Mark J Cowley

Mark J Cowley

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Mark J Cowley

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Increased Diagnostic Yield of Spastic Paraplegia with or Without Cerebellar Ataxia Through Whole-Genome Sequencing.

Cerebellum 2019 Aug;18(4):781-790

Department of Neurology, Movement Disorder Center, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea.

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http://dx.doi.org/10.1007/s12311-019-01038-0DOI Listing
August 2019

Mutational Patterns in Metastatic Cutaneous Squamous Cell Carcinoma.

J Invest Dermatol 2019 Jul 23;139(7):1449-1458.e1. Epub 2019 Jan 23.

Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia; Children's Cancer Institute, Kensington, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, Sydney, Australia.

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http://dx.doi.org/10.1016/j.jid.2019.01.008DOI Listing
July 2019

Population data improves variant interpretation in autosomal dominant polycystic kidney disease.

Genet Med 2019 06 29;21(6):1425-1434. Epub 2018 Oct 29.

Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.

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http://www.nature.com/articles/s41436-018-0324-x
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http://dx.doi.org/10.1038/s41436-018-0324-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6677146PMC
June 2019

Biparental inheritance of mitochondrial DNA in humans is not a common phenomenon.

Genet Med 2019 Jun 7. Epub 2019 Jun 7.

Murdoch Children's Research Institute, Melbourne, Australia.

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http://dx.doi.org/10.1038/s41436-019-0568-0DOI Listing
June 2019

Response to Brodehl et al.

Genet Med 2019 05 28;21(5):1248-1249. Epub 2018 Sep 28.

Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.

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http://www.nature.com/articles/s41436-018-0292-1
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http://dx.doi.org/10.1038/s41436-018-0292-1DOI Listing
May 2019

Next-Generation Sequencing and Emerging Technologies.

Semin Thromb Hemost 2019 May 16. Epub 2019 May 16.

Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.

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http://dx.doi.org/10.1055/s-0039-1688446DOI Listing
May 2019

High Degree of Genetic Heterogeneity for Hereditary Cerebellar Ataxias in Australia.

Cerebellum 2019 Feb;18(1):137-146

Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.

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http://dx.doi.org/10.1007/s12311-018-0969-7DOI Listing
February 2019

Cryptic intronic NBAS variant reveals the genetic basis of recurrent liver failure in a child.

Mol Genet Metab 2019 01 11;126(1):77-82. Epub 2018 Dec 11.

Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.ymgme.2018.12.002DOI Listing
January 2019

Seave: a comprehensive web platform for storing and interrogating human genomic variation.

Bioinformatics 2019 01;35(1):122-125

Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.

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https://academic.oup.com/bioinformatics/article/35/1/122/504
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http://dx.doi.org/10.1093/bioinformatics/bty540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298057PMC
January 2019

Oral malignant gastrointestinal neuroectodermal tumour with junctional component mimicking mucosal melanoma.

Pathology 2018 Oct 31;50(6):648-653. Epub 2018 Aug 31.

Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Medical School, The University of Sydney, Sydney, NSW, Australia; Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.

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http://dx.doi.org/10.1016/j.pathol.2018.07.002DOI Listing
October 2018

Expanding the spectrum of mutations and novel insights into disease mechanisms.

Mol Genet Metab Rep 2018 Sep 20;16:46-51. Epub 2018 Jul 20.

Department of Neurogenetics, Kolling Institute, Royal North Shore Hospital, St. Leonards, NSW, Australia.

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http://dx.doi.org/10.1016/j.ymgmr.2018.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6072801PMC
September 2018

Whole Genome Sequencing Improves Outcomes of Genetic Testing in Patients With Hypertrophic Cardiomyopathy.

J Am Coll Cardiol 2018 07;72(4):419-429

Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia; Department of Cardiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.jacc.2018.04.078DOI Listing
July 2018

A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures.

Cell 2018 02;172(5):924-936.e11

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.02.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832058PMC
February 2018

Evaluation of Streck BCT and PAXgene Stabilised Blood Collection Tubes for Cell-Free Circulating DNA Studies in Plasma.

Mol Diagn Ther 2017 Oct;21(5):563-570

School of Women's and Children's Health, Lowy Cancer Research Centre, University of New South Wales, Kensington, NSW, 2052, Australia.

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http://dx.doi.org/10.1007/s40291-017-0284-xDOI Listing
October 2017

A De Novo Mutation in the Sodium-Activated Potassium Channel KCNT2 Alters Ion Selectivity and Causes Epileptic Encephalopathy.

