Publications

Casillo SM, Gatesman TA…Vaske OM…Pollack IF, Agnihotri S, et al. An ERK5-PFKFB3 axis regulates glycolysis and represents a therapeutic vulnerability in pediatric diffuse midline glioma. Cell Rep. 2024 Jan 23;43(1):113557. doi: 10.1016/j.celrep.2023.113557. PMID: 38113141

Lilly JV, Rokita JL…Vaske OM…Resnick AC, Waanders AJ, et al. The children’s brain tumor network (CBTN) – Accelerating research in pediatric central nervous system tumors through collaboration and open science. Neoplasia. 2023 Jan;35:100846. doi: 10.1016/j.neo.2022.100846. PMID: 36335802

Flores-Toro JA, Jagu S, Kibbe WA, Doroshow JH, et al. The Childhood Cancer Data Initiative: Using the Power of Data to Learn From and Improve Outcomes for Every Child and Young Adult With Pediatric Cancer. J Clin Oncol. 2023 Aug 20;41(24):4045-4053. doi: 10.1200/JCO.22.02208. PMID: 37267580

Leong SP, Witz IP,  Vaske OM, Witte M, et al. Cancer microenvironment and genomics: evolution in process. Clin Exp Metastasis. 2022 Feb;39(1):85-99. doi: 10.1007/s10585-021-10097-9. PMID:33970362

Golbourn BJ, Halbert ME…Vaske OM…Mack SC, Agnihotri S, et al. Loss of MAT2A compromises methionine metabolism and represents a vulnerability in H3K27M mutant glioma by modulating the epigenome. Nat Cancer. 2022 May;3(5):629-648. doi: 10.1038/s43018-022-00348-3. PMID: 35422502

Chun-On P, Hinchie AM, Vaske OM, Greider CW, Alder JK, et al. TPP1 promoter mutations cooperate with TERT promoter mutations to lengthen telomeres in melanoma. Science. 2022 Nov 11;378(6620):664-668. doi: 10.1126/science.abq0607. PMID: 36356143

Sanders LM, Chandra R,  Salama SR, Vaske OM, et al. Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors. Commun Biol. 2022 Dec 13;5(1):1367. doi: 10.1038/s42003-022-04075-4.PMID: 36513728

Beale HC, Roger JM, Haussler D, Vaske OM, et al. The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets. Gigascience. 2021 Mar 13;10(3):giab011. doi: 10.1093/gigascience/giab011.PMID: 33712853

Thornlow B, Hinrichs AS…Vaske O…Kilpatrick AM, Corbett-Detig R, et al. A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. bioRxiv [Preprint]. 2021 Apr 6:2021.04.05.438352. doi: 10.1101/2021.04.05.438352.PMID: 33851162

Kerlavage AR, Kirchhoff AC…Vaske O…Nadaf S, Kibbe WA, et al. Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer. JCO Clin Cancer Inform. 2021 Aug;5:881-896. doi: 10.1200/CCI.21.00040. PMID: 34428097 

Woods AD, Purohit R…Vaske O… Keller C, Wadhwa A, et al. Metastatic pediatric sclerosing epithelioid fibrosarcoma. Cold Spring Harb Mol Case Stud. 2021 Oct 19;7(5):a006093. doi: 10.1101/mcs.a006093. PMID: 34362827 

Thakur S, Jain M… Vaske O…Murguia-Favela L, Narendran A, et al. Identification and in vitro validation of neoantigens for immune activation against high-risk pediatric leukemia cells. Hum Vaccin Immunother. 2021 Dec 2;17(12):5558-5562. doi: 10.1080/21645515.2021.2001243. PMID: 34844524 

Reed MR, Lyle AG, Vaske OM, Rodriguez A, et al. A Functional Precision Medicine Pipeline Combines Comparative Transcriptomics and Tumor Organoid Modeling to Identify Bespoke Treatment Strategies for Glioblastoma. Cells. 2021 Dec 2;10(12):3400. doi: 10.3390/cells10123400.PMID: 34943910

Chang T, Draper JM, Vaske O, Stone MD, Sanford JR, et al. A method for campus-wide SARS-CoV-2 surveillance at a large public university. PLoS One. 2021 Dec 17;16(12):e0261230. doi: 10.1371/journal.pone.0261230.PMID: 34919584

Vivian J, Eizenga JM, Beale HC, Vaske OM, Paten B. Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples. JCO Clin Cancer Inform. 2020 Feb;4:160-170. doi: 10.1200/CCI.19.00095. PMID: 32097024

Pfeil J, Sanders LM, Haussler D, Vaske OM, et al. Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. PLoS Comput Biol. 2020 Apr 10;16(4):e1007753. doi: 10.1371/journal.pcbi.1007753. PMID: 32275708

Castilla-Vallmanya L, Selmer KK…Vaske OM…Grinberg D, Amiel J, et al. Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7. Genet Med. 2020 Jul;22(7):1215-1226. doi: 10.1038/s41436-020-0792-7..PMID: 32376980

