Matthew Jensen

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

A global view of human centromere variation and evolution

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

Quantifying the impact of genetic mutations on enhancer dynamics

The paper quantifies how genetic mutations affect enhancer activity and gene expression using a novel method and identifies TF-specific regulatory programs and enhancer-gene relationships.

Genetic modifiers and ascertainment drive variable expressivity of complex disorders

The paper examines how modifier variants affect clinical outcomes in individuals with primary disease variants, showing context-dependent phenotypic associations and synergistic interactions.

Complex genetic variation in nearly complete human genomes

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

Digital phenotyping from wearables using AI characterizes psychiatric disorders and identifies genetic associations

This paper uses wearable data and AI to identify genetic associations with psychiatric disorders by creating intermediate phenotypes from continuous physiological features.

A comprehensive catalog of 3D genome organization in diverse human genomes facilitates understanding of the impact of structural variation on chromatin structure

The paper develops a Hi-C analysis pipeline to catalog TADs and loops in human genomes and quantifies the impact of SVs on chromatin structure and gene expression.

Homomorphic Encryption: An Application to Polygenic Risk Scores

This paper applies fully homomorphic encryption to compute polygenic risk scores securely, showing high accuracy and feasibility with synthetic and real data.

Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

Single-cell genomics and regulatory networks for 388 human brains

The paper processes single-nuclei multi-omics data from 388 human brains to identify regulatory elements and build cell-type networks, revealing changes in aging and neuropsychiatric disorders.

Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex

The paper generates a molecular neuroanatomical map of the human prefrontal cortex using spatial transcriptomics and single nucleus RNA-sequencing, revealing novel spatial domains and cell-cell interactions linked to psychiatric disorders.

Assortative mating and parental genetic relatedness drive the pathogenicity of variably expressive variants

The paper examines how assortative mating and parental genetic relatedness influence the pathogenicity of variably expressive variants in neurodevelopmental disorders.

Functional assessment of the "two-hit" model for neurodevelopmental defects in Drosophila and X. laevis

The paper tests a 'two-hit' model for neurodevelopmental defects by examining interactions between 16p12.1 homologs and 'second-hit' genes in Drosophila and Xenopus laevis, finding genetic interactions in 63% of tested pairs.

Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion

The paper investigates how gene expression changes from a 16p12.1 deletion and second-hit variants contribute to phenotypic variability in developmental delay.

The chromatin remodeler ISWI acts during Drosophila development to regulate adult sleep

The paper identifies ISWI as a chromatin remodeler required for adult sleep in Drosophila, with distinct developmental roles in sleep and other behaviors.

Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development

The paper systematically analyzes non-neuronal defects in Drosophila models of pathogenic copy-number variant genes, identifying developmental issues in multiple tissues and signaling pathways.

Gene discoveries in autism are biased towards comorbidity with intellectual disability

The paper identifies genetic factors in autism that contribute to comorbidity with intellectual disability, showing increased risk for ID with specific variants.

NCBP2 modulates neurodevelopmental defects of the 3q29 deletion in Drosophila and X. laevis models

This study identifies NCBP2 as a key modifier gene in the 3q29 deletion, showing it enhances developmental defects through disrupted apoptosis and cell cycle mechanisms in Drosophila and Xenopus models.

A machine-learning approach for accurate detection of copy-number variants from exome sequencing

CN-Learn improves CNV detection from exome sequencing by integrating multiple callers and machine learning, achieving higher precision and recall than individual methods or Venn diagram approaches.

An interaction-based model for neuropsychiatric features of copy-number variants

The paper proposes an interaction-based model to explain neuropsychiatric features of copy-number variants by considering gene interactions within CNV regions.

Rare variants in the genetic background modulate the expressivity of neurodevelopmental disorders

The paper shows that rare secondary mutations in functionally intolerant genes affect the expressivity of neurodevelopmental disorders in individuals with primary mutations.

Pervasive epistasis modulates neurodevelopmental defects of the autism-associated 16p11.2 deletion

The paper identifies genetic interactions within the 16p11.2 deletion that modulate neurodevelopmental phenotypes in Drosophila and links these interactions to human brain networks.

Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity

This study introduces two novel metrics to assess coverage uniformity in whole exome sequencing data, revealing local and global non-uniformity across platforms and genomic regions.