Archive of

Publications

Our main scientific interests lie in modeling and understanding the dynamics of biological systems through the lens of genomics. Our work focuses on three distinct topics: Cancer, Infectious Diseases, and Electronic Health Records.

Archive of recent publications

This archive links to our published work.

2024 | 2023 |2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011

2006-2010 | 1999-2005

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2024

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2023

  • "Smoother: A Unified and Modular Framework for Incorporating Structural Dependency in Spatial Omics Data"

    AUTHORS: Jiayu Su, Jean-Baptiste Reynier, Xi Fu, Guojie Zhong, Jiahao Jiang, Rydberg Supo Escalante, Yiping Wang, Luis Aparicio, Benjamin Izar, David A Knowles, Raul Rabadan

    Genome Biology. 2023 December 18. doi: 10.1186/s13059-023-03138-x

  • "A pan-cancer analysis implicates human NKIRAS1 as a tumor-suppressor gene"

    AUTHORS: Thomas S. Postler, Anqi Wang, Francesco G. Brundu, Pingzhang Wang, Zikai Wu, Kelly E. Butler, Yenkel Grinberg-Bleyer, Suneeta Krishnareddy, Stephen M. Lagana, Anjali Saqi, Andrea Oeckinghaus, Raul Rabadan, and Sankar Ghosh

    Proceedings of the National Academy of Sciences. 2023 November 6. doi: 10.1073/pnas.2312595120

  • "GET: a foundation model of transcription across human cell types"

    AUTHORS: Xi Fu, Shentong Mo, Anqi Shao, Anouchka Laurent, Alejandro Buendia, Adolfo A. Ferrando, Alberto Ciccia, Yanyan Lan, Teresa Palomero, David M. Owens, Eric P. Xing, Raul Rabadan

    bioRxiv. 2023 September 24. doi: 10.1101/2023.09.24.559168

  • "ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion"

    AUTHORS: Demis Menolfi, Brian J. Lee, Hanwen Zhang, Wenxia Jiang, Nicole E. Bowen, Yunyue Wang, Junfei Zhao, Antony Holmes, Steven Gershik, Raul Rabadan, Baek Kim, Shan Zha

    Nature Communications. 2023 June 19. doi: 10.1038/s41467-023-39332-5

  • "A transposase-derived gene required for human brain development"

    AUTHORS: Jubierre Zapater L, Rodriguez Fos E, Planas-Felix M, Lewis S, Cameron D, Demarest P, Nabila A, Zhao J, Bergin P, Reed C, Yamada M, Socci N, Hayes M, Rabadan R, Torrents D, Kruer MC, Toth M, Kentsis A

    bioRxiv. 2023 April 28. doi:10.1101/2023.04.28.538770

  • "Inverse agonists of RAR/RXR signaling as lineage-specific anti-tumor agents against human Adenoid Cystic Carcinoma "

    AUTHORS: Sara Viragova, PhD, Luis Aparicio, PhD, Pierangela Palmerini, PhD, Junfei Zhao, PhD, Luis E Valencia Salazar, BA, Alexandra Schurer, MS, Anika Dhuri, Debashis Sahoo, PhD, Christopher A Moskaluk, MD, Raul Rabadan, PhD, Piero Dalerba, MD

    Journal of the National Cancer Institute. 2023 April 11. doi:10.1093/jnci/djad062

  • "Checkpoint kinase 1/2 inhibition potentiates anti-tumoral immune response and sensitizes gliomas to immune checkpoint blockade"

    AUTHORS: Crismita Dmello, Junfei Zhao, Li Chen, Andrew Gould, Brandyn Castro, Victor A. Arrieta, Daniel Y. Zhang, Kwang-Soo Kim, Deepak Kanojia, Peng Zhang, Jason Miska, Ragini Yeeravalli, Karl Habashy, Ruth Saganty, Seong Jae Kang, Jawad Fares, Connor Liu, Gavin Dunn, Elizabeth Bartom, Matthew J. Schipma, Patrick D. Hsu, Mahmoud S. Alghamri, Maciej S. Lesniak, Amy B. Heimberger, Raul Rabadan, Catalina Lee-Chang & Adam M. Sonabend

    Nature Communications. 2023 March 22. doi:10.1038/s41467-023-36878-2

  • "Benchmarking of microbiome detection tools on RNA-seq synthetic databases according to diverse conditions"

    AUTHORS: Francisco Jurado-Rueda, Lola Alonso-Guirado, Tomin E Perea-Chamblee, Oliver T Elliott, Ioan Filip, Raúl Rabadán, Núria Malats

    Bioinformatics Advances. 2023 February 22. doi:10.1093/bioadv/vbad014

  • "Genomic landscape of virus-associated cancers"

    AUTHORS: Karen Gomez, Gianluca Schiavoni, Yoonhee Nam, Jean-Baptiste Reynier, Cole Khamnei, Michael Aitken, Giuseppe Palmieri, Antonio Cossu, Arnold Levine, Carel van Noesel, Brunangelo Falini, Laura Pasqualucci, Enrico Tiacci, Raul Rabadan

    medRxiv. 2023 February 16. doi: 10.1101/2023.02.14.23285775

  • "Pervasiveness of HLA allele-specific expression loss across tumor types"

    AUTHORS: Ioan Filip, Anqi Wang, Oleksandr Kravets, Rose Orenbuch, Junfei Zhao, Tomin E. Perea-Chamblee, Gulam A. Manji, Evangelina López de Maturana, Núria Malats, Kenneth P. Olive, Raul Rabadan

    Genome Medicine. 2023 February 9. doi: 10.1186/s13073-023-01154-x

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2022

  • "Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization"

    AUTHORS: Jennifer Zagelbaum, Allana Schooley, Junfei Zhao, Benjamin R. Schrank, Elsa Callen, Shan Zha, Max E. Gottesman, André Nussenzweig, Raul Rabadan, Job Dekker, Jean Gautier

    Nature Structural & Molecular Biology. 2022 December 23. doi:10.1038/s41594-022-00893-6

  • "Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis"

    AUTHORS: Debra Van Egeren, Khushi Kohli, Jeremy L Warner, Philippe L Bedard, Gregory Riely, Eva Lepisto, Deborah Schrag, Michele LeNoue-Newton, Paul Catalano, Kenneth L Kehl, Franziska Michor, for the AACR Project GENIE Consortium represented by Shawn Sweeney

    AACR Project GENIE Consortium represented by Shawn Sweeney: Michael Fiandalo, Margaret Foti, Yekaterina Khotskaya, Jocelyn Lee, Nicole Peters, Shawn Sweeney, Jean Abraham, James D Brenton, Carlos Caldas, Gary Doherty, Birgit Nimmervoll, Karen Pinilla, Jose-Ezequiel Martin, Oscar M Rueda, Stephen-John Sammut, Dilrini Silva, Kajia Cao, Allison P Heath, Marilyn Li, Jena Lilly, Suzanne MacFarland, John M Maris, Jennifer L Mason, Allison M Morgan, Adam Resnick, Mark Welsh, Yuankun Zhu, Bruce Johnson, Yvonne Li, Lynette Sholl, Ron Beaudoin, Roshni Biswas, Ethan Cerami, Oya Cushing, Deepa Dand, Matthew Ducar, Alexander Gusev, William C Hahn, Kevin Haigis, Michael Hassett, Katherine A Janeway, Pasi Jänne, Arundhati Jawale, Jason Johnson, Kenneth L Kehl, Priti Kumari, Valerie Laucks, Eva Lepisto, Neal Lindeman, James Lindsay, Amanda Lueders, Laura Macconaill, Monica Manam, Tali Mazor, Diana Miller, Ashley Newcomb, John Orechia, Andrea Ovalle, Asha Postle, Daniel Quinn, Brendan Reardon, Barrett Rollins, Priyanka Shivdasani, Angela Tramontano, Eliezer Van Allen, Stephen C Van Nostrand, Jonathan Bell, Michael B Datto, Michelle Green, Chris Hubbard, Shannon J McCall, Niharika B Mettu, John H Strickler, Fabrice Andre, Benjamin Besse, Marc Deloger, Semih Dogan, Antoine Italiano, Yohann Loriot, Lacroix Ludovic, Stefan Michels, Jean Scoazec, Alicia Tran-Dien, Gilles Vassal, Christopher E Freeman, Susan J Hsiao, Matthew Ingham, Jiuhong Pang, Raul Rabadan, Lira Camille Roman, Richard Carvajal, Raymond DuBois, Maria E Arcila, Ryma Benayed, Michael F Berger, Marufur Bhuiya, A Rose Brannon, Samantha Brown, Debyani Chakravarty, Cynthia Chu, Ino de Bruijn, Jesse Galle, Jianjiong Gao, Stu Gardos, Benjamin Gross, Ritika Kundra, Andrew L Kung, Marc Ladanyi, Jessica A Lavery, Xiang Li, Aaron Lisman, Brooke Mastrogiacomo, Caroline McCarthy, Chelsea Nichols, Angelica Ochoa, Katherine S Panageas, John Philip, Shirin Pillai, Gregory J Riely, Hira Rizvi, Julia Rudolph, Charles L Sawyers, Deborah Schrag, Nikolaus Schultz, Julian Schwartz, Robert Sheridan, David Solit, Avery Wang, Manda Wilson, Ahmet Zehir, Hongxin Zhang, Gaofei Zhao, Lailah Ahmed, Philippe L Bedard, Jeffrey P Bruce, Helen Chow, Sophie Cooke, Samantha Del Rossi, Sam Felicen, Sevan Hakgor, Prasanna Jagannathan, Suzanne Kamel-Reid, Geeta Krishna, Natasha Leighl, Zhibin Lu, Alisha Nguyen, Leslie Oldfield, Demi Plagianakos, Trevor J Pugh, Alisha Rizvi, Peter Sabatini, Elizabeth Shah, Nitthusha Singaravelan, Lillian Siu, Gunjan Srivastava, Natalie Stickle, Tracy Stockley, Marian Tang, Carlos Virtaenen, Stuart Watt, Celeste Yu, Brady Bernard, Carlo Bifulco, Julie L Cramer, Soohee Lee, Brian Piening, Sheila Reynolds, Joseph Slagel, Paul Tittel, Walter Urba, Jake VanCampen, Roshanthi Weerasinghe, Alyssa Acebedo, Justin Guinney, Xindi Guo, Haley Hunter-Zinck, Thomas Yu, Kristen Dang, Valsamo Anagnostou, Alexander Baras, Julie Brahmer, Christopher Gocke, Robert B Scharpf, Jessica Tao, Victor E Velculescu, Shlece Alexander, Neil Bailey, Philip Gold, Mariska Bierkens, Jan de Graaf, Jan Hudeček, Gerrit A Meijer, Kim Monkhorst, Kris G Samsom, Joyce Sanders, Gabe Sonke, Jelle Ten Hoeve, Tony van de Velde, José van den Berg, Emile Voest, George Steinhardt, Sabah Kadri, Wanjari Pankhuri, Peng Wang, Jeremy Segal, Christine Moung, Carlos Espinosa-Mendez, Henry J Martell, Courtney Onodera, Ana Quintanar Alfaro, E Alejandro Sweet-Cordero, Eric Talevich, Michelle Turski, Laura Van't Veer, Amanda Wren, Susana Aguilar, Rodrigo Dienstmann, Francesco Mancuso, Paolo Nuciforo, Josep Tabernero, Cristina Viaplana, Ana Vivancos, Ingrid Anderson, Sandip Chaugai, Joseph Coco, Daniel Fabbri, Doug Johnson, Leigh Jones, Xuanyi Li, Christine Lovly, Sanjay Mishra, Kathleen Mittendorf, Li Wen, Yuanchu James Yang, Chen Ye, Marilyn Holt, Michele L LeNoue-Newton, Christine M Micheel, Ben H Park, Samuel M Rubinstein, Thomas Stricker, Lucy Wang, Jeremy Warner, Meijian Guan, Guangxu Jin, Liang Liu, Umit Topaloglu, Cetin Urtis, Wei Zhang, Michael D'Eletto, Stephen Hutchison, Janina Longtine, Zenta Walther

    Nature Scientific Reports. 2022 November 9. doi: 10.1038/s41598-022-21448-1

  • "Loss of PBRM1 Alters Promoter Histone Modifications and Activates ALDH1A1 to Drive Renal Cell Carcinoma"

    AUTHORS: David A. Schoenfeld; Royce Zhou; Sakellarios Zairis; William Su; Nicole Steinbach; Deepti Mathur; Ankita Bansal; Alexis L. Zachem; Bertilia Tavarez; Dan Hasson; Emily Bernstein; Raul Rabadan; Ramon Parsons 

    Molecular Cancer Research. 2022 August 5. https://doi.org/10.1158/1541-7786.MCR-21-1039

  • "Glioma progression is shaped by genetic evolution and microenvironment interactions"

    AUTHORS: Frederick S Varn, Kevin C Johnson, Jan Martinek, Jason T Huse, MacLean P Nasrallah, Pieter Wesseling, Lee A D Cooper, Tathiane M Malta, Taylor E Wade, Thais S Sabedot , Daniel Brat, Peter V Gould, Adelheid Wöehrer, Kenneth Aldape, Azzam Ismail, Santhosh K Sivajothi , Floris P Barthel, Hoon Kim, Emre Kocakavuk, Nazia Ahmed, Kieron White, Indrani Datta, Hyo-Eun Moon, Steven Pollock, Christine Goldfarb, Ga-Hyun Lee, Luciano Garofano, Kevin J Anderson, Djamel Nehar-Belaid, Jill S Barnholtz-Sloan, Spyridon Bakas, Annette T Byrne, Fulvio D'Angelo, Hui K Gan, Mustafa Khasraw, Simona Migliozzi, D Ryan Ormond, Sun Ha Paek, Erwin G Van Meir, Annemiek M E Walenkamp, Colin Watts, Tobias Weiss, Michael Weller, Karolina Palucka, Lucy F Stead, Laila M Poisson, Houtan Noushmehr, Antonio Iavarone, Roel G W Verhaak, GLASS Consortium

    Glass Consortium: Frederick S Varn, Kevin C Johnson, Jan Martinek, Jason T Huse, MacLean P Nasrallah, Pieter Wesseling, Lee A D Cooper, Tathiane M Malta, Taylor E Wade, Thais S Sabedot, Daniel Brat, Peter V Gould, Adelheid Wöehrer, Kenneth Aldape, Azzam Ismail, Santhosh K Sivajothi, Floris P Barthel, Hoon Kim, Emre Kocakavuk, Nazia Ahmed, Kieron White, Indrani Datta, Hyo-Eun Moon, Steven Pollock, Christine Goldfarb, Ga-Hyun Lee, Luciano Garofano, Kevin J Anderson, Djamel Nehar-Belaid, Jill S Barnholtz-Sloan, Spyridon Bakas, Annette T Byrne, Fulvio D'Angelo, Hui K Gan, Mustafa Khasraw, Simona Migliozzi, D Ryan Ormond, Sun Ha Paek, Erwin G Van Meir, Annemiek M E Walenkamp, Colin Watts, Tobias Weiss, Michael Weller, Kristin D Alfaro, Samirkumar B Amin, David M Ashley, Christoph Bock, Andrew Brodbelt, Ketan R Bulsara, Ana Valeria Castro, Jennifer M Connelly, Joseph F Costello, John F de Groot, Gaetano Finocchiaro, Pim J French, Anna Golebiewska, Ann C Hau, Chibo Hong, Craig Horbinski, Kasthuri S Kannan, Mathilde Cm Kouwenhoven, Anna Lasorella, Peter S LaViolette, Keith L Ligon, Allison K Lowman, Shwetal Mehta, Hrvoje Miletic, Annette M Molinaro, Ho Keung Ng, Simone P Niclou, Johanna M Niers, Joanna J Phillips, Raul Rabadan, Ganesh Rao, Guido Reifenberger, Nader Sanai, Susan C Short, Peter Sillevis Smitt, Andrew E Sloan, Marion Smits, James M Snyder, Hiromichi Suzuki, Ghazaleh Tabatabai, Georgette Tanner, William H Tomaszewski, Michael Wells, Bart A Westerman, Helen Wheeler, Jichun Xie, W K Alfred Yung, Gelareh Zadeh, Junfei Zhao, Karolina Palucka, Lucy F Stead, Laila M Poisson, Houtan Noushmehr, Antonio Iavarone, Roel Gw Verhaak

    Cell. 2022 June 9. doi: 10.1016/j.cell.2022.04.038

  • "Neoadjuvant chemoradiation alters the immune microenvironment in pancreatic ductal adenocarcinoma"

    AUTHORS: Robyn D. Gartrell, Thomas Enzler, Pan S. Kim, Benjamin T. Fullerton, Ladan Fazlollahi, Andrew X. Chen, Hanna E. Minns, Subha Perni, Stuart P. Weisberg, Emanuelle M. Rizk, Samuel Wang, Eun Jeong Oh, Xinzheng V. Guo, Codruta Chiuzan, Gulam A. Manji, Susan E. Bates, John Chabot, Beth Schrope, Michael Kluger, Jean Emond, Raul Rabadán, Donna Farber, Helen E. Remotti, David P. Horowitz, Yvonne M. Saenger

    OncoImmunology. 2022 May 5. doi: 10.1080/2162402X.2022.2066767

  • "Oncogenic Vav1-Myo1f induces therapeutically targetable macrophage-rich tumor microenvironment in peripheral T cell lymphoma"

    AUTHORS: Jose R Cortes, Ioan Filip, Robert Albero, Juan A Patiño-Galindo, S Aidan Quinn, Wen-Hsuan W Lin, Anouchka P Laurent, Bobby B Shih, Jessie A Brown, Anisha J Cooke, Adam Mackey, Jonah Einson, Sakellarios Zairis, Alfredo Rivas-Delgado, Maria Antonella Laginestra, Stefano Pileri, Elias Campo, Govind Bhagat, Adolfo A Ferrando, Raul Rabadan, Teresa Palomero

    Cell Rep. 2022 Apr 19. doi: 10.1016/j.celrep.2022.110695.

