Jonathan L. Sebat

Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats

The paper identifies non-SNP variants as significant regulators of gene expression and addiction-related traits in HS rats using joint cis-eQTL analysis.

Determinants of functional burden pleiotropy and gene dosage responses across human traits

The paper develops FunBurd to analyze gene dosage effects on 43 traits in UK-Biobank, finding pleiotropy and non-monotonic responses linked to genetic constraint and brain-specific mechanisms.

Combinatorial effects of gene dosage, polygenic background and environment on complex traits

The paper examines how gene dosage, polygenic background, and environment influence complex traits like height and BMI using large-scale data from multiple cohorts.

Long-Read Genome Sequencing Improves Detection and Functional Interpretation of Structural and Repeat Variants in Autism

This study shows that long-read genome sequencing improves detection of structural and repeat variants in autism and links them to functional consequences.

Effects of gene dosage on cognitive ability: A function-based association study across brain and non-brain processes

The paper identifies a CNV duplication associated with higher cognitive ability and shows gene-dosage effects differ between deletions and duplications across biological processes.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The paper presents an improved rat reference genome, mRatBN7.2, which enhances genomic, transcriptomic, and proteomics data mapping and identifies millions of genetic variations across rat strains.

DeepMosaic: Control-independent mosaic single nucleotide variant detection using deep convolutional neural networks

DeepMosaic detects mosaic single nucleotide variants without control samples using deep convolutional neural networks, achieving high accuracy and uncovering many variants missed by existing methods.

A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex

This study shows that autism spectrum disorder risk is influenced by rare variants, polygenic risk, and sex, with sex-specific effects on genetic liability and behavioral traits.

Genomic architecture of autism spectrum disorder from comprehensive whole-genome sequence annotation

This study identifies 135 ASD-associated protein-coding genes using whole-genome sequencing data from 11,312 individuals and exome sequencing from over 18,000 trios, with a false discovery rate of 80%.

Polymorphic SNPs, short tandem repeats and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains

The paper identifies genetic variants responsible for gene expression differences between C57BL/6 and C57BL/10 mouse substrains.

Cortical Organoids Model Early Brain Development Disrupted by 16p11.2 Copy Number Variants in Autism

This study uses cortical organoids derived from patients with 16p11.2 CNV to show altered neurodevelopmental processes, including changes in organoid size, neuronal maturation, and migration.

Temporal stability of human sperm mosaic mutations results in life-long threat of transmission to offspring

The paper analyzes sperm mosaic mutations in healthy males, finding that many are stable over time and pose a lifelong transmission risk to offspring.

Customized de novo mutation detection for any variant calling pipeline: SynthDNM

SynthDNM is a classifier that adapts to new variant calling pipelines by using simulated training examples to accurately detect de novo mutations.

Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling

This study shows that Cul3 haploinsufficiency in mice causes social and cognitive deficits, cortical volume reduction, and cytoskeletal defects, which are rescued by RhoA inhibition.

MutPred2: inferring the molecular and phenotypic impact of amino acid variants

MutPred2 identifies pathogenic amino acid variants, predicts their molecular mechanisms, and validates their functional impact in neurodevelopmental disorders.

Quantification of autism recurrence risk by direct assessment of paternal sperm mosaicism

The paper quantifies autism recurrence risk by detecting paternal sperm mosaicism through single molecule genotyping and whole genome sequencing.

Common DNA sequence variation influences 3-dimensional conformation of the human genome

This study identifies DNA sequence variants that influence 3D chromatin conformation and links them to gene expression and disease risk.

Oligogenic effects of 16p11.2 copy number variation on craniofacial development

The paper investigates the oligogenic effects of 16p11.2 copy number variation on craniofacial development across species, showing that individual genes and their combinations influence facial structure.

Multi-platform discovery of haplotype-resolved structural variation in human genomes

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

Paternally inherited noncoding structural variants contribute to autism

This study identifies rare paternally-inherited structural variants contributing to autism by disrupting noncoding regions and coding genes, with differential parental contributions.

SV2: Accurate Structural Variation Genotyping and De Novo Mutation Detection

SV2 is a machine-learning algorithm that improves structural variant genotyping and detects de novo mutations from paired-end sequencing data.