ATEC23 Challenge: Automated prediction of treatment effectiveness in ovarian cancer using histopathological images. - Wang, Ching-Wei; Firdi, Nabila Puspita; Chu, Tzu-Chiao; Faiz, Mohammad Faiz Iqbal; Iqbal, Mohammad Zafar; Li, Yifan; Yang, Bo; Mallya, Mayur; Bashashati, Ali; Li, Fei; Wang, Haipeng; Lu, Mengkang; et al. (Medical Image Anal., 2025)

AI-driven 3D Spatial Transcriptomics. - Almagro-Pérez, Cristina; Song, Andrew H.; Weishaupt, Luca L.; Kim, Ahrong; Jaume, Guillaume; Williamson, Drew F. K.; Hemker, Konstantin; Lu, Ming Y.; Singh, Kritika; Chen, Bowen; Le, Long Phi; Baras, Alexander S.; et al. (CoRR, 2025)

Multi-scale relational graph convolutional network for multiple instance learning in histopathology images. - Bazargani, Roozbeh; Fazli, Ladan; Gleave, Martin E.; Goldenberg, Larry; Bashashati, Ali; Salcudean, Septimiu E. (Medical Image Anal., 2024)

How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval. - Fradkin, Philip; Moghadam, Puria Azadi; Suri, Karush; Wenkel, Frederik; Bashashati, Ali; Sypetkowski, Maciej; Beaini, Dominique (2024)

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

Benchmarking Histopathology Foundation Models for Ovarian Cancer Bevacizumab Treatment Response Prediction from Whole Slide Images. - Mallya, Mayur; Mirabadi, Ali Khajegili; Farahani, Hossein; Bashashati, Ali (CoRR, 2024)

How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval. - Fradkin, Philip; Azadi, Puria; Suri, Karush; Wenkel, Frederik; Bashashati, Ali; Sypetkowski, Maciej; Beaini, Dominique (CoRR, 2024)

Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images. - Nakhli, Ramin; Moghadam, Puria Azadi; Mi, Haoyang; Farahani, Hossein; Baras, Alexander; Gilks, C. Blake; Bashashati, Ali (2023)

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

ALL-IN: ALocal GLobal Graph-Based DIstillatioN Model for Representation Learning of Gigapixel Histopathology Images With Application In Cancer Risk Assessment. - Azadi, Puria; Suderman, Jonathan; Nakhli, Ramin; Rich, Katherine; Asadi, Maryam; Kung, Sonia; Oo, Htoo; Keyes, Mira; Farahani, Hossein; MacAulay, Calum; Goldenberg, Larry; Black, Peter; et al. (2023)

A novel H&E color augmentation for domain invariance classification of unannotated histopathology prostate cancer images. - Bazargani, Roozbeh; Chen, Wanwen; Sadeghian, Sadaf; Asadi, Maryam; Boschman, Jeffrey; Darbandsari, Amirali; Bashashati, Ali; Salcudean, Septimiu E. (2023)

A Morphology Focused Diffusion Probabilistic Model for Synthesis of Histopathology Images. - Moghadam, Puria Azadi; Dalen, Sanne Van; Martin, Karina C.; Lennerz, Jochen K.; Yip, Stephen; Farahani, Hossein; Bashashati, Ali (2023)

AMIGO: Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images. - Nakhli, Ramin; Moghadam, Puria Azadi; Mi, Haoyang; Farahani, Hossein; Baras, Alexander; Gilks, C. Blake; Bashashati, Ali (CoRR, 2023)

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

CCRL: Contrastive Cell Representation Learning. - Nakhli, Ramin; Darbandsari, Amirali; Farahani, Hossein; Bashashati, Ali (2022)

CCRL: Contrastive Cell Representation Learning. - Nakhli, Ramin; Darbandsari, Amirali; Farahani, Hossein; Bashashati, Ali (CoRR, 2022)

