2018 Publications
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Phf6 loss enhances HSC self-renewal driving tumor initiation and leukemia stem cell activity in T-ALL.
Wendorff AA, Quinn SA, Rashkovan M, Madubata CJ, Ambesi-Impiombato A, Litzow MR, Tallman MS, Paietta E, Paganin M, Basso G, Gastier-Foster JM, Loh ML, Rabadan R, Van Vlierberghe P, Ferrando AA.

Dose-response modeling in high-throughput cancer drug screenings: A case study with recommendations for practitioners.
Wesley Tansey, Kathy Li, Haoran Zhang, Scott W Linderman, Raul Rabadan, David M Blei, Chris H Wiggins

Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations.
Jason K Sa, Seung Won Choi, Junfei Zhao, Yeri Lee, Jing Zhang, Doo‐Sik Kong, Jung Won Choi, Ho Jun Seol, Jung‐Il Lee, Antonio Iavarone, Raul Rabadan, Do‐Hyun Nam.

Topological Data Analysis of Single-cell Hi-C Contact Maps.
Mathieu Carriere, Raul Rabadan

A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes.
Ahrim Youn, Kyung In Kim, Raul Rabadan, Benjamin Tycko, Yufeng Shen, Shuang Wang

Suppression of GATA3 Binding Drives Selective Abrogation of NOTCH1-MYC Enhancer Activity By Nucleosome Invasion in Thymocyte Development and Leukemia.
Laura Belver, Alexander Y Yang, Daniel Herranz, Aidan Quinn, Francesco G Brundu, Pablo Perez-Duran, Silvia Alvarez, Devya Gurung, Pedro P Rocha, Ramya Raviram, Marissa Rashkovan, Raul Rabadan, Adolfo A Ferrando

High Throughput Droplet Single-Cell Genotyping of Transcriptomes (GoT) Reveals the Cell Identity Dependency of the Transcriptional Output of Somatic Mutations.
Anna S Nam, Kyu-Tae Kim, Ronan Chaligne, Franco Izzo, Chelston Ang, Nathaniel Omans, Alessandro Pastore, Justin Taylor, Alicia Alonso, Wayne Tam, Ronald Hoffman, Joseph Scandura, Raul Rabadan, Omar I Abdel-Wahab, Peter Smibert, Dan A Landau.

Mutations in the RNA Splicing Factor SF3B1 Promote Transformation through MYC Stabilization.
Akihide Yoshimi, Zhaoqi Liu, Wang Jiguang, Hana Cho, Stanley C Lee, Michelle Ki, Lillian E Bitner, Timothy Chu, Anthony R Mato, Peter P Ruvolo, Giulia Fabbri, Laura Pasqualucci, Raul Rabadan, Omar I Abdel-Wahab

DDIS-13. UNDERSTANDING GLIOBLASTOMA SUSCEPTIBILITY TO TOP2-TARGETING DRUGS FOR PERSONALIZED THERAPY.
Chidiebere Awah, Edgar Gonzalez-Buendía, Junfei Zhao, Eric Feldstein, Li Chen, Aayushi Mahajan, Louisa Warnke, Lu Wang, Cheol Park, Jan Winter, Silvana Konermann, Ali Shilatifard, C David James, Raul Rabadan, Patrick Hsu, Mukesh Bansal, Atique Ahmed, Adam Sonabend

The Holdout Randomization Test: Principled and Easy Black Box Feature Selection.
W Tansey, V Veitch, H Zhang, R Rabadan, DM Blei

Blastic plasmacytoid dendritic cell neoplasm: genomics mark epigenetic dysregulation as a primary therapeutic target.
Maria Rosaria Sapienza, Francesco Abate, Federica Melle, Stefania Orecchioni, Fabio Fuligni, Maryam Etebari, Valentina Tabanelli, Maria Antonella Laginestra, Alessandro Pileri, Giovanna Motta, Maura Rossi, Claudio Agostinelli, Elena Sabattini, Nicola Pimpinelli, Mauro Truni, Brunangelo Falini, Lorenzo Cerroni, Giovanna Talarico, Rossana Piccioni, Stefano Amente, Valentina Indio, Giuseppe Tarantino, Francesco Brundu, Marco Paulli, Emilio Berti, Fabio Facchetti, Gaetano Ivan Dellino, Francesco Bertolini, Claudio Tripodo, Raul Rabadan, Stefano A. Pileri

