Our Publications

Researchers associated with the UC Santa Cruz Treehouse Initiative write publications in pediatric cancer, and other related fields.

Holly C Beale, Jacquelyn M Roger, Matthew A Cattle, Liam T McKay, Drew K A Thompson, Katrina Learned, A Geoffrey Lyle, Ellen T Kephart, Rob Currie, Du Linh Lam, Lauren Sanders, Jacob Pfeil, John Vivian, Isabel Bjork, Sofie R Salama, David Haussler, Olena M Vaske, The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasetsGigaScience, Volume 10, Issue 3, March 2021, giab011. doi:10.1093/gigascience/giab011


Pfeil J, Sanders L, Anastopoulos I, Lyle A, Weinstein A, Xue Y, Blair A, Beale H, Lee A, Leung S, Dinh P, Shah A, Breese M, Devine W, Bjork I, Salama S, Sweet-Cordero E, Haussler D, Vaske O. Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. PLOS Computational Biology. April 2020. 16. e1007753. doi: 10.1371/journal.pcbi.1007753.

Rao A, Madejska A, Pfeil J, Paten B, Salama S, Haussler D. ProTECT—Prediction of T-Cell Epitopes for Cancer TherapyFrontiers in Immunology. 2020;11:2873. Published Nov 10, 2020. doi:10.3389/fimmu.2020.483296

Sanders, LM, Cheney, A, Seninge, L, et al. Identification of a differentiation stall in epithelial mesenchymal transition in histone H3–mutant diffuse midline gliomaGigaScience9(12). doi:10.1093/gigascience/giaa136.


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

Koncar R.F., Dey B.R., Stanton A.-C.J., Agrawal N., Wassell M.L., McCarl L.H., Locke A.L., Sanders L., Morozova-Vaske O., Myers M.I., Hamilton R.L., Carcaboso A.M., Kohanbash G., Hu B., Amankulor N.M., Felker J., Kambhampati M., Nazarian J., Becher O.J., James C.D., Hashizume R., Broniscer A., Pollack I.F. and Agnihotri S. Identification of Novel RAS Signaling Therapeutic Vulnerabilities in Diffuse Intrinsic Pontine Gliomas. Cancer Research. Posted June 14, 2019. doi:10.1158/0008-5472.CAN-18-3521

Learned K, Durbin A, Currie R, Kephart E, Beale H, Sanders L, Pfeil J, Goldstein T, Salama S, Haussler D, Morozova Vaske O, Bjork I. Barriers to accessing public cancer genomic data. Scientific Data. 20 June 2019. 

Rao A, Madejska A.A., Pfeil J, Paten B, Salama S.R., Haussler D. ProTECT – Prediction of T-cell Epitopes for Cancer Therapy. bioRxiv preprint. Posted July 09, 2019. doi:10.1101/696526

Sanders L, Cheney A, Beale H, Kephart E, Bjork I, Pfeil J, Salama S, Haussler D, Morozova O. Shared dysregulation of long non-coding RNA and developmental gene networks in histone H3 K27M gliomas and PF-A ependymomas. Journal of Clinical Oncology. 26 May 2019.

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

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

Vaske O.M. and Haussler D. Data sharing for pediatric cancers. Science. Posted March 15, 2019. doi:10.1126/science.aax2739

Vivian J. Tools for Large-scale Genomic Analysis and Gene Expression Outlier Modeling for Precision Therapeutics. UC Santa Cruz; 2019.

Vivian J., Eizenga J.M., Beale H.C., Vaske O.M., and Paten, B. Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples. JCO Clinical Cancer Informatics, (4), Posted June 06, 2019. doi:10.1200/CCI.19.00095

Zhang C, Sharma R, Satbir T, Cheney A, Vaske O, Sanders L, Boklan J, Lewis V.A., Anderson R, Kovalchuk O, Lacayo N.J., Narendran A. and Bielamowicz K.J. Establishing a Novel in Vitro Informed Precision Clinical Trial Pathway for Refractory Pediatric Leukemia. Blood, [online]. Posted November 13, 2019. doi:10.1182/blood-2019-131444


Newton Y, Rassekh SR, Deyell RJ, Shen Y, Jones MR, Dunham C, Yip S, Leelakumari S, Zhu J, McColl D, Swatloski T, Salama SR, Ng T, Hendson G, Lee AF, Ma Y, Moore R, Mungall AJ, Haussler D, Stuart J, Jantzen C, Laskin J, Jones SJM, Marra MA, Morozova O; Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer. JCO Precision Oncology 2018 :2, 1-16

Pfeil J, Thornton A, Durbin A, Kephart E, Beale H, Sanders L, Bjork I, Morozova O, Salama SR, Haussler D; Gene expression analysis for improved subtyping of high-risk neuroblastoma. Journal of Clinical Oncology 2018 36:15_suppl, 10559-10559.

