Modeling Global and local Codon Bias with Deep Language Models. - Masaki Stanley Fujimoto; Paul M. Bodily; Cole A. Lyman; Andrew J. Jacobsen; Quinn Snell; Mark J. Clement (BIBE, 2017)

Genome Polymorphism Detection Through Relaxed de Bruijn Graph Construction. - M. Stanley Fujimoto; Cole A. Lyman; Anton Suvorov; Paul M. Bodily; Quinn Snell; Keith A. Crandall; Seth M. Bybee; Mark J. Clement (BIBE, 2017)

Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs. - Cole A. Lyman; M. Stanley Fujimoto; Anton Suvorov; Paul M. Bodily; Quinn Snell; Keith A. Crandall; Seth M. Bybee; Mark J. Clement (BIBE, 2017)

The PepSeq Pipeline: Software for Antimicrobial Motif Discovery in Randomly-Generated Peptide Libraries. - Tanner D. Jensen; Kristi A. Bresciano; Emma Dallon; M. Stanley Fujimoto; Cole A. Lyman; Enoch Stewart; Joel Griffitts; Mark J. Clement (BCB, 2018)

Feedback Regulation of Immune Response to Maximum Exercise in Gulf War Illness. - Cole A. Lyman; Mark J. Clement; Travis J. A. Craddock; Mary Fletcher; Nancy G. Klimas; Gordon Broderick (BCB, 2019)

When the How Outweighs the What: the Pivotal Importance of Context. - Cole A. Lyman; Connor Anderson 001; Matthew C. Morris; Umesh K. Nandal; Marianna J. Martindale; Mark J. Clement; Gordon Broderick (BIBM, 2019)

Predicting the Immune Response to Repurposed Drugs in Coronavirus-induced Cytokine Storm. - Matthew C. Morris; Cole A. Lyman; Spencer Richman; Hong Bao Cao; Chris Cheadle; Gordon Broderick (BIBE, 2020)

Hacking the Immune Response to Infection in Chronic Obstructive Pulmonary Disease. - Matthew C. Morris; Spencer Richman; Cole A. Lyman; Jun Qu; Manoj J. Mammen; Sanjay Sethi; Gordon Broderick (BIBE, 2020)

Kcollections: A Fast and Efficient Library for K-mers. - M. Stanley Fujimoto; Cole A. Lyman; Mark J. Clement (IPDPS Workshops, 2020)

High Fidelity Modeling of Pulse Dynamics using Logic Networks. - Cole A. Lyman; Matthew C. Morris; Spencer Richman; Hong Bao Cao; Antony Scerri; Chris Cheadle; Gordon Broderick (BIBM, 2021)

Leveraging Drug-Target Interaction Data for the Translation of Computational Models into Clinically Actionable Interventions. - Spencer C. Richmanz; Cole A. Lyman; Matthew C. Morris; Hongbao Cao; Anastasia Nesterovay; Anton Yuryevy; Chris Cheadle; Gordon Broderick (BIBM, 2021)