Joel S Parker

Joel S Parker

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An Immunocompetent Mouse Model of HPV16(+) Head and Neck Squamous Cell Carcinoma.

Cell Rep 2019 Nov;29(6):1660-1674.e7

Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oral and Craniofacial Health Sciences, UNC Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Biomedical Research Imaging Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.10.005DOI Listing
November 2019

B Cells and T Follicular Helper Cells Mediate Response to Checkpoint Inhibitors in High Mutation Burden Mouse Models of Breast Cancer.

Cell 2019 Nov;179(5):1191-1206.e21

Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.10.028DOI Listing
November 2019

Improved indel detection in DNA and RNA via realignment with ABRA2.

Bioinformatics 2019 Sep;35(17):2966-2973

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735753PMC
September 2019

A functional role for the cancer disparity-linked genes, CRYβB2 and CRYβB2P1, in the promotion of breast cancer.

Breast Cancer Res 2019 09 11;21(1):105. Epub 2019 Sep 11.

Department of Biological and Biomedical Sciences, North Carolina Central University, 1801 Fayetteville Street, Mary Townes Science Complex, Durham, NC, 27707, USA.

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http://dx.doi.org/10.1186/s13058-019-1191-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6739962PMC
September 2019

Histone deacetylase 11 inhibition promotes breast cancer metastasis from lymph nodes.

Nat Commun 2019 Sep 13;10(1):4192. Epub 2019 Sep 13.

UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.

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http://dx.doi.org/10.1038/s41467-019-12222-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6744422PMC
September 2019

Genetic determinants of cellular addiction to DNA polymerase theta.

Nat Commun 2019 Sep 19;10(1):4286. Epub 2019 Sep 19.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.

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http://dx.doi.org/10.1038/s41467-019-12234-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753077PMC
September 2019

Identification of a Robust Methylation Classifier for Cutaneous Melanoma Diagnosis.

J Invest Dermatol 2019 Jun 6;139(6):1349-1361. Epub 2018 Dec 6.

Department of Dermatology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

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http://dx.doi.org/10.1016/j.jid.2018.11.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535139PMC
June 2019

Prognostic value of B cells in cutaneous melanoma.

Genome Med 2019 05 28;11(1):36. Epub 2019 May 28.

Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.

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http://dx.doi.org/10.1186/s13073-019-0647-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6540526PMC
May 2019

I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms.

Genome Biol 2019 03 7;20(1):52. Epub 2019 Mar 7.

Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599, NC, USA.

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http://dx.doi.org/10.1186/s13059-019-1640-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404283PMC
March 2019

Cells exhibiting strong promoter activation in vivo display features of senescence.

Proc Natl Acad Sci U S A 2019 02 25;116(7):2603-2611. Epub 2019 Jan 25.

Curriculum in Genetics and Molecular Biology, University of North Carolina School of Medicine, Chapel Hill, NC 27599;

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http://dx.doi.org/10.1073/pnas.1818313116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377452PMC
February 2019

Male breast cancer: a disease distinct from female breast cancer.

Breast Cancer Res Treat 2019 Jan 28;173(1):37-48. Epub 2018 Sep 28.

Breast Unit, Champalimaud Clinical Center/Champalimaud Foundation, Lisbon, Portugal.

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http://dx.doi.org/10.1007/s10549-018-4921-9DOI Listing
January 2019

RNA-Sequencing of Umbilical Cord Blood to Investigate Spontaneous Preterm Birth: A Pilot Study.

AJP Rep 2019 Jan 7;9(1):e60-e66. Epub 2019 Mar 7.

Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, North Carolina.

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http://dx.doi.org/10.1055/s-0039-1678717DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6406026PMC
January 2019

A Monolayer of Primary Colonic Epithelium Generated on a Scaffold with a Gradient of Stiffness for Drug Transport Studies.

Anal Chem 2018 11 30;90(22):13331-13340. Epub 2018 Oct 30.

Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States and North Carolina State University, Raleigh, North Carolina 27607, United States.

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http://pubs.acs.org/doi/10.1021/acs.analchem.8b02845
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http://dx.doi.org/10.1021/acs.analchem.8b02845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339567PMC
November 2018

ZFX Mediates Non-canonical Oncogenic Functions of the Androgen Receptor Splice Variant 7 in Castrate-Resistant Prostate Cancer.

