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Items: 20

1.

Deep Learning Implicitly Handles Tissue Specific Phenomena to Predict Tumor DNA Accessibility and Immune Activity.

Wnuk K, Sudol J, Givechian KB, Soon-Shiong P, Rabizadeh S, Szeto C, Vaske C.

iScience. 2019 Oct 25;20:119-136. doi: 10.1016/j.isci.2019.09.018. Epub 2019 Sep 14.

2.

A20 and ABIN1 Suppression of a Keratinocyte Inflammatory Program with a Shared Single-Cell Expression Signature in Diverse Human Rashes.

Harirchian P, Lee J, Hilz S, Sedgewick AJ, Perez White BE, Kesling MJ, Mully T, Golovato J, Gray M, Mauro TM, Purdom E, Kim EA, Sbitany H, Bhutani T, Vaske CJ, Benz SC, Cho RJ, Cheng JB.

J Invest Dermatol. 2019 Jun;139(6):1264-1273. doi: 10.1016/j.jid.2018.10.046. Epub 2018 Dec 10.

PMID:
30543901
3.

Data-Independent Acquisition Mass Spectrometry To Quantify Protein Levels in FFPE Tumor Biopsies for Molecular Diagnostics.

Kim YJ, Sweet SMM, Egertson JD, Sedgewick AJ, Woo S, Liao WL, Merrihew GE, Searle BC, Vaske C, Heaton R, MacCoss MJ, Hembrough T.

J Proteome Res. 2019 Jan 4;18(1):426-435. doi: 10.1021/acs.jproteome.8b00699. Epub 2018 Dec 12.

PMID:
30481034
4.

Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution.

Cheng JB, Sedgewick AJ, Finnegan AI, Harirchian P, Lee J, Kwon S, Fassett MS, Golovato J, Gray M, Ghadially R, Liao W, Perez White BE, Mauro TM, Mully T, Kim EA, Sbitany H, Neuhaus IM, Grekin RC, Yu SS, Gray JW, Purdom E, Paus R, Vaske CJ, Benz SC, Song JS, Cho RJ.

Cell Rep. 2018 Oct 23;25(4):871-883. doi: 10.1016/j.celrep.2018.09.006.

5.

Polyoma virus-associated carcinomas of the urologic tract: a clinicopathologic and molecular study.

Sirohi D, Vaske C, Sanborn Z, Smith SC, Don MD, Lindsey KG, Federman S, Vankalakunti M, Koo J, Bose S, Peralta-Venturina M, Ziffle JV, Grenert JP, Miller S, Chiu C, Amin MB, Simko JP, Stohr BA, Luthringer DJ.

Mod Pathol. 2018 Sep;31(9):1429-1441. doi: 10.1038/s41379-018-0065-z. Epub 2018 May 15.

6.

Cell of origin and mutation pattern define three clinically distinct classes of sebaceous carcinoma.

North JP, Golovato J, Vaske CJ, Sanborn JZ, Nguyen A, Wu W, Goode B, Stevers M, McMullen K, Perez White BE, Collisson EA, Bloomer M, Solomon DA, Benz SC, Cho RJ.

Nat Commun. 2018 May 14;9(1):1894. doi: 10.1038/s41467-018-04008-y.

7.

Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome.

Aure MR, Vitelli V, Jernström S, Kumar S, Krohn M, Due EU, Haukaas TH, Leivonen SK, Vollan HK, Lüders T, Rødland E, Vaske CJ, Zhao W, Møller EK, Nord S, Giskeødegård GF, Bathen TF, Caldas C, Tramm T, Alsner J, Overgaard J, Geisler J, Bukholm IR, Naume B, Schlichting E, Sauer T, Mills GB, Kåresen R, Mælandsmo GM, Lingjærde OC, Frigessi A, Kristensen VN, Børresen-Dale AL, Sahlberg KK; OSBREAC.

Breast Cancer Res. 2017 Mar 29;19(1):44. doi: 10.1186/s13058-017-0812-y.

8.

FOXM1 cistrome predicts breast cancer metastatic outcome better than FOXM1 expression levels or tumor proliferation index.

