Publications

2018
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

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

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

2017
Clonal Evolution Mechanisms and Collateral Sensitivity to Impdh Inhibitor Therapy in Relapsed Lymphoblastic Leukemia
Chelsea Dieck, Gannie Tzoneva, Koichi Oshima, Alberto Ambesi-Impiombato, Marta Sanchez-Martin, Maria Luisa Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Julie M Gastier-Foster, Mignon L Loh, Renate Kirschner-Schwabe, Chioma Madubata, Raul Rabadan, Adolfo A Ferrando

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

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.

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.

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

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

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

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.

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.

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.

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

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.

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.

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.

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.

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.

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+.
* 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

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.

2016
Evolutionary scalpels for dissecting tumor ecosystems.
Daniel I.S. Rosenbloom , Pablo G. Camara, Tim Chu, Raul Rabadan.

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.

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.

A Theory of Taxonomy.
Guido D'Amico, Raul Rabadan, Matthew Kleban.

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.

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.

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+.
* 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.

Genomic data analysis in tree spaces.
Sakellarios Zairis, Hossein Khiabanian, Andrew J. Blumberg, Raul Rabadan.

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.

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.

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.

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.

Reprogramming eukaryotic translation with ligand-responsive synthetic RNA switches.
Anzalone AV, Lin AJ, Zairis S, Rabadan R, Cornish VW.

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.

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.

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.

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.

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.

Applying Topological Principles to Genomic Analysis.
Kevin Emmett, Joseph M. Chan, Daniel S. Rosenbloom, and Raul Rabadan.

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.

Quantifying Reticulation in Phylogenetic Complexes Using Homology.
Kevin Emmett and Raul Rabadan.
BICT 2015 (Accepted).

Multiscale Topology of Chromatin Folding.
Kevin Emmett, Benjamin Schweinhart, and Raul Rabadan.
BICT 2015 (Accepted).

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.

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+.
* 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.

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.

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.

WE-D-BRB-03: Geometrization of Tumor Evolution.
Raul Rabadan.

JAK-STAT in lymphoproliferative disorders.
R. Rabadan, G. Inghirami.

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.

Inference of ancestral recombination graphs through topological data analysis.
P. G. Camara, A. J. Levine and R. Rabadan.

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+.
* 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‡.
‡ 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.

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‡.
* 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.
* 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*.
* 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.

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.

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.

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.
* 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.

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.
* 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.
* 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‡.
* 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.

Moduli Spaces of Phylogenetic Trees Describing Tumor Evolutionary Patterns.
Sakellarios Zairis, Hossein Khiabanian, Andrew Blumberg, and Raul Rabadan.

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.

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.

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.

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.

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.
* 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.

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‡.
* 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.

2013
SAVI: a statistical algorithm for variant frequency identification.
Vladimir Trifonov, Laura Pasqualucci, Enrico Tiacci, Brunangelo Falini, Raul Rabadan.

Topology of viral evolution.
Chan JM, Carlsson G, Rabadan R.

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‡.
* 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.

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.

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*.
* 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.

MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples.
Trifonov V, Pasqualucci L, Dalla Favera R, Rabadan R.

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.‡
* 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.

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.

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.

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‡.
* 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‡.
* 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*.
* Corresponding authors.

How many neutrophils are enough (redux, redux)?
Silverstein SC, Rabadan R.

Drug-drug interaction through molecular structure similarity analysis.
Vilar S, Harpaz R, Uriarte E, Santana L, Rabadan R, Friedman C.

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.

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.

Viral Reassortment as an information exchange between viral segments.
Greenbaum B, Li O, Poon L, Levine A, Rabadan R.

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.

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.

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.

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.

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.

Discovering disease associations by integrating electronic clinical data and medical literature.
Holmes A B, Hawson A, Liu F, Friedman C, Khiabanian H, Rabadan R.

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

BRAF Mutations in Hairy-Cell Leukemia (reply).
Tiacci E, Rabadan R, Falini B.

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*.
* 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.

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.

Understanding the Origins of a Pandemic Virus.
Hernandez C X, Chan J, Khiabanian H, Rabadan R

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.

Biclustering of Adverse Drug Events in FDA’s Spontaneous Reporting System.
Harpaz R, Perez H, Chase H S, Rabadan R, Hripcsak G, Friedman C

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.

Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data.
Trifonov V, Pascualucci L, Dalla-Favera R, Rabadan R.

Frequency Analysis Techniques for the Identification of Viral Genetic Data.
Vladimir Trifonov, Raul Rabadan.

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.

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.

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.

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.

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.

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.

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.

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.

Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Pandemic Influenza.
Alexander Solovyov, Benjamin Greenbaum, Gustavo Palacios, W. Ian Lipkin, Raul Rabadan.

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.

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.

