Shoba Ranganathan

Shoba Ranganathan

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Shoba Ranganathan

Publications by authors named "Shoba Ranganathan"

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Bioinformatics approaches for improving seminal plasma proteome analysis.

Theriogenology 2019 Oct 31;137:43-49. Epub 2019 May 31.

Department of Molecular Sciences, Macquarie University, Sydney, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.theriogenology.2019.05.036DOI Listing
October 2019

APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018.

BMC Genomics 2019 Apr 18;19(Suppl 9):266. Epub 2019 Apr 18.

Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.

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http://dx.doi.org/10.1186/s12864-019-5582-8DOI Listing
April 2019

Applications of machine learning in GPCR bioactive ligand discovery.

Curr Opin Struct Biol 2019 Apr 18;55:66-76. Epub 2019 Apr 18.

Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2019.03.022DOI Listing
April 2019

Structural bioinformatics analysis of variants on GPCR function.

Curr Opin Struct Biol 2019 Apr 4;55:161-177. Epub 2019 Jun 4.

Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2019.04.007DOI Listing
April 2019

Editorial overview: Theory and simulation: demystifying GPCRs - structure, function and drug design.

Curr Opin Struct Biol 2019 Apr;55:vi-viii

Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2019.07.004DOI Listing
April 2019

iSwathX: an interactive web-based application for extension of DIA peptide reference libraries.

Bioinformatics 2019 Feb;35(3):538-539

Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.

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http://dx.doi.org/10.1093/bioinformatics/bty660DOI Listing
February 2019

Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε.

BMC Bioinformatics 2019 Feb 4;19(Suppl 13):342. Epub 2019 Feb 4.

Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.

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http://dx.doi.org/10.1186/s12859-018-2373-1DOI Listing
February 2019

PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acids.

Sci Rep 2018 12 18;8(1):17923. Epub 2018 Dec 18.

Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan.

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http://dx.doi.org/10.1038/s41598-018-36203-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299098PMC
December 2018

Role of solvent accessibility for aggregation-prone patches in protein folding.

Sci Rep 2018 08 27;8(1):12896. Epub 2018 Aug 27.

Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia.

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http://dx.doi.org/10.1038/s41598-018-31289-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6110721PMC
August 2018

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses.

BMC Genomics 2018 May 9;19(Suppl 2):88. Epub 2018 May 9.

School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore.

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http://dx.doi.org/10.1186/s12864-018-4461-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954268PMC
May 2018

De Novo Peptide Sequencing: Deep Mining of High-Resolution Mass Spectrometry Data.

Methods Mol Biol 2017 ;1549:119-134

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

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http://dx.doi.org/10.1007/978-1-4939-6740-7_10DOI Listing
February 2018

A Systematic Bioinformatics Approach to Identify High Quality Mass Spectrometry Data and Functionally Annotate Proteins and Proteomes.

Methods Mol Biol 2017 ;1549:163-176

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

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http://dx.doi.org/10.1007/978-1-4939-6740-7_13DOI Listing
February 2018

Molecular Dynamics Pinpoint the Global Fluorine Effect in Balanoid Binding to PKCε and PKA.

J Chem Inf Model 2018 02 27;58(2):511-519. Epub 2018 Jan 27.

Department of Molecular Sciences, Macquarie University , Sydney, NSW 2109, Australia.

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http://dx.doi.org/10.1021/acs.jcim.7b00504DOI Listing
February 2018

A bioinformatics potpourri.

BMC Genomics 2018 01 19;19(Suppl 1):920. Epub 2018 Jan 19.

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

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http://dx.doi.org/10.1186/s12864-017-4326-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780851PMC
January 2018

Human Prestin: A Candidate PE1 Protein Lacking Stringent Mass Spectrometric Evidence?

J Proteome Res 2017 12 21;16(12):4531-4535. Epub 2017 Sep 21.

Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, ‡Department of Biomedical Science, Faculty of Medicine and Health Sciences, and §Department of Physics and Astronomy, Faculty of Science and Engineering, Macquarie University , 4 Wally's Walk, North Ryde, New South Wales 2109, Australia.

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http://dx.doi.org/10.1021/acs.jproteome.7b00354DOI Listing
December 2017

Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases.

BMC Bioinformatics 2017 12 28;18(Suppl 16):572. Epub 2017 Dec 28.

Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.

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http://dx.doi.org/10.1186/s12859-017-1955-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751415PMC
December 2017

Prediction of interface residue based on the features of residue interaction network.

J Theor Biol 2017 11 15;432:49-54. Epub 2017 Aug 15.

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

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http://dx.doi.org/10.1016/j.jtbi.2017.08.014DOI Listing
November 2017

Divergent response of homologous ATP sites to stereospecific ligand fluorination for selectivity enhancement.

Org Biomol Chem 2017 Feb 25;15(7):1570-1574. Epub 2017 Jan 25.

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

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http://dx.doi.org/10.1039/c7ob00129kDOI Listing
February 2017

Accelerating the search for the missing proteins in the human proteome.

Nat Commun 2017 01 24;8:14271. Epub 2017 Jan 24.

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

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http://dx.doi.org/10.1038/ncomms14271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5286205PMC
January 2017

2016 update on APBioNet's annual international conference on bioinformatics (InCoB).

BMC Genomics 2016 12 22;17(Suppl 13):1036. Epub 2016 Dec 22.

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

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http://dx.doi.org/10.1186/s12864-016-3362-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259860PMC
December 2016

Bioinformatics and systems biology research update from the 15 International Conference on Bioinformatics (InCoB2016).

BMC Bioinformatics 2016 Dec 22;17(Suppl 19):524. Epub 2016 Dec 22.

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

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http://dx.doi.org/10.1186/s12859-016-1409-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259976PMC
December 2016

Systems Proteomics View of the Endogenous Human Claudin Protein Family.

J Proteome Res 2016 Feb 12;15(2):339-59. Epub 2016 Jan 12.

Department of Chemistry, Department of Molecular Biosciences, and Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777318PMC
February 2016

GIW and InCoB are advancing bioinformatics in the Asia-Pacific.

BMC Bioinformatics 2015 Dec 18;16(Suppl 18):I1. Epub 2015 Dec 18.

Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599.

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http://dx.doi.org/10.1186/1471-2105-16-S18-I1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389036PMC
December 2015

Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock.

Biotechnol Adv 2015 Nov 27;33(6 Pt 1):980-91. Epub 2015 May 27.

The Genome Institute, Washington University in St. Louis, MO 63108, USA; Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:

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http://dx.doi.org/10.1016/j.biotechadv.2015.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4746232PMC
November 2015

Introduction to selected papers from GIW/InCoB 2015.

J Bioinform Comput Biol 2015 Oct;13(5):1502003

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http://dx.doi.org/10.1142/S0219720015020035DOI Listing
October 2015

Linking structural features of protein complexes and biological function.

Protein Sci 2015 Sep 14;24(9):1486-94. Epub 2015 Jul 14.

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

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http://dx.doi.org/10.1002/pro.2736DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570542PMC
September 2015

Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions.

Mol Ther Methods Clin Dev 2015 29;2:15015. Epub 2015 Apr 29.

Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead , Westmead, Australia ; The University of Sydney, Discipline of Paediatrics and Child Health , Westmead, Australia.

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http://dx.doi.org/10.1038/mtm.2015.15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445430PMC
June 2015

Structure-based clustering of major histocompatibility complex (MHC) proteins for broad-based T-cell vaccine design.

Methods Mol Biol 2014 ;1184:503-11

Institute of High Performance Computing, 1 Fusionopolis Way, #16-16, Connexis North Tower, Singapore, 138632, Singapore,

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http://link.springer.com/10.1007/978-1-4939-1115-8_27
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http://dx.doi.org/10.1007/978-1-4939-1115-8_27DOI Listing
March 2015

Protein-protein interactions and prediction: a comprehensive overview.

