Teaching

Courses taught at the Indian Institute of Science:

• Jan (2026 - 2021), Algorithmic Foundations of Big Data Biology
• Aug (2025, 2022 - 2021): Introduction to Scalable Systems (with Sathish Vadhiyar)

Courses taught on NPTEL:

• Jan (2026-2025), Algorithms in Computational Biology and Sequence Analysis

A collection of lecture slides on bioinformatics topics:

Introduction and warmup

• Molecular biology and high-throughput sequencing
• Dynamic range minimum query
• Bitvector rank and select

Strings and exact matching

• Z-algorithm
• Suffix array
• Suffix array construction
• Suffix trie
• Suffix tree
• Suffix tree construction
• Suffix tree applications
• Burrows Wheeler Transform (BWT)
• Reversing the BWT
• FM-index

Sequence alignment

• Edit distance
• Global and semi-global alignment
• Local alignment
• Gap penalty
• Statistical significance of alignments

Heuristics for sequence alignment

• Motivation
• Maximal unique matches
• Chaining
• Chaining with gap cost

Genome assembly

• Introduction
• Shortest common superstring
• Greedy algorithm
• Assembly using de Bruijn graphs

Demos on real data

• Indexing of 400,000 SARS-CoV-2 genomes
• Genome resequencing