Selected
Publications
Our main scientific interests lie in modeling and understanding the dynamics of biological
systems through the lens of genomics. Our work focuses on three distinct topics:
Cancer, Infectious Diseases, and Electronic Health Records.
This page contains links to Selected Publications. We also have a full Publications Archive.
“Computing The Role Of Alternative Splicing In Cancer”
AUTHORS: Zhaoqi Liu, Raul Rabadan.
Trends In Cancer. 2021 Jan 23. doi: 10.1016/j.trecan.2020.12.015
“Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia”
AUTHORS: Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown, Juan Angel Patiño-Galindo, Timothy Chu, Aidan Quinn, Thomas Gunning, Laura Belver, Alberto Ambesi-Impiombato, Valeria Tosello, Zhengqiang Wang, Maria Luisa Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Milagros Balbin, Concepcion Nicolas, Julie M. Gastier-Foster, Meenakshi Devidas, Mignon L. Loh, Elisabeth Paietta, Martin S. Tallman, Jacob M. Rowe, Mark Litzow, Mark D. Minden, Jules Meijerink, Raul Rabadan+, Adolfo Ferrando+.
Nature Cancer. 2020 Oct 19. doi: 10.1038/s43018-020-00124-1.
“A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors”
AUTHORS: Laura Crowley, Francesco Cambuli, Luis Aparicio, Maho Shibata, Brian D Robinson, Shouhong Xuan, Weiping Li, Hanina Hibshoosh, Massimo Loda, Raul Rabadan+, Michael M Shen+.
*These authors have contributed equally to this work. +Corresponding authors.
“Identification of Relevant Genetic Alterations in Cancer using Topological Data Analysis.”
AUTHORS: Raúl Rabadán+, Yamina Mohamedi, Udi Rubin, Tim Chu, Oliver Elliott, Luis Arnés, Santiago Cal, Álvaro J. Obaya, Arnold J. Levine+, Pablo G. Cámara+.
*These authors have contributed equally to this work. +Corresponding authors.
Nature Commun. 2020 July 30. doi: 10.1038/s41467-020-17659-7.
“Topological Data Analysis for Genomics and Evolution: Topology in Biology.”
AUTHORS: Raul Rabadan and Andrew J. Blumberg.
“A Random Matrix Theory Approach to Denoise Single-Cell Data”
AUTHORS: Luis Aparicio, Mykola Bordyuh, Andrew Blumberg, Raul Rabadan.
“Genomic Characterization of HIV-Associated Plasmablastic Lymphoma Identifies Pervasive Mutations in the JAK–STAT Pathway.”
AUTHORS: Zhaoqi Liu, Ioan Filip, Karen Gomez, Dewaldt Engelbrecht, Shabnum Meer, Pooja N. Lalloo, Pareen Patel, Yvonne Perner, Junfei Zhao, Jiguang Wang, Laura Pasqualucci, Raul Rabadan and Pascale Willem.
Blood Cancer Discovery. 2020 June 10. doi:10.1158/2643-3230.BCD-20-0051
“Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulation.”
AUTHORS: Liu Z, Zhang J, Sun Y, Perea-Chamblee TE, Manley JL, Rabadan R.
Proc Natl Acad Sci U S A. 2020 Apr 24. pii: 201922622. doi: 10.1073/pnas.1922622117.
“Mutations in the RNA splicing factor SF3B1 promote tumorigenesis through MYC stabilization.”
AUTHORS: Liu Z, Yoshimi A, Wang J, Cho H, Chun-Wei Lee S, Ki M, Bitner L, Chu T, Shah H, Liu B, Mato AR, Ruvolo P, Fabbri G, Pasqualucci L, Abdel-Wahab O, Rabadan R.
Cancer Discov. 2020 Mar 18. pii: CD-19-1330. doi: 10.1158/2159-8290.CD-19-1330.
“HLA Typing from RNA Sequencing and Applications to Cancer.”
AUTHORS: Rose Orenbuch, Ioan Filip, Raul Rabadan+.
*These authors have contributed equally to this work. +Corresponding authors.
Bioinformatics for Cancer Immunotherapy. 2020 March 03. pp. 71-92
“arcasHLA: high resolution HLA typing from RNAseq.”
AUTHORS: Orenbuch R, Filip I, Comito D, Shaman J, Pe'er I, Rabadan R.
Bioinformatics. 2019 Jun 7. pii: btz474. doi: 10.1093/bioinformatics/btz474.
“Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.”
AUTHORS: 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.
Nat Med. 2019 Feb 11. doi: 10.1038/s41591-019-0349-y.
“Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy.”
AUTHORS: 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.