A. Bashashati

A. Bashashati, J. Boschman, R. McCallum, 2022, Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society.

Molecular profiling and molecular classification of endometrioid ovarian carcinomas.

A. Bashashati, S. Shah, D. Huntsman, 2019, Gynecologic oncology.

Tumor-associated antigen PRAME exhibits dualistic functions that are targetable in diffuse large B cell lymphoma

Allen W. Zhang, R. Gascoyne, D. Scott, 2020, The Journal of clinical investigation.

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

Ali Bashashati, Richard A. Moore, Gavin Ha, 2017, Nature Genetics.

The coming 15 years in gynaecological pathology: digitisation, artificial intelligence, and new technologies

A. Bashashati, D. Huntsman, D. Farnell, 2020, Histopathology.

TITLE: TERT promoter mutation in adult granulosa cell tumor of the ovary RUNNING TITLE: TERT promoter mutation in AGCT AUTHORS:

A. Bashashati, H. Horlings, C. Gilks, 2017 .

Tumor-associated antigen PRAME exhibits dualistic functions that are targetable in diffuse large B cell lymphoma

Allen W. Zhang, Lauren C. Chong, R. Gascoyne, 2020, The Journal of clinical investigation.

Deep learning-based histotype diagnosis of ovarian carcinoma whole-slide pathology images

A. Bashashati, D. Huntsman, M. Köbel, 2022, Modern Pathology.

A Morphology Focused Diffusion Probabilistic Model for Synthesis of Histopathology Images

Puria Azadi Moghadam, A. Bashashati, J. Lennerz, 2022, 2023 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV).

LYMPHOID NEOPLASIA An RCOR1 loss – associated gene expression signature identi ﬁ es a prognostically signi ﬁ cant DLBCL subgroup

Ryan D. Morin, R. Gascoyne, L. Sehn, 2015 .

Regulation of pH by Carbonic Anhydrase 9 Mediates Survival of Pancreatic Cancer Cells With Activated KRAS in Response to Hypoxia.

S. C. Chafe, A. Bashashati, S. Shah, 2019, Gastroenterology.

Diffuse large B-cell lymphoma: reduced CD20 expression is associated with an inferior survival.

Ryan R Brinkman, Ali Bashashati, Angela Brooks-Wilson, 2009, Blood.

Multi-Scale Relational Graph Convolutional Network for Multiple Instance Learning in Histopathology Images

S. Salcudean, A. Bashashati, M. Gleave, 2022, ArXiv.

Kronos: a workflow assembler for genome analytics and informatics

Sohrab P. Shah, Ali Bashashati, Ryan D. Morin, 2016, bioRxiv.

Deep learning-based histotype diagnosis of ovarian carcinoma whole-slide pathology images

A. Bashashati, D. Huntsman, M. Köbel, 2022, Modern Pathology.

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates

Ali Bashashati, Martin Hirst, Kaston Leung, 2016, Proceedings of the National Academy of Sciences.

Towards Development of a 3-State Self-Paced Brain-Computer Interface

Gary E. Birch, Rabab Kreidieh Ward, Ali Bashashati, 2007, Comput. Intell. Neurosci..

Automatic user customization for improving the performance of a self-paced brain interface system

Gary E. Birch, Rabab Kreidieh Ward, Ali Bashashati, 2006, Medical and Biological Engineering and Computing.

A hybrid genetic algorithm approach for improving the performance of the LF-ASD brain computer interface

Gary E. Birch, Rabab Kreidieh Ward, Ali Bashashati, 2005, Proceedings. (ICASSP '05). IEEE International Conference on Acoustics, Speech, and Signal Processing, 2005..

Improving the performance of the LF-ASD brain computer interface by means of genetic algorithm

G.E. Birch, M. Fatourechi, R.K. Ward, 2004, Proceedings of the Fourth IEEE International Symposium on Signal Processing and Information Technology, 2004..

An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup.

Ryan D. Morin, R. Gascoyne, D. Scott, 2015, Blood.

Molecular and Genetic Characterization of MHC Deficiency Identifies EZH2 as Therapeutic Target for Enhancing Immune Recognition.

Ryan D. Morin, R. Gascoyne, D. Scott, 2019, Cancer discovery.

Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models

Ali Bashashati, Yi Kan Wang, Steven McKinney, 2019, PLoS Comput. Biol..

Targeting Hypoxia-Induced Carbonic Anhydrase IX Enhances Immune-Checkpoint Blockade Locally and Systemically

S. C. Chafe, A. Bashashati, S. Shah, 2019, Cancer Immunology Research.

Synthesis of diagnostic quality cancer pathology images by generative adversarial networks

Yiping Wang, Anne Mills, Ali Bashashati, 2020, The Journal of pathology.

Synthesis of diagnostic quality cancer pathology images

Yiping Wang, Steven J.M. Jones, Ali Bashashati, 2020, bioRxiv.

