Genomics

Genomics for Biomedical Drug Discovery 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 Overview

 

FEBRUARY 02, 2022

Course Overview 

  • Course structure, expectations, and intended outcomes.
  • Applications of bioinformatics (Introduction to Bioinformatics Course),
  • Examples in Biomedical Research
  • Pharma R & D and Agriculture

Associated online resources:

Bioinformatics in R and Python

 

FEBRUARY 09, 2022

Bioinformatics in R and Python 

  • Working with sequences DNA
  • RNA and Protein sequences

Associated online resource:

Next Generation Sequencing history and applications

 

FEBRUARY 16, 2022

NGS history & applications

  • History of NGS
  • Overview of DNA structure
  • DNA variations: Point mutations
  • Deletions, Duplication, Frame Shift
  • Types of Genomics sequencing: Targeted, Whole Genome, Whole Exome
  • Advancements & Challenges
  • Current application of NGS in Biomedical Drug designing and Discovery

Associated online resources:

 

FEBRUARY 21, 2022 at 1 PM CST

LIVE QnA Session
Introduction to genomics

 

FEBRUARY 23, 2022

Introduction  to Genomics

  • Technologies for DNA and RNA sequencing: Microarray, High Throughput Sequencing, qPCR (Introduction to Genomics Course)
  • Advantages and applications of NGS: Illumina, Nanopore and PacBio
  • Computational challenges with short-read sequencing (Big Data)

Associated online resources: 
Genomics and Cancer

 

MARCH 03, 2022

Genomics 1: Cancer 

  • Biology of genetics
  • To identify genetic variants and visualization using the  Integrative Genomics Viewer.

Associated online resource:

Introduction to NGS Genomic Project

 

MARCH 10, 2022

 

Introduction to NGS Genomic Projects

  • Planning Genomics bioinformatics analysis: literature review
  • Compiling a primary dataset
  • Developing an analysis plan

Associated online resource: 

NGS Analysis

 

MARCH 17, 2022

Gen. Sequence Analysis

  • Multiple sequence alignment
  • Phylogenetic tree reconstruction
Associated online resource: 

MARCH 18, 2022 at 1 PM CST

LIVE QnA Session
Mutations and Variant Analysis

 

MARCH 24, 2022

Mutations and Variant Analysis 

  • Germline and Somatic mutations
  • Practical Assignment Analysis 
  • Visualization using Genome Browser
Associated online resource: 

 

Sequence structure and function

 

MARCH 31, 2022

Sequence, structure, and function 

  • Multiple Sequence Alignment
  • Visualizing and filtering alignment R-CODE

Associated online resource:  

 

MARCH 31, 2022 at 1 PM CST

LIVE QnA Session

 

If you need help finalizing registration, contact Farhana Musarrat (email: fmusar1@lsu.edu). You have to register for the orientation using the form below. For LSU or LBRN members, you can complete your registration via BIOMMED iLab link below - 

Register for the Online Mentor Guided Training Program

LBRN certificate

Training Certificate from the Louisiana Biomedical Research Network or LSU BioMMED:

  • Certification of Training Requirement Completion
  • Recognition within the Network and Other IDeA States
  • Advancement for Research, Faculty and Student participants within the LBRN Network
  • Training certification for LSU through the Center for Biotechnology and Biomolecular Medicine at the Louisiana State University