Key Topics Covered:

SESSIONS

TOPICS

Bioinformatics in Translational Oncology Research

• The cancer problem – complexity of cancer biology and typical challenges in diagnostics (organs, tissues, cells).
• Molecular factors in tumor development, growth and metastasis.
• Overview of clinical and molecular data types and features (phenotype-genotype relationship).

Associated Online Resources:

• Modeling Cancer Precision Medicine

Next generation Sequencing: Analysis of DNA Variation

• Introduction to Next generation Sequencing: shotgun sequencing reads
• The need for structured data and associated bioinformatics methods: processing (germline and somatic mutations)
• Analysis (mapping, detecting variants) and interpretation (significant and insignificant mutations, etc.)
  
  

Associated Online Resources: 

• Introduction to Genomics
• Advanced Genomics Overview
• Mutability Analysis & Interpretation

Processing Next Generation Sequencing Data

• An overview of RNA-seq
• Read quality and pre-processing
• Mapping on reference genome using various tactics (alignment and alignment-free quantification)
• Quantification of genes and transcripts.
• Summary of structured data: visualization (PCA) & biological significance (annotation and interpretation). 

Associated Online Resources:

• RNA-seq and NGS sequencing
• RNA Quantification
• Data Preparation for Downstream Analysis
• Principal component Analysis (PCA ):Tutorial

 Machine Learning for Gene Expression Data

• Data exploration using dimensionality reduction and clustering
• Classification and discriminant analysis for labeled datasets
• Unsupervised and Supervised Machine Learning

Associated Online Resources:

• Dimensionality reduction: PCA, t-SNE & visualization
• Machine Learning methods
• Unsupervised Machine Learning (Clustering)
• Supervised Machine Learning

 Oncology Data Sources: Raw Data and Public Databases

• NCBI (National Center for Biotechnology Information): SRA, GEO, RefSeq and other repositories of publicly available research data.
• TCGA: The Cancer Genome Atlas and the multi-center project for cancer research studies as a case study for oncology data mining.
• COSMIC: database of mutation variants and their impact on disease phenotype and treatment in cancer.

Associated Online Resources:

• NCBI : SRA, GEO, RefSeq
• TCGA
• COSMIC

NGS: Viral Genomes in the Host Transcriptome

• Oncolytic viruses and their role in tumor development
• Inflammation and tissue damage.
• Using alignment, annotation, and non-mapped reads to detect viral genomes in clinical samples.
• Alignment to databases of viral genomes.

Associated Online Resources:

• RNA-seq and NGS sequencing
• Genomic Variation in NGS Data: Practical

• Multiple sequence alignment and phylogenetic analysis
• Preparation of Data: Assembled genome sequences
• Selecting appropriate genomic sequences for a full pipeline

Associated Online Resources:

• Multiple Sequence Alignment - visualizing and filtering alignment
• Comparing DNA sequences using Phylogenetic Analysis

 Workflows and pipelines in bioinformatics

• Logic behind various: Workflows and pipelines
• Utilizing the right references: What to do if we have FASTA/FASTQ files?
• Which databases to use: Detection of viral genomes by mapping on databases.
• Interpretation of Phylogenetic Analysis: Evolutionary relationships between genomes, evolutionary time.

Associated Online Resources:

• Phylogenetic Analysis
• Comparing DNA sequences using Phylogenetic Analysis

From Infection to Pandemic: Viral Adaptation

• The origin of human infection with MERS, SARS, and SARS-2 pandemics.
• Activation of immune response and cytokine storm caused by viral replication.
• Scarring, inflammation and cancer.

Associated Online Resources:

• COVID-19 Origin & Pathogenesis of SARS-COV2

Host-Pathogen Interaction

• Host response to viral replication and the implications for cell, organ and tissue.
• Viral strategies for exploitation of host cellular machinery in viral protein production. 

Associated Online Resources:

• COVID-19 Origin & Pathogenesis of SARS-COV2