Protein Pept Lett 2014 ;21(8):779-89

Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, NSW, Australia.

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http://dx.doi.org/10.2174/09298665113209990056DOI Listing
February 2015

Characterization of the interaction between heterodimeric αvβ6 integrin and urokinase plasminogen activator receptor (uPAR) using functional proteomics.

J Proteome Res 2014 Dec 29;13(12):5956-64. Epub 2014 Oct 29.

Australian School of Advanced Medicine, Faculty of Human Sciences, ‡Department of Chemistry and Biomolecular Sciences, and §Department of Engineering, Faculty of Science, Macquarie University , Sydney, NSW 2109, Australia.

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http://dx.doi.org/10.1021/pr500849xDOI Listing
December 2014

A site for direct integrin αvβ6·uPAR interaction from structural modelling and docking.

J Struct Biol 2014 Mar 11;185(3):327-35. Epub 2014 Jan 11.

Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, NSW, Australia; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2014.01.001DOI Listing
March 2014

Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome.

J Proteome Res 2014 Jan 13;13(1):76-83. Epub 2013 Dec 13.

Department of Chemistry and Biomolecular Sciences and ‡ARC Centre of Excellence in Bioinformatics, Macquarie University , Sydney, NSW 2109, Australia.

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http://pubs.acs.org/doi/10.1021/pr400794x
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http://dx.doi.org/10.1021/pr400794xDOI Listing
January 2014

Unlocking the puzzling biology of the black Périgord truffle Tuber melanosporum.

J Proteome Res 2013 Dec 6;12(12):5349-56. Epub 2013 Nov 6.

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

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http://dx.doi.org/10.1021/pr400650cDOI Listing
December 2013

APBioNet-transforming bioinformatics in the Asia-Pacific region.

PLoS Comput Biol 2013 Oct 31;9(10):e1003317. Epub 2013 Oct 31.

Perdana University Graduate School of Medicine, Selangor Darul Ehsan, Malaysia ; Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814852PMC
October 2013

Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs).

BMC Genomics 2012 13;13 Suppl 7:S8. Epub 2012 Dec 13.

Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-13-S7-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546426PMC
June 2013

Advances in translational bioinformatics and population genomics in the Asia-Pacific.

BMC Genomics 2012 13;13 Suppl 7:S1. Epub 2012 Dec 13.

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

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http://dx.doi.org/10.1186/1471-2164-13-S7-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521394PMC
June 2013

An analysis of the transcriptome of Teladorsagia circumcincta: its biological and biotechnological implications.

BMC Genomics 2012 13;13 Suppl 7:S10. Epub 2012 Dec 13.

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

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http://dx.doi.org/10.1186/1471-2164-13-S7-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521389PMC
June 2013

Functional annotation of the human chromosome 7 "missing" proteins: a bioinformatics approach.

J Proteome Res 2013 Jun 11;12(6):2504-10. Epub 2013 Jan 11.

Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, NSW, Australia.

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http://dx.doi.org/10.1021/pr301082pDOI Listing
June 2013

InCoB2012 Conference: from biological data to knowledge to technological breakthroughs.

BMC Bioinformatics 2012 13;13 Suppl 17:S1. Epub 2012 Dec 13.

Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka 820-8502, Japan.

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http://dx.doi.org/10.1186/1471-2105-13-S17-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521245PMC
May 2013

TranSeqAnnotator: large-scale analysis of transcriptomic data.

BMC Bioinformatics 2012 13;13 Suppl 17:S24. Epub 2012 Dec 13.

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

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http://dx.doi.org/10.1186/1471-2105-13-S17-S24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521237PMC
May 2013

Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework.

BMC Syst Biol 2013 Feb 6;7:12. Epub 2013 Feb 6.

ARC Centre of Excellence in Bioinformatics and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.

