Stephan Sanders

This paper introduces SpliceAI2, a deep learning model that improves identification and quantification of splice-altering variants and their effects on transcripts and disease.

This study shows ML-assisted directed evolution improves AAV capsid manufacturing efficiency 41-fold compared to directed evolution alone.

This study identifies how the polyglutamine tract in the androgen receptor regulates muscle growth and atrophy by altering transcriptional activity and chromatin binding.

The paper identifies a cross-tissue splicing signature as a biomarker for ReNU syndrome, distinguishing affected individuals from controls with high specificity.

The paper identifies an RA-autoregulatory loop in the developing PFC that maintains RA signaling and defines cortical areal identities.

The paper identifies 253 autism-associated genes using rare variation from 62,429 individuals and finds pleiotropy across physiological systems and developmental disorders.

The paper provides guidance for classifying variants in snRNA genes and introduces RNUdb, a tool to support variant annotation and classification.

The paper develops ASO Atlas, a database of RNase H-mediated ASO sequences and their efficacy, and trains OligoAI, a deep learning model to predict ASO efficacy based on sequence and chemical features, reducing screening effort by 5.72-fold.

The paper creates a genome-wide map of homozygous deletions in 125,730 individuals, identifying novel rare disease genes and variants.

The paper uses spatial transcriptomics to identify brain regions enriched for ASD and schizophrenia genes in mice, finding the thalamus, cortex, and hippocampus as key areas.

The paper uses STARMAPS to analyze single-cell RNA sequencing data and identifies spatial and temporal patterns of ASD-associated gene enrichment in specific brain regions.

The paper identifies transcriptional and epigenomic differences in Brodmann Area 22 in autism, linking them to RFX3-dependent networks and verbal ability.

The paper presents a framework for prioritizing targets and patients for antisense oligonucleotide therapies in rare diseases, focusing on equitable and systematic decision-making.

The paper maps gene expression responses to loss of 1,947 disease-associated genes across the mouse brain using Perturb-seq, revealing cell-type-specific essentiality and transcriptional programs.

The paper identifies human-specific transcriptomic and regulatory features in the cerebellum, including ZP2's role in synapse development and regulation.

The paper engineers AAV9 capsids to enhance extracellular vesicle loading through rational design and directed evolution, achieving up to threefold increased EV-AAV yield and improved transduction efficiency.

This study identifies uORF elements regulating BDNF translation and demonstrates that disrupting uORFs can upregulate BDNF expression in cell culture.

This study identifies 5'UTR exons containing uORFs as targets for splice-switching to increase protein translation in haploinsufficient disease genes.

This study examines common and rare variant genetic contributions to autism in African Americans, highlighting differences in genetic effects and polygenic score transferability between European and African ancestries.

The paper identifies cell-type-specific molecular and regulatory changes in D1 striosome medium spiny neurons and astrocytes in ASD using single-nucleus multiomic profiling in human putamen.

The paper identifies active human neural enhancers and CRISPRa gRNAs that upregulate NDD risk genes, providing a resource for cis-regulatory therapy development.

The paper estimates the proportion of genetic diagnoses in a pediatric cohort that are amenable to antisense oligonucleotide therapy, finding 4.9% eligible or likely eligible.

This study shows that CRISPR activation can rescue electrophysiological deficits in SCN2A haploinsufficiency by increasing the expression of the remaining functional allele in mice and human neurons.

The paper identifies biallelic variants in RNU4-2 causing a recessive neurodevelopmental syndrome with distinct white matter changes, expanding the known genotypic and phenotypic spectrum of RNU4-2-related disorders.

The paper presents consensus guidelines for assessing pathogenic variants' eligibility for antisense oligonucleotide treatments, including classification criteria and considerations for different therapeutic approaches.

The paper describes a CRISPRa screening method combining multiplex perturbations with sc-RNA-seq to identify cell-type-specific regulatory elements and their target genes.

CWAS-Plus identifies noncoding variant associations in whole-genome sequencing data using cell-type-specific functional data, finding links to autism and Alzheimer's disease.

This paper conducts a genome-wide association meta-analysis of age at onset of walking, identifying 11 loci and showing genetic correlations with ADHD, BMI, intelligence, and brain structure.

The paper combines massively parallel reporter assays and mouse transgenic assays to study the functional impact of non-coding variants on neuronal enhancer activity, finding strong correlations and additional pleiotropic effects.

This study shows that Ank2 and Scn2a work together in dendrites of neocortical neurons, linking their dysfunction to autism spectrum disorder.