Osteosarcoma Explorer: A Data Commons with Clinical, Genomic, Protein, and Tissue Imaging Data for Osteosarcoma Research Yang DM*,#, Zhou Q#, Cline L, Cheng X, Luo D, Lai H, Li Y, Jin KW, Yao B, Leavey PJ, Rakheja D, Lo T, Hall D, Barkauskas DA, Shulman DS, Janeway K, Khanna C, Gorlick R, Menzies C, Zhan X, Xiao G, Skapek SX, Xu L, Klesse LJ, Crompton BD, Xie Y*.
JCO Clinical Cancer Informatics (2023): e2300104.

Development of a data model and data commons for germ cell tumors Ci B#, Yang DM#, Krailo M, Xia C, Yao B, Luo D, Zhou Q, Xiao G, Xu L, Skapek SX, Murray MM, Amatruda JF, Klosterkemper L, Shaikh F, Faure-Conter C, Fresneau B, Volchenboum SL, Stoneham S, Lopes LF, Nicholson J, Frazier AL, Xie Y.
JCO Clinical Cancer Informatics (2020). DOI: 10.1200/CCI.20.00025

Developing and Using a Data Commons for Understanding the Molecular Characteristics of Germ Cell Tumors Ci B, Lin SY, Yao B, Luo D, Xu L, Krailo M, Murray MJ, Amatruda JF, Frazier AL, Xie Y.
Methods in molecular biology (Clifton, N.J.). 2021. 2195. 263-275. PubMed PMID: 32852769; PubMed Central ID: Publication Status: Published

LCE: an open web portal to explore gene expression and clinical associations in lung cancer Xie Y, Zhou Q, Xiao G, Cai L, Lin S, Huffman K, Heymach J, Yang L, Tang H, Minna J, Ci B, Zhou Y, Luo D, Girard L, Yao B, Allen J, Gazdar A, Wistuba I.
Oncogene 2018 Dec 7. 38. 14. 2551-2564. PubMed PMID: 30532070; PubMed Central ID: PMC6477796; Publication Status: Published

Exon skipping in genes encoding lineage-defining myogenic transcription factors in rhabdomyosarcoma Butler E, Xu L, Rakheja D, Schwettmann B, Toubbeh S, Guo L, Kim J, Skapek SX, Zheng Y
Cold Spring Harbor Molecular Case Studies 2022 Aug. 8. 5. a006190. PubMed PMID: 35933111; PubMed Central ID: PMC9528969; Publication Status: Published

Cross-Talk Between Histone Methyltransferases and Demethylases Regulate REST Transcription During Neurogenesis Swaminathan J, Maegawa S, Shaik S, Sharma A, Bravo-Alegria J, Guo L, Xu L, Harmanci A, Gopalakrishnan V
Frontiers in Oncology 2022 May 6. 12. 855167. PubMed PMID: 35600406; PubMed Central ID: PMC9120943; Publication Status: Published

Serum Small RNA Sequencing and miR-375 Assay Do Not Identify the Presence of Pure Teratoma at Postchemotherapy Retroperitoneal Lymph Node Dissection Lafin JT, Kenigsberg AP, Meng X, Abe D, Savelyeva A, Singla N, Woldu SL, Lotan Y, Mauck RJ, Lewis CM, Margulis V, Wong D, Jia L, Kapur P, Xu L, Speir RW, Chesnut GT, Frazier AL, Strand DW, Coleman N, Murray MJ, Amatruda JF, Bagrodia A.
European urology open science 2021 Apr. 26. 83-87. PubMed PMID: 33997822; PubMed Central ID: PMC8121258; Publication Status: Published

REST promotes ETS1-dependent vascular growth in medulloblastoma Shaik S, Maegawa S, Haltom AR, Wang F, Xiao X, Dobson T, Sharma A, Yang Y, Swaminathan J, Kundra V, Li XN, Schadler K, Harmanci A, Xu L, Gopalakrishnan V.
Molecular oncology 2021 May. 15. 5. 1486-1506. PubMed PMID: 33469989; PubMed Central ID: PMC8096796; Publication Status: Published

Real-World Application of Pre-Orchiectomy miR-371a-3p Test in Testicular Germ Cell Tumor Management Badia RR, Abe D, Wong D, Singla N, Savelyeva A, Chertack N, Woldu SL, Lotan Y, Mauck R, Ouyang D, Meng X, Lewis CM, Majmudar K, Jia L, Kapur P, Xu L, Frazier AL, Margulis V, Strand DW, Coleman N, Murray MJ, Amatruda JF, Lafin JT, Bagrodia A
The Journal of urology 2021 Jan. 205. 1. 137-144. PubMed PMID: 32856980; PubMed Central ID: Publication Status: Published

HDAC6 promotes growth, migration/invasion, and self-renewal of rhabdomyosarcoma Pham TQ, Robinson K, Xu L, Pavlova MN, Skapek SX, Chen EY
Oncogene 2021 Jan. 40. 3. 578-591. PubMed PMID: 33199827; PubMed Central ID: PMC7855743; Publication Status: Published

Functional imaging of RAS pathway targeting in malignant peripheral nerve sheath tumor cells and xenografts Butler E, Schwettmann B, Geboers S, Hao G, Kim J, Nham K, Sun X, Laetsch TW, Xu L, Williams NS, Skapek SX
Pediatric blood & cancer 2020 Dec. 67. 12. e28639. PubMed PMID: 32975370; PubMed Central ID: Publication Status: Published

Deep Learning of Rhabdomyosarcoma Pathology Images for Classification and Survival Outcome Prediction Zhang X, Wang S, Rudzinski ER, Agarwal S, Rong R, Barkauskas DA, Daescu O, Furman L, Venkatramani R, Xie Y, Xiao G, Leavey P
The American Journal of Pathology 2022 Jun. 192. 6. 917-925. PubMed PMID: 35390316; PubMed Central ID: PMC9194647; Publication Status: Published

Bayesian Modeling Identifies PLAG1 as a Key Regulator of Proliferation and Survival in Rhabdomyosarcoma Cells Zheng Y, Xu L, Hassan M, Zhou X, Zhou Q, Rakheja D, Skapek SX
Molecular cancer research MCR. 2020 Mar. 18. 3. 364-374. PubMed PMID: 31757836; PubMed Central ID: PMC7056573; Publication Status: Published