Saniya Khullar
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View article: Integration of Nuclear Receptors into a Schwann cell Gene Regulatory Network
Integration of Nuclear Receptors into a Schwann cell Gene Regulatory Network Open
Peripheral nerve function depends on the proper formation and maintenance of Schwann cells. During development, large diameter axons are enveloped by single, myelinating Schwann cells whereas clusters of small diameter axons are surrounded…
View article: Network-based drug repurposing for psychiatric disorders using single-cell genomics
Network-based drug repurposing for psychiatric disorders using single-cell genomics Open
Neuropsychiatric disorders lack effective treatments due to a limited understanding of the underlying cellular and molecular mechanisms. To address this, we integrated population-scale single-cell genomics data and analyzed 23 cell-type-le…
View article: Cell-type-resolved genetic regulatory variation shapes inflammatory bowel disease risk
Cell-type-resolved genetic regulatory variation shapes inflammatory bowel disease risk Open
Most genetic variants associated with complex diseases lie in non-coding regions, complicating efforts to identify effector genes and relevant cell types. Here, we map cis-eQTLs across 2.2 million single cells from blood and intestinal bio…
View article: Coordinated Immune-Extracellular Matrix Transcriptional Changes Drive Brain Metastatic Progression in Lung Adenocarcinoma
Coordinated Immune-Extracellular Matrix Transcriptional Changes Drive Brain Metastatic Progression in Lung Adenocarcinoma Open
View article: NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation
NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation Open
Motivation Transcription factor (TF) coordination plays a key role in gene regulation via direct and/or indirect protein–protein interactions (PPIs) and co-binding to regulatory elements on DNA. Single-cell technologies facilitate gene exp…
View article: Network-based drug repurposing for psychiatric disorders using single-cell genomics
Network-based drug repurposing for psychiatric disorders using single-cell genomics Open
Neuropsychiatric disorders lack effective treatments due to a limited understanding of underlying cellular and molecular mechanisms. To address this, we integrated population-scale single-cell genomics data and analyzed cell-type-level gen…
View article: Conserved transcription factors coordinate synaptic gene expression through repression
Conserved transcription factors coordinate synaptic gene expression through repression Open
Chemical synapses are the primary sites of communication in the nervous system. Synapse formation is a complex process involving hundreds of proteins that must be expressed in two cells at the same time. We find that synaptic genes are bro…
View article: Single-cell genomics and regulatory networks for 388 human brains
Single-cell genomics and regulatory networks for 388 human brains Open
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, …
View article: Massively parallel characterization of regulatory elements in the developing human cortex
Massively parallel characterization of regulatory elements in the developing human cortex Open
Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogat…
View article: Single-cell genomics and regulatory networks for 388 human brains
Single-cell genomics and regulatory networks for 388 human brains Open
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei,…
View article: DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype–phenotype prediction
DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype–phenotype prediction Open
View article: NetREm Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation
NetREm Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation Open
Transcription factor (TF) coordination plays a key role in target gene (TG) regulation via protein-protein interactions (PPIs) and DNA co-binding to regulatory elements. Single-cell technologies facilitate gene expression measurement for i…
View article: Species-specific FMRP regulation of RACK1 is critical for prenatal cortical development
Species-specific FMRP regulation of RACK1 is critical for prenatal cortical development Open
View article: Age-maintained human neurons demonstrate a developmental loss of intrinsic neurite growth ability
Age-maintained human neurons demonstrate a developmental loss of intrinsic neurite growth ability Open
Injury to adult mammalian central nervous system (CNS) axons results in limited regeneration. Rodent studies have revealed a developmental switch in CNS axon regenerative ability, yet whether this is conserved in humans is unknown. Using h…
View article: BOMA, a machine-learning framework for comparative gene expression analysis across brains and organoids
BOMA, a machine-learning framework for comparative gene expression analysis across brains and organoids Open
Our machine-learning framework, brain and organoid manifold alignment (BOMA), first performs a global alignment of developmental gene expression data between brains and organoids. It then applies manifold learning to locally refine the ali…