Mol Cell 2018 10 27;72(2):341-354.e6. Epub 2018 Sep 27.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.08.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214474PMC
October 2018

Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality.

mSystems 2018 Sep-Oct;3(5). Epub 2018 Sep 25.

Lineberger Comprehensive Cancer Center, School of Medicine at the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

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http://dx.doi.org/10.1128/mSystems.00081-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156273PMC
September 2018

Gene expression-phenotype associations in adults with eosinophilic esophagitis.

Dig Liver Dis 2018 08 27;50(8):804-811. Epub 2018 Mar 27.

Department of Genetics, University of Chapel Hill, NC, United States.

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http://dx.doi.org/10.1016/j.dld.2018.03.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6059985PMC
August 2018

Meta-analysis of airway epithelium gene expression in asthma.

Eur Respir J 2018 05 17;51(5). Epub 2018 May 17.

Dept of Genetics, University of North Carolina, Chapel Hill, NC, USA.

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http://dx.doi.org/10.1183/13993003.01962-2017DOI Listing
May 2018

The Chromatin Remodeler BPTF Activates a Stemness Gene-Expression Program Essential for the Maintenance of Adult Hematopoietic Stem Cells.

Stem Cell Reports 2018 03 15;10(3):675-683. Epub 2018 Feb 15.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22136711183004
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http://dx.doi.org/10.1016/j.stemcr.2018.01.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5918338PMC
March 2018

Identification of Germline Variants in Tumor Genomic Sequencing Analysis.

J Mol Diagn 2018 01;20(1):123-125

Department of Pathology and Laboratory Medicine, The University of North Carolina School of Medicine, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina. Electronic address:

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http://dx.doi.org/10.1016/j.jmoldx.2017.09.008DOI Listing
January 2018

Combined kinase inhibitors of MEK1/2 and either PI3K or PDGFR are efficacious in intracranial triple-negative breast cancer.

Neuro Oncol 2017 Oct;19(11):1481-1493

Lineberger Comprehensive Cancer Center, Departments of Genetics, Pharmacology, Pathology & Laboratory Medicine, Laboratory Animal Medicine, Biostatistics, and Medicine, Divisions of Neuropathology, Hematology/Oncology, School of Medicine, and Neurology and Neurosciences Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.

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http://dx.doi.org/10.1093/neuonc/nox052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737524PMC
October 2017

Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations.

Nat Commun 2017 05 26;8:15290. Epub 2017 May 26.

Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China.

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http://dx.doi.org/10.1038/ncomms15290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5477513PMC
May 2017

Immunophenotyping and Transcriptomic Outcomes in PDX-Derived TNBC Tissue.

Mol Cancer Res 2017 04 30;15(4):429-438. Epub 2016 Dec 30.

BD Technologies, Research Triangle Park, Durham, North Carolina.

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http://dx.doi.org/10.1158/1541-7786.MCR-16-0286-TDOI Listing
April 2017

Amplification of SOX4 promotes PI3K/Akt signaling in human breast cancer.

Breast Cancer Res Treat 2017 04 7;162(3):439-450. Epub 2017 Feb 7.

Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, CINJ 4558, New Brunswick, NJ, 08903, USA.

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http://dx.doi.org/10.1007/s10549-017-4139-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5334195PMC
April 2017

SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.

Genome Biol 2017 04 8;18(1):66. Epub 2017 Apr 8.

Section of Genetic Medicine, Department of Medicine, The University of Chicago, 900 East 57th Street, KCBD 3220A, Chicago, IL, 60637, USA.

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http://dx.doi.org/10.1186/s13059-017-1193-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385048PMC
April 2017

Tumor-homing cytotoxic human induced neural stem cells for cancer therapy.

Sci Transl Med 2017 02;9(375)

Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1126/scitranslmed.aah6510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6719790PMC
February 2017

An Oral Selective Alpha-1A Adrenergic Receptor Agonist Prevents Doxorubicin Cardiotoxicity.

JACC Basic Transl Sci 2017 Feb;2(1):39-53

University of North Carolina School of Medicine, McAllister Heart Institute; UNC School of Medicine, Division of Cardiology.

