Metastasis claims 90% of all cancer-related deaths and remains clinically insuperable. The hallmarks of metastases are processes known as Epithelial to Mesenchymal Transition (EMT) and its reverse Mesenchymal to Epithelial Transition (MET) that enable primary carcinoma cells to migrate and start new tumors at distant organs. I will present an integrated theoretical and experimental approach that elucidates how cancer cells undergo EMT and MET, and how these transitions affect their ability to initiate new tumors.
Cellular Senescence
Held usually at 3:30pm on Fridays, TGIF discussions are informal talks on current scientific topics and events.
Bioinformatics in Influenza surveillance: From sequence to structure to molecular mechanisms with the FluSurver
Bioinformatics can play an important role in infectious disease surveillance and research from epidemiological data processing with geographic and temporal visualization to comparing genome phylogenies and structural modelling of mutations. As a classical example, interest in new influenza outbreaks as well as regular surveillance of circulating seasonal strains produce a constant flow of influenza genome sequences that need to be analysed and interpreted for epidemiological and phenotypic features.
Network Pharmacology
Held usually at 3:30pm on Fridays, TGIF discussions are informal talks on current scientific topics and events.
CellMiner databases, tools, and molecular pharmacologic applications
Understanding the influences of molecular alterations on pharmacological responses in the omic sense is at the fore of the effort to make oncology treatments more effective and specific. At present, however, this remains a field in its infancy. The NCI-60 cancerous cell lines provide a premier set of databases and tools for systems molecular pharmacological studies.
Overview of the Galaxy platform for analysis of genomics data
Modern genomics research requires complex computational processing to integrate, analyze, and extract meaning from large, disparate datasets. While a multitude of commercial and open source bioinformatics applications are available, it is difficult to assemble a collection of tools that work together seamlessly to perform the required analysis. Even more difficult is performing analysis in a manner that documents the data, algorithms, and processing steps such that the results are easily published and reproducible.
Cancer Systems Genomics
Abstract – I will describe my work with the NCI TARGET Pediatric Acute Myeloid Leukemia consortium in which we are integrating data from 197 cancer whole genome sequences with mRNA and miRNA expression and DNA-methylation data, including verification of DNA variants via targeted re-sequencing, and frequency validation of confirmed variants in 650 additional patients.
Introduction to Next Generation Sequencing Data Analysis (May 2016)
Introduction to Next Generation Sequencing Data Analysis (May 2016) by the Core Facility for Bioinformatics
Noises and dynamics in cells: Mathematical modeling in systems biology
One important aspect in the systems biology is to gain understanding in the systems level with molecular basis. With molecular basis in the model, new treatment or genetic perturbation can be designed in order to change the systems behavior. In this talk, I’ll focus on the methodology and an application for simulating a biological system, particularly for systems with noises.
Genome Assembly, Annotation and Variant Calling Training And Workshop (May 2016)
Genome Assembly, Annotation and Variant Calling Training and Workshop (May 2016) by Core Facility for Bioinformatics