Publications

2019
The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Raul Rabadan and Andrew J. Blumberg.
Cambridge University Press. 2019. ISBN-13: 978-1107159549.

arcasHLA: high resolution HLA typing from RNAseq.
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.
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.
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.
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.
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.
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.
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.
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.

2018
Phf6 loss enhances HSC self-renewal driving tumor initiation and leukemia stem cell activity in T-ALL.
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.

Dose-response modeling in high-throughput cancer drug screenings: A case study with recommendations for practitioners.
Wesley Tansey, Kathy Li, Haoran Zhang, Scott W Linderman, Raul Rabadan, David M Blei, Chris H Wiggins
arXiv preprint. 2018 Dec 13. arXiv:1812.05691

Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

2017
Repurposing Dasatinib for Ibrutinib-Resistant Diffuse Large B-Cell Lymphoma.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

2016
Evolutionary scalpels for dissecting tumor ecosystems.
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.
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.
Lorin Crawford, Anthea Monod, Andrew X. Chen, Sayan Mukherjee, Raúl Rabadán.
arXiv. 2016 November. arXiv:1611.06818 [stat.AP].

A Theory of Taxonomy.
Guido D'Amico, Raul Rabadan, Matthew Kleban.
arXiv. 2016 November. arXiv:1611.03890 [physics.soc-ph].

The genetics of nodal marginal zone lymphoma.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

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.
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.
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.
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.
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.
Kevin Emmett and Raul Rabadan.
BICT 2015 (Accepted).
arXiv:1511.01429 [q-bio.QM].

Multiscale Topology of Chromatin Folding.
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.
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.
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.
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.
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.
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.
Raul Rabadan.
Med Phys. 2015 Jun;42(6):3666. doi: 10.1118/1.4925927.

JAK-STAT in lymphoproliferative disorders.
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.
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.
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.
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.
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.
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.
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.
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.
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.

2014
Darwin, Lamarck, or Baldwin: Applying Evolutionary Algorithms to Machine Learning Techniques.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

2013
SAVI: a statistical algorithm for variant frequency identification.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

2012
GAB2 induces tumor angiogenesis in NRAS-driven melanoma.
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.
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.
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.
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)?
Silverstein SC, Rabadan R.
J Clin Invest. 2012 Jul 23:1-4.

Drug-drug interaction through molecular structure similarity analysis.
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.
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.
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.
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.
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.

2011
Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness.
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.
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.
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.
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.
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.
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).
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.
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.
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.
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.
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.
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.
Harpaz R, Perez H, Chase H S, Rabadan R, Hripcsak G, Friedman C
Nature Clinical Pharmacology & Therapeutics 2011 Feb;89(2):243-50.

2010
Genome-Wide Analysis Reveals Frequent Inactivating Mutations of Acetyltransferase Genes In B-Cell Lymphoma.
Pasqualucci L, Dominguez-Sola D, Chiarenza A, Fabbri G, Grunn A, Trifonov V, Kasper L H, Lerach S, Jing M, Rossi D, Mullighan C, Gaidano G, Rabadan R, Brindle P K, and Dalla-Favera R.
Blood (ASH Annual Meeting Abstracts) Nov 2010;116:474.

The Genome of Chronic Lymphocytic Leukemia.
Fabbri G, Trifonov V, Rossi D, Elliott O, Chan J M, Rinaldi A, Kwee I, Bertoni F, Gaidano G, Pasqualucci L, Rabadan R, and Dalla-Favera R.
Blood (ASH Annual Meeting Abstracts) Nov 2010;116:51.

Network Analysis of Global Influenza Spread.
Chan J, Holmes A, Rabadan R.
PLoS Comput Biol 2010;6(11):e1001005. doi:10.1371/journal.pcbi.1001005.

Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data.
Trifonov V, Pascualucci L, Dalla-Favera R, Rabadan R.
Nature Preceedings <http://dx.doi.org/10101/npre.2010.5037.1>
2010 arXiv:1010.4328v1.

Frequency Analysis Techniques for the Identification of Viral Genetic Data.
Vladimir Trifonov, Raul Rabadan.
mBio 2010 Aug 24;1(3):e00156-10.

Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus.
Wong EH, Smith DK, Rabadan R, Peiris M, Poon LL.
BMC Evol Biol 2010 Aug 19;10:253

Young and Early Career Investigators: Report from a Global HIV Vaccine Enterprise Working Group.
Dan H Barouch, Thumbi Ndung’u, Galit Alter, Timothy Cardozo, Bhavna Chohan, Jacques Fellay, Nicole Frahm, Jonathan Fuchs, Al Leslie, Yong Liu, Penny Moore, Raul Rabadan.
Nature Preceedings Sept 2010; doi:10.1038/npre.2010.4800.2

Signs of the 2009 Influenza Pandemic in the New York-Presbyterian Electronic Health Records.
Hossein Khiabanian, Antony B Holmes, Brendan J Kelly, Mrinalini Gururaj, George Hripcsak, Raul Rabadan.
PLoS One 2010;5(9):e12658. doi:10.1371/journal.pone.0012658.