  • "Dose–response modeling in high-throughput cancer drug screenings: an end-to-end approach"

    AUTHORS: Wesley Tansey, Kathy Li, Haoran Zhang, Scott W Linderman, Raul Rabadan, David M Blei, Chris H Wiggins

    Biostatisics. 2022 April 13. doi: 10.1093/biostatistics/kxaa047

  • "Subversion of serotonin-receptor signaling in osteoblasts by kynurenine drives Acute Myeloid Leukemia"

    AUTHORS: Marta Galan-Diez, Florence Borot, Abdullah Mahmood Ali, Junfei Zhao, Eva Gil-Iturbe, Xiaochuan Shan, Na Luo, Yongfeng Liu, Xi-Ping Huang, Brygida Bisikirska, Rossella Labella, Irwin Kurland, Bryan L Roth, Matthias Quick, Siddhartha Mukherjee, Raul Rabadan, Martin Carroll, Azra Raza and Stavroula Kousteni.

    Cancer Discovery. 2022 April 01; 12(4): 1106–1127. doi:10.1158/2159-8290.

  • "Topological data analysis identifies emerging adaptive mutations in SARS-CoV-2"

    AUTHORS: Michael Bleher, Lukas Hahn, Juan Ángel Patiño-Galindo, Mathieu Carrière, Ulrich Bauer, Raúl Rabadán, Andreas Ott

    medRxiv. 2022 February 14. doi: 10.1101/2021.06.10.21258550

  • "Implications of Selection Bias Due to Delayed Study Entry in Clinical Genomic Studies"

    AUTHORS: Samantha Brown, Jessica A Lavery, Ronglai Shen, Axel S Martin, Kenneth L Kehl, Shawn M Sweeney, Eva M Lepisto, Hira Rizvi, Caroline G McCarthy, Nikolaus Schultz, Jeremy L Warner, Ben Ho Park, Philippe L Bedard 5, Gregory J Riely, Deborah Schrag, Katherine S Panageas; AACR Project GENIE Consortium

    AACR Project GENIE Consortium: Shawn Sweeney, Margaret Foti, Yekaterina Khotskaya, Michael Fiandalo, Benjamin Gross, Nikolaus Schultz, Brooke Mastrogiacomo, Mahdi Sarmardy, Marilyn Li, Adam Resnick, Angela Waanders, Jena Lilly, Richard Carvajal, Raul Rabadan, Matthew Ingham, Susan Hsaio, Jean Abraham, James Brenton, Oscar Rueda, Carlos Caldas, Mikel Valgañón, Dilrini Silva, Chris Boursnell, Raquel Garcia, Ezequiel Rodriguez, Birgit Nimmervoll, Ethan Cerami, Matthew Ducar, Priti Kumari, Neal Lindeman, Laura MacConnaill, John Orechia, Deborah Schrag, Priyanka Shivdasani, Eliezer Van Allen, Jason Johnson, Pasi Jänne, Eva Lepisto, Michael Hassett, Sindy Pimentel, Parin Sripakdeevong, Katherine Janeway, Jason M Johnson, Matthew Meyerson, Daniel Quinn, Oya Cushing, Kevin Haigis, Diana Miller, Kenneth Kehl, Alexander Gustav, Angela Tramontano, Simon Arango Baquero, Jonathan Bell, Michelle Green, Shannon McCall, Michael Datto, Fabien Calvo, Fabrice Andre, Meurice Guillaume, Semih Dogan, Lacroix Ludovic, Jean Scoazec, Monica Ardenos, Gilles Vassal, Stefan Michels, Victor Velculescu, Alexander Baras, Christopher Gocke, Julie Brahmer, Charles Sawyers, David Solit, Stu Gardos, Mike Berger, Marc Ladanyi, Gregory Riely, Joseph Sirintrapun, Katherine Panageas, Ari Caroline, Stacy Thomas, Andrew Zarski, Ahmet Zehir, Alexia Iasonosa, John Philip, Samantha Brown, Andrew Kung, Ritika Kundra, Julia Rudolph, Jessica Lavery, Hira Rivzi, Julian Schwartz, Caroline McCarthy, Maufur Bhuiya, Axel Martin, Cynthia Chu, Raymond DuBois, Tony van de Velde, Geritt Meijer, Hugo Horlings, Harm van Tinteren, Martijn Lolkema, Les Nijman, Mariska Bierkens, Jelle Hoeve, Emilie Voest, Annemieke Hiemstra, Gabe Sonke, Jacques Craenmehr, Jan Hudecek, Kim Monkhorst, Walter Urba, Brady Bernard, Brian Piening, Carlo Bifulco, Paul Tittel, Julie Cramer, Justin Guinney, Thomas Yu, Xindi Guo, Alyssa Acebedo, Philip Gold, Neil Bailey, Sabah Kadri, Jeremy Segal, Wanjari Pankhuri, Peng Wang, Steinhardt George, Moung Christine, Laura Van't Veer, Eric Talevich, Amanda Wren, Alejandro Sweet-Cordero, Michelle Turski, Philippe Bedard, Suzanne KamelReid, Zhibin Lu, Trevor Pugh, Lillian Siu, Stuart Watt, Natasha Leighl, Celeste Yu, Lailah Ahmed, Geeta Krishna, Carlos Virtaenen, Helen Chow, Demi Plagianakos, Samantha Del Rossi, Nitthusha Singaravelan, Sevan Hakgor, Nazish Qazi, Alisha Nguyen, Natalie Stickle, Thomas Stricker, Christine Micheel, Ingrid Anderson, Leigh Jones, Lucy Wang, Christine Lovly, Michele LeNoue Newton, Ben Park, Jeremy Warner, Daniel Fabbri, Joseph Coco, Chen Ye, Sandip Chaugai, Sanjay Mishra, Yuanchu James Yang, Li Wen, Rodrigo Dienstmann, Susana Aguilar Izquierdo, Cristina Viaplana Donato, Francesco Mancuso, Umit Topaloglu, Liang Liu, Meijian Guan, Wei Zhang, Guangxu Jin, James Knight, Michael D'Eletto, E Zeynep Ormay, Shrikant Mane, Kaya Bilguvar, Walther Zenta, Daniel Dykas

    JAMA Oncology. 2022 February 8. doi: 10.1001/jamaoncol.2021.5153.

  • "Phenotypic dissection of epithelial lineages and therapeutic manipulation of differentiation programs in human Adenoid Cystic Carcinomas (ACCs)"

    AUTHORS: Sara Viragova, Luis Aparicio, Junfei Zhao, Luis E Valencia Salazar, Alexandra Schurer, Anika Dhuri, Debashis Sahoo, Christopher A Moskaluk, Raul Rabadan, Piero Dalerba

    bioRxiv. 2022 January 21. doi: 10.1101/2022.01.19.476843

  • "SF3B1 mutant-induced missplicing of MAP3K7 causes anemia in myelodysplastic syndromes"

    AUTHORS: Yen K Lieu, Zhaoqi Liu, Abdullah M Ali, Xin Wei, Alex Penson, Jian Zhang, Xiuli An, Raul Rabadan, Azra Raza, James L Manley, Siddhartha Mukherjee

    Proc Natl Acad Sci USA. 2022 January 4. doi: 0.1073/pnas.2111703119

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2021

  • "A Targetable Bone Marrow-Niche Axis for the Treatment of Acute Myeloid Leukemia"

    AUTHORS: Marta Galan-Diez, Florence Borot, Abdullah M Ali, Junfei Zhao, Eva Gil-Iturbe, Xiaochuan Shan, Xi-Ping Huang, Irwin Kurland, Bryan L Roth, Matthias Quick, Siddhartha Mukherjee, Raul Rabadan, Martin P Carroll, Azra Raza, Stavroula Kousteni

    Blood. 2021 November 23. doi: 10.1182/blood-2021-147741

  • "HHV-6 in the Lymphoma Microenvironment: Both Chicken and Egg?"

    AUTHORS: Genevieve M Crane, Dmitry Tychinin, Anton Karelin, Aleksandr Cherdintsev, Olga Kudryashova, Evgeniy Egorov, Sandrine Degryse, Nikita Kotlov, Alexander Bagaev, Joseph Casano, Jonathan Reichel, Lisa Giulino Roth, Mikhail Roshal, Sakellarios Zairis, Raul Rabadan, Olivier Elemento, Giorgio Inghirami, Ethel Cesarman

    Blood. 2021 November 23. doi: 10.1182/blood-2021-146336

  • "A Phase I Study of the Combination of Pexidartinib and Sirolimus to Target Tumor-Associated Macrophages in Unresectable Sarcoma and Malignant Peripheral Nerve Sheath Tumors."

    AUTHORS: Gulam A. Manji, Brian A. Van Tine, Shing M. Lee, Alexander G. Raufi, Ilenia Pellicciotta, Angela C. Hirbe, Jaya Pradhan, Andrew Chen, Raul Rabadan, Gary K. Schwartz.

    American Association for Cancer Research. 2021 Sept 7. doi: 10.1158/1078-0432.CCR-21-1779

  • "A persistent look at how tumours evade therapy."

    AUTHORS: Karen Gomez, Raul Rabadan.

    Nature. 2021 Aug 11. doi: 10.1038/d41586-021-02117-1

  • "Transcriptional control of CBX5 by the RNA-binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia"

    AUTHORS: Camila Prieto, Diu T. T. Nguyen, Zhaoqi Liu, Justin Wheat, Alexendar Perez, Saroj Gourkanti, Timothy Chou, Ersilia Barin, Anthony Velleca, Thomas Rohwetter, Arthur Chow, James Taggart, Angela M. Savino, Katerina Hoskova, Meera Dhodapkar, Alexandra Schurer, Trevor S. Barlowe, Ly P. Vu, Christina Leslie, Ulrich Steidl, Raul Rabadan, Michael G. Kharas.

    Nature Cancer. 2021 July 5. doi: 10.1038/s43018-021-00220-w

  • “The Holdout Randomization Test: Principled and Easy Black Box Feature Selection.”

    AUTHORS: W Tansey, V Veitch, H Zhang, R Rabadan, DM Blei.

    Journal of Computational and Graphical Statistics. 2021 June 17. doi: 10.1080/10618600.2021.1923520

  • "iPLA2β-mediated lipid detoxification controls p53-driven ferroptosis independent of GPX4"

    AUTHORS: Delin Chen, Bo Chu, Xin Yang, Zhaoqi Liu, Ying Jin, Ning Kon, Raul Rabadan, Xuejun Jiang, Brent R. Stockwell, Wei Gu.

    Nature Comm. 2021 June 15. doi: 10.1038/s41467-021-23902-6

  • "Genetic mechanisms of HLA-I loss and immune escape in diffuse large B cell lymphoma"

    AUTHORS: Marco Fangazio, Erik Ladewig, Karen Gomez, Laura Garcia-Ibanez, Rahul Kumar, Julie Teruya-Feldstein, Davide Rossi, Ioan Filip, Qiang Pan-Hammarström, Giorgio Inghirami, Renzo Boldorini, German Ott, Annette M. Staiger, Björn Chapuy, Gianluca Gaidano, Govind Bhagat, Katia Basso, Raul Rabadan, Laura Pasqualucci, Riccardo Dalla-Favera.

    Proc Natl Acad Sci U S A. 2021 June 1. doi: 10.1073/pnas.2104504118

  • “Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker”

    AUTHORS: Andrew X. Chen, Robyn D. Gartrell, Junfei Zhao, Pavan S. Upadhyayula, Wenting Zhao, Jinzhou Yuan, Hanna E. Minns, Athanassios Dovas, Jeffrey N. Bruce, Anna Lasorella, Antonio Iavarone, Peter Canoll, Peter A. Sims, Raul Rabadan.

    Genome Med. 2021 May 7. doi: 10.1186/s13073-021-00906-x

  • “Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations”

    AUTHORS: Silvia Affo, Ajay Nair, Francesco Brundu, Aashreya Ravichandra, Sonakshi Bhattacharjee, Michitaka Matsuda, LiKang Chin, Aveline Filliol, Wen Wen, Xinhua Song, Aubrianna Decker, Jeremy Worley, Jorge Matias Caviglia, Lexing Yu, Deqi Yin, Yoshinobu Saito, Thomas Savage, Rebecca G. Wells, Matthias Mack, Lars Zender, Nicholas Arpaia, Helen E. Remotti, Raul Rabadan, Peter Sims, Anne-Laure Leblond, Achim Weber, Marc-Oliver Riener, Brent R. Stockwell, Jellert Gaublomme, Josep M. Llovet, Raghu Kalluri, George K. Michalopoulos, Ekihiro Seki, Daniela Sia, Xin Chen, Andrea Califano, Robert F. Schwabe.

    Cancer Cell. 2021 April 29. doi: 10.4049/jimmunol.2000051

  • “Pregnancy Specific Glycoproteins: A Possible Mediator of Immune Tolerance of Cancers”

    AUTHORS: Junfei Zhao, Raul Rabadan, Arnold J. Levine.

    Journal of Cellular Immunology. 2021 April 14.

  • "PDK1 is Required for Maintenance of CD4+ Foxp3+ Regulatory T Cell Function"

    AUTHORS: Hyunju Oh, Jingyao Zhao, Yenkel Grinberg-Bleyer, Thomas S. Postler, Pingzhang Wang, Sung-Gyoo Park, Raul Rabadan, Matthew S. Hayden, Sankar Ghosh.

    J Immunol. 2021 Mar 31. doi: 10.4049/jimmunol.2000051

  • “Functional Interrogation Of DNA Damage Response Variants With Base Editing Screens”

    AUTHORS: Raquel Cuella-Martin, Samuel B.Hayward, Xiao Fan, Xiao Chen, Jen-Wei Huang, Angelo Taglialatela, Giuseppe Leuzzi, Junfei Zhao, Raul Rabadan, Chao Lu, Yufeng Shen, Alberto Ciccia.

