On the Distribution of Lexical Features at Multiple Levels of Analysis. - Fatemeh Almodaresi; Lyle H. Ungar; Vivek Kulkarni; Mohsen Zakeri; Salvatore Giorgi; H. Andrew Schwartz (ACL (2), 2017)

Improved data-driven likelihood factorizations for transcript abundance estimation. - Mohsen Zakeri; Avi Srivastava; Fatemeh Almodaresi; Rob Patro (Bioinform., 2017)

Towards Selective-Alignment: Bridging the Accuracy Gap between Alignment-Based and Alignment-Free Transcript Quantification. - Hirak Sarkar; Mohsen Zakeri; Laraib Malik; Rob Patro (BCB, 2018)

Optimizing the accuracy of Lightweight Methods for Short Read Alignment and Quantification. - Mohsen Zakeri (2021)

PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index. - Fatemeh Almodaresi; Mohsen Zakeri; Rob Patro (Bioinform., 2021)

Sigmoni: classification of nanopore signal with a compressed pangenome index. - Vikram Shivakumar; Omar Y. Ahmed; Sam Kovaka; Mohsen Zakeri; Ben Langmead (Bioinform., 2024)

EvANI benchmarking workflow for evolutionary distance estimation. - Sina Majidian; Stephen Hwang; Mohsen Zakeri; Ben Langmead (Briefings Bioinform., 2025)