Geographic Dependence, Surveillance, and Origins of the 2009 Influenza A (H1N1) Virus.
Trifonov V, Khiabanian H, Rabadan R.

Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA Identify Mediators of the Host Innate Immune System.
Greenbaum B, Rabadan R, Levine A.

Cluster Analysis of the Origin of the New Influenza A(H1N1).
A Solovyov, G Palacios, T Briese, W I Lipkin, R Rabadan.

The origin of the recent swine influenza A(H1N1) virus infecting humans.
Trifonov V, Khiabanian H, Greenbaum B, Rabadan R.

Differences in Patient Age Distribution between Influenza A Subtypes.
Khiabanian H, Farrell G, St. George K, Rabadan R.

Reassortment patterns in Swine influenza viruses.
Khiabanian H, Trifonov V, Rabadan R.

The Emergence of 2009 H1N1 Pandemic Influenza.
Greenbaum B, Trifonov V, Khiabanian H, Levine A, Rabadan R.

Spectral Signatures of Photon-Particle Oscillations from Celestial Objects.
Doron Chelouche, Raul Rabadan, Sergey Pavlov, Francisco Castejon.

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.

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.

Anomalies in the Influenza Genome Database: New Biology or Lab Errors?
Michael Krasnitz, Arnold Levine, Raul Rabadan.

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.

Patterns of Evolution and Host Gene Mimicry in Influenza and other RNA Viruses.
B.Greenbaum, Arnold J. Levine, Gyan Bhanot, Raul Rabadan.

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.

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.

Non-random reassortment in human influenza A viruses.
Raul Rabadan, Arnold Levine, Michael Krasnitz.

2007
Evolution of the Influenza A Virus: Some New Advances.
Rabadan R, Robins H.

2006
Comparison of Avian and Human Influenza A Viruses Reveals a Mutational Bias on the Viral Genomes.
Rabadan R, Levine A, Robins H.

Photon regeneration from pseudoscalars at X-ray laser facilities.
Raul Rabadan, Andreas Ringwald, Kris Sigurdson.

2005
Constraints on light pseudoscalars from colliders and photonregeneration experiments in X-ray facilities.
Raul Rabadan.

Collider bounds on pseudoscalars coupling to gauge bosons.
Matthew Kleban, Raul Rabadan.

Non-perturbative orientifold transitions at the conifold.
Kentaro Hori, Kazuo Hosomichi, David C Page, Raul Rabadan, Johannes Walcher.

Stability in asymptotically AdS spaces.
Kleban M, Porrati M, Rabadan R.

2004
Poincare recurrences and topological diversity.
Kleban M, Porrati M, Rabadan R.

Boundary rigidity and holography.
Porrati M, Rabadan R.

On bouncing brane worlds, S-branes and branonium cosmology.
C P Burgess, F Quevedo, R Rabadan, G Tasinato, I Zavala.

D-brane chemistry.
C P Burgess, N E Grandi, F Quevedo, R Rabadan.

2003
Branonium.
C P Burgess, P Martineau, F Quevedo, R Rabadan.

(Re)constructing dimensions.
Raul Rabadan, Gary Shiu.

2002
Dilaton tadpoles and D-brane interactions in compact spaces.
Raul Rabadan, Frederic Zamora.

Complex structure moduli stability in toroidal compactifications.
Juan Garcia-Bellido, Raul Rabadan.

M theory lift of brane anti-brane systems and localized closed string tachyons.
Raul Rabadan, Joan Simon.

Inflationary scenarios from branes at angles.
Juan Garcia-Bellido, Raul Rabadan, Frederic Zamora.

Branes at angles, torons, stability and supersymmetry.
Rabadan R.

2001
Getting just the standard model at intersecting branes.
Luis E Ibanez, F Marchesano, R Rabadan.

D=4 Chiral String Compactifications from Intersecting Branes.
G Aldazabal, S Franco, Luis E Ibanez, R Rabadan, A M Uranga.

Intersecting Brane Worlds.
G Aldazabal, S Franco, Luis E Ibanez, R Rabadan, A M Uranga.

Type IIB Orientifolds without Untwisted Tadpoles, and non-BPS D-branes.
R Rabadan, A M Uranga.

D = 4, N=1 orientifolds with vector structure.
Matthias Klein, Raul Rabadan.

2000
Z(N) x Z(M) orientifolds with and without discrete torsion.
Matthias Klein, Raul Rabadan.

Orientifolds with discrete torsion.
Mathias Klein, Raul Rabadan.

Orientifolding the conifold.
J Park, R Rabadan, A M Uranga.

N=1 type IIA brane configurations, chirality and T duality.
J Park, R Rabadan, A M Uranga.

Sigma model anomalies in compact D = 4, N=1 type IIB orientifolds and Fayet-Iliopoulos terms.
Luis E Ibanez, R Rabadan, A M Uranga.

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.