Elucidating the Interplay of Genes and Environment in Autism Using Genomic and Exposure Data from Large Populations

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Project Description

Autism spectrum disorder (ASD) is a multifactorial neurodevelopmental condition influenced by both genetic and environmental factors. While rare and common genetic variants have identified over 250 ASD-associated genes and copy number variants (CNVs), the mechanisms through which environmental exposures modify genetic susceptibility remain poorly understood. A major barrier to progress has been insufficient sample size to rigorously investigate gene-environment interactions (G×E). To address this gap, we are applying novel data analytic approaches to genetic and exposure data in large biobank cohorts. This project we will investigate prenatal exposures and early-life environmental factors in one of our deeply phenotyped cohorts (ABCD, HBCD and MoBa) with genome-wide genetic data, neurodevelopmental assesments.

Integrative analysis of functional pathways, cells and brain regions across phenotypic dimensions of the autism spectrum

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Project Description

This project is applying integrative approaches, combining genetic association data in autism with detailed functional information on gene networks and cell-type and spatial expression of genes to define specific dimensions of phenotype and function within the autism spectrum

Understanding the connection of nuclear shape to gene expression

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Project Description

Hypothesis that chromatin's contribution to nuclear mechanics enables the inference of expressed genes.

- investigate morphological pathways in the transition from monomorphonuclear to polymorphonuclear cells during differentiation using data-driven and biophysical models

- connect morphological pathways to gene expression profiles

Nathan Tran

First Name
Nathan
Last Name
Tran
Student Status
Graduate Student
Email
nat011@ucsd.edu
Major
Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics
Completed Degrees

B.S., Computational & Systems Biology, University of California Los Angeles, 2025

BISB Training Grant
No
Special Funding or Awards

2025-28 Trainee on National Library of Medicine (NLM) Training Grant Fellowship Program

Safa Saeed

First Name
Safa
Last Name
Saeed
Student Status
Graduate Student
Email
sasaeed@ucsd.edu
Major
Bioinformatics and Systems Biology
Completed Degrees

B.S., Bioengineering: Bioinformatics, University of California, San Diego, 2025

BISB Training Grant
No
Special Funding or Awards

2025-26 Trainee on NIH Training Grant in Bioinformatics

Junxi Feng

First Name
Junxi
Last Name
Feng
Student Status
Graduate Student
Email
juf009@ucsd.edu
Major
Bioinformatics and Systems Biology
Completed Degrees

B.S., Computational and Systems Biology, University of California, Los Angeles, 2023
M.S., Computational Biology and Quantitative Genetics, Harvard University, 2025

BISB Training Grant
No