Genomics

Genomics Data Analysis is an online bioinformatics training program that will provide an in-depth overview of concepts and analytical tools used to study genomic variation. The program is designed to introduce students, clinicians and researchers to the role and the applications of Genomic Data Analysis to study genomic variation and apply genomics in translational sciences to improve diagnostic accuracy, predict which drugs are likely to be effective in patients, and contribute to the monitoring, treatment and diseases in individuals and populations.

Each week, participants will meet online to discuss various aspects of NGS data processing, genomic data analysis, and interpretation. After the first introductory lectures, participants will have the opportunity to get guidance and work on curated datasets or develop independent projects that leverage the tools and concepts covered in this program.

Key Topics Covered:

  Big data, HPC and cloud computing

Many types of omics data require step-by-step preparation, exploration, annotation, and visualization to understand. The T-BioInfo platform was designed for big multi-omics data analysis hiding the complexities of data with a user-friendly and intuitive interface that eliminates the need for coding and advanced machine learning algorithms for data integration and mining.

 NGS: omics data types and use cases

A program that embeds data-driven concepts into biological projects, spanning the student learning journey from observer to participant in research. Project-based learning for big data bioinformatics is to go beyond the theory with real datasets, projects, and expert mentors. Work with curated datasets from publicly available repositories with easy-to-follow tutorials.

 Computational pipelines for data processing

Data processing for Next Generation Sequencing, Mass-Spectroscopy, Structural and phenotypic data. Build and adapt pipelines using similar approaches to data mapping, quantification, and annotation that are used to prepare data for downstream statistical analysis, train machine learning models and annotate features.

 Introduction to Programming: R and Python
Online bioinformatics coding exercises to learn and explore R and Python scripting and understand how to analyze and visualize -omics data to extract meaningful insights from large biological datasets. Learn, practice, and achieve bioinformatics greatness with concise exercises and interesting challenges right in the comfort of your browser!

Program Syllabus: OmicsLogic Genomics 

 
SESSIONS TITLE TOPICS TO BE COVERED
Genomics Data Analysis: Course Overview 

Associated online course/resource:

Genomics Data Analysis: Course Overview 

  • Next Generation Sequencing Data
  • Omics Data Molecular Determinants of a Phenotype
  • Overview of Mutations & Variations
  • Course structure, expectations, and intended outcomes.
  • Topics: Applications of bioinformatics (Introduction to Bioinformatics Course),
  • Examples in Biomedical Research,
  • Pharma R & D and Agriculture
Access to the educational portal (https://learn.omicslogic.com) & analytical server (server.t-bio.info)
Slide2

Associated online course/resource

Unraveling Genomics & Working with DNA sequences using R

  • Understanding of DNA Variation 
  • DNA sequences and alignment in R
  • NGS processing, data formats & technical challenges
  • Mapping, read alignment & section of variants
  • Next steps for whole exome data analysis
  • Working with DNA sequences in R
  • Pairwise Sequence Alignment
  • Multiple Sequence Alignment
  • RNA and Protein sequences (Exploring PDB)
  • Genomic Variations
  • Working with DNA sequences in R using OmicsLogic Code Block & Google Collab Notebook 
Next Generation Sequencing: An overview of history & applications

Associated online course/resource:

Next Generation Sequencing: An overview of history & applications

  • History of NGS
  • Overview of DNA structure
  • DNA variations: Point mutations
  • Deletions, Duplication, Frame Shift
  • File Formats: FASTq, FASTA, SVL, BAM, GTF
  • Types of Genomics sequencing: Targeted, Whole Genome, Whole Exome
  • Advancements & Challenges
  • Current application of NGS in Biomedical Drug designing and Discovery
  • Analysis of Genomic Data on T-Bio info Server
     

    Suggested Reading:

    Long walk to genomics: History and current approaches to genome sequencing and assembly

Introduction to Genome Sequencing Techniques & Hands-on with Datasets

Associated online course/resource: 

