Research from AIM Lab

Publications

How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval

Puria Azadi Moghadam, Fradkin Philip, Karush Suri, Frederik Wenkel, Ali Bashashati, Maciej Sypetkowski, Dominique Beaini
A Deep Learning Approach for the Identification of the Molecular Subtypes of Pancreatic Ductal Adenocarcinoma Based on Whole Slide Pathology Images

Pouya Ahmadvand, Hossein Farahani, David Farnell, Amirali Darbandsari, James Topham, Joanna Karasinska, Jessica Nelson, Julia Naso, Steven Jones, Daniel Renouf, David Schaeffer, Ali Bashashati
ATEC23 Challenge: Automated Prediction of Treatment Effectiveness in Ovarian Cancer Using Histopathological Images

CW Wang, NP Firdi, TC Chu, MF Faiz, MZ Iqbal, Y Li, B Yang, M Mallya, A Bashashati, F Li, H Wang
Benchmarking Histopathology Foundation Models for Ovarian Cancer Bevacizumab Treatment Response Prediction from Whole Slide Images

Mayur Mallya, Ali Khajegili Mirabadi, Hossein Farahani, Ali Bashashati
Benchmarking Bulk and Single-Cell Variant Calling Approaches on Chromium scRNA-seq and scATAC-seq Libraries

Wiens MVJ, Farahani H, Scott RW, Underhill TM, Bashashati A
AI-Based Histopathology Image Analysis Reveals a Distinct Subset of Endometrial Cancers

Darbandsari A, Farahani H, Asadi M, Wiens M, Cochrane D, Khajegili Mirabadi A, Jamieson A, Farnell D, Ahmadvand P, Douglas M, Leung S, Abolmaesumi P, Jones SJM, Talhouk A, Kommoss S, Gilks CB, Huntsman DG, Singh N, McAlpine JN, Bashashati A
VOLTA: An Environment-Aware Contrastive Cell Representation Learning for Histopathology

Ramin Nakhli, Katherine Rich, Allen Zhang, Amirali Darbandsari, Elahe Shenasa, Sydney Thiessen, Katy Milne, Jessica McAlpine, Brad Nelson, C Blake Gilk, Hossein Farahani, Ali Bashashati
Practical Application of Deep Learning in Diagnostic Neuropathology - Reimagining a Histological Asset in the Era of Precision Medicine

Rich K, Tosefsky K, Martin KC, Bashashati A, Yip S
Multi-Scale Relational Graph Convolutional Network for Multiple Instance Learning in Histopathology Images

R Bazargani, L Fazli, M Gleave, L Goldenberg, A Bashashati, S Salcudean
Prostate Cancer Risk Stratification by Digital Histopathology and Deep Learning

Y Shao, R Bazargani, D Karimi, J Wang, L Fazli, SL Goldenberg, ME Gleave, PC Black, A Bashashati, S Salcudean
Learning Generalizable AI Models for Multi-Center Histopathology Image Classification

M Asadi-Aghbolaghi, A Darbandsari, A Zhang, A Contreras-Sanz, J Boschman, P Ahmadvand, M Köbel, D Farnell, DG Huntsman, A Churg, PC Black, G Wang, CB Gilks, H Farahani, A Bashashati
Harmonized Molecular Classification; Assessment of a Single-Test ProMisE NGS Tool

A Jamieson, MK McConechy, A Lum, S Leung, EF Thompson, J Senz, A Talhouk, DG Huntsman, A Bashashati, CB Gilks, JN McAlpine
CO-PILOT: Dynamic Top-Down Point Cloud with Conditional Neighborhood Aggregation for Multi-Gigapixel Histopathology Image Representation

Ramin Nakhli, Allen Zhang, Ali Khajegili, Katherine Rich, Maryam Asadi, C. Blake Gilks, Hossein Farahani, Ali Bashashati
ALL-IN: A Local Global Graph-based Distillation Model for Representation Learning of Gigapixel Histopathology Images With Application In Cancer Risk Assessment

Puria Azadi, Jonothan Suderman, Ramin Nakhli, Katherine Rich, Maryam Asadi, Sonia Kung, Htoo Zarni, M. Keyes, Hossein Farahani, Calum McAulay, Larry Goldenberg, Peter Black, Ali Bashashati
Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images

Ramin Nakhli, Puria Azadi Moghadam, Haoyang Mi, Hossein Farahani, Alexander Baras, Blake Gilks, Ali Bashashati
Artificial Intelligence and Pathomics: Prostate Cancer

Puria Azadi, Ali Bashashati, Larry Goldenberg
A Morphology Focused Diffusion Probabilistic Model for Synthesis of Histopathology Images

Puria Azadi Moghadam, Sanne van Delen, Karina C. Martin, Jochen Lennerz, Stephen Yip, Hossein Farahani, Ali Bashashati
A Novel H&E Color Augmentation for Unannotated Domain Invariance Histopathology Prostate Cancer Classification

Roozbeh Bazargani, Wanwen Chen, Sadaf Sadeghian, Maryam Asadi, Jeffrey Boschman, Amirali Darbandsari, Ali Bashashati, Septimiu Salcudean
Gastrointestinal Symptoms and the Severity of COVID-19: Disorders of Gut-Brain Interaction Are an Outcome

Ramin Ebrahim Nakhli, Aaron Shanker, Irene Sarosiek, Jeffrey Boschman, Karina Espino, Solmaz Sigaroodi, Ihsan Al Bayati, Sherif Elhanafi, Amin Sadeghi, Jerzy Sarosiek, Marc J Zuckerman, Ali Rezaie, Richard W McCallum, Max J Schmulson, Ali Bashashati, Mohammad Bashashati
AI for Prostate Cancer Diagnosis - Hype or Today’s Reality?