Heart and skeletal muscle inflammation of farmed salmon is associated with infection with a novel reovirus.
Gustavo Palacios, Marie Lovoll, Torstein Tengs, Mady Hornig, Stephen Hutchison, Jeffrey Hui, Ruth-Torill Kongtorp, Nazir Savji, Ana Bussetti, Alexander Solovyov, Anja Kristoffersen, Christopher Celone, Craig Street, Vladimir Trifonov, David Hirshberg, Raul Rabadan, Michael Egholm, Espen Rimstad, W. Ian Lipkin.
PLoS One 2010;5(7):e11487. doi:10.1371/journal.pone.0011487.

ParMap, an Algorithm for the Identification of Complex Genomic Variations in Nextgen Sequencing Data.
Hossein Khiabanian, Pieter Van Vlierberghe, Teresa Palomero, Adolfo A. Ferrando, Raul Rabadan.
BMC Research Notes 2010 May 27;3(1):147.

Differential levels of transcription of p53-regulated genes by the arginine/proline polymorphism: p53 with arginine at codon 72 favors apoptosis.
Jeong B S, Hu W, Belyi V, Rabadan R, Levine A.
FASEB J 2010 May;24(5):1347-53.

PHF6 mutations in T-cell acute lymphoblastic leukemia.
Van Vlierberghe P, Palomero T, Khiabanian H, Van der Meulen J, Castillo M, Van Roy N, De Moerloose B, Philippé J, González-García S, Toribio M, Taghon T, Zuurbier L, Cauwelier B, Harrison C, Schwab C, Pisecker M, Strehl S, Langerak A, Gecz J, Sonneveld E, Pieters R, Paietta E, Rowe J, Wiernik P, Benoit Y, Soulier J, Poppe B, Yao X, Cordon-Cardo C, Meijerink J, Rabadan R, Speleman F, Ferrando A.
Nature Genetics 2010 March 14;42:338–342.

Molecular characterization of severe and mild cases of influenza A (H1N1) 2009 strain from Argentina.
Baumeister E, Palacios G, Cisterna D, Solovyov A, Hui J, Savji N, Bussetti A V, Campos A, Pontoriero A, Jabado O J, Street C, Hirschberg D L, Rabadan R, Alonio V, Molina V, Hutchison S, Egholm M, Lipkin W I.
Medicina (B Aires) 2010;70(6):518-23.

Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Pandemic Influenza.
Alexander Solovyov, Benjamin Greenbaum, Gustavo Palacios, W. Ian Lipkin, Raul Rabadan.
PLoS Currents 2010 Jan 29;2:RRN1147. doi:10.1371/currents.RRN1147.

2009
Next Generation Syndromic Surveillance: Molecular Epidemiology, Electronic Health Records and the Pandemic Influenza A (H1N1) Virus.
Raul Rabadan, Farzad Mostashari, Neil Calman, George Hripcsak.
PLoS Currents 2009 Aug 22;1:RRN1012. doi:10.1371/currents.RRN1012.

The Contribution of the PB1-F2 Protein to the Fitness of Influenza A Viruses and its Recent Evolution in the 2009 Influenza A (H1N1) Pandemic Virus.
Vladimir Trifonov, Vincent Racaniello, Raul Rabadan.
PLoS Currents 2009 Aug 21;1:RRN1006. doi:10.1371/currents.RRN1006.

Geographic Dependence, Surveillance, and Origins of the 2009 Influenza A (H1N1) Virus.
Trifonov V, Khiabanian H, Rabadan R.
The New England Journal of Medicine 2009 Jul 9;361(2):115–119.

Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA Identify Mediators of the Host Innate Immune System.
Greenbaum B, Rabadan R, Levine A.
PLoS One 2009 Jun 18;4(6):e5969. doi:10.1371/journal.pone.0005969.

Cluster Analysis of the Origin of the New Influenza A(H1N1).
A Solovyov, G Palacios, T Briese, W I Lipkin, R Rabadan.
Eurosurveillance 2009 May 28;14(21).

The origin of the recent swine influenza A(H1N1) virus infecting humans.
Trifonov V, Khiabanian H, Greenbaum B, Rabadan R.
Eurosurveillance 2009 April 30;14(17).

Differences in Patient Age Distribution between Influenza A Subtypes.
Khiabanian H, Farrell G, St. George K, Rabadan R.
PLoS One 2009;4(8):e6832. doi:10.1371/journal.pone.0006832.