    Cell. 2021 Feb 18. doi: 10.1016/j.cell.2021.01.041

  • “Global Patterns Of Recombination Across Human Viruses”

    AUTHORS: Juan Ángel Patiño-Galindo, Ioan Filip, Raul Rabadan.

    Molecular Biology and Evolution. 2021 Feb 15. doi: 10.1093/molbev/msab046

  • “Comprehensive Characterization Of Protein-Protein Interactions Perturbed By Disease Mutations”

    AUTHORS: Feixiong Cheng, Junfei Zhao, Yang Wang, Weiqiang Lu, Zehui Liu, Yadi Zhou, William R. Martin, Ruisheng Wang, Jin Huang, Tong Hao, Hong Yue, Jing Ma, Yuan Hou, Jessica A. Castrillon, Jiansong Fang, Justin D. Lathia, Ruth A. Keri, Felice C. Lightstone, Elliott Marshall Antman, Raul Rabadan, David E. Hill, Charis Eng, Marc Vidal, Joseph Loscalzo.

    Nature Genetics. 2021 Feb 08. doi: 10.1038/s41588-020-00774-y

  • “Computing The Role Of Alternative Splicing In Cancer”

    AUTHORS: Zhaoqi Liu, Raul Rabadan.

    Trends In Cancer. 2021 Jan 23. doi: 10.1016/j.trecan.2020.12.015

  • “FYN-TRAF3IP2 Induces NF-κB Signaling-Driven Peripheral T-cell Lymphoma”

    AUTHORS: Christine S. Moon, Clara Reglero, Jose R. Cortes, S. Aidan Quinn, Silvia Alvarez, Junfei Zhao, Wen-Hsuan W. Lin, Anisha J. Cooke, Francesco Abate, Craig R. Soderquist, Claudia Fiñana, Giorgio Inghirami, Elias Campo, Govind Bhagat, Raul Rabadan, Teresa Palomero, Adolfo A. Ferrando.

    Nature Cancer. 2021 Jan 13. doi: 10.1038/s43018-020-00161-w

  • “The UVSSA Complex Alleviates MYC-driven Transcription Stress”

    AUTHORS: Mai Sato, Andrew Walter Liebau, Zhaoqi Liu, Lizhi Liu, Raul Rabadan, Jean Gautier.

    Journal of Cell Biology. 2021 Jan 06. doi: 10.1083/jcb.201807163

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2020

  • “Double Empirical Bayes Testing”

    AUTHORS: Wesley Tansey, Yixin Wang, Raul Rabadan, David Blei.

    International Statistical Review. 2020 Nov 25. doi: 10.1111/insr.12430

  • “High Tumor Mutational Burden and T-cell Activation are Associated with Long-Term Response to Anti-PD1 Therapy in Lynch Syndrome Recurrent Glioblastoma Patient”

    AUTHORS: Elena Anghileri, Natalia Di Ianni, Rosina Paterra, Tiziana Langella, Junfei Zhao, Marica Eoli, Monica Patane, Bianca Pollo, Valeria Cuccarini, Antonio Iavarone, Raul Rabadan, Gaetano Finocchiaro, Serena Pellegatta.

    Cancer Immunol Immunother. 2020 Nov 03. doi: 10.1007/s00262-020-02769-4

  • “Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia”

    AUTHORS: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown, Juan Angel Patiño-Galindo, Timothy Chu, Aidan Quinn, Thomas Gunning, Laura Belver, Alberto Ambesi-Impiombato, Valeria Tosello, Zhengqiang Wang, Maria Luisa Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Milagros Balbin, Concepcion Nicolas, Julie M. Gastier-Foster, Meenakshi Devidas, Mignon L. Loh, Elisabeth Paietta, Martin S. Tallman, Jacob M. Rowe, Mark Litzow, Mark D. Minden, Jules Meijerink, Raul Rabadan+, Adolfo Ferrando+.

    *These authors have contributed equally to this work. +Corresponding authors.

    Nature Cancer. 2020 October 19. doi: doi.org/10.1038/s43018-020-00124-1

  • “Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state”

    AUTHORS: Daniela Cerezo-Wallis, Marta Contreras-Alcalde, Kevin Troulé, Xavier Catena, Cynthia Mucientes, Tonantzin G. Calvo, Estela Cañón, Cristina Tejedo, Paula C. Pennacchi, Sabrina Hogan, Peter Kölblinger, Héctor Tejero, Andrew X. Chen, Nuria Ibarz, Osvaldo Graña-Castro, Lola Martinez, Javier Muñoz, Pablo Ortiz-Romero, José L. Rodriguez-Peralto, Gonzalo Gómez-López, Fátima Al-Shahrour, Raúl Rabadán, Mitchell P. Levesque, David Olmeda, María S. Soengas.

    Nature Medicine. 2020 Oct 19. doi: 10.1038/s41591-020-1073-3.

  • “A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance”

    AUTHORS: Juan M. Arriaga, Sukanya Panja, Mohammed Alshalalfa, Junfei Zhao, Min Zou, Arianna Giacobbe, Chioma J. Madubata, Jaime Yeji Kim, Antonio Rodriguez, Ilsa Coleman, Renu K. Virk, Hanina Hibshoosh, Onur Ertunc, Büşra Ozbek, Julia Fountain, R. Jeffrey Karnes, Jun Luo, Emmanuel S. Antonarakis, Peter S. Nelson, Felix Y. Feng, Mark A. Rubin, Angelo M. De Marzo, Raul Rabadan, Peter A. Sims, Antonina Mitrofanova, Cory Abate-Shen.

    Nature Cancer. 2020 Oct 19. doi: 10.1038/s43018-020-00125-0.

  • “ A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors”

    AUTHORS: Laura Crowley, Francesco Cambuli, Luis Aparicio, Maho Shibata, Brian D Robinson, Shouhong Xuan, Weiping Li, Hanina Hibshoosh, Massimo Loda, Raul Rabadan+, Michael M Shen+.

    eLife 2020;9:e59465 doi: 10.7554/eLife.59465.

    *These authors have contributed equally to this work. +Corresponding authors.

  • “Mutant SF3B1 promotes AKT and NF-kB driven mammary tumorigenesis”

    AUTHORS: Bo Liu, Zhaoqi Liu, Sisi Chen, Michelle Ki, Caroline Erickson, Jorge S. Reis-Filho, Benjamin H. Durham, Qing Chang, Elisa de Stanchina, Yiwei Sun, Raul Rabadan, Omar Abdel-Wahab, Sarat Chandarlapaty.

    J Clin Invest. 2020 Oct 8. doi: 10.1172/JCI138315.

  • “CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining”

    AUTHORS: Xiaobin S. Wang, Junfei Zhao, Foon Wu-Baer, Zhengping Shao, Brian J. Lee, Olivia M. Cupo, Raul Rabadan, Jean Gautier, Richard Baer, Shan Zha.

    Proc Natl Acad Sci U S A. 2020 Sept 28. doi: 10.1073/pnas.2010972117.

  • “A Novel JAK1 Mutant Breast Implant-Associated Anaplastic Large Cell Lymphoma Patient-Derived Xenograft Fostering Pre-Clinical Discoveries”

    AUTHORS: Danilo Fiore, Luca Vincenzo Cappelli, Paul Zumbo, Jude M. Phillips, Zhaoqi Liu, Shuhua Cheng, Liron Yoffe, Paola Ghione, Federica Di Maggio, Ahmet Dogan, Inna Khodos, Elisa de Stanchina, Joseph Casano, Clarisse Kayembe, Wayne Tam, Doron Betel, Robin Foa’, Leandro Cerchietti, Raul Rabadan, Steven Horwitz, David M. Weinstock, Giorgio Inghirami.

    Cancers. 2020; 12(6):1603. doi:10.3390/cancers12061603

  • “A Random Matrix Theory Approach to Denoise Single-Cell Data”

    AUTHORS: Luis Aparicio, Mykola Bordyuh, Andrew Blumberg, Raul Rabadan.

    Patterns. 2020 June 12. doi: 10.1016/j.patter.2020.100035

  • “Genomic Characterization of HIV-Associated Plasmablastic Lymphoma Identifies Pervasive Mutations in the JAK–STAT Pathway.”

    AUTHORS: Zhaoqi Liu, Ioan Filip, Karen Gomez, Dewaldt Engelbrecht, Shabnum Meer, Pooja N. Lalloo, Pareen Patel, Yvonne Perner, Junfei Zhao, Jiguang Wang, Laura Pasqualucci, Raul Rabadan and Pascale Willem.

    Blood Cancer Discovery. 2020 June 10. doi:10.1158/2643-3230.BCD-20-0051

  • “Understanding Coronavirus (Understanding Life)”

    AUTHOR: Raul Rabadan.

    Cambridge University Press 2020 ISBN-13: 978-1108826716.

  • “Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulation.”

    AUTHORS: Liu Z, Zhang J, Sun Y, Perea-Chamblee TE, Manley JL, Rabadan R.

    Proc Natl Acad Sci U S A. 2020 Apr 24. pii: 201922622. doi: 10.1073/pnas.1922622117.

  • “Mutations in the RNA splicing factor SF3B1 promote tumorigenesis through MYC stabilization.”

    AUTHORS: Liu Z, Yoshimi A, Wang J, Cho H, Chun-Wei Lee S, Ki M, Bitner L, Chu T, Shah H, Liu B, Mato AR, Ruvolo P, Fabbri G, Pasqualucci L, Abdel-Wahab O, Rabadan R.

    Cancer Discov. 2020 Mar 18. pii: CD-19-1330. doi: 10.1158/2159-8290.CD-19-1330.

  • “MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas.”

    AUTHORS: Barbara Oldrini, Nuria Vaquero-Siguero, Quanhua Mu, Paula Kroon, Ying Zhang, Marcos Galán-Ganga, Zhaoshi Bao, Zheng Wang, Hanjie Liu, Jason K Sa, Junfei Zhao, Hoon Kim, Sandra Rodriguez-Perales, Do-Hyun Nam, Roel GW Verhaak, Raul Rabadan, Tao Jiang, Jiguang Wang, Massimo Squatrito.

    Nature Communcations. 2020 August 04. doi: doi.org/10.1038/s41467-020-17717-0

  • “HLA Typing from RNA Sequencing and Applications to Cancer.”

    AUTHORS: Rose Orenbuch, Ioan Filip, Raul Rabadan+.

    Bioinformatics for Cancer Immunotherapy. 2020 March 03. pp. 71-92

    *These authors have contributed equally to this work. +Corresponding authors.

  • “Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma.”

    AUTHORS: Gartrell-Corrado RD, Chen AX, Rizk EM, Marks DK, Bogardus MH, Hart TD, Silverman AM, Bayan CY, Finkel GG, Barker LW, Komatsubara KM, Carvajal RD, Horst BA, Chang R, Monod A, Rabadan R, Saenger YM.

    Cancer Res. 2020 Mar 1;80(5):1078-1087. doi: 10.1158/0008-5472.CAN-19-2039.

  • “MREC: a fast and versatile framework for aligning and matching point clouds with applications to single cell molecular data.”

    AUTHORS: Andrew J. Blumberg, Mathieu Carriere, Michael A. Mandell, Raul Rabadan, Soledad Villar.

    arXiv preprint. 2020 Feb 20. arXiv:2001.01666

  • “Abstract P3-03-01: Double PIK3CA mutations in cis drive oncogene addiction and enhance sensitivity to PI3K alpha inhibitors in breast cancer.”

    AUTHORS: Neil Vasan, Pedram Razavi, Jared L Johnson, Hong Shao, Timothy Wilson, Frauke Schimmoller, Hardik Shah, Alesia Antoine, Erik Ladewig, Alexander Gorelick, Ting-Yu Lin, Eneda Toska, Guotai Xu, Abiha Kazmi, Matthew T Chang, Barry S. Taylor, Maura N. Dickler, Komal Jhaveri, Sarat Chandarlapaty, Raul Rabadan, Ed Reznik, Melissa L Smith, Robert Sebra, Lori Friedman, Lewis C Cantley, Maurizio Scaltriti and José Baselga.

    Cancer Research. 2020 Feb 15. P3-03-01-P3-03-01. doi:10.1158/1538-7445.SABCS19-P3-03-01.

  • “Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2.”

    AUTHORS: Juan Ángel Patiño-Galindo, Ioan Filip, Ratul Chowdhury, Costas D. Maranas, Peter K. Sorger, Mohammed AlQuraishi, Raul Rabadan+.

    Genome Medicine. 2021 August 06. doi: doi.org/10.1186/s13073-021-00943-6

    *These authors have contributed equally to this work. +Corresponding authors.

  • “Identification of Relevant Genetic Alterations in Cancer using Topological Data Analysis.”

    AUTHORS: Raúl Rabadán+, Yamina Mohamedi, Udi Rubin, Tim Chu, Oliver Elliott, Luis Arnés, Santiago Cal, Álvaro J. Obaya, Arnold J. Levine+, Pablo G. Cámara+.

    *These authors have contributed equally to this work. +Corresponding authors.

    Nature Commun. 2020 July 30. doi: 10.1038/s41467-020-17659-7.

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2019

  • “Can patient selection and neoadjuvant administration resuscitate PD-1 inhibitors for glioblastoma?”

    AUTHORS: Arrieta VA, Iwamoto F, Lukas RV, Sachdev S, Rabadan R, Sonabend AM.

    J Neurosurg. 2019 Dec 6:1-6. doi: 10.3171/2019.9.JNS192523.

  • “Secretome analysis of patient-derived GBM tumor spheres identifies midkine as a potent therapeutic target.”

    AUTHORS: Han S, Shin H, Lee JK, Liu Z, Rabadan R, Lee J, Shin J, Lee C, Yang H, Kim D, Kim SH, Kim J, Oh JW, Kong DS, Lee JI, Seol HJ, Choi JW, Kang HJ, Nam DH.

    Exp Mol Med. 2019 Dec 6;51(12):1-11. doi: 10.1038/s12276-019-0351-y.

  • “Longitudinal molecular trajectories of diffuse glioma in adults.”

    AUTHORS: Barthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HK, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCM, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JM, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JK, Schuster M, Shaw BL, Short SC, Smitt PAS, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, De Groot JF, Stead LF, Verhaak RGW; GLASS Consortium.

    Nature. 2019 Dec;576(7785):112-120. doi: 10.1038/s41586-019-1775-1. Epub 2019 Nov 20.

  • “Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers.”

    AUTHORS: Sa JK, Hwang JR, Cho YJ, Ryu JY, Choi JJ, Jeong SY, Kim J, Kim MS, Paik ES, Lee YY, Choi CH, Kim TJ, Kim BG, Bae DS, Lee Y, Her NG, Shin YJ, Cho HJ, Kim JY, Seo YJ, Koo H, Oh JW, Lee T, Kim HS, Song SY, Bae JS, Park WY, Han HD, Ahn HJ, Sood AK, Rabadan R, Lee JK, Nam DH, Lee JW.

    Genome Biol. 2019 Nov 26;20(1):253. doi: 10.1186/s13059-019-1848-3.

  • “Role of Vav1 Genomic Alterations in T-Cell Differentiation and Transformation in Peripheral T-Cell Lymphoma.”

    AUTHORS: Jose Rodriguez Cortes, PhD, Anisha R. Cooke, Aidan Quinn, Ioan Filip, PhD, Juan Angel Patino, PhD, Raul Rabadan, PhD, Adolfo A. Ferrando, MD PhD, Teresa Palomero, PhD.

    Blood. 2019 Nov 13. doi: https://doi.org/10.1182/blood-2019-129438

  • “RNA Sequencing of Hodgkin Lymphoma Reed-Sternberg Cells Uncovers a Plasma Cell Signature and Escape from NK Cell Recognition.”

