2019 Publications
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Can patient selection and neoadjuvant administration resuscitate PD-1 inhibitors for glioblastoma?
Arrieta VA, Iwamoto F, Lukas RV, Sachdev S, Rabadan R, Sonabend AM.

Secretome analysis of patient-derived GBM tumor spheres identifies midkine as a potent therapeutic target.
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.

Longitudinal molecular trajectories of diffuse glioma in adults.
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.

Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers.
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.

Role of Vav1 Genomic Alterations in T-Cell Differentiation and Transformation in Peripheral T-Cell Lymphoma.
Jose Rodriguez Cortes, PhD, Anisha R. Cooke, Aidan Quinn, Ioan Filip, PhD, Juan Angel Patino, PhD, Raul Rabadan, PhD, Adolfo A. Ferrando, MD PhD, Teresa Palomero, PhD.

RNA Sequencing of Hodgkin Lymphoma Reed-Sternberg Cells Uncovers a Plasma Cell Signature and Escape from NK Cell Recognition.
Ethel Cesarman, MD PhD, Mikhail Roshal, MD PhD, Jonathan Reichel, PhD, Wagner Florian, PhD, Bhavneet Binder, Sakellarios Zairis, Jouliana Sadek, PhD, Joshua Brody, MD, Raul Rabadan, PhD, Sandeep Dave, MD.

IMMU-42. CD8+ T-CELLS MEDIATE IMMUNOEDITING, AND INFLUENCE GENOTYPE, TUMOR ONCOGENIC PATHWAYS AND MICROENVIRONMENT DURING PROGRESSION OF MURINE GLIOMAS.
J Robert Kane, Junfei Zhao, Takashi Tsujiuchi, Brice Laffleur, Aayushi Mahajan, Ganesh Rao, Angeliki Mela, Crismita Dmello, Victor A Arrieta, Li Chen, Daniel Y Zhang, Catalina Lee-Chang, Ting Xiao, Gerson Rothschild, Uttiya Basu, Craig Horbinski, Maciej S Lesniak, Amy Heimberger, Raul Rabadan, Peter D Canoll, Adam Sonabend.

Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors.
Neil Vasan, Pedram Razavi, Jared L Johnson, Hong Shao, Hardik Shah, Alesia Antoine, Erik Ladewig, Alexander Gorelick, Ting-Yu Lin, Eneda Toska, Guotai Xu, Abiha Kazmi, Matthew T Chang, Barry S Taylor, Maura N Dickler, Komal Jhaveri, Sarat Chandarlapaty, Raul Rabadan, Ed Reznik, Melissa L Smith, Robert Sebra, Frauke Schimmoller, Timothy R Wilson, Lori S Friedman, Lewis C Cantley, Maurizio Scaltriti, José Baselga.

Predicting Clinical Outcomes in Glioblastoma: An Application of Topological and Functional Data Analysis.
Lorin Crawford, Anthea Monod, Andrew X Chen, Sayan Mukherjee, Raúl Rabadán.

The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function.
Singer RA, Arnes L, Cui Y, Wang J, Gao Y, Guney MA, Burnum-Johnson KE, Rabadan R, Ansong C, Orr G, Sussel L.

Gata3-controlled nucleosome eviction drives Myc enhancer activity in T-cell development and leukemia.
Belver L, Yang AY, Albero R, Herranz D, Brundu FG, Quinn SA, Perez-Duran P, Alvarez S, Gianni F, Rashkovan M, Gurung D, Rocha PP, Raviram R, Reglero C, Cortes JR, Cooke AJ, Wendorff AA, Cordo V, Meijerink JP, Rabadan R, Ferrando AA.

A Structure-Informed Atlas of Human-Virus Interactions.
Gorka Lasso, Sandra V. Mayer, Evandro R. Winkelmann, Tim Chu, Oliver Elliott, Juan Angel Patino-Galindo, Kernyu Park, Raul Rabadan, Barry Honig, Sagi D. Shapira.

Tissue-Resident Memory T Cells Mediate Immune Homeostasis in the Human Pancreas Through the PD-1/PD-L1 Pathway.
Stuart Weisberg, Dustin J Carpenter, Michael Chait, Pranay Dogra, Robyn D Gartrell-Corrado, Andrew X Chen, Sean Campbell, Wei` Liu, Pooja Saraf, Mark E Snyder, Masaru Kubota, Nichole M Danzl, Beth A Schrope, Raul Rabadan, Yvonne Saenger, Xiaojuan Chen, Donna Farberi.

Disease-Causing Mutations in SF3B1 Alter Splicing by Disrupting Interaction with SUGP1.
Jian Zhang, Abdullah M Ali, Yen K Lieu, Zhaoqi Liu, Jianchao Gao, Raul Rabadan, Azra Raza, Siddhartha Mukherjee, James L Manley.

Repurposing dasatinib for diffuse large B cell lymphoma.
Scuoppo C, Wang J, Persaud M, Mittan SK, Basso K, Pasqualucci L, Rabadan R, Inghirami G, Grandori C, Bosch F, Dalla-Favera R.

2003-Acute Myeloid Leukemia Cells Seize Serotonin Signaling in Osteoblasts to Engraft and Proliferate.
Marta Galan-Diez, Junfei Zhao, Raul Rabadan, Stavroula Kousteni.

