Rameen Beroukhim (R Beroukhim)

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 32

Top Topics

Newly Diagnosed

Papillary Thyroid

Top Venues

Nature communications

bioRxiv : the preprint server for biology

Clinical cancer research : an official journal of the American Association for Cancer Research

Nature reviews. Cancer

This page only lists publications with an associated author ORCID identifier.

Publications

Wolu Chukwu, Siyun Lee, Alexander Crane, Shu Zhang, Sophie Webster, Ipsa Mittra, Marcin Imielinski, Rameen Beroukhim, Frank P B Dubios, Simona Dalin
Comparison of germline and somatic structural variants in cancers reveal systematic differences in variant generating and selection processes. bioRxiv : the preprint server for biology (2024)
Wolu Chukwu, Siyun Lee, Alexander Crane, Shu Zhang, Sophie Webster, Ipsa Mittra, Marcin Imielinski, Rameen Beroukhim, Frank P B Dubios, Simona Dalin
Comparison of germline and somatic structural variants in cancers reveal systematic differences in variant generating and selection processes. bioRxiv : the preprint server for biology (2024)
Frank P B Dubios, Nikos Sidiropoulos, Joachim Weischenfeldt, Rameen Beroukhim
Publisher Correction: Structural variations in cancer and the 3D genome. Nature reviews. Cancer (2024)
Mary Jane Lim-Fat, J Bryan Iorgulescu, Rifaquat Rahman, Varun M Bhave, Alona Muzikansky, Eleanor Woodward, Sydney Whorral, Marie Allen, Mehdi Touat, Xiaomei Li, Gongwen Xu, Jay Patel, Elizabeth R Gerstner, Jayashree Kalpathy-Cramer, Gilbert Youssef, Ugonma N Chukwueke, J Ricardo McFaline-Figueroa, Lakshmi Nayak, Eudocia Quant Lee, David A Reardon, Rameen Beroukhim, Raymond Y Huang, Wenya Linda Bi, Keith L Ligon, Patrick Yung Wen
Clinical and Genomic Predictors of Adverse Events in Newly Diagnosed Glioblastoma. Clinical cancer research : an official journal of the American Association for Cancer Research 30 (7) (2024)
Wolu Chukwu, Siyun Lee, Alexander Crane, Shu Zhang, Sophie Webster, Ipsa Mittra, Marcin Imielinski, Rameen Beroukhim, Frank P B Dubios, Simona Dalin
Comparison of germline and somatic structural variants in cancers reveal systematic differences in variant generating and selection processes. bioRxiv : the preprint server for biology (2024)
Sean A Misek, Aaron Fultineer, Jérémie Kalfon, Javad Noorbakhsh, Isabella Boyle, Priyanka Roy, Joshua M Dempster, Lia Petronio, Katherine Huang, Alham Saadat, Thomas Green, Adam Brown, John G Doench, David E Root, James M McFarland, Rameen Beroukhim, Jesse S Boehm
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries. Nature communications 15 (1) (2024)
Sean A Misek, Aaron Fultineer, Jérémie Kalfon, Javad Noorbakhsh, Isabella Boyle, Priyanka Roy, Joshua M Dempster, Lia Petronio, Katherine Huang, Alham Saadat, Thomas Green, Adam Brown, John G Doench, David E Root, James M McFarland, Rameen Beroukhim, Jesse S Boehm
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries. Nature communications 15 (1) (2024)
Wolu Chukwu, Siyun Lee, Alexander Crane, Shu Zhang, Sophie Webster, Ipsa Mittra, Marcin Imielinski, Rameen Beroukhim, Frank P B Dubios, Simona Dalin
Comparison of germline and somatic structural variants in cancers reveal systematic differences in variant generating and selection processes. bioRxiv : the preprint server for biology (2024)
Sean A Misek, Aaron Fultineer, Jérémie Kalfon, Javad Noorbakhsh, Isabella Boyle, Priyanka Roy, Joshua M Dempster, Lia Petronio, Katherine Huang, Alham Saadat, Thomas Green, Adam Brown, John G Doench, David E Root, James M McFarland, Rameen Beroukhim, Jesse S Boehm
