Publications

Researchers associated with the UC Santa Cruz Treehouse Initiative write publications in pediatric cancer, and other related fields.
2019

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. 

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.

2018

Goldman M, Craft B, Brooks AN, Zhu J, Haussler, D; The UCSC Xena Platform for cancer genomics data visualization and interpretationbioRxiv, 2018. doi: 10.1101/326470.

Newton YRassekh SR, Deyell RJShen YJones MR, Dunham CYip SLeelakumari SZhu JMcColl DSwatloski TSalama SR, Ng THendson GLee AFMa YMoore RMungall AJHaussler D, Stuart J, Jantzen CLaskin JJones SJMMarra MA, Morozova O; Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed CancerJCO Precision Oncology 2018 :21-16.

Pfeil JThornton ADurbin AKephart EBeale HSanders LBjork IMorozova OSalama SR, Haussler D; Gene expression analysis for improved subtyping of high-risk neuroblastomaJournal of Clinical Oncology 2018 36:15_suppl, 10559-10559.

Sanders LRose-Dey BBeale HKephart EPfeil JMorozova OAgnihotri SSalama SRHaussler D; Comparative gene expression analysis for identifying clinically relevant overexpressed genes in childhood brain tumorsJournal of Clinical Oncology 2018 36:15_supple14033-e14033.

Toor JS, Rao AA, McShan AC, Yarmarkovich M, Nerli S, Yamaguchi K, Madejska AA, Nguyen S, Tripathi S, Maris JM, Salama SR, Haussler D, Sgourakis NG;  A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope ConformationsFront Immunol. 2018 Jan 30;9:99. doi: 10.3389/fimmu.2018.00099. eCollection 2018. PMID:29441070 | PMCID:PMC5797543

2017

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.

Birger C, Hanna MSalinas E, Neff JSaksena GLivitz DRosebrock DStewart C, Leshchiner I, Baumann AVoet DCibulskis KBanks E, Philippakis AGetz G; FireCloud, a scalable cloud-based platform for collaborative genome analysis: Strategies for reducing and controlling costsbioRxiv (2017): 209494.

Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A, Nikiforova MN; Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American PathologistsJ Mol Diagn. 2017 Jan;19(1):4-23. doi: 10.1016/j.jmoldx.2016.10.002. Review. PMID:27993330 | PMCID:PMC5707196

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.

Savage, N; Getting data sharing right to help fulfill the promise of cancer genomics. Cell 168.4 (2017): 551-554.

2016

Hao, Y; Computational modeling for identification of low-frequency single nucleotide variants. Indiana University, Purdue University Indianapolis. ScholarWorks, 2015.

Heynen GJ, Nevedomskaya E, Palit S, Jagalur Basheer N, Lieftink C, Schlicker A, Zwart W, Bernards R, Bajpe PK;  Mastermind-Like 3 Controls Proliferation and Differentiation in Neuroblastoma. Mol Cancer Res. 2016 May;14(5):411-22. doi: 10.1158/1541-7786.MCR-15-0291-T. Epub 2016 Jan 19. PMID:26785999

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

2014

Goldman M, Craft B, Swatloski T, Cline M, Morozova O, Diekhans M, Haussler D, Zhu J; The UCSC Cancer Genomics Browser: update 2015.  Nucleic Acids Res. 2015 Jan;43(Database issue):D812-7. doi: 10.1093/nar/gku1073. Epub 2014 Nov 11. PMID:25392408 | PMCID:PMC4383911

Krishna A, Biryukov M, Trefois C, Antony PM, Hussong R, Lin J, Heinäniemi M, Glusman G, Köglsberger S, Boyd O, van den Berg BH, Linke D, Huang D, Wang K, Hood L, Tholey A, Schneider R, Galas DJ, Balling R, May P; Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson’s disease. BMC Genomics. 2014 Dec 20;15:1154. doi: 10.1186/1471-2164-15-1154. PMID:25528190 | PMCID:PMC4367834

Kumar A, Fan D, Dipette DJ, Singh US; Sparstolonin B, a novel plant derived compound, arrests cell cycle and induces apoptosis in N-myc amplified and N-myc nonamplified neuroblastoma cells. PLoS One. 2014 May 1;9(5):e96343. doi: 10.1371/journal.pone.0096343. eCollection 2014. Erratum in: PLoS One. 2016;11(7):e0159082. PMID:24788776 | PMCID:PMC4006872

Wilks C, Cline MS, Weiler E, Diehkans M, Craft B, Martin C, Murphy D, Pierce H, Black J, Nelson D, Litzinger B, Hatton T, Maltbie L, Ainsworth M, Allen P, Rosewood L, Mitchell E, Smith B, Warner J, Groboske J, Telc H, Wilson D, et al.; The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Database (Oxford). 2014 Sep 29;2014. pii: bau093. doi: 10.1093/database/bau093. Print 2014. PMID:25267794 | PMCID:PMC4178372

2013

Pchelintsev NA, McBryan T, Rai TS, van Tuyn J, Ray-Gallet D, Almouzni G, Adams PD; Placing the HIRA histone chaperone complex in the chromatin landscape. Cell Rep. 2013 Apr 25;3(4):1012-9. doi: 10.1016/j.celrep.2013.03.026. Epub 2013 Apr 18. PMID: 23602572 | PMCID: PMC3974909 

Romania P, Castellano A, Surace C, Citti A, De Ioris MA, Sirleto P, De Mariano M, Longo L, Boldrini R, Angioni A, Locatelli F, Fruci D; High-resolution array CGH profiling identifies Na/K transporting ATPase interacting 2 (NKAIN2) as a predisposing candidate gene in neuroblastoma. PLoS One. 2013 Oct 25;8(10):e78481. doi: 10.1371/journal.pone.0078481. eCollection 2013. PMID: 24205241 | PMCID: PMC3808344