Chirag Jain
Assistant Professor
Pratiksha Trust Young Investigator
Department of Computational and Data Sciences
Indian Institute of Science
My research lab develops efficient computational algorithms for data-intensive problems in biology. In response to challenging computational problems, we design solutions that are provably-good, scalable in practice, and useful for life scientists to draw new insights from high-throughput data.
Prior to my appointment at IISc, I was working as a post-doctoral fellow with Adam Phillippy at the National Institutes of Health. In 2019, I received Ph.D. at Georgia Tech, where I was advised by Srinivas Aluru for my dissertation work. I did my bachelors in computer science at Indian Institute of Technology Delhi. I'm a recipient of the Pratiksha Trust Young Investigator Award and Georgia Tech College of Computing Dissertation Award.
I am looking for bright students and postdocs to join my lab. Interested folks are welcome to contact me. See projects and publications to learn about our work.
Research Interests
• Bioinformatics / computational biology
• Algorithms for genome sequencing
• Applied graph / combinatorial / discrete algorithms
• Algorithms design and analysis
• High performance computing
Teaching
[2023 January] DS202: Algorithmic Foundations of Big Data Biology
[2022 August] DS221: Introduction to Scalable Systems (jointly with Sathish Vadhiyar, Matthew Jacob)
Selected Publications
Weighted minimizer sampling improves long read mapping
C Jain, A Rhie, H Zhang, C Chu, B Walenz, S Koren, A Phillippy. ISMB 2020
On the complexity of sequence to graph alignment
C Jain, ⇔ H Zhang, Yu Gao, S Aluru. RECOMB 2019
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
A Dilthey, C Jain, S Koren, A Phillippy. Nature Comm. 2019
Accelerating sequence alignment to graphs
C Jain, S Misra, H Zhang, A Dilthey, S Aluru. IEEE IPDPS 2019 (GT news)
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
C Jain, L Rodriguez, A Phillippy, K Konstantinidis, S Aluru. Nature Comm. 2018 (GT news)
A fast approximate algorithm for mapping long reads to large reference databases
C Jain, A Dilthey, S Koren, S Aluru, A Phillippy. RECOMB 2017
Selected Awards
• NERSC HPC Achievement Award 2022 (news: HPCWire ) • Pratiksha Trust Young Investigator Award 2020 • Georgia Tech College of Computing Dissertation Award 2020 • Best Poster Award RECOMB 2019 • ACM Supercomputing Reproducibility Award 2016 (news: CACM, HPCWire, SC, insideHPC ) • NVIDIA Award for Best Paper using GPU Technologies IEEE HiPC 2014