View article: Predicting brain-regional gene regulatory networks from multi-omics for Alzheimer’s disease phenotypes and Covid-19 severity
Predicting brain-regional gene regulatory networks from multi-omics for Alzheimer’s disease phenotypes and Covid-19 severity Open
Neuroinflammation and immune dysregulation play a key role in Alzheimer’s disease (AD) and are also associated with severe Covid-19 and neurological symptoms. Also, genome-wide association studies found many risk single nucleotide polymorp…
View article: Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex
Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex Open
View article: DeepGAMI: Deep biologically guided auxiliary learning for multimodal integration and imputation to improve phenotype prediction
DeepGAMI: Deep biologically guided auxiliary learning for multimodal integration and imputation to improve phenotype prediction Open
Genotype-phenotype association is found in many biological systems, such as brain-related diseases and behavioral traits. Despite the recent improvement in the prediction of phenotypes from genotypes, they can be further improved and expla…
View article: Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease Open
Dysregulation of gene expression in Alzheimer’s disease (AD) remains elusive, especially at the cell type level. Gene regulatory network, a key molecular mechanism linking transcription factors (TFs) and regulatory elements to govern gene …
View article: DeepGAMI: Deep auxiliary learning for multi-modal integration and estimation to improve genotype-phenotype prediction
DeepGAMI: Deep auxiliary learning for multi-modal integration and estimation to improve genotype-phenotype prediction Open
Genotype-phenotype association is found in many biological systems such as brains and brain diseases. However, predicting phenotypes from genotypes remains challenging, primarily due to complex underlying molecular and cellular mechanisms.…
View article: DeepGAMI: Deep auxiliary learning for multi-modal integration and estimation to improve genotype-phenotype prediction
DeepGAMI: Deep auxiliary learning for multi-modal integration and estimation to improve genotype-phenotype prediction Open
Genotype-phenotype association is found in many biological systems such as brains and brain diseases. However, predicting phenotypes from genotypes remains challenging, primarily due to complex underlying molecular and cellular mechanisms.…
View article: DeepGAMI: Deep auxiliary learning for multi-modal integration and estimation to improve genotype-phenotype prediction
DeepGAMI: Deep auxiliary learning for multi-modal integration and estimation to improve genotype-phenotype prediction Open
Genotype-phenotype association is found in many biological systems such as brains and brain diseases. However, predicting phenotypes from genotypes remains challenging, primarily due to complex underlying molecular and cellular mechanisms.…
View article: Bringing machine learning to research on intellectual and developmental disabilities: taking inspiration from neurological diseases
Bringing machine learning to research on intellectual and developmental disabilities: taking inspiration from neurological diseases Open
View article: Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease Open
Dysregulation of gene expression in Alzheimer’s disease (AD) remains elusive, especially at the cell type level. Gene regulatory network, a key molecular mechanism linking transcription factors (TFs) and regulatory elements to govern targe…
View article: Additional file 1 of Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex
Additional file 1 of Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex Open
Additional file 1. Candidate trans-eQTLs with pooled FDR<0.25 in DLPFC.
View article: Additional file 4 of Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex
Additional file 4 of Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex Open
Additional file 4. trans-eQTLs with permutation FDR<0.25 in DLPFC.
View article: Additional file 5 of Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex
Additional file 5 of Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex Open
Additional file 5. Mediation analysis results for candidate trans-eQTLs.
View article: Additional file 2 of Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex
Additional file 2 of Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex Open
Additional file 2. trans-eQTLs with pooled FDR<0.05 in DLPFC.
View article: Additional file 3 of Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex
Additional file 3 of Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex Open
Additional file 3. trans-eGenes with gene level FDR<0.25 in DLPFC.
View article: Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex
Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex Open
Psychiatric disorders exact immense human and economic tolls in societies globally. Underlying many of these disorders is a complex repertoire of genomic variants that influence the expression of genes involved in pathways and processes in…