Reassortment patterns in Swine influenza viruses.
Khiabanian H, Trifonov V, Rabadan R.
PLoS One 2009 Oct 7;4(10):e7366. doi:10.1371/journal.pone.0007366.

The Emergence of 2009 H1N1 Pandemic Influenza.
Greenbaum B, Trifonov V, Khiabanian H, Levine A, Rabadan R.
Rappuoli R, Del Giudice G (eds): Influenza Vaccines for the Future. Birkhaeuser, 2009.

Spectral Signatures of Photon-Particle Oscillations from Celestial Objects.
Doron Chelouche, Raul Rabadan, Sergey Pavlov, Francisco Castejon.
The Astrophysical Journal Supplement 2009;180(1):1-29. doi:10.1088/0067-0049/180/1/1.
arXiv:0806.0411v1.

2008
A recoding method to improve the humoral immune response to an HIV DNA vaccine.
Huang Y, Krasnitz M, Rabadan R, Witten D M, Song Y, Levine A J, Ho D D, Robins H.
PLoS One 2008;3(9):e3214. doi:10.1371/journal.pone.0003214.

Spectroscopic Constraints on (pseudo-)Scalar Particles from Compact Astrophysical Objects.
Doron Chelouche, Raul Rabadan, Sergey Pavlov, Francisco Castejon.
Proceedings for the 4th Patras Workshop on Axions, WIMPs and WISPs.
2008 arXiv:0810.3009v1.

Anomalies in the Influenza Genome Database: New Biology or Lab Errors?
Michael Krasnitz, Arnold Levine, Raul Rabadan.
J Virol 2008 Sept;82(17):8947–8950. doi:10.1128/JVI.00101-08.

Mitochondrial DNA Haplogroup D4a is a Marker for Extreme Longevity in Japan.
E Bilal, R Rabadan, G Alexe, N Fuku, H Ueno, Y Nishigaki, Y Fujita, M Ito, Y Arai, N Hirose, A Ruckenstein, G Bhanot, M Tanaka.
PLoS One 2008 Jun 11;3(6):e2421. doi:10.1371/journal.pone.0002421.

Patterns of Evolution and Host Gene Mimicry in Influenza and other RNA Viruses.
B.Greenbaum, Arnold J. Levine, Gyan Bhanot, Raul Rabadan.
PLoS Pathog 2008 Jun;4(6):e1000079. doi:10.1371/journal.ppat.1000079.

An information-theoretic analysis of genetics, gender and age in cancer patients.
Gurinder Singh Atwal, Raul Rabadan, Guillermina Lozano, Louise C Strong, Mariëlle W G Ruijs, Marjanka K Schmidt, Laura J van't Veer, Heli Nevanlinna, Johanna Tommiska, Kristiina Aittomäki, Gaelle Bougeard, Thierry Frebourg, Arnold J Levine, Gareth L Bond.
PLoS One 2008 Apr 9;3(4):e1951. doi:10.1371/journal.pone.0001951.

Highly Conserved Regions of Influenza A Virus Polymerase Gene Segments Are Critical for Efficient Viral RNA Packaging.
Glenn A Marsh, Raul Rabadan, Arnold J Levine, Peter Palese.
J Virol 2008 March;82(5):2295-2304.

Non-random reassortment in human influenza A viruses.
Raul Rabadan, Arnold Levine, Michael Krasnitz.
Influenza and Other Respiratory Viruses 2008 Jan;2(1):9-22.

2007
Evolution of the Influenza A Virus: Some New Advances.
Rabadan R, Robins H.
Evolutionary Bioinformatics Online 2007;3:299–307.

2006
Comparison of Avian and Human Influenza A Viruses Reveals a Mutational Bias on the Viral Genomes.
Rabadan R, Levine A, Robins H.
J Virol 2006 Dec;80(23):11887-91.

Photon regeneration from pseudoscalars at X-ray laser facilities.
Raul Rabadan, Andreas Ringwald, Kris Sigurdson.
Phys. Rev. Lett. 2006;96(11):110407. doi:10.1103/PhysRevLett.96.110407.

2005
Constraints on light pseudoscalars from colliders and photonregeneration experiments in X-ray facilities.
Raul Rabadan.
2005 http://arxiv.org/abs/hep-ph/0511103.

Collider bounds on pseudoscalars coupling to gauge bosons.
Matthew Kleban, Raul Rabadan.
2005 arXiv:hep-ph/0510183v2.

Non-perturbative orientifold transitions at the conifold.
Kentaro Hori, Kazuo Hosomichi, David C Page, Raul Rabadan, Johannes Walcher.
Journal of High Energy Physics 2005;0510:026.
arXiv:hep-th/0506234v2.

