Precision medicine is changing the way we understand, diagnose and treat major life-threatening diseases. The transformation is driven by high-throughput molecular data from patients, animal models, and large-scale experiments.
In this program, we will explore how the various -omics data types can be analyzed to understand the basic biology associated with viruses & hosts, cancer onset & development and outcomes and see how large-scale clinical trials and experiments provide an opportunity to improve precision medicine. In the later part of the program, we will learn about virology and immunology and the use of bioinformatics for infectious disease research, diagnostics as well as drug and vaccine development.
Cancer biology: changes in organs, tissues, and cells, Molecular factors in tumor development and metastasis, Clinical and molecular data in oncology studies, Analyzing the...
Processing (germline and somatic mutations) Analysis (mapping, detecting variants) Interpretation (variant types and significance)
Quality Control and the role of pre-processing, Mapping strategies: alignment to transcriptome or genome Quantification and Visualization of Gene Expression
Data exploration using dimensionality reduction and clustering, Classification and discriminant analysis for labeled datasets, Unsupervised & Supervised Machine Learning
National Center for Biotechnology Information (NCBI)Sequence Read Archive (SRA), Gene Expression Omnibus (GEO)The Cancer Genome Atlas (TCGA), COSMIC
Overview of NGS: reads, sequences, file formats, alignment, annotation, and non-mapped reads, Alignment to databases of viral genomes
Multiple sequence alignment and Phylogenetic Analysis, Preparation of data: assembled genome sequences, Selecting appropriate genomic sequences for a full pipeline
The logic behind various Workflows and Pipelines, Finding and using the right References & Databases Approaches to Interpretation of Visual Outputs
Example Project: the origin of Coronavirus pandemics: MERS, SARS, and SARS-2 outbreaks
Interaction between pathogen and host response, Analysis of gene expression to capture immune responses, Implications for vaccine design: factors for consideration.
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