2014 Publications
← Return to Complete Publication Listing

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.