A5054597616- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- RNA regulation and disease
- Immunotherapy and Immune Responses
- Parasite Biology and Host Interactions
- Chromosomal and Genetic Variations
- Aquaculture disease management and microbiota
- Circular RNAs in diseases
- Cancer Genomics and Diagnostics
- Monoclonal and Polyclonal Antibodies Research
- interferon and immune responses
- vaccines and immunoinformatics approaches
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Parasites and Host Interactions
- Epigenetics and DNA Methylation
- Cancer-related molecular mechanisms research
Brown University
2017-2023
New York University
2020
DNA methylation plays a critical role in establishing and maintaining cellular identity. However, it is frequently dysregulated during tumor development closely intertwined with other genetic alterations. Here, we leveraged multi-omic profiling of 687 tumors matched non-involved adjacent tissues from the kidney, brain, pancreas, lung, head neck, endometrium to identify aberrant associated RNA protein abundance changes build Pan-Cancer catalog. We uncovered lineage-specific epigenetic drivers...
The nearest neighbor model and associated dynamic programming algorithms allow for the efficient estimation of RNA secondary structure Boltzmann ensemble. However because a given only contains fraction possible helices that could form from sequence, ensemble is multimodal. Several methods exist clustering structures finding those modes. less focus to exploring underlying reasons this multimodality: presence conflicting basepairs. Information theory, or more specifically mutual information,...
Abstract Manipulation of host phenotypes by parasites is hypothesized to be an adaptive strategy enhancing parasite transmission across hosts and generations. Characterizing the molecular mechanisms manipulation important advance our understanding host–parasite coevolution. The trematode ( Levinseniella byrdi ) known alter colour behaviour its amphipod Orchestia grillus presumably increasing predation amphipods which enhances through life cycle. We sampled 24 infected uninfected from a salt...
<h3>Background</h3> Repetitive elements are suppressed in normal tissues but commonly expressed cancer, where methylation changes can lead to their reactivation. Combined with dysregulation of splicing machinery, this leads an increase the number RNA repeat-gene 'fusions': transcripts derived from junctions between protein-coding genes and repetitive elements. These fusions have potential be a rich source highly tumor-specific cancer vaccine targets. <h3>Methods</h3> ROME has developed...
Repetitive elements are now known to have relevant cellular functions, including self-complementary sequences that form double stranded (ds) RNA. There numerous pathways determine the fate of endogenous dsRNA, and misregulation dsRNA is a driver autoimmune disease, particularly in brain. Unfortunately, alignment high-throughput, short-read repeat poses dilemma: Such may align equally well multiple genomic locations. In order differentiate elements, current methods depend on sequence...
Abstract Changes in the DNA copy number of genes (copy variation/CNV) are widespread many cancers and affect expression tumor suppressors oncogenes. Many these CNVs arise from chromosomal aberrations that result improperly repaired damage. LINE-1 retrotransposons - genomic elements cut then reverse transcribe themselves into gap expressed likely contribute to damage CNV cancer cells. Using multi-omic data CPTAC, we developed cloud-based tools on NCI funded Cancer Genomics Cloud measure RNA,...