Zhenlin Ju

Zhenlin Ju

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Sequential Therapy with PARP and WEE1 Inhibitors Minimizes Toxicity while Maintaining Efficacy.

Cancer Cell 2019 Jun;35(6):851-867.e7

Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Cell, Development and Cancer Biology, Oregon Health and Sciences University, Portland, OR 97201, USA; Knight Cancer Institute, Portland, OR 97201, USA.

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http://dx.doi.org/10.1016/j.ccell.2019.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642675PMC
June 2019

Neomorphic PDGFRA extracellular domain driver mutations are resistant to PDGFRA targeted therapies.

Nat Commun 2018 11 2;9(1):4583. Epub 2018 Nov 2.

Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.

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http://www.nature.com/articles/s41467-018-06949-w
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http://dx.doi.org/10.1038/s41467-018-06949-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214970PMC
November 2018

Essential roles of mitochondrial biogenesis regulator Nrf1 in retinal development and homeostasis.

Mol Neurodegener 2018 10 17;13(1):56. Epub 2018 Oct 17.

Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin St., MSB 7.024, Houston, TX, 77030, USA.

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https://molecularneurodegeneration.biomedcentral.com/article
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http://dx.doi.org/10.1186/s13024-018-0287-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192121PMC
October 2018

DNA-Methyltransferase 1 Induces Dedifferentiation of Pancreatic Cancer Cells through Silencing of Krüppel-Like Factor 4 Expression.

Clin Cancer Res 2017 Sep 28;23(18):5585-5597. Epub 2017 Jun 28.

Department Gastroenterology Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.

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http://dx.doi.org/10.1158/1078-0432.CCR-17-0387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5600846PMC
September 2017

Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays.

Cancer Cell 2017 02;31(2):225-239

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501076PMC
February 2017

Proteomic Characterization of Head and Neck Cancer Patient-Derived Xenografts.

Mol Cancer Res 2016 Mar 18;14(3):278-86. Epub 2015 Dec 18.

Department of Otolaryngology, University of Pittsburgh, Pittsburgh, Pennsylvania. Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania. Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, California.

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http://dx.doi.org/10.1158/1541-7786.MCR-15-0354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4794346PMC
March 2016

Spatial normalization of reverse phase protein array data.

PLoS One 2014 12;9(12):e97213. Epub 2014 Dec 12.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0097213PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264691PMC
January 2016

The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers.

Cancer Cell 2015 Oct 1;28(4):515-528. Epub 2015 Oct 1.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15356108150030
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http://dx.doi.org/10.1016/j.ccell.2015.08.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4605878PMC
October 2015

ARID1A Deficiency Impairs the DNA Damage Checkpoint and Sensitizes Cells to PARP Inhibitors.

Cancer Discov 2015 Jul 11;5(7):752-67. Epub 2015 Jun 11.

Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Medical Oncology, Tongji Hospital, Tongji Medical College, The Huazhong University of Science and Technology, Wuhan, P.R. China.

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http://cancerdiscovery.aacrjournals.org/cgi/doi/10.1158/2159
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http://dx.doi.org/10.1158/2159-8290.CD-14-0849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497871PMC
July 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

Development of a robust classifier for quality control of reverse-phase protein arrays.

Bioinformatics 2015 Mar 6;31(6):912-8. Epub 2014 Nov 6.

Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu736DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4375399PMC
March 2015

Prognostic relevance of acquired uniparental disomy in serous ovarian cancer.

Mol Cancer 2015 Feb 3;14:29. Epub 2015 Feb 3.

Departments of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12943-015-0289-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320828PMC
February 2015

A comprehensive comparison of normalization methods for loading control and variance stabilization of reverse-phase protein array data.

Cancer Inform 2014 16;13:109-17. Epub 2014 Oct 16.

Department of Bioinformatics and Computational Biology, Unit 1410, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://journals.sagepub.com/doi/10.4137/CIN.S13329
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http://dx.doi.org/10.4137/CIN.S13329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213190PMC
November 2014

Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer.

Proc Natl Acad Sci U S A 2014 Jan 6;111(3):1114-9. Epub 2014 Jan 6.

Departments of Otolaryngology, Pharmacology and Chemical Biology, Structural Biology, and Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213.

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http://dx.doi.org/10.1073/pnas.1319551111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3903220PMC
January 2014

TCPA: a resource for cancer functional proteomics data.

Nat Methods 2013 Nov 15;10(11):1046-7. Epub 2013 Sep 15.

1] Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA. [2].

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http://dx.doi.org/10.1038/nmeth.2650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076789PMC
November 2013

Soft tissue sarcoma subtypes exhibit distinct patterns of acquired uniparental disomy.

BMC Med Genomics 2012 Dec 5;5:60. Epub 2012 Dec 5.

Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA.