Ali Bashashati, S Larry Goldenberg
CCRL: Contrastive Cell Representation Learning

Ramin Ebrahim Nakhli, Amirali Darbandsari, Hossein Farahani, Ali Bashashati
Tumor Associated Antigen PRAME Exhibits Dualistic Functions That Are Targetable in Diffuse Large B-Cell Lymphoma

Katsuyoshi Takata, Lauren C Chong, Daisuke Ennishi, Tomohiro Aoki, Michael Yu Li, Avinash Thakur, Shannon Healy, Elena Viganò, Tao Dao, Daniel Kwon, Gerben Duns, Julie S Nielsen, Susana Ben-Neriah, Ethan Tse, Stacy S Hung, Merrill Boyle, Sung Soo Mun, Christopher M Bourne, Bruce Woolcock, Adèle H Telenius, Makoto Kishida, Shinya Rai, Allen W Zhang, Ali Bashashati, Saeed Saberi, Gianluca D'Antonio, Brad H Nelson, Sohrab P Shah, Pamela A Hoodless, Ari M Melnick, Randy D Gascoyne, Joseph M Connors, David A Scheinberg, Wendy Béguelin, David W Scott, Christian Steidl
Deep Learning-Based Histotype Diagnosis of Ovarian Carcinoma Whole-Slide Pathology Images

Hossein Farahani, Jeffrey Boschman, David Farnell, Amirali Darbandsari, Allen Zhang, Pouya Ahmadvand, Ashley van Spankeren, Steven Jones, Martin Koebel, David Huntsman, C Blake Gilks, Naveena Singh, Ali Bashashati
The Utility of Color Normalization for AI-Based Diagnosis of Hematoxylin and Eosin-Stained Pathology Images

Jeffrey Boschman, Hossein Farahani, Amirali Darbandsari, Pouya Ahmadvand, Ashley Van Spankeren, David Farnell, Adrian Levine, Julia R. Naso, Andrew Churg, Steven Jones, Stephen Yip, Martin Koebel, David Huntsman, Blake Gilks, Ali Bashashati
Deep Learning-Based Classification Distinguishes Sarcomatoid Malignant Mesotheliomas from Benign Spindle Cell Mesothelial Proliferations

Julia R. Naso, Adrian B. Levine, Hossein Farahani, Lucian R. Chirieac, Sanja Dacic, Joanne L. Wright, Chi Lai, Hui-Min Yang, Steven J. M. Jones, Ali Bashashati, Stephen Yip, Andrew Churg
Adult-Type Granulosa Cell Tumor of the Ovary: A FOXL2-Centric Disease

Jessica A Pilsworth, Dawn R Cochrane, Samantha J Neilson, Bahar H Moussavi, Daniel Lai, Asl? D Munzur, Janine Senz, Yi Kan Wang, Sina Zareian, Ali Bashashati, Adele Wong, Jacqueline Keul, Annette Staebler, Hannah S van Meurs, Hugo M Horlings, Stefan Kommoss, Friedrich Kommoss, Esther Oliva, Anniina EM Färkkilä, Blake Gilks, David G Huntsman
Endometrial cancer molecular risk stratification is equally prognostic for endometrioid ovarian carcinoma

Pauline Krämer, Aline Talhouk, Mary Anne Brett, Derek S. Chiu, Evan S. Cairns, Daniëlla A. Scheunhage, Rory F. L. Hammond, David Farnell, Tayyebeh M. Nazeran, Marcel Grube, Zhouchunyang Xia, Janine Senz, Samuel Leung, Lukas Feil, Jana Pasternak, Katherine Dixon, Andreas Hartkopf, Bernhard Krämer, Sara Brucker, Florian Heitz, Andreas du Bois, Philipp Harter, Felix K. F. Kommoss, Hans-Peter Sinn, Sabine Heublein, Friedrich Kommoss, Hans-Walter Vollert, Ranjit Manchanda, Cornelis D. de Kroon, Hans W. Nijman, Marco de Bruyn, Emily F. Thompson, Ali Bashashati, Jessica N. McAlpine, Naveena Singh, Anna V. Tinker, Annette Staebler, Tjalling Bosse, Stefan Kommoss, Martin Köbel, Michael S. Anglesio
Synthesis of diagnostic quality cancer pathology images

Adrian B. Levine, Jason Peng, David Farnell, Mitchell Nursey, Yiping Wang, Julia R. Naso, Hezhen Ren, Hossein Farahani, Colin Chen, Derek Chiu, Aline Talhouk, Brandon Sheffield, Maziar Riazy, Philip P. Ip, Carlos Parra-Herran, Anne Mills, Naveena Singh, Basile Tessier-Cloutier, Taylor Salisbury, Jonathan Lee, Tim Salcudean, Steven J.M. Jones, David G. Huntsman, C. Blake Gilks, Stephen Yip, Ali Bashashati
Synthesis of high resolution glioma pathology images using generative adversarial networks

Adrian Levine, Jason Peng, David Farnell, Mitchell Nursey, Yiping Wang, Steven Jones, C Blake Gilks, Ali Bashashati, Stephen Yip
Classification of Epithelial Ovarian Carcinoma Whole-Slide Pathology Images Using Deep Transfer Learning

Yiping Wang, David Farnell, Hossein Farahani, Mitchell Nursey, Basile Tessier-Cloutier, Steven J. M. Jones, David G. Huntsman, C. Blake Gilks, Ali Bashashati
TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma

Daisuke Ennishi, Shannon Healy, Ali Bashashati, Saeed Saberi, Christoffer Hother, Anja Mottok, Fong Chun Chan, Lauren Chong, Libin Abraham, Robert Kridel, Merrill Boyle, Barbara Meissner, Tomohiro Aoki, Katsuyoshi Takata, Bruce W. Woolcock, Elena Viganò, Michael Gold, Laurie L. Molday, Robert S. Molday, Adele Telenius, Michael Y. Li, Nicole Wretham, Nancy Dos Santos, Mark Wong, Natasja N. Viller, Robert A. Uger, Gerben Duns, Abigail Baticados, Angel Madero, Brianna N. Bristow, Pedro Farinha, Graham W. Slack, Susana Ben-Neriah, Daniel Lai, Allen W. Zhang, Sohrab Salehi, Hennady P. Shulha, Derek S. Chiu, Sara Mostafavi, Alina S. Gerrie, Da Wei Huang, Christopher Rushton, Diego Villa, Laurie H. Sehn, Kerry J. Savage, Andrew J. Mungall, Andrew P. Weng, Marcel B. Bally, Ryan D. Morin, Gabriela V. Cohen Freue, Louis M. Staudt, Joseph M. Connors, Marco A. Marra, Sohrab P. Shah, Randy D. Gascoyne, David W. Scott, Christian Steidl
Generation of Synthetic Ovarian Carcinoma Microscopic Images for Proficiency Testing

