James E Korkola

James E Korkola

UNVERIFIED PROFILE

Are you James E Korkola?   Register this Author

Register author
James E Korkola

James E Korkola

Publications by authors named "James E Korkola"

Are you James E Korkola?   Register this Author

44Publications

1093Reads

46Profile Views

Annot: a Django-based sample, reagent, and experiment metadata tracking system.

BMC Bioinformatics 2019 Nov 1;20(1):542. Epub 2019 Nov 1.

Department of Biomedical Engineering and OHSU Center for Spatial Systems Biomedicine, OHSU, Portland, OR, 97201, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-019-3147-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6824123PMC
November 2019

Using Microarrays to Interrogate Microenvironmental Impact on Cellular Phenotypes in Cancer.

J Vis Exp 2019 05 21(147). Epub 2019 May 21.

Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health and Science University;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3791/58957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736605PMC
May 2019

Kinome rewiring reveals AURKA limits PI3K-pathway inhibitor efficacy in breast cancer.

Nat Chem Biol 2018 08 25;14(8):768-777. Epub 2018 Jun 25.

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41589-018-0081-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6051919PMC
August 2018

Microenvironment-Mediated Mechanisms of Resistance to HER2 Inhibitors Differ between HER2+ Breast Cancer Subtypes.

Cell Syst 2018 Mar 14;6(3):329-342.e6. Epub 2018 Mar 14.

Department of Biomedical Engineering, Knight Cancer Institute, OHSU Center for Spatial Systems Biomedicine, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S24054712183005
Publisher Site
http://dx.doi.org/10.1016/j.cels.2018.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5927625PMC
March 2018

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

Authors:
Alexandra B Keenan Sherry L Jenkins Kathleen M Jagodnik Simon Koplev Edward He Denis Torre Zichen Wang Anders B Dohlman Moshe C Silverstein Alexander Lachmann Maxim V Kuleshov Avi Ma'ayan Vasileios Stathias Raymond Terryn Daniel Cooper Michele Forlin Amar Koleti Dusica Vidovic Caty Chung Stephan C Schürer Jouzas Vasiliauskas Marcin Pilarczyk Behrouz Shamsaei Mehdi Fazel Yan Ren Wen Niu Nicholas A Clark Shana White Naim Mahi Lixia Zhang Michal Kouril John F Reichard Siva Sivaganesan Mario Medvedovic Jaroslaw Meller Rick J Koch Marc R Birtwistle Ravi Iyengar Eric A Sobie Evren U Azeloglu Julia Kaye Jeannette Osterloh Kelly Haston Jaslin Kalra Steve Finkbiener Jonathan Li Pamela Milani Miriam Adam Renan Escalante-Chong Karen Sachs Alex Lenail Divya Ramamoorthy Ernest Fraenkel Gavin Daigle Uzma Hussain Alyssa Coye Jeffrey Rothstein Dhruv Sareen Loren Ornelas Maria Banuelos Berhan Mandefro Ritchie Ho Clive N Svendsen Ryan G Lim Jennifer Stocksdale Malcolm S Casale Terri G Thompson Jie Wu Leslie M Thompson Victoria Dardov Vidya Venkatraman Andrea Matlock Jennifer E Van Eyk Jacob D Jaffe Malvina Papanastasiou Aravind Subramanian Todd R Golub Sean D Erickson Mohammad Fallahi-Sichani Marc Hafner Nathanael S Gray Jia-Ren Lin Caitlin E Mills Jeremy L Muhlich Mario Niepel Caroline E Shamu Elizabeth H Williams David Wrobel Peter K Sorger Laura M Heiser Joe W Gray James E Korkola Gordon B Mills Mark LaBarge Heidi S Feiler Mark A Dane Elmar Bucher Michel Nederlof Damir Sudar Sean Gross David F Kilburn Rebecca Smith Kaylyn Devlin Ron Margolis Leslie Derr Albert Lee Ajay Pillai

Cell Syst 2018 01 29;6(1):13-24. Epub 2017 Nov 29.

NIH, Bethesda, MD 20892, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2017.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799026PMC
January 2018

Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics.

Sci Data 2017 11 7;4:170166. Epub 2017 Nov 7.

HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/sdata.2017.166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5674849PMC
November 2017

Mechanism and Role of SOX2 Repression in Seminoma: Relevance to Human Germline Specification.

Stem Cell Reports 2016 05 28;6(5):772-783. Epub 2016 Apr 28.

Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stemcr.2016.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939754PMC
May 2016

A genetic strategy for single and combinatorial analysis of miRNA function in mammalian hematopoietic stem cells.

Stem Cells 2010 Feb;28(2):287-96

Center for Cell Engineering Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/stem.257DOI Listing
February 2010

Molecular events in germ cell tumours: linking chromosome-12 gain, acquisition of pluripotency and response to cisplatin.

BJU Int 2009 Nov;104(9 Pt B):1334-8

Cell Biology Division, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1464-410X.2009.08855.xDOI Listing
November 2009

Interferon-alpha resistance associated genes in renal cell carcinoma identified by expression profiling.

J Urol 2007 Apr;177(4):1264-8; discussion 1268

Department of Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.juro.2006.11.087DOI Listing
April 2007

Constitutive gene expression predisposes morphogen-mediated cell fate responses of NT2/D1 and 27X-1 human embryonal carcinoma cells.

Stem Cells 2007 Mar 30;25(3):771-8. Epub 2006 Nov 30.

Cell Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1634/stemcells.2006-0271DOI Listing
March 2007

Biology and genetics of adult male germ cell tumors.

J Clin Oncol 2006 Dec;24(35):5512-8

Cell Biology Program and Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.

View Article

Download full-text PDF

Source
http://jco.ascopubs.org/content/24/35/5512.full.pdf
Web Search
http://www.jco.org/cgi/doi/10.1200/JCO.2006.08.4285
Publisher Site
http://dx.doi.org/10.1200/JCO.2006.08.4285DOI Listing
December 2006

Transcriptional program associated with IFN-alpha response of renal cell carcinoma.

J Interferon Cytokine Res 2006 Mar;26(3):156-70

Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/jir.2006.26.156DOI Listing
March 2006

Down-regulation of stem cell genes, including those in a 200-kb gene cluster at 12p13.31, is associated with in vivo differentiation of human male germ cell tumors.

Cancer Res 2006 Jan;66(2):820-7

Cell Biology Program and Departments of Medicine, Epidemiology and Biostatistics, and Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/0008-5472.CAN-05-2445DOI Listing
January 2006

Gene expression-based classification of nonseminomatous male germ cell tumors.

Oncogene 2005 Jul;24(32):5101-7

Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/sj.onc.1208694DOI Listing
July 2005

Bladder cancer outcome and subtype classification by gene expression.

Clin Cancer Res 2005 Jun;11(11):4044-55

Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94143-0808, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1078-0432.CCR-04-2409DOI Listing
June 2005

Clonality of lobular carcinoma in situ and synchronous invasive lobular carcinoma.

Cancer 2004 Jun;100(12):2562-72

Department of Surgery, University of California-San Francisco, San Francisco, California 94115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/cncr.20273DOI Listing
June 2004

Differentiation of lobular versus ductal breast carcinomas by expression microarray analysis.

Cancer Res 2003 Nov;63(21):7167-75

Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA.

View Article

Download full-text PDF

Source
November 2003

Optimizing stringency for expression microarrays.

Biotechniques 2003 Oct;35(4):828-35

University of California San Francisco, San Francisco, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2144/03354mt04DOI Listing
October 2003

Cyclin D1 is necessary but not sufficient for anchorage-independent growth of rat mammary tumor cells and is associated with resistance of the Copenhagen rat to mammary carcinogenesis.

Oncogene 2003 May;22(22):3452-62

Molecular and Cell Biology Research, Sunnybrook and Women's College Health Sciences Centre, Toronto, ON, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/sj.onc.1206411DOI Listing
May 2003

Tissue-specific resistance to cancer development in the rat: phenotypes of tumor-modifier genes.

Carcinogenesis 2002 Jan;23(1):1-9

Department of Medical Biophysics, Faculty of Medicine, University of Toronto, 150 College Street, Toronto M5S 3E2, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/carcin/23.1.1DOI Listing
January 2002