Sara Mostafavi
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Pet ownership and risk of depression: a systematic review and meta-analysis Open
This study reveals a complex relationship between pet ownership and depression. Cat ownership is linked to a higher risk, while dog ownership shows mixed results. Overall, pet ownership isn't significantly associated with depression, highl…
View article: GAME: Genomic API for Model Evaluation
GAME: Genomic API for Model Evaluation Open
The rapid expansion of genomics datasets and the application of machine learning has produced sequence-to-activity genomics models with ever-expanding capabilities. However, benchmarking these models on practical applications has been chal…
View article: The Power of Collective Design: Co-Creating Healing-Centered Mental Health Care for Refugee and Immigrant Families
The Power of Collective Design: Co-Creating Healing-Centered Mental Health Care for Refugee and Immigrant Families Open
Refugee and immigrant communities face a host of dynamic health challenges. This essay discusses the importance of prioritizing the impacts of resettlement on mental health and provides examples of how creating a collective network of cult…
Deep genomic models of allele-specific measurements Open
Allele-specific quantification of sequencing data, such as gene expression, allows for a causal investigation of how DNA sequence variations influence cis gene regulation. Current methods for analyzing allele-specific measurements for caus…
Investigating Data Size, Sequence Diversity, and Model Complexity in MPRA-based Sequence-to-Function Prediction Open
We created the MPRA Dataset Collection (MDC), a curated resource of MPRA data from 12 studies comprising over 150 million labeled DNA subsequences. These datasets include both random and natural genomic sequences paired with diverse functi…
Contrasting genetic predisposition and diagnosis in psychiatric disorders: A multi-omic single-nucleus analysis of the human OFC Open
Psychiatric disorders like schizophrenia, bipolar disorder, and major depressive disorder exhibit substantial genetic and clinical overlap. However, their molecular architecture remains elusive due to their polygenic nature and complex bra…
A scalable approach to investigating sequence-to-expression prediction from personal genomes Open
A key promise of sequence-to-functon(S2F) models is their ability to evaluate arbitrary sequence inputs, providing a robust framework for understanding genotype-phenotype relationships. However, despite strong performance across genomic lo…
A scalable approach to investigating sequence-to-function predictions from personal genomes Open
Sequence-to-function (S2F) models hold the promise of evaluating arbitrary DNA sequences, providing a powerful framework for linking genotype to phenotype. Yet, despite strong performance across genomic loci, these models often struggle to…
Refining sequence-to-activity models by increasing model resolution Open
Decoding the cis-regulatory syntax that controls gene expression is essential for improving our understanding of cell differentiation and disease. To identify regulatory motifs and their regulatory syntax, deep learning based sequence-to-a…
THE ADOPTION OF ARTIFICIAL INTELLIGENCE IN HIGHER EDUCATION: A QUANTITATIVE ANALYSIS USING STRUCTURAL EQUATION MODELING Open
Global businesses have actively embraced the digital industry. The education sector also utilizes digital tools to enhance personalized learning and promote equity in education. New frontiers have been established in education through the …
View article: Microheterogeneity in the Kinetics and Sex-Specific Response to Type I IFN
Microheterogeneity in the Kinetics and Sex-Specific Response to Type I IFN Open
The response to type I IFNs involves the rapid induction of prototypical IFN signature genes (ISGs). It is not known whether the tightly controlled ISG expression observed at the cell population level correctly represents the coherent resp…
Contrasting genetic predisposition and diagnosis in psychiatric disorders: a multi-omic single-nucleus analysis of the human orbitofrontal cortex Open
Psychiatric disorders like schizophrenia, bipolar disorder, and major depressive disorder exhibit significant genetic and clinical overlap. However, their molecular architecture remains elusive due to their polygenic nature and complex bra…
View article: Sex-dependent placental methylation quantitative trait loci provide insight into the prenatal origins of childhood onset traits and conditions
Sex-dependent placental methylation quantitative trait loci provide insight into the prenatal origins of childhood onset traits and conditions Open
Molecular quantitative trait loci (QTLs) allow us to understand the biology captured in genome-wide association studies (GWASs). The placenta regulates fetal development and shows sex differences in DNA methylation. We therefore hypothesiz…
Recurrent cannabis-induced catatonia: a case report and comprehensive systematic literature review Open
Background Catatonia presents itself as a complex neuropsychiatric syndrome, giving rise to various motor, speech, and behavioral challenges. It is noteworthy that approximately 10% of psychiatric hospital admissions can be attributed to t…
Quick and effective approximation of <i>in silico</i> saturation mutagenesis experiments with first-order Taylor expansion Open
To understand the decision process of genomic sequence-to-function models, various explainable AI algorithms have been proposed. These methods determine the importance of each nucleotide in a given input sequence to the model’s predictions…
Impact on splicing in<i>Saccharomyces cerevisiae</i>of random 50-base sequences inserted into an intron Open
Intron splicing is a key regulatory step in gene expression in eukaryotes. Three sequence elements required for splicing—5′ and 3′ splice sites and a branchpoint—are especially well-characterized in Saccharomyces cerevisiae , but our under…
View article: A germline heterozygous dominant negative <i>IKZF2</i> variant causing syndromic primary immune regulatory disorder and ICHAD
A germline heterozygous dominant negative <i>IKZF2</i> variant causing syndromic primary immune regulatory disorder and ICHAD Open
Monogenic defects that impair the control of inflammation and tolerance lead to profound immune dysregulation, including autoimmunity and atopy. Studying these disorders reveals important molecular and cellular factors that regulate human …
View article: A Parkinson’s disease genetic risk score associates with blood DNAm on chromosome 17
A Parkinson’s disease genetic risk score associates with blood DNAm on chromosome 17 Open
Although Parkinson’s disease (PD) coincides with altered immune functioning, there are few reproducible associations between blood DNA methylation (DNAm) and PD case-control status. Integrative analyses of genotype and blood DNAm can addre…
ExplaiNN: interpretable and transparent neural networks for genomics Open
Deep learning models such as convolutional neural networks (CNNs) excel in genomic tasks but lack interpretability. We introduce ExplaiNN, which combines the expressiveness of CNNs with the interpretability of linear models. ExplaiNN can p…