Publications

26 Results (Filters Applied)
  • Imieliński Lab 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

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

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 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

Nature Biotechnology. 2022 May 30.

Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing.

Aditya S. Deshpande, Netha Ulahannan, Matthew Pendleton, Xiaoguang Dai, Lynn Ly, Julie M. Behr, Stefan Schwenk, Will Liao, Michael A. Augello, Carly Tyer, Priyesh Rughani, Sarah Kudman, Huasong Tian, Hannah G. Otis, Emily Adney, David Wilkes, Juan Miguel Mosquera, Christopher E. Barbieri, Ari Melnick, David Stoddart, Daniel J. Turner, Sissel Juul, Eoghan Harrington & Marcin Imieliński

Nature Communications. 2022 Apr. 28.

Somatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression.

Thomas G. Paulson, Patricia C. Galipeau, Kenji M. Oman, Carissa A. Sanchez, Mary K. Kuhner, Lucian P. Smith, Kevin Hadi, Minita Shah, Kanika Arora, Jennifer Shelton, Molly Johnson, Andre Corvelo, Carlo C. Maley, Xiaotong Yao, Rashesh Sanghvi, Elisa Venturini, Anne-Katrin Emde, Benjamin Hubert, Marcin Imielinski, Nicolas Robine, Brian J. Reid & Xiaohong Li

Cell Reports Medicine. 2022 Feb. 15.

System-wide transcriptome damage and tissue identity loss in COVID-19 patients.

Jiwoon Park, Jonathan Foox, Tyler Hether, David C. Danko, Sarah Warren, Youngmi Kim, Jason Reeves, Daniel J. Butler, Christopher Mozsary, Joel Rosiene, Alon Shaiber, Evan E. Afshin, Matthew MacKay, Andre´ F. Rendeiro, Yaron Bram, Vasuretha Chandar, Heather Geiger, Arryn Craney, Priya Velu, Ari M. Melnick, Iman Hajirasouliha, Afshin Beheshti, Deanne Taylor, Amanda Saravia-Butler, Urminder Singh, Eve Syrkin Wurtele, Jonathan Schisler, Samantha Fennessey, Andre´ Corvelo, Michael C. Zody, Soren Germer, Steven Salvatore, Shawn Levy, Shixiu Wu, Nicholas P. Tatonetti, Sagi Shapira,22 Mirella Salvatore,8,23 Lars F. Westblade,7,8 Melissa Cushing,7 Hanna Rennert,7 Alison J. Kriegel,24 Olivier Elemento, Marcin Imielinski, Charles M. Rice, Alain C. Borczuk, Cem Meydan, Robert E. Schwartz, and Christopher E. Mason

PNAS. 2021 Apr. 13.

Integrated mutational landscape analysis of uterine leiomyosarcomas.

Jungmin Choi, Aranzazu Manzano, Weilai Dong, Stefania Bellone, Elena Bonazzoli, Luca Zammataro, Xiaotong Yao, Aditya Deshpande, Samir Zaidi, Adele Guglielmi, Barbara Gnutti, Nupur Nagarkatti, Joan R. Tymon-Rosario, Justin Harold, Dennis Mauricio, Burak Zeybek, Gulden Menderes, Gary Altwerger, Kyungjo Jeong, Siming Zhao, Natalia Buza, Pei Hui, Antonella Ravaggi, Eliana Bignotti, Chiara Romani, Paola Todeschini, Laura Zanotti, Franco Odicino, Sergio Pecorelli, Laura Ardighieri, Kaya Bilguvar, Charles M. Quick, Dan-Arin Silasi, Gloria S. Huang, Vaagn Andikyan, Mitchell Clark, Elena Ratner, Masoud Azodi, Marcin Imielinski, Peter E. Schwartz, Ludmil B. Alexandrov, Richard P. Lifton, Joseph Schlessinger, and Alessandro D. Santin

Cell. 2021 Apr. 7.

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes.

Stefan C. Dentro, Ignaty Leshchiner, Kerstin Haase, Maxime Tarabichi, Jeff Wintersinger, Amit G. Deshwar, Kaixian Yu, Yulia Rubanova, Geoff Macintyre, Jonas Demeulemeester,Ignacio Vazquez-Garcıa, Kortine Kleinheinz, Dimitri G. Livitz, Salem Malikic,15 Nilgun Donmez, Subhajit Sengupta, Pavana Anur, Clemency Jolly, Marek Cmero, Daniel Rosebrock,Steven E. Schumacher, Yu Fan, Matthew Fittall, Ruben M. Drews, Xiaotong Yao, Thomas B.K. Watkins, Juhee Lee, Matthias Schlesner, Hongtu Zhu, David J. Adams, Nicholas McGranahan, Charles Swanton, Gad Getz, Paul C. Boutros, Marcin Imielinski, Rameen Beroukhim, S. Cenk Sahinalp, Yuan Ji, Martin Peifer, Inigo Martincorena, Florian Markowetz, Ville Mustonen, Ke Yuan, Moritz Gerstung, Paul T. Spellman, Wenyi Wang, Quaid D. Morris, David C. Wedge, Peter Van Loo, and on behalf of the PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium

Nature Communications. 2021 March 12.

Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions

Daniel J Butler, Christopher Mozsary, Cem Meydan, David C Danko, Jonathan Foox, Joel Rosiene, Alon Shaiber, Ebrahim Afshinnekoo, Matthew MacKay, Fritz J Sedlazeck, Nikolay A Ivanov, Maria A Sierra, Diana Pohle, Michael Zeitz, Undina Gisladottir, Craig D Westover, Krista Ryon, Benjamin Young, Chandrima Bhattacharya, Phyllis Ruggiero, Bradley W Langhorst, Nathan A Tanner, Justyn Gawrys, Dmitry Meleshko, Dong Xu, Jenny Xiang, Angelika Iftner, Daniela Bezdan, John Sipley, Lin Cong, Arryn Craney, Priya Velu, Ari Melnick, Iman A Hajirasouliha, Thomas Iftner, Mirella Salvatore, Massimo Loda, Lars F Westblade, Shawn Levy, Melissa Cushing, Nicholas P Tatonetti, Marcin Imielinski, Hanna Rennert, Christopher Mason

Cell Reports. 2021 Feb. 2.

Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway.

Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, Lee JJ, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N; TCGA Research Network, Meyerson M, Govindan R, Imielinski M

Nature. 2020 December 9.

Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture.

Nevin Yusufova, Andreas Kloetgen, Matt Teater, Adewola Osunsade, Jeannie M. Camarillo, Christopher R. Chin, Ashley S. Doane, Bryan J. Venters, Stephanie Portillo-Ledesma, Joseph Conway, Jude M. Phillip, Olivier Elemento, David W. Scott, Wendy Béguelin, Jonathan D. Licht, Neil L. Kelleher, Louis M. Staudt, Arthur I. Skoultchi, Michael-Christopher Keogh, Effie Apostolou, Christopher E. Mason, Marcin Imielinski, Tamar Schlick, Yael David, Aristotelis Tsirigos, C. David Allis, Alexey A. Soshnev, Ethel Cesarman & Ari M. Melnick.

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