Sanders LM, Cheney A,  Salama SR, Vaske OM, et al. Identification of a differentiation stall in epithelial mesenchymal transition in histone H3-mutant diffuse midline glioma. Gigascience. 2020 Dec 15;9(12):giaa136. doi: 10.1093/gigascience/giaa136. PMID: 33319914

Petralia F, Tignor N, Rood BR, Wang P; Children’s Brain Tumor Network; Clinical Proteomic Tumor Analysis Consortium, et al. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. Cell. 2020 Dec 23;183(7):1962-1985.e31. doi: 10.1016/j.cell.2020.10.044. PMID: 33242424 

Vaske OM, Haussler D. Data sharing for pediatric cancers. Science. 2019 Mar 15;363(6432):1125. doi: 10.1126/science.aax2739.PMID: 30872493 

Learned K, Durbin A, Vaske OM, Bjork IM, et al. Barriers to accessing public cancer genomic data. Sci Data. 2019 Jun 20;6(1):98. doi: 10.1038/s41597-019-0096-4.PMID: 31222016 

Vaske OM, Bjork I, Goldstein TC, Haussler D, et al. Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer. JAMA Netw Open. 2019 Oct 2;2(10):e1913968. doi: 10.1001/jamanetworkopen.2019.13968.PMID: 31651965

Sanders LM, Rangaswami A, Sweet-Cordero EA, Vaske OM, et al. Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor. Cold Spring Harb Mol Case Stud. 2019 Oct 23;5(5):a004317. doi: 10.1101/mcs.a004317. PMID: 31645344 

Bjork I, Peralez J, Haussler D, Spunt SL, Vaske OM. Data sharing for clinical utility. Cold Spring Harb Mol Case Stud. 2019 Oct 23;5(5):a004689. doi: 10.1101/mcs.a004689. Print 2019 Oct.PMID: 31645349

Rokita JL, Rathi KS…Vaske OM…Wheeler DA, Maris JM, et all. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Rep. 2019 Nov 5;29(6):1675-1689.e9. doi: 10.1016/j.celrep.2019.09.071.PMID: 31693904

Newton Y, Rassekh SR, Marra MA, Morozova O, et al. Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer. JCO Precis Oncol. 2018;2:PO.17.00198. doi: 10.1200/PO.17.00198. PMID: 31372595 

Mittal, K., Cooper, G.W., et al. (2024). Targeting TRIP13 in favorable histology Wilms tumor with nuclear export inhibitors synergizes with doxorubicin. Commun Biol 7, 1–13. doi: 10.1038/s42003-024-06140-6. PMID: 38383600

Wang Y, Gao B, Wang XS, Lan L, et al. Meiotic protein SYCP2 confers resistance to DNA-damaging agents through R-loop-mediated DNA repair. Nat Commun. 2024 Feb 21;15(1):1568. doi: 10.1038/s41467-024-45693-2.PMID: 38383600 

Comitani, F., Nash, J.O. et al. Diagnostic classification of childhood cancer using multiscale transcriptomics. Nat Med. 2023 29, 656–666. 10.1038/s41591-023-02221-x.

Zhao G, Newbury P, Chen B, Hashizume R, et al. Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma. Acta Neuropathol Commun. 2022 Oct 23;10(1):150. doi: 10.1186/s40478-022-01463-z.PMID: 36274161 

Warren A, Chen Y, Tsherniak A, McFarland JM, et al. Global computational alignment of tumor and cell line transcriptional profiles. Nat Commun. 2021 Jan 4;12(1):22. doi: 10.1038/s41467-020-20294-x.PMID: 33397959 

Zeng B, Glicksberg BS, Chow C, Chen B, et al. OCTAD: an open workspace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features. Nat Protoc. 2021 Feb;16(2):728-753. doi: 10.1038/s41596-020-00430-z. Epub 2020 Dec 23.PMID: 33361798

Pan M, Wright WC, Easton J, Geeleher P, et al. The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma. Nat Commun. 2021 Nov 9;12(1):6468. doi: 10.1038/s41467-021-26640-x.PMID: 34753908 

Savary C, Kim A, Blum Y, de Tayrac M, et al. Depicting the genetic architecture of pediatric cancers through an integrative gene network approach. Sci Rep. 2020 Jan 27;10(1):1224. doi: 10.1038/s41598-020-58179-0.PMID: 31988326 

Gupta A, Taslim C, Tullius BP, Cripe TP. Therapeutic modulation of the CD47-SIRPα axis in the pediatric tumor microenvironment: working up an appetite. Cancer Drug Resist. 2020 May 11;3(3):550-562. doi: 10.20517/cdr.2020.12. PMID: 35582455 

Gupta A, Belsky JA, Cottrell CE, Setty BA, et al. Infantile fibrosarcoma-like tumor driven by novel RBPMS-MET fusion consolidated with cabozantinib. Cold Spring Harb Mol Case Stud. 2020 Oct 7;6(5):a005645. doi: 10.1101/mcs.a005645. PMID: 33028644

Song J, Zhao Q, Xu Y, Zhu L. A signature of 29 immune-related genes pairs to predict prognosis in patients with neuroblastoma. Int Immunopharmacol. 2020 Nov;88:106994. doi: 10.1016/j.intimp.2020.106994. PMID: 33182060