A Multi-species Functional Embedding Integrating Sequence and Network Structure. - Mark D. M. Leiserson; Jason Fan; Anthony Cannistra; Inbar Fried; Tim Lim; Thomas Schaffner; Mark Crovella; Benjamin J. Hescott (RECOMB, 2018)

Matrix (factorization) reloaded: flexible methods for imputing genetic interactions with cross-species and side information. - Jason Fan; Xuan Cindy Li; Mark Crovella; Mark D. M. Leiserson (Bioinform., 2020)

Perplexity: evaluating transcript abundance estimation in the absence of ground truth. - Jason Fan; Skylar Chan; Rob Patro (Algorithms Mol. Biol., 2022)

ScalpelSig Designs Targeted Genomic Panels from Data to Detect Activity of Mutational Signatures. - Nicholas Franzese; Jason Fan; Roded Sharan; Mark D. M. Leiserson (J. Comput. Biol., 2022)

Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing. - Jason Fan; Jamshed Khan; Giulio Ermanno Pibiri; Rob Patro (RECOMB, 2023)

Analyzing and indexing huge reference sequence collections. - Jason Fan (2023)

Meta-colored Compacted de Bruijn Graphs. - Giulio Ermanno Pibiri; Jason Fan; Rob Patro (RECOMB, 2024)

Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs*. - Alessio Campanelli; Giulio Ermanno Pibiri; Jason Fan; Rob Patro (J. Comput. Biol., 2024)

Fulgor: a fast and compact k-mer index for large-scale matching and color queries. - Jason Fan; Jamshed Khan; Noor Pratap Singh; Giulio Ermanno Pibiri; Rob Patro (Algorithms Mol. Biol., 2024)