Jingchun Zhu

Jingchun Zhu

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Jingchun Zhu

Jingchun Zhu

Publications by authors named "Jingchun Zhu"

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Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer.

Authors:
Olena M Vaske Isabel Bjork Sofie R Salama Holly Beale Avanthi Tayi Shah Lauren Sanders Jacob Pfeil Du L Lam Katrina Learned Ann Durbin Ellen T Kephart Rob Currie Yulia Newton Teresa Swatloski Duncan McColl John Vivian Jingchun Zhu Alex G Lee Stanley G Leung Aviv Spillinger Heng-Yi Liu Winnie S Liang Sara A Byron Michael E Berens Adam C Resnick Norman Lacayo Sheri L Spunt Arun Rangaswami Van Huynh Lilibeth Torno Ashley Plant Ivan Kirov Keri B Zabokrtsky S Rod Rassekh Rebecca J Deyell Janessa Laskin Marco A Marra Leonard S Sender Sabine Mueller E Alejandro Sweet-Cordero Theodore C Goldstein David Haussler

JAMA Netw Open 2019 Oct 2;2(10):e1913968. Epub 2019 Oct 2.

University of California, Santa Cruz Genomics Institute, Santa Cruz.

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http://dx.doi.org/10.1001/jamanetworkopen.2019.13968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822083PMC
October 2019

Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer.

Authors:
Yulia Newton S Rod Rassekh Rebecca J Deyell Yaoqing Shen Martin R Jones Chris Dunham Stephen Yip Sreeja Leelakumari Jingchun Zhu Duncan McColl Teresa Swatloski Sofie R Salama Tony Ng Glenda Hendson Anna F Lee Yussanne Ma Richard Moore Andrew J Mungall David Haussler Joshua M Stuart Colleen Jantzen Janessa Laskin Steven J M Jones Marco A Marra Olena Morozova

JCO Precis Oncol 2018 19;2. Epub 2018 Apr 19.

University of California Santa Cruz Genomics Institute, Mailstop CBSE, 1156 High St, Santa Cruz, CA 95064.

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http://dx.doi.org/10.1200/PO.17.00198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6675034PMC
April 2018

Toil enables reproducible, open source, big biomedical data analyses.

Authors:
John Vivian Arjun Arkal Rao Frank Austin Nothaft Christopher Ketchum Joel Armstrong Adam Novak Jacob Pfeil Jake Narkizian Alden D Deran Audrey Musselman-Brown Hannes Schmidt Peter Amstutz Brian Craft Mary Goldman Kate Rosenbloom Melissa Cline Brian O'Connor Megan Hanna Chet Birger W James Kent David A Patterson Anthony D Joseph Jingchun Zhu Sasha Zaranek Gad Getz David Haussler Benedict Paten

Nat Biotechnol 2017 04;35(4):314-316

Computational Genomics Lab, UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA.

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http://dx.doi.org/10.1038/nbt.3772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546205PMC
April 2017

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

N Engl J Med 2016 Jan 4;374(2):135-45. Epub 2015 Nov 4.

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https://www.genome.gov/Multimedia/Slides/TCGA4/06_Linehan.pd
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http://www.nejm.org/doi/abs/10.1056/NEJMoa1505917
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http://dx.doi.org/10.1056/NEJMoa1505917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775252PMC
January 2016

A Distributed Network for Intensive Longitudinal Monitoring in Metastatic Triple-Negative Breast Cancer.

Authors:
C Anthony Blau Arturo B Ramirez Sibel Blau Colin C Pritchard Michael O Dorschner Stephen C Schmechel Timothy J Martins Elisabeth M Mahen Kimberly A Burton Vitalina M Komashko Amie J Radenbaugh Katy Dougherty Anju Thomas Christopher P Miller James Annis Jonathan R Fromm Chaozhong Song Elizabeth Chang Kellie Howard Sharon Austin Rodney A Schmidt Michael L Linenberger Pamela S Becker Francis M Senecal Brigham H Mecham Su-In Lee Anup Madan Roy Ronen Janusz Dutkowski Shelly Heimfeld Brent L Wood Jackie L Stilwell Eric P Kaldjian David Haussler Jingchun Zhu

J Natl Compr Canc Netw 2016 01;14(1):8-17

Center for Cancer Innovation, University of Washington, Seattle, Washington

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http://www.jnccn.org/content/14/1/8.full.pdf
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4970582PMC
http://dx.doi.org/10.6004/jnccn.2016.0003DOI Listing
January 2016

RADIA: RNA and DNA integrated analysis for somatic mutation detection.

Authors:
Amie J Radenbaugh Singer Ma Adam Ewing Joshua M Stuart Eric A Collisson Jingchun Zhu David Haussler

PLoS One 2014 18;9(11):e111516. Epub 2014 Nov 18.

University of California Santa Cruz Genomics Institute, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America; Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111516PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236012PMC
July 2015

The UCSC Cancer Genomics Browser: update 2015.

Authors:
Mary Goldman Brian Craft Teresa Swatloski Melissa Cline Olena Morozova Mark Diekhans David Haussler Jingchun Zhu

Nucleic Acids Res 2015 Jan 11;43(Database issue):D812-7. Epub 2014 Nov 11.

Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA

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http://dx.doi.org/10.1093/nar/gku1073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383911PMC
January 2015

Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: a workshop report: the RPPA (Reverse Phase Protein Array) society.

Authors:
Rehan Akbani Karl-Friedrich Becker Neil Carragher Ted Goldstein Leanne de Koning Ulrike Korf Lance Liotta Gordon B Mills Satoshi S Nishizuka Michael Pawlak Emanuel F Petricoin Harvey B Pollard Bryan Serrels Jingchun Zhu

Mol Cell Proteomics 2014 Jul 28;13(7):1625-43. Epub 2014 Apr 28.