Somatic mutations and cell identity linked by Genotyping of Transcriptomes.
Nam AS, Kim KT, Chaligne R, Izzo F, Ang C, Taylor J, Myers RM, Abu-Zeinah G, Brand R, Omans ND, Alonso A, Sheridan C, Mariani M, Dai X, Harrington E, Pastore A, Cubillos-Ruiz JR, Tam W, Hoffman R, Rabadan R, Scandura JM, Abdel-Wahab O, Smibert P, Landau DA.

TOP2B Enzymatic Activity on Promoters and Introns Modulates Multiple Oncogenes in Human Gliomas.
Edgar Gonzalez-Buendia, Junfei Zhao, Lu Wang, Subhas Mukherjee, Stacy A Marshall, Eric Feldstein, Daniel Zhang, Catalina Lee-Chang, Aayushi Mahajan, Li Chen, Ronald Realubit, Charles Karan, Lisa Magnuson, Craig Horbinski, Jann N Sarkaria, Ahmed Mohyeldin, Ichiro Nakano, Charles D James, Daniel J Brat, Atique Ahmed, Peter Canoll, Raul Rabadan, Ali Shilatifard, Adam M Sonabend.

High density of CD68+ HLA-DR-macrophages in the stroma of primary melanoma correlates with an unfavorable immune microenvironment as assessed by Digital Spatial Profiling.
Emanuelle M Rizk, Andrew Chen, Andrew M Silverman, Douglas K Marks, Raul Rabadan, Kit Fuhrman, Alison VanSchoiack, Yan Liang, Joseph Beechem, Yvonne M Saenger, Robyn D Gartrell.

Double PIK3CA mutations in cis enhance oncogene activation and sensitivity to PI3K alpha inhibitors in breast cancer.
Neil Vasan, Pedram Razavi, Jared Johnson, Hong Shao, Hardik Shah, Alesia Antoine, Erik Ladewig, Alexander Gorelick, Eneda Toska, Guotai Xu, Abiha Kazmi, Matthew T Chang, Barry S Taylor, Maura N Dickler, Komal Jhaveri, Raul Rabadan, Ed Reznik, Melissa L Smith, Robert Sebra, Lewis C Cantley, Maurizio Scaltriti, Jose Baselga.

Topological Data Analysis for Genomics and Evolution: Topology in Biology.
Raul Rabadan and Andrew J. Blumberg.

arcasHLA: high resolution HLA typing from RNAseq.
Orenbuch R, Filip I, Comito D, Shaman J, Pe'er I, Rabadan R.

Novel insights into the genetics and epigenetics of MALT lymphoma unveiled by next generation sequencing analyses.
Cascione L, Rinaldi A, Bruscaggin A, Tarantelli C, Arribas AJ, Kwee I, Pecciarini L, Mensah AA, Spina V, Chung EYL, Terzi di Bergamo L, Dirnhofer S, Tzankov A, Miranda RN, Young KH, Traverse-Glehen A, Gaidano G, Swerdlow SH, Gascoyne R, Rabadan R, Ponzoni M, Bhagat G, Rossi D, Zucca E, Bertoni F.

The 2019 Mathematical Oncology Roadmap.
Rockne RC, Hawkins-Daarud A, Swanson KR, Sluka JP, Glazier JA, Macklin P, Hormuth D, Jarrett AM, Lima EABDF, Oden J, Biros G, Yankeelov TE, Curtius K, Bakir IA, Wodarz D, Komarova N, Aparicio L, Bordyuh M, Rabadan R, Finley S, Enderling H, Caudell JJ, Moros EG, Anderson ARA, Gatenby R, Kaznatcheev A, Jeavons P, Krishnan N, Pelesko J, Wadhwa RR, Yoon N, Nichol D, Marusyk A, Hinczewski M, Scott JG.

Complete Regression of Advanced Pancreatic Ductal Adenocarcinomas upon Combined Inhibition of EGFR and C-RAF.
Blasco MT, Navas C, Martín-Serrano G, Graña-Castro O, Lechuga CG, Martín-Díaz L, Djurec M, Li J, Morales-Cacho L, Esteban-Burgos L, Perales-Patón J, Bousquet-Mur E, Castellano E, Jacob HKC, Cabras L, Musteanu M, Drosten M, Ortega S, Mulero F, Sainz B Jr, Dusetti N, Iovanna J, Sánchez-Bueno F, Hidalgo M, Khiabanian H, Rabadán R, Al-Shahrour F, Guerra C, Barbacid M.

Longitudinal active sampling for respiratory viral infections across age groups.
Galanti M, Birger R, Ud-Dean M, Filip I, Morita H, Comito D, Anthony S, Freyer GA, Ibrahim S, Lane B, Ligon C, Rabadan R, Shittu A, Tagne E, Shaman J.

Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.
Zhao J, Chen AX, Gartrell RD, Silverman AM, Aparicio L, Chu T, Bordbar D, Shan D, Samanamud J, Mahajan A, Filip I, Orenbuch R, Goetz M, Yamaguchi JT, Cloney M, Horbinski C, Lukas RV, Raizer J, Rae AI, Yuan J, Canoll P, Bruce JN, Saenger YM, Sims P, Iwamoto FM, Sonabend AM, Rabadan R.

Interrogation of eukaryotic stop codon readthrough signals by in vitro RNA selection.
Anzalone AV, Zairis S, Lin AJ, Rabadan R, Cornish VW.

Rates of asymptomatic respiratory virus infection across age groups.
Galanti M, Birger R, Ud-Dean M, Filip I, Morita H, Comito D, Anthony S, Freyer GA, Ibrahim S, Lane B, Matienzo N, Ligon C, Rabadan R, Shittu A, Tagne E, Shaman J.