Publications

Multiomics and deep learning dissect regulatory syntax in human development

Betty B Liu^*, Selin Jessa^*, Samuel H Kim^*, Yan Ting Ng^*, Soon Il Higashino, Georgi K Marinov, Derek C Chen, Benjamin E Parks, Li Li, Tri C Nguyen, Austin T Wang, Sean K Wang, Meng How Tan, Serena Y Tan, Michael Kosicki, Len A Pennacchio, Eyal Ben-David, Anca M Pasca, Anshul Kundaje^{^}, Kyle K H Farh^{^}, William J Greenleaf^{^}

Selin's postdoc work using deep learning in a new fetal single-cell atlas to study the organization of transcription factor binding sites in human development, and where they're perturbed in complex traits. Highlighted in Nature Genetics.

Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells

Tong Wang, Selin Jessa, Georgi K Marinov, Sandy Klemm, Anshul Kundaje, William J Greenleaf

We present a new assay, beCasKAS, to sensitively detect off-target edits from CRISPR base editors, and show how non-coding off-target genome edits can be triaged for epigenetic dysregulation in silico using deep learning.

FOXR2 targets LHX6+/DLX+ neural lineages to drive CNS neuroblastoma

Selin Jessa^*, Antonella De Cola^*, Bhavyaa Chandarana^*, Michael McNicholas, Steven Hébert, Adam Ptack, Damien Faury, Jessica W Tsai, Andrey Korshunov, Timothy N Phoenix, Benjamin Ellezam, David T W Jones, Michael D Taylor, Pratiti Bandopadhayay, Manav Pathania^{^}, Nada Jabado^{^}, Claudia L Kleinman^{^}

K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas

Selin Jessa^*, Abdulshakour Mohammadnia^*, Ashot S Harutyunyan^*, Maud Hulswit, Srinidhi Varadharajan, Hussein Lakkis, Nisha Kabir, Zahedeh Bashardanesh, Steven Hébert, Damien Faury, Maria C Vladoiu, Samantha Worme, Marie Coutelier, Brian Krug, Augusto Faria Andrade, Manav Pathania, Andrea Bajic, Alexander G Weil, Benjamin Ellezam, Jeffrey Atkinson, Roy W R Dudley, Jean-Pierre Farmer, Sebastien Perreault, Benjamin A Garcia, Valérie Larouche, Mathieu Blanchette, Livia Garzia, Aparna Bhaduri, Keith L Ligon, Pratiti Bandopadhayay, Michael D Taylor, Stephen C Mack, Nada Jabado^{^}, Claudia L Kleinman^{^}

Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis

Carol C L Chen^*, Shriya Deshmukh^*, Selin Jessa^*, Djihad Hadjadj^*, Véronique Lisi, Augusto Faria Andrade, Damien Faury, Wajih Jawhar, Rola Dali, Hiromichi Suzuki, Manav Pathania, Deli A, Frank Dubois, Eleanor Woodward, Steven Hébert, Marie Coutelier, Jason Karamchandani, Steffen Albrecht, Sebastian Brandner, Nicolas De Jay, Tenzin Gayden, Andrea Bajic, Ashot S Harutyunyan, Dylan M Marchione, Leonie G Mikael, Nikoleta Juretic, Michele Zeinieh, Caterina Russo, Nicola Maestro, Angelia V Bassenden, Peter Hauser, József Virga, Laszlo Bognar, Almos Klekner, Michal Zapotocky, Ales Vicha, Lenka Krskova, Katerina Vanova, Josef Zamecnik, David Sumerauer, Paul G Ekert, David S Ziegler, Benjamin Ellezam, Mariella G Filbin, Mathieu Blanchette, Jordan R Hansford, Dong-Anh Khuong-Quang, Albert M Berghuis, Alexander G Weil, Benjamin A Garcia, Livia Garzia, Stephen C Mack, Rameen Beroukhim, Keith L Ligon, Michael D Taylor, Pratiti Bandopadhayay, Christoph Kramm, Stefan M Pfister, Andrey Korshunov, Dominik Sturm, David T W Jones, Paolo Salomoni, Claudia L Kleinman^{^}, Nada Jabado^{^}

Stalled developmental programs at the root of pediatric brain tumors

Selin Jessa, Alexis Blanchet-Cohen, Brian Krug, Maria Vladoiu, Marie Coutelier, Damien Faury, Brice Poreau, Nicolas De Jay, Steven Hébert, Jean Monlong, W Todd Farmer, Laura K Donovan, Yixing Hu, Melissa K McConechy, Florence M G Cavalli, Leonie G Mikael, Benjamin Ellezam, Maxime Richer, Andréa Allaire, Alexander G Weil, Jeffrey Atkinson, Jean-Pierre Farmer, Roy W R Dudley, Valerie Larouche, Louis Crevier, Steffen Albrecht, Mariella G Filbin, Hervé Sartelet, Pierre-Eric Lutz, Corina Nagy, Gustavo Turecki, Santiago Costantino, Peter B Dirks, Keith K Murai, Guillaume Bourque, Jiannis Ragoussis, Livia Garzia, Michael D Taylor^{^}, Nada Jabado^{^}, Claudia L Kleinman^{^}

Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart

Andrew R Marderstein^{*^}, Soumya Kundu^*, Evin M Padhi, Salil Deshpande, Austin Wang, Esther Robb, Ying Sun, Chang M Yun, Diego Pomales-Matos, Yilin Xie, Daniel Nachun, Selin Jessa, Anshul Kundaje^{^}, Stephen B Montgomery^{^}

A unified lexicon of predictive DNA sequence motifs from ENCODE transcription factor binding and chromatin accessibility assays

Salil Deshpande, Chang M. Yun, Vivekanandan Ramalingam, Vivian Hecht, Aman Patel, Anusri Pampari, Selin Jessa, Ryan Zhao, Austin Wang, Anshul Kundaje

TULIPs decorate the three-dimensional genome of PFA ependymoma

Michael J Johnston, John J Y Lee, Bo Hu, Ana Nikolic, Elham Hasheminasabgorji, Audrey Baguette, Seungil Paik, Haifen Chen, Sachin Kumar, Carol C L Chen, Selin Jessa, Polina Balin, Vernon Fong, Melissa Zwaig, Kulandaimanuvel Antony Michealraj, Xun Chen, Yanlin Zhang, Srinidhi Varadharajan, Pierre Billon, Nikoleta Juretic, Craig Daniels, Amulya Nageswara Rao, Caterina Giannini, Eric M Thompson, Miklos Garami, Peter Hauser, Timea Pocza, Young Shin Ra, Byung-Kyu Cho, Seung-Ki Kim, Kyu-Chang Wang, Ji Yeoun Lee, Wieslawa Grajkowska, Marta Perek-Polnik, Sameer Agnihotri, Stephen Mack, Benjamin Ellezam, Alex Weil, Jeremy Rich, Guillaume Bourque, Jennifer A Chan, V Wee Yong, Mathieu Lupien, Jiannis Ragoussis, Claudia Kleinman, Jacek Majewski, Mathieu Blanchette, Nada Jabado, Michael D Taylor, Marco Gallo

Mapping Angiopoietin1 expression in the developing and adult brain

Xin Wei, Selin Jessa, Claudia L Kleinman, Timothy N Phoenix

Epigenetically defined therapeutic targeting in H3.3G34R/V high-grade gliomas

Stefan R Sweha, Chan Chung, Siva Kumar Natarajan, Pooja Panwalkar, Matthew Pun, Amer Ghali, Jill Bayliss, Drew Pratt, Anand Shankar, Visweswaran Ravikumar, Arvind Rao, Marcin Cieslik, Kari Wilder-Romans, Andrew J Scott, Daniel R Wahl, Selin Jessa, Claudia L Kleinman, Nada Jabado, Alan Mackay, Chris Jones, Daniel Martinez, Mariarita Santi, Alexander R Judkins, Viveka Nand Yadav, Tingting Qin, Timothy N Phoenix, Carl J Koschmann, Suzanne J Baker, Arul M Chinnaiyan, Sriram Venneti

ZFTA-RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma

Amir Arabzade, Yanhua Zhao, Srinidhi Varadharajan, Hsiao-Chi Chen, Selin Jessa, Bryan Rivas, Austin J Stuckert, Minerva Solis, Alisha Kardian, Dana Tlais, Brian J Golbourn, Ann-Catherine J Stanton, Yuen San Chan, Calla Olson, Kristen L Karlin, Kathleen Kong, Robert Kupp, Baoli Hu, Sarah G Injac, Madeline Ngo, Peter R Wang, Luz A De Leon, Felix Sahm, Daisuke Kawauchi, Stefan M Pfister, Charles Y Lin, H Courtney Hodges, Irtisha Singh, Thomas F Westbrook, Murali M Chintagumpala, Susan M Blaney, Donald W Parsons, Kristian W Pajtler, Sameer Agnihotri, Richard J Gilbertson, Joanna Yi, Nada Jabado, Claudia L Kleinman, Kelsey C Bertrand, Benjamin Deneen, Stephen C Mack

chromswitch: A flexible method to detect chromatin state switches

Selin Jessa, Claudia L Kleinman

Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma

Sarah E Arthur, Aixiang Jiang, Bruno M Grande, Miguel Alcaide, Razvan Cojocaru, Christopher K Rushton, Anja Mottok, Laura K Hilton, Prince Kumar Lat, Eric Y Zhao, Luka Culibrk, Daisuke Ennishi, Selin Jessa, Lauren Chong, Nicole Thomas, Prasath Pararajalingam, Barbara Meissner, Merrill Boyle, Jordan Davidson, Kevin R Bushell, Daniel Lai, Pedro Farinha, Graham W Slack, Gregg B Morin, Sohrab Shah, Dipankar Sen, Steven J M Jones, Andrew J Mungall, Randy D Gascoyne, Timothy E Audas, Peter Unrau, Marco A Marra, Joseph M Connors, Christian Steidl, David W Scott, Ryan D Morin

Enhancing knowledge discovery from cancer genomics data with Galaxy

Marco A Albuquerque, Bruno M Grande, Elie J Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K Grewal, Sohrab P Shah, Paul C Boutros, Ryan D Morin

Healthcare for All!: Access to healthcare for migrants with precarious status in the Parc-Extension neighbourhood of Montreal, Quebec

Selin Jessa