Stability in asymptotically AdS spaces.
Kleban M, Porrati M, Rabadan R.
Journal of High Energy Physics 2005;0508:016.
arXiv:hep-th/0409242v1.

2004
Poincare recurrences and topological diversity.
Kleban M, Porrati M, Rabadan R.
Journal of High Energy Physics 2004;0410:030.
arXiv:hep-th/0407192v2.

Boundary rigidity and holography.
Porrati M, Rabadan R.
Journal of High Energy Physics 2004;0401:034.
arXiv:hep-th/0312039v2.

On bouncing brane worlds, S-branes and branonium cosmology.
C P Burgess, F Quevedo, R Rabadan, G Tasinato, I Zavala.
Journal of Cosmology and Astroparticle Physics 2004;0402:008.
arXiv:hep-th/0310122v2.

D-brane chemistry.
C P Burgess, N E Grandi, F Quevedo, R Rabadan.
Journal of High Energy Physics 2004;0401:067.
arXiv:hep-th/0310010v2.

2003
Branonium.
C P Burgess, P Martineau, F Quevedo, R Rabadan.
Journal of High Energy Physics 2003;0306:037.
arXiv:hep-th/0303170v1.

(Re)constructing dimensions.
Raul Rabadan, Gary Shiu.
Journal of High Energy Physics 2003;0305:045.
arXiv:hep-th/0212144v2.

2002
Dilaton tadpoles and D-brane interactions in compact spaces.
Raul Rabadan, Frederic Zamora.
Journal of High Energy Physics 2002;0212:052.
arXiv:hep-th/0207178v3.

Complex structure moduli stability in toroidal compactifications.
Juan Garcia-Bellido, Raul Rabadan.
Journal of High Energy Physics 2002;0205:042.
arXiv:hep-th/0203247v2.

M theory lift of brane anti-brane systems and localized closed string tachyons.
Raul Rabadan, Joan Simon.
Journal of High Energy Physics 2002;0205:045.
arXiv:hep-th/0203243v2.

Inflationary scenarios from branes at angles.
Juan Garcia-Bellido, Raul Rabadan, Frederic Zamora.
Journal of High Energy Physics 2002;0201:036.
arXiv:hep-th/0112147v2.

Branes at angles, torons, stability and supersymmetry.
Rabadan R.
Nuclear Physics B 2002;620(1-2):152-180.
arXiv:hep-th/0107036v3.

2001
Getting just the standard model at intersecting branes.
Luis E Ibanez, F Marchesano, R Rabadan.
Journal of High Energy Physics 2001;0111:002.
arXiv:hep-th/0105155v2.

D=4 Chiral String Compactifications from Intersecting Branes.
G Aldazabal, S Franco, Luis E Ibanez, R Rabadan, A M Uranga.
Journal of Mathematical Physics 2001;42:3103-3126.
arXiv:hep-th/0011073v3.

Intersecting Brane Worlds.
G Aldazabal, S Franco, Luis E Ibanez, R Rabadan, A M Uranga.
Journal of High Energy Physics 2001;0102:047.
arXiv:hep-ph/0011132v3.

Type IIB Orientifolds without Untwisted Tadpoles, and non-BPS D-branes.
R Rabadan, A M Uranga.
Journal of High Energy Physics 2001;0101:029.
arXiv:hep-th/0009135v2.

D = 4, N=1 orientifolds with vector structure.
Matthias Klein, Raul Rabadan.
Nuclear Physics B 2001;596(1-2):197-230.
arXiv:hep-th/0007087v2.

2000
Z(N) x Z(M) orientifolds with and without discrete torsion.
Matthias Klein, Raul Rabadan.
Journal of High Energy Physics 2000;0010:049.
arXiv:hep-th/0008173v2.

Orientifolds with discrete torsion.
Mathias Klein, Raul Rabadan.
Journal of High Energy Physics 2000;0007:040.
arXiv:hep-th/0002103v2.

Orientifolding the conifold.
J Park, R Rabadan, A M Uranga.
Nuclear Physics B 2000;570(1-2):38-80.
arXiv:hep-th/9907086v2.

N=1 type IIA brane configurations, chirality and T duality.
J Park, R Rabadan, A M Uranga.
Nuclear Physics B 2000;570(1-2):3-37.
arXiv:hep-th/9907074v2.

Sigma model anomalies in compact D = 4, N=1 type IIB orientifolds and Fayet-Iliopoulos terms.
Luis E Ibanez, R Rabadan, A M Uranga.
Nuclear Physics B 2000;576(1-3):285-312.
arXiv:hep-th/9905098v1.

1999
Anomalous U(1)’s in type I and type IIB D = 4, N=1 string vacua.
Luis E Ibanez, R Rabadan, A M Uranga.
Nuclear Physics B 1999;542(1-2):112-138.
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