Publications by authors named "Shivashankar H Nagaraj"

33Publications

Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data.

Am J Hum Genet 2020 08;107(2):175-182

Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA 6004, Australia; The Western Australian Register of Developmental Anomalies, Department of Health, Government of Western Australia, Perth, WA 6004, Australia; School of Medicine, Division of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2020.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7413856PMC
August 2020

Analysis of the (PAR4) Single Nucleotide Polymorphism () in an Indigenous Australian Population.

Front Genet 2020 30;11:432. Epub 2020 Apr 30.

Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.

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http://dx.doi.org/10.3389/fgene.2020.00432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7204273PMC
April 2020

A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping.

Brief Bioinform 2019 Nov 27. Epub 2019 Nov 27.

School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.

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http://dx.doi.org/10.1093/bib/bbz121DOI Listing
November 2019

Targeting Epithelial Mesenchymal Plasticity in Pancreatic Cancer: A Compendium of Preclinical Discovery in a Heterogeneous Disease.

Cancers (Basel) 2019 Nov 7;11(11). Epub 2019 Nov 7.

Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia.

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http://dx.doi.org/10.3390/cancers11111745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896204PMC
November 2019

Multi-Omics Characterization of the Spontaneous Mesenchymal-Epithelial Transition in the PMC42 Breast Cancer Cell Lines.

J Clin Med 2019 Aug 19;8(8). Epub 2019 Aug 19.

Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia.

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http://dx.doi.org/10.3390/jcm8081253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723942PMC
August 2019

Interrogation of Phenotypic Plasticity between Epithelial and Mesenchymal States in Breast Cancer.

J Clin Med 2019 Jun 21;8(6). Epub 2019 Jun 21.

Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia.

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http://dx.doi.org/10.3390/jcm8060893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6617164PMC
June 2019

Targeting epithelial-mesenchymal plasticity in cancer: clinical and preclinical advances in therapy and monitoring.

Biochem J 2017 09 20;474(19):3269-3306. Epub 2017 Sep 20.

Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia

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http://dx.doi.org/10.1042/BCJ20160782DOI Listing
September 2017

Whole-genome characterization of chemoresistant ovarian cancer.

Nature 2015 May;521(7553):489-94

1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Department of Pathology, University of Melbourne, Parkville, Victoria 3052, Australia [3] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia [4] Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK [5] Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3052, Australia.

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http://dx.doi.org/10.1038/nature14410DOI Listing
May 2015

PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization.

J Proteome Res 2015 May 17;14(5):2255-66. Epub 2015 Apr 17.

§Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland G61 1BD, United Kingdom.

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http://dx.doi.org/10.1021/acs.jproteome.5b00029DOI Listing
May 2015

Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline.

Mol Cell Proteomics 2013 Nov 23;12(11):3388-97. Epub 2013 Jul 23.

G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India;

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http://dx.doi.org/10.1074/mcp.M112.027169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820949PMC
November 2013

Molecular cloning and characterisation of ovine dual oxidase 2.

Gene 2012 May 20;500(1):40-6. Epub 2012 Mar 20.

CSIRO Livestock Industries, St Lucia, Queensland, Australia.

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http://dx.doi.org/10.1016/j.gene.2012.03.052DOI Listing
May 2012

Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.

PLoS One 2011 23;6(9):e25457. Epub 2011 Sep 23.

Computational and Systems Biology, CSIRO Livestock Industries, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0025457PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179510PMC
February 2012

A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer.

BMC Syst Biol 2011 Feb 26;5:35. Epub 2011 Feb 26.

Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation, Division of Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St, Lucia, Brisbane, Queensland 4067, Australia.

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http://dx.doi.org/10.1186/1752-0509-5-35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051904PMC
February 2011

Chronic exposure to anabolic steroids induces the muscle expression of oxytocin and a more than fiftyfold increase in circulating oxytocin in cattle.

Physiol Genomics 2011 May 15;43(9):467-78. Epub 2011 Feb 15.

Australian Cooperative Research Centre for Beef Genetic Technologies, University of New England, Armidale, New South Wales.