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries. Nature communications 15 (1) (2024)
Mary Jane Lim-Fat, J Bryan Iorgulescu, Rifaquat Rahman, Varun M Bhave, Alona Muzikansky, Eleanor Woodward, Sydney Whorral, Marie Allen, Mehdi Touat, Xiaomei Li, Gongwen Xu, Jay Patel, Elizabeth R Gerstner, Jayashree Kalpathy-Cramer, Gilbert Youssef, Ugonma N Chukwueke, J Ricardo McFaline-Figueroa, Lakshmi Nayak, Eudocia Quant Lee, David A Reardon, Rameen Beroukhim, Raymond Y Huang, Wenya Linda Bi, Keith L Ligon, Patrick Yung Wen
Clinical and Genomic Predictors of Adverse Events in Newly Diagnosed Glioblastoma. Clinical cancer research : an official journal of the American Association for Cancer Research 30 (7) (2024)
Mary Jane Lim-Fat, J Bryan Iorgulescu, Rifaquat Rahman, Varun M Bhave, Alona Muzikansky, Eleanor Woodward, Sydney Whorral, Marie Allen, Mehdi Touat, Xiaomei Li, Gongwen Xu, Jay Patel, Elizabeth R Gerstner, Jayashree Kalpathy-Cramer, Gilbert Youssef, Ugonma N Chukwueke, J Ricardo McFaline-Figueroa, Lakshmi Nayak, Eudocia Quant Lee, David A Reardon, Rameen Beroukhim, Raymond Y Huang, Wenya Linda Bi, Keith L Ligon, Patrick Yung Wen
Clinical and genomic predictors of adverse events in newly diagnosed glioblastoma. Clinical cancer research : an official journal of the American Association for Cancer Research (2024)
Juliann Shih, Shahab Sarmashghi, Nadja Zhakula-Kostadinova, Shu Zhang, Yohanna Georgis, Stephanie H Hoyt, Michael S Cuoco, Galen F Gao, Liam F Spurr, Ashton C Berger, Gavin Ha, Veronica Rendo, Hui Shen, Matthew L Meyerson, Andrew D Cherniak, Alison M Taylor, Rameen Beroukhim
Cancer aneuploidies are shaped primarily by effects on tumour fitness. Nature (2023)
Anne-Florence Blandin, Ross M Giglio, Maya Srikanth Graham, Guadalupe Garcia, Seth Malinowski, Jared K Woods, Shakti Ramkissoon, Lori Ramkissoon, Frank P B Dubios, Kathleen Schoolcraft, Jessica W Tsai, Dayle K Wang, Robert Jones, Jayne Vogelzang, Kristine Pelton, Sarah Becker, Fiona Watkinson, Claire Sinai, Elizabeth F Cohen, Matthew A Booker, Michael Yevgeniy Tolstorukov, Veerle Haemels, Liliana Christova Goumnerova, Karen D Wright, Mark W Kieran, Katie Pricola Fehnel, David A Reardon, Arnault Tauziède-Espariat, Rishi R Lulla, Benjamin Carcamo, Stanley Chaleff, Alain Charest, Frederik De Smet, Azra H Ligon, Adrian M Dubuc, Melanie Pages, Pascale Varlet, Patrick Yung Wen, Brian M Alexander, Susan N Chi, Sanda Alexandrescu, Ralf Kittler, Robert Bachoo, Pratiti Bandopadhayay, Rameen Beroukhim, Keith L Ligon
ALK amplification and rearrangements are recurrent targetable events in congenital and adult glioblastoma. Clinical cancer research : an official journal of the American Association for Cancer Research (2023)
Wolu Chukwu, Siyun Lee, Alexander Crane, Shu Zhang, Ipsa Mittra, Marcin Imielinski, Rameen Beroukhim, Frank P B Dubios, Simona Dalin
Genomic sequence context differs between germline and somatic structural variants allowing for their differentiation in tumor samples without paired normals. bioRxiv : the preprint server for biology (2023)
Wolu Chukwu, Siyun Lee, Alexander Crane, Shu Zhang, Ipsa Mittra, Marcin Imielinski, Rameen Beroukhim, Frank P B Dubios, Simona Dalin
Genomic sequence context differs between germline and somatic structural variants allowing for their differentiation in tumor samples without paired normals. bioRxiv : the preprint server for biology (2023)
