Publications

2018

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.