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Raúl Rabadán

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Raúl Rabadán (born 1974) is a Spanish-American theoretical physicist and computational biologist. He is currently the Gerald and Janet Carrus Professor in the Department of Systems Biology, Biomedical Informatics and Surgery at Columbia University. He is the director of the Program for Mathematical Genomics at Columbia University and director of the Center for Topology of Cancer Evolution and Heterogeneity. At Columbia, he has put together a highly interdisciplinary lab with researchers from the fields of mathematics, physics, computer science, engineering, and medicine, with the common goal of solving pressing biomedical problems through quantitative computational models. Rabadan's current interest focuses on uncovering patterns of evolution in biological systems—in particular, viruses and cancer.

Raúl Rabadán
Born1974 (age 49–50)
Alma materAutonomous University of Madrid (Ph.D. 2001)
Scientific career
FieldsTheoretical physics
Computational biology
Genomics
Mathematical biology
InstitutionsColumbia University
Institute for Advanced Study
CERN
Websiterabadan.c2b2.columbia.edu

Career

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Rabadan is an expert on mathematical approaches to biological systems, genomics of cancer and infectious diseases. He received his PhD in string theory phenomenology, specifically the physics of string compactifications and intersecting D-brane configurations in the Universidad Autonoma de Madrid, Spain. In his more recent research in physics he has studied the information paradox of black holes in the context of the Anti-de Sitter/Conformal Field Theory duality, and has proposed several experiments to search for axions. Since 2005 he has focused his research program on theoretical and computational problems in biology. From 2001 to 2003, Rabadan was a fellow at the Theoretical Physics Division at CERN, the European Organization for Nuclear Research, in Geneva, Switzerland. In 2003 he joined the Physics Group of the School of Natural Sciences at the Institute for Advanced Study.

Since 2008 Rabadan has been a professor at Columbia University, in New York. His applied quantitative approaches to modeling and understanding the dynamics of biological systems through the lens of genomics. He has focused his research on the evolution of two of such biological systems: cancer and infectious diseases. In particular, he has been working in the identification of driver mechanisms of evolutionary processes, characterize key process dynamics and elucidate epistasic interactions. Rabadan is interested in understanding the evolution of infectious agents through the analysis of their genome, in particular RNA viruses like influenza and coronaviruses. His work in this area includes elucidating the origin of the influenza A virus subtype H1N1.[1][2]

Rabadan's work in cancer genomics has led to the identification of driver alterations in hairy cell leukemia,[3] diffuse large B-cell lymphoma,[4][5] T-cell acute lymphoblastic leukemia,[6][7] chronic lymphocytic leukemia,[8][9][10][11] splenic marginal zone lymphoma[12] and glioblastoma multiforme;[13][14][15] and to the identification of recurrent alterations, which lead to therapy resistance, using longitudinal data in T-cell acute lymphoblastic leukemia. He is currently studying the role of non-coding RNA in cancer.[16][17] Recently, he has been working on the application of topological data analysis to large scale genomic data and transcriptomic single cell data.[18][19][20][21][22]

Rabadan's scientific work has led to more than 200 peer-reviewed scientific publications, including in high impact factor journals (New England Journal of Medicine, Nature, Science, Nature Genetics, Nature Medicine, Cell, among others). Several of his results have been featured by the international press, including CNN, the New York Times, the Wall Street Journal, the Associated Press, Reuters International, and The Economist.

Books

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In 2019 Rabadan together with Andrew Blumberg, a topologist at the University of Texas, published a book Topological Data Analysis for Genomics and Evolution in Cambridge University Press. The books explores biology in the age of Big Data. This book introduces the central ideas and techniques of topological data analysis and its specific applications to biology, including the evolution of viruses, bacteria and humans, genomics of cancer, and single cell characterization of developmental processes.

In 2020 Rabadan published Understanding Coronavirus in Cambridge University Press. The book provides a concise and accessible introduction provides answers to the most common questions surrounding coronavirus for a general audience, including an introduction about the origin and evolution of this virus, the relation to SARS and other respiratory viruses, among other.

