Matthew T. Maurano

Genome writing and Targeted Delivery of the NKX6-3/ANK1 gene cluster and its Type 2 Diabetes GWAS Variants to Human iPSCs

This paper introduces a method to deliver synthetic haplotypes containing T2D GWAS variants to hiPSCs to study their functional impact on differentiation.

Iterative improvement of deep learning models using synthetic regulatory genomics

The paper fine-tunes the Enformer model using synthetic regulatory sequences to improve its predictive performance on non-reference sequences.

Genome writing to dissect consequences of SVA retrotransposon disease X-Linked Dystonia Parkinsonism

The paper genomically rewrote a mouse Taf1 allele with a human XDP patient-derived TAF1 allele, revealing that intronic SVA retrotransposons reduce TAF1 levels and cause neurodegeneration.

Synthetic genomic dissection of enhancer context sensitivity and synergy

The paper identifies context-dependent enhancer synergy in mouse embryonic stem cells, showing that enhancers can significantly boost neighboring DHS activity and that this synergy depends on distance and specific transcription factor sequences.

Genomic context sensitizes regulatory elements to genetic disruption

The paper investigates how genomic context affects enhancer function by analyzing the murine Igf2/H19 locus and shows that regulatory elements depend on their native surroundings.

Structural characterization of a polymorphic repeat at the CACNA1C schizophrenia locus

The paper characterizes a VNTR in CACNA1C associated with schizophrenia, showing linkage to risk variants and reduced gene expression.

Mouse genomic rewriting and tailoring: synthetic Trp53 and humanized ACE2

This paper introduces mSwAP-In, a method for efficient genome rewriting in mouse embryonic stem cells, demonstrating its use for Trp53 and ACE2 locus modifications to create more accurate disease models.

Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus

The paper uses synthetic regulatory genomics to study Sox2 expression in mESCs, finding that some enhancer regions are context-dependent and can enhance core regulatory elements.

Genomic analysis of a synthetic reversed sequence reveals default chromatin states in yeast and mammalian cells

The paper introduces a reversed synthetic locus into yeast and mouse genomes to study default chromatin states, finding widespread transcription in yeast but not in mouse.

Genomic context sensitivity of insulator function

The paper investigates how genomic context affects CTCF insulator function by analyzing reporter activity across various genomic configurations.

An Effector Index to Predict Causal Genes at GWAS Loci

The paper introduces the Effector Index, an algorithm to predict causal genes at GWAS loci using genomic features, achieving 85% AUC in type 2 diabetes validation.

Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation

The paper uses synthetic genomic reconstitution to study Hox cluster regulation, finding that distal enhancers are required for full transcriptional output while chromatin remodeling can occur without them.

Tissue context determines the penetrance of regulatory DNA variation

The paper quantifies how tissue context influences the effect of regulatory DNA variants on transcription factor activity using allelic accessibility maps in mice.

De novo assembly, delivery and expression of a 101 kb human gene in mouse cells

The paper describes a pipeline for de novo assembly, delivery, and expression of a 101 kb human gene in mouse cells, demonstrating functional evaluation of a full-length gene.

Big DNA as a tool to dissect an age-related macular degeneration-associated haplotype

The paper introduces a method to assemble synthetic haplotypes for functional analysis of AMD-associated variants, demonstrating its application to the 10q26 risk region.

An Atlas of Human and Murine Genetic Influences on Osteoporosis

This paper identifies 518 genetic loci associated with bone mineral density and fracture risk, validates causal genes in mice, and provides insights for osteoporosis drug development.