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http://dx.doi.org/10.1016/j.jacbts.2016.10.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343290PMC
February 2017

Genomic Analysis of Immune Cell Infiltrates Across 11 Tumor Types.

J Natl Cancer Inst 2016 11 22;108(11). Epub 2016 Jun 22.

Affiliations of authors: Lineberger Comprehensive Cancer Center (MDI, JSP, KAH, JSS, CMP, BGV), Curriculum in Genetics and Molecular Biology (MDI, JSP), Department of Medicine (JSS, BGV), Department of Genetics (KAH, CMP), Department of Microbiology and Immunology (JSS), and Department of Pathology & Laboratory Medicine (CMP), University of North Carolina, Chapel Hill, Chapel Hill, NC.

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http://jnci.oxfordjournals.org/content/108/11/djw144.full.pd
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https://academic.oup.com/jnci/article-lookup/doi/10.1093/jnc
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http://dx.doi.org/10.1093/jnci/djw144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5241901PMC
November 2016

Chemotherapy and Stem Cell Transplantation Increase p16 Expression, a Biomarker of T-cell Aging.

EBioMedicine 2016 Sep 21;11:227-238. Epub 2016 Aug 21.

Department of Medicine, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA; Department of Genetics, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S23523964163037
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049997PMC
http://dx.doi.org/10.1016/j.ebiom.2016.08.029DOI Listing
September 2016

Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next-generation Sequencing.

Appl Immunohistochem Mol Morphol 2016 08;24(7):490-5

*Department of Pathology and Laboratory Medicine †Lineberger Comprehensive Cancer Center ‡Department of Medicine, Division of Medical Oncology, The University of North Carolina, Chapel Hill, NC.

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http://dx.doi.org/10.1097/PAI.0000000000000215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791202PMC
August 2016

G Protein Coupled Receptor Kinase 3 Regulates Breast Cancer Migration, Invasion, and Metastasis.

PLoS One 2016 6;11(4):e0152856. Epub 2016 Apr 6.

Thurston Arthritis Research Center and the Department of Medicine, Division of Rheumatology, Allergy, and Immunology, University of North Carolina, Chapel Hill, NC 27599, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152856PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822790PMC
August 2016

Alternate Metabolic Programs Define Regional Variation of Relevant Biological Features in Renal Cell Carcinoma Progression.

Clin Cancer Res 2016 06 19;22(12):2950-9. Epub 2016 Jan 19.

UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.

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http://clincancerres.aacrjournals.org/content/early/2016/01/
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http://clincancerres.aacrjournals.org/cgi/doi/10.1158/1078-0
Publisher Site
http://dx.doi.org/10.1158/1078-0432.CCR-15-2115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911278PMC
June 2016

Mutation of androgen receptor N-terminal phosphorylation site Tyr-267 leads to inhibition of nuclear translocation and DNA binding.

PLoS One 2015 7;10(5):e0126270. Epub 2015 May 7.

Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126270PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423977PMC
May 2016

Identification of mRNA isoform switching in breast cancer.

BMC Genomics 2016 Mar 3;17:181. Epub 2016 Mar 3.

Department of Genetics, University of North Carolina, 27599, Chapel Hill, NC, USA.

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http://dx.doi.org/10.1186/s12864-016-2521-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778320PMC
March 2016