Classification of Epithelial Ovarian Carcinoma Whole-Slide Pathology Images Using Deep Transfer Learning pdf

Yiping Wang, Ali Bashashati, David Farnell, 2020, ArXiv.

Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden

Yi Kan Wang, A. Bashashati, M. Marra, 2015, The Journal of pathology.

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data

Sohrab P. Shah, Ali Bashashati, Ryan D. Morin, 2012, Bioinform..

LINE-1 retrotransposon-mediated DNA transductions in endometriosis associated ovarian cancers.

Yi Kan Wang, A. Bashashati, S. Shah, 2017, Gynecologic oncology.

Genetic profiling of MYC and BCL2 in diffuse large B-cell lymphoma determines cell-of-origin-specific clinical impact.

Ryan D. Morin, R. Gascoyne, D. Scott, 2017, Blood.

Adult‐type granulosa cell tumor of the ovary: a FOXL2‐centric disease

Yi Kan Wang, A. Bashashati, H. Horlings, 2021, The journal of pathology. Clinical research.

TERT promoter mutation in adult granulosa cell tumor of the ovary

Yi Kan Wang, A. Bashashati, S. Shah, 2018, Modern Pathology.

The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

Richard A. Moore, Yi Kan Wang, Scott D. Brown, 2017, bioRxiv.

TITLE : TERT promoter mutation in adult granulosa cell tumor of the ovary RUNNING TITLE : TERT mutation in adult granulosa cell tumor

A. Bashashati, S. Shah, H. Horlings, 2017 .

Kronos: a workflow assembler for genome analytics and informatics

Sohrab P. Shah, Ali Bashashati, Paul C. Boutros, 2016, bioRxiv.

Deep-learning based classification distinguishes sarcomatoid malignant mesotheliomas from benign spindle cell mesothelial proliferations

Adrian B Levine, A. Bashashati, L. Chirieac, 2021, Modern Pathology.

The driver landscape of sporadic chordoma

Matthew D. Young, M. Stratton, T. Nielsen, 2017, Nature Communications.

Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation

P. Sorensen, A. Bashashati, S. Shah, 2019, Communications Biology.

A survey of signal processing algorithms in brain–computer interfaces based on electrical brain signals

Rabab K Ward, Ali Bashashati, Mehrdad Fatourechi, 2007, Journal of neural engineering.

The genomic landscape of epithelioid sarcoma cell lines and tumours

T. Nielsen, A. Bashashati, S. Shah, 2016, The Journal of pathology.

Synchronous Endometrial and Ovarian Carcinomas: Evidence of Clonality.

Yi Kan Wang, A. Bashashati, S. Shah, 2015, Journal of the National Cancer Institute.

VOLTA: an Environment-Aware Contrastive Cell Representation Learning for Histopathology

Allen W. Zhang, A. Bashashati, C. Gilks, 2023, ArXiv.

The utility of color normalization for AI‐based diagnosis of hematoxylin and eosin‐stained pathology images

Adrian B Levine, Stephen S. F. Yip, A. Bashashati, 2021, The Journal of pathology.

TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma

Ryan D. Morin, Allen W. Zhang, Lauren C. Chong, 2020, Nature Medicine.

Per‐channel basis normalization methods for flow cytometry data

Ryan R Brinkman, Ali Bashashati, Thomas Lumley, 2009, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection

Farshid S. Garmaroudi, B. McManus, A. Bashashati, 2010, Proceedings of the National Academy of Sciences.

Automated analysis of multidimensional flow cytometry data improves diagnostic accuracy between mant

Gholamreza Haffari, Arvind Gupta, Habil Zare, 2011 .

A Survey of Flow Cytometry Data Analysis Methods

Ali Bashashati, Ryan Remy Brinkman, A. Bashashati, 2009, Adv. Bioinformatics.

Merging Mixture Components for Cell Population Identification in Flow Cytometry

Greg Finak, Raphael Gottardo, Ali Bashashati, 2009, Adv. Bioinformatics.

Double-Hit Gene Expression Signature Defines a Distinct Subgroup of Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma.

Ryan D. Morin, R. Gascoyne, D. Scott, 2019, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Brain-computer interface design for asynchronous control applications: improvements to the LF-ASD asynchronous brain switch

Gary E. Birch, Ali Bashashati, Steven G. Mason, 2004, IEEE Transactions on Biomedical Engineering.

Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation

P. Sorensen, A. Bashashati, S. Shah, 2019, Communications Biology.

A Comprehensive Survey of Brain Interface Technology Designs

Karla Felix Navarro, M. Fatourechi, S. G. Mason, 2007, Annals of Biomedical Engineering.

User Customization of the Feature Generator of an Asynchronous Brain Interface

Rabab K. Ward, Gary E. Birch, Ali Bashashati, 2006, Annals of Biomedical Engineering.

A New Design of the Asynchronous Brain Computer Interface Using the Knowledge of the Path of Features

G.E. Birch, R.K. Ward, A. Bashashati, 2005, Conference Proceedings. 2nd International IEEE EMBS Conference on Neural Engineering, 2005..