    AUTHORS: Ethel Cesarman, MD PhD, Mikhail Roshal, MD PhD, Jonathan Reichel, PhD, Wagner Florian, PhD, Bhavneet Binder, Sakellarios Zairis, Jouliana Sadek, PhD, Joshua Brody, MD, Raul Rabadan, PhD, Sandeep Dave, MD.

    Blood. 2019 Nov 13. doi:https://doi.org/10.1182/blood-2019-131163

  • “IMMU-42. CD8+ T-CELLS MEDIATE IMMUNOEDITING, AND INFLUENCE GENOTYPE, TUMOR ONCOGENIC PATHWAYS AND MICROENVIRONMENT DURING PROGRESSION OF MURINE GLIOMAS.”

    AUTHORS: J Robert Kane, Junfei Zhao, Takashi Tsujiuchi, Brice Laffleur, Aayushi Mahajan, Ganesh Rao, Angeliki Mela, Crismita Dmello, Victor A Arrieta, Li Chen, Daniel Y Zhang, Catalina Lee-Chang, Ting Xiao, Gerson Rothschild, Uttiya Basu, Craig Horbinski, Maciej S Lesniak, Amy Heimberger, Raul Rabadan, Peter D Canoll, Adam Sonabend.

    Neuro-Oncology. 2019 Nov 11. Vol.21, Page vi128,doi: https://doi.org/10.1093/neuonc/noz175.534

  • “Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors.”

    AUTHORS: Neil Vasan, Pedram Razavi, Jared L Johnson, Hong Shao, Hardik Shah, Alesia Antoine, Erik Ladewig, Alexander Gorelick, Ting-Yu Lin, Eneda Toska, Guotai Xu, Abiha Kazmi, Matthew T Chang, Barry S Taylor, Maura N Dickler, Komal Jhaveri, Sarat Chandarlapaty, Raul Rabadan, Ed Reznik, Melissa L Smith, Robert Sebra, Frauke Schimmoller, Timothy R Wilson, Lori S Friedman, Lewis C Cantley, Maurizio Scaltriti, José Baselga.

    Science. 2019 Nov 08. Vol. 366, Issue 6466, pp. 714-723 doi: 10.1126/science.aaw9032

  • “Predicting Clinical Outcomes in Glioblastoma: An Application of Topological and Functional Data Analysis.”

    AUTHORS: Lorin Crawford, Anthea Monod, Andrew X Chen, Sayan Mukherjee, Raúl Rabadán.

    Journal of the American Statistical Association. 2019 Oct 17. doi: https://doi.org/10.1080/01621459.2019.1671198

  • “The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function.”

    AUTHORS: Singer RA, Arnes L, Cui Y, Wang J, Gao Y, Guney MA, Burnum-Johnson KE, Rabadan R, Ansong C, Orr G, Sussel L.

    Cell Metab. 2019 Oct 10. pii: S1550-4131(19)30516-9. doi: 10.1016/j.cmet.2019.09.013.

  • “Gata3-controlled nucleosome eviction drives Myc enhancer activity in T-cell development and leukemia.”

    AUTHORS: Belver L, Yang AY, Albero R, Herranz D, Brundu FG, Quinn SA, Perez-Duran P, Alvarez S, Gianni F, Rashkovan M, Gurung D, Rocha PP, Raviram R, Reglero C, Cortes JR, Cooke AJ, Wendorff AA, Cordo V, Meijerink JP, Rabadan R, Ferrando AA.

    Cancer Discov. 2019 Sep 13. pii: CD-19-0471. doi: 10.1158/2159-8290.CD-19-0471.

  • “A Structure-Informed Atlas of Human-Virus Interactions.”

    AUTHORS: Gorka Lasso, Sandra V. Mayer, Evandro R. Winkelmann, Tim Chu, Oliver Elliott, Juan Angel Patino-Galindo, Kernyu Park, Raul Rabadan, Barry Honig, Sagi D. Shapira.

    Cell. 2019 Sep 5;178(6):1526-1541.e16. doi: 10.1016/j.cell.2019.08.005. Epub 2019 Aug 29.

  • “Tissue-Resident Memory T Cells Mediate Immune Homeostasis in the Human Pancreas Through the PD-1/PD-L1 Pathway.”

    AUTHORS: Stuart Weisberg, Dustin J Carpenter, Michael Chait, Pranay Dogra, Robyn D Gartrell-Corrado, Andrew X Chen, Sean Campbell, Wei` Liu, Pooja Saraf, Mark E Snyder, Masaru Kubota, Nichole M Danzl, Beth A Schrope, Raul Rabadan, Yvonne Saenger, Xiaojuan Chen, Donna Farberi.

    Cell Reports. 2019 Aug 31. doi: 10.2139/ssrn.3445675.

  • “Disease-Causing Mutations in SF3B1 Alter Splicing by Disrupting Interaction with SUGP1.”

    AUTHORS: Jian Zhang, Abdullah M Ali, Yen K Lieu, Zhaoqi Liu, Jianchao Gao, Raul Rabadan, Azra Raza, Siddhartha Mukherjee, James L Manley.

    Molecular Cell. 2019 Aug 29. doi: 10.1016/j.molcel.2019.07.017

  • “Repurposing dasatinib for diffuse large B cell lymphoma.”

    AUTHORS: Scuoppo C, Wang J, Persaud M, Mittan SK, Basso K, Pasqualucci L, Rabadan R, Inghirami G, Grandori C, Bosch F, Dalla-Favera R.

    Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):16981-16986. doi: 10.1073/pnas.1905239116.

  • “2003-Acute Myeloid Leukemia Cells Seize Serotonin Signaling in Osteoblasts to Engraft and Proliferate.”

    AUTHORS: Marta Galan-Diez, Junfei Zhao, Raul Rabadan, Stavroula Kousteni.

    Experimental Hematology. 2019 Aug 1. doi: 10.1016/j.exphem.2019.06.278

  • “Somatic mutations and cell identity linked by Genotyping of Transcriptomes.”

    AUTHORS: Nam AS, Kim KT, Chaligne R, Izzo F, Ang C, Taylor J, Myers RM, Abu-Zeinah G, Brand R, Omans ND, Alonso A, Sheridan C, Mariani M, Dai X, Harrington E, Pastore A, Cubillos-Ruiz JR, Tam W, Hoffman R, Rabadan R, Scandura JM, Abdel-Wahab O, Smibert P, Landau DA.

    Nature. 2019 Jul;571(7765):355-360. doi: 10.1038/s41586-019-1367-0.

  • “TOP2B Enzymatic Activity on Promoters and Introns Modulates Multiple Oncogenes in Human Gliomas.”

    AUTHORS: Edgar Gonzalez-Buendia, Junfei Zhao, Lu Wang, Subhas Mukherjee, Stacy A Marshall, Eric Feldstein, Daniel Zhang, Catalina Lee-Chang, Aayushi Mahajan, Li Chen, Ronald Realubit, Charles Karan, Lisa Magnuson, Craig Horbinski, Jann N Sarkaria, Ahmed Mohyeldin, Ichiro Nakano, Charles D James, Daniel J Brat, Atique Ahmed, Peter Canoll, Raul Rabadan, Ali Shilatifard, Adam M Sonabend.

    Cancer Cell. 2019 Jul 8. doi: 10.2139/ssrn.3414699.

  • “High density of CD68+ HLA-DR-macrophages in the stroma of primary melanoma correlates with an unfavorable immune microenvironment as assessed by Digital Spatial Profiling.”

    AUTHORS: Emanuelle M Rizk, Andrew Chen, Andrew M Silverman, Douglas K Marks, Raul Rabadan, Kit Fuhrman, Alison VanSchoiack, Yan Liang, Joseph Beechem, Yvonne M Saenger, Robyn D Gartrell.

    American Association for Cancer Research. 2019 Jul 1. doi: 10.1158/1538-7445.AM2019-2798.

  • “Double PIK3CA mutations in cis enhance oncogene activation and sensitivity to PI3K alpha inhibitors in breast cancer.”

    AUTHORS: Neil Vasan, Pedram Razavi, Jared Johnson, Hong Shao, Hardik Shah, Alesia Antoine, Erik Ladewig, Alexander Gorelick, Eneda Toska, Guotai Xu, Abiha Kazmi, Matthew T Chang, Barry S Taylor, Maura N Dickler, Komal Jhaveri, Raul Rabadan, Ed Reznik, Melissa L Smith, Robert Sebra, Lewis C Cantley, Maurizio Scaltriti, Jose Baselga.

    American Association for Cancer Research. 2019 Jul 1. doi: 10.1158/1538-7445.AM2019-3917.

  • “Topological Data Analysis for Genomics and Evolution: Topology in Biology.”

    AUTHORS: Raul Rabadan and Andrew J. Blumberg.

    Cambridge University Press. 2019. ISBN-13: 978-1107159549.

  • “arcasHLA: high resolution HLA typing from RNAseq.”

    AUTHORS: Orenbuch R, Filip I, Comito D, Shaman J, Pe'er I, Rabadan R.

    Bioinformatics. 2019 Jun 7. pii: btz474. doi: 10.1093/bioinformatics/btz474.

  • “Novel insights into the genetics and epigenetics of MALT lymphoma unveiled by next generation sequencing analyses.”

    AUTHORS: Cascione L, Rinaldi A, Bruscaggin A, Tarantelli C, Arribas AJ, Kwee I, Pecciarini L, Mensah AA, Spina V, Chung EYL, Terzi di Bergamo L, Dirnhofer S, Tzankov A, Miranda RN, Young KH, Traverse-Glehen A, Gaidano G, Swerdlow SH, Gascoyne R, Rabadan R, Ponzoni M, Bhagat G, Rossi D, Zucca E, Bertoni F.

    Haematologica. 2019 Apr 24. pii: haematol.2018.214957. doi: 10.3324/haematol.2018.214957.

  • “The 2019 Mathematical Oncology Roadmap.”

    AUTHORS: Rockne RC, Hawkins-Daarud A, Swanson KR, Sluka JP, Glazier JA, Macklin P, Hormuth D, Jarrett AM, Lima EABDF, Oden J, Biros G, Yankeelov TE, Curtius K, Bakir IA, Wodarz D, Komarova N, Aparicio L, Bordyuh M, Rabadan R, Finley S, Enderling H, Caudell JJ, Moros EG, Anderson ARA, Gatenby R, Kaznatcheev A, Jeavons P, Krishnan N, Pelesko J, Wadhwa RR, Yoon N, Nichol D, Marusyk A, Hinczewski M, Scott JG.

    Phys Biol. 2019 Apr 16. doi: 10.1088/1478-3975/ab1a09.

  • “Complete Regression of Advanced Pancreatic Ductal Adenocarcinomas upon Combined Inhibition of EGFR and C-RAF.”

    AUTHORS: Blasco MT, Navas C, Martín-Serrano G, Graña-Castro O, Lechuga CG, Martín-Díaz L, Djurec M, Li J, Morales-Cacho L, Esteban-Burgos L, Perales-Patón J, Bousquet-Mur E, Castellano E, Jacob HKC, Cabras L, Musteanu M, Drosten M, Ortega S, Mulero F, Sainz B Jr, Dusetti N, Iovanna J, Sánchez-Bueno F, Hidalgo M, Khiabanian H, Rabadán R, Al-Shahrour F, Guerra C, Barbacid M.

    Cancer Cell. 2019 Apr 15;35(4):573-587.e6. doi: 10.1016/j.ccell.2019.03.002.

  • “Longitudinal active sampling for respiratory viral infections across age groups.”

    AUTHORS: Galanti M, Birger R, Ud-Dean M, Filip I, Morita H, Comito D, Anthony S, Freyer GA, Ibrahim S, Lane B, Ligon C, Rabadan R, Shittu A, Tagne E, Shaman J.

    Influenza Other Respir Viruses. 2019 Feb 15. doi: 10.1111/irv.12629.

  • “Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.”

    AUTHORS: Zhao J, Chen AX, Gartrell RD, Silverman AM, Aparicio L, Chu T, Bordbar D, Shan D, Samanamud J, Mahajan A, Filip I, Orenbuch R, Goetz M, Yamaguchi JT, Cloney M, Horbinski C, Lukas RV, Raizer J, Rae AI, Yuan J, Canoll P, Bruce JN, Saenger YM, Sims P, Iwamoto FM, Sonabend AM, Rabadan R.

    Nat Med. 2019 Feb 11. doi: 10.1038/s41591-019-0349-y.

  • “Interrogation of eukaryotic stop codon readthrough signals by in vitro RNA selection.”

    AUTHORS: Anzalone AV, Zairis S, Lin AJ, Rabadan R, Cornish VW.

    Biochemistry. 2019 Jan 30. doi: 10.1021/acs.biochem.8b01280.

  • “Rates of asymptomatic respiratory virus infection across age groups.”

    AUTHORS: Galanti M, Birger R, Ud-Dean M, Filip I, Morita H, Comito D, Anthony S, Freyer GA, Ibrahim S, Lane B, Matienzo N, Ligon C, Rabadan R, Shittu A, Tagne E, Shaman J.

    Epidemiol Infect. 2019 Jan;147:e176. doi: 10.1017/S0950268819000505.

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2018

  • “Phf6 loss enhances HSC self-renewal driving tumor initiation and leukemia stem cell activity in T-ALL.”

    AUTHORS: Wendorff AA, Quinn SA, Rashkovan M, Madubata CJ, Ambesi-Impiombato A, Litzow MR, Tallman MS, Paietta E, Paganin M, Basso G, Gastier-Foster JM, Loh ML, Rabadan R, Van Vlierberghe P, Ferrando AA.

    Cancer Discov. 2018 Dec 19. pii: CD-18-1005. doi: 10.1158/2159-8290.CD-18-1005.

  • “Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations.”

    AUTHORS: Jason K Sa, Seung Won Choi, Junfei Zhao, Yeri Lee, Jing Zhang, Doo‐Sik Kong, Jung Won Choi, Ho Jun Seol, Jung‐Il Lee, Antonio Iavarone, Raul Rabadan, Do‐Hyun Nam.

    International Journal of Cancer. 2018 Dec 11. doi:10.1002/ijc.32054

  • “Topological Data Analysis of Single-cell Hi-C Contact Maps.”

    AUTHORS: Mathieu Carriere, Raul Rabadan

    arXiv preprint. 2018 Dec 4. arXiv:1812.01360

  • “A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes.”

    AUTHORS: Ahrim Youn, Kyung In Kim, Raul Rabadan, Benjamin Tycko, Yufeng Shen, Shuang Wang

    BMC Medical Genomics. 2018 Nov. doi:10.1186/s12920-018-0425-z

  • “Suppression of GATA3 Binding Drives Selective Abrogation of NOTCH1-MYC Enhancer Activity By Nucleosome Invasion in Thymocyte Development and Leukemia.”

    AUTHORS: Laura Belver, Alexander Y Yang, Daniel Herranz, Aidan Quinn, Francesco G Brundu, Pablo Perez-Duran, Silvia Alvarez, Devya Gurung, Pedro P Rocha, Ramya Raviram, Marissa Rashkovan, Raul Rabadan, Adolfo A Ferrando

    Blood. 2018 Nov 29. doi:10.1182/blood-2018-99-119423

  • “High Throughput Droplet Single-Cell Genotyping of Transcriptomes (GoT) Reveals the Cell Identity Dependency of the Transcriptional Output of Somatic Mutations.”

    AUTHORS: Anna S Nam, Kyu-Tae Kim, Ronan Chaligne, Franco Izzo, Chelston Ang, Nathaniel Omans, Alessandro Pastore, Justin Taylor, Alicia Alonso, Wayne Tam, Ronald Hoffman, Joseph Scandura, Raul Rabadan, Omar I Abdel-Wahab, Peter Smibert, Dan A Landau.

    Blood. 2018 Nov 21. doi:10.1182/blood-2018-99-119236

  • “Mutations in the RNA Splicing Factor SF3B1 Promote Transformation through MYC Stabilization.”