A Morphology Focused Diffusion Probabilistic Model for Synthesis of Histopathology Images. - Moghadam, Puria Azadi; Dalen, Sanne Van; Martin, Karina C.; Lennerz, Jochen K.; Yip, Stephen; Farahani, Hossein; Bashashati, Ali (CoRR, 2022)

Multi-Scale Relational Graph Convolutional Network for Multiple Instance Learning in Histopathology Images. - Bazargani, Roozbeh; Fazli, Ladan; Goldenberg, Larry; Gleave, Martin E.; Bashashati, Ali; Salcudean, Septimiu E. (CoRR, 2022)

Classification of Epithelial Ovarian Carcinoma Whole-Slide Pathology Images Using Deep Transfer Learning. - Wang, Yiping; Farnell, David; Farahani, Hossein; Nursey, Mitchell; Tessier-Cloutier, Basile; Jones, Steven J. M.; Huntsman, David G.; Gilks, C. Blake; Bashashati, Ali (CoRR, 2020)

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

Bayesian optimization of BCI parameters. - Bashashati, Hossein; Ward, Rabab K.; Bashashati, Ali (2016)

Neural Network Conditional Random Fields for Self-Paced Brain Computer Interfaces. - Bashashati, Hossein; Ward, Rabab K.; Bashashati, Ali; Mohamed, Amr M. (2016)

Hidden Markov Support Vector Machines for Self-Paced Brain Computer Interfaces. - Bashashati, Hossein; Ward, Rabab K.; Bashashati, Ali (2015)

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. - Ding, Jiarui; Bashashati, Ali; Roth, Andrew; Oloumi, Arusha; Tse, Kane; Zeng, Thomas; Haffari, Gholamreza; Hirst, Martin; Marra, Marco A.; Condon, Anne; Aparicio, Sam; Shah, Sohrab P. (Bioinform., 2012)

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. - Roth, Andrew; Ding, Jiarui; Morin, Ryan D.; Crisan, Anamaria; Ha, Gavin; Giuliany, Ryan; Bashashati, Ali; Hirst, Martin; Turashvili, Gulisa; Oloumi, Arusha; Marra, Marco A.; Aparicio, Sam; et al. (Bioinform., 2012)

Random forests-based 2D-to-3D video conversion. - Pourazad, Mahsa T.; Nasiopoulos, Panos; Bashashati, Ali (2010)

Merging Mixture Components for Cell Population Identification in Flow Cytometry. - Finak, Greg; Bashashati, Ali; Brinkman, Ryan Remy; Gottardo, Raphael (Adv. Bioinformatics, 2009)

A Survey of Flow Cytometry Data Analysis Methods. - Bashashati, Ali; Brinkman, Ryan Remy (Adv. Bioinformatics, 2009)

Towards Development of a 3-State Self-Paced Brain-Computer Interface. - Bashashati, Ali; Ward, Rabab K.; Birch, Gary E. (Comput. Intell. Neurosci., 2007)

Automatic user customization for improving the performance of a self-paced brain interface system. - Fatourechi, Mehrdad; Bashashati, Ali; Birch, Gary E.; Ward, Rabab K. (Medical Biol. Eng. Comput., 2006)

An experimental study to investigate the effects of a motion tracking electromagnetic sensor during EEG data acquisition. - Bashashati, Ali; Noureddin, Borna; Ward, Rabab K.; Lawrence, Peter D.; Birch, Gary E. (IEEE Trans. Biomed. Eng., 2006)

Detection of Hand Extension Movements in the Context of a 3-State Asynchronous Brain Interface. - Bashashati, Ali; Ward, Rabab K.; Birch, Gary E. (2006)

A hybrid genetic algorithm approach for improving the performance of the LF-ASD brain computer interface. - Fatourechi, Mehrdad; Bashashati, Ali; Ward, Rabab K.; Birch, Gary E. (2005)

Brain-computer interface design for asynchronous control applications: improvements to the LF-ASD asynchronous brain switch. - Borisoff, Jaimie F.; Mason, Steven G.; Bashashati, Ali; Birch, Gary E. (IEEE Trans. Biomed. Eng., 2004)