Anne-Florence Blandin, Ross M Giglio, Maya Srikanth Graham, Guadalupe Garcia, Seth Malinowski, Jared K Woods, Shakti Ramkissoon, Lori Ramkissoon, Frank P B Dubios, Kathleen Schoolcraft, Jessica W Tsai, Dayle K Wang, Robert Jones, Jayne Vogelzang, Kristine Pelton, Sarah Becker, Fiona Watkinson, Claire Sinai, Elizabeth F Cohen, Matthew A Booker, Michael Yevgeniy Tolstorukov, Veerle Haemels, Liliana Christova Goumnerova, Karen D Wright, Mark W Kieran, Katie Pricola Fehnel, David A Reardon, Arnault Tauziède-Espariat, Rishi R Lulla, Benjamin Carcamo, Stanley Chaleff, Alain Charest, Frederik De Smet, Azra H Ligon, Adrian M Dubuc, Melanie Pages, Pascale Varlet, Patrick Yung Wen, Brian M Alexander, Susan N Chi, Sanda Alexandrescu, Ralf Kittler, Robert Bachoo, Pratiti Bandopadhayay, Rameen Beroukhim, Keith L Ligon
ALK amplification and rearrangements are recurrent targetable events in congenital and adult glioblastoma. Clinical cancer research : an official journal of the American Association for Cancer Research (2023)
Prasidda Khadka, Zachary J Reitman, Sophie Lu, Graham Buchan, Gabrielle Gionet, Frank Dubois, Diana M Carvalho, Juliann Shih, Shu Zhang, Noah F Greenwald, Travis Zack, Ofer Shapira, Kristine Pelton, Rachel Hartley, Heather Bear, Yohanna Georgis, Spandana Jarmale, Randy Melanson, Kevin Bonanno, Kathleen Schoolcraft, Peter G Miller, Alexandra L Condurat, Elizabeth M Gonzalez, Kenin Qian, Eric Morin, Jaldeep Langhnoja, Leslie E Lupien, Veronica Rendo, Jeromy Digiacomo, Dayle K Wang, Kevin Ning Zhou, Rushil Kumbhani, Maria E Guerra Garcia, Claire E Sinai, Sarah Becker, Rachel Schneider, Jayne Vogelzang, Karsten Krug, Amy Goodale, Tanaz Abid, Zohra Kalani, Frederica Piccioni, Rameen Beroukhim, Nicole S Persky, David E Root, Angel Montero Carcaboso, Benjamin L Ebert, Christine Fuller, Ozgun Babur, Mark W Kieran, Chris Jones, Hasmik Keshishian, Keith L Ligon, Steven A Carr, Timothy N Phoenix, Pratiti Bandopadhayay
PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation. Nature communications 13 (1) (2022)
Frank P B Dubios, Nikos Sidiropoulos, Joachim Weischenfeldt, Rameen Beroukhim
Structural variations in cancer and the 3D genome. Nature reviews. Cancer 22 (9) (2022)
Frank P B Dubios, Ofer Shapira, Noah F Greenwald, Travis Zack, Jeremiah Wala, Jessica W Tsai, Alexander Crane, Audrey Baguette, Djihad Hadjadj, Ashot S Harutyunyan, Kiran H Kumar, Mirjam Blattner-Johnson, Jayne Vogelzang, Cecilia Sousa, Kyung Shin Kang, Claire Sinai, Dayle K Wang, Prasidda Khadka, Kathleen Lewis, Lan Nguyen, Hayley Malkin, Patricia Ho, Ryan O'Rourke, Shu Zhang, Rose Gold, Davy Deng, Jonathan Serrano, Matija Snuderl, Chris Jones, Karen D Wright, Susan N Chi, Jacques Grill, Claudia L Kleinman, Liliana Christova Goumnerova, Nada Jabado, David T W Jones, Mark W Kieran, Keith L Ligon, Rameen Beroukhim, Pratiti Bandopadhayay
Structural variants shape driver combinations and outcomes in pediatric high-grade glioma. Nature cancer 3 (8) (2022)
Yael Cohen-Sharir, James M McFarland, Mai Abdusamad, Carolyn Marquis, Sara V Bernhard, Mariya Kazachkova, Helen Tang, Marica R Ippolito, Kathrin Laue, Johanna Zerbib, Heidi L H Malaby, Andrew Jones, Lisa-Marie Stautmeister, Irena Bockaj, René Wardenaar, Nicholas Lyons, Ankur K Nagaraja, Adam J Bass, Diana Carolina Johanna Spierings, Floris Foijer, Rameen Beroukhim, Stefano Santaguida, Todd R Golub, Jason Stumpff, Zuzana Storchová, Uri Ben-David
Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition. Nature 590 (7846) (2021)
Camilo Jaimes, Sridhar Vajapeyam, D Brown, Pei-Chi Kao, Clement Ma, L Greenspan, Nalin Gupta, Liliana Christova Goumnerova, Pratiti Bandopadhayay, Frank P B Dubios, Noah F Greenwald, Travis Zack, O Shapira, Rameen Beroukhim, Keith L Ligon, Susan N Chi, Mark W Kieran, Karen D Wright, T Young Poussaint
