Teaching [Back]

Student Mentorship

I have designed and virtually delivered an Introductory Bioinformatics course to two graduate students at Queen’s University (Kingston, Ontario, Canada). The course outline was follows:

Title: Bioinformatics analysis methods for the analysis of Mycobacterium tuberculosis whole genome sequencing (WGS) data.
Description: This course introduces bioinformatics approaches used for the analysis of Mycobacterium tuberculosis (Mtb) WGS data. The focus is on such topics as fundamental approaches for WGS data analysis and Linux command line use; application of various tools/software and databases; software methods for quality check trimming, read mapping, alignment manipulation and visualization, and quality evaluation of de novo assemblies; and finding specific sequences of interest from a given assembly using BLAST search.
Duration: 8th July 2021 – 9th September 2021
Number of lectures: 10
Course schedule: The material (i.e., lecture slides and data for hands-on practices) for this course was provided to the students by email before each lecture. Students have recorded all the virtual lectures. Homework for students after each lecture was included in the slides. Students were not evaluated because they undertook this course as non-credit.
Learning outcomes: At the end of this course students should be able to do the following:

1. Download and install required command-line software.
2. Check the basic quality and tell whether the WGS samples are good or bad.
3. To trim and remove the adapter contamination
4. Align the WGS data against the reference genome and visualize the output file.
5. Examine assembled genomes using NCBI BLAST for any contamination and/or hybrid sequences, and to check whether the assembly belongs to the Mtb reference genome or not.
6. Identify and extract specific gene sequences of interest from the given assembly.
7. Check whether the quality of the assembly is good or bad.

Guest Faculty (Teaching; 2006(1 month)) at Guru Jambheshwar University of Science and Technology, Hisar, India

Course: Introductory Bioinformatics (MBT-525)
Class: M.Sc. Biotechnology
Number of lectures: 16

Invited Talks at Workshops

Conducted by Department of Biophysics (2009-2012), AIIMS, New Delhi, INDIA
*Also conducted hands-on practical sessions (as Instructor) in all workshops.

1. Introduction to microarray (2012)
2. Database searching and sequence alignment tool demo (2011)
3. Sequence alignment tools(2010)
4. Introduction to databases and demo on sequence alignment(2010)
5. Basic of perl scripting (2009)

Students Supervison

Supervised and managed 7 graduate and undergraduate students in their dissertation projects.