Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language. - Haitham Elmarakeby; Mostafa Arefiyan; Elijah Myers; Song Li; Ruth Grene; Lenwood S. Heath (J. Comput. Biol., 2017)

Deep Learning for Biological Problems. - Haitham Elmarakeby (2017)

Biologically informed deep neural network for prostate cancer discovery. - Haitham Elmarakeby; Justin Hwang; Rand Arafeh; Jett Crowdis; Sydney Gang; David Liu; Saud H. AlDubayan; Keyan Salari; Steven Kregel; Camden Richter; Taylor E. Arnoff; Jihye Park; et al. (Nat., 2021)

Empirical evaluation of language modeling to ascertain cancer outcomes from clinical text reports. - Haitham Elmarakeby; Pavel S. Trukhanov; Vidal M. Arroyo; Irbaz Bin Riaz; Deborah Schrag; Eliezer M. Van Allen; Kenneth L. Kehl (BMC Bioinform., 2023)