Adrian Levine, Chien Chen Peng, David Farnell, Basile Tessier-Cloutier, Mitchell Nursey, Davood Karimi, Steven Jones, Septimiu Salcudean, David Huntsman, Stephen Yip
Endometrial Cancer Molecular Risk Stratification is Equally Prognostic for Endometrioid Ovarian Carcinoma

Pauline Krämer, Aline Talhouk, Mary Anne Brett, Derek S. Chiu, Evan S. Cairns, Daniëlla A. Scheunhage, Rory F.L. Hammond, David Farnell, Tayyebeh M. Nazeran, Marcel Grube, Zhouchunyang Xia, Janine Senz, Samuel Leung, Lukas Feil, Jana Pasternak, Katherine Dixon, Andreas Hartkopf, Bernhard Krämer, Sara Brucker, Florian Heitz, Andreas du Bois, Philipp Harter, Felix K.F. Kommoss, Hans-Peter Sinn, Sabine Heublein, Friedrich Kommoss, Hans-Walter Vollert, Ranjit Manchanda, Cornelis D. de Kroon, Hans W. Nijman, Marco de Bruyn, Emily F. Thompson, Ali Bashashati, Jessica N. McAlpine, Naveena Singh, Anna V. Tinker, Annette Staebler, Tjalling Bosse, Stefan Kommoss, Martin Köbel, Michael S. Anglesio
The coming 15~years in gynaecological pathology: digitisation, artificial intelligence, and new technologies

David A Farnell, David Huntsman, Ali Bashashati
Abstract GMM-047: GENOMIC CHARACTERIZATION OF ADULT-TYPE GRANULOSA CELL TUMORS: IMPLICATIONS FOR PATHOGENESIS AND TREATMENT OF RECURRENT DISEASE

Jessica A. Pilsworth, Dawn R. Cochrane, Samantha Neilson, Anniina E.M. Färkkilä, Hugo M. Horlings, Satoshi Yanagida, Janine Senz, Yi Kan Wang, Bahar Moussavi, Daniel Lai, Ali Bashashati, Jacqueline Keul, Adele Wong, Hannah van Meurs, Sara Y. Brucker, Florin-Andrei Taran, Bernhard Krämer, Annette Staebler, Esther Oliva, Sohrab P. Shah, Stefan Kommoss, Friedrich Kommoss, C. Blake Gilks, David G. Huntsman
Molecular profiling and molecular classification of endometrioid ovarian carcinomas

Paulina Cybulska, Arnaud Da Cruz Paula, Jill Tseng, Mario M. Leitao Jr, Ali Bashashati, David G. Huntsman, Tayyebeh M. Nazeran, Carol Aghajanian, Nadeem R. Abu-Rustum, Deborah F. DeLair, Sohrab P. Shah, Britta Weigelt
Regulation of pH by Carbonic Anhydrase 9 Mediates Survival of Pancreatic Cancer Cells With Activated KRAS in Response to Hypoxia

Paul C. McDonald, Shawn C. Chafe, Wells S. Brown, Saeed Saberi, Mridula Swayampakula, Geetha Venkateswaran, Oksana Nemirovsky, Jordan A. Gillespie, Joanna M. Karasinska, Steve E. Kalloger, Claudiu T. Supuran, David F. Schaeffer, Ali Bashashati, Sohrab P. Shah, James T. Topham, Donald T. Yapp, Jinyang Li, Daniel J. Renouf, Ben Z. Stanger, Shoukat Dedhar
Abstract 3480:TMEM30Aloss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma

Shannon Healy, Daisuke Ennishi, Ali Bashashati, Saeed Saberi, Christoffer Hother, Anja Mottok, Fong Chun Chan, Lauren Chong, Robert Kridel, Merrill Boyle, Barbara Meissner, Tomohiro Aoki, Katsuyoshi Takata, Bruce W. Woolcock, Elena Vigano, Libin Abraham, Michael Gold, Adele Telenius, Pedro Farinha, Graham Slack, Susana Ben-Neriah, Daniel Lai, Allen W. Zhang, Sohrab Salehi, Hennady P. Shulha, Derek S. Chiu, Sara Mostafavi, Alina S. Gerrie, Diego Villa, Laurie H. Sehn, Kerry J. J. Savage, Andrew J. J. Mungall, Andrew P. Weng, Marcel Bally, Ryan D. Morin, Gabriela V. Cohen Freue, Joseph M. Connors, Marco A. Marra, Sohrab P. Shah, Randy D. Gascoyne, David W. Scott, Christian Steidl, Ulrich Steidl
Targeting Hypoxia-Induced Carbonic Anhydrase IX Enhances Immune-Checkpoint Blockade Locally and Systemically

Shawn C. Chafe, Paul C. McDonald, Saeed Saberi, Oksana Nemirovsky, Geetha Venkateswaran, Samantha Burugu, Dongxia Gao, Alberto Delaidelli, Alastair H. Kyle, Jennifer H.E. Baker, Jordan A. Gillespie, Ali Bashashati, Andrew I. Minchinton, Youwen Zhou, Sohrab P. Shah, Shoukat Dedhar
Molecular profiling of endometrioid ovarian carcinomas

P Cybulska, ADC Paula, JH Tseng, A Bashashati, D Huntsman, NR Abu-Rustum, D DeLair, SP Shah, B Weigelt
Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation

Alborz Mazloomian, Shinsuke Araki, Momoko Ohori, Amal M. El-Naggar, Damian Yap, Ali Bashashati, Shoichi Nakao, Poul H. Sorensen, Atsushi Nakanishi, Sohrab Shah, Samuel Aparicio
Molecular and Genetic Characterization of MHC Deficiency Identifies EZH2 as Therapeutic Target for Enhancing Immune Recognition

Daisuke Ennishi, Katsuyoshi Takata, Wendy Béguelin, Gerben Duns, Anja Mottok, Pedro Farinha, Ali Bashashati, Saeed Saberi, Merrill Boyle, Barbara Meissner, Susana Ben-Neriah, Bruce W. Woolcock, Adèle Telenius, Daniel Lai, Matt Teater, Robert Kridel, Kerry J. Savage, Laurie H. Sehn, Ryan D. Morin, Marco A. Marra, Sohrab P. Shah, Joseph M. Connors, Randy D. Gascoyne, David W. Scott, Ari M. Melnick, Christian Steidl
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
Double-Hit Gene Expression Signature Defines a Distinct Subgroup of Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma

Daisuke Ennishi, Aixiang Jiang, Merrill Boyle, Brett Collinge, Bruno M. Grande, Susana Ben-Neriah, Christopher Rushton, Jeffrey Tang, Nicole Thomas, Graham W. Slack, Pedro Farinha, Katsuyoshi Takata, Tomoko Miyata-Takata, Jeffrey Craig, Anja Mottok, Barbara Meissner, Saeed Saberi, Ali Bashashati, Diego Villa, Kerry J. Savage, Laurie H. Sehn, Robert Kridel, Andrew J. Mungall, Marco A. Marra, Sohrab P. Shah, Christian Steidl, Joseph M. Connors, Randy D. Gascoyne, Ryan D. Morin, David W. Scott
The Double-Hit Gene Expression Signature Defines a Clinically and Biologically Distinct Subgroup within GCB-DLBCL

Daisuke Ennishi, Aixiang Jiang, Merrill Boyle, Brett Collinge, Bruno M. Grande, Susana Ben-Neriah, Graham W Slack, Pedro Farinha, Diego Villa, Anja Mottok, Barbara Meissner, Saeed Saberi, Ali Bashashati, Kerry J Savage, Laurie H Sehn, Robert Kridel, Marco A. Marra, Sohrab P Shah, Christian Steidl, Joseph M. Connors, Randy D. Gascoyne, Ryan D. Morin, David W. Scott
Somatic PRAME Deletions Are Associated with Decreased Immunogenicity, Apoptosis Resistance and Poor Outcomes in Diffuse Large B-Cell Lymphoma

Katsuyoshi Takata, Daisuke Ennishi, Ali Bashashati, Saeed Saberi, Elena Viganò, Shannon Healy, Julie S Nielsen, Gianluca D′ Antonio, Brad H Nelson, Sohrab P Shah, Joseph M Connors, Randy D. Gascoyne, David W. Scott, Christian Steidl
Abstract B22: Capturing L1 retrotransposon-mediated DNA transductions in endometriosis associated ovarian cancers as a way to track tumor development

Zhouchunyang Xia, Dawn Cochrane, Michael Anglesio, Winnie Yang, Miguel Alcaide, Tayyebeh Nazeran, Janine Senz, Amy Lum, Ali Bashashati, Yikan Wang, Ryan Morin, Sohrab Shah, David Huntsman
Abstract PR13: TERT is frequently mutated in adult-type granulosa cell tumors of the ovary compared to other malignant sex cord-stromal tumors

Jessica A. Pilsworth, Dawn R. Cochrane, Zhouchunyang Xia, Geraldine Aubert, Anniina E. M. Färkkilä, Hugo M. Horlings, Satoshi Yanagida, Winnie Yang, Jamie L. P. Lim, Yikan Wang, Ali Bashashati, Jacqueline Keul, Adele Wong, Esther Oliva, Sohrab P. Shah, Stefan Kommoss, Friedrich Kommoss, Peter M. Lansdorp, Duncan M. Baird, David G. Huntsman
Abstract B22: Capturing L1 retrotransposon-mediated DNA transductions in endometriosis associated ovarian cancers as a way to track tumor development

Zhouchunyang Xia, Dawn Cochrane, Michael Anglesio, Winnie Yang, Miguel Alcaide, Tayyebeh Nazeran, Janine Senz, Amy Lum, Ali Bashashati, Yikan Wang, Ryan Morin, Sohrab Shah, David Huntsman
TERT promoter mutation in adult granulosa cell tumor of the ovary

Jessica A. Pilsworth, Dawn R. Cochrane, Zhouchunyang Xia, Geraldine Aubert, Anniina E. M. Färkkilä, Hugo M. Horlings, Satoshi Yanagida, Winnie Yang, Jamie L. P. Lim, Yi Kan Wang, Ali Bashashati, Jacqueline Keul, Adele Wong, Kevin Norris, Sara Y. Brucker, Florin-Andrei Taran, Bernhard Krämer, Annette Staebler, Hannah van Meurs, Esther Oliva, Sohrab P. Shah, Stefan Kommoss, Friedrich Kommoss, C. Blake Gilks, Duncan M. Baird, David G. Huntsman
Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer

Allen W. Zhang, Andrew McPherson, Katy Milne, David R. Kroeger, Phineas T. Hamilton, Alex Miranda, Tyler Funnell, Nicole Little, Camila P.E. de Souza, Sonya Laan, Stacey LeDoux, Dawn R. Cochrane, Jamie L.P. Lim, Winnie Yang, Andrew Roth, Maia A. Smith, Julie Ho, Kane Tse, Thomas Zeng, Inna Shlafman, Michael R. Mayo, Richard Moore, Henrik Failmezger, Andreas Heindl, Yi Kan Wang, Ali Bashashati, Diljot S. Grewal, Scott D. Brown, Daniel Lai, Adrian N.C. Wan, Cydney B. Nielsen, Curtis Huebner, Basile Tessier-Cloutier, Michael S. Anglesio, Alexandre Bouchard-Côté, Yinyin Yuan, Wyeth W. Wasserman, C. Blake Gilks, Anthony N. Karnezis, Samuel Aparicio, Jessica N. McAlpine, David G. Huntsman, Robert A. Holt, Brad H. Nelson, Sohrab P. Shah
Integrated single-nucleotide and structural variation signatures of DNA-repair deficient human cancers

