Publications by authors named "Fiona McCarthy"

58Publications

Chickspress: a resource for chicken gene expression.

Database (Oxford) 2019 01;2019

School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson AZ, USA.

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http://dx.doi.org/10.1093/database/baz058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556980PMC
January 2019

Leveraging Experimental Details for an Improved Understanding of Host-Pathogen Interactome.

Curr Protoc Bioinformatics 2018 03;61(1):8.26.1-8.26.12

Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi.

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http://dx.doi.org/10.1002/cpbi.44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060636PMC
March 2018

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms.

J Vis Exp 2017 05 9(123). Epub 2017 May 9.

BIO5 Institute, University of Arizona; The School of Plant Sciences, University of Arizona; Genetics GIDP, University of Arizona.

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http://dx.doi.org/10.3791/55009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607918PMC
May 2017

Acute Ischemia Induced by High-Density Culture Increases Cytokine Expression and Diminishes the Function and Viability of Highly Purified Human Islets of Langerhans.

Transplantation 2017 11;101(11):2705-2712

1 Department of Surgery, University of Arizona, Tucson, AZ. 2 Department of Physiological Sciences GIDP, University of Arizona, Tucson, AZ. 3 School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ. 4 Department of Physiology, University of Arizona, Tucson, AZ. 5 Sanofi-Aventis Group, Tucson, AZ. 6 Icagen, Inc., Tucson, AZ. 7 Department of Surgery, SUNY Upstate Medical University, Syracuse, NY.

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http://dx.doi.org/10.1097/TP.0000000000001714DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6319561PMC
November 2017

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology.

Integr Comp Biol 2016 12 17;56(6):1183-1191. Epub 2016 Sep 17.

Romberg Tiburon Center for Environmental Studies and Department of Biology, San Francisco State University, Tiburon, CA 94920, USA.

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http://dx.doi.org/10.1093/icb/icw083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5146710PMC
December 2016

HPIDB 2.0: a curated database for host-pathogen interactions.

Database (Oxford) 2016 3;2016. Epub 2016 Jul 3.

Institute for Genomics, Biocomputing and Biotechnology, College of Veterinary Medicine, Institute for Genomics, Mississippi State University, Mississippi State, MS 39762, USA

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http://dx.doi.org/10.1093/database/baw103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930832PMC
November 2017

Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates.

Front Neurosci 2015 7;9:361. Epub 2015 Oct 7.

Genetics GIDP, University of Arizona Tucson, AZ, USA ; BIO5 Institute, University of Arizona Tucson, AZ, USA ; The School of Plant Sciences, University of Arizona Tucson, AZ, USA.

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http://journal.frontiersin.org/Article/10.3389/fnins.2015.00
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http://dx.doi.org/10.3389/fnins.2015.00361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595791PMC
October 2015

Third Report on Chicken Genes and Chromosomes 2015.

Authors:
Michael Schmid Jacqueline Smith David W Burt Bronwen L Aken Parker B Antin Alan L Archibald Chris Ashwell Perry J Blackshear Clarissa Boschiero C Titus Brown Shane C Burgess Hans H Cheng William Chow Derrick J Coble Amanda Cooksey Richard P M A Crooijmans Joana Damas Richard V N Davis Dirk-Jan de Koning Mary E Delany Thomas Derrien Takele T Desta Ian C Dunn Matthew Dunn Hans Ellegren Lél Eöry Ionas Erb Marta Farré Mario Fasold Damarius Fleming Paul Flicek Katie E Fowler Laure Frésard David P Froman Valerie Garceau Paul P Gardner Almas A Gheyas Darren K Griffin Martien A M Groenen Thomas Haaf Olivier Hanotte Alan Hart Julien Häsler S Blair Hedges Jana Hertel Kerstin Howe Allen Hubbard David A Hume Pete Kaiser Darek Kedra Stephen J Kemp Christophe Klopp Kalmia E Kniel Richard Kuo Sandrine Lagarrigue Susan J Lamont Denis M Larkin Raman A Lawal Sarah M Markland Fiona McCarthy Heather A McCormack Marla C McPherson Akira Motegi Stefan A Muljo Andrea Münsterberg Rishi Nag Indrajit Nanda Michael Neuberger Anne Nitsche Cedric Notredame Harry Noyes Rebecca O'Connor Elizabeth A O'Hare Andrew J Oler Sheila C Ommeh Helio Pais Michael Persia Frédérique Pitel Likit Preeyanon Pablo Prieto Barja Elizabeth M Pritchett Douglas D Rhoads Charmaine M Robinson Michael N Romanov Max Rothschild Pierre-François Roux Carl J Schmidt Alisa-Sophia Schneider Matthew G Schwartz Steve M Searle Michael A Skinner Craig A Smith Peter F Stadler Tammy E Steeves Claus Steinlein Liang Sun Minoru Takata Igor Ulitsky Qing Wang Ying Wang Wesley C Warren Jonathan M D Wood David Wragg Huaijun Zhou