References

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  1. ^ Trifonov, V., Khiabanian, H., Greenbaum, B. & Rabadan, R. The origin of the recent swine influenza A(H1N1) virus infecting humans. Euro Surveill 14 (2009).
  2. ^ Trifonov, V.; Khiabanian, H.; Rabadan, R. (2009). "Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus". N Engl J Med. 361 (2): 115–119. doi:10.1056/NEJMp0904572. PMID 19474418.
  3. ^ Tiacci, E.; et al. (2011). "BRAF mutations in hairy-cell leukemia". N Engl J Med. 364 (24): 2305–2315. doi:10.1056/NEJMoa1014209. PMC 3689585. PMID 21663470.
  4. ^ Pasqualucci, L.; et al. (2011). "Inactivating mutations of acetyltransferase genes in B-cell lymphoma". Nature. 471 (7337): 189–195. Bibcode:2011Natur.471..189P. doi:10.1038/nature09730. PMC 3271441. PMID 21390126.
  5. ^ Pasqualucci, L.; et al. (2011). "Analysis of the coding genome of diffuse large B-cell lymphoma". Nat Genet. 43 (9): 830–837. doi:10.1038/ng.892. PMC 3297422. PMID 21804550.
  6. ^ Van Vlierberghe, P.; et al. (2010). "PHF6 mutations in T-cell acute lymphoblastic leukemia". Nat Genet. 42 (4): 338–342. doi:10.1038/ng.542. PMC 2847364. PMID 20228800.
  7. ^ Tzoneva, G.; et al. (2013). "Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL". Nat Med. 19 (3): 368–371. doi:10.1038/nm.3078. PMC 3594483. PMID 23377281.
  8. ^ Rossi, D. et al. Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia. Blood 119, 521-529, doi:10.1182/blood-2011-09-379966 (2012).
  9. ^ Rossi, D.; et al. (2012). "Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia". Blood. 121 (8): 1403–1412. doi:10.1182/blood-2012-09-458265. PMC 3578955. PMID 23243274.
  10. ^ Rossi, D.; et al. (2011). "Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness". Blood. 118 (26): 6904–6908. doi:10.1182/blood-2011-08-373159. PMC 3245210. PMID 22039264.
  11. ^ 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. Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia. eLife 2014 Dec 11; doi:10.7554/eLife.02869 PMID 25496728.
  12. ^ Rossi, D.; et al. (2012). "The coding genome of splenic marginal zone lymphoma:activation of NOTCH2 and other pathways regulating marginal zone development". J Exp Med. 209 (9): 1537–1551. doi:10.1084/jem.20120904. PMC 3428941. PMID 22891273.
  13. ^ Singh, D. et al. Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma. Science, doi:10.1126/science.1220834.
  14. ^ Jiguang Wang, Emanuela Cazzato, Erik Ladewig, Veronique Frattini, Daniel 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 Blumberg, Anna Lasorella, Do-Hyun Nam, Gaetano Finocchiaro, Antonio Iavarone, Raul Rabadan, Clonal Evolution of Glioblastoma under Therapy, Nature Genetics 2016 June 6. doi:10.1038/ng.3590.
  15. ^ Veronique Frattini, Vladimir Trifonov, Joseph Minhow Chan, Angelica Castano, Marie Lia, Francesco Abate, Stephen T. Keir, Alan X. Ji, Pietro Zoppoli, Francesco Niola, Carla Danussi, Igor Dolgalev, Paola Porrati, Serena Pellegatta, Adriana Heguy, Gaurav Gupta, David J. Pisapia, Peter Canoll, Jeffrey N. Bruce, Roger E. McLendon, Hai Yan, Ken Aldape, Gaetano Finocchiaro, Tom Mikkelsen, Gilbert G. Privé, Darell D. Bigner, Anna Lasorella, Raul Rabadan, Antonio Iavarone. The integrated landscape of driver genomic alterations in glioblastoma. Nature Genetics 2013 Aug 5. doi:10.1038/ng.2734. PMC 3677224.
  16. ^ E. Pefanis, J. Wang, G. Rothschild, J. Lim, J. Chao, R. Rabadan, AN. Economides, U. Basu. Antisense non-coding RNA transcription targets AID to divergently transcribed genes in the B cell genome. Nature 514, 389–393 ( co-corresponding authors).
  17. ^ 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. RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity. Cell 2015 May; doi:10.1016/j.cell.2015.04.034
  18. ^ Chan, J. M.; Carlsson, G.; Rabadan, R. (2013). "Topology of viral evolution". Proc Natl Acad Sci U S A. 110 (46): 18566–18571. Bibcode:2013PNAS..11018566C. doi:10.1073/pnas.1313480110. PMC 3831954. PMID 24170857.
  19. ^ K. Emmett, R. R. Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis. Lecture Notes in Computer Science (LNCS) (2014).
  20. ^ Camara, Pablo G.; Rosenbloom, Daniel I. S.; Emmett, Kevin J.; Levine, Arnold J.; Rabadan, Raul (2016). "Fine-scale resolution of human recombination using topological data analysis". Cell Systems. 3 (1): 83–94. doi:10.1016/j.cels.2016.05.008. PMC 4965322. PMID 27345159.
  21. ^ S. Zairis, A. Blumberg, H. Khiabanian, R. Rabadan. Moduli spaces of phylogenetic trees describing tumor evolutionary patterns. Lecture Notes in Computer Science (LNCS) 2014. Volume 8609, pp 528-539. 2.
  22. ^ Rizvi, Abbas H.; Camara, Pablo G.; Kandror, Elena K.; Roberts, Thomas J.; Schieren, Ira; Maniatis, Tom; Rabadan, Raul (June 2017). "Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development". Nature Biotechnology. 35 (6): 551–560. doi:10.1038/nbt.3854. ISSN 1546-1696. PMC 5569300. PMID 28459448.
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