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http://dx.doi.org/10.1186/1752-0509-7-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605242PMC
February 2013

Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference.

BMC Bioinformatics 2011 30;12 Suppl 13:S1. Epub 2011 Nov 30.

Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia.

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http://dx.doi.org/10.1186/1471-2105-12-S13-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278825PMC
August 2012

In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance.

BMC Bioinformatics 2011 30;12 Suppl 13:S25. Epub 2011 Nov 30.

Dept. of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia.

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http://dx.doi.org/10.1186/1471-2105-12-S13-S25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278842PMC
August 2012

An ethnobotanical study of medicinal plants used by the Yaegl Aboriginal community in northern New South Wales, Australia.

J Ethnopharmacol 2012 Jan 11;139(1):244-55. Epub 2011 Nov 11.

Indigenous Bioresources Research Group, Macquarie University, North Ryde, Sydney 2109, Australia.

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http://dx.doi.org/10.1016/j.jep.2011.11.008DOI Listing
January 2012

A comparative structural bioinformatics analysis of inherited mutations in β-D-Mannosidase across multiple species reveals a genotype-phenotype correlation.

BMC Genomics 2011 Nov 30;12 Suppl 3:S22. Epub 2011 Nov 30.

Department of Chemistry and Biomolecular Sciences and ARC center of excellence in Bioinformatics, Macquarie University, NSW 2109, Australia.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-12-S3-S22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333182PMC
November 2011

InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia.

BMC Genomics 2011 Nov 30;12 Suppl 3:S1. Epub 2011 Nov 30.

Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan.

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http://dx.doi.org/10.1186/1471-2164-12-S3-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333168PMC
November 2011

In silico secretome analysis approach for next generation sequencing transcriptomic data.

BMC Genomics 2011 Nov 30;12 Suppl 3:S14. Epub 2011 Nov 30.

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

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http://dx.doi.org/10.1186/1471-2164-12-S3-S14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333173PMC
November 2011

Structural diversity of biologically interesting datasets: a scaffold analysis approach.

J Cheminform 2011 Aug 8;3:30. Epub 2011 Aug 8.

Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia.

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http://dx.doi.org/10.1186/1758-2946-3-30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179739PMC
August 2011

MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures.

Bioinformatics 2011 Apr 23;27(8):1192-3. Epub 2011 Feb 23.

Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, NSW, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btr104DOI Listing
April 2011

Understanding TR binding to pMHC complexes: how does a TR scan many pMHC complexes yet preferentially bind to one.

PLoS One 2011 Feb 22;6(2):e17194. Epub 2011 Feb 22.

Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017194PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3043089PMC
February 2011

Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010).

BMC Genomics 2010 Dec 2;11 Suppl 4:S1. Epub 2010 Dec 2.

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

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http://dx.doi.org/10.1186/1471-2164-11-S4-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005919PMC
December 2010

InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010.

BMC Bioinformatics 2010 Oct 15;11 Suppl 7:S1. Epub 2010 Oct 15.

Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka 820-8502, Japan.

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http://dx.doi.org/10.1186/1471-2105-11-S7-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957677PMC
October 2010

Network analysis of human protein location.

BMC Bioinformatics 2010 Oct 15;11 Suppl 7:S9. Epub 2010 Oct 15.

ARC Centre of Excellence in Bioinformatics and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW, Australia.

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http://dx.doi.org/10.1186/1471-2105-11-S7-S9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957692PMC
October 2010

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing.

Nucleic Acids Res 2010 Sep 3;38(17):e171. Epub 2010 Aug 3.

Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia.

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http://dx.doi.org/10.1093/nar/gkq667DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943614PMC
September 2010

pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes.

Immunome Res 2010 Sep 27;6 Suppl 1:S2. Epub 2010 Sep 27.

Department of Chemistry and Biomolecular Sciences and ARC Center of Excellence in Bioinformatics, Macquarie University, NSW 2109, Australia.