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Authors:
W Marston Linehan Paul T Spellman Christopher J Ricketts Chad J Creighton Suzanne S Fei Caleb Davis David A Wheeler Bradley A Murray Laura Schmidt Cathy D Vocke Myron Peto Abu Amar M Al Mamun Eve Shinbrot Anurag Sethi Samira Brooks W Kimryn Rathmell Angela N Brooks Katherine A Hoadley A Gordon Robertson Denise Brooks Reanne Bowlby Sara Sadeghi Hui Shen Daniel J Weisenberger Moiz Bootwalla Stephen B Baylin Peter W Laird Andrew D Cherniack Gordon Saksena Scott Haake Jun Li Han Liang Yiling Lu Gordon B Mills Rehan Akbani Mark D M Leiserson Benjamin J Raphael Pavana Anur Donald Bottaro Laurence Albiges Nandita Barnabas Toni K Choueiri Bogdan Czerniak Andrew K Godwin A Ari Hakimi Thai H Ho James Hsieh Michael Ittmann William Y Kim Bhavani Krishnan Maria J Merino Kenna R Mills Shaw Victor E Reuter Ed Reznik Carl S Shelley Brian Shuch Sabina Signoretti Ramaprasad Srinivasan Pheroze Tamboli George Thomas Satish Tickoo Kenneth Burnett Daniel Crain Johanna Gardner Kevin Lau David Mallery Scott Morris Joseph D Paulauskis Robert J Penny Candace Shelton W Troy Shelton Mark Sherman Eric Thompson Peggy Yena Melissa T Avedon Jay Bowen Julie M Gastier-Foster Mark Gerken Kristen M Leraas Tara M Lichtenberg Nilsa C Ramirez Tracie Santos Lisa Wise Erik Zmuda John A Demchok Ina Felau Carolyn M Hutter Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean C Zenklusen Jiashan Zhang Brenda Ayala Julien Baboud Sudha Chudamani Jia Liu Laxmi Lolla Rashi Naresh Todd Pihl Qiang Sun Yunhu Wan Ye Wu Adrian Ally Miruna Balasundaram Saianand Balu Rameen Beroukhim Tom Bodenheimer Christian Buhay Yaron S N Butterfield Rebecca Carlsen Scott L Carter Hsu Chao Eric Chuah Amanda Clarke Kyle R Covington Mahmoud Dahdouli Ninad Dewal Noreen Dhalla Harsha V Doddapaneni Jennifer A Drummond Stacey B Gabriel Richard A Gibbs Ranabir Guin Walker Hale Alicia Hawes D Neil Hayes Robert A Holt Alan P Hoyle Stuart R Jefferys Steven J M Jones Corbin D Jones Divya Kalra Christie Kovar Lora Lewis Jie Li Yussanne Ma Marco A Marra Michael Mayo Shaowu Meng Matthew Meyerson Piotr A Mieczkowski Richard A Moore Donna Morton Lisle E Mose Andrew J Mungall Donna Muzny Joel S Parker Charles M Perou Jeffrey Roach Jacqueline E Schein Steven E Schumacher Yan Shi Janae V Simons Payal Sipahimalani Tara Skelly Matthew G Soloway Carrie Sougnez Angela Tam Donghui Tan Nina Thiessen Umadevi Veluvolu Min Wang Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Jane Zhou Jason Bedford Fengju Chen Yao Fu Mark Gerstein David Haussler Katayoon Kasaian Phillip Lai Shiyun Ling Amie Radenbaugh David Van Den Berg John N Weinstein Jingchun Zhu Monique Albert Iakovina Alexopoulou Jeremiah J Andersen J Todd Auman John Bartlett Sheldon Bastacky Julie Bergsten Michael L Blute Lori Boice Roni J Bollag Jeff Boyd Erik Castle Ying-Bei Chen John C Cheville Erin Curley Benjamin Davies April DeVolk Rajiv Dhir Laura Dike John Eckman Jay Engel Jodi Harr Ronald Hrebinko Mei Huang Lori Huelsenbeck-Dill Mary Iacocca Bruce Jacobs Michael Lobis Jodi K Maranchie Scott McMeekin Jerome Myers Joel Nelson Jeremy Parfitt Anil Parwani Nicholas Petrelli Brenda Rabeno Somak Roy Andrew L Salner Joel Slaton Melissa Stanton R Houston Thompson Leigh Thorne Kelinda Tucker Paul M Weinberger Cynthia Winemiller Leigh Anne Zach Rosemary Zuna

A Role for Widely Interspaced Zinc Finger (WIZ) in Retention of the G9a Methyltransferase on Chromatin.

J Biol Chem 2015 Oct 3;290(43):26088-102. Epub 2015 Sep 3.

the Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599,

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http://dx.doi.org/10.1074/jbc.M115.654459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4646261PMC
October 2015

Spatially distinct neutrophil responses within the inflammatory lesions of pneumonic plague.

MBio 2015 Oct 13;6(5):e01530-15. Epub 2015 Oct 13.

Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

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http://dx.doi.org/10.1128/mBio.01530-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4620470PMC
October 2015

Tumor Heterogeneity: Focus on the Leaves, the Trees, or the Forest?