Cytogenet Genome Res 2015 14;145(2):78-179. Epub 2015 Jul 14.

Department of Human Genetics, University of Würzburg, Würzburg, Germany.

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http://dx.doi.org/10.1159/000430927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120589PMC
October 2015

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://jarvislab.net/wp-content/uploads/2012/02/Green-et-al-
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http://www.sciencemag.org/cgi/doi/10.1126/science.1254449
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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

Transgenic soya bean seeds accumulating β-carotene exhibit the collateral enhancements of oleate and protein content traits.

Plant Biotechnol J 2015 May 14;13(4):590-600. Epub 2014 Nov 14.

School of Plant Sciences/BIO5 Institute, University of Arizona, Tucson, AZ, USA.

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http://dx.doi.org/10.1111/pbi.12286DOI Listing
May 2015

De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.

PLoS One 2014 12;9(5):e96855. Epub 2014 May 12.

Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America; Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096855PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018402PMC
January 2015

Inflammatory cytokines in human pancreatic cancer.

Cancer Lett 2014 Apr 20;345(2):157-63. Epub 2013 Jul 20.

Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary, University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.canlet.2013.07.014DOI Listing
April 2014

Interestingness measures and strategies for mining multi-ontology multi-level association rules from gene ontology annotations for the discovery of new GO relationships.

J Biomed Inform 2013 Oct 11;46(5):849-56. Epub 2013 Jul 11.

Department of Computer Science and Engineering, Mississippi State University, MS, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2013.06.012DOI Listing
October 2013

Current clinical immunotherapy targets in advanced nonsmall cell lung cancer (NSCLC).

J Leukoc Biol 2013 Dec 21;94(6):1201-6. Epub 2013 May 21.

1.Barts Cancer Institute, Queen Mary, University of London, Charterhouse Square, London, EC1M 6BQ, UK.

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http://dx.doi.org/10.1189/jlb.0313121DOI Listing
December 2013

Developing a biocuration workflow for AgBase, a non-model organism database.

Database (Oxford) 2012 17;2012:bas038. Epub 2012 Nov 17.

Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, MS 39762, USA.

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http://dx.doi.org/10.1093/database/bas038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500517PMC
April 2013

Cross-Ontology multi-level association rule mining in the Gene Ontology.

PLoS One 2012 12;7(10):e47411. Epub 2012 Oct 12.

Department of Computer Science and Engineering, Mississippi State University, Mississippi State, MS, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0047411PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3470562PMC
February 2013

Transcriptome-based differentiation of closely-related Miscanthus lines.

PLoS One 2012 10;7(1):e29850. Epub 2012 Jan 10.

Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029850PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3254643PMC
May 2012

The proteogenomic mapping tool.

BMC Bioinformatics 2011 Apr 22;12:115. Epub 2011 Apr 22.

Department of Computer Science & Engineering, Mississippi State University, MS, USA.

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http://dx.doi.org/10.1186/1471-2105-12-115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107813PMC
April 2011

AgBase: supporting functional modeling in agricultural organisms.

Nucleic Acids Res 2011 Jan 12;39(Database issue):D497-506. Epub 2010 Nov 12.

Department of Basic Sciences, College of Veterinary Medicine, PO Box 6100, Mississippi State University, MS 39762, USA.