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http://dx.doi.org/10.1152/physiolgenomics.00226.2010DOI Listing
May 2011

Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle.

BMC Genomics 2011 Jan 12;12:23. Epub 2011 Jan 12.

Computational and Systems Biology, CSIRO Food Futures Flagship and CSIRO Livestock Industries, 306 Carmody Rd, St. Lucia, Brisbane, Queensland 4067, Australia.

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http://dx.doi.org/10.1186/1471-2164-12-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025955PMC
January 2011

The interplay between evolution, regulation and tissue specificity in the Human Hereditary Diseasome.

BMC Genomics 2010 Dec 2;11 Suppl 4:S23. Epub 2010 Dec 2.

CSIRO Livestock Industries, Queensland Bioscience Precinct, St. Lucia, Queensland, Australia.

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http://dx.doi.org/10.1186/1471-2164-11-S4-S23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005915PMC
December 2010

Association weight matrix for the genetic dissection of puberty in beef cattle.

Proc Natl Acad Sci U S A 2010 Aug 19;107(31):13642-7. Epub 2010 Jul 19.

Cooperative Research Centre for Beef Genetic Technologies, Queensland Bioscience Precinct, Brisbane, QLD, Australia.

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http://dx.doi.org/10.1073/pnas.1002044107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922254PMC
August 2010

Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data.

Bioinformatics 2010 Apr 9;26(7):896-904. Epub 2010 Feb 9.

Bioinformatics Group, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Brisbane, Queensland 4067, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btq051DOI Listing
April 2010

Needles in the EST haystack: large-scale identification and analysis of excretory-secretory (ES) proteins in parasitic nematodes using expressed sequence tags (ESTs).

PLoS Negl Trop Dis 2008 Sep 24;2(9):e301. Epub 2008 Sep 24.

Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia.

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http://dx.plos.org/10.1371/journal.pntd.0000301
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http://dx.doi.org/10.1371/journal.pntd.0000301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553489PMC
September 2008

Proteomics analysis of the excretory/secretory component of the blood-feeding stage of the hookworm, Ancylostoma caninum.

Mol Cell Proteomics 2009 Jan 26;8(1):109-21. Epub 2008 Aug 26.

Helminth Biology Laboratory, Division of Infectious Diseases, Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M800206-MCP2
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http://dx.doi.org/10.1074/mcp.M800206-MCP200DOI Listing
January 2009

High-throughput functional annotation and data mining with the Blast2GO suite.

Nucleic Acids Res 2008 Jun 29;36(10):3420-35. Epub 2008 Apr 29.

Bioinformatics Department, Centro de Investigación Principe Felipe, Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gkn176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2425479PMC
June 2008

Transcriptional changes in the hookworm, Ancylostoma caninum, during the transition from a free-living to a parasitic larva.

PLoS Negl Trop Dis 2008 Jan 9;2(1):e130. Epub 2008 Jan 9.

Helminth Biology Laboratory, Division of Infectious Diseases and Immunology, Queensland Institute of Medical Research, Herston, Queensland, Australia.

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http://dx.plos.org/10.1371/journal.pntd.0000130
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http://dx.doi.org/10.1371/journal.pntd.0000130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2217673PMC
January 2008

A transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus.

BMC Genomics 2007 Sep 5;8:311. Epub 2007 Sep 5.

Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia.

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http://dx.doi.org/10.1186/1471-2164-8-311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2131760PMC
September 2007

ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform.

Nucleic Acids Res 2007 Jul 1;35(Web Server issue):W143-7. Epub 2007 Jun 1.

Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.

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http://dx.doi.org/10.1093/nar/gkm378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933243PMC
July 2007

A hitchhiker's guide to expressed sequence tag (EST) analysis.

Brief Bioinform 2007 Jan 23;8(1):6-21. Epub 2006 May 23.

Department of Chemistry and Biomolecular Sciences & Biotechnology Research Institute, Macquarie University, Sydney, Australia.

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http://dx.doi.org/10.1093/bib/bbl015DOI Listing
January 2007