| 2025 | EASE | Exploring Zero-Shot App Review Classification with ChatGPT: Challenges and Potential. | Mohit Chaudhary, Chirag Jain, Preethu Rose Anish |
| 2025 | RECOMB | Integer Programming Framework for Pangenome-Based Genome Inference. | Ghanshyam Chandra, Md. Helal Hossen, Stephan Scholz, Alexander T. Dilthey, Daniel Gibney, Chirag Jain |
| 2025 | WABI | Haplotype-Aware Long-Read Error Correction. | Parvesh Barak, Daniel Gibney, Chirag Jain |
| 2024 | COLING | Generating Clarification Questions for Disambiguating Contracts. | Anmol Singhal, Chirag Jain, Preethu Rose Anish, Arkajyoti Chakraborty, Smita Ghaisas |
| 2024 | EMNLP | Refining App Reviews: Dataset, Methodology, and Evaluation. | Amrita Singh, Chirag Jain, Mohit Chaudhary, Preethu Anish |
| 2024 | HRI | DRAWBOT: Making Everyday Objects Interactive. | Chirag Jain, Hunter L. Brown, Heather Knight |
| 2024 | ISIT | On the Coverage Required for Diploid Genome Assembly. | Daanish Mahajan, Chirag Jain, Navin Kashyap |
| 2024 | RECOMB | Haplotype-Aware Sequence Alignment to Pangenome Graphs. | Ghanshyam Chandra, Daniel Gibney, Chirag Jain |
| 2023 | CIT | Securing E-Voting using Hyperledger Fabric: A Permissioned Blockchain Approach. | Chirag Jain, Luv Gupta, Manav Ranawat, Varsha Hole |
| 2023 | HiPC | A Lossless Compression Pipeline for Petabyte-Scale Whole Genome Sequencing Data. | Ajeya Bhat, Sai Manasa Chadalavada, Nagakishore Jammula, Chirag Jain, Yogesh Simmhan |
| 2023 | RE | Automated Identification of Security and Privacy Requirements from Software Engineering Contracts. | Chirag Jain, Preethu Rose Anish, Smita Ghaisas |
| 2023 | RE | A Transformer-based Approach for Abstractive Summarization of Requirements from Obligations in Software Engineering Contracts. | Chirag Jain, Preethu Rose Anish, Amrita Singh, Smita Ghaisas |
| 2023 | RECOMB | Sequence to Graph Alignment Using Gap-Sensitive Co-linear Chaining. | Ghanshyam Chandra, Chirag Jain |
| 2023 | WABI | Co-Linear Chaining on Pangenome Graphs. | Jyotshna Rajput, Ghanshyam Chandra, Chirag Jain |
| 2022 | RECOMB | Co-linear Chaining with Overlaps and Gap Costs. | Chirag Jain, Daniel Gibney, Sharma V. Thankachan |
| 2020 | ICMI | It's Not What They Play, It's What You Hear: Understanding Perceived vs. Induced Emotions in Hindustani Classical Music. | Amogh Gulati, Brihi Joshi, Chirag Jain, Jainendra Shukla |
| 2019 | RECOMB | On the Complexity of Sequence to Graph Alignment. | Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru |
| 2019 | WABI | Validating Paired-End Read Alignments in Sequence Graphs. | Chirag Jain, Haowen Zhang, Alexander T. Dilthey, Srinivas Aluru |
| 2018 | AAAI | Production Ready Chatbots: Generate if Not Retrieve. | Aniruddha Tammewar, Monik Pamecha, Chirag Jain, Apurva Nagvenkar, Krupal Modi |
| 2017 | RECOMB | A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases. | Chirag Jain, Alexander T. Dilthey, Sergey Koren, Srinivas Aluru, Adam M. Phillippy |
| 2016 | HPDC | A Self-Correcting Connected Components Algorithm. | Piyush Sao, Oded Green, Chirag Jain, Richard W. Vuduc |
| 2015 | SC | A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications. | Patrick Flick, Chirag Jain, Tony Pan, Srinivas Aluru |
| 2014 | HiPC | Fine-grained GPU parallelization of pairwise local sequence alignment. | Chirag Jain, Subodh Kumar |
| 2008 | ICIP | A low-complexity, motion-robust, spatio-temporally adaptive video de-noiser with in-loop noise estimation. | Chirag Jain, Sriram Sethuraman |