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http://dx.doi.org/10.1093/nar/gkq1115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013706PMC
January 2011

Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences.

BMC Bioinformatics 2010 Oct 7;11 Suppl 6:S9. Epub 2010 Oct 7.

Department of Basic Sciences, Mississippi State University, Mississippi State, MS 39762, USA.

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http://dx.doi.org/10.1186/1471-2105-11-S6-S9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026383PMC
October 2010

GOModeler--a tool for hypothesis-testing of functional genomics datasets.

BMC Bioinformatics 2010 Oct 7;11 Suppl 6:S29. Epub 2010 Oct 7.

Department of Computer Science and Engineering, Mississippi State University, MS, USA.

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http://dx.doi.org/10.1186/1471-2105-11-S6-S29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026376PMC
October 2010

Proteome profile of the developing maize (Zea mays L.) rachis.

Proteomics 2010 Aug;10(16):3051-5

Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, MS 39762, USA.

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http://dx.doi.org/10.1002/pmic.200900833DOI Listing
August 2010

Re-annotation is an essential step in systems biology modeling of functional genomics data.

PLoS One 2010 May 14;5(5):e10642. Epub 2010 May 14.

Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010642PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871057PMC
May 2010

Transcriptional and pathway analysis in the hypothalamus of newly hatched chicks during fasting and delayed feeding.

BMC Genomics 2010 Mar 9;11:162. Epub 2010 Mar 9.

Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1186/1471-2164-11-162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848243PMC
March 2010

Structural and functional-annotation of an equine whole genome oligoarray.

BMC Bioinformatics 2009 Oct 8;10 Suppl 11:S8. Epub 2009 Oct 8.

Department of Clinical Sciences, College of Veterinary Medicine, Mississippi State University, PO Box 6100, Mississippi State, MS, 39762, USA.

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http://dx.doi.org/10.1186/1471-2105-10-S11-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3226197PMC
October 2009

Facilitating functional annotation of chicken microarray data.

BMC Bioinformatics 2009 Oct 8;10 Suppl 11:S2. Epub 2009 Oct 8.

Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.

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http://dx.doi.org/10.1186/1471-2105-10-S11-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3226191PMC
October 2009

The Chicken Gene Nomenclature Committee report.

BMC Genomics 2009 Jul 14;10 Suppl 2:S5. Epub 2009 Jul 14.

Department of Genomics and Genetics, Roslin Institute and Royal (Dick) School of Veterinary Studies, Midlothian, UK.

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http://dx.doi.org/10.1186/1471-2164-10-S2-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2966335PMC
July 2009

Introduction to the proceedings of the Avian Genomics and Gene Ontology Annotation Workshop.

BMC Genomics 2009 Jul 14;10 Suppl 2:I1. Epub 2009 Jul 14.

Department of Computer Science and Engineering, Mississippi State University, Mississippi State, MS 39762, USA.

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http://dx.doi.org/10.1186/1471-2164-10-S2-I1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2966328PMC
July 2009

Understanding animal viruses using the Gene Ontology.

Trends Microbiol 2009 Jul 2;17(7):328-35. Epub 2009 Jul 2.

Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.

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http://dx.doi.org/10.1016/j.tim.2009.04.006DOI Listing
July 2009

ArrayIDer: automated structural re-annotation pipeline for DNA microarrays.

BMC Bioinformatics 2009 Jan 23;10:30. Epub 2009 Jan 23.

Department of Basic Science, PO Box 6100, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762,USA.

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http://dx.doi.org/10.1186/1471-2105-10-30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2636773PMC
January 2009

Sequential detergent extraction prior to mass spectrometry analysis.

Methods Mol Biol 2009 ;528:110-8

Department of Basic Sciences, Mississippi State University, MS 39762, USA.

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http://dx.doi.org/10.1007/978-1-60327-310-7_7DOI Listing
March 2009

The essential and non-essential genes of Bovine herpesvirus 1.

J Gen Virol 2008 Nov;89(Pt 11):2851-2863

Department of Primary Industries and Fisheries, St Lucia, Brisbane, QLD, Australia.

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http://dx.doi.org/10.1099/vir.0.2008/002501-0DOI Listing
November 2008

Gene Ontology annotation quality analysis in model eukaryotes.