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http://dx.doi.org/10.1186/1745-7580-6-S1-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946780PMC
September 2010

Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases.

BMC Genomics 2009 Dec 3;10 Suppl 3:S11. Epub 2009 Dec 3.

Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, NSW 2109, Australia.

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http://dx.doi.org/10.1186/1471-2164-10-S3-S11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788363PMC
December 2009

A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation.

BMC Genomics 2009 Dec 3;10 Suppl 3:S33. Epub 2009 Dec 3.

Department of Chemistry and Biomolecular Sciences and ARC center of excellence in Bioinformatics, Macquarie University, NSW 2109, Australia.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-10-S3-S33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788387PMC
December 2009

A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the "-omics" era.

BMC Genomics 2009 Dec 3;10 Suppl 3:S36. Epub 2009 Dec 3.

Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-10-S3-S36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788390PMC
December 2009

A multi-factor model for caspase degradome prediction.

BMC Genomics 2009 Dec 3;10 Suppl 3:S6. Epub 2009 Dec 3.

Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.

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http://dx.doi.org/10.1186/1471-2164-10-S3-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788393PMC
December 2009

Towards a career in bioinformatics.

BMC Bioinformatics 2009 Dec 3;10 Suppl 15:S1. Epub 2009 Dec 3.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788349PMC
December 2009

Physiochemical property space distribution among human metabolites, drugs and toxins.

BMC Bioinformatics 2009 Dec 3;10 Suppl 15:S10. Epub 2009 Dec 3.

Department of Chemistry and Biomolecular Sciences & ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788350PMC
December 2009

A comprehensive assessment of N-terminal signal peptides prediction methods.

BMC Bioinformatics 2009 Dec 3;10 Suppl 15:S2. Epub 2009 Dec 3.

Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis, Singapore.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788353PMC
December 2009

Secretome: clues into pathogen infection and clinical applications.

Genome Med 2009 Nov 30;1(11):113. Epub 2009 Nov 30.

Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia.

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http://dx.doi.org/10.1186/gm113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808748PMC
November 2009

Advanced in silico analysis of expressed sequence tag (EST) data for parasitic nematodes of major socio-economic importance--fundamental insights toward biotechnological outcomes.

Biotechnol Adv 2009 Jul-Aug;27(4):439-48. Epub 2009 Apr 2.

Department of Chemistry and Biomolecular Sciences and Australian Research Council (ARC) Centre of Excellence in Bioinformatics, Macquarie University, Sydney, New South Wales 2109, Australia.

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http://dx.doi.org/10.1016/j.biotechadv.2009.03.005DOI Listing
September 2009

An integrated transcriptomics and proteomics analysis of the secretome of the helminth pathogen Fasciola hepatica: proteins associated with invasion and infection of the mammalian host.

Mol Cell Proteomics 2009 Aug 14;8(8):1891-907. Epub 2009 May 14.

Institute for the Biotechnology of Infectious Diseases, University of Technology Sydney, Ultimo, Sydney, New South Wales 2007, Australia.

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http://dx.doi.org/10.1074/mcp.M900045-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2722771PMC
August 2009

Improved insights into the transcriptomes of the human hookworm Necator americanus--fundamental and biotechnological implications.

Biotechnol Adv 2009 Mar-Apr;27(2):122-32. Epub 2008 Oct 18.

Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia.

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July 2009

Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse.