Sanders L, Rose-Dey B, Beale H, Kephart E, Pfeil J, Morozova O, Agnihotri S, Salama SR, Haussler D; Comparative gene expression analysis for identifying clinically relevant overexpressed genes in childhood brain tumors. Journal of Clinical Oncology 2018 36:15_suppl, e14033-e14033.


Beale H, Lam DLVivian JNewton Y, Shah AT, Bjork IGoldstein TBrooks A, Stuart J, Salama SSweet-Cordero AHaussler D, Morozova O. Identifying confidently measured genes in single pediatric cancer patient samples using RNA sequencing. (2017): 2466-2466.

Morozova ONewton YShah ABeale HLam DL, Vivian JBjork IGoldstein TStuart JSalama SSweet-Cordero A, Haussler D; Abstract 4890: A pan-cancer analysis framework for incorporating gene expression information into clinical interpretation of pediatric cancer genomic data(2017): 4890-4890.

Morozova O, Salama S, Bjork I Goldstein TMueller SSender LSweet-Cordero AHaussler D, California Kids Cancer Comparison Team; Comparative genomic analysis for pediatric cancer patients evaluated in a California Initiative to Advance Precision Medicine Demonstration Project. (2017): TPS10578-TPS10578.


Morozova ONewton YCline MYip S, Rao A, Stuart JGoldstein TSalama SDeyell RRassekh Rod. S, Haussler D; Abstract PR14: Harnessing the power of big data to advance pediatric cancer care. American Association for Cancer Research, 2016. doi: 10.1158/1538-7445.PEDCA15-PR14 

Newton, Y; Discovering molecular patterns with therapeutic implications in large-cohort heterogeneous cross-cancer data. UC Santa Cruz, 2016. ProQuest ID: Newton_ucsc_0036E_11177. Merritt ID: ark:/13030/m5m66797. Retrieved from https://escholarship.org/uc/item/9sd1t5jb


Morozova O, Newton Y, Cline M, Zhu J, Learned K, Stuart J, Salama S, Arceci R, Haussler D. Abstract LB-212: Treehouse Childhood Cancer Project: a resource for sharing and multiple cohort analysis of pediatric cancer genomics data. Cancer Res August 1 2015 (75) (15 Supplement) LB-212. doi: 10.1158/1538-7445.AM2015-LB-212

Publications That Use Treehouse Data or Resources

Researchers use Treehouse’s resources or publicly available, processed data for their analysis: Treehouse is granted permission to use the data; we run it through our pipelines and make our processed data public as part of our compendium.


Warren, A., Chen, Y., Jones, A. et al. Global computational alignment of tumor and cell line transcriptional profilesNat Commun 12, 22 (2021). doi: 10.1038/s41467-020-20294-x

Zeng, B., Glicksberg, B.S., Newbury, P. et al. OCTAD: an open workspace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features. Nat Protoc 16, 728–753 (2021). doi: 10.1038/s41596-020-00430-z

Pan M et al. The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma. February 25, 2021. doi: 10.1101/2021.02.25.432934.


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;3. doi: 10.20517/cdr.2020.12

Gupta, A., Belsky, J., Schieffer, K., Leraas, K., Varga, E., McGrath, S., Koo, S., Magrini, V., Wilson, R., White, P., Mardis, E., Jatana, K., Cottrell, C. and Setty, B., 2020. Infantile fibrosarcoma–like tumor driven by novel RBPMS-MET fusion consolidated with cabozantinibMolecular Case Studies, 6(5), p.a005645.

Savary C, Kim A, Lespagnol A, Gandemer V, Pellier I, Andrieu C, Pagès G, Galibert M, Yna Blum Y, de Tayrac M. Depicting the genetic architecture of pediatric cancers through an integrative gene network approach. Sci Rep 10, 1224 (2020)

Song J, Zhao Q, Xu Y, Zhu L. A signature of 29 immune-related genes pairs to predict prognosis in patients with neuroblastomaInternational Immunopharmacology 2020; 88. doi: 10.1016/j.intimp.2020.106994

Warren A, Jones A, Shibue T, Hahn WC, Boehm JS, Vazquez F,Tsherniak A, McFarland JM. Global computational alignment of tumor and cell line transcriptional profiles. bioRxiv. March 26, 2020.

Wong, M., Mayoh, C., Lau, L.M.S. et al. Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancerNat Med (2020). October 2020. doi: 10.1038/s41591-020-1072-4