    Akihide Yoshimi, Zhaoqi Liu, Wang Jiguang, Hana Cho, Stanley C Lee, Michelle Ki, Lillian E Bitner, Timothy Chu, Anthony R Mato, Peter P Ruvolo, Giulia Fabbri, Laura Pasqualucci, Raul Rabadan, Omar I Abdel-Wahab

    Blood. 2018 Nov 21. doi:10.1182/blood-2018-99-110328

  • “DDIS-13. UNDERSTANDING GLIOBLASTOMA SUSCEPTIBILITY TO TOP2-TARGETING DRUGS FOR PERSONALIZED THERAPY.”

    AUTHORS: Chidiebere Awah, Edgar Gonzalez-Buendía, Junfei Zhao, Eric Feldstein, Li Chen, Aayushi Mahajan, Louisa Warnke, Lu Wang, Cheol Park, Jan Winter, Silvana Konermann, Ali Shilatifard, C David James, Raul Rabadan, Patrick Hsu, Mukesh Bansal, Atique Ahmed, Adam Sonabend

    Neuro-Oncology. 2018 Nov 05. doi:10.1093/neuonc/noy148.290

  • “The Holdout Randomization Test: Principled and Easy Black Box Feature Selection.”

    AUTHORS: W Tansey, V Veitch, H Zhang, R Rabadan, DM Blei

    arXiv preprint. 2018 Nov 1. arXiv:1811.00645

  • “Blastic plasmacytoid dendritic cell neoplasm: genomics mark epigenetic dysregulation as a primary therapeutic target.”

    AUTHORS: Maria Rosaria Sapienza, Francesco Abate, Federica Melle, Stefania Orecchioni, Fabio Fuligni, Maryam Etebari, Valentina Tabanelli, Maria Antonella Laginestra, Alessandro Pileri, Giovanna Motta, Maura Rossi, Claudio Agostinelli, Elena Sabattini, Nicola Pimpinelli, Mauro Truni, Brunangelo Falini, Lorenzo Cerroni, Giovanna Talarico, Rossana Piccioni, Stefano Amente, Valentina Indio, Giuseppe Tarantino, Francesco Brundu, Marco Paulli, Emilio Berti, Fabio Facchetti, Gaetano Ivan Dellino, Francesco Bertolini, Claudio Tripodo, Raul Rabadan, Stefano A. Pileri

    Haematologica. October 2018. doi:10.3324/haematol.2018.202093

  • “Quasi-universality in single-cell sequencing data.”

    AUTHORS: L Aparicio, M Bordyuh, AJ Blumberg, R Rabadan

    arXiv preprint. 2018 Oct 5. arXiv:1810.03602

  • “Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy.”

    AUTHORS: Jin-Ku Lee, Zhaoqi Liu, Jason K. Sa, Sang Shin, Jiguang Wang, Mykola Bordyuh, Hee Jin Cho, Oliver Elliott, Timothy Chu, Seung Won Choi, Daniel I. S. Rosenbloom, In-Hee Lee, Yong Jae Shin, Hyun Ju Kang, Donggeon Kim, Sun Young Kim, Moon-Hee Sim, Jusun Kim, Taehyang Lee, Yun Jee Seo, Hyemi Shin, Mijeong Lee, Sung Heon Kim, Yong-Jun Kwon, Jeong-Woo Oh, Minsuk Song, Misuk Kim, Doo-Sik Kong, Jung Won Choi, Ho Jun Seol, Jung-Il Lee, Seung Tae Kim, Joon Oh Park, Kyoung-Mee Kim, Sang-Yong Song, Jeong-Won Lee, Hee-Cheol Kim, Jeong Eon Lee, Min Gew Choi, Sung Wook Seo, Young Mog Shim, Jae Ill Zo, Byong Chang Jeong, Yeup Yoon, Gyu Ha Ryu, Nayoung K. D. Kim, Joon Seol Bae, Woong-Yang Park, Jeongwu Lee, Roel G. W. Verhaak, Antonio Iavarone, Jeeyun Lee, Raul Rabadan, Do-Hyun Nam.

    Nat Genet. 2018 Sep 27. doi: 10.1038/s41588-018-0209-6.

  • “Distinct genomic profile and specific targeted drug responses in adult cerebellar glioblastoma.”

    AUTHORS: Hee Jin Cho, Junfei Zhao, Sang Won Jung, Erik Ladewig, Doo-Sik Kong, Yeon-Lim Suh, Yeri Lee, Donggeon Kim, Sun Hee Ahn, Mykola Bordyuh, Hyun Ju Kang, Jason K Sa, Yun Jee Seo, Sung Tae Kim, Do Hoon Lim, Yun-Sik Dho, Jung-Il Lee, Ho Jun Seol, Jung Won Choi, Woong-Yang Park, Chul-Kee Park, Raul Rabadan, Do-Hyun Nam.

    Neuro-Oncology. July 2018. doi:10.1093/neuonc/noy123

  • “Copy number profiling across glioblastoma populations has implications for clinical trial design.”

    AUTHORS: Patrick J Cimino, Lisa McFerrin, Hans-Georg Wirsching, Sonali Arora, Hamid Bolouri, Raul Rabadan, Michael Weller, Eric C Holland.

    Neuro-Oncology. July 2018. doi:10.1093/neuonc/noy108

  • “Quantitative compositional and spatial analysis of tumor microenvironment (TME) in primary melanoma.”

    AUTHORS: Robyn D Gartrell, Andrew Chen, Douglas K Marks, Thomas D Hart, Gen Li, Alan Wu, Yan Lu, Camden Esancy, Zoe Blake, Bret Taback, Raul Rabadan, Howard L Kaufman, Charles G Drake, Basil Horst, Anthea Monod, Yvonne Saenger.

    Cancer Research. Volume 78, Issue 13. July 2018. doi:10.1158/1538-7445.AM2018-2091

  • “On statistical modeling of sequencing noise in high depth data to assess tumor evolution.”

    Raul Rabadan, Gyan Bhanot, Sonia Marsilio, Nicholas Chiorazzi, Laura Pasqualucci, Hossein Khiabanian.

    Journal of Statistical Physics. Volume 172. July 2018. doi:10.1007/s1095

  • “The possibility of cancer immune editing in gliomas. A critical review.”

    AUTHORS: Víctor A Arrieta, Bernardo Cacho-Díaz, Junfei Zhao, Raul Rabadan, Li Chen, Adam M Sonabend.

    OncoImmunology. Volume 7, 2018 - Issue 7. doi:10.1080/2162402X.2018.1445458.

  • “Black Box FDR.”

    AUTHORS: Wesley Tansey, Yixin Wang, David M Blei, Raul Rabadan.

    arXiv. 2018. preprint arXiv:1806.03143.

  • “Correlation of immune infiltration of cytotoxic T cells and activated microglia in glioblastoma (GBM) post anti-PD1 therapy with response.”

    AUTHORS: Andrew Silverman, Robyn Denise Gartrell, Junfei Zhao, Syeda Sabeeka Batool, Thomas D Hart, Syed Shabee Hasan, James H Garvin, George Zanazzi, Fabio Massaiti Iwamoto, Raul Rabadan, Peter Canoll, Yvonne M Saenger.

    Journal of Clinical Oncology 36, no. 15_suppl (May 20 2018) 2055-2055.doi:10.1200/JCO.2018.36.15_suppl.2055.

  • “The Egyptian rousette genome reveals unexpected features of bat antiviral immunity.”

    AUTHORS: Stephanie S Pavlovich, Sean P Lovett, Galina Koroleva, Jonathan C Guito, Catherine E Arnold, Elyse R Nagle, Kirsten Kulcsar, Albert Lee, Françoise Thibaud-Nissen, Adam J Hume, Elke Mühlberger, Luke S Uebelhoer, Jonathan S Towner, Raul Rabadan, Mariano Sanchez-Lockhart, Thomas B Kepler, Gustavo Palacios.

    Cell. Volume 173, Issue 5, 17 May 2018, Pages 1098-1110.e18. doi:10.1016/j.cell.2018.03.070.

  • “Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma.”

    AUTHORS: Enrico Tiacci, Erik Ladewig, Gianluca Schiavoni, Alex Penson, Elisabetta Fortini, Valentina Pettirossi, Yuchun Wang, Ariele Rosseto, Alessandra Venanzi, Sofija Vlasevska, Roberta Pacini, Simonetta Piattoni, Alessia Tabarrini, Alessandra Pucciarini, Barbara Bigerna, Alessia Santi, Alessandro M Gianni, Simonetta Viviani, Antonello Cabras, Stefano Ascani, Barbara Crescenzi, Cristina Mecucci, Laura Pasqualucci, Raul Rabadan, Brunangelo Falini.

    Blood [12 Apr 2018, 131(22):2454-2465]. doi:10.1182/blood-2017-11-814913.

  • “Quantifying genetic innovation: Mathematical foundations for the topological study of reticulate evolution.”

    AUTHORS: Michael Lesnick, Raúl Rabadán, Daniel Rosenbloom.

    arXiv. 2018. preprint arXiv:1804.01398.

  • “Increased HOXA5 expression provides a selective advantage for gain of whole chromosome 7 in IDH wild-type glioblastoma.”

    AUTHORS: Patrick J Cimino, Youngmi Kim, Hua-Jun Wu, Jes Alexander, Hans-Georg Wirsching, Frank Szulzewsky, Ken Pitter, Tatsuya Ozawa, Jiguang Wang, Julio Vazquez, Sonali Arora, Raul Rabadan, Ross Levine, Franziska Michor, Eric C Holland.

    Genes & Dev. 2018. 32: 512-523. doi:10.1101/gad.312157.118.

  • “Quantitative Analysis of Immune Infiltrates in Primary Melanoma.”

    AUTHORS: Robyn D Gartrell, Douglas K Marks, Thomas D Hart, Gen Li, Danielle R Davari, Alan Wu, Zoë Blake, Yan Lu, Kayleigh N Askin, Anthea Monod, Camden L Esancy, Edward C Stack, Dan Tong Jia, Paul M Armenta, Yichun Fu, Daisuke Izaki, Bret Taback, Raul Rabadan, Howard L Kaufman, Charles G Drake, Basil A Horst, Yvonne M Saenger.

    Cancer Immunology Research, April 2018, Volume 6, Issue 4 .doi:10.1158/2326-6066.CIR-17-0360.

  • “Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma.”

    AUTHORS: Luis Arnes, Zhaoqi Liu, Jiguang Wang, Hans Carlo Maurer, Irina Sagalovskiy, Marta Sanchez-Martin, Nikhil Bommakanti, Diana C Garofalo, Dina A Balderes, Lori Sussel, Kenneth P Olive, Raul Rabadan.

    Gut Published Online First: 10 February 2018. doi: 10.1136/gutjnl-2017-314353.

  • “Genetic landscape of ultra-stable chronic lymphocytic leukemia patients.”

    AUTHORS: S Raponi, I Del Giudice, M Marinelli, J Wang, L Cafforio, C Ilari, A Piciocchi, M Messina, S Bonina, S Tavolaro, M Bordyuh, P Mariglia, N Peragine, FR Mauro, S Chiaretti, S Molica, M Gentile, A Visentin, L Trentin, GM Rigolin, A Cuneo, F Diop, D Rossi, G Gaidano, A Guarini, R Rabadan, R Foà.

    Annals of Oncology, Volume 29, Issue 4, 1 April 2018, Pages 966–972, doi:10.1093/annonc/mdy021.

  • “Saa3 is a key mediator of the protumorigenic properties of cancer-associated fibroblasts in pancreatic tumors.”

    AUTHORS: Magdolna Djurec, Osvaldo Graña, Albert Lee, Kevin Troulé, Elisa Espinet, Lavinia Cabras, Carolina Navas, María Teresa Blasco, Laura Martín-Díaz, Miranda Burdiel, Jing Li, Zhaoqi Liu, Mireia Vallespinós, Francisco Sanchez-Bueno, Martin R Sprick, Andreas Trumpp, Bruno Sainz, Fátima Al-Shahrour, Raul Rabadan, Carmen Guerra, Mariano Barbacid.

    PNAS 2018. doi:10.1073/pnas.1717802115.

  • “Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia.”

    AUTHORS: Gannie Tzoneva, Chelsea L Dieck, Koichi Oshima, Alberto Ambesi-Impiombato, Marta Sánchez-Martín, Chioma J Madubata, Hossein Khiabanian, Jiangyan Yu, Esme Waanders, Ilaria Iacobucci, Maria Luisa Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Julie M Gastier-Foster, Mignon L Loh, Renate Kirschner-Schwabe, Charles G Mullighan, Raul Rabadan, Adolfo A Ferrando.

    Nature volume 553, pages 511–514 (25 January 2018) doi:10.1038/nature25186.

  • “Precision Medicine for Acute Kidney Injury (AKI): Redefining AKI by Agnostic Kidney Tissue Interrogation and Genetics.”

    AUTHORS: Krzysztof Kiryluk, Andrew S Bomback, Yim-Ling Cheng, Katherine Xu, Pablo G Camara, Raul Rabadan, Peter A Sims, Jonathan Barasch.

    Nephrology. January 2018. doi:10.1016/j.semnephrol.2017.09.006.

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2017

  • “Repurposing Dasatinib for Ibrutinib-Resistant Diffuse Large B-Cell Lymphoma.”

    AUTHORS: Claudio Scuoppo, Wang Jiguang, Mirjana Persaud, Sandeep Mittan, Laura Pasqualucci, Raul Rabadan, Carla Grandori, Riccardo Dalla-Favera.

    Blood 2017 130:3843.

  • “Somatic CLL mutations occur at multiple distinct hematopoietic maturation stages: documentation and cautionary note regarding cell fraction purity.”

    AUTHORS: S Marsilio, H Khiabanian, G Fabbri, S Vergani, C Scuoppo, E Montserrat, EJ Shpall, M Hadigol, P Marin, KR Rai, R Rabadan, S Devereux, L Pasqualucci, N Chiorazzi.

    Leukemia.05 December 2017.doi:10.1038/leu.2017.343.

  • “Gene-08. Pharmacologic Modulation Of Myc And Pdgfra By Targeting Topoisomerase Ii On Gliomas.”

    AUTHORS: Edgar Gonzalez-Buendia, Eric Feldstein, Junfei Zhao, Aayushi Mahajan, Ronald Realubit, Charles Karan, Raul Rabadan, Adam M Sonabend.

    Neuro-Oncology. 19(suppl_6):vi94, NOV 2017 DOI: 10.1093/neuonc/nox168.383.

  • “Restoration of Replication Fork Stability in BRCA1-and BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers.”

    AUTHORS: Angelo Taglialatela, Silvia Alvarez, Giuseppe Leuzzi, Vincenzo Sannino, Lepakshi Ranjha, Jen-Wei Huang, Chioma Madubata, Roopesh Anand, Brynn Levy, Raul Rabadan, Petr Cejka, Vincenzo Costanzo, Alberto Ciccia.

    Molecular Cell. 2017 Sep. doi: 10.1016/j.molcel.2017.09.036.

  • “Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas.”

    AUTHORS: Chioma J Madubata, Alireza Roshan-Ghias, Timothy Chu, Samuel Resnick, Junfei Zhao, Luis Arnes, Jiguang Wang & Raul Rabadan.

    npj Genomic Medicine. 2017 Oct. doi:10.1038/s41525-017-0032-5.

  • “Refined karyotype-based prognostic stratification of chronic lymphocytic leukemia with a low-and very-low-risk genetic profile.”

    AUTHORS: ID Giudice, GM Rigolin, S Raponi, L Cafforio, C Ilari, J Wang, M Bordyuh, A Piciocchi, M Marinelli, M Nanni, S Tavolaro, M Filetti, A Bardi, E Tammiso, E Volta, M Negrini, E Saccenti, FR Mauro, D Rossi, G Gaidano, A Guarini, R Rabadan, A Cuneo, R Foà.

    Leukemia. 2017 Sep. doi: 10.1038/leu.2017.292.

  • “An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function.”

