Alexander E. Urban
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View article: Multi-platform framework for mapping somatic retrotransposition in human tissues
Multi-platform framework for mapping somatic retrotransposition in human tissues Open
Mobile element insertions (MEI) shape the human genome in both germline and somatic tissues. While inherited MEIs are well characterized, mapping somatic MEIs (sMEI) in non-cancer tissues remains challenging due to their low allelic fracti…
Effect of cortisol on cortical organoids: Building a “stress in a dish” model system Open
Exposure to chronic stress and traumatic experiences impacts brain health and development, which may lead to Post Traumatic Stress Disorder (PTSD), other mental health conditions, or altered resilience. Although certain behavioral and soci…
View article: Peripheral Complement C4 Protein in Schizophrenia: Association with Gene Copy Number and Immune Cell Subtypes
Peripheral Complement C4 Protein in Schizophrenia: Association with Gene Copy Number and Immune Cell Subtypes Open
The lack of disease-modifying treatments for schizophrenia necessitates the exploration of novel aspects of its pathophysiology, including innate immune mechanisms in the periphery. C4 protein activation, associated with the complement cas…
Prioritizing disease-related rare variants by integrating gene expression data Open
Rare variants, comprising the vast majority of human genetic variations, are likely to have more deleterious impact in the context of human diseases compared to common variants. Here we present carrier statistic, a statistical framework to…
View article: Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints
Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints Open
We developed a generally applicable method, CRISPR/Cas9-targeted long-read sequencing (CTLR-Seq), to resolve, haplotype-specifically, the large and complex regions in the human genome that had been previously impenetrable to sequencing ana…
View article: Mapping recurrent mosaic copy number variation in human neurons
Mapping recurrent mosaic copy number variation in human neurons Open
When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development…
Prioritizing disease-related rare variants by integrating gene expression data Open
Rare variants, comprising a vast majority of human genetic variations, are likely to have more deleterious impact on human diseases compared to common variants. Here we present carrier statistic, a statistical framework to prioritize disea…
Prioritizing disease-related rare variants by integrating gene expression data Open
Rare variants, comprising a vast majority of human genetic variations, are likely to have more deleterious impact on human diseases compared to common variants. Here we present carrier statistic, a statistical framework to prioritize disea…
View article: Mutations in human DNA methyltransferase <i>DNMT1</i> induce specific genome-wide epigenomic and transcriptomic changes in neurodevelopment
Mutations in human DNA methyltransferase <i>DNMT1</i> induce specific genome-wide epigenomic and transcriptomic changes in neurodevelopment Open
DNA methyltransferase type 1 (DNMT1) is a major enzyme involved in maintaining the methylation pattern after DNA replication. Mutations in DNMT1 have been associated with autosomal dominant cerebellar ataxia, deafness and narcolepsy (ADCA-…
View article: Cell-type specific global reprogramming of the transcriptome and epigenome in induced neurons with the 16p11.2 neuropsychiatric CNVs
Cell-type specific global reprogramming of the transcriptome and epigenome in induced neurons with the 16p11.2 neuropsychiatric CNVs Open
Copy number variants (CNVs), either deletions or duplications, at the 16p11.2 locus in the human genome are known to increase the risk for autism spectrum disorders (ASD), schizophrenia, and several other developmental conditions. Here, we…
Modeling ionic transport and disorder in crystalline electrodes using percolation theory Open
Solid ionic conductors are essential components of batteries and fuel cells. In many cases, ionic conduction through crystalline materials with substitutional disorder can be modeled with atomic-scale lattice model percolation simulations.…
View article: Simulated sulfur K-edge X-ray absorption spectroscopy database of lithium thiophosphate solid electrolytes
Simulated sulfur K-edge X-ray absorption spectroscopy database of lithium thiophosphate solid electrolytes Open
X-ray absorption spectroscopy (XAS) is a premier technique for materials characterization, providing key information about the local chemical environment of the absorber atom. In this work, we develop a database of sulfur K-edge XAS spectr…
View article: Control-independent mosaic single nucleotide variant detection with DeepMosaic
Control-independent mosaic single nucleotide variant detection with DeepMosaic Open
Mosaic variants (MVs) reflect mutagenic processes during embryonic development and environmental exposure, accumulate with aging and underlie diseases such as cancer and autism. The detection of noncancer MVs has been computationally chall…
View article: Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability
Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability Open
We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 with schizophrenia, and 59 with autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, brains had 20 to 60 detectable…
Understanding the Onset of Surface Degradation in LiNiO2 Cathodes Open
Nickel-based layered oxides offer an attractive platform for the development of energy-dense cobalt-free cathodes for lithium-ion batteries but suffer from degradation via oxygen gas release during electrochemical cycling. While such degra…
Hyperexcitable arousal circuits drive sleep instability during aging Open
Sleep quality declines with age; however, the underlying mechanisms remain elusive. We found that hyperexcitable hypocretin/orexin (Hcrt/OX) neurons drive sleep fragmentation during aging. In aged mice, Hcrt neurons exhibited more frequent…
View article: Somatic mutations reveal hypermutable brains and are associated with neuropsychiatric disorders
Somatic mutations reveal hypermutable brains and are associated with neuropsychiatric disorders Open
Somatic mutations have causative roles in many diseases and contribute to neuropsychiatric disorders. Here, we analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 with schizophrenia, and 59 with autism) for somatic sin…
AI-Aided Mapping of the Structure-Composition-Conductivity Relationships of Glass-Ceramic Lithium Thiophosphate Electrolytes Open
Lithium thiophosphates (LPS) with the composition (Li$_2$S)$_x$(P$_2$S$_5$)$_{1-x}$ are among the most promising prospective electrolyte materials for solid-state batteries (SSBs), owing to their superionic conductivity at room temperature…
Doubly Stabilized Perovskite Nanocrystal Luminescence Downconverters Open
Halide perovskite nanocrystals (NCs) have emerged as a promising material for applications ranging from light-emitting diodes (LEDs) to solar cells and photodetectors. Still, several issues impede the realization of the nanocrystals' full …
View article: 1010i-CGATGT_S1_L001_R1_001.fastq.gz
1010i-CGATGT_S1_L001_R1_001.fastq.gz Open
DNA methylation data across 5x10^6 CpG loci, derived from buccal cells of 6-month-old infants. Method is bisulfite treatment followed by next-generation sequencing using Illumina SeqCap Epi Enrichment platform.