An Informatics Framework for Knowledge Representation and Reconciliation of Disease Pathways. - Yulia Innokenteva; Olha Kholod; Fei He 005; Duolin Wang; Richard D. Hammer; Dong Xu 002; Dmitriy Shin (AMIA, 2019)

Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning. - Fei He 005; Duolin Wang; Yulia Innokenteva; Olha Kholod; Dmitriy Shin; Dong Xu 002 (BIBM, 2019)

Mutational Forks: Inferring Deregulated Flow of Signal Transduction Based on Patient-Specific Mutations. - Olha Kholod; Zhen Lyu; Jonathan B. Mitchem; Peter J. Tonellato; Trupti Joshi; Dmitriy Shin (BIBM, 2019)

Modeling of Contextual Information in Knowledge Graphs of Diagnostic Reports. - Pericles S. Giannaris; Cynthia Tang; Olha Kholod; Steve Hanson; Chi-Ren Shyu; Richard D. Hammer; Dong Xu 002; Dmitriy Shin (SWH@ISWC, 2019)

Identifying patient-specific flow of signal transduction perturbed by multiple single-nucleotide alterations. - Olha Kholod; Chi-Ren Shyu; Jonathan B. Mitchem; Jussuf T. Kaifi; Dmitriy Shin (Quant. Biol., 2020)

Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles. - Fei He 005; Joshua Thompson; Ziting Mao; Yijie Ren; Yulia I. Nussbaum; Olha Kholod; Dmitriy Shin; Mark Hannink; Mihail Popescu; Dong Xu 002 (BIBM, 2021)