¶Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California;

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http://www.mcponline.org/lookup/doi/10.1074/mcp.O113.034918
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http://dx.doi.org/10.1074/mcp.O113.034918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083105PMC
July 2014

Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser.

Authors:
Melissa S Cline Brian Craft Teresa Swatloski Mary Goldman Singer Ma David Haussler Jingchun Zhu

Sci Rep 2013 Oct 2;3:2652. Epub 2013 Oct 2.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz.

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http://dx.doi.org/10.1038/srep02652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3788369PMC
October 2013

The UCSC Cancer Genomics Browser: update 2013.

Authors:
Mary Goldman Brian Craft Teresa Swatloski Kyle Ellrott Melissa Cline Mark Diekhans Singer Ma Chris Wilks Josh Stuart David Haussler Jingchun Zhu

Nucleic Acids Res 2013 Jan 29;41(Database issue):D949-54. Epub 2012 Oct 29.

Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gks1008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531186PMC
January 2013

A DNA hypermethylation module for the stem/progenitor cell signature of cancer.

Authors:
Hariharan Easwaran Sarah E Johnstone Leander Van Neste Joyce Ohm Tim Mosbruger Qiuju Wang Martin J Aryee Patrick Joyce Nita Ahuja Dan Weisenberger Eric Collisson Jingchun Zhu Srinivasan Yegnasubramanian William Matsui Stephen B Baylin

Genome Res 2012 May 5;22(5):837-49. Epub 2012 Mar 5.

The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins and the Johns Hopkins Medical Institutions, Baltimore, MD 21117, USA.

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http://genome.cshlp.org/content/early/2012/03/09/gr.131169.1
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http://genome.cshlp.org/cgi/doi/10.1101/gr.131169.111
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http://dx.doi.org/10.1101/gr.131169.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337430PMC
May 2012

Human tRNA genes function as chromatin insulators.

Authors:
Jesse R Raab Jonathan Chiu Jingchun Zhu Sol Katzman Sreenivasulu Kurukuti Paul A Wade David Haussler Rohinton T Kamakaka

EMBO J 2012 Jan 15;31(2):330-50. Epub 2011 Nov 15.

Department of MCD Biology, University of California, Santa Cruz, CA, USA.

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http://dx.doi.org/10.1038/emboj.2011.406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261562PMC
January 2012

The Human Epigenome Browser at Washington University.

Authors:
Xin Zhou Brett Maricque Mingchao Xie Daofeng Li Vasavi Sundaram Eric A Martin Brian C Koebbe Cydney Nielsen Martin Hirst Peggy Farnham Robert M Kuhn Jingchun Zhu Ivan Smirnov W James Kent David Haussler Pamela A F Madden Joseph F Costello Ting Wang

Nat Methods 2011 Nov 29;8(12):989-90. Epub 2011 Nov 29.

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http://www.nature.com/articles/nmeth.1772
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http://dx.doi.org/10.1038/nmeth.1772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552640PMC
November 2011

The UCSC Cancer Genomics Browser: update 2011.

Authors:
J Zachary Sanborn Stephen C Benz Brian Craft Christopher Szeto Kord M Kober Laurence Meyer Charles J Vaske Mary Goldman Kayla E Smith Robert M Kuhn Donna Karolchik W James Kent Joshua M Stuart David Haussler Jingchun Zhu

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

Department of Biomolecular Engineering, Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkq1113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013705PMC
January 2011

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

Authors:
Charles J Vaske Stephen C Benz J Zachary Sanborn Dent Earl Christopher Szeto Jingchun Zhu David Haussler Joshua M Stuart

Bioinformatics 2010 Jun;26(12):i237-45

Howard Hughes Medical Institute, UC Santa Cruz, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881367PMC
June 2010

The UCSC Cancer Genomics Browser.

Authors:
Jingchun Zhu J Zachary Sanborn Stephen Benz Christopher Szeto Fan Hsu Robert M Kuhn Donna Karolchik John Archie Marc E Lenburg Laura J Esserman W James Kent David Haussler Ting Wang

Nat Methods 2009 Apr;6(4):239-40

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http://dx.doi.org/10.1038/nmeth0409-239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5027375PMC
April 2009

Comparative genomics search for losses of long-established genes on the human lineage.

Authors:
Jingchun Zhu J Zachary Sanborn Mark Diekhans Craig B Lowe Tom H Pringle David Haussler

PLoS Comput Biol 2007 Dec;3(12):e247

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0030247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134963PMC
December 2007

A Bayesian network driven approach to model the transcriptional response to nitric oxide in Saccharomyces cerevisiae.

Authors:
Jingchun Zhu Ashwini Jambhekar Aaron Sarver Joseph DeRisi

PLoS One 2006 Dec 20;1:e94. Epub 2006 Dec 20.

Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000094PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1762306PMC
December 2006

The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum.

Authors:
Zbynek Bozdech Manuel Llinás Brian Lee Pulliam Edith D Wong Jingchun Zhu Joseph L DeRisi

PLoS Biol 2003 Oct 18;1(1):E5. Epub 2003 Aug 18.

Department of Biochemistry and Biophysics, University of California, San Francisco, USA.

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http://dx.plos.org/10.1371/journal.pbio.0000005
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http://dx.doi.org/10.1371/journal.pbio.0000005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC176545PMC
October 2003

Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray.

Authors:
Zbynek Bozdech Jingchun Zhu Marcin P Joachimiak Fred E Cohen Brian Pulliam Joseph L DeRisi

Genome Biol 2003 31;4(2):R9. Epub 2003 Jan 31.

Department of Biochemistry and Biophysics, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151308PMC
http://dx.doi.org/10.1186/gb-2003-4-2-r9DOI Listing
March 2003