    AUTHORS: Oh H, Grinberg-Bleyer Y, Liao W, Maloney D, Wang P, Wu Z, Wang J, Bhatt DM, Heise N, Schmid RM, Hayden MS, Klein U, Rabadan R, Ghosh S.

    Immunity. 2017 Sep 1. pii: S1074-7613(17)30368-0. doi: 10.1016/j.immuni.2017.08.010.

  • “Tropical Sufficient Statistics for Persistent Homology with a Parametric Application to Infectious Viral Disease.”

    AUTHORS: Anthea Monod, Sara Kališnik Verovšek, Juan Ángel Patiño-Galindo, Lorin Crawford.

    arXiv. 2017 Sept. arXiv:1709.02647 [math.ST].

  • “Geometry and topology of genomic data.”

    AUTHORS: A.J. Blumberg and R. Rabadan.

    Chapter 64 in J.E. Goodman, J. O'Rourke, and C.D. Toth, editors.

    Handbook of Discrete and Computational Geometry, 2nd edition, CRC Press, Boca Raton, FL, 2017, pp. 1735-1773.

  • “Reprogramming Cancer Associated Fibroblasts as a therapeutic approach against Pancreatic Ductal Adenocarcinoma.”

    AUTHORS: Magdolna Djurec, Kevin Troule, Osvaldo Graña, Albert Lee, Raúl Rabadán, Carmen Guerra, Mariano Barbacid.

    Pancreatology. 2017 Jul. doi: 10.1016/j.pan.2017.05.175.

  • “The B-cell receptor controls fitness of MYC-driven lymphoma cells via GSK3β inhibition.”

    AUTHORS: Varano G, Raffel S, Sormani M, Zanardi F, Lonardi S, Zasada C, Perucho L, Petrocelli V, Haake A, Lee AK, Bugatti M, Paul U, Van Anken E, Pasqualucci L, Rabadan R, Siebert R, Kempa S, Ponzoni M, Facchetti F, Rajewsky K, Casola S.

    Nature. 2017 Jun 8;546(7657):302-306. doi: 10.1038/nature22353. Epub 2017 May 31.

  • “p53 maintains baseline expression of multiple tumor suppressor genes.”

    AUTHORS: Pappas K, Xu J, Zairis S, Resnick-Silverman L, Abate F, Steinbach N, Ozturk S, Saal LH, Su T, Cheung P, Schmidt H, Aaronson SA, Hibshoosh H, Manfredi JJ, Rabadan R, Parsons R.

    Mol Cancer Res. 2017 May 8. doi: 10.1158/1541-7786.MCR-17-0089.

  • “Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development.”

    AUTHORS: Abbas H Rizvi, Pablo G Camara, Elena K Kandror, Thomas J Roberts, Ira Schieren, Tom Maniatis & Raul Rabadan.

    Nature Biotechnology. 2017 May. doi:10.1038/nbt.3854

  • “Nuclear Proximity of Mtr4 to RNA Exosome Restricts DNA Mutational Asymmetry.”

    AUTHORS: Lim J, Giri PK, Kazadi D, Laffleur B, Zhang W, Grinstein V, Pefanis E, Brown LM, Ladewig E, Martin O, Chen Y, Rabadan R, Boyer F, Rothschild G, Cogné M, Pinaud E, Deng H, Basu U.

    Cell. 2017 Apr 20;169(3):523-537.e15. doi: 10.1016/j.cell.2017.03.043.

  • “Germ-Cell-Specific Inflammasome Component NLRP14 Negatively Regulates Cytosolic Nucleic Acid Sensing to Promote Fertilization.”

    AUTHORS: Abe T, Lee A, Sitharam R, Kesner J, Rabadan R, Shapira SD.

    Immunity. 2017 Apr 18;46(4):621-634. doi: 10.1016/j.immuni.2017.03.020.

  • “Spatiotemporal genomic architecture informs precision oncology in glioblastoma.”

    AUTHORS: Lee JK*, Wang J*, Sa JK*, Ladewig E*, Lee HO, Lee IH, Kang HJ, Rosenbloom DS, Camara PG, Liu Z, van Nieuwenhuizen P, Jung SW, Choi SW, Kim J, Chen A, Kim KT, Shin S, Seo YJ, Oh JM, Shin YJ, Park CK, Kong DS, Seol HJ, Blumberg A, Lee JI, Iavarone A, Park WY+, Rabadan R+, Nam DH+.

    Nat Genet. 2017 Apr. doi: 10.1038/ng.3806.

    * These authors have contributed equally to this work. +Corresponding authors.

  • “Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas.”

    AUTHORS: Francesco Abate, Ana C. da Silva-Almeida, Sakellarios Zairis, Javier Robles-Valero, Lucile Couronne, Hossein Khiabanian, S. Aidan Quinn, Mi-Yeon Kim, Maria Antonella Laginestra, Christine Kim, Danilo Fiore, Govind Bhagat, Miguel Angel Piris, Elias Campo, Izidore S. Lossos, Olivier A. Bernard, Giorgio Inghirami, Stefano Pileri, Xosé R. Busteo, Raul Rabadan, Adolfo A. Ferrando, and Teresa Palomero.

    PNAS. 2017 January. doi: 10.1073/pnas.1608839114.

  • “Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration.”

    AUTHORS: Uhlemann AC, McAdam PR, Sullivan SB, Knox JR, Khiabanian H, Rabadan R, Davies PR, Fitzgerald JR, Lowy FD.

    MBio. 2017 Jan 17;8(1). pii: e01375-16. doi: 10.1128/mBio.01375-16.

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2016

  • “Evolutionary scalpels for dissecting tumor ecosystems.”

    AUTHORS: Daniel I.S. Rosenbloom , Pablo G. Camara, Tim Chu, Raul Rabadan.

    BBA-Reviews on Cancer. 2016 December. doi: 10.1016/j.bbcan.2016.11.005.

  • “Genomic Characterization of Dysplastic Nevi Unveils Implications for Diagnosis of Melanoma.”

    AUTHORS: Melamed RD, Aydin IT, Rajan GS, Phelps R, Silvers DN, Emmett KJ, Brunner G, Rabadan R, Celebi JT.

    J Invest Dermatol. 2016 Nov. doi: 10.1016/j.jid.2016.11.017.

  • “Topological Summaries of Tumor Images Improve Prediction of Disease Free Survival in Glioblastoma Multiforme.”

    AUTHORS: Lorin Crawford, Anthea Monod, Andrew X. Chen, Sayan Mukherjee, Raúl Rabadán.

    arXiv. 2016 November. arXiv:1611.06818 [stat.AP].

  • “A Theory of Taxonomy.”

    AUTHORS: Guido D'Amico, Raul Rabadan, Matthew Kleban.

    arXiv. 2016 November. arXiv:1611.03890 [physics.soc-ph].

  • “The genetics of nodal marginal zone lymphoma.”

    AUTHORS: Valeria Spina, Hossein Khiabanian, Monica Messina, Sara Monti, Luciano Cascione, Alessio Bruscaggin, Elisa Spaccarotella, Antony B. Holmes, Luca Arcaini, Marco Lucioni, Fabrizio Tabbò, Sakellarios Zairis, Fary Diop, Michaela Cerri, Sabina Chiaretti, Roberto Marasca, Maurilio Ponzoni, Silvia Deaglio, Antonio Ramponi, Enrico Tiacci, Laura Pasqualucci, Marco Paulli, Brunangelo Falini, Giorgio Inghirami, Francesco Bertoni, Robin Foà, Raul Rabadan, Gianluca Gaidano and Davide Rossi.

    Blood. 2016 September. doi:10.1182/blood-2016-02-696757.

  • “Genetic Landscape and Gene Expression Profile of Chronic Lymphocytic Leukemia Patients with Ultra-Stable Disease.”

    AUTHORS: Ilaria Del Giudice, Sara Raponi, Marilisa Marinelli, Jiguang Wang, Luciana Cafforio, Caterina Ilari, Monica Messina, Silvia Bonina, Simona Tavolaro, Mykola Bordyuh, Francesca Romana Mauro, Sabina Chiaretti, Davide Rossi, Gianluca Gaidano, Anna Guarini, Raul Rabadan, Robin Foà.

    Clinical Lymphoma, Myeloma, & Leukemia. 2016 Sept. doi: 10.1016/j.clml.2016.07.061.

  • “Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia.”

    AUTHOR: Koichi Oshima*, Hossein Khiabanian*, Ana C. da Silva-Almeida, Gannie Tzoneva, Francesco Abate, Alberto Ambesi-Impiombato, Marta Sanchez-Martin, Zachary Carpenter, Alex Penson, Arianne Perez-Garcia, Cornelia Eckert, Concepción Nicolas, Milagros Balbin, Maria Luisa Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Julie M. Gastier-Foster, Meenakshi Devidas, Mignon L. Loh, Renate Kirschner-Schwabe, Teresa Palomero+, Raul Rabadan+, and Adolfo A. Ferrando+.

    PNAS. 2016 August. doi: 10.1073/pnas.1608420113.

    * These authors have contributed equally to this work. +Corresponding authors.

  • “Inference of Ancestral Recombination Graphs through Topological Data Analysis.”

    AUTHORS: Pablo G. Cámara, Arnold J. Levine, Raúl Rabadán.

    PLOS Computational Biology. 2016 August. doi: 10.1371/journal.pcbi.1005071.

  • “Genomic data analysis in tree spaces.”

    AUTHORS: Sakellarios Zairis, Hossein Khiabanian, Andrew J. Blumberg, Raul Rabadan.

    arXiv. 2016 July. arXiv:1607.07503 [q-bio.GN].

  • “Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination.”

    AUTHORS: Pablo G. Camara, Daniel I.S. Rosenbloom, Kevin J. Emmett, Arnold J. Levine, Raul Rabadan.

    Cell Systems. 2016 June. doi: 10.1016/j.cels.2016.05.008.

  • “Kinase-dead ATM protein is highly oncogenic and can be preferentially targeted by Topo-isomerase I inhibitors.”

    AUTHORS: Kenta Yamamoto, Jiguang Wang, Lisa Sprinzen, Jun Xu, Christopher J Haddock, Chen Li, Brian J Lee, Denis G Loredan, Wenxia Jiang, Alessandro Vindigni, Dong Wang, Raul Rabadan, and Shan Zha.

    eLife. 2016 June 15. doi: 10.7554/eLife.14709.

  • “Clonal evolution of glioblastoma under therapy.”

    AUTHORS: Jiguang Wang, Emanuela Cazzato, Erik Ladewig, Veronique Frattini, Daniel I S Rosenbloom, Sakellarios Zairis, Francesco Abate, Zhaoqi Liu, Oliver Elliott, Yong-Jae Shin, Jin-Ku Lee, In-Hee Lee, Woong-Yang Park, Marica Eoli, Andrew J Blumberg, Anna Lasorella, Do-Hyun Nam, Gaetano Finocchiaro, Antonio Iavarone, Raul Rabadan.

    Nature Genetics. 2016 June 6. doi: 10.1038/ng.3590.

  • “A Case of T-cell Acute Lymphoblastic Leukemia Relapsed As Myeloid Acute Leukemia.”

    AUTHORS: Paganin M, Buldini B, Germano G, Seganfreddo E, Meglio AD, Magrin E, Grillo F, Pigazzi M, Rizzari C, Cazzaniga G, Khiabanian H, Palomero T, Rabadan R, Ferrando AA, Basso G.

    Pediatric Blood Cancer. 2016 May 3. doi: 10.1002/pbc.26054.

  • “Reprogramming eukaryotic translation with ligand-responsive synthetic RNA switches.”

    AUTHORS: Anzalone AV, Lin AJ, Zairis S, Rabadan R, Cornish VW.

    Nat Methods. 2016 Mar 21. doi: 10.1038/nmeth.3807.

  • “Prognostic and therapeutic role of targetable lesions in B-lineage acute lymphoblastic leukemia without recurrent fusion genes.”

    AUTHORS: Messina M, Chiaretti S, Wang J, Fedullo AL, Peragine N, Gianfelici V, Piciocchi A, Brugnoletti F, Di Giacomo F, Pauselli S, Holmes AB, Puzzolo MC, Ceglie G, Apicella V, Mancini M, Te Kronnie G, Testi AM, Vitale A, Vignetti M, Guarini A, Rabadan R, Foà R.

    Oncotarget. 2016 Feb 12. doi: 10.18632/oncotarget.7356.

  • “Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.”

    AUTHORS: Ceccarelli M, Barthel FP, Malta TM, Sabedot TS, Salama SR, Murray BA, Morozova O, Newton Y, Radenbaugh A, Pagnotta SM, Anjum S, Wang J, Manyam G, Zoppoli P, Ling S, Rao AA, Grifford M, Cherniack AD, Zhang H, Poisson L, Carlotti CG Jr, Tirapelli DP, Rao A, Mikkelsen T, Lau CC, Yung WK, Rabadan R, Huse J, Brat DJ, Lehman NL, Barnholtz-Sloan JS, Zheng S, Hess K, Rao G, Meyerson M, Beroukhim R, Cooper L, Akbani R, Wrensch M, Haussler D, Aldape KD, Laird PW, Gutmann DH; TCGA Research Network, Noushmehr H, Iavarone A, Verhaak RG.

    Cell. 2016 Jan 28;164(3):550-63. doi: 10.1016/j.cell.2015.12.028.

  • “Clinical Impact of Small Subclones Harboring NOTCH1, SF3B1 or BIRC3 Mutations in Chronic Lymphocytic Leukemia.”

    AUTHORS: Rasi S, Khiabanian H, Ciardullo C, Terzi-di-Bergamo L, Monti S, Spina V, Bruscaggin A, Cerri M, Deambrogi C, Martuscelli L, Biasi A, Spaccarotella E, De Paoli L, Gattei V, Foà R, Rabadan R, Gaidano G, Rossi D.

    Haematologica. 2016 Jan 27. pii: haematol.2015.136051.

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2015

  • “Clonality Analysis of Immunoglobulin Gene Rearrangement by Next-Generation Sequencing in Endemic Burkitt Lymphoma Suggests Antigen Drive Activation of BCR as Opposed to Sporadic Burkitt Lymphoma.”

    AUTHORS: Teresa Amato, Francesco Abate, Pierpaolo Piccaluga, Michele Iacono, Chiara Fallerini, Alessandra Renieri, Giulia De Falco, Maria Raffaella Ambrosio, Vaselious Mourmouras, Martin Ogwang, Valeria Calbi, Raul Rabadan, Michael Hummel, Stefano Pileri, Lorenzo Leoncini, Cristiana Bellan.

    Am Journ of Clinical Pathology. 2015 Dec 28; 145:116-127. doi: 10.1093/ajcp/aqv011.

  • “De novo transcriptome reconstruction and annotation of the Egyptian rousette bat.”

    AUTHORS: Lee AK, Kulcsar KA, Elliott O, Khiabanian H, Nagle ER, Jones ME, Amman BR, Sanchez-Lockhart M, Towner JS, Palacios G, Rabadan R.

    BMC Genomics. 2015 Dec 7;16:1033. doi: 10.1186/s12864-015-2124-x.

  • “Applying Topological Principles to Genomic Analysis.”

    AUTHORS: Kevin Emmett, Joseph M. Chan, Daniel S. Rosenbloom, and Raul Rabadan.

    Microbe. 2015 Nov; Vol. 10, Num. 11. pp 467-473.

  • “Inter- and intra-patient clonal and subclonal heterogeneity of chronic lymphocytic leukaemia: evidences from circulating and lymph nodal compartments.”

    AUTHORS: Del Giudice I, Marinelli M, Wang J, Bonina S, Messina M, Chiaretti S, Ilari C, Cafforio L, Raponi S, Mauro FR, Di Maio V, De Propris MS, Nanni M, Ciardullo C, Rossi D, Gaidano G, Guarini A, Rabadan R, Foà R.

    Br J Haematol. 2015 Nov 24. doi: 10.1111/bjh.13859.