Tyler Funnell, Allen Zhang, Yu-Jia Shiah, Diljot Grewal, Robert Lesurf, Steven McKinney, Ali Bashashati, Yi Kan Wang, Paul C. Boutros, Sohrab P. Shah
Genetic Characterization and Clinical Impact of Loss of MHC Class I and II Expression in De Novo Diffuse Large B-Cell Lymphoma

Daisuke Ennishi, Anja Mottok, Pedro Farinha, Fong Chun Chan, Ali Bashashati, Saeed Saberi, Barbara Meissner, Merrill Boyle, Susana Ben-Neriah, Robert Kridel, Kerry J Savage, Laurie H. Sehn, Ryan D. Morin, Marco A Marra, Sohrab P Shah, Joseph M Connors, Randy D. Gascoyne, David W. Scott, Christian Steidl
LINE-1 retrotransposon-mediated DNA transductions in endometriosis associated ovarian cancers

Zhouchunyang Xia, Dawn R. Cochrane, Michael S. Anglesio, Yi Kan Wang, Tayyebeh Nazeran, Basile Tessier-Cloutier, Melissa K. McConechy, Janine Senz, Amy Lum, Ali Bashashati, Sohrab P. Shah, David G. Huntsman
The driver landscape of sporadic chordoma

Patrick S. Tarpey, Sam Behjati, Matthew D. Young, Inigo Martincorena, Ludmil B. Alexandrov, Sarah J. Farndon, Charlotte Guzzo, Claire Hardy, Calli Latimer, Adam P. Butler, Jon W. Teague, Adam Shlien, P. Andrew Futreal, Sohrab Shah, Ali Bashashati, Farzad Jamshidi, Torsten O. Nielsen, David Huntsman, Daniel Baumhoer, Sebastian Brandner, Jay Wunder, Brendan Dickson, Patricia Cogswell, Josh Sommer, Joanna J. Phillips, M. Fernanda Amary, Roberto Tirabosco, Nischalan Pillay, Stephen Yip, Michael R. Stratton, Adrienne M. Flanagan, Peter J. Campbell
Abstract 3381: TERT promoter mutation in granulosa cell tumours of the ovary: Prevalence and prognostic significance

Jessica A. Pilsworth, Dawn R. Cochrane, Zhouchunyang Xia, Hugo M. Horlings, Winnie Yang, Melissa K. McConechy, Satoshi Yanagida, Anniina E. Färkkilä, Adele P. Wong, Genny Trigo-Gonzalez, S.W. Grace Cheng, Yikan Wang, Ali Bashashati, Gregg B. Morin, Esther Oliva, Sohrab P. Shah, David G. Huntsman
Abstract 2445: Integrative genetic analysis identifies therapeutic relevance of cell of origin-specific genetic alterations in diffuse large B-cell lymphoma

Daisuke Ennishi, Ali Bashashati, Saeed Saberi, Anja Mottok, Barbara Meissner, Merrill Boyle, Susana Ben-Neriah, Robert Kridel, Kerry J. Savage, Laurie H. Sehn, Joseph M. Connors, Ryan D. Morin, Marco A. Marra, Sohrab P. Shah, Christian Steidl, David W. Scott, Randy D. Gascoyne
Kronos: a workflow assembler for genome analytics and informatics

M. Jafar Taghiyar, Jamie Rosner, Diljot Grewal, Bruno M. Grande, Radhouane Aniba, Jasleen Grewal, Paul C. Boutros, Ryan D. Morin, Ali Bashashati, Sohrab P. Shah
CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion

Jerry F. Tien, Alborz Mazloomian, S.-W. Grace Cheng, Christopher S. Hughes, Christalle C.T. Chow, Leanna T. Canapi, Arusha Oloumi, Genny Trigo-Gonzalez, Ali Bashashati, James Xu, Vicky C.-D. Chang, Sohrab P. Shah, Samuel Aparicio, Gregg B. Morin
Abstract DPOC-014: BEYOND CODING MUTATIONS: USING RETROTRANSPOSONS TO PREDICT OVARIAN CANCER DEVELOPMENT

Zhouchunyang Xia, Dawn Cochrane, Michael S Anglesio, Tayyebeh M Nazeran, Janine Senz, Amy Lum, Ali Bashashati, Yi Kan Wang, Sohrab P Shah, David Huntsman
Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

Yi Kan Wang, Ali Bashashati, Michael S Anglesio, Dawn R Cochrane, Diljot S Grewal, Gavin Ha, Andrew McPherson, Hugo M Horlings, Janine Senz, Leah M Prentice, Anthony N Karnezis, Daniel Lai, Mohamed R Aniba, Allen W Zhang, Karey Shumansky, Celia Siu, Adrian Wan, Melissa K McConechy, Hector Li-Chang, Alicia Tone, Diane Provencher, Manon de Ladurantaye, Hubert Fleury, Aikou Okamoto, Satoshi Yanagida, Nozomu Yanaihara, Misato Saito, Andrew J Mungall, Richard Moore, Marco A Marra, C Blake Gilks, Anne-Marie Mes-Masson, Jessica N McAlpine, Samuel Aparicio, David G Huntsman, Sohrab P Shah
Genetic profiling of MYC and BCL2 in diffuse large B-cell lymphoma determines cell-of-origin–specific clinical impact

Daisuke Ennishi, Anja Mottok, Susana Ben-Neriah, Hennady P. Shulha, Pedro Farinha, Fong Chun Chan, Barbara Meissner, Merrill Boyle, Christoffer Hother, Robert Kridel, Daniel Lai, Saeed Saberi, Ali Bashashati, Sohrab P. Shah, Ryan D. Morin, Marco A. Marra, Kerry J. Savage, Laurie H. Sehn, Christian Steidl, Joseph M. Connors, Randy D. Gascoyne, David W. Scott
The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

