Publications

94 Results (Filters Applied)
  • Cancer x
Nature Genetics. 2023 Nov. 9.

Most large structural variants in cancer genomes can be detected without long reads.

Zi-Ning Choo, Julie M. Behr, Aditya Deshpande, Kevin Hadi, Xiaotong Yao, Huasong Tian, Kaori Takai, George Zakusilo, Joel Rosiene, Arnaud Da Cruz Paula, Britta Weigelt, Jeremy Setton, Nadeem Riaz, Simon N. Powell, Klaus Busam, Alexander N. Shoushtari, Charlotte Ariyan, Jorge Reis-Filho, Titia de Lange & Marcin Imieliński

NPJ Precision Oncology. 2023 Sept. 13.

Evolution of structural rearrangements in prostate cancer intracranial metastases.

Francesca Khani, William F. Hooper, Xiaofei Wang, Timothy R. Chu, Minita Shah, Lara Winterkorn, Michael Sigouros, Vincenza Conteduca, David Pisapia, Sara Wobker, Sydney Walker, Julie N. Graff, Brian Robinson, Juan Miguel Mosquera, Andrea Sboner, Olivier Elemento, Nicolas Robine & Himisha Beltran

Nature. 2023 Aug. 16.

Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers.

Jeremy Setton, Kevin Hadi, Zi-Ning Choo, Katherine S. Kuchin, Huasong Tian, Arnaud Da Cruz Paula, Joel Rosiene, Pier Selenica, Julie Behr, Xiaotong Yao, Aditya Deshpande, Michael Sigouros, Jyothi Manohar, Jones T. Nauseef, Juan-Miguel Mosquera, Olivier Elemento, Britta Weigelt, Nadeem Riaz, Jorge S. Reis-Filho, Simon N. Powell & Marcin Imieliński

Cell Stem Cell. 2023 Aug. 14.

Single-cell multi-omics defines the cell-type specific impact of splicing aberrations in human hematopoietic clonal outgrowths.

Mariela Cortés-López, Paulina Chamely, Allegra G. Hawkins, Robert F. Stanley, Ariel D. Swett, Saravanan Ganesan, Tarek H. Mouhieddine, Xiaoguang Dai, Lloyd Kluegel, Celine Chen, Kiran Batta, Nili Furer, Rahul S. Vedula, John Beaulaurier, Alexander W. Drong, Scott Hickey, Neville Dusaj, Gavriel Mullokandov, Adam M. Stasiw, Jiayu Su, Ronan Chaligné, Sissel Juul, Eoghan Harrington, David A. Knowles, Catherine J. Potenski, Daniel H. Wiseman, Amos Tanay, Liran Shlush, Robert C. Lindsley, Irene M. Ghobrial, Justin Taylor, Omar Abdel-Wahab, Federico Gaiti, Dan A. Landau

Nature. 2023 June 7.

Epigenetic dysregulation from chromosomal transit in micronuclei.

Albert S. Agustinus, Duaa Al-Rawi, Bhargavi Dameracharla, Ramya Raviram, Bailey S. C. L. Jones, Stephanie Stransky, Lorenzo Scipioni, Jens Luebeck, Melody Di Bona, Danguole Norkunaite, Robert M. Myers, Mercedes Duran, Seongmin Choi, Britta Weigelt, Shira Yomtoubian, Andrew McPherson, Eléonore Toufektchan, Kristina Keuper, Paul S. Mischel, Vivek Mittal, Sohrab P. Shah, John Maciejowski, Zuzana Storchova, Enrico Gratton, Peter Ly, Dan Landau, Mathieu F. Bakhoum, Richard P. Koche, Simone Sidoli, Vineet Bafna, Yael David & Samuel F. Bakhoum

Blood Cancer Discovery. 2023 Feb. 1.

Molecular evolution of classic Hodgkin lymphoma revealed through whole genome sequencing of Hodgkin and Reed Sternberg cells.

