28 Result(s)
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Leonardo Collado-Torres
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Article
Open AccessAnalysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry
Ancestral differences in genomic variation affect the regulation of gene expression; however, most gene expression studies have been limited to European ancestry samples or adjusted to identify ancestry-indepe...
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Open AccessSex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus
Schizophrenia is a complex neuropsychiatric disorder with sexually dimorphic features, including differential symptomatology, drug responsiveness, and male incidence rate. Prior large-scale transcriptome analy...
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Open AccessTrkB-dependent regulation of molecular signaling across septal cell types
The lateral septum (LS), a GABAergic structure located in the basal forebrain, is implicated in social behavior, learning, and memory. We previously demonstrated that expression of tropomyosin kinase receptor ...
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Open AccessChallenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets
Deconvolution of cell mixtures in “bulk” transcriptomic samples from homogenate human tissue is important for understanding disease pathologies. However, several experimental and computational challenges imped...
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Open AccessData-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue
We define and identify a new class of control genes for next-generation sequencing called total RNA expression genes (TREGs), which correlate with total RNA abundance in cell types of different sizes and trans...
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Open AccessBiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data
Bisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of cancer, psychiatric disorders, and many other conditions. Raw data generat...
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Comment on: What genes are differentially expressed in individuals with schizophrenia? A systematic review
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Analysis of the caudate nucleus transcriptome in individuals with schizophrenia highlights effects of antipsychotics and new risk genes
Most studies of gene expression in the brains of individuals with schizophrenia have focused on cortical regions, but subcortical nuclei such as the striatum are prominently implicated in the disease, and curr...
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Open AccessspatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the ...
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Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways
Recent genetic studies have identified variants associated with bipolar disorder (BD), but it remains unclear how brain gene expression is altered in BD and how genetic risk for BD may contribute to these alte...
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Open Accessrecount3: summaries and queries for large-scale RNA-seq expression and splicing
We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to th...
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Open AccessGenome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk
DNA methylation (DNAm) is an epigenetic regulator of gene expression and a hallmark of gene-environment interaction. Using whole-genome bisulfite sequencing, we have surveyed DNAm in 344 samples of human postm...
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Open AccessCorrection to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses
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Open AccessSPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
RNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with it. In practice, there are a large number of individual steps a researcher must perform ...
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Publisher Correction: Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
A Correction to this paper has been published: https://doi.org/10.1038/s41593-021-00817-5.
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Article
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
We used the 10x Genomics Visium platform to define the spatial topography of gene expression in the six-layered human dorsolateral prefrontal cortex. We identified extensive layer-enriched expression signature...
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Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome
Cigarette smoking during pregnancy is a major public health concern. While there are well-described consequences in early child development, there is very little known about the effects of maternal smoking on ...
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Profiling gene expression in the human dentate gyrus granule cell layer reveals insights into schizophrenia and its genetic risk
Specific cell populations may have unique contributions to schizophrenia but may be missed in studies of homogenate tissue. Here laser capture microdissection followed by RNA sequencing (LCM-seq) was used to t...
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Open AccessRegulatory sites for splicing in human basal ganglia are enriched for disease-relevant information
Genome-wide association studies have generated an increasing number of common genetic variants associated with neurological and psychiatric disease risk. An improved understanding of the genetic control of gen...
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Open AccessDissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs
Human induced pluripotent stem cells (hiPSCs) are a powerful model of neural differentiation and maturation. We present a hiPSC transcriptomics resource on corticogenesis from 5 iPSC donor and 13 subclonal lin...