Allen W. Zhang, Andrew McPherson, Katy Milne, David R. Kroeger, Phineas T. Hamilton, Alex Miranda, Tyler Funnell, Sonya Laan, Dawn R. Cochrane, Jamie L.P. Lim, Winnie Yang, Andrew Roth, Maia A. Smith, Camila de Souza, Julie Ho, Kane Tse, Thomas Zeng, Inna Shlafman, Michael R. Mayo, Richard Moore, Henrik Failmezger, Andreas Heindl, Yi Kan Wang, Ali Bashashati, Scott D. Brown, Daniel Lai, Adrian N. C. Wan, Cydney B. Nielsen, Alexandre Bouchard-Côté, Yinyin Yuan, Wyeth W. Wasserman, C. Blake Gilks, Anthony N. Karnezis, Samuel Aparicio, Jessica N. McAlpine, David G. Huntsman, Robert A. Holt, Brad H. Nelson, Sohrab P. Shah
Neural Network Conditional Random Fields for Self-Paced Brain Computer Interfaces

Hossein Bashashati, Rabab K. Ward, Ali Bashashati, Amr Mohamed
Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study

Robert Kridel, Fong Chun Chan, Anja Mottok, Merrill Boyle, Pedro Farinha, King Tan, Barbara Meissner, Ali Bashashati, Andrew McPherson, Andrew Roth, Karey Shumansky, Damian Yap, Susana Ben-Neriah, Jamie Rosner, Maia A. Smith, Cydney Nielsen, Eva Giné, Adele Telenius, Daisuke Ennishi, Andrew Mungall, Richard Moore, Ryan D. Morin, Nathalie A. Johnson, Laurie H. Sehn, Thomas Tousseyn, Ahmet Dogan, Joseph M. Connors, David W. Scott, Christian Steidl, Marco A. Marra, Randy D. Gascoyne, Sohrab P. Shah
Targeted Sequencing Reveals Novel Gene Mutations Associated with Transformation and Early Progression in Follicular Lymphoma

Robert Kridel, Fong Chun Chan, Anja Mottok, Merrill Boyle, Pedro Farinha, King Tan, Barbara Meissner, Ali Bashashati, Susana Ben-Neriah, Eva Gine, Daisuke Ennishi, Andrew J. Mungall, Ryan D. Morin, Nathalie A. Johnson, Laurie H. Sehn, Thomas Tousseyn, Ahmet Dogan, Joseph M. Connors, David W. Scott, Christian Steidl, Marco A. Marra, Randy D. Gascoyne, Sohrab P. Shah
Divergent Modes of Tumor Evolution Underlie Histological Transformation and Early Progression of Follicular Lymphoma

Fong Chun Chan, Robert Kridel, Anja Mottok, Merrill Boyle, Pedro Farinha, King Tan, Barbara Meissner, Ali Bashashati, Andrew McPherson, Andrew Roth, Karey Shumansky, Damian Yap, Susana Ben-Neriah, Jamie Rosner, Maia A. Smith, Cydney Nielsen, Adele Telenius, Daisuke Ennishi, Andrew J. Mungall, Richard Moore, Ryan D. Morin, Nathalie A. Johnson, Laurie H Sehn, Joseph M. Connors, David W Scott, Christian Steidl, Marco A. Marra, Randy D Gascoyne, Sohrab P. Shah
Frequent Genetic Alterations of PI3K-AKT Pathway and Their Clinical Significance in Germinal Center B-Cell-like Diffuse Large B-Cell Lymphoma

Daisuke Ennishi, Ali Bashashati, Saeed Saberi, Anja Mottok, Barbara Meissner, Merrill Boyle, Susana Ben-Neriah, Robert Kridel, David Dominguez-Sola, Kerry J Savage, Laurie H Sehn, Joseph M. Connors, Ryan D. Morin, Marco A. Marra, Sohrab P. Shah, Christian Steidl, David W. Scott, Randy D Gascoyne
Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates

Kaston Leung, Anders Klaus, Bill K. Lin, Emma Laks, Justina Biele, Daniel Lai, Ali Bashashati, Yi-Fei Huang, Radhouane Aniba, Michelle Moksa, Adi Steif, Anne-Marie Mes-Masson, Martin Hirst, Sohrab P. Shah, Samuel Aparicio, Carl L. Hansen
Abstract LB-324: Genomic consequences of aberrant DNA repair stratify ovarian cancer histotypes

Yikan Wang, Ali Bashashati, Michael S. Anglesio, Dawn Cochrane, Diljot Grewal, Hugo Horlings, Anthony Karnezis, Anne-Marie Mes-Masson, Aikou Okamoto, Satoshi Yanagida, Nozomu Yanaihara, Misato Saito, Blake Gilks, Jessica McAlpine, Samuel Aparicio, David Huntsman, Sohrab Shah
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer

Andrew McPherson, Andrew Roth, Emma Laks, Tehmina Masud, Ali Bashashati, Allen W Zhang, Gavin Ha, Justina Biele, Damian Yap, Adrian Wan, Leah M Prentice, Jaswinder Khattra, Maia A Smith, Cydney B Nielsen, Sarah C Mullaly, Steve Kalloger, Anthony Karnezis, Karey Shumansky, Celia Siu, Jamie Rosner, Hector Li Chan, Julie Ho, Nataliya Melnyk, Janine Senz, Winnie Yang, Richard Moore, Andrew J Mungall, Marco A Marra, Alexandre Bouchard-Côté, C Blake Gilks, David G Huntsman, Jessica N McAlpine, Samuel Aparicio, Sohrab P Shah
Synchronous Endometrial and Ovarian Carcinomas: Evidence of Clonality

Michael S. Anglesio, Yi Kan Wang, Madlen Maassen, Hugo M. Horlings, Ali Bashashati, Janine Senz, Robertson Mackenzie, Diljot S. Grewal, Hector Li-Chang, Anthony N. Karnezis, Brandon S. Sheffield, Melissa K. McConechy, Friedrich Kommoss, Florin A. Taran, Annette Staebler, Sohrab P. Shah, Diethelm Wallwiener, Sara Brucker, C. Blake Gilks, Stefan Kommoss, David G. Huntsman
Bayesian optimization of BCI parameters

Hossein Bashashati, Rabab K. Ward, Ali Bashashati
User-customized brain computer interfaces using Bayesian optimization

Hossein Bashashati, Rabab K Ward, Ali Bashashati
Abstract PR07: Synchronous ovarian and endometrial carcinomas: The case for pseudo-metastasis.

