Stephen R Piccolo

Stephen R Piccolo

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Stephen R Piccolo

Stephen R Piccolo

Publications by authors named "Stephen R Piccolo"

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Metastatic colon adenocarcinoma has a significantly elevated expression of IL-10 compared with primary colon adenocarcinoma tumors.

Cancer Biol Ther 2018 10;19(10):913-920. Epub 2018 May 10.

a Department of Microbiology and Molecular Biology , Brigham Young University , Provo UT.

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http://dx.doi.org/10.1080/15384047.2017.1360453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300346PMC
September 2019

Functional and transcriptomic characterization of carboplatin-resistant A2780 ovarian cancer cell line.

Biol Res 2019 Mar 21;52(1):13. Epub 2019 Mar 21.

Laboratorio de Patología Molecular, Centro de Excelencia en Medicina Traslacional-Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Avenida Alemania #0478, 3th Floor, Temuco, Chile.

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http://dx.doi.org/10.1186/s40659-019-0220-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6427839PMC
March 2019

Remote sensing tree classification with a multilayer perceptron.

PeerJ 2019 28;7:e6101. Epub 2019 Feb 28.

Department of Biology, Brigham Young University, Provo, UT, United States of America.

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http://dx.doi.org/10.7717/peerj.6101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397751PMC
February 2019

Potential new biomarkers for endometrial cancer.

Cancer Cell Int 2019 21;19:19. Epub 2019 Jan 21.

1Department of Microbiology and Molecular Biology, Brigham Young University, 3142 LSB, Provo, UT 84602 USA.

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http://dx.doi.org/10.1186/s12935-019-0731-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341571PMC
January 2019

Genome Sequencing and RNA-Motif Analysis Reveal Novel Damaging Noncoding Mutations in Human Tumors.

Mol Cancer Res 2018 07 28;16(7):1112-1124. Epub 2018 Mar 28.

Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain.

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http://dx.doi.org/10.1158/1541-7786.MCR-17-0601DOI Listing
July 2018

Curated compendium of human transcriptional biomarker data.

Sci Data 2018 04 17;5:180066. Epub 2018 Apr 17.

Department of Biology, Brigham Young University, Provo, Utah 84602, USA.

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http://dx.doi.org/10.1038/sdata.2018.66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5903354PMC
April 2018

Classifying cancer genome aberrations by their mutually exclusive effects on transcription.

BMC Med Genomics 2017 12 21;10(Suppl 4):66. Epub 2017 Dec 21.

Department of Biology, Brigham Young University, Provo, UT, 84602, USA.

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http://dx.doi.org/10.1186/s12920-017-0303-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763295PMC
December 2017

A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer.

JCO Clin Cancer Inform 2017 11;1:1-15

Fatemeh Seyednasrollah and Laura L. Elo, Turku Centre for Biotechnology; University of Turku; Åbo Akademi University, Turku, Finland; Devin C. Koestler, University of Kansas Medical Center, Kansas City, KS; Tao Wang, University of Texas Southwestern Medical Center, Dallas, TX; Stephen R. Piccolo, Brigham Young University, Provo; University of Utah, Salt Lake City, Utah, UT; Roberto Vega, Russell Greiner, and Luke Kumar, University of Alberta; Alberta Innovates Centre for Machine Learning, Edmonton, Alberta, Canada; Christiane Fuchs, Helmholtz Zentrum München, Neuherberg; Technische Universität München, Garching, Germany; Eyal Gofer, The Hebrew University, Jerusalem, Israel; Russell D. Wolfinger, SAS Institute, Cary, NC; Kimberly Kanigel Winner and James C. Costello, University of Colorado, Anschutz Medical Campus, Aurora, CO; Chris Bare, Elias Chaibub Neto, Thomas Yu, Thea Norman, and Justin Guinney, Sage Bionetworks, Seattle, WA; Liji Shen and Fang Liz Zhou, Sanofi, Bridgewater, NJ; Kald Abdallah, AstraZeneca, Gaithersburg, MD; Gustavo Stolovitzky, IBM Research, Yorktown Heights; Howard I. Scher, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Howard R. Soule, Prostate Cancer Foundation, Santa Monica; Charles J. Ryan, University of California, San Francisco, CA; Christopher J. Sweeney, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA; and Oliver Sartor, Tulane University, New Orleans, LA.