Cell Rep 2017 Oct;21(4):926-933

Pharmacology and Toxicology, University at Buffalo - The State University of New York, Buffalo, NY 14214, USA; Program for Neuroscience, University at Buffalo - The State University of New York, Buffalo, NY 14214, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.09.088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5687820PMC
October 2017

A SLC39A8 variant causes manganese deficiency, and glycosylation and mitochondrial disorders.

J Inherit Metab Dis 2017 03 19;40(2):261-269. Epub 2016 Dec 19.

Genetic Metabolic Disorders Research Unit, The Children's Hospital at Westmead, KRI, Level 3, Locked Bag 4001, Westmead, NSW, 2145, Australia.

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http://dx.doi.org/10.1007/s10545-016-0010-6DOI Listing
March 2017

Hypermutation In Pancreatic Cancer.

Gastroenterology 2017 01 15;152(1):68-74.e2. Epub 2016 Nov 15.

Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Department of Surgery, Bankstown Hospital, Bankstown, Sydney, New South Wales, Australia; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales Australia, Liverpool, New South Wales, Australia; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00165085163518
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http://dx.doi.org/10.1053/j.gastro.2016.09.060DOI Listing
January 2017

Genomic analyses identify molecular subtypes of pancreatic cancer.

Authors:
Peter Bailey David K Chang Katia Nones Amber L Johns Ann-Marie Patch Marie-Claude Gingras David K Miller Angelika N Christ Tim J C Bruxner Michael C Quinn Craig Nourse L Charles Murtaugh Ivon Harliwong Senel Idrisoglu Suzanne Manning Ehsan Nourbakhsh Shivangi Wani Lynn Fink Oliver Holmes Venessa Chin Matthew J Anderson Stephen Kazakoff Conrad Leonard Felicity Newell Nick Waddell Scott Wood Qinying Xu Peter J Wilson Nicole Cloonan Karin S Kassahn Darrin Taylor Kelly Quek Alan Robertson Lorena Pantano Laura Mincarelli Luis N Sanchez Lisa Evers Jianmin Wu Mark Pinese Mark J Cowley Marc D Jones Emily K Colvin Adnan M Nagrial Emily S Humphrey Lorraine A Chantrill Amanda Mawson Jeremy Humphris Angela Chou Marina Pajic Christopher J Scarlett Andreia V Pinho Marc Giry-Laterriere Ilse Rooman Jaswinder S Samra James G Kench Jessica A Lovell Neil D Merrett Christopher W Toon Krishna Epari Nam Q Nguyen Andrew Barbour Nikolajs Zeps Kim Moran-Jones Nigel B Jamieson Janet S Graham Fraser Duthie Karin Oien Jane Hair Robert Grützmann Anirban Maitra Christine A Iacobuzio-Donahue Christopher L Wolfgang Richard A Morgan Rita T Lawlor Vincenzo Corbo Claudio Bassi Borislav Rusev Paola Capelli Roberto Salvia Giampaolo Tortora Debabrata Mukhopadhyay Gloria M Petersen Donna M Munzy William E Fisher Saadia A Karim James R Eshleman Ralph H Hruban Christian Pilarsky Jennifer P Morton Owen J Sansom Aldo Scarpa Elizabeth A Musgrove Ulla-Maja Hagbo Bailey Oliver Hofmann Robert L Sutherland David A Wheeler Anthony J Gill Richard A Gibbs John V Pearson Nicola Waddell Andrew V Biankin Sean M Grimmond

Nature 2016 Mar 24;531(7592):47-52. Epub 2016 Feb 24.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1038/nature16965DOI Listing
March 2016

Asparagine Synthetase Deficiency causes reduced proliferation of cells under conditions of limited asparagine.

Mol Genet Metab 2015 Nov 14;116(3):178-86. Epub 2015 Aug 14.

Sydney Children's Hospital, High Street Randwick NSW 2031, Australia; University of New South Wales, High Street, Sydney, NSW 2052, Australia; Seals Molecular Genetics, POW Hospital Campus, Barker Street, Randwick, Sydney, NSW 2031, Australia. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10967192153004
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http://dx.doi.org/10.1016/j.ymgme.2015.08.007DOI Listing
November 2015

Whole genomes redefine the mutational landscape of pancreatic cancer.

Nature 2015 Feb;518(7540):495-501

1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia [2] Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK.

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http://dx.doi.org/10.1038/nature14169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4523082PMC
February 2015

Clinical and pathologic features of familial pancreatic cancer.

Cancer 2014 Dec 14;120(23):3669-75. Epub 2014 Oct 14.