Francesco Maura, Bachisio Ziccheddu, Jenny Z Xiang, Bhavneet Bhinder, Joel Rosiene, Federico Abascal, Kylee H Maclachlan, Kenneth Wha Eng, Manik Uppal, Feng He, Wei Zhang, Qi Gao, Venkata D Yellapantula, Vicenta Trujillo-Alonso, Sunita I Park, Matthew J Oberley, Elizabeth Ruckdeschel, Megan S Lim, Gerald B Wertheim, Matthew J Barth, Terzah M Horton, Andriy Derkach, Alexandra E Kovach, Christopher J Forlenza, Yanming Zhang, Ola Landgren, Craig H Moskowitz, Ethel Cesarman, Marcin Imielinski, Olivier Elemento, Mikhail Roshal, Lisa Giulino-Roth

Cold Spring Harbor Molecular Case Studies. 2022 Dec. 28.

Whole-genome characterization of myoepithelial carcinomas of the soft tissue.

Joanna Cyrta, Joel Rosiene, Rohan Bareja, Sarah Kudman, Wael Al Zoughbi, Samaneh Motanagh, David C Wilkes, Kenneth Eng, Tuo Zhang, Evan Sticca, Susan Mathew, Mark A Rubin, Andrea Sboner, Olivier Elemento, Brian P Rubin, Marcin Imielinski, Juan Miguel Mosquera

Nature. 2022 Dec. 14.

Recurrent repeat expansions in human cancer genomes.

Graham S. Erwin, Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu, Christian R. Hoerner, Shannon M. White, Lucia Ramirez, Ananya Vadlakonda, Alekhya Vadlakonda, Konor von Kraut, Julia Park, Charlotte M. Brannon, Daniel A. Sumano, Raushun A. Kirtikar, Alicia A. Erwin, Thomas J. Metzner, Ryan K. C. Yuen, Alice C. Fan, John T. Leppert, Michael A. Eberle, Mark Gerstein & Michael P. Snyder

JCO Precision Oncology. 2022 Dec. 8.

Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care.

Edwin Cuppen, Olivier Elemento, Richard Rosenquist, Svetlana Nikic, Maarten IJzerman, Isabelle Durand Zaleski, Geert Frederix, Lars-Åke Levin, Charles G Mullighan, Reinhard Buettner, Trevor J Pugh, Sean Grimmond, Carlos Caldas, Fabrice Andre, Ilse Custers, Elias Campo, Hans van Snellenberg, Anna Schuh, Hidewaki Nakagawa, Christof von Kalle, Torsten Haferlach, Stefan Fröhling, Vaidehi Jobanputra

Nature. 2022 Nov. 30.

Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer.

Andrew L. H. Webster, Mathijs A. Sanders, Krupa Patel, Ralf Dietrich, Raymond J. Noonan, Francis P. Lach, Ryan R. White, Audrey Goldfarb, Kevin Hadi, Matthew M. Edwards, Frank X. Donovan, Remco M. Hoogenboezem, Moonjung Jung, Sunandini Sridhar, Tom F. Wiley, Olivier Fedrigo, Huasong Tian, Joel Rosiene, Thomas Heineman, Jennifer A. Kennedy, Lorenzo Bean, Rasim O. Rosti, Rebecca Tryon, Ashlyn-Maree Gonzalez, Allana Rosenberg, Ji-Dung Luo, Thomas S. Carroll, Sanjana Shroff, Michael Beaumont, Eunike Velleuer, Jeff C. Rastatter, Susanne I. Wells, Jordi Surrallés, Grover Bagby, Margaret L. MacMillan, John E. Wagner, Maria Cancio, Farid Boulad, Theresa Scognamiglio, Roger Vaughan, Kristin G. Beaumont, Amnon Koren, Marcin Imielinski, Settara C. Chandrasekharappa, Arleen D. Auerbach, Bhuvanesh Singh, David I. Kutler, Peter J. Campbell & Agata Smogorzewska

This work was partially supported by a gift from the Simons Foundation.