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Items: 18

1.

Gene Copy Number Estimation From Targeted Next Generation Sequencing Of Prostate Cancer Biopsies: Analytic Validation and Clinical Qualification.

Seed G, Yuan W, Mateo J, Carreira S, Bertan C, Lambros M, Boysen G, Ferraldeschi R, Miranda S, Figueiredo I, Riisnaes R, Crespo M, Nava Rodrigues D, Talevich E, Robinson DR, Kunju LP, Wu YM, Lonigro R, Sandhu S, Chinnayan A, de Bono JS.

Clin Cancer Res. 2017 Jul 27. pii: clincanres.0972.2017. doi: 10.1158/1078-0432.CCR-17-0972. [Epub ahead of print]

PMID:
28751446
2.

Genomic profiling of breast secretory carcinomas reveals distinct genetics from other breast cancers and similarity to mammary analog secretory carcinomas.

Krings G, Joseph NM, Bean GR, Solomon D, Onodera C, Talevich E, Yeh I, Grenert JP, Hosfield E, Crawford ED, Jordan RC, van Zante A, Zaloudek C, Shin SJ, Chen YY.

Mod Pathol. 2017 Aug;30(8):1086-1099. doi: 10.1038/modpathol.2017.32. Epub 2017 May 26.

PMID:
28548128
3.

Targeted next-generation sequencing of pediatric neuro-oncology patients improves diagnosis, identifies pathogenic germline mutations, and directs targeted therapy.

Kline CN, Joseph NM, Grenert JP, van Ziffle J, Talevich E, Onodera C, Aboian M, Cha S, Raleigh DR, Braunstein S, Torkildson J, Samuel D, Bloomer M, Campomanes AGA, Banerjee A, Butowski N, Raffel C, Tihan T, Bollen AW, Phillips JJ, Korn WM, Yeh I, Bastian BC, Gupta N, Mueller S, Perry A, Nicolaides T, Solomon DA.

Neuro Oncol. 2017 May 1;19(5):699-709. doi: 10.1093/neuonc/now254.

PMID:
28453743
4.

Genomic profiling of malignant peritoneal mesothelioma reveals recurrent alterations in epigenetic regulatory genes BAP1, SETD2, and DDX3X.

Joseph NM, Chen YY, Nasr A, Yeh I, Talevich E, Onodera C, Bastian BC, Rabban JT, Garg K, Zaloudek C, Solomon DA.

Mod Pathol. 2017 Feb;30(2):246-254. doi: 10.1038/modpathol.2016.188. Epub 2016 Nov 4.

5.

Genomic profiling of malignant phyllodes tumors reveals aberrations in FGFR1 and PI-3 kinase/RAS signaling pathways and provides insights into intratumoral heterogeneity.

Liu SY, Joseph NM, Ravindranathan A, Stohr BA, Greenland NY, Vohra P, Hosfield E, Yeh I, Talevich E, Onodera C, Van Ziffle JA, Grenert JP, Bastian BC, Chen YY, Krings G.

Mod Pathol. 2016 Sep;29(9):1012-27. doi: 10.1038/modpathol.2016.97. Epub 2016 Jun 3.

PMID:
27255162
6.

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.

Talevich E, Shain AH, Botton T, Bastian BC.

PLoS Comput Biol. 2016 Apr 21;12(4):e1004873. doi: 10.1371/journal.pcbi.1004873. eCollection 2016 Apr.

7.

Identification and classification of small molecule kinases: insights into substrate recognition and specificity.

Oruganty K, Talevich EE, Neuwald AF, Kannan N.

BMC Evol Biol. 2016 Jan 6;16:7. doi: 10.1186/s12862-015-0576-x.

8.

The Genetic Evolution of Melanoma from Precursor Lesions.

Shain AH, Yeh I, Kovalyshyn I, Sriharan A, Talevich E, Gagnon A, Dummer R, North J, Pincus L, Ruben B, Rickaby W, D'Arrigo C, Robson A, Bastian BC.

N Engl J Med. 2015 Nov 12;373(20):1926-36. doi: 10.1056/NEJMoa1502583.

9.

Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway.

Shain AH, Garrido M, Botton T, Talevich E, Yeh I, Sanborn JZ, Chung J, Wang NJ, Kakavand H, Mann GJ, Thompson JF, Wiesner T, Roy R, Olshen AB, Gagnon A, Gray JW, Huh N, Hur JS, Busam KJ, Scolyer RA, Cho RJ, Murali R, Bastian BC.

Nat Genet. 2015 Oct;47(10):1194-9. doi: 10.1038/ng.3382. Epub 2015 Sep 7.

10.

Activating MET kinase rearrangements in melanoma and Spitz tumours.

Yeh I, Botton T, Talevich E, Shain AH, Sparatta AJ, de la Fouchardiere A, Mully TW, North JP, Garrido MC, Gagnon A, Vemula SS, McCalmont TH, LeBoit PE, Bastian BC.

Nat Commun. 2015 May 27;6:7174. doi: 10.1038/ncomms8174.

11.

ProKinO: a unified resource for mining the cancer kinome.

McSkimming DI, Dastgheib S, Talevich E, Narayanan A, Katiyar S, Taylor SS, Kochut K, Kannan N.

Hum Mutat. 2015 Feb;36(2):175-86. doi: 10.1002/humu.22726.

12.

Prediction and prioritization of rare oncogenic mutations in the cancer Kinome using novel features and multiple classifiers.

U M, Talevich E, Katiyar S, Rasheed K, Kannan N.

PLoS Comput Biol. 2014 Apr 17;10(4):e1003545. doi: 10.1371/journal.pcbi.1003545. eCollection 2014 Apr.

13.

Global analysis of protein expression and phosphorylation of three stages of Plasmodium falciparum intraerythrocytic development.

Pease BN, Huttlin EL, Jedrychowski MP, Talevich E, Harmon J, Dillman T, Kannan N, Doerig C, Chakrabarti R, Gygi SP, Chakrabarti D.

J Proteome Res. 2013 Sep 6;12(9):4028-45. doi: 10.1021/pr400394g. Epub 2013 Aug 26.

14.

Structural and evolutionary adaptation of rhoptry kinases and pseudokinases, a family of coccidian virulence factors.

Talevich E, Kannan N.

BMC Evol Biol. 2013 Jun 6;13:117. doi: 10.1186/1471-2148-13-117.

15.

Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython.

Talevich E, Invergo BM, Cock PJ, Chapman BA.

BMC Bioinformatics. 2012 Aug 21;13:209. doi: 10.1186/1471-2105-13-209.

16.

An evolutionary perspective on the kinome of malaria parasites.

Talevich E, Tobin AB, Kannan N, Doerig C.

Philos Trans R Soc Lond B Biol Sci. 2012 Sep 19;367(1602):2607-18. doi: 10.1098/rstb.2012.0014. Review.

17.

Structural and evolutionary divergence of eukaryotic protein kinases in Apicomplexa.

Talevich E, Mirza A, Kannan N.

BMC Evol Biol. 2011 Nov 2;11:321. doi: 10.1186/1471-2148-11-321.

18.

Co-conserved features associated with cis regulation of ErbB tyrosine kinases.

Mirza A, Mustafa M, Talevich E, Kannan N.

PLoS One. 2010 Dec 13;5(12):e14310. doi: 10.1371/journal.pone.0014310.

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