Yau C, Meyer L, Benz S, Vaske C, Scott G, Egan B, Labhart P, Pourmand N, Benz CC.

Breast Cancer Res Treat. 2015 Nov;154(1):23-32. doi: 10.1007/s10549-015-3589-7. Epub 2015 Oct 12.

PMID:
26456572
9.

Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53.

Quigley D, Silwal-Pandit L, Dannenfelser R, Langerød A, Vollan HK, Vaske C, Siegel JU, Troyanskaya O, Chin SF, Caldas C, Balmain A, Børresen-Dale AL, Kristensen V.

Mol Cancer Res. 2015 Mar;13(3):493-501. doi: 10.1158/1541-7786.MCR-14-0387. Epub 2014 Oct 28.

10.

Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing.

Lee MC, Lopez-Diaz FJ, Khan SY, Tariq MA, Dayn Y, Vaske CJ, Radenbaugh AJ, Kim HJ, Emerson BM, Pourmand N.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):E4726-35. doi: 10.1073/pnas.1404656111. Epub 2014 Oct 22.

11.

JARID1B is a luminal lineage-driving oncogene in breast cancer.

Yamamoto S, Wu Z, Russnes HG, Takagi S, Peluffo G, Vaske C, Zhao X, Moen Vollan HK, Maruyama R, Ekram MB, Sun H, Kim JH, Carver K, Zucca M, Feng J, Almendro V, Bessarabova M, Rueda OM, Nikolsky Y, Caldas C, Liu XS, Polyak K.

Cancer Cell. 2014 Jun 16;25(6):762-77. doi: 10.1016/j.ccr.2014.04.024.

12.

Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM.

Sedgewick AJ, Benz SC, Rabizadeh S, Soon-Shiong P, Vaske CJ.

Bioinformatics. 2013 Jul 1;29(13):i62-70. doi: 10.1093/bioinformatics/btt229.

13.

The UCSC Interaction Browser: multidimensional data views in pathway context.

Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D, Stuart JM.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W218-24. doi: 10.1093/nar/gkt473. Epub 2013 Jun 8.

14.

Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.

Kristensen VN, Vaske CJ, Ursini-Siegel J, Van Loo P, Nordgard SH, Sachidanandam R, Sørlie T, Wärnberg F, Haakensen VD, Helland Å, Naume B, Perou CM, Haussler D, Troyanskaya OG, Børresen-Dale AL.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2802-7. doi: 10.1073/pnas.1108781108. Epub 2011 Sep 9.

15.

The UCSC Cancer Genomics Browser: update 2011.

Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J.

Nucleic Acids Res. 2011 Jan;39(Database issue):D951-9. doi: 10.1093/nar/gkq1113. Epub 2010 Nov 8.

16.

Voltage-gated Na+ channel SCN5A is a key regulator of a gene transcriptional network that controls colon cancer invasion.

House CD, Vaske CJ, Schwartz AM, Obias V, Frank B, Luu T, Sarvazyan N, Irby R, Strausberg RL, Hales TG, Stuart JM, Lee NH.

Cancer Res. 2010 Sep 1;70(17):6957-67. doi: 10.1158/0008-5472.CAN-10-1169. Epub 2010 Jul 22.

17.

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.

Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM.

Bioinformatics. 2010 Jun 15;26(12):i237-45. doi: 10.1093/bioinformatics/btq182.

18.

Inferring disease-related pathways using a probabilistic epistasis model.

Kanabar PN, Vaske CJ, Yeang CH, Yildiz FH, Stuart JM.

Pac Symp Biocomput. 2009:480-91.

19.

A factor graph nested effects model to identify networks from genetic perturbations.

Vaske CJ, House C, Luu T, Frank B, Yeang CH, Lee NH, Stuart JM.

PLoS Comput Biol. 2009 Jan;5(1):e1000274. doi: 10.1371/journal.pcbi.1000274. Epub 2009 Jan 30.

20.

Gene prediction and verification in a compact genome with numerous small introns.

Tenney AE, Brown RH, Vaske C, Lodge JK, Doering TL, Brent MR.

Genome Res. 2004 Nov;14(11):2330-5. Epub 2004 Oct 12.

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