The Kinghorn Cancer Center, Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.

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http://dx.doi.org/10.1002/cncr.28863DOI Listing
December 2014

A preexistent hypoxic gene signature predicts impaired islet graft function and glucose homeostasis.

Cell Transplant 2013 31;22(11):2147-59. Epub 2012 Oct 31.

Diabetes and Obesity Research Program, Garvan Institute, Darlinghurst, New South Wales, Australia.

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http://dx.doi.org/10.3727/096368912X658728DOI Listing
May 2014

Clinical and molecular characterization of HER2 amplified-pancreatic cancer.

Genome Med 2013 31;5(8):78. Epub 2013 Aug 31.

Kinghorn Cancer Centre and Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia ; Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK ; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK.

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http://dx.doi.org/10.1186/gm482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978667PMC
May 2014

BCL-2 hypermethylation is a potential biomarker of sensitivity to antimitotic chemotherapy in endocrine-resistant breast cancer.

Mol Cancer Ther 2013 Sep 16;12(9):1874-85. Epub 2013 Jul 16.

Corresponding Author: Andrew Stone, Garvan Institute of Medical Research, L9 TKCC, 370 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia.

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http://dx.doi.org/10.1158/1535-7163.MCT-13-0012DOI Listing
September 2013

Understanding pancreatic cancer genomes.

J Hepatobiliary Pancreat Sci 2013 Aug;20(6):549-56

The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, Australia; Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia.

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http://dx.doi.org/10.1007/s00534-013-0610-6DOI Listing
August 2013

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

Authors:
Andrew V Biankin Nicola Waddell Karin S Kassahn Marie-Claude Gingras Lakshmi B Muthuswamy Amber L Johns David K Miller Peter J Wilson Ann-Marie Patch Jianmin Wu David K Chang Mark J Cowley Brooke B Gardiner Sarah Song Ivon Harliwong Senel Idrisoglu Craig Nourse Ehsan Nourbakhsh Suzanne Manning Shivangi Wani Milena Gongora Marina Pajic Christopher J Scarlett Anthony J Gill Andreia V Pinho Ilse Rooman Matthew Anderson Oliver Holmes Conrad Leonard Darrin Taylor Scott Wood Qinying Xu Katia Nones J Lynn Fink Angelika Christ Tim Bruxner Nicole Cloonan Gabriel Kolle Felicity Newell Mark Pinese R Scott Mead Jeremy L Humphris Warren Kaplan Marc D Jones Emily K Colvin Adnan M Nagrial Emily S Humphrey Angela Chou Venessa T Chin Lorraine A Chantrill Amanda Mawson Jaswinder S Samra James G Kench Jessica A Lovell Roger J Daly Neil D Merrett Christopher Toon Krishna Epari Nam Q Nguyen Andrew Barbour Nikolajs Zeps Nipun Kakkar Fengmei Zhao Yuan Qing Wu Min Wang Donna M Muzny William E Fisher F Charles Brunicardi Sally E Hodges Jeffrey G Reid Jennifer Drummond Kyle Chang Yi Han Lora R Lewis Huyen Dinh Christian J Buhay Timothy Beck Lee Timms Michelle Sam Kimberly Begley Andrew Brown Deepa Pai Ami Panchal Nicholas Buchner Richard De Borja Robert E Denroche Christina K Yung Stefano Serra Nicole Onetto Debabrata Mukhopadhyay Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Steven Gallinger Ralph H Hruban Anirban Maitra Christine A Iacobuzio-Donahue Richard D Schulick Christopher L Wolfgang Richard A Morgan Rita T Lawlor Paola Capelli Vincenzo Corbo Maria Scardoni Giampaolo Tortora Margaret A Tempero Karen M Mann Nancy A Jenkins Pedro A Perez-Mancera David J Adams David A Largaespada Lodewyk F A Wessels Alistair G Rust Lincoln D Stein David A Tuveson Neal G Copeland Elizabeth A Musgrove Aldo Scarpa James R Eshleman Thomas J Hudson Robert L Sutherland David A Wheeler John V Pearson John D McPherson Richard A Gibbs Sean M Grimmond

Nature 2012 Nov 24;491(7424):399-405. Epub 2012 Oct 24.

The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, Sydney, New South Wales 2010, Australia.

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http://dx.doi.org/10.1038/nature11547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530898PMC
November 2012

Influence of atrial fibrillation on microRNA expression profiles in left and right atria from patients with valvular heart disease.

Physiol Genomics 2012 Feb 6;44(3):211-9. Epub 2011 Dec 6.

