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 melanoma. Cancer Res. 2020 Jan 16. pii: canres.2039.2019. doi: 10.1158/0008-5472.CAN-19-2039. 

Weisberg SP, Carpenter DJ, Chait M, Dogra P, Gartrell-Corrado RD, Chen AX, Campbell S, Liu W, Saraf P, Snyder ME, Kubota M, Danzl NM, Schrope BA, Rabadan R, Saenger Y, Chen X, Farber DL. Tissue-Resident Memory T Cells Mediate Immune Homeostasis in the Human Pancreas through the PD-1/PD-L1 Pathway. Cell Rep. 2019 Dec 17;29(12):3916-3932.e5. doi: 10.1016/j.celrep.2019.11.056.

Arrieta VA, Iwamoto F, Lukas RV, Sachdev S, Rabadan R, Sonabend AM. Can patient selection and neoadjuvant administration resuscitate PD-1 inhibitors for glioblastoma? J Neurosurg. 2019 Dec 6:1-6. doi: 10.3171/2019.9.JNS192523. 

Han S, Shin H, Lee JK, Liu Z, Rabadan R, Lee J, Shin J, Lee C, Yang H, Kim D, Kim SH, Kim J, Oh JW, Kong DS, Lee JI, Seol HJ, Choi JW, Kang HJ, Nam DH. Secretome analysis of patient-derived GBM tumor spheres identifies midkine as a potent therapeutic target. Exp Mol Med. 2019 Dec 6;51(12):147. doi: 10.1038/s12276-019-0351-y.

Sa JK, Hwang JR, Cho YJ, Ryu JY, Choi JJ, Jeong SY, Kim J, Kim MS, Paik ES, Lee YY, Choi CH, Kim TJ, Kim BG, Bae DS, Lee Y, Her NG, Shin YJ, Cho HJ, Kim JY, Seo YJ, Koo H, Oh JW, Lee T, Kim HS, Song SY, Bae JS, Park WY, Han HD, Ahn HJ, Sood AK, Rabadan R, Lee JK, Nam DH, Lee JW. Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers. Genome Biol. 2019 Nov 26;20(1):253. doi: 10.1186/s13059-019-1848-3.

Barthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HK, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCM, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JM, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JK, Schuster M, Shaw BL, Short SC, Smitt PAS, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, De Groot JF, Stead LF, Verhaak RGW; GLASS Consortium. Longitudinal molecular trajectories of diffuse glioma in adults. Nature. 2019 Dec;576(7785):112-120. doi: 10.1038/s41586-019-1775-1. 

Vasan N, Razavi P, Johnson JL, Shao H, Shah H, Antoine A, Ladewig E, Gorelick A, Lin TY, Toska E, Xu G, Kazmi A, Chang MT, Taylor BS, Dickler MN, Jhaveri K, Chandarlapaty S, Rabadan R, Reznik E, Smith ML, Sebra R, Schimmoller F, Wilson TR, Friedman LS, Cantley LC, Scaltriti M, Baselga J. Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors. Science. 2019 Nov 8;366(6466):714-723. doi: 10.1126/science.aaw9032.

Singer RA, Arnes L, Cui Y, Wang J, Gao Y, Guney MA, Burnum-Johnson KE, Rabadan R, Ansong C, Orr G, Sussel L. The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function. Cell Metab. 2019 Dec 3;30(6):1091-1106.e8. doi: 10.1016/j.cmet.2019.09.013. Epub 2019 Oct 10.

Belver L, Yang AY, Albero R, Herranz D, Brundu FG, Quinn SA, Pérez-Durán P, Álvarez S, Gianni F, Rashkovan M, Gurung D, Rocha PP, Raviram R, Reglero C, Cortés JR, Cooke AJ, Wendorff AA, Cordó V, Meijerink JP, Rabadan R, Ferrando AA. GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia. Cancer Discov. 2019 Dec;9(12):1774-1791. doi: 10.1158/2159-8290.CD-19-0471. 

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.

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.

Raponi S, Del Giudice I, Marinelli M, Wang J, Cafforio L, Ilari C, Piciocchi A, Messina M, Bonina S, Tavolaro S, Bordyuh M, Mariglia P, Peragine N, Mauro FR, Chiaretti S, Molica S, Gentile M, Visentin A, Trentin L, Rigolin GM, Cuneo A, Diop F, Rossi D, Gaidano G, Guarini A, Rabadan R, Foà R.  Genetic Landscape of Ultra-Stable Chronic Lymphocytic Leukemia Patients. Ann Oncol. 2018 Jan 22.

Djurec M, Graña O, Lee A, Troulé K, Espinet E, Cabras L, Navas C, Blasco MT, Martín-Díaz L, Burdiel M, Li J, Liu Z, Vallespinós M, Sanchez-Bueno F, Sprick MR, Trumpp A, Sainz B Jr., Al-Shahrour F, Rabadan R, Guerra C, Barbacid M. Saa3 is a key mediator of the protumorigenic properties of cancer-associated fibroblasts in pancreatic tumors. Proc Natl Acad Sci U S A. 2018 Feb 6;115(6):E1147-E1156

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 17.

Kiryluk K, Bomback AS, Cheng YL, Xu K, Camara PG, Rabadan R, Sims PA, Barasch J. Precision Medicine for Acute Kidney Injury (AKI): Redefining AKI by Agnostic Kidney Tissue Interrogation and Genetics. Semin Nephrol. 2018 Jan.

D'Amico G, Rabadan R, Kleban M. A Random Categorization Model for Hierarchical Taxonomies. Sci Rep. 2017 Dec 6;7(1):17051.