MR Imaging Correlates for Molecular and Mutational Analyses in Children with Diffuse Intrinsic Pontine Glioma. AJNR. American journal of neuroradiology 41 (5) (2020)
Caitlin A Nichols, William J Gibson, Meredith S Brown, Jack A Kosmicki, John P Busanovich, Hope Wei, Laura M Urbanski, Naomi Curimjee, Ashton C Berger, Galen F Gao, Andrew D Cherniak, Sirano Dhe-Paganon, Brenton R Paolella, Rameen Beroukhim
Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities. Nature communications 11 (1) (2020)
Oana M Enache, Veronica Rendo, Mai Abdusamad, Daniel Lam, Desiree Davison, Sangita Pal, Naomi Currimjee, Julian Hess, Sasha Pantel, Anwesha Nag, Aaron R Thorner, John G Doench, Francisca Vazquez, Rameen Beroukhim, Todd R Golub, Uri Ben-David
Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nature genetics 52 (7) (2020)
Nilay S Sethi, Osamu Kikuchi, Gina N Duronio, Matthew D Stachler, James M McFarland, Ruben Ferrer-Luna, Yanxi Zhang, Chunyang Bao, Roderick Bronson, Deepa Patil, Francisco Sanchez-Vega, Jie-Bin Liu, Ewa Sicinska, Jean-Bernard Lazaro, Keith L Ligon, Rameen Beroukhim, Adam J Bass
Early TP53 alterations engage environmental exposures to promote gastric premalignancy in an integrative mouse model. Nature genetics 52 (2) (2020)
Mehdi Touat, Yvonne Y Li, Adam N Boynton, Liam F Spurr, J Bryan Iorgulescu, Craig L Bohrson, Isidro Cortes-Ciriano, Cristina Birzu, Jack E Geduldig, Kristine Pelton, Mary Jane Lim-Fat, Sangita Pal, Ruben Ferrer-Luna, Shakti H Ramkissoon, Frank Dubois, Charlotte Bellamy, Naomi Currimjee, Juliana Bonardi, Kenin Qian, Patricia Ho, Seth Malinowski, Leon Taquet, Robert E Jones, Aniket Shetty, Kin-Hoe Chow, Radwa Sharaf, Dean Pavlick, Lee A Albacker, Nadia Younan, Capucine Baldini, Maïté Verreault, Marine Giry, Erell Guillerm, Samy Ammari, Frédéric Beuvon, Karima Mokhtari, Agusti Alentorn, Caroline Dehais, Caroline Houillier, Florence Laigle-Donadey, Dimitri Psimaras, Eudocia Q Lee, Lakshmi Nayak, J Ricardo McFaline-Figueroa, Alexandre Carpentier, Philippe Cornu, Laurent Capelle, Bertrand Mathon, Jill S Barnholtz-Sloan, Arnab Chakravarti, Wenya Linda Bi, E Antonio Chiocca, Katie Pricola Fehnel, Sanda Alexandrescu, Susan N Chi, Daphne Haas-Kogan, Tracy T Batchelor, Garrett M Frampton, Brian M Alexander, Raymond Y Huang, Azra H Ligon, Florence Coulet, Jean-Yves Delattre, Khê Hoang-Xuan, David M Meredith, Sandro Santagata, Alex Duval, Marc Sanson, Andrew D Cherniak, Patrick Y Wen, David A Reardon, Aurélien Marabelle, Peter J Park, Ahmed Idbaih, Rameen Beroukhim, Pratiti Bandopadhayay, Franck Bielle, Keith L Ligon
Mechanisms and therapeutic implications of hypermutation in gliomas. Nature 580 (7804) (2020)
Pratiti Bandopadhayay, Frederica Piccioni, Ryan O'Rourke, Patricia Ho, Elizabeth M Gonzalez, Graham Buchan, Kenin Qian, Gabrielle Gionet, Emily Girard, Margo Coxon, Matthew G Rees, Lisa Brenan, Frank Dubois, Ofer Shapira, Noah F Greenwald, Melanie Pages, Amanda Balboni Iniguez, Brenton R Paolella, Alice Meng, Claire Sinai, Giovanni Roti, Neekesh V Dharia, Amanda Creech, Benjamin Tanenbaum, Prasidda Khadka, Adam Tracy, Hong L Tiv, Andrew L Hong, Shannon Coy, Rumana Rashid, Jia-Ren Lin, Glenn S Cowley, Fred C Lam, Amy Goodale, Yenarae Lee, Kathleen Schoolcraft, Francisca Vazquez, William C Hahn, Aviad Tsherniak, James E Bradner, Michael B Yaffe, Till Milde, Stefan M Pfister, Jun Qi, Monica Schenone, Steven A Carr, Keith L Ligon, Mark W Kieran, Sandro Santagata, James M Olson, Prafulla C Gokhale, Jacob D Jaffe, David E Root, Kimberly Stegmaier, Cory M Johannessen, Rameen Beroukhim
Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nature communications 10 (1) (2019)
Andrew L Hong, Yuen-Yi Tseng, Jeremiah A Wala, Won-Jun Kim, Bryan D Kynnap, Mihir B Doshi, Guillaume Kugener, Gabriel J Sandoval, Thomas P Howard, Ji Li, Xiaoping Yang, Michelle Tillgren, Mahmhoud Ghandi, Abeer Sayeed, Rebecca Deasy, Abigail Ward, Brian McSteen, Katherine M Labella, Paula Keskula, Adam Tracy, Cora Connor, Catherine M Clinton, Alanna J Church, Brian D Crompton, Katherine A Janeway, Barbara Van Hare, David Sandak, Ole Gjoerup, Pratiti Bandopadhayay, Paul A Clemons, Stuart L Schreiber, David E Root, Prafulla C Gokhale, Susan N Chi, Elizabeth A Mullen, Charles Wm Roberts, Cigall Kadoch, Rameen Beroukhim, Keith L Ligon, Jesse S Boehm, William C Hahn
Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition. eLife 8 (2019)
Zachary J Reitman, Brenton R Paolella, Guillaume Bergthold, Kristine Pelton, Sarah Becker, Robert Jones, Claire E Sinai, Hayley Malkin, Ying Huang, Leslie Grimmet, Zachary T Herbert, Yu Sun, Jessica L Weatherbee, John A Alberta, John F Daley, Orit Rozenblatt-Rosen, Alexandra L Condurat, Kenin Qian, Prasidda Khadka, Rosalind A Segal, Daphne Haas-Kogan, Mariella G Filbin, Mario L Suvà, Aviv Regev, Charles D Stiles, Mark W Kieran, Liliana Christova Goumnerova, Keith L Ligon, Alex K Shalek, Pratiti Bandopadhayay, Rameen Beroukhim
Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells. Nature communications 10 (1) (2019)
Uri Ben-David, Rameen Beroukhim, Todd R Golub
Genomic evolution of cancer models: perils and opportunities. Nature reviews. Cancer 19 (2) (2019)
Abhishek A Chakraborty, Tuomas Laukka, Matti Myllykoski, Alison E Ringel, Matthew A Booker, Michael Yevgeniy Tolstorukov, Yuzhong Jeff Meng, Samuel R Meier, Rebecca B Jennings, Amanda L Creech, Zachary T Herbert, Samuel K McBrayer, Benjamin A Olenchock, Jacob D Jaffe, Marcia C Haigis, Rameen Beroukhim, Sabina Signoretti, Peppi Karppinen, William G Kaelin
Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate. Science (New York, N.Y.) 363 (6432) (2019)
Jeremiah A Wala, Pratiti Bandopadhayay, Noah F Greenwald, Ryan O'Rourke, Ted Sharpe, Chip Stewart, Steven E Schumacher, Yilong Li, Joachim Weischenfeldt, Xiaotong Yao, Chad Nusbaum, Peter Campbell, Gad A Getz, Matthew L Meyerson, Cheng-Zhong Zhang, Marcin Imielinski, Rameen Beroukhim
SvABA: genome-wide detection of structural variants and indels by local assembly. Genome research 28 (4) (2018)
Mariella G Filbin, Michael Mints, Volker Hovestadt, McKenzie L Shaw, Leah E Escalante, Nathan D Mathewson, Cyril Neftel, Nelli Frank, Kristine Pelton, Christine M Hebert, Christine Haberler, Keren Yizhak, Johannes Gojo, Kristof Egervari, Christopher Mount, Peter van Galen, Dennis M Bonal, Quang-De Nguyen, Alexander Beck, Claire Sinai, Thomas Czech, Christian Dorfer, Liliana Goumnerova, Cinzia Lavarino, Angel Montero Carcaboso, Jaume Mora, Ravindra Mylvaganam, Christina C Luo, Andreas Peyrl, Mara Popović, Amedeo A Azizi, Tracy T Batchelor, Matthew P Frosch, Maria Martinez-Lage, Mark W Kieran, Pratiti Bandopadhayay, Rameen Beroukhim, Gerhard Fritsch, Gad A Getz, Orit Rozenblatt-Rosen, Kai W Wucherpfennig, David N Louis, Michelle Monje, Irene Slavc, Keith L Ligon, Todd R Golub, Aviv Regev, Bradley E Bernstein, Mario L Suvà
Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science (New York, N.Y.) 360 (6386) (2018)