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http://dx.doi.org/10.1186/1755-8794-5-60DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3541987PMC
December 2012

An efficient procedure for protein extraction from formalin-fixed, paraffin-embedded tissues for reverse phase protein arrays.

Proteome Sci 2012 Sep 24;10(1):56. Epub 2012 Sep 24.

Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1186/1477-5956-10-56DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561137PMC
September 2012

Combined Src and ER blockade impairs human breast cancer proliferation in vitro and in vivo.

Breast Cancer Res Treat 2011 Jul 29;128(1):69-78. Epub 2010 Jul 29.

Braman Family Breast Cancer Institute, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, 33136, USA.

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http://dx.doi.org/10.1007/s10549-010-1024-7DOI Listing
July 2011

Integrative analysis of proteomic signatures, mutations, and drug responsiveness in the NCI 60 cancer cell line set.

Mol Cancer Ther 2010 Feb 2;9(2):257-67. Epub 2010 Feb 2.

Department of Melanoma Medical Oncology and Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 0904, Houston, TX 77030, USA.

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http://dx.doi.org/10.1158/1535-7163.MCT-09-0743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085051PMC
February 2010

Integrated Molecular and Clinical Analysis of AKT Activation in Metastatic Melanoma.

Clin Cancer Res 2009 Dec;15(24):7538-7546

Authors' Affiliations: Departments of Melanoma Medical Oncology, Systems Biology, Biostatistics, Cancer Medicine, Surgical Oncology, Cancer Biology, and Pathology, University of Texas M. D. Anderson Cancer Center, Houston, Texas; and Lovelace Respiratory Research Institute, Albuquerque, New Mexico.

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http://dx.doi.org/10.1158/1078-0432.CCR-09-1985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805170PMC
December 2009

Genomic approaches in the identification of hypoxia biomarkers in model fish species.

J Exp Mar Bio Ecol 2009 Dec;381(Suppl 1):S180-S187

Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.

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http://dx.doi.org/10.1016/j.jembe.2009.07.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782826PMC
December 2009

Comparison of gene expression responses to hypoxia in viviparous (Xiphophorus) and oviparous (Oryzias) fishes using a medaka microarray.

Comp Biochem Physiol C Toxicol Pharmacol 2009 Mar 21;149(2):258-65. Epub 2008 Nov 21.

Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S15320456080031
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http://dx.doi.org/10.1016/j.cbpc.2008.11.005DOI Listing
March 2009

Genomic resources for Xiphophorus research.

Zebrafish 2006 ;3(1):11-22

Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666-4616, USA.

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http://dx.doi.org/10.1089/zeb.2006.3.11DOI Listing
April 2008

DNA microarray technology in toxicogenomics of aquatic models: methods and applications.

Comp Biochem Physiol C Toxicol Pharmacol 2007 Feb 3;145(1):5-14. Epub 2006 Jun 3.

Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666, USA.

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http://dx.doi.org/10.1016/j.cbpc.2006.04.017DOI Listing
February 2007

Multiple tissue gene expression analyses in Japanese medaka (Oryzias latipes) exposed to hypoxia.

Comp Biochem Physiol C Toxicol Pharmacol 2007 Feb 30;145(1):134-44. Epub 2006 Jun 30.

Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666-4616, USA.

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http://dx.doi.org/10.1016/j.cbpc.2006.06.012DOI Listing
February 2007

p21 delays tumor onset by preservation of chromosomal stability.

Proc Natl Acad Sci U S A 2006 Dec 14;103(52):19842-7. Epub 2006 Dec 14.

Department of Cancer Genetics and Pathology, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0606343104
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http://dx.doi.org/10.1073/pnas.0606343104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1702317PMC
December 2006

An in silico mining for simple sequence repeats from expressed sequence tags of zebrafish, medaka, Fundulus, and Xiphophorus.

In Silico Biol 2005 ;5(5-6):439-63

Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.

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May 2006

Application of protein lysate microarrays to molecular marker verification and quantification.

Proteome Sci 2005 Nov 10;3. Epub 2005 Nov 10.

Department of Molecular Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1186/1477-5956-3-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1334216PMC
November 2005

Expression profile of the channel catfish spleen: analysis of genes involved in immune functions.

Mar Biotechnol (NY) 2002 Dec;4(6):526-36

The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA.

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http://link.springer.com/content/pdf/10.1007/s10126-002-0067
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http://link.springer.com/10.1007/s10126-002-0067-0
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http://dx.doi.org/10.1007/s10126-002-0067-0DOI Listing
December 2002

Transcriptome analysis of channel catfish (Ictalurus punctatus): initial analysis of gene expression and microsatellite-containing cDNAs in the skin.

Gene 2002 Feb;285(1-2):157-68

The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA.

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http://dx.doi.org/10.1016/s0378-1119(02)00414-6DOI Listing
February 2002