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http://dx.doi.org/10.1200/CCI.17.00018DOI Listing
November 2017

Systems Approaches to Cancer Biology.

Cancer Res 2016 12 18;76(23):6774-6777. Epub 2016 Nov 18.

Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia.

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http://dx.doi.org/10.1158/0008-5472.CAN-16-1580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5135591PMC
December 2016

A cloud-based workflow to quantify transcript-expression levels in public cancer compendia.

Sci Rep 2016 12 16;6:39259. Epub 2016 Dec 16.

Department of Biology, Brigham Young University, Provo, Utah, USA.

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http://dx.doi.org/10.1038/srep39259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159871PMC
December 2016

Tools and techniques for computational reproducibility.

Gigascience 2016 07 11;5(1):30. Epub 2016 Jul 11.

Department of Computer Science, Brigham Young University, Provo, UT, USA.

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http://dx.doi.org/10.1186/s13742-016-0135-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940747PMC
July 2016

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.

Authors:
Genevera I Allen Nicola Amoroso Catalina Anghel Venkat Balagurusamy Christopher J Bare Derek Beaton Roberto Bellotti David A Bennett Kevin L Boehme Paul C Boutros Laura Caberlotto Cristian Caloian Frederick Campbell Elias Chaibub Neto Yu-Chuan Chang Beibei Chen Chien-Yu Chen Ting-Ying Chien Tim Clark Sudeshna Das Christos Davatzikos Jieyao Deng Donna Dillenberger Richard J B Dobson Qilin Dong Jimit Doshi Denise Duma Rosangela Errico Guray Erus Evan Everett David W Fardo Stephen H Friend Holger Fröhlich Jessica Gan Peter St George-Hyslop Satrajit S Ghosh Enrico Glaab Robert C Green Yuanfang Guan Ming-Yi Hong Chao Huang Jinseub Hwang Joseph Ibrahim Paolo Inglese Anandhi Iyappan Qijia Jiang Yuriko Katsumata John S K Kauwe Arno Klein Dehan Kong Roland Krause Emilie Lalonde Mario Lauria Eunjee Lee Xihui Lin Zhandong Liu Julie Livingstone Benjamin A Logsdon Simon Lovestone Tsung-Wei Ma Ashutosh Malhotra Lara M Mangravite Taylor J Maxwell Emily Merrill John Nagorski Aishwarya Namasivayam Manjari Narayan Mufassra Naz Stephen J Newhouse Thea C Norman Ramil N Nurtdinov Yen-Jen Oyang Yudi Pawitan Shengwen Peng Mette A Peters Stephen R Piccolo Paurush Praveen Corrado Priami Veronica Y Sabelnykova Philipp Senger Xia Shen Andrew Simmons Aristeidis Sotiras Gustavo Stolovitzky Sabina Tangaro Andrea Tateo Yi-An Tung Nicholas J Tustison Erdem Varol George Vradenburg Michael W Weiner Guanghua Xiao Lei Xie Yang Xie Jia Xu Hojin Yang Xiaowei Zhan Yunyun Zhou Fan Zhu Hongtu Zhu Shanfeng Zhu

Alzheimers Dement 2016 06 11;12(6):645-53. Epub 2016 Apr 11.

School of Computer Science, Fudan University, Shanghai, Shanghai, China; Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, Shanghai, China; Centre for Computational Systems Biology, Fudan University, Shanghai, China.

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http://dx.doi.org/10.1016/j.jalz.2016.02.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474755PMC
June 2016

Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types.

Oncotarget 2016 Jun;7(23):35044-55

Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou, China.

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http://dx.doi.org/10.18632/oncotarget.9037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5085208PMC
June 2016

Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.

Mol Syst Biol 2016 Mar 10;12(3):860. Epub 2016 Mar 10.

Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT, USA Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4812528PMC
http://dx.doi.org/10.15252/msb.20156506DOI Listing
March 2016

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results.

Bioinformatics 2015 Nov 24;31(22):3666-72. Epub 2015 Jul 24.

Department of Biology, Brigham Young University, Provo, UT 84604, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804769PMC
November 2015

Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

BMC Med Genomics 2015 Nov 4;8:72. Epub 2015 Nov 4.

Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT, USA.

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http://dx.doi.org/10.1186/s12920-015-0145-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4634735PMC
November 2015

Inferring pathway dysregulation in cancers from multiple types of omic data.

Genome Med 2015 26;7(1):61. Epub 2015 Jun 26.