CD20 mutations involving the rituximab epitope are rare in diffuse large B-cell lymphomas and are not a significant cause of R-CHOP failure

R. Gascoyne, L. Sehn, J. Connors, 2009, Haematologica.

Comparing Different Classifiers in Sensory Motor Brain Computer Interfaces

Rabab K. Ward, Gary E. Birch, Dezhong Yao, 2015, PloS one.

CCRL: Contrastive Cell Representation Learning

A. Bashashati, H. Farahani, Amirali Darbandsari, 2022, ECCV Workshops.

An automatic method to generate ensemble averages of movement-related potentials for individuals with spinal cord injuries

A. Bashashati, R. Ward, A. Bashashati, 2004, The 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

AMIGO: Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images

Puria Azadi Moghadam, A. Bashashati, C. Gilks, 2023, ArXiv.

The driver landscape of sporadic chordoma

Matthew D. Young, M. Stratton, T. Nielsen, 2017, Nature Communications.

Artificial intelligence-based histopathology image analysis identifies a novel subset of endometrial cancers with distinct genomic features and unfavourable outcome

A. Talhouk, A. Bashashati, C. Gilks, 2023, medRxiv.

Bayesian optimization of BCI parameters

Rabab Kreidieh Ward, Ali Bashashati, Hossein Bashashati, 2016, 2016 IEEE Canadian Conference on Electrical and Computer Engineering (CCECE).

User-customized brain computer interfaces using Bayesian optimization

Rabab K Ward, Ali Bashashati, Hossein Bashashati, 2016, Journal of neural engineering.

Detection of Hand Extension Movements in the Context of a 3-State Asynchronous Brain Interface

Gary E. Birch, Rabab Kreidieh Ward, Ali Bashashati, 2006, 2006 IEEE International Conference on Acoustics Speech and Signal Processing Proceedings.

An experimental study to investigate the effects of a motion tracking electromagnetic sensor during EEG data acquisition

Gary E. Birch, Rabab Kreidieh Ward, Ali Bashashati, 2006, IEEE Transactions on Biomedical Engineering.

O005/#638 ProMisE-2: a one step DNA-based endometrial cancer molecular classifier

A. Talhouk, S. Leung, A. Bashashati, 2022, Oral Abstracts (Regular and Late-Breaking Submission).

Reduction in multi-lineage and erythroid progenitors distinguishes myelodysplastic syndromes from non-malignant cytopenias.

A. Bashashati, A. Karsan, C. Eaves, 2009, Leukemia research.

with an inferior survival Diffuse large B-cell lymphoma: reduced CD20 expression is associated

J. Connors, M. Boyle, A. Bashashati, 2013 .

Harmonized molecular classification; assessment of a single-test ProMisE NGS tool.

A. Talhouk, S. Leung, A. Bashashati, 2023, Gynecologic Oncology.

Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images

Puria Azadi Moghadam, A. Bashashati, B. Gilks, 2023, 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR).

Artificial Intelligence and Pathomics

A. Bashashati, S. Goldenberg, Puria Azadi Moghadam, 2023, Urologic clinics of North America.

Automated analysis of multidimensional flow cytometry data improves diagnostic accuracy between mantle cell lymphoma and small lymphocytic lymphoma.

N. Aghaeepour, R. Gascoyne, J. Connors, 2011, American journal of clinical pathology.

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer

Richard A. Moore, Allen W. Zhang, A. Bashashati, 2016, Nature Genetics.

Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study

Ryan D. Morin, Richard A. Moore, E. Giné, 2016, PLoS medicine.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

A. Bashashati, M. Marra, A. McPherson, 2014, Genome research.

Integrative analysis of genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer Supplemental Material

A. Bashashati, M. Marra, M. Hirst, 2012 .

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

F. Markowetz, S. Tavaré, A. Børresen-Dale, 2012, Nature.

GRASP: GRAph-Structured Pyramidal Whole Slide Image Representation

Ali Khajegili Mirabadi, A. Bashashati, C. Gilks, 2024, ArXiv.

Effect of eye-blinks on a self-paced brain interface design

Rabab K. Ward, Gary E. Birch, Ali Bashashati, 2007, Clinical Neurophysiology.

CO-PILOT: Dynamic Top-Down Point Cloud with Conditional Neighborhood Aggregation for Multi-Gigapixel Histopathology Image Representation

Ali Khajegili Mirabadi, A. Bashashati, Allen Zhang, 2023, 2023 IEEE/CVF International Conference on Computer Vision (ICCV).

Multi-Scale Relational Graph Convolutional Network for Multiple Instance Learning in Histopathology Images

S. Salcudean, A. Bashashati, M. Gleave, 2022, Medical Image Anal..

Fractal dimension-based EEG biofeedback system

Rabab K. Ward, Gary E. Birch, Ali Bashashati, 2003, Proceedings of the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (IEEE Cat. No.03CH37439).