Sequence to Graph Alignment Using Gap-Sensitive Co-linear Chaining. - Ghanshyam Chandra; Chirag Jain (RECOMB, 2023)

Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs. - Ghanshyam Chandra; Chirag Jain (J. Comput. Biol., 2023)

Haplotype-Aware Sequence Alignment to Pangenome Graphs. - Ghanshyam Chandra; Daniel Gibney; Chirag Jain (RECOMB, 2024)

Co-linear chaining on pangenome graphs. - Jyotshna Rajput; Ghanshyam Chandra; Chirag Jain (Algorithms Mol. Biol., 2024)

Integer Programming Framework for Pangenome-Based Genome Inference. - Ghanshyam Chandra; Md. Helal Hossen; Stephan Scholz; Alexander T. Dilthey; Daniel Gibney; Chirag Jain (RECOMB, 2025)