BMC Genomics 2009 Jul 7;10 Suppl 1:S5. Epub 2009 Jul 7.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709266PMC
July 2009

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Authors:
Christine G Elsik Ross L Tellam Kim C Worley Richard A Gibbs Donna M Muzny George M Weinstock David L Adelson Evan E Eichler Laura Elnitski Roderic Guigó Debora L Hamernik Steve M Kappes Harris A Lewin David J Lynn Frank W Nicholas Alexandre Reymond Monique Rijnkels Loren C Skow Evgeny M Zdobnov Lawrence Schook James Womack Tyler Alioto Stylianos E Antonarakis Alex Astashyn Charles E Chapple Hsiu-Chuan Chen Jacqueline Chrast Francisco Câmara Olga Ermolaeva Charlotte N Henrichsen Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Felix Kokocinski Melissa Landrum Donna Maglott Kim Pruitt Victor Sapojnikov Stephen M Searle Victor Solovyev Alexandre Souvorov Catherine Ucla Carine Wyss Juan M Anzola Daniel Gerlach Eran Elhaik Dan Graur Justin T Reese Robert C Edgar John C McEwan Gemma M Payne Joy M Raison Thomas Junier Evgenia V Kriventseva Eduardo Eyras Mireya Plass Ravikiran Donthu Denis M Larkin James Reecy Mary Q Yang Lin Chen Ze Cheng Carol G Chitko-McKown George E Liu Lakshmi K Matukumalli Jiuzhou Song Bin Zhu Daniel G Bradley Fiona S L Brinkman Lilian P L Lau Matthew D Whiteside Angela Walker Thomas T Wheeler Theresa Casey J Bruce German Danielle G Lemay Nauman J Maqbool Adrian J Molenaar Seongwon Seo Paul Stothard Cynthia L Baldwin Rebecca Baxter Candice L Brinkmeyer-Langford Wendy C Brown Christopher P Childers Timothy Connelley Shirley A Ellis Krista Fritz Elizabeth J Glass Carolyn T A Herzig Antti Iivanainen Kevin K Lahmers Anna K Bennett C Michael Dickens James G R Gilbert Darren E Hagen Hanni Salih Jan Aerts Alexandre R Caetano Brian Dalrymple Jose Fernando Garcia Clare A Gill Stefan G Hiendleder Erdogan Memili Diane Spurlock John L Williams Lee Alexander Michael J Brownstein Leluo Guan Robert A Holt Steven J M Jones Marco A Marra Richard Moore Stephen S Moore Andy Roberts Masaaki Taniguchi Richard C Waterman Joseph Chacko Mimi M Chandrabose Andy Cree Marvin Diep Dao Huyen H Dinh Ramatu Ayiesha Gabisi Sandra Hines Jennifer Hume Shalini N Jhangiani Vandita Joshi Christie L Kovar Lora R Lewis Yih-Shin Liu John Lopez Margaret B Morgan Ngoc Bich Nguyen Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Rita A Wright Christian Buhay Yan Ding Shannon Dugan-Rocha Judith Herdandez Michael Holder Aniko Sabo Amy Egan Jason Goodell Katarzyna Wilczek-Boney Gerald R Fowler Matthew Edward Hitchens Ryan J Lozado Charles Moen David Steffen James T Warren Jingkun Zhang Readman Chiu Jacqueline E Schein K James Durbin Paul Havlak Huaiyang Jiang Yue Liu Xiang Qin Yanru Ren Yufeng Shen Henry Song Stephanie Nicole Bell Clay Davis Angela Jolivet Johnson Sandra Lee Lynne V Nazareth Bella Mayurkumar Patel Ling-Ling Pu Selina Vattathil Rex Lee Williams Stacey Curry Cerissa Hamilton Erica Sodergren David A Wheeler Wes Barris Gary L Bennett André Eggen Ronnie D Green Gregory P Harhay Matthew Hobbs Oliver Jann John W Keele Matthew P Kent Sigbjørn Lien Stephanie D McKay Sean McWilliam Abhirami Ratnakumar Robert D Schnabel Timothy Smith Warren M Snelling Tad S Sonstegard Roger T Stone Yoshikazu Sugimoto Akiko Takasuga Jeremy F Taylor Curtis P Van Tassell Michael D Macneil Antonio R R Abatepaulo Colette A Abbey Virpi Ahola Iassudara G Almeida Ariel F Amadio Elen Anatriello Suria M Bahadue Fernando H Biase Clayton R Boldt Jeffery A Carroll Wanessa A Carvalho Eliane P Cervelatti Elsa Chacko Jennifer E Chapin Ye Cheng Jungwoo Choi Adam J Colley Tatiana A de Campos Marcos De Donato Isabel K F de Miranda Santos Carlo J F de Oliveira Heather Deobald Eve Devinoy Kaitlin E Donohue Peter Dovc Annett Eberlein Carolyn J Fitzsimmons Alessandra M Franzin Gustavo R Garcia Sem Genini Cody J Gladney Jason R Grant Marion L Greaser Jonathan A Green Darryl L Hadsell Hatam A Hakimov Rob Halgren Jennifer L Harrow Elizabeth A Hart Nicola Hastings Marta Hernandez Zhi-Liang Hu Aaron Ingham Terhi Iso-Touru Catherine Jamis Kirsty Jensen Dimos Kapetis Tovah Kerr Sari S Khalil Hasan Khatib Davood Kolbehdari Charu G Kumar Dinesh Kumar Richard Leach Justin C-M Lee Changxi Li Krystin M Logan Roberto Malinverni Elisa Marques William F Martin Natalia F Martins Sandra R Maruyama Raffaele Mazza Kim L McLean Juan F Medrano Barbara T Moreno Daniela D Moré Carl T Muntean Hari P Nandakumar Marcelo F G Nogueira Ingrid Olsaker Sameer D Pant Francesca Panzitta Rosemeire C P Pastor Mario A Poli Nathan Poslusny Satyanarayana Rachagani Shoba Ranganathan Andrej Razpet Penny K Riggs Gonzalo Rincon Nelida Rodriguez-Osorio Sandra L Rodriguez-Zas Natasha E Romero Anne Rosenwald Lillian Sando Sheila M Schmutz Libing Shen Laura Sherman Bruce R Southey Ylva Strandberg Lutzow Jonathan V Sweedler Imke Tammen Bhanu Prakash V L Telugu Jennifer M Urbanski Yuri T Utsunomiya Chris P Verschoor Ashley J Waardenberg Zhiquan Wang Robert Ward Rosemarie Weikard Thomas H Welsh Stephen N White Laurens G Wilming Kris R Wunderlich Jianqi Yang Feng-Qi Zhao