Cancer Cell 2015 Aug;28(2):149-50

Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2015.07.011DOI Listing
August 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Reply to Alexander S. Parker, Brad C. Leibovich, Jeanette E. Eckel-Passow, John C. Cheville's letter to the editor re: Samira A. Brooks, A. Rose Brannon, Joel S. Parker, et al. ClearCode34: a prognostic risk predictor for localized clear cell renal cell carcinoma. Eur Urol 2014;66:77-84.

Eur Urol 2014 Nov 15;66(5):e92. Epub 2014 Jul 15.

UNC Lineberger Cancer Center, Chapel Hill, NC, USA; Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

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http://dx.doi.org/10.1016/j.eururo.2014.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4294998PMC
November 2014

ABRA: improved coding indel detection via assembly-based realignment.

Bioinformatics 2014 Oct 6;30(19):2813-5. Epub 2014 Jun 6.

Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu376DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173014PMC
October 2014

An integrated genomics approach identifies drivers of proliferation in luminal-subtype human breast cancer.

Nat Genet 2014 Oct 24;46(10):1051-9. Epub 2014 Aug 24.

1] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [4] Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

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http://dx.doi.org/10.1038/ng.3073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300117PMC
October 2014

Molecular features and survival outcomes of the intrinsic subtypes within HER2-positive breast cancer.

J Natl Cancer Inst 2014 Aug 19;106(8). Epub 2014 Aug 19.

: Breast Cancer Unit (AP, BA, MV, JC), Department of Medical Oncology (AP, BA, MV, JC, JT), and Translational Genomics Group (AP, MV), Vall d'Hebron Institute of Oncology Barcelona, Spain; Lineberger Comprehensive Cancer Center (LAC, JSP, CMP), Department of Genetics (CMP), and Department of Pathology and Laboratory Medicine (CMP), University of North Carolina, Chapel Hill, NC; Memorial Sloan-Kettering Cancer Center, New York (JB).

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http://dx.doi.org/10.1093/jnci/dju152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151853PMC
August 2014

ClearCode34: A prognostic risk predictor for localized clear cell renal cell carcinoma.

Eur Urol 2014 Jul 25;66(1):77-84. Epub 2014 Feb 25.

UNC Lineberger Cancer Center, Chapel Hill, NC, USA; Department of Medicine, Division of Hematology and Oncology, and Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S03022838140016
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http://dx.doi.org/10.1016/j.eururo.2014.02.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058355PMC
July 2014

Prognostic B-cell signatures using mRNA-seq in patients with subtype-specific breast and ovarian cancer.

Clin Cancer Res 2014 Jul 10;20(14):3818-29. Epub 2014 Jun 10.

Authors' Affiliations: Lineberger Comprehensive Cancer Center; Medicine; Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina

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http://dx.doi.org/10.1158/1078-0432.CCR-13-3368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102637PMC
July 2014

Integrated RNA and DNA sequencing improves mutation detection in low purity tumors.

Nucleic Acids Res 2014 Jul 26;42(13):e107. Epub 2014 Jun 26.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Internal Medicine, Division of Medical Oncology, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA

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http://dx.doi.org/10.1093/nar/gku489DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117748PMC
July 2014

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

BMC Genomics 2014 Jun 2;15:419. Epub 2014 Jun 2.

Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill NC 27599, USA.

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http://dx.doi.org/10.1186/1471-2164-15-419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070569PMC
June 2014

Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology.

Proc Natl Acad Sci U S A 2014 Feb 11;111(8):3110-5. Epub 2014 Feb 11.

Department of Genetics, Department of Medicine, Division of Hematology/Oncology, Department of Surgery, Department of Pathology and Laboratory Medicine, and Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.

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http://dx.doi.org/10.1073/pnas.1318376111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3939870PMC
February 2014

Characterization of cell lines derived from breast cancers and normal mammary tissues for the study of the intrinsic molecular subtypes.

Breast Cancer Res Treat 2013 Nov 27;142(2):237-55. Epub 2013 Oct 27.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB7295, Chapel Hill, NC, 27599, USA.

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http://dx.doi.org/10.1007/s10549-013-2743-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832776PMC
November 2013