Nucleic Acids Res 2008 Feb 10;36(2):e12. Epub 2008 Jan 10.

Department of Basic Sciences, Mississippi State University, Mississippi 39762, USA.

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http://dx.doi.org/10.1093/nar/gkm1167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2241866PMC
February 2008

Prediction of peptides observable by mass spectrometry applied at the experimental set level.

BMC Bioinformatics 2007 Nov 1;8 Suppl 7:S23. Epub 2007 Nov 1.

Department of Biochemistry & Molecular Biology, Mississippi State University, MS, USA.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/1471-2105-8-S7-S23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099492PMC
November 2007

Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome.

BMC Genomics 2007 Nov 19;8:425. Epub 2007 Nov 19.

Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.

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http://dx.doi.org/10.1186/1471-2164-8-425DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2204016PMC
November 2007

Non-electrophoretic differential detergent fractionation proteomics using frozen whole organs.

Rapid Commun Mass Spectrom 2007 ;21(23):3905-9

College of Veterinary Medicine, PO Box 6100, Mississippi State University, MS 39762-6100, USA.

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http://doi.wiley.com/10.1002/rcm.3287
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http://dx.doi.org/10.1002/rcm.3287DOI Listing
January 2008

AgBase: a unified resource for functional analysis in agriculture.

Nucleic Acids Res 2007 Jan 29;35(Database issue):D599-603. Epub 2006 Nov 29.

Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, PO Box 6100, Mississippi, MS 39762, USA.

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http://dx.doi.org/10.1093/nar/gkl936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1751552PMC
January 2007

AgBase: a functional genomics resource for agriculture.

BMC Genomics 2006 Sep 8;7:229. Epub 2006 Sep 8.

Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.

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http://dx.doi.org/10.1186/1471-2164-7-229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618847PMC
September 2006

Modeling a whole organ using proteomics: the avian bursa of Fabricius.

Proteomics 2006 May;6(9):2759-71

Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762-6100, USA.

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http://dx.doi.org/10.1002/pmic.200500648DOI Listing
May 2006

Differential detergent fractionation for non-electrophoretic eukaryote cell proteomics.

J Proteome Res 2005 Mar-Apr;4(2):316-24

College of Veterinary Medicine, PO Box 6100, Mississippi State University, Mississippi 39762, USA.

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http://dx.doi.org/10.1021/pr049842dDOI Listing
July 2005

Genetic analysis of bovine viral diarrhoea viruses from Australia.

Vet Microbiol 2005 Mar 26;106(1-2):1-6. Epub 2005 Jan 26.

Department of Primary Industries and Fisheries, Level 6 North, Queensland Biosciences Precinct, 306 Carmody Road, Brisbane, Qld 4072, Australia.

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http://dx.doi.org/10.1016/j.vetmic.2004.10.024DOI Listing
March 2005

Construction of a gene inactivation library for Bovine herpesvirus 1 using infectious clone technology.

Methods Mol Biol 2005 ;292:387-400

Department of Primary Industries, Agency for Food and Fibre Sciences, St. Lucia, Queensland, Australia.

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http://dx.doi.org/10.1385/1-59259-848-x:387DOI Listing
March 2005

Rapid and efficient construction of recombinant bovine herpesvirus 1 genomes.

J Virol Methods 2003 Feb;107(2):269-74

Queensland Agricultural Biotechnology Centre, Agency for Food and Fibre Sciences, Gehrmann Laboratories, Research Road, 4072, Queensland, Brisbane, Australia.

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http://dx.doi.org/10.1016/s0166-0934(02)00226-4DOI Listing
February 2003

Construction and manipulation of an infectious clone of the bovine herpesvirus 1 genome maintained as a bacterial artificial chromosome.

J Virol 2002 Jul;76(13):6660-8

Queensland Agricultural Biotechnology Centre, Agency for Food and Fibre Sciences, Gehrmann Laboratories, Research Road, St. Lucia, Queensland 4072, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC136292PMC
http://dx.doi.org/10.1128/jvi.76.13.6660-6668.2002DOI Listing
July 2002