JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. - Anthony Mathelier; Xiaobei Zhao; Allen W. Zhang; François Parcy; Rebecca Worsley-Hunt; David J. Arenillas; Sorana Buchman; Chih-Yu Chen; Alice Yi Chou; Hans Ienasescu; Jonathan S. Lim; Casper Shyr; et al. (Nucleic Acids Res., 2014)

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. - Anthony Mathelier; Oriol Fornes; David J. Arenillas; Chih-Yu Chen; Grégoire Denay; Jessica J. Y. Lee; Wenqiang Shi; Casper Shyr; Ge Tan; Rebecca Worsley-Hunt; Allen W. Zhang; François Parcy; et al. (Nucleic Acids Res., 2016)

Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models. - Tyler Funnell; Allen W. Zhang; Diljot Grewal; Steven McKinney; Ali Bashashati; Yi Kan Wang; Sohrab P. Shah (PLoS Comput. Biol., 2019)

CO-PILOT: Dynamic Top-Down Point Cloud with Conditional Neighborhood Aggregation for Multi-Gigapixel Histopathology Image Representation. - Ramin Nakhli; Allen W. Zhang; Ali Khajegili Mirabadi; Katherine Rich; Maryam Asadi; C. Blake Gilks; Hossein Farahani; Ali Bashashati (ICCV, 2023)

VOLTA: an Environment-Aware Contrastive Cell Representation Learning for Histopathology. - Ramin Nakhli; Allen Zhang 002; Hossein Farahani; Amirali Darbandsari; Elahe Shenasa; Sidney Thiessen; Katy Milne; Jessica McAlpine; Brad Nelson; C. Blake Gilks; Ali Bashashati (CoRR, 2023)

GRASP: GRAph-Structured Pyramidal Whole Slide Image Representation. - Ali Khajegili Mirabadi; Graham Archibald; Amirali Darbandsari; Alberto Contreras-Sanz; Ramin Ebrahim Nakhli; Maryam Asadi; Allen Zhang 002; C. Blake Gilks; Peter Black; Gang Wang; Hossein Farahani; Ali Bashashati (CoRR, 2024)