2015 Publications
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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.