Bioinformatics for Infectious Diseases: Training & Research Support Program

Bioinformatics for Infectious Diseases is a program developed in collaboration with Noguchi Memorial Institute for Medical Research (NMIMR), Ghana’s leading biomedical research institute at the University of Ghana. The program is designed to introduce students, clinicians and researchers to the role and the applications of bioinformatics to the study of pathogenic microorganisms and their interaction with the host and vectors. 

Using examples from peer-reviewed publications, participants will learn to apply bioinformatics tools to publicly available genomic and transcriptomic data on Plasmodium falciparum, Ebolavirus, Sars-COV-2, Mycobacterium tuberculosis and other pathogens. The program will last for 1 month and will  include 12 online sessions, 6 asynchronous courses and several specially curated datasets to support research projects with a focus on Malaria (Plasmodium falciparum) and COVID-19 (SARS-COV-2). In addition, we will work with the community of researchers at the University of Ghana and University of Haifa, Israel, where the Tauber Bioinformatics Research Center members will showcase their research in the area of 

• Pathogen Population genetics (signatures of pressure response)
• Host-pathogen-vector interaction
• Multi-omics integration

The program will be led by Omics Logic mentors who have considerable expertise with virology, immunology and bioinformatics. A group of research participants from the University of Ghana will be led by their Principal Investigator: Dr. Anita Ghansah (aghansah2013@gmail.com) and Dr. Bright Abu. and other researchers from the Noguchi Memorial Research Institute and Rhodes University (SA).

What is the significance of Bioinformatics for Infectious Diseases?

Genomics and bioinformatics have contributed immensely to our understanding of infectious diseases: from disease pathogenesis, to the mechanisms of host-pathogen interaction, spread of antimicrobial resistance, and host immune responses. As a result, the emergence of genomic medicine has substantially advanced our ability to detect, study and treat infectious diseases. These achievements came as a result of a close collaboration between computer scientists and biologists, placing bioinformatics at the center of current advances in this domain.

Before the program starts, we will conduct open sessions for those joining any of the upcoming training phases and explain how the program will work, giving them examples of topics, research activities, outcomes and data.

Host pathogen Interaction

You can now watch the video here – https://youtu.be/5tEykxIepHw

Training schedule

This program is divided up into several phases intended to cover important topics relevant to infectious disease research and bioinformatics. In each phase, we include several free webinars that will be highlighted in this schedule.

Free Webinar: Preparing for Analysis: Formulating your question and finding publicly accessible data. (Jan. 25, 2020)

Pre-registration link: https://edu.tbioinfo.com/infectious-diseases-noguchi-program

Phase 1: Introduction to Bioinformatics for Infectious Diseases 

Overview: 1 month program with 7 sessions online sessions and asynchronous resources in between

The program will include tutorial projects on various pathogens (Ebola, Covid, Tuberculosis, EV-D68) as well as specific topics related to Malaria and COVID-19

This phase of the program will culminate in short research proposals that will be presented in an open Session: Overview Student Research Projects – Feb 22, 2021

Phase 2: Bioinformatics Research Project Development

To support the development of projects based on the research proposals they have developed in phase 1 of the program, we will hold several sessions to guide proper analysis planning and execution. To do so, we will explore various topics related to infectious diseases, such as:

In the context of this training program, many of the projects we have been developing will be used as examples: Mutation profiling of EBOLA virus outbreaks, Origin and Pathogenesis of Novel Coronavirus, as well as novel techniques on low-frequency mutation studies involving cirseq.

In this 2 months program, participants will gain access to tutorials and practical examples that will illustrate:

• Analysis methods and tools for genomic and transcriptomic data analysis of host-pathogen interactions
• Methods to study relationships based on local and global multiple sequence alignment (MSA)
• Phylogenetic analysis and evolutionary studies used for genome ancestry and population fitness
• Chemical and structural implications of sequence variation mapped on PDB models
• Host-pathogen interaction and treatment response

For the duration of this program, participants will gain access to research tools, training and mentor support, helping translate bioinformatics into a practical toolkit for research. The included resources are:

• Course Access – (access to edu.t-bio.info portal)
• Coding platform –  (access to coding challenges on code.omicslogic.com)
• Interactive Sessions –  (guided ZOOM sessions with a Trainer)
• 3 projects –   (Use-case examples on edu.t-bio.info)
• Mentor Support – (one-on-one technical support, guidance with projects, etc.)
• Education Cloud Pipelines – (Additional 30 days for project development)

How to Register?

1. Program details can be found here: https://infectious-diseases.omicslogic.com/
2. To register, first click on “Get Started”
3. Select a membership (Basic, Intermediate, Advanced) of your choice
4. Add your card details and checkout
5. To Register for the full program(2 months), please select the advanced option.

Scholarships

For scholarship request, please fill up the form here – https://edu.tbioinfo.com/scholarship-2021

The scholarships we offer are designed to help motivated, talented and promising students to benefit from special training and research opportunities. The criteria for approval include a reasonable need, indication of extra effort that the participant is willing to put into the program and time commitment needed to go beyond the regular training. 

This will likely include keeping a regular record of topics covered, detailed “lab journal” entry and participation in student-facing presentations about the learned topics. Here is an example of what such presentations might include: https://youtu.be/eV1mNlbTwqs

 For any questions about the program and its resources, please reach out to – marketing@pine.bio