A5075356427- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Molecular Biology Techniques and Applications
- Machine Learning in Bioinformatics
- Hepatitis C virus research
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Protein Structure and Dynamics
- HIV, Drug Use, Sexual Risk
- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- Pneumocystis jirovecii pneumonia detection and treatment
- Reproductive System and Pregnancy
- CRISPR and Genetic Engineering
- Blood properties and coagulation
- HIV/AIDS Research and Interventions
- Cancer Genomics and Diagnostics
- Neurogenetic and Muscular Disorders Research
- Platelet Disorders and Treatments
- Pregnancy and Medication Impact
- Bone Metabolism and Diseases
- Adenosine and Purinergic Signaling
- Advanced Causal Inference Techniques
University of Pennsylvania
2014-2020
Target (United States)
2018-2019
GlaxoSmithKline (United States)
2018-2019
South College
2018
College of New Jersey
2010
RNA localization involves cis-motifs that are recognized by RNA-binding proteins (RBP), which then mediate to specific sub-cellular compartments. is critical for many different cell functions, e.g., in neuronal dendrites, a step long-lasting synaptic potentiation. However, there little consensus regarding RNAs localized and the role of alternative isoforms localization. A comprehensive catalog can help dissect RBP/RNA interactions motifs. Here, we utilize single sequencing approach profile...
Excessive bone resorption by osteoclasts (OCs) can result in serious clinical outcomes, including loss that may weaken skeletal or periodontal strength. Proper homeostasis and strength are maintained balancing OC function with the bone-forming of osteoblasts. Unfortunately, current treatments broadly inhibit differentiation also interfere coupled formation. We therefore identified a factor, purinergic receptor P2X5 is highly expressed during maturation phase, which we show here plays no...
Many R packages have been developed for transcriptome analysis but their use often requires familiarity with and integrating results of different scripts to wrangle the datatypes. Furthermore, exploratory data analyses generate multiple derived datasets such as subsets or transformations, which can be difficult track. Here we present PIVOT, an R-based platform that wraps open source a uniform user interface graphical management allows non-programmers interactively explore transcriptomics...
Non-alcoholic fatty liver disease (NAFLD) is a leading form of chronic with large unmet need. steatohepatitis (NASH), progressive variant NAFLD, can lead to fibrosis, cirrhosis, and hepatocellular carcinoma. To identify potential new therapeutics for NASH, we used computational approach based on Connectivity Map (CMAP) analysis, which pointed us bromodomain extra-terminal motif (BET) inhibitors treating NASH. experimentally validate this hypothesis, tested small-molecule inhibitor the BET...
Osteoclasts are multinucleated, giant cells derived from myeloid progenitors. While receptor activator of NF-κB ligand (RANKL) stimulation is the primary driver osteoclast differentiation, additional signaling further contributes to maturation. Here, we demonstrate that immunoglobulin superfamily member 11 (IgSF11), whose expression increases during regulates differentiation through interaction with postsynaptic density protein 95 (PSD-95), a scaffold multiple domains. IgSF11 deficiency in...
Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function—for example, recruiting specific RNA-binding protein then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences doing...
Abstract Recognition of protein structural fold is the starting point for many structure prediction tools and function inference. Fold computationally demanding recognizing novel folds difficult such that majority proteins have not been annotated classification. Here we describe a new machine learning approach using feature space can be used accurate recognition all 1,221 currently known inference unknown folds. We show our method achieves better than 94% accuracy even when only one training...
The increasing number of annotated genome sequences in public databases has made it possible to study the length distributions and domain composition proteins at unprecedented resolution. To identify factors that influence protein metazoans, we performed an analysis all domain-annotated from a total 49 animal species Ensembl (v.56) or EnsemblMetazoa (v.3). Our results indicate constraints are not fixed as linear function count can vary based on content. presence repeating domains was...
Abstract RNA localization to neuronal dendrites is critical step for long-lasting synaptic potentiation, but there little consensus regarding which RNAs are localized and the role of alternative isoforms in localization. Using independent RNA-sequencing from soma same neuron, we deeply profiled sub-cellular transcriptomes assess extent variability dendritic individual hippocampal neurons, including an assessment differential 3’UTR isoforms. We identified 2,225 RNAs, 298 cases...
Abstract Many R packages have been developed for transcriptome analysis but their use often requires familiarity with and integrating results of different is difficult. Here we present PIVOT, an R-based application a uniform user interface graphical data management that allows non-programmers to conveniently access various bioinformatics tools interactively explore transcriptomics data. PIVOT supports many popular open source provides extensive set statistical manipulations. A graph-based...
ABSTRACT Recognition of protein structural fold is the starting point for many structure prediction tools and function inference. Fold computationally demanding recognizing novel folds difficult such that majority proteins have not been annotated classification. Here we describe a new machine learning approach using feature space can be used accurate recognition all 1,221 currently known inference unknown folds. We show our method achieves better than 96% accuracy even when only one training...
Abstract Although most canonical somatic cancer mutations have now been cataloged, only a fraction are amenable to drug discovery efforts. These limited targets with gain of function and druggable protein domains. Examples include kinases such as FLT3 metabolic enzymes IDH1/2. However, excluded from this list undruggable mutations, KRAS, or tumor suppressors which acquire loss APC. The concept synthetic lethality is being used address gap in discovery. Cells carry these directly become...