genes involved in skeletal and facial development, despite small individual effects.

Human and mouse essentiality screens as a resource for disease gene discovery

The paper integrates gene essentiality data from human and mouse screens to classify genes into FUSIL categories, identifying developmental lethal genes associated with rare diseases.

Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis

This study identifies insertion sites in 40 transgenic mouse lines, revealing frequent disruptions of endogenous genes and structural variations.

Noninvasive sleep monitoring in large-scale screening of knock-out mice reveals novel sleep-related genes

The paper identifies 122 novel sleep-related genes from a large-scale knockout mouse study using non-invasive sleep monitoring.