Michael S. Anglesio, Yi Kan Wang, Madlen Maassen, Hugo M. Horlings, Ali Bashashati, Blake Gilks, Stefan Kommoss, David G. Huntsman
Pamidronate functionalized nanoconjugates for targeted therapy of focal skeletal malignant osteolysis

Qian Yin, Li Tang, Kaimin Cai, Rong Tong, Rachel Sternberg, Xujuan Yang, Lawrence W. Dobrucki, Luke B. Borst, Debra Kamstock, Ziyuan Song, William G. Helferich, Jianjun Cheng, Timothy M. Fan
The genomic landscape of epithelioid sarcoma cell lines and tumours

Farzad Jamshidi, Ali Bashashati, Karey Shumansky, Brendan Dickson, Nalan Gokgoz, Jay S Wunder, Irene L Andrulis, Alexander J Lazar, Sohrab P Shah, David G Huntsman, Torsten O Nielsen
Hidden Markov Support Vector Machines for Self-Paced Brain Computer Interfaces

Hossein Bashashati, Rabab K. Ward, Ali Bashashati
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types

Jiarui Ding, Melissa K. McConechy, Hugo M. Horlings, Gavin Ha, Fong Chun Chan, Tyler Funnell, Sarah C. Mullaly, Jüri Reimand, Ali Bashashati, Gary D. Bader, David Huntsman, Samuel Aparicio, Anne Condon, Sohrab P. Shah
Abstract AS18: The somatic mutational landscape of endometriosis associated ovarian cancers and precursor lesions

Michael S Anglesio, Ali Bashashati, Yikan Wang, Gavin Ha, Janine Senz, Winnie Yang, Steve E Kalloger, Leah M Prentice, Satoshi Yanagida, Clara Salamanca, Galina Soukhatcheva, Anthony Kazernis, Hector Chang, Anne-Marie Mes-Mason, Aikou Okamoto, Marco A Marra, Blake Gilks, Sohrab P Shah, David G Huntsman
Comparing Different Classifiers in Sensory Motor Brain Computer Interfaces

Hossein Bashashati, Rabab K. Ward, Gary E. Birch, Ali Bashashati
Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden

Michael S Anglesio, Ali Bashashati, Yi Kan Wang, Janine Senz, Gavin Ha, Winnie Yang, Mohamed R Aniba, Leah M Prentice, Hossein Farahani, Hector Li Chang, Anthony N Karnezis, Marco A Marra, Paul J Yong, Martin Hirst, Blake Gilks, Sohrab P Shah, David G Huntsman
An RCOR1 loss–associated gene expression signature identifies a prognostically significant DLBCL subgroup

Fong Chun Chan, Adele Telenius, Shannon Healy, Susana Ben-Neriah, Anja Mottok, Raymond Lim, Marie Drake, Sandy Hu, Jiarui Ding, Gavin Ha, David W. Scott, Robert Kridel, Ali Bashashati, Sanja Rogic, Nathalie Johnson, Ryan D. Morin, Lisa M. Rimsza, Laurie Sehn, Joseph M. Connors, Marco A. Marra, Randy D. Gascoyne, Sohrab P. Shah, Christian Steidl
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

Peter Eirew, Adi Steif, Jaswinder Khattra, Gavin Ha, Damian Yap, Hossein Farahani, Karen Gelmon, Stephen Chia, Colin Mar, Adrian Wan, Emma Laks, Justina Biele, Karey Shumansky, Jamie Rosner, Andrew McPherson, Cydney Nielsen, Andrew J. L. Roth, Calvin Lefebvre, Ali Bashashati, Camila de Souza, Celia Siu, Radhouane Aniba, Jazmine Brimhall, Arusha Oloumi, Tomo Osako, Alejandra Bruna, Jose L. Sandoval, Teresa Algara, Wendy Greenwood, Kaston Leung, Hongwei Cheng, Hui Xue, Yuzhuo Wang, Dong Lin, Andrew J. Mungall, Richard Moore, Yongjun Zhao, Julie Lorette, Long Nguyen, David Huntsman, Connie J. Eaves, Carl Hansen, Marco A. Marra, Carlos Caldas, Sohrab P. Shah, Samuel Aparicio
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

Gavin Ha, Andrew Roth, Jaswinder Khattra, Julie Ho, Damian Yap, Leah M. Prentice, Nataliya Melnyk, Andrew McPherson, Ali Bashashati, Emma Laks, Justina Biele, Jiarui Ding, Alan Le, Jamie Rosner, Karey Shumansky, Marco A. Marra, C. Blake Gilks, David G. Huntsman, Jessica N. McAlpine, Samuel Aparicio, Sohrab P. Shah
Abstract LB-312: The somatic mutational landscape of ovarian clear cell carcinoma and its precursor lesions

Ali Bashashati, Michael Anglesio, Yikan Wang, Gavin Ha, Janine Senz, Winnie Yang, Steve Kalloger, Leah Prentice, Satoshi Yanagida, Clara Salamanca, Galina Soukhatcheva, Anthony Karnezis, Hector Chang, Martin Hirst, Anne-Marie Mes-Mason, Aikou Okamoto, Marco Marra, Blake Gilks, Sohrab Shah, David Huntsman
Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling

Ali Bashashati, Gavin Ha, Alicia Tone, Jiarui Ding, Leah M Prentice, Andrew Roth, Jamie Rosner, Karey Shumansky, Steve Kalloger, Janine Senz, Winnie Yang, Melissa McConechy, Nataliya Melnyk, Michael Anglesio, Margaret TY Luk, Kane Tse, Thomas Zeng, Richard Moore, Yongjun Zhao, Marco A Marra, Blake Gilks, Stephen Yip, David G Huntsman, Jessica N McAlpine, Sohrab P Shah
DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer

Ali Bashashati, Gholamreza Haffari, Jiarui Ding, Gavin Ha, Kenneth Lui, Jamie Rosner, David G Huntsman, Carlos Caldas, Samuel A Aparicio, Sohrab P Shah
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

Gavin Ha, Andrew Roth, Daniel Lai, Ali Bashashati, Jiarui Ding, Rodrigo Goya, Ryan Giuliany, Jamie Rosner, Arusha Oloumi, Karey Shumansky
The genomic and transcriptomic architecture of 2, 000 breast tumours reveals novel subgroups

Christina Curtis, , Sohrab P. Shah, Suet-Feung Chin, Gulisa Turashvili, Oscar M. Rueda, Mark J. Dunning, Doug Speed, Andy G. Lynch, Shamith Samarajiwa, Yinyin Yuan, Stefan Gräf, Gavin Ha, Gholamreza Haffari, Ali Bashashati, Roslin Russell, Steven McKinney, Anita Langerød, Andrew Green, Elena Provenzano, Gordon Wishart, Sarah Pinder, Peter Watson, Florian Markowetz, Leigh Murphy, Ian Ellis, Arnie Purushotham, Anne-Lise Børresen-Dale, James D. Brenton, Simon Tavaré, Carlos Caldas, Samuel Aparicio
The clonal and mutational evolution spectrum of primary triple-negative breast cancers

Sohrab P. Shah, Andrew Roth, Rodrigo Goya, Arusha Oloumi, Gavin Ha, Yongjun Zhao, Gulisa Turashvili, Jiarui Ding, Kane Tse, Gholamreza Haffari, Ali Bashashati, Leah M. Prentice, Jaswinder Khattra, Angela Burleigh, Damian Yap, Virginie Bernard, Andrew McPherson, Karey Shumansky, Anamaria Crisan, Ryan Giuliany, Alireza Heravi-Moussavi, Jamie Rosner, Daniel Lai, Inanc Birol, Richard Varhol, Angela Tam, Noreen Dhalla, Thomas Zeng, Kevin Ma, Simon K. Chan, Malachi Griffith, Annie Moradian, S.-W. Grace Cheng, Gregg B. Morin, Peter Watson, Karen Gelmon, Stephen Chia, Suet-Feung Chin, Christina Curtis, Oscar M. Rueda, Paul D. Pharoah, Sambasivarao Damaraju, John Mackey, Kelly Hoon, Timothy Harkins, Vasisht Tadigotla, Mahvash Sigaroudinia, Philippe Gascard, Thea Tlsty, Joseph F. Costello, Irmtraud M. Meyer, Connie J. Eaves, Wyeth W. Wasserman, Steven Jones, David Huntsman, Martin Hirst, Carlos Caldas, Marco A. Marra, Samuel Aparicio
B Cells With High Side Scatter Parameter by Flow Cytometry Correlate With Inferior Survival in Diffuse Large B-Cell Lymphoma

Ali Bashashati, Nathalie A. Johnson, Alireza Hadj Khodabakhshi, Matthew D. Whiteside, Habil Zare, David W. Scott, Kenneth Lo, Raphael Gottardo, Fiona S.L. Brinkman, Joseph M. Connors, Graham W. Slack, Randy D. Gascoyne, Andrew P. Weng, Ryan R. Brinkman
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data

Andrew Roth, Jiarui Ding, Ryan Morin, Anamaria Crisan, Gavin Ha, Ryan Giuliany, Ali Bashashati, Martin Hirst, Gulisa Turashvili, Arusha Oloumi, Marco A. Marra, Samuel Aparicio, Sohrab P. Shah
Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data

Jiarui Ding, Ali Bashashati, Andrew Roth, Arusha Oloumi, Kane Tse, Thomas Zeng, Gholamreza Haffari, Martin Hirst, Marco A. Marra, Anne Condon, Samuel Aparicio, Sohrab P. Shah
Automated Analysis of Multidimensional Flow Cytometry Data Improves Diagnostic Accuracy Between Mantle Cell Lymphoma and Small Lymphocytic Lymphoma

Habil Zare, Ali Bashashati, Robert Kridel, Nima Aghaeepour, Gholamreza Haffari, Joseph M. Connors, Randy D. Gascoyne, Arvind Gupta, Ryan R. Brinkman, Andrew P. Weng
BIOINFORMATICS TO BEDSIDE: AN AUTOMATED AND GENERALIZABLE MULTIDIMENSIONAL FLOW CYTOMETRY DATA ANALYSIS APPROACH IMPROVES DIAGNOSTIC ACCURACY BETWEEN MANTLE CELL LYMPHOMA AND SMALL LYMPHOCYTIC LYMPHOMA

Ryan R Brinkman, Habil Zare, Robert Kridel, Nima Aghaepour, Gholamreza Haffari, Josef M Connors, Randy D Gascoyne, Arvind Gupta, Andrew P Weng, Ali Bashashati
A Random Forests-based approach for estimating depth of human body gestures using a single video camera

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

Mahsa T. Pourazad, Panos Nasiopoulos, Ali Bashashati
Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection

Farshid S Garmaroudi, David Marchant, Xiaoning Si, Abbas Khalili, Ali Bashashati, Brian W Wong, Aline Tabet, Raymond T Ng, Kevin Murphy, Honglin Luo
Per-channel basis normalization methods for flow cytometry data

Florian Hahne, Alireza Hadj Khodabakhshi, Ali Bashashati, Chao-Jen Wong, Randy D. Gascoyne, Andrew P. Weng, Vicky Seyfert-Margolis, Katarzyna Bourcier, Adam Asare, Thomas Lumley, Robert Gentleman, Ryan R. Brinkman

Generation of Synthetic Ovarian Carcinoma Microscopic Images for Proficiency Testing