Marsilio S, Khiabanian H, Fabbri G, Vergani S, Scuoppo C, Montserrat E, Shpall EJ, Hadigol M, Marin P, Rai KR, Rabadan R, Devereux S, Pasqualucci L, Chiorazzi N. Somatic CLL mutations occur at multiple distinct hematopoietic maturation stages: documentation and cautionary note regarding cell fraction purity.  Leukemia. 2017 Dec 5.

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.

Taglialatela A, Alvarez S, Leuzzi G, Sannino V, Ranjha L, Huang JW, Madubata C, Anand R, Levy B, Rabadan R, Cejka P, Costanzo V, Ciccia A. Restoration of Replication Fork Stability in BRCA1- and BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers. Mol Cell. 2017 Oct 19.

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. 2017 Sep 19.

Gong Q, Wang C, Zhang W, Iqbal J, Hu Y, Greiner TC, Cornish A, Kim JH, Rabadan R, Abate F, Wang X, Inghirami GG, McKeithan TW, Chan WC. Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data. Sci Rep. 2017 Sep 12.

Oh H, Grinberg-Bleyer Y, Liao W, Maloney D, Wang P, Wu Z, Wang J, Bhatt DM, Heise N, Schmid RM, Hayden MS, Klein U, Rabadan R, Ghosh S. An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function.  Immunity. 2017 Sep 19. Epub 2017 Sep 7.

Varano G, Raffel S, Sormani M, Zanardi F, Lonardi S, Zasada C, Perucho L, Petrocelli V, Haake A, Lee AK, Bugatti M, Paul U, Van Anken E, Pasqualucci L, Rabadan R, Siebert R, Kempa S, Ponzoni M, Facchetti F, Rajewsky K, Casola S. The B-cell receptor controls fitness of MYC-driven lymphoma cells via GSK3β inhibition.  Nature. 2017 Jun 8. Epub 2017 May 31.

Pappas K, Xu J, Zairis S, Resnick-Silverman L, Abate F, Steinbach N, Ozturk S, Saal LH, Su T, Cheung P, Schmidt H, Aaronson S, Hibshoosh H, Manfredi J, Rabadan R, Parsons R. p53 Maintains Baseline Expression of Multiple Tumor Suppressor Genes. Mol Cancer Res. 2017 Aug;15. Epub 2017 May 8.

Rizvi AH, Camara PG, Kandror EK, Roberts TJ, Schieren I, Maniatis T, Rabadan R.  Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development. Nat Biotechnol. 2017 Jun. Epub 2017 May 1.

Lim J, Giri PK, Kazadi D, Laffleur B, Zhang W, Grinstein V, Pefanis E, Brown LM, Ladewig E, Martin O, Chen Y, Rabadan R, Boyer F, Rothschild G, Cogné M, Pinaud E, Deng H, Basu U. Nuclear Proximity of Mtr4 to RNA Exosome Restricts DNA Mutational Asymmetry. Cell. 2017 Apr 20.

Abe T, Lee A, Sitharam R, Kesner J, Rabadan R, Shapira S. Germ-Cell-Specific Inflammasome Component NLRP14 Negatively Regulates Cytosolic Nucleic Acid Sensing to Promote Fertilization. Immunity. 2017 Apr 18.

Tzoneva G, Perez-Garcia A, Carpenter Z, Khiabanian H, Tosello V, Allegretta M, Paietta E, Racevskis J, Rowe JM, Tallman MS, Paganin M, Basso G, Hof J, Kirschner-Schwabe R, Palomero T, Rabadan R, Ferrando A. Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL . Nat Med. 2013 Mar;19(3):368-71.

Singh D, Chan JM, Zoppoli P, Niola F, Sullivan R, Castano A, Liu EM, Reichel J, Porrati P, Pellegatta S, Qiu K, Gao Z, Ceccarelli M, Riccardi R, Brat DJ, Guha A, Aldape K, Golfinos JG, Zagzag D, Mikkelsen T, Finocchiaro G, Lasorella A, Rabadan R, Iavarone A. Transforming fusions of FGFR and TACC genes in human glioblastoma . Science. 2012 Sep 7;337(6099):1231-5.

Greenbaum B, Li O, Poon L, Levine A, Rabadan R. Viral reassortment as an information exchange between viral segments . Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3341-6.

Dapito D H, Mencin A, Gwak G Y, Pradere J P, Jang M K, Mederacke I, Caviglia J M, Khiabanian H, Adeyemi A, Bataller R, Lefkowitch J H, Bower M, Friedman R, Sartor R B, Rabadan R, Schwabe R F. Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4 . Cancer Cell. 2012 April 17;21(4):504-516.

Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliott O, Chan J, Bhagat G, Chadburn A, Gaidano G, Mullighan CG, Rabadan R, Dalla-Favera R. Analysis of the coding genome of diffuse large B-cell lymphoma . Nat Genet. 2011 Jul 31;43(9):830-7.

Tiacci E, Trifonov V, Schiavoni G, Holmes A, Kern W, Martelli MP, Pucciarini A, Bigerna B, Pacini R, Wells VA, Sportoletti P, Pettirossi V, Mannucci R, Elliott O, Liso A, Ambrosetti A, Pulsoni A, Forconi F, Trentin L, Semenzato G, Inghirami G, Capponi M, Di Raimondo F, Patti C, Arcaini L, Musto P, Pileri S, Haferlach C, Schnittger S, Pizzolo G, Foà R, Farinelli L, Haferlach T, Pasqualucci L, Rabadan R, Falini B. BRAF mutations in hairy-cell leukemia . N Engl J Med. 2011 Jun 16;364(24):2305-15.

Trifonov V, Khiabanian H, Rabadan R. Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus . N Engl J Med. 2009 Jul 9;361(2):115–119.