Department of Oncological Sciences, University of Utah, Salt Lake City, UT USA ; Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT USA.

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http://dx.doi.org/10.1186/s13073-015-0189-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499940PMC
July 2015

ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways.

Bioinformatics 2015 Jun 22;31(11):1745-53. Epub 2015 Jan 22.

Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118 USA, Department of Biomedical Informatics and Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112 USA Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118 USA, Department of Biomedical Informatics and Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112 USA.

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http://dx.doi.org/10.1093/bioinformatics/btv031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443674PMC
June 2015

Genomic classification of the RAS network identifies a personalized treatment strategy for lung cancer.

Mol Oncol 2014 Oct 20;8(7):1339-54. Epub 2014 May 20.

Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA; Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA. Electronic address:

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http://doi.wiley.com/10.1016/j.molonc.2014.05.005
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http://dx.doi.org/10.1016/j.molonc.2014.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450766PMC
October 2014

Robust meta-analysis shows that glioma transcriptional subtyping complements traditional approaches.

Cell Oncol (Dordr) 2014 Oct 21;37(5):317-29. Epub 2014 Aug 21.

Department of Biochemistry, University of Utah, 15 North Medical Drive East, Rm 5800, Salt Lake City, UT, 84112, USA,

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http://dx.doi.org/10.1007/s13402-014-0190-8DOI Listing
October 2014

Clinical and molecular models of glioblastoma multiforme survival.

Int J Data Min Bioinform 2013 ;7(3):245-65

Department of Pharmacology and Toxicology, University of Utah, 201 Presidents Circle, Salt Lake City, 84112 UT, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018825PMC
March 2014

A field guide to genomics research.

PLoS Biol 2014 Jan 7;12(1):e1001744. Epub 2014 Jan 7.

Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, United States of America ; Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1001744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3883637PMC
January 2014

Multiplatform single-sample estimates of transcriptional activation.

Proc Natl Acad Sci U S A 2013 Oct 15;110(44):17778-83. Epub 2013 Oct 15.

Departments of Pharmacology and Toxicology, and Oncological Sciences, The University of Utah, Salt Lake City, UT 84112.

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http://dx.doi.org/10.1073/pnas.1305823110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816418PMC
October 2013

A single-sample microarray normalization method to facilitate personalized-medicine workflows.

Genomics 2012 Dec 19;100(6):337-44. Epub 2012 Aug 19.

Department of Pharmacology and Toxicology, University of Utah, 201 Presidents Circle, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1016/j.ygeno.2012.08.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3508193PMC
December 2012

Menthol induces cell-cycle arrest in PC-3 cells by down-regulating G2/M genes, including polo-like kinase 1.

Biochem Biophys Res Commun 2012 Jun 9;422(3):436-41. Epub 2012 May 9.

Department of Physiology, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.

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https://linkinghub.elsevier.com/retrieve/pii/S0006291X120087
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http://dx.doi.org/10.1016/j.bbrc.2012.05.010DOI Listing
June 2012

Multiplicity: an organizing principle for cancers and somatic mutations.

BMC Med Genomics 2011 Jun 29;4:52. Epub 2011 Jun 29.

Department of Biomedical Informatics, University of Utah, 26 South 2000 East, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1186/1755-8794-4-52DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150236PMC
June 2011

Predicting phenotypic severity of uncertain gene variants in the RET proto-oncogene.

PLoS One 2011 Mar 30;6(3):e18380. Epub 2011 Mar 30.

Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018380PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068179PMC
March 2011

Evaluation of genetic risk scores for lipid levels using genome-wide markers in the Framingham Heart Study.

BMC Proc 2009 Dec 15;3 Suppl 7:S46. Epub 2009 Dec 15.

Department of Biomedical Informatics, School of Medicine, University of Utah, 26 South 2000 East, Salt Lake City, Utah 84112, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795945PMC
http://dx.doi.org/10.1186/1753-6561-3-s7-s46DOI Listing
December 2009

Polygenic model for predicting breast cancer risk via genome-wide polymorphisms.

AMIA Annu Symp Proc 2008 Nov 6:1094. Epub 2008 Nov 6.

University of Utah, Salt Lake City, UT, USA.

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November 2008

Somatic mutation signatures of cancer.

AMIA Annu Symp Proc 2008 Nov 6:202-6. Epub 2008 Nov 6.

University of Utah, UT, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655983PMC
November 2008