Quasi-universality in single-cell sequencing data.
L Aparicio, M Bordyuh, AJ Blumberg, R Rabadan

Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy.
Jin-Ku Lee, Zhaoqi Liu, Jason K. Sa, Sang Shin, Jiguang Wang, Mykola Bordyuh, Hee Jin Cho, Oliver Elliott, Timothy Chu, Seung Won Choi, Daniel I. S. Rosenbloom, In-Hee Lee, Yong Jae Shin, Hyun Ju Kang, Donggeon Kim, Sun Young Kim, Moon-Hee Sim, Jusun Kim, Taehyang Lee, Yun Jee Seo, Hyemi Shin, Mijeong Lee, Sung Heon Kim, Yong-Jun Kwon, Jeong-Woo Oh, Minsuk Song, Misuk Kim, Doo-Sik Kong, Jung Won Choi, Ho Jun Seol, Jung-Il Lee, Seung Tae Kim, Joon Oh Park, Kyoung-Mee Kim, Sang-Yong Song, Jeong-Won Lee, Hee-Cheol Kim, Jeong Eon Lee, Min Gew Choi, Sung Wook Seo, Young Mog Shim, Jae Ill Zo, Byong Chang Jeong, Yeup Yoon, Gyu Ha Ryu, Nayoung K. D. Kim, Joon Seol Bae, Woong-Yang Park, Jeongwu Lee, Roel G. W. Verhaak, Antonio Iavarone, Jeeyun Lee, Raul Rabadan, Do-Hyun Nam.

Distinct genomic profile and specific targeted drug responses in adult cerebellar glioblastoma.
Hee Jin Cho, Junfei Zhao, Sang Won Jung, Erik Ladewig, Doo-Sik Kong, Yeon-Lim Suh, Yeri Lee, Donggeon Kim, Sun Hee Ahn, Mykola Bordyuh, Hyun Ju Kang, Jason K Sa, Yun Jee Seo, Sung Tae Kim, Do Hoon Lim, Yun-Sik Dho, Jung-Il Lee, Ho Jun Seol, Jung Won Choi, Woong-Yang Park, Chul-Kee Park, Raul Rabadan, Do-Hyun Nam.

Copy number profiling across glioblastoma populations has implications for clinical trial design.
Patrick J Cimino, Lisa McFerrin, Hans-Georg Wirsching, Sonali Arora, Hamid Bolouri, Raul Rabadan, Michael Weller, Eric C Holland.

Quantitative compositional and spatial analysis of tumor microenvironment (TME) in primary melanoma.
Robyn D Gartrell, Andrew Chen, Douglas K Marks, Thomas D Hart, Gen Li, Alan Wu, Yan Lu, Camden Esancy, Zoe Blake, Bret Taback, Raul Rabadan, Howard L Kaufman, Charles G Drake, Basil Horst, Anthea Monod, Yvonne Saenger.

On statistical modeling of sequencing noise in high depth data to assess tumor evolution.
Raul Rabadan, Gyan Bhanot, Sonia Marsilio, Nicholas Chiorazzi, Laura Pasqualucci, Hossein Khiabanian.

The possibility of cancer immune editing in gliomas. A critical review.
Víctor A Arrieta, Bernardo Cacho-Díaz, Junfei Zhao, Raul Rabadan, Li Chen, Adam M Sonabend.

Black Box FDR.
Wesley Tansey, Yixin Wang, David M Blei, Raul Rabadan.

Correlation of immune infiltration of cytotoxic T cells and activated microglia in glioblastoma (GBM) post anti-PD1 therapy with response.
Andrew Silverman, Robyn Denise Gartrell, Junfei Zhao, Syeda Sabeeka Batool, Thomas D Hart, Syed Shabee Hasan, James H Garvin, George Zanazzi, Fabio Massaiti Iwamoto, Raul Rabadan, Peter Canoll, Yvonne M Saenger.

The Egyptian rousette genome reveals unexpected features of bat antiviral immunity.
Stephanie S Pavlovich, Sean P Lovett, Galina Koroleva, Jonathan C Guito, Catherine E Arnold, Elyse R Nagle, Kirsten Kulcsar, Albert Lee, Françoise Thibaud-Nissen, Adam J Hume, Elke Mühlberger, Luke S Uebelhoer, Jonathan S Towner, Raul Rabadan, Mariano Sanchez-Lockhart, Thomas B Kepler, Gustavo Palacios.

Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma.
Enrico Tiacci, Erik Ladewig, Gianluca Schiavoni, Alex Penson, Elisabetta Fortini, Valentina Pettirossi, Yuchun Wang, Ariele Rosseto, Alessandra Venanzi, Sofija Vlasevska, Roberta Pacini, Simonetta Piattoni, Alessia Tabarrini, Alessandra Pucciarini, Barbara Bigerna, Alessia Santi, Alessandro M Gianni, Simonetta Viviani, Antonello Cabras, Stefano Ascani, Barbara Crescenzi, Cristina Mecucci, Laura Pasqualucci, Raul Rabadan, Brunangelo Falini.

Quantifying genetic innovation: Mathematical foundations for the topological study of reticulate evolution.
Michael Lesnick, Raúl Rabadán, Daniel Rosenbloom.

Increased HOXA5 expression provides a selective advantage for gain of whole chromosome 7 in IDH wild-type glioblastoma.
Patrick J Cimino, Youngmi Kim, Hua-Jun Wu, Jes Alexander, Hans-Georg Wirsching, Frank Szulzewsky, Ken Pitter, Tatsuya Ozawa, Jiguang Wang, Julio Vazquez, Sonali Arora, Raul Rabadan, Ross Levine, Franziska Michor, Eric C Holland.

Quantitative Analysis of Immune Infiltrates in Primary Melanoma.
Robyn D Gartrell, Douglas K Marks, Thomas D Hart, Gen Li, Danielle R Davari, Alan Wu, Zoë Blake, Yan Lu, Kayleigh N Askin, Anthea Monod, Camden L Esancy, Edward C Stack, Dan Tong Jia, Paul M Armenta, Yichun Fu, Daisuke Izaki, Bret Taback, Raul Rabadan, Howard L Kaufman, Charles G Drake, Basil A Horst, Yvonne M Saenger.

Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma.
Luis Arnes, Zhaoqi Liu, Jiguang Wang, Hans Carlo Maurer, Irina Sagalovskiy, Marta Sanchez-Martin, Nikhil Bommakanti, Diana C Garofalo, Dina A Balderes, Lori Sussel, Kenneth P Olive, Raul Rabadan.

Genetic landscape of ultra-stable chronic lymphocytic leukemia patients.
S Raponi, I Del Giudice, M Marinelli, J Wang, L Cafforio, C Ilari, A Piciocchi, M Messina, S Bonina, S Tavolaro, M Bordyuh, P Mariglia, N Peragine, FR Mauro, S Chiaretti, S Molica, M Gentile, A Visentin, L Trentin, GM Rigolin, A Cuneo, F Diop, D Rossi, G Gaidano, A Guarini, R Rabadan, R Foà.

Saa3 is a key mediator of the protumorigenic properties of cancer-associated fibroblasts in pancreatic tumors.
Magdolna Djurec, Osvaldo Graña, Albert Lee, Kevin Troulé, Elisa Espinet, Lavinia Cabras, Carolina Navas, María Teresa Blasco, Laura Martín-Díaz, Miranda Burdiel, Jing Li, Zhaoqi Liu, Mireia Vallespinós, Francisco Sanchez-Bueno, Martin R Sprick, Andreas Trumpp, Bruno Sainz, Fátima Al-Shahrour, Raul Rabadan, Carmen Guerra, Mariano Barbacid.

Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia.
Gannie Tzoneva, Chelsea L Dieck, Koichi Oshima, Alberto Ambesi-Impiombato, Marta Sánchez-Martín, Chioma J Madubata, Hossein Khiabanian, Jiangyan Yu, Esme Waanders, Ilaria Iacobucci, Maria Luisa Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Julie M Gastier-Foster, Mignon L Loh, Renate Kirschner-Schwabe, Charles G Mullighan, Raul Rabadan, Adolfo A Ferrando.

Precision Medicine for Acute Kidney Injury (AKI): Redefining AKI by Agnostic Kidney Tissue Interrogation and Genetics.
Krzysztof Kiryluk, Andrew S Bomback, Yim-Ling Cheng, Katherine Xu, Pablo G Camara, Raul Rabadan, Peter A Sims, Jonathan Barasch.