Gilad Barshad
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View article: Using Functional Genomic Data in Monocytes/Macrophages and Genotyping to Nominate Disease-Driving Single Nucleotide Polymorphisms and Target Genes in Juvenile Idiopathic Arthritis
Using Functional Genomic Data in Monocytes/Macrophages and Genotyping to Nominate Disease-Driving Single Nucleotide Polymorphisms and Target Genes in Juvenile Idiopathic Arthritis Open
Introduction GWAS have identified multiple regions that confer risk for juvenile idiopathic arthritis (JIA). However, identifying the single nucleotide polymorphisms (SNPs) that drive disease risk is impeded by the SNPs’ that identify risk…
View article: Evolution of promoter-proximal pausing enabled a new layer of transcription control
Evolution of promoter-proximal pausing enabled a new layer of transcription control Open
View article: Evolution of promoter-proximal pausing enabled a new layer of transcription control
Evolution of promoter-proximal pausing enabled a new layer of transcription control Open
Promoter-proximal pausing of RNA polymerase II (Pol II) is a key regulatory step during transcription. Despite the central role of pausing in gene regulation, we do not understand the evolutionary processes that led to the emergence of Pol…
View article: Meiotic gene transcription programs are mediated by A-MYB and BRDT-dependent RNA polymerase II pause release during mammalian prophase I
Meiotic gene transcription programs are mediated by A-MYB and BRDT-dependent RNA polymerase II pause release during mammalian prophase I Open
During meiotic prophase I, germ cells must balance transcriptional activation with meiotic recombination and chromosome synapsis, biological processes requiring extensive changes to chromatin state and structure. Here we explored the inter…
View article: Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes
Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes Open
In the Methods subsection entitled "Control for age, gender, and cause of death," the text has been changed as follows: Control for age, gender, and cause of deathTo control for the possible contribution of age, gender, and cause of death …
View article: RNA polymerase II and PARP1 shape enhancer-promoter contacts
RNA polymerase II and PARP1 shape enhancer-promoter contacts Open
How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we studied enhancer-promoter contact architecture and communication by integrating data from nucleosome-resolution genomic…
View article: RNA polymerase II and PARP1 shape enhancer-promoter contacts
RNA polymerase II and PARP1 shape enhancer-promoter contacts Open
How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we studied enhancer-promoter contact architecture and communication by integrating data from nucleosome-resolution genomic…
View article: Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells Open
Motivation Quantification of isoform abundance has been extensively studied at the mature RNA level using RNA-seq but not at the level of precursor RNAs using nascent RNA sequencing. Results We address this problem with a new computational…
View article: Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) Highlights Pre-RNA Isoform Diversity in Human Cells
Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) Highlights Pre-RNA Isoform Diversity in Human Cells Open
Quantification of mature-RNA isoform abundance from RNA-seq data has been extensively studied, but much less attention has been devoted to quantifying the abundance of distinct precursor RNAs based on nascent RNA sequencing data. Here we a…
View article: Multiple stages of evolutionary change in anthrax toxin receptor expression in humans
Multiple stages of evolutionary change in anthrax toxin receptor expression in humans Open
The advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease influenced human evolution, we studied changes in human expression of anthrax toxin receptor 2 ( ANTXR2 ), whic…
View article: Disease-causing mutations in subunits of OXPHOS complex I affect their physical interactions
Disease-causing mutations in subunits of OXPHOS complex I affect their physical interactions Open
Mitochondrial complex I (C1) is the largest multi-subunit oxidative phosphorylation (OXPHOS) protein complex. Recent availability of a high-resolution human C1 structure, and from two non-human mammals, enabled predicting the impact of mut…
View article: Supplemental Dataset S3: Relative correlation heatmaps for splice-variants of genes with more than one transcript highly OXPHOS correlated across tissues.
Supplemental Dataset S3: Relative correlation heatmaps for splice-variants of genes with more than one transcript highly OXPHOS correlated across tissues. Open
Supplemental Dataset S3 of: Barshad et al (2018). Genome Research, 28(7): 952-967.
View article: Supplemental Dataset S1: Correlation heat maps for OXPHOS genes and splice variants expression patterns in 48 human tissues.
Supplemental Dataset S1: Correlation heat maps for OXPHOS genes and splice variants expression patterns in 48 human tissues. Open
Supplemental Dataset S1 of: Barshad et al (2018). Genome Research, 28(7): 952-967.
View article: Oxidative-phosphorylation genes from the mitochondrial and nuclear genomes co-express in all human tissues except for the ancient brain
Oxidative-phosphorylation genes from the mitochondrial and nuclear genomes co-express in all human tissues except for the ancient brain Open
In humans, oxidative phosphorylation (OXPHOS), the cellular energy producer, harbors ∼90 nuclear DNA (nDNA)- and mitochondrial DNA (mtDNA)-encoded subunits. Although nDNA- and mtDNA-encoded OXPHOS proteins physically interact, their transc…
View article: Mitochondrial Involvement in Vertebrate Speciation? The Case of Mito-nuclear Genetic Divergence in Chameleons
Mitochondrial Involvement in Vertebrate Speciation? The Case of Mito-nuclear Genetic Divergence in Chameleons Open
Compatibility between the nuclear (nDNA) and mitochondrial (mtDNA) genomes is important for organismal health. However, its significance for major evolutionary processes such as speciation is unclear, especially in vertebrates. We previous…