  • “Quantifying Reticulation in Phylogenetic Complexes Using Homology.”

    AUTHORS: Kevin Emmett and Raul Rabadan.

    BICT 2015 (Accepted).

    arXiv:1511.01429 [q-bio.QM].

  • “Multiscale Topology of Chromatin Folding.”

    AUTHORS: Kevin Emmett, Benjamin Schweinhart, and Raul Rabadan.

    BICT 2015 (Accepted).

    arXiv:1511.01426 [q-bio.GN].

  • "Distinct Viral and Mutational Spectrum of Endemic Burkitt Lymphoma."

    AUTHORS: Abate F, Ambrosio MR, Mundo L, Laginestra MA, Fuligni F, Rossi M, Zairis S, Gazaneo S, De Falco G, Lazzi S, Bellan C, Rocca BJ, Amato T, Marasco E, Etebari M, Ogwang M, Calbi V, Ndede I, Patel K, Chumba D, Piccaluga PP, Pileri S, Leoncini L, Rabadan R.

    PLoS Pathog. 2015 Oct 15;11(10):e1005158. doi: 10.1371/journal.ppat.1005158.

  • “The mutational landscape of CTCL and Sézary syndrome.”

    AUTHORS: Ana Carolina da Silva Almeida*, Francesco Abate*, Hossein Khiabanian, Estela Martinez-Escala, Joan Guitart, Cornelis P. Tensen, Maarten H. Vermeer, Raul Rabadan+, Adolfo Ferrando+ and Teresa Palomero+.

    Nat Genet. 2015 Dec;47(12):1465-70. doi: 10.1038/ng.3442.

    * These authors have contributed equally to this work. +Corresponding authors.

  • “Transcriptomics identify CD9 as a marker of murine IL-10-competent regulatory B cells.”

    AUTHORS: Jianbo Sun, Jiguang Wang, Evangelos Pefanis, Jaime Chao, Gerson Rothschild, Isao Tachibana, Jun Kui Chen, Ivaylo I. Ivanov, Raul Rabadan, Yoshito Takeda, Uttiya Basu.

    Cell Rep. 2015 Nov 10;13(6):1110-7. doi: 10.1016/j.celrep.2015.09.070.

  • “Identification of a new subclass of ALK negative ALCL expressing aberrant levels of ERBB4 transcripts.”

    AUTHORS: Scarfò I, Pellegrino E, Mereu E, Kwee I, Agnelli L, Bergaggio E, Garaffo G, Vitale N, Caputo M, Machiorlatti R, Circosta P, Abate F, Barreca A, Novero D, Mathew S, Rinaldi A, Tiacci E, Serra S, Deaglio S, Neri A, Falini B, Rabadan R, Bertoni F, Inghirami G, Piva R.

    Blood. 2015 Oct 13. pii: blood-2014-12-614503.

  • “Generation of live attenuated influenza virus using codon usage bias.”

    AUTHORS: Fan RL, Valkenburg SA, Wong CK, Li OT, Nicholls JM, Rabadan R, Peiris JS, Poon LL.

    J Virol. 2015 Aug 12; pii: JVI.01443-15.

  • “WE-D-BRB-03: Geometrization of Tumor Evolution.”

    AUTHOR: Raul Rabadan.

    Med Phys. 2015 Jun;42(6):3666. doi: 10.1118/1.4925927.

  • “JAK-STAT in lymphoproliferative disorders.”

    AUTHORS: R. Rabadan, G. Inghirami.

    Oncoscience. 2015 Aug 11;2(9):737-8.

  • “A disease-associated mutation in SRSF2 misregulates splicing by altering RNA binding affinities.”

    AUTHORS: Jian Zhang, Yen K. Lieu, Abdullah M. Ali, Alex Penson, Kathryn S. Reggio, Raul Rabadan, Azra Raza, Siddhartha Mukherjee and James L. Manley.

    PNAS 2015 Aug;112(34):E4726-E4734. doi: 10.1073/pnas.1514105112.

  • “Inference of ancestral recombination graphs through topological data analysis.”

    AUTHORS: P. G. Camara, A. J. Levine and R. Rabadan.

    arXiv 2015 May; arXiv:1505.05815.

  • “RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity.”

    AUTHORS: Evangelos Pefanis*, Jiguang Wang*, Gerson Rothschild*, Junghyun Lim*, David Kazadi, Jianbo Sun, Alexander Federation, Jaime Chao, Oliver Elliott, Zhi-Ping Liu, Aris N. Economides, James E. Bradner, Raul Rabadan+, Uttiya Basu+.

    Cell 2015 May; doi: 10.1016/j.cell.2015.04.034.

    * These authors have contributed equally to this work. +Corresponding authors.

  • “An information theoretic method to identify combinations of genomic alterations that promote glioblastoma.”

    AUTHORS: Rachel D. Melamed, Jiguang Wang, Antonio Iavarone‡, and Raul Rabadan‡.

    Journal of Molecular Cell Biology 2015 May 4; doi: 10.1093/jmcb/mjv026.

    ‡ These authors have contributed equally to this work.

  • “Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes.”

    AUTHORS: Rachel D. Melamed, Kevin J. Emmett, Chioma Madubata, Andrey Rzhetsky, Raul Rabadan.

    Nature Communications 2015 April 30; doi:10.1038/ncomms8033.

  • “Convergent Mutations and Kinase Fusions Lead to Oncogenic STAT3 Activation in Anaplastic Large Cell Lymphoma.”

    AUTHORS: Ramona Crescenzo*, Francesco Abate*, Elena Lasorsa*, Fabrizio Tabbo, Marcello Gaudiano, Nicoletta Chiesa, Filomena Di Giacomo, Elisa Spaccarotella, Luigi Barbarossa, Elisabetta Ercole, Maria Todaro, Michela Boi, Andrea Acquaviva, Elisa Ficarra, Domenico Novero, Andrea Rinaldi, Thomas Tousseyn, Andreas Rosenwald, Lukas Kenner, Lorenzo Cerroni, Alexander Tzankov, Maurilio Ponzoni, Marco Paulli, Dennis Weisenburger, Wing C. Chan, Javeed Iqbal, Miguel A. Piris, Alberto Zamo, Carmela Ciardullo, Davide Rossi, Gianluca Gaidano, Stefano Pileri, Enrico Tiacci, Brunangelo Falini, Leonard D. Shultz, Laurence Mevellec, Jorge E. Vialard, Roberto Piva, Francesco Bertoni, Raul Rabadan‡, Giorgio Inghirami‡.

    Cancer Cell 2015 April 13. doi:10.1016/j.ccell.2015.03.006.

    * These authors have contributed equally to this work. ‡ These authors have contributed equally to this work.

  • “Network propagation reveals novel genetic features predicting drug response of cancer cell lines.”

    AUTHORS: Jiguang Wang*, Judith Kribelbauer*, Raul Rabadan.

    Current Bioinformatics 2015; Vol 11; doi: 10.2174/1574893611666160125222144.

    * These authors have contributed equally to this work.

  • “High-resolution genomic surveillance of 2014 ebolavirus using shared subclonal variants.”

    AUTHORS: Kevin J Emmett, Albert K Lee, Hossein Khiabanian*, Raul Rabadan*.

    PLOS Currents Outbreaks 2015 Feb 9; doi: 10.1371/currents.outbreaks.c7fd7946ba606c982668a96bcba43c90.

    * These authors have contributed equally to this work.

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2014

  • “Darwin, Lamarck, or Baldwin: Applying Evolutionary Algorithms to Machine Learning Techniques.”

    AUTHORS: Holzinger, A.; Blanchard, D.; Bloice, M.; Holzinger, K.; Palade, V.; Rabadan, R.

    Web Intelligence (WI) and Intelligent Agent Technologies (IAT), 2014 IEEE/WIC/ACM International Joint Conferences 2014, Volume: 2 Pages: 449 - 453, DOI: 10.1109/WI-IAT.2014.132

  • “A Targetable GATA2-IGF2 Axis Confers Aggressiveness in Lethal Prostate Cancer.”

    AUTHORS: Samuel J. Vidal, Veronica Rodriguez-Bravo, S. Aidan Quinn, Ruth Rodriguez-Barrueco, Amaia Lujambio, Estrelania Williams, Xiaochen Sun, Janis de la Iglesia-Vicente, Albert Lee, Ben Readhead, Xintong Chen, Matthew Galsky, Berta Esteve, Daniel P. Petrylak, Joel T. Dudley, Raul Rabadan, Jose M. Silva, Yujin Hoshida, Scott W. Lowe, Carlos Cordon-Cardo, Josep Domingo-Domenech.

    Cancer Cell 2014 Nov; doi: http://dx.doi.org/10.1016/j.ccell.2014.11.013.

  • “A novel patient derived tumorgraft model with TRAF1-ALK anaplastic large cell lymphoma translocation.”

    AUTHORS: F Abate, M Todaro, J-A van der Krogt, M Boi, I Landra, R Machiorlatti, F Tabbo, K Messana, A Barreca, D Novero, M Gaudiano, S Aliberti, F Di Giacomo, T Tousseyn, E Lasorsa, R Crescenzo, L Bessone, E Ficarra, A Acquaviva, A Rinaldi, M Ponzoni, D L Longo, S Aime, M Cheng, B Ruggeri, P P Piccaluga, S Pileri, E Tiacci, B Falini, B Pera-Gresely, L Cerchietti, J Iqbal, W C Chan, L D Shultz, I Kwee, R Piva, I Wlodarska, R Rabadan, F Bertoni and G Inghirami the European T-cell Lymphoma Study Group.

    Leukemia 2014 Dec 23; doi: 10.1038/leu.2014.347.

  • “Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia.”

    AUTHORS: Jiguang Wang*, Hossein Khiabanian*, Davide Rossi*, Giulia Fabbri, Valter Gattei, Francesco Forconi, Luca Laurenti, Roberto Marasca, Giovanni Del Poeta, Robin Foà, Laura Pasqualucci, Gianluca Gaidano, Raul Rabadan.

    eLife 2014 Dec 11; doi: 10.7554/eLife.02869.

    * These authors have contributed equally to this work.

  • “Viral diversity and clonal evolution from unphased genomic data.”

    AUTHORS: Hossein Khiabanian, Zachary Carpenter, Jeffrey Kugelman, Joseph Chan, Vladimir Trifonov, Elyse Nagle, Travis Warren, Patrick Iversen, Sina Bavari, Gustavo Palacios and Raul Rabadan.

    BMC Genomics 2014, 15(Suppl 6):S17 doi:10.1186/1471-2164-15-S6-S17.

  • “Transcriptome reconstruction and annotation of cynomolgus and African green monkey.”

    AUTHORS: Albert Lee*, Hossein Khiabanian*, Jeffrey Kugelman, Oliver Elliott, Elyse Nagle, Guo-Yun Yu, Travis Warren, Gustavo Palacios, and Raul Rabadan.

    BMC Genomics 2014, 15:846. doi:10.1186/1471-2164-15-846.

    * These authors have contributed equally to this work.

  • “Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.”

    AUTHORS: Francesco Abate*, Sakellarios Zairis*, Elisa Ficarra, Andrea Acquaviva, Chris H Wiggins, Veronique Frattini, Anna Lasorella, Antonio Iavarone, Giorgio Inghirami and Raul Rabadan.

    BMC Systems Biology 2014 Sept 4. 8:97. doi:10.1186/s12918-014-0097-z.

    * These authors have contributed equally to this work.

  • “Noncoding RNA transcription targets AID to divergently transcribed loci in B cells.”

    AUTHORS: Evangelos Pefanis*, Jiguang Wang*, Gerson Rothschild*, Junghyun Lim, Jaime Chao, Raul Rabadan‡, Aris N. Economides, Uttiya Basu‡.

    Nature 2014 Oct 16;514(7522):389-93. doi: 10.1038/nature13580.

    * These authors have contributed equally to this work. ‡ These authors have contributed equally to this work.

  • “Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis.”

    AUTHORS: Kevin Emmett and Raul Rabadan.

    Lecture Notes in Computer Science (LNCS) 2014. Volume 8609, pp 540-551.

    arXiv:1406.1219.

  • “Moduli Spaces of Phylogenetic Trees Describing Tumor Evolutionary Patterns.”

    AUTHORS: Sakellarios Zairis, Hossein Khiabanian, Andrew Blumberg, and Raul Rabadan.

    Lecture Notes in Computer Science 2014. Volume 8609, pp 528-539. doi: 10.1007/978-3-319-09891-3_48.

    arXiv:1410.0980 [full version].

  • “The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland.”

    AUTHORS: Llobet-Navas D, Rodríguez-Barrueco R, Castro V, Ugalde AP, Sumazin P, Jacob-Sendler D, Demircan B, Castillo-Martín M, Putcha P, Marshall N, Villagrasa P, Chan J, Sanchez-Garcia F, Pe'er D, Rabadán R, Iavarone A, Cordón-Cardó C, Califano A, López-Otín C, Ezhkova E, Silva JM.

    Genes Dev 2014 Apr 1;28(7):765-8.

  • “Network Propagation Reveals Novel Genetic Features Predicting Drug Response of Cancer Cell Lines.”

    AUTHORS: Jiguang Wang, Judith Kribelbauer, and Raul Rabadan.

    M. Basu, Y. Pan, and J. Wang (Eds.): ISBRA 2014, LNBI 8492, pp. 386--386. Springer International Publishing Switzerland (2014).

  • “Data-driven discovery of seasonally linked diseases from an Electronic Health Records system.”

    AUTHORS: R Melamed, H Khiabanian, R Rabadan.

    BMC Bioinformatics 2014. 15(Suppl 6):S3 doi:10.1186/1471-2105-15-S6-S3.

  • “Parametric Inference Using Persistence Diagrams: A Case Study in Population Genetics.”

    AUTHORS: K Emmett, D Rosenbloom, P Camara, R Rabadan.

    International Conference on Machine Learning (ICML) Workshop on Topological Methods in Machine Learning June 2014.

    arXiv:1406.4582

  • “Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness.”

    AUTHORS: Monica Messina, Ilaria Del Giudice, Hossein Khiabanian, Davide Rossi, Sabina Chiaretti, Silvia Rasi, Valeria Spina, Antony B. Holmes, Marilisa Marinelli, Giulia Fabbri, Alfonso Piciocchi, Francesca R. Mauro, Anna Guarini, Gianluca Gaidano, Riccardo Dalla-Favera, Laura Pasqualucci, Raul Rabadan, and Robin Foà.

    Blood Prepublished online 2014 Feb 18. doi:10.1182/blood-2013-10-534271.

  • “Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia.”

    AUTHORS: Rossi D*, Khiabanian H*, Spina V, Ciardullo C, Bruscaggin A, Famà R, Rasi S, Monti S, Deambrogi C, De Paoli L, Wang J, Gattei V, Guarini A, Foà R, Rabadan R, Gaidano G.

    Blood Prepublished online 2014 Feb 5. doi:10.1182/blood-2013-11-539726.

    * These authors have contributed equally to this work.

  • “Leukaemogenesis induced by an activating β-catenin mutation in osteoblasts.”

    AUTHORS: Aruna Kode, John S. Manavalan, Ioanna Mosialou, Govind Bhagat, Chozha V. Rathinam, Na Luo, Hossein Khiabanian, Albert Lee, Vundavalli V. Murty, Richard Friedman, Andrea Brum, David Park, Naomi Galili, Siddhartha Mukherjee, Julie Teruya-Feldstein, Azra Raza, Raul Rabadan, Ellin Berman, Stavroula Kousteni.

    Nature 2014 Jan 15. doi:10.1038/nature12883.

  • “Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas.”

    AUTHORS: Palomero T*, Couronné L*, Khiabanian H*, Kim MY, Ambesi-Impiombato A, Perez-Garcia A, Carpenter Z, Abate F, Allegretta M, Haydu JE, Jiang X, Lossos IS, Nicolas C, Balbin M, Bastard C, Bhagat G, Piris MA, Campo E, Bernard OA, Rabadan R‡, Ferrando AA‡.

