Bacterial Comparative Genomics
Unraveling Evolutionary Threads: Exploring Bacterial Diversity Through Comparative Genomics
MODE
Online/ e-LMS
Online/ e-LMS
TYPE
Self Paced
Self Paced
LEVEL
Moderate
Moderate
DURATION
1 Month
1 Month
VIDEO LENGTH
4.5
4.5
Program Aim
The aim of the program on Bacterial Comparative Genomics is to equip participants with advanced knowledge and practical skills essential for analyzing bacterial genomes through comparative genomics methodologies. By the conclusion of the program, participants will possess the expertise needed to conduct sophisticated genomic analyses and contribute to advancements in bacterial genomics research.
About Program
Explore the intricacies of bacterial genomics in our Advanced program on Bacterial Comparative Genomics. Designed for higher education audiences, this virtual program provides an immersive experience into the analysis of bacterial genomes using cutting-edge bioinformatics tools and techniques. Participants will gain practical skills in processing read data, performing de novo assembly, annotating genomes, and conducting comparative analyses to uncover the evolutionary dynamics and functional diversity of bacterial species.
Program Objectives
- Provide participants with the technical proficiency required to process and analyze read data for bacterial genomes.
- Enable participants to perform de novo assembly, genome annotation, and comparative genomic analyses using state-of-the-art bioinformatics tools.
- Foster an understanding of bacterial genome evolution, genetic diversity, and functional genomics.
- Familiarize participants with tools for identifying antimicrobial resistance genes and conducting pangenome analyses to elucidate bacterial genome dynamics.
- Introduce participants to Comparative Genomics Webservers for further exploration and analysis of bacterial genomes.
Program Structure
Module 1:
- Installing genomics tools with Conda
- Obtaining reads Data
- Perform QC and Trimming of Data
- Perform de novo assembly using spades
Module 2:
- Polish the draft assembly using pilon
- Reordering contigs against a reference genome using ragtag
- Multi-locus sequence typing
- Annotate the draft genome using prokka
Module 3:
- Look for antimicrobial resistance genes using abricate
- Perform Pangenome Analysis
- Overview of Comparative Genomics Webserver like BV-BRC
Requirements:
• Working knowledge of Linux OS system is a must for the program
• PC with Linux operating system or Microsoft Windows Subsystem for Linux (see this link: https://www.freecodecamp.org/news/how-to-install-wsl2-windows-subsystem-for-linux-2-on-windows-10/)
• Install conda. For installing conda in the Windows sub-system see the link: https://medium.com/@parham.motameni/install-conda-on-wsl2-2e76d1e03229
Program Eligibility
- Educational Background: Candidates should typically hold a Bachelor’s degree in a relevant field such as Biology, Microbiology, Genetics, Bioinformatics, or a related discipline. Some programs may require a higher degree such as a Master’s or Ph.D.
- Research Experience: Previous research experience in microbiology, genomics, or bioinformatics is often preferred. This could include coursework, internships, or hands-on laboratory experience.
- Skills and Knowledge: Candidates should have a strong foundation in molecular biology, genetics, and bioinformatics. Proficiency in relevant software and programming languages commonly used in genomic analysis (such as Python, R, or Perl) may be required.
- Interest in Comparative Genomics: Applicants should demonstrate a keen interest in studying bacterial diversity, evolution, and genomic variations across different species or strains. Familiarity with concepts in comparative genomics and evolutionary biology is beneficial.
- Collaborative Attitude: Successful candidates should be able to work effectively in a collaborative research environment. Strong communication skills and the ability to work as part of a multidisciplinary team are often valued.
- Motivation and Commitment: Candidates should demonstrate a genuine passion for research in bacterial genomics and a strong commitment to advancing scientific knowledge in the field.
- Academic Record: A strong academic record, demonstrated through transcripts and recommendation letters, may be required for admission to some programs.
- Specific Program Requirements: Depending on the program, additional eligibility criteria such as language proficiency, GRE scores, or specific prerequisites may apply. Applicants should carefully review the program requirements before applying.
Program Outcomes
- Proficiency in Genomic Data Analysis: Participants will master techniques for processing, analyzing, and interpreting genomic data, including read data QC, de novo assembly, and annotation, enabling them to conduct sophisticated genomic analyses.
- Mastery of Bioinformatics Tools: Participants will gain hands-on experience with essential bioinformatics tools such as SPAdes, Pilon, RagTag, Prokka, and Abricate, equipping them with practical skills for genomic data analysis in research and industry settings.