Introduction to Genome Sequencing Techniques & Hands-on with Datasets

  • Technologies for DNA and RNA sequencing: Microarray, High Throughput Sequencing, qPCR 
  • Mapping/Alignment to Reference Genome
  • Allele Frequency 
  • Advantages and applications of NGS: Illumina, Nanopore and PacBio
  • Computational challenges with short-read sequencing (Big Data)
  • Exploring MalariaGen for hands-on analysis on T-Bioinfo Server
Understanding Genomic Variations and Hands-On with IGV

Associated online course/resource:

Understanding Genomic Variations and Hands-On with IGV

  • Next Generation Sequencing(NGS) Data
  • Sequencing read based on length
  • Sequencing technology
  • Illumina Sequencing Technology
  • Nanopore Sequencing Technology
  • Significance of DNA variation
  • DNA variant calling (VCF File)
  • DNA Aberration: In/Dels
  • Tuberculosis Drug Resistance
  • Ebola Virus: Transmission & Vaccine Design 
  • Identification of genetic variants and visualization using the Integrative Genomics Viewer.
Introduction to NGS Genomic Projects

Big Data Repositories:

Pubmed: https://pubmed.ncbi.nlm.nih.gov/

NCBI SRA: https://www.ncbi.nlm.nih.gov/sra

NCBI Virus: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/

GEO: https://www.ncbi.nlm.nih.gov/geo/

Introduction to NGS Genomic Projects

  • Project Examples
  • Origin and Pathogenesis of the Novel Coronavirus
  • Phylogenetic Analysis
  • Multiple Sequence Alignment
  • Key protein components responsible for Pathogenicity
  • Designing a Bioinformatics Project
  • Steps to be followed for project development
  • Choosing a topic for your project
  • Exploring Big Data Repositories
  • Compiling a primary dataset
  • Developing an analysis plan
  • Mutation Cell line Hands-on analysis on T-Bioinfo Server

Associated online course/resource: 

Mutability & Phylogenetic Analysis: Tools & Applications

Associated online course/resource:  

Mutability & Phylogenetic Analysis: Tools & Applications

  • Multiple sequence alignment
  • Mutability Pipeline
  • What is machine learning?
  • Types of machine learning
  • Dimensionality Reduction
  • Principal Component Analysis
  • Phylogenetic tree reconstruction
  • Methods for the estimation of reproduction number (RO)
  • Applications of Phylogenetic tree: Analysis based on sequence & metadata
  • Phylogenetic analysis
  • Hands-on with Phylogenetic tree graphic viewer: FigTree
  • Hands-on with Ugene

FigTree: http://tree.bio.ed.ac.uk/software/figtree/

Ugene: http://ugene.net/

Mutations and Variant Analysis

 

Mutations and Variant Analysis 

  • Differential Mutation Analysis
  • Germline and Somatic Mutations 
  • Practical Assignment Analysis and Visualization using Genome Browser

Associated online course/resource: 



Sequence, Structure and Function 

Example Projects on Genomics Data Analysis on OmicsLogic Learn Portal

Sequence, Structure, and Function 

  • Multiple Sequence Alignment
  • Practical Hands-on with Ugene
  • Visualizing and filtering alignment R-CODE
  • Genome Wide Association Studies
  • Important Terms
  • HapMap Project
  • GWAS Methods
  • Case Study: Tuberculosis Infection & Treatment: Finding Drug Resistant Variants
  • Practical Hands-on with GWAS Pipeline on T-Bioinfo Server
  • Exploring NCBI Bioproject to extract data
  • Result Analysis and Biological Interpretation 

Now that you have the required expertise for Genomic Data Analysis, let's get started with your Research Project. To learn more about the Research Fellowship Program, visit: Omics Logic - Research Fellowship Program

Research Proposal Form: Form (hsforms.com)

 

Register for the Upcoming Webinar Session: