Publications

2020

Rabadan R, Yamina Mohamedi, Udi Rubin, Tim Chu, Adam N Alghalith,  Oliver Elliott, Luis Arnés, Santiago Cal, Álvaro J Obaya, Arnold J Levine, Pablo G Cámara Identification of relevant genetic alterations in cancer using topological data analysis PMCID: PMC7393176
DOI: 10.1038/s41467-020-17659-7 July 2020

Zhaoqi Liu, Ioan Filip, Karen Gomez, Dewaldt Engelbrecht, Shabnum Meer, Pooja N. Lalloo, Pareen Patel, Yvonne Perner, Junfei Zhao, Jiguang Wang, Laura Pasqualucci*, Rabadan R* and Pascale Willem*. Genomic Characterization of HIV-Associated Plasmablastic Lymphoma Identifies Pervasive Mutations in the JAK–STAT Pathway. * Co-last Authors. Blood Cancer Discovery. 2020 June 10. doi:10.1158/2643-3230.BCD-20-0051

Liu Z, Zhang J, Sun Y, Perea-Chamblee TE, Manley JL, Rabadan R. Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulationPNAS 2020 Apr 24. pii: 201922622. doi: 10.1073/pnas.1922622117. May 2020

Gartrell-Corrado RD, Chen AX, Rizk EM, Marks DK, Bogardus MH, Hart TD, Silverman AM, Bayan CY, Finkel GG, Barker LW, Komatsubara KM, Carvajal RD, Horst BA, Chang R, Monod A, Rabadan R, Saenger YM. Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary MelanomaCancer Res. 2020 Mar 1;80(5):1078-1087. doi: 10.1158/0008-5472.CAN-19-2039. Mar 2020

Rose Orenbuch, Ioan Filip, Devon Comito, Jeffrey Shaman, Itsik Pe’er, Rabadan R arcasHLA: high-resolution HLA typing from RNAseq Bioinformatics 36 (1), 33-40 11 2020 Jan 2020

2019

Laura Belver, Alexander Y Yang, Robert Albero, Daniel Herranz, Francesco G Brundu, S Aidan Quinn, Pablo Pérez-Durán, Silvia Álvarez, Francesca Gianni, Marissa Rashkovan, Devya Gurung, Pedro P Rocha, Ramya Raviram, Clara Reglero, Jose R Cortés, Anisha J Cooke, Agnieszka A Wendorff, Valentina Cordó, Jules P Meijerink, Rabadan R, Adolfo A Ferrando Gata3-controlled nucleosome eviction drives Myc enhancer activity in T-cell development and leukemia Cancer discovery 9 (12), 1774-1791 Dec 2019

Floris P Barthel, Kevin C Johnson, Frederick S Varn, Anzhela D Moskalik, Georgette Tanner, Emre Kocakavuk, Kevin J Anderson, Olajide Abiola, Kenneth Aldape, Kristin D Alfaro, Donat Alpar, Samirkumar B Amin, David M Ashley, Pratiti Bandopadhayay, Jill S Barnholtz-Sloan, Rameen Beroukhim, Christoph Bock, Priscilla K Brastianos, Daniel J Brat, Andrew R Brodbelt, Alexander F Bruns, Ketan R Bulsara, Aruna Chakrabarty, Arnab Chakravarti, Jeffrey H Chuang, Elizabeth B Claus, Elizabeth J Cochran, Jennifer Connelly, Joseph F Costello, Gaetano Finocchiaro, Michael N Fletcher, Pim J French, Hui K Gan, Mark R Gilbert, Peter V Gould, Matthew R Grimmer, Antonio Iavarone, Azzam Ismail, Michael D Jenkinson, Mustafa Khasraw, Hoon Kim, Mathilde CM Kouwenhoven, Peter S LaViolette, Meihong Li, Peter Lichter, Keith L Ligon, Allison K Lowman, Tathiane M Malta, Tali Mazor, Kerrie L McDonald, Annette M Molinaro, Do-Hyun Nam, Naema Nayyar, Ho Keung Ng, Chew Yee Ngan, Simone P Niclou, Johanna M Niers, Houtan Noushmehr, Javad Noorbakhsh, D Ryan Ormond, Chul-Kee Park, Laila M Poisson, Rabadan R, Bernhard Radlwimmer, Ganesh Rao, Guido Reifenberger, Jason K Sa, Michael Schuster, Brian L Shaw, Susan C Short, Peter A Sillevis Smitt, Andrew E Sloan, Marion Smits, Hiromichi Suzuki, Ghazaleh Tabatabai, Erwin G Van Meir, Colin Watts, Michael Weller, Pieter Wesseling, Bart A Westerman, Georg Widhalm, Adelheid Woehrer, WK Alfred Yung, Gelareh Zadeh, Jason T Huse, John F De Groot, Lucy F Stead, Roel GW Verhaak Longitudinal molecular trajectories of diffuse glioma in adults Nature 576 (7785), 112-120 Nov 2019

Jian Zhang, Abdullah M Ali, Yen K Lieu, Zhaoqi Liu, Jianchao Gao, Rabadan R, Azra Raza, Siddhartha Mukherjee, James L Manley Disease-causing mutations in SF3B1 alter splicing by disrupting interaction with SUGP1 Molecular cell 76 (1), 82-95. e7 Oct 2019

Claudio Scuoppo, Jiguang Wang, Mirjana Persaud, Sandeep K Mittan, Katia Basso, Laura Pasqualucci, Rabadan R, Giorgio Inghirami, Carla Grandori, Francesc Bosch, Riccardo Dalla-Favera Repurposing dasatinib for diffuse large B cell lymphoma Proceedings of the National Academy of Sciences 116 (34), 16981-16986 Aug 2019

Anna S Nam, Kyu-Tae Kim, Ronan Chaligne, Franco Izzo, Chelston Ang, Justin Taylor, Robert M Myers, Ghaith Abu-Zeinah, Ryan Brand, Nathaniel D Omans, Alicia Alonso, Caroline Sheridan, Marisa Mariani, Xiaoguang Dai, Eoghan Harrington, Alessandro Pastore, Juan R Cubillos-Ruiz, Wayne Tam, Ronald Hoffman, Rabadan R, Joseph M Scandura, Omar Abdel-Wahab, Peter Smibert, Dan A Landau Somatic mutations and cell identity linked by Genotyping of Transcriptomes Nature 571 (7765), 355-360 Jul 2019

Luis Arnes, Zhaoqi Liu, Jiguang Wang, Carlo Maurer, Irina Sagalovskiy, Marta Sanchez-Martin, Nikhil Bommakanti, Diana C Garofalo, Dina A Balderes, Lori Sussel, Kenneth P Olive, Rabadan R Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma Gut 68 (3), 499-511 May 2019

María Teresa Blasco, Carolina Navas, Guillermo Martín-Serrano, Osvaldo Graña-Castro, Carmen G Lechuga, Laura Martín-Díaz, Magdolna Djurec, Jing Li, Lucia Morales-Cacho, Laura Esteban-Burgos, Javier Perales-Patón, Emilie Bousquet-Mur, Eva Castellano, Harrys KC Jacob, Lavinia Cabras, Monica Musteanu, Matthias Drosten, Sagrario Ortega, Francisca Mulero, Bruno Sainz Jr, Nelson Dusetti, Juan Iovanna, Francisco Sánchez-Bueno, Manuel Hidalgo, Hossein Khiabanian, Rabadan R, Fátima Al-Shahrour, Carmen Guerra, Mariano Barbacid Complete regression of advanced pancreatic ductal adenocarcinomas upon combined inhibition of EGFR and C-RAF Cancer cell 35 (4), 573-587. e6 Apr 2019

Junfei Zhao, Andrew X Chen, Robyn D Gartrell, Andrew M Silverman, Luis Aparicio, Tim Chu, Darius Bordbar, David Shan, Jorge Samanamud, Aayushi Mahajan, Ioan Filip, Rose Orenbuch, Morgan Goetz, Jonathan T Yamaguchi, Michael Cloney, Craig Horbinski, Rimas V Lukas, Jeffrey J Raizer, Ali I Rae, Jinzhou Yuan, Peter Canoll, Jeffrey N Bruce, Yvonne M Saenger, Peter Sims, Fabio M Iwamoto, Adam M Sonabend, Rabadan R Author Correction: Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma (Nature Medicine, (2019), 25, 3,(462-469), 10.1038/s41591-019-0349-y) Nature medicine 25 (6) Mar 2019

Agnieszka A Wendorff, S Aidan Quinn, Marissa Rashkovan, Chioma J Madubata, Alberto Ambesi-Impiombato, Mark R Litzow, Martin S Tallman, Elisabeth Paietta, Maddalena Paganin, Giuseppe Basso, Julie M Gastier-Foster, Mignon L Loh, Rabadan R, Pieter Van Vlierberghe, Adolfo A Ferrando Phf6 loss enhances HSC self-renewal driving tumor initiation and leukemia stem cell activity in T-ALL Cancer discovery 9 (3), 436-451 Mar 2019

Andrew V Anzalone, Sakellarios Zairis, Annie J Lin, Rabadan R, Virginia W Cornish Interrogation of Eukaryotic Stop Codon Readthrough Signals by in Vitro RNA Selection Biochemistry 58 (8), 1167-1178 Feb 2019

2018

Cho HJ, Zhao J, Jung SW, Ladewig E, Kong D, Suh Y, Lee Y, Kim D, Ahn SH, Bordyuh M, Kang HJ, Sa J, Seo YJ, Kim ST, Lim DH, Dho Y, Lee J, Seol HJ, Won Choi J, Park W, Park C, Rabadan R,  Nam D. Distinct genomic profile and specific targeted drug responses in adult cerebellar glioblastoma. Neuro Oncol. 2018 Jul 31. doi: 10.1093/neuonc/noy123. [Epub ahead of print]

Tansey W, Wang Y, Blei DM, Rabadan R. Black Box FDR. Arxiv, Preprint. Jun 2018.

Arrieta VA, Cacho-Díaz B, Zhao J, Rabadan R, Chen L, Sonabend AM. The possibility of cancer immune editing in gliomas. A critical review. Oncoimmunology. 2018 Apr 9;7(7):e1445458. doi: 10.1080/2162402X.2018.1445458. eCollection 2018.

Cimino PJ, Kim Y, Wu HJ, Alexander J, Wirsching HG, Szulzewsky F, Pitter K, Ozawa T, Wang J, Vazquez J, Arora S, Rabadan R, Levine R, Michor F, Holland EC. Increased HOXA5 expression provides a selective advantage for gain of whole chromosome 7 in IDH wild-type glioblastoma. Genes Dev. 2018 Apr 1;32(7-8):512-523. doi: 10.1101/gad.312157.118. Epub 2018 Apr 9.

Gartrell RD, Marks DK, Hart TD, Li G, Davari DR, Wu A, Blake Z, Lu Y, Askin KN, Monod A, Esancy CL, Stack EC, Jia DT, Armenta PM, Fu Y, Izaki D, Taback B, Rabadan R, Kaufman HL, Drake CG, Horst BA, Saenger YM. Quantitative Analysis of Immune Infiltrates in Primary Melanoma. Cancer Immunol Res. 2018 Feb 21. pii: canimm.0360.2017. doi: 10.1158/2326-6066.CIR-17-0360. [Epub ahead of print]

Arnes L, Liu Z, Wang J, Carlo Maurer H, Sagalovskiy I, Sanchez-Martin M, Bommakanti N, Garofalo DC, Balderes DA, Sussel L, Olive KP, Rabadan R. Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma. Gut. 2018 Feb 10. pii: gutjnl-2017-314353. doi: 10.1136/gutjnl-2017-314353. [Epub ahead of print]

Tzoneva G, Dieck CL, Oshima K, Ambesi-Impiombato A, Sánchez-Martín M, Madubata CJ, Khiabanian H, Yu J, Waanders E, Iacobucci I, Sulis ML, Kato M, Koh K, Paganin M, Basso G, Gastier-Foster JM, Loh ML, Kirschner-Schwabe R, Mullighan CG, Rabadan R, Ferrando AA. Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia. Nature. 2018 Jan 25;553(7689):511-514. doi: 10.1038/nature25186. Epub 2018 Jan 17.

2017

Madubata CJ, Roshan-Ghias A, Chu T, Resnick S, Zhao J, Arnes L, Wang J, Rabadan R. Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas. NPJ Genom Med. 2017 Oct. 3.doi: 10.1038/s41525-017-0032-5.

Giudice ID, Rigolin GM, Raponi S, Cafforio L, Ilari C, Wang J, Bordyuh M, Piciocchi A, Marinelli M, Nanni M, Tavolaro S, Filetti M, Bardi A, Tammiso E, Volta E, Negrini M, Saccenti E, Mauro FR, Rossi D, Gaidano G, Guarini A, Rabadan R, Cuneo A, Foà R. Refined karyotype-based prognostic stratification of chronic lymphocytic leukemia with a low- and very-low-risk genetic profile. Leukemia. 2018 Feb;32(2):543-546. doi: 10.1038/leu.2017.292. Epub 2017 Sep 19.

Rabadan R, Bhanot G, Marsilio S, Chiorazzi N, Pasqualucci L, Khiabanian H. On statistical modeling of sequencing noise in high depth data to assess tumor evolution. bioRxiv. Sept. 4, 2017. doi: https://doi.org/10.1101/128587

D’Amico G, Rabadan R, Kleban M. A Random Categorization Model for Hierarchical TaxonomiesScientific Reports, volume 7, Article number: 17051. April 2017. doi:10.1038/s41598-017-17168-6

Lasorella A, Sanson M, Iavarone A. FGFR-TACC gene fusions in human glioma. Neuro Oncol. 2017 Apr 1;19(4):475-483. doi: 10.1093/neuonc/now240.

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. Spatiotemporal genomic architecture informs precision oncology in glioblastoma. Nat Genet. 2017 Apr.  Epub 2017 Mar 6. doi 10.1038/ng.3806

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. p53 maintains baseline expression of multiple tumor suppressor genes. Mol Cancer Res. 2017 May 8. pii: molcanres.0089.2017. doi: 10.1158/1541-7786.MCR-17-0089.

Rizvi AH, Camara PG, Kandror EK, Roberts TJ, Schieren I, Maniatis T, Rabadan RSingle-cell topological RNA-seq analysis reveals insights into cellular differentiation and development.Nat Biotechnol. 2017 May 1. doi: 10.1038/nbt.3854. [Epub ahead of print]

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. Spatiotemporal genomic architecture informs precision oncology in glioblastoma.Nat Genet. 2017 Apr;49(4):594-599. doi: 10.1038/ng.3806. Epub 2017 Mar 6.

Rabadan R, Marsilio S, Chiorazzi N, Pasqualucci L, Khiabanian HHighly sensitive detection of small variants in multi-sample ultra-deep tumor sequencing. bioRxiv, 128587

2016

Camara PG. Topological methods for genomics: present and future directions. Curr Opin Syst. Biol. 2017 Feb. Epub 2016 Dec. doi: 10.1016/j.coisb.2016.12.007.

Anzalone AV, Lin AJ, Zairis S, Rabadan R, Cornish VW. Reprogramming eukaryotic translation with ligand-responsive synthetic RNA switches. Nat Methods. 2016 May. Epub Mar 2016. DOI:10.1038/nmeth.3807.

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, Foa R, Rabadan R, Gaidano G, Rossi D. Clinical impact of small subclones harboring NOTCH1, SF3B1 or BIRC3 mutations in chronic lymphocytic leukemia. Haematologica. 2016 Apr. Epub 2016 Jan 27.doi: 10.3324/haematol.2015.136051.

Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbo F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M,  Falini B, Inghirami G, Bertoni F, Foa R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sept 8. Epub 2016 Jun 22. doi: 10.1182/blood-2016-02-696757.

Yamamoto K, Wang J, Sprinzen L, Xu J, Haddock CJ, Li C, Lee BJ, Loredan DG, Jiang W, Vindigni A, Wang D, Rabadan R, Zha S. Kinase-dead ATM protein is highly oncogenic and can be preferentially targeted by Topo-isomerase I inhibitors. Elife. 2016 Jun 15.doi: 10.7554/eLife.14709.

De Sano L, Caravagna G, Ramazzotti D, Graudenzi A, Mauri G, Mishra B, Antoniotti M. TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. Bioinformatics. 2016 Jun 15;32(12):1911-3. doi: 10.1093/bioinformatics/btw035. Epub 2016 Feb 9. PubMed PMID: 26861821.

Rosenbloom D, Camara P, Chu T, Rabadan R. Evolutionary scalpels for dissecting tumor ecosystems. Science Direct, 2016

Crawford L, Monod A, Chen A, Mukherjee S, Rabadan R. Topological Summaries of Tumor Images Improve Prediction of Disease Free Survival in Glioblastoma Multiforme. arXiv, 2016

Oshimaa K, Khiabanian H, da Silva-Almeida A, Tzoneva G, Abate F, Ambesi-Impiombato A, Sanchez-Martin M, Carpenter Z, Penson A, Perez-Garcia A, Eckert C, Nicolas C, Balbin M, Luisa Sulis M, Kato M, Koh L, Paganin M, Basso G, Gastier-Foster J, Devidas M, Loh M, Kirschner-Schwabe R, Palomero T, Rabadan R, Ferrando A. Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphobastic leukemia. PNAS, 2016

Camara P, Levine A, Rabadan R. Inference of Ancestral Recombination Graphs through Topological Data Analysis. PLoS, 2016

Zairis S, Khiabanian H, Blumberg A, Rabadan R. Genomic data analysis in tree spaces. arXiv, 2016

Camara P, Rosenbloom D, Emmett K, Levine A, Rabadan R. Topological Data Analysis Generates High-Resoultion, Genome-wide Maps of Human Recombination. Cell Systems, 2016

Caravagna G, Graudenzi A, Ramazzotti D, Sanz-Pamplona R, De Sano L, Mauri G, Moreno V, Antoniotti M, Mishra B. Algorithmic methods to infer the evolutionary trajectories in cancer progression Proc Natl Acad Sci U S A. 2016 Jul 12; 113(28): E4025–E4034. Published online 2016 Jun 28. doi: 10.1073/pnas.1520213113

Wang J, Cazzato E, Ladewig E, Frattini V, Rosenbloom DI, Zairis S, Abate F, Liu Z, Elliott O, Shin YJ, Lee JK, Lee IH, Park WY, Eoli M, Blumberg AJ, Lasorella A, Nam DH, Finocchiaro G, Iavarone A, Rabadan R. Clonal evolution of glioblastoma under therapy. Nat Genet. 2016 Jul;48(7):768-76. doi: 10.1038/ng.3590. Epub 2016 Jun 6.

Yang X, Debonneuil E, Zhavoronkov A, Mishra B. Cancer megafunds with in silico and in vitro validation: accelerating cancer drug discovery via financial engineering without financial crisisOncotarget. 2016 Sep 6; 7(36): 57671–57678. Published online 2016 Jun 3. doi: 10.18632/oncotarget.9808

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. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell, 2016.

2015

Emmett K, Schweinhart B, Rabadan R. Multiscale Topology of Chromatin Folding. BICT, 2015.

Emmett K, Rabadan RQuantifying Reticulation in Phylogenetic Complexes Using Homology. BICT, 2015.

Emmett K, Chan J, Rosenbloom D, Rabadan RApplying Topological Principles to Genomic Analysis. Microbe, 2015.

M Antoniotti, G Caravagna, L De Sano, A Graudenzi, G Mauri, et al. Design of the TRONCO BioConductor Package for TRanslational ONCOlogy. bioRxiv, 2015.

Bose, S., Wan, Z., Carr, A., Rizvi, A.H., Vieira, G., Pe’er, D., Sims, P.AScalable microfluidics for single cell RNA printing and sequencing. Genome Biology, 2015.

Cámara PG, Levine AJ, Rabadán R. Inference of ancestral recombination graphs through topological data analysis. ArXiv, 2015.