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View article: Fer governs mTORC1 regulating pathways and sustains viability of pancreatic ductal adenocarcinoma cells
Fer governs mTORC1 regulating pathways and sustains viability of pancreatic ductal adenocarcinoma cells Open
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers with a high percentage of morbidity. The deciphering and identification of novel targets and tools for intervening with its adverse progression are therefore of immens…
View article: From promoter motif to cardiac function: a single DPE motif affects transcription regulation and organ function <i>in vivo</i>
From promoter motif to cardiac function: a single DPE motif affects transcription regulation and organ function <i>in vivo</i> Open
Transcription initiates at the core promoter, which contains distinct core promoter elements. Here, we highlight the complexity of transcriptional regulation by outlining the effect of core promoter-dependent regulation on embryonic develo…
View article: ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements
ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements Open
Motivation Prediction and identification of core promoter elements and transcription factor binding sites is essential for understanding the mechanism of transcription initiation and deciphering the biological activity of a specific locus.…
View article: An affinity for brainstem microglia in pediatric high grade gliomas of brainstem origin
An affinity for brainstem microglia in pediatric high grade gliomas of brainstem origin Open
Background High-grade gliomas (HGG) in children have a devastating prognosis and occur in a remarkable spatiotemporal pattern. Diffuse midline gliomas (DMG), including diffuse intrinsic pontine gliomas (DIPG), typically occur in mid-childh…
View article: An affinity for brainstem microglia in pediatric high-grade gliomas of brainstem origin
An affinity for brainstem microglia in pediatric high-grade gliomas of brainstem origin Open
Background High-grade gliomas (HGG) in children have a devastating prognosis and occur in a remarkable spatiotemporal pattern. Diffuse midline gliomas (DMG), including diffuse intrinsic pontine gliomas (DIPG), typically occur in mid-childh…
View article: Quantitative Analysis of Differential Expression of HOX Genes in Multiple Cancers
Quantitative Analysis of Differential Expression of HOX Genes in Multiple Cancers Open
Transcription factors encoded by Homeobox (HOX) genes play numerous key functions during early embryonic development and differentiation. Multiple reports have shown that mis-regulation of HOX gene expression plays key roles in the develop…
View article: Detecting horizontal gene transfer: a probabilistic approach
Detecting horizontal gene transfer: a probabilistic approach Open
Background Horizontal gene transfer (HGT) is the event of a DNA sequence being transferred between species not by inheritance. HGT is a crucial factor in prokaryotic evolution and is a significant source for genomic novelty resulting in an…
View article: Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay
Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay Open
The integrative analysis of high-throughput reporter assays, machine learning, and profiles of epigenomic chromatin state in a broad array of cells and tissues has the potential to significantly improve our understanding of noncoding regul…
View article: Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes
Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes Open
The regulation of transcription initiation is critical for developmental and cellular processes. RNA polymerase II (Pol II) is recruited by the basal transcription machinery to the core promoter where Pol II initiates transcription. The co…
View article: Comparative genomic analysis of mollicutes with and without a chaperonin system
Comparative genomic analysis of mollicutes with and without a chaperonin system Open
The GroE chaperonin system, which comprises GroEL and GroES, assists protein folding in vivo and in vitro. It is conserved in all prokaryotes except in most, but not all, members of the class of mollicutes. In Escherichia coli, about 60 pr…
View article: Detecting Horizontal Gene Transfer between Closely Related Taxa
Detecting Horizontal Gene Transfer between Closely Related Taxa Open
Horizontal gene transfer (HGT), the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distingu…