Science 2009 Apr;324(5926):522-8

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http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009

Emerging strengths in Asia Pacific bioinformatics.

BMC Bioinformatics 2008 Dec 12;9 Suppl 12:S1. Epub 2008 Dec 12.

Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia.

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http://dx.doi.org/10.1186/1471-2105-9-S12-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638166PMC
December 2008

Flanking signal and mature peptide residues influence signal peptide cleavage.

BMC Bioinformatics 2008 Dec 12;9 Suppl 12:S15. Epub 2008 Dec 12.

Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.

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http://dx.doi.org/10.1186/1471-2105-9-S12-S15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638155PMC
December 2008

CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge.

BMC Bioinformatics 2008 Dec 12;9 Suppl 12:S25. Epub 2008 Dec 12.

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

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http://dx.doi.org/10.1186/1471-2105-9-S12-S25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638165PMC
December 2008

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

Critical technologies for bioinformatics.

Brief Bioinform 2008 Jul 22;9(4):261-2. Epub 2008 May 22.

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http://dx.doi.org/10.1093/bib/bbn025DOI Listing
July 2008

A practical guide to structure-based prediction of MHC-binding peptides.

Methods Mol Biol 2007 ;409:301-8

Department of Chemistry, Macquarie University, New South Wales, Australia.

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http://dx.doi.org/10.1007/978-1-60327-118-9_22DOI Listing
June 2008

Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors.

BMC Bioinformatics 2008 ;9 Suppl 1:S22

Computational Biology Group, Temasek Life Sciences Laboratory, 1 Reseach Link National University of Singapore, Singapore 117604.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-9-S1-S22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2259423PMC
April 2008