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Although Aβ peptides are causative agents in Alzheimer's disease (AD), the underlying mechanisms are still elusive. We report that Aβ42 induces a translational block by activating AMPK, thereby inhibiting the mTOR pathway. This translational block leads to widespread ER stress, which activates JNK3. JNK3 in turn phosphorylates APP at T668, thereby(More)
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level. miRNAs are highly expressed in cells of the immune and nervous system, attesting to their importance in Neuroimmunology. Besides their involvement in modulation of physiological and pathological processes, miRNAs hold high promise as disease(More)
Many biologically significant processes, such as cell differentiation and cell cycle progression, gene transcription and DNA replication, chromosome stability and epigenetic silencing etc. depend on the crucial interactions between cellular proteins and DNA. Chromatin immunoprecipitation (ChIP) is an important experimental technique for studying(More)
BACKGROUND Chronic lymphocytic leukemia (CLL) is the most common adult leukemia. It is a highly heterogeneous disease, and can be divided roughly into indolent and progressive stages based on classic clinical markers. Immunoglobin heavy chain variable region (IgVH) mutational status was found to be associated with patient survival outcome, and biomarkers(More)
Throughput from sequencing instruments has been increasing in an unprecedented speed, leading to an explosion of the next-generation sequencing (NGS) data, and challenges in storing, managing, and analyzing these datasets. Parallelism is the key in handling large-scale data, and some progress has been made in parallelizing important steps, like sequence(More)
Current treatments for acute myeloid leukemia (AML) are designed to target rapidly dividing blast populations with limited success in eradicating the functionally distinct leukemia stem cell (LSC) population, which is postulated to be responsible for disease resistance and relapse. We have previously reported high miR-126 expression levels to be associated(More)
Next Generation Sequencing is highly resource intensive. NGS Tasks related to data processing, management and analysis require high-end computing servers or even clusters. Additionally, processing NGS experiments requires suitable storage space and significant manual interaction. At The Ohio State University's Biomedical Informatics Shared Resource, we(More)
Differential expression detection for RNA-seq experiments is often biased by normalization algorithms due to their sensitivity to parametric assumptions on the gene count distributions, extreme values of gene expression, gene length and total number of sequence reads. To overcome limitations of current methodologies, we developed Differential Feature Index(More)
New high-throughput sequencing technologies can generate millions of short sequences in a single experiment. As the size of the data increases, comparison of multiple experiments on different cell lines under different experimental conditions becomes a big challenge. In this paper, we investigate ways to compare multiple ChIP-sequencing experiments. We(More)
The increasing availability of structurally aligned protein families has made it possible to use statistical methods to discover regions of interpositional dependencies of residue identity. Such dependencies amongst residues often have structural or functional implications, and their discovery can supply valuable constraints that assist in the refinement of(More)