    Nat Genet. 2014 Feb;46(2):166-70. doi: 10.1038/ng.2873.

    * These authors have contributed equally to this work. ‡ These authors have contributed equally to this work.

  • “Genetics of Follicular Lymphoma Transformation.”

    AUTHORS: Pasqualucci L, Khiabanian H, Fangazio M, Vasishtha M, Messina M, Holmes AB, Ouillette P, Trifonov V, Rossi D, Tabbò F, Ponzoni M, Chadburn A, Murty VV, Bhagat G, Gaidano G, Inghirami G, Malek SN, Rabadan R, Dalla-Favera R.

    Cell Rep. 2014 Jan 2. pii: S2211-1247(13)00785-7. doi: 10.1016/j.celrep.2013.12.027.

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2013

  • “SAVI: a statistical algorithm for variant frequency identification.”

    AUTHORS: Vladimir Trifonov, Laura Pasqualucci, Enrico Tiacci, Brunangelo Falini, Raul Rabadan.

    BMC Systems Biology 2013 Oct 14. doi: 10.1186/1752-0509-7-S2-S2.

  • “Topology of viral evolution.”

    AUTHORS: Chan JM, Carlsson G, Rabadan R.

    Proc Natl Acad Sci USA 2013 Oct 29. doi: 10.1073/pnas.1313480110.

  • “Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome.”

    AUTHORS: Giulia Fabbri*, Hossein Khiabanian*, Antony B. Holmes, Jiguang Wang, Monica Messina, Charles G. Mullighan, Laura Pasqualucci, Raul Rabadan‡, and Riccardo Dalla-Favera‡.

    The Journal of Experimental Medicine 2013 Oct 14. doi: 10.1084/jem.20131448.

    * These authors have contributed equally to this work. ‡ These authors have contributed equally to this work.

  • “A nondegenerate code of deleterious variants in mendelian Loci contributes to complex disease risk.”

    AUTHORS: Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, White KP, Rzhetsky A.

    Cell. 2013 Sep 26;155(1):70-80. doi: 10.1016/j.cell.2013.08.030.

  • “E3-ubiquitin ligase Nedd4 determines the fate of AID-associated RNA polymerase II in B cells.”

    AUTHORS: Sun J, Keim CD, Wang J, Kazadi D, Oliver PM, Rabadan R, Basu U.

    Genes Dev. 2013 Aug 15;27(16):1821-33. doi: 10.1101/gad.210211.112.

  • “The integrated landscape of driver genomic alterations in glioblastoma.”

    AUTHORS: Frattini V, Trifonov V, Chan JM, Castano A, Lia M, Abate F, Keir ST, Ji AX, Zoppoli P, Niola F, Danussi C, Dolgalev I, Porrati P, Pellegatta S, Heguy A, Gupta G, Pisapia DJ, Canoll P, Bruce JN, McLendon RE, Yan H, Aldape K, Finocchiaro G, Mikkelsen T, Privé GG, Bigner DD, Lasorella A*, Rabadan R*, Iavarone A*.

    Nature Genetics 2013 Aug 05. doi:10.1038/ng.2734.

    * These authors have contributed equally to this work.

  • “Beyond NPM-anaplastic lymphoma kinase driven lymphomagenesis: alternative drivers in anaplastic large cell lymphoma.”

    AUTHORS: Tabbò F, Ponzoni M, Rabadan R, Bertoni F, Inghirami G; European T-cell Lymphoma Study Group.

    Current Opinion in Hematology 2013 Jul;20(4):374-81. doi: 10.1097/MOH.0b013e3283623c07.

  • “MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples.”

    AUTHORS: Trifonov V, Pasqualucci L, Dalla Favera R, Rabadan R.

    BMC Systems Biology 2013 Mar 25;7:25. doi: 10.1186/1752-0509-7-25.

  • “Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL.”

    AUTHORS: Tzoneva G*, Perez-Garcia A*, Carpenter Z*, Khiabanian H, Tosello V, Allegretta M, Paietta E, Racevskis J, Rowe J, Tallman M, Paganin M, Basso G, Hof J, Kirschner-Schwabe R, Palomero T‡, Rabadan R‡, Ferrando A.‡

    Nature Medicine 2013 February 03. doi:10.1038/nm.3078.

    * These authors have contributed equally to this work. ‡ These authors have contributed equally to this work.

  • “Quantifying Pathogen Surveillance Using Temporal Genomic Data.”

    AUTHORS: Joseph Chan, Raul Rabadan.

    mBio 2013 January 29;4(1). doi: 10.1128/mBio.00524-12.

  • “Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia.”

    AUTHORS: Rossi D, Rasi S, Spina V, Bruscaggin A, Monti S, Ciardullo C, Deambrogi C, Khiabanian H, Serra R, Bertoni F, Forconi F, Laurenti L, Marasca R, Dal-Bo M, Rossi FM, Bulian P, Nomdedeu J, Del Poeta G, Gattei V, Pasqualucci L, Rabadan R, Foà R, Dalla-Favera R, Gaidano G.

    Blood 2013 Feb 21;121(8):1403-12. doi: 10.1182/blood-2012-09-458265.

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2012

  • “GAB2 induces tumor angiogenesis in NRAS-driven melanoma.”

    AUTHORS: Yang Y, Wu J, Demir A, Castillo-Martin M, Melamed RD, Zhang G, Fukunaga-Kanabis M, Perez-Lorenzo R, Zheng B, Silvers DN, Brunner G, Wang S, Rabadan R, Cordon-Cardo C, Celebi JT.

    Oncogene 2012 Aug 27. doi: 10.1038/onc.2012.367.

  • “The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development.”

    AUTHORS: Davide Rossi*, Vladimir Trifonov*, Marco Fangazio*, Alessio Bruscaggin, Silvia Rasi, Valeria Spina, Sara Monti, Tiziana Vaisitti, Francesca Arruga, Rosella Famà, Carmela Ciardullo, Mariangela Greco, Stefania Cresta, Daniela Piranda, Antony Holmes, Giulia Fabbri, Monica Messina, Andrea Rinaldi, Jiguang Wang, Claudio Agostinelli, Pier Paolo Piccaluga, Marco Lucioni, Fabrizio Tabbò, Roberto Serra, Silvia Franceschetti, Clara Deambrogi, Giulia Daniele, Valter Gattei, Roberto Marasca, Fabio Facchetti, Luca Arcaini, Giorgio Inghirami, Francesco Bertoni, Stefano A. Pileri, Silvia Deaglio, Robin Foà, Riccardo Dalla-Favera‡, Laura Pasqualucci‡, Raul Rabadan‡, and Gianluca Gaidano‡.

    The Journal of Experimental Medicine 2012 August. doi: 10.1084/jem.20120904.

    * These authors have contributed equally to this work. ‡ These authors have contributed equally to this work.

  • “Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma.”

    AUTHORS: Devendra Singh*, Joseph Minhow Chan*, Pietro Zoppoli*, Francesco Niola*, Ryan Sullivan, Angelica Castano, Eric Minwei Liu, Jonathan Reichel, Paola Porrati, Serena Pellegatta, Kunlong Qiu, Zhibo Gao, Michele Ceccarelli, Riccardo Riccardi, Daniel J. Brat, Abhijit Guha, Ken Aldape, John G. Golfinos, David Zagzag, Tom Mikkelsen, Gaetano Finocchiaro, Anna Lasorella‡, Raul Rabadan‡, Antonio Iavarone‡.

    Science 2012 10.1126/science.1220834.

    * These authors have contributed equally to this work. ‡ These authors have contributed equally to this work.

  • “Emergence of Fatal Avian Influenza in New England Harbor Seals.”

    AUTHORS: S. J. Anthony*, J. A. St. Leger, K. Pugliares, H. S. Ip, J. M. Chan, Z. W. Carpenter, I. Navarrete-Macias, M. Sanchez-Leon, J. T. Saliki, J. Pedersen, W. Karesh, P. Daszak, R. Rabadan*, T. Rowles, and W. I. Lipkin*.

    mBio 2012 July 31;3(4). doi: 10.1128/mBio.00166-12.

    * Corresponding authors.

  • “How many neutrophils are enough (redux, redux)?”

    AUTHORS: Silverstein SC, Rabadan R.

    J Clin Invest. 2012 Jul 23:1-4.

  • “Drug-drug interaction through molecular structure similarity analysis.”

    AUTHORS: Vilar S, Harpaz R, Uriarte E, Santana L, Rabadan R, Friedman C.

    J Am Med Inform Assoc. 2012 May 30.

  • “Promotion of Hepatocellular Carcinoma by the Intestinal Microbiota and TLR4.”

    AUTHORS: Dapito D H, Mencin A, Gwak G Y, Pradere J P, Jang M K, Mederacke I, Caviglia J M, Khiabanian H, Adeyemi A, Bataller R, Lefkowitch J H, Bower M, Friedman R, Sartor R B, Rabadan R, Schwabe R F.

    Cancer Cell 2012 April 17;21(4):504-516.

  • “Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia.”

    AUTHORS: Ntziachristos P, Tsirigos A, Van Vlierberghe P, Nedjic J, Trimarchi T, Sol Flaherty M, Ferres-Marco D, da Ros V, Tang Z, Siegle J, Asp P, Hadler M, Rigo I, De Keersmaecker K, Patel J, Huynh T, Utro F, Poglio S, Samon J B, Paietta E, Racevskis J, Rowe J, Rabadan R, Levine R L, Brown S, Pflumio F, Dominguez M, Ferrando A, Aifantis I.

    Nature Medicine 2012 Jan. doi:10.1038/nm.2651. Epublication ahead of print.

  • “Viral Reassortment as an information exchange between viral segments.”

    AUTHORS: Greenbaum B, Li O, Poon L, Levine A, Rabadan R.

    PNAS 2012 Published online before print. doi:10.1073/pnas.1113300109.

  • “Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia.”

    AUTHORS: Rossi D, Rasi S, Fabbri G, Spina V, Fangazio M, Forconi F, Marasca R, Laurenti L, Bruscaggin A, Cerri M, Monti S, Cresta S, Famà R, De Paoli L, Bulian P, Gattei V, Guarini A, Deaglio S, Capello D, Rabadan R, Pasqualucci L, Dalla-Favera R, Foà R, Gaidano G.

    Blood 2012 Jan 12;119(2):521-529. doi:10.1182/blood-2011-09-379966.

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2011

  • “Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness.”

    AUTHORS: Rossi D, Bruscaggin A, Spina V, Rasi S, Khiabanian H, Messina M, Fangazio M, Vaisitti T, Monti S, Chiaretti S, Guarini A, Del Giudice I, Cerri M, Cresta S, Deambrogi C, Gargiulo E, Gattei V, Forconi F, Bertoni F, Deaglio S, Rabadan R, Pasqualucci L, Foà R, Dalla-Favera R, Gaidano G.

    Blood 2011 Dec 22;118(26):6904-6908.

  • “Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis.”

    AUTHORS: Vilar S, Harpaz R, Chase HS, Costanzi S, Rabadan R, Friedman C.

    J Am Med Inform Assoc 2011 Dec;18 Suppl 1:i73-i80.

  • “Whole-exome sequencing identifies mutations of BCOR in acute myeloid leukemia with normal karyotype.”

    AUTHORS: Grossmann V, Tiacci E, Holmes AB, Kohlmann A, Martelli MP, Kern W, Spanhol-Rosseto A, Klein HU, Dugas M, Schindela S, Trifonov V, Schnittger S, Haferlach C, Bassan R, Wells VA, Spinelli O, Chan J, Rossi R, Baldoni S, De Carolis L, Goetze K, Serve H, Peceny R, Kreuzer KA, Oruzio D, Specchia G, Di Raimondo F, Fabbiano F, Sborgia M, Liso A, Farinelli L, Rambaldi A, Pasqualucci L, Rabadan R, Haferlach T, Falini B.

    Blood 2011 Dec 1:118(23):6153-6163.

  • “Analysis of the coding genome of diffuse large B-cell lymphoma.”

    AUTHORS: Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliott O, Chan J, Bhagat G, Chadburn A, Gaidano G, Mullighan CG, Rabadan R, Dalla-Favera R.

    Nature Genetics 2011 Jul 31;43(9):830-7.

  • “Discovering disease associations by integrating electronic clinical data and medical literature.”

    AUTHORS: Holmes A B, Hawson A, Liu F, Friedman C, Khiabanian H, Rabadan R.

    PLoS One 2011;6(6):e21132. doi:10.1371/journal.pone.0021132.

  • “BRAF Mutations in Hairy-Cell Leukemia.”

    AUTHORS: Tiacci E, Trifonov V, Schiavoni G, Holmes A, Kern W, Martelli MP, Pucciarini A, Bigerna B, Pacini R, Wells VA, Sportoletti P, Pettirossi V, Mannucci R, Elliott O, Liso A, Ambrosetti A, Pulsoni A, Forconi F, Trentin L, Semenzato G, Inghirami G, Capponi M, Di Raimondo F, Patti C, Arcaini L, Musto P, Pileri S, Haferlach C, Schnittger S, Pizzolo G, Foà R, Farinelli L, Haferlach T, Pasqualucci L, Rabadan R*, Falini B*.

    The New England Journal of Medicine 2011 Jun 16;364(24):2305-15.

    * These authors have contributed equally to this work.

  • “BRAF Mutations in Hairy-Cell Leukemia (reply).”

    AUTHORS: Tiacci E, Rabadan R, Falini B.

    The New England Journal of Medicine 2011 Jun 16;365(10):961-962.

  • “Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation.”

    AUTHORS: Fabbri G, Rasi S, Rossi D, Trifonov V, Khiabanian H, Ma J, Grunn A, Fangazio M, Capello D, Monti S, Cresta S, Gargiulo E, Forconi F, Guarini A, Arcaini L, Paulli M, Laurenti L, Larocca LM, Marasca R, Gattei V, Oscier D, Bertoni F, Mullighan CG, Foá R, Pasqualucci L*, Rabadan R*, Dalla-Favera R*, Gaidano G*.

    The Journal of Experimental Medicine 2011 Jun 13;208:1389-1401.

    * These authors have contributed equally to this work.

  • “Identifying Hosts of Families of Viruses: A Machine Learning Approach.”

    “Identifying Hosts of Families of Viruses: A Machine Learning Approach.”AUTHORS: Raj A, Dewar M, Palacios G, Rabadan R, Wiggins C H.

    PLoS ONE 2011; 6(12): e27631. doi:10.1371/journal.pone.0027631.

  • “Oligonucleotide Motifs That Disappear During the Evolution of Influenza in Humans Increase IFN-alpha secretion by Plasmacytoid Dendritic Cells.”

    AUTHORS: Jimenez-Baranda S, Greenbaum B, Manches O, Handler J, Rabadan R, Levine A, Bhardwaj N.

    J Virol April 2011;85(8):3893-3904.

  • “Understanding the Origins of a Pandemic Virus.”

    AUTHORS: Hernandez C X, Chan J, Khiabanian H, Rabadan R

    2011 arXiv:1104.4568.

    Columbia University Academic Commons, AC:P:9893.

  • “Inactivating mutations of acetyltransferase genes in B-cell lymphoma.”

    AUTHORS: Pasqualucci L, Dominguez-Sola D, Chiarenza A, Fabbri G, Grunn A, Trifonov V, Kasper LH, Lerach S, Tang H, Ma J, Rossi D, Murty V, Mullighan C, Gaidano G, Rabadan R, Brindle P, Dalla-Favera R.

    Nature 2011 March 10;471(7337):189–195.

  • “Biclustering of Adverse Drug Events in FDA’s Spontaneous Reporting System.”

    AUTHORS: Harpaz R, Perez H, Chase H S, Rabadan R, Hripcsak G, Friedman C

    Nature Clinical Pharmacology & Therapeutics 2011 Feb;89(2):243-50.

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2006-2010

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1999-2005