Molecular Cardiology Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne 8008, Victoria, Australia.

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http://dx.doi.org/10.1152/physiolgenomics.00111.2011DOI Listing
February 2012

PINA v2.0: mining interactome modules.

Nucleic Acids Res 2012 Jan 8;40(Database issue):D862-5. Epub 2011 Nov 8.

Cancer Research Program, Peter Wills Bioinformatics Centre, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244997PMC
January 2012

Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry.

Mol Biosyst 2011 Nov 2;7(11):2997-3005. Epub 2011 Aug 2.

Cancer Pharmacology Unit, ANZAC Research Institute and Discipline of Medicine, The University of Sydney, Sydney, Australia.

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http://dx.doi.org/10.1039/c1mb05236eDOI Listing
November 2011

Evaluation of the NOD/SCID xenograft model for glucocorticoid-regulated gene expression in childhood B-cell precursor acute lymphoblastic leukemia.

BMC Genomics 2011 Nov 17;12:565. Epub 2011 Nov 17.

Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, Randwick, NSW 2031, Australia.

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http://dx.doi.org/10.1186/1471-2164-12-565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228854PMC
November 2011

Identification of novel GH-regulated pathway of lipid metabolism in adipose tissue: a gene expression study in hypopituitary men.

J Clin Endocrinol Metab 2011 Jul 11;96(7):E1188-96. Epub 2011 May 11.

Pituitary Research Unit, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Sydney, Australia.

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http://dx.doi.org/10.1210/jc.2010-2679DOI Listing
July 2011

An early inflammatory gene profile in visceral adipose tissue in children.

Int J Pediatr Obes 2011 Jun 24;6(2-2):e360-3. Epub 2011 May 24.

Institute of Endocrinology and Diabetes, The Children's Hospital, University of Sydney , Westmead , Australia .

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http://dx.doi.org/10.3109/17477166.2011.575152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829917PMC
June 2011

A sustained dietary change increases epigenetic variation in isogenic mice.

PLoS Genet 2011 Apr 21;7(4):e1001380. Epub 2011 Apr 21.

Victor Chang Cardiac Research Institute, University of New South Wales, Sydney, Australia.

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http://dx.doi.org/10.1371/journal.pgen.1001380DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080854PMC
April 2011

Cold adaptation in the marine bacterium, Sphingopyxis alaskensis, assessed using quantitative proteomics.

Environ Microbiol 2010 Oct;12(10):2658-76

School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.

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http://dx.doi.org/10.1111/j.1462-2920.2010.02235.xDOI Listing
October 2010

Detection of growth hormone doping by gene expression profiling of peripheral blood.

J Clin Endocrinol Metab 2009 Dec 29;94(12):4703-9. Epub 2009 Oct 29.

Pituitary Research Unit, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst New South Wales 2010, Sydney, Australia.

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http://dx.doi.org/10.1210/jc.2009-1038DOI Listing
December 2009

Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling.

Mol Cell Proteomics 2009 Oct 14;8(10):2227-42. Epub 2009 Jul 14.

School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.

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http://dx.doi.org/10.1074/mcp.M800462-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758752PMC
October 2009

Intra- and inter-individual genetic differences in gene expression.

Mamm Genome 2009 May 8;20(5):281-95. Epub 2009 May 8.

School of Biotechnology and Biomolecular Sciences, The University of New South Wales, NSW, Australia.

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http://dx.doi.org/10.1007/s00335-009-9181-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690833PMC
May 2009

Gene-expression profiling of gram-positive and gram-negative sepsis in critically ill patients.

Crit Care Med 2008 Apr;36(4):1125-8

Department of Intensive Care Medicine, Nepean Hospital and Western Clinical School, University of Sydney, Penrith, NSW 2750, Australia.

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http://dx.doi.org/10.1097/CCM.0b013e3181692c0bDOI Listing
April 2008

The influence of genetic variation on gene expression.

Genome Res 2007 Dec;17(12):1707-16

School of Biotechnology and Biomolecular Sciences, University of New South Wales, Randwick, NSW 2052, Australia.

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http://dx.doi.org/10.1101/gr.6981507DOI Listing
December 2007

Genetic dissection of gene regulation in multiple mouse tissues.

Mamm Genome 2006 Jun 12;17(6):490-5. Epub 2006 Jun 12.

School of Biotechnology and Biomolecular Sciences, University of New South Wales, Botany Street, Sydney, NSW 2052, Australia.

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http://dx.doi.org/10.1007/s00335-005-0186-9DOI Listing
June 2006