- Understanding of Comparative Genomics Principles: Participants will develop a deep understanding of comparative genomics principles and methodologies, enabling them to investigate bacterial genome evolution, genetic diversity, and functional genomics.
- Identification of Antimicrobial Resistance Genes: Participants will acquire the expertise to identify antimicrobial resistance genes and interpret their significance in the context of public health, clinical microbiology, and antibiotic drug development.
- Pangenome Analysis Skills: Participants will learn pangenome analysis techniques to explore bacterial genome dynamics, population genomics, and evolutionary biology research, providing valuable insights into microbial ecology and adaptation.
- Effective Communication of Genomic Findings: Participants will enhance their communication skills to effectively present genomic findings and insights, facilitating scientific discourse, writing research papers, and collaborating with interdisciplinary teams.
- Problem-Solving Abilities in Bioinformatics: Participants will develop problem-solving skills to address complex challenges in genomic data analysis, enabling them to overcome technical hurdles and advance genomic research agendas.
- Linux OS Proficiency: Participants will gain strong foundational knowledge in Linux OS for bioinformatics analysis, empowering them to navigate command-line interfaces and perform computational analyses efficiently, essential for academic research and industrial applications.
Fee Structure
Standard Fee: INR 4,998 USD 110
Discounted Fee: INR 2499 USD 55
Certificate
Program Assesment
- Research Objectives: Evaluate how well-defined and relevant the research objectives of the program are. Assess whether they address important questions in bacterial genomics, such as understanding evolutionary relationships, characterizing genomic variations, or elucidating mechanisms of antibiotic resistance.
- Methodologies and Approaches: Assess the appropriateness and rigor of the methodologies and approaches used in the program. Consider the use of cutting-edge genomic technologies, bioinformatics tools, and computational analyses to study bacterial genomes and interpret genomic data.
- Interdisciplinary Collaboration: Evaluate the extent of interdisciplinary collaboration within the program. Assess how effectively researchers from diverse fields such as microbiology, genomics, bioinformatics, and evolutionary biology collaborate to address complex questions in bacterial genomics.
- Publication and Dissemination of Findings: Assess the quantity and quality of research outputs generated by the program, including publications in peer-reviewed journals, conference presentations, and contributions to scientific literature. Evaluate the impact of the program’s findings on advancing knowledge in the field of bacterial genomics.
- Training and Capacity Building: Evaluate the program’s effectiveness in training and capacity building. Assess whether it provides opportunities for students, early-career researchers, and trainees to gain hands-on experience in bacterial genomics research and develop essential skills in genomic analysis and bioinformatics.
- Collaboration with Industry and Healthcare: Assess whether the program fosters collaboration with industry partners and healthcare institutions to translate research findings into practical applications, such as developing diagnostic tools, vaccines, or therapeutics targeting bacterial pathogens.
- Impact on Public Health and Society: Evaluate the broader impact of the program on public health and society. Assess whether research outcomes contribute to understanding bacterial pathogenesis, informing public health policies, and addressing challenges related to antibiotic resistance and infectious diseases.
- Sustainability and Future Directions: Assess the sustainability of the program and its potential for future growth and innovation. Consider whether it has secured funding, established partnerships, and developed strategies for long-term success and expansion in the field of bacterial genomics.
Program Deliverables
- Lecture Slides: A complete set of slides covering all topics from basic genomics to advanced comparative techniques.
- Video Lectures: Recorded expert lectures on genome sequencing, data analysis, and interpretation.
- Interactive Modules: Online modules for hands-on learning of software tools and databases used in bacterial comparative genomics.
- Bioinformatics Software Suite: Licenses or free access to key bioinformatics software used for sequence alignment, genome assembly, and annotation.
- Genomic Databases: Access to major bacterial genomic databases and tutorials on how to use them for comparative studies.
Future Career Prospects
- Advanced Research and Development: Lead cutting-edge research projects in academic, governmental, or private sectors focusing on microbial genomics, antibiotic resistance, and pathogen evolution.
- Biotech and Pharmaceutical Leadership: Take on senior roles in biotechnology and pharmaceutical companies developing new antibiotics, vaccines, and microbial products.
- Public Health and Epidemiology: Direct public health initiatives and policy development using genomic data to control and prevent infectious diseases.
- Bioinformatics and Data Science: Specialize in bioinformatics, developing new tools and algorithms for analyzing complex genomic datasets.
- Regulatory and Bioethics: Engage in regulatory, ethical, and policy roles, ensuring that genomic technologies are developed and implemented responsibly.
