Publications by authors named "Joshua W K Ho"

77Publications

Computed tomography-based deep-learning prediction of neoadjuvant chemoradiotherapy treatment response in esophageal squamous cell carcinoma.

Radiother Oncol 2020 Sep 15;154:6-13. Epub 2020 Sep 15.

Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China; Guangdong Esophageal Cancer Institute, Guangzhou, China. Electronic address:

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http://dx.doi.org/10.1016/j.radonc.2020.09.014DOI Listing
September 2020

Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads.

F1000Res 2019 4;8:1587. Epub 2019 Sep 4.

Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia.

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http://dx.doi.org/10.12688/f1000research.19426.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459848PMC
October 2020

A High-Throughput Genome-Integrated Assay Reveals Spatial Dependencies Governing Tcf7l2 Binding.

Cell Syst 2020 Sep 9;11(3):315-327.e5. Epub 2020 Sep 9.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Hubrecht Institute, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2020.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7530048PMC
September 2020

Biophysical Review's 'meet the editors series'-a profile of Joshua W. K. Ho.

Authors:
Joshua W K Ho

Biophys Rev 2020 Aug 28;12(4):745-748. Epub 2020 Jul 28.

School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.

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http://dx.doi.org/10.1007/s12551-020-00744-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7429651PMC
August 2020

Hactive: a smartphone application for heart rate profiling.

Biophys Rev 2020 Aug 14;12(4):777-779. Epub 2020 Jul 14.

Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.

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http://dx.doi.org/10.1007/s12551-020-00731-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7429606PMC
August 2020

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data.

Genome Biol 2020 07 8;21(1):167. Epub 2020 Jul 8.

School of Mathematics and Statistics, Faculty of Science, The University of Sydney, Camperdown, 2006, Australia.

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http://dx.doi.org/10.1186/s13059-020-02071-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341584PMC
July 2020

Challenges and emerging systems biology approaches to discover how the human gut microbiome impact host physiology.

Biophys Rev 2020 Aug 7;12(4):851-863. Epub 2020 Jul 7.

School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.

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http://dx.doi.org/10.1007/s12551-020-00724-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7429608PMC
August 2020

Introduction to the Special Issue on GIW/ABACBS 2019.

Authors:
Joshua W K Ho

J Bioinform Comput Biol 2020 02;18(1):2002001

School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China.

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http://dx.doi.org/10.1142/S0219720020020011DOI Listing
February 2020

dv-trio: a family-based variant calling pipeline using DeepVariant.

Bioinformatics 2020 Jun;36(11):3549-3551

Victor Chang Cardiac Research Institute, Sydney, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btaa116DOI Listing
June 2020

Cellular diversity and lineage trajectory: insights from mouse single cell transcriptomes.

Development 2020 01 24;147(2). Epub 2020 Jan 24.

School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.

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http://dx.doi.org/10.1242/dev.179788DOI Listing
January 2020

Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco.

BMC Genomics 2019 Dec 30;20(Suppl 10):927. Epub 2019 Dec 30.

Victor Chang Cardiac Research Institute, 405 Liverpool St, Darlinghurst, 2010, New South Wales, Australia.

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http://dx.doi.org/10.1186/s12864-019-6341-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936136PMC
December 2019

Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding.

Epigenetics Chromatin 2019 06 13;12(1):36. Epub 2019 Jun 13.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1186/s13072-019-0273-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6567924PMC
June 2019

Discovery of perturbation gene targets via free text metadata mining in Gene Expression Omnibus.

Comput Biol Chem 2019 Jun 24;80:152-158. Epub 2019 Mar 24.

Victor Chang Cardiac Research Institute, Sydney, Australia; University of New South Wales, Sydney, Australia; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.

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https://linkinghub.elsevier.com/retrieve/pii/S14769271193019
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http://dx.doi.org/10.1016/j.compbiolchem.2019.03.014DOI Listing
June 2019

Ultrafast clustering of single-cell flow cytometry data using FlowGrid.

BMC Syst Biol 2019 04 5;13(Suppl 2):35. Epub 2019 Apr 5.

Victor Chang Cardiac Research Institute, Sydney, Australia.

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http://dx.doi.org/10.1186/s12918-019-0690-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449887PMC
April 2019

Big data: the elements of good questions, open data, and powerful software.

Biophys Rev 2019 Feb 25;11(1):1-3. Epub 2019 Jan 25.

Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.

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http://dx.doi.org/10.1007/s12551-019-00500-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381355PMC
February 2019

Host and microbiome multi-omics integration: applications and methodologies.

Biophys Rev 2019 Feb 9;11(1):55-65. Epub 2019 Jan 9.

State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.

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http://link.springer.com/10.1007/s12551-018-0491-7
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http://dx.doi.org/10.1007/s12551-018-0491-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381360PMC
February 2019

Identification of active signaling pathways by integrating gene expression and protein interaction data.

BMC Syst Biol 2018 12 31;12(Suppl 9):120. Epub 2018 Dec 31.

School of Medicine, Western Sydney University, Campbelltown, NSW, Australia.

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http://dx.doi.org/10.1186/s12918-018-0655-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311899PMC
December 2018

C3: An R package for cross-species compendium-based cell-type identification.

Comput Biol Chem 2018 Dec 9;77:187-192. Epub 2018 Oct 9.

Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S14769271183015
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http://dx.doi.org/10.1016/j.compbiolchem.2018.10.003DOI Listing
December 2018

A Screening Approach to Identify Clinically Actionable Variants Causing Congenital Heart Disease in Exome Data.

Circ Genom Precis Med 2018 03;11(3):e001978

From the Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (J.O.S., H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.); Faculty of Science (J.O.S., S.L.D.) and Faculty of Medicine (H.C., D.T.H., E.I., E.G., D.B.S., J.W.K.H., R.M.G., G.C., S.L.D.), University of New South Wales, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Heart Centre for Children (G.M.B., G.F.S., D.S.W.), Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, New South Wales, Australia (G.M.B., G.F.S., D.S.W.); Genetic Services of Western Australia, Perth (K.H., N.P.); Sydney Children's Hospitals Network, New South Wales, Australia (G.F.S.); Institute of Health and Biomedical Innovation, Queensland University of Technology (P.L., E.L.D.); Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia (E.L.D.); University of Queensland, Brisbane (E.L.D.); and School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia (N.P.).

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http://dx.doi.org/10.1161/CIRCGEN.117.001978DOI Listing
March 2018

Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest.

BMC Genomics 2018 01 19;19(Suppl 1):929. Epub 2018 Jan 19.

Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.

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http://dx.doi.org/10.1186/s12864-017-4340-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780765PMC
January 2018

iSyTE 2.0: a database for expression-based gene discovery in the eye.

Nucleic Acids Res 2018 01;46(D1):D875-D885

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.

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http://dx.doi.org/10.1093/nar/gkx837DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753381PMC
January 2018

An Embryonic and Induced Pluripotent Stem Cell Model for Ovarian Granulosa Cell Development and Steroidogenesis.

Reprod Sci 2018 05 31;25(5):712-726. Epub 2017 Aug 31.

1 Division of Reproductive Endocrinology and Infertility, Department of Obstetrics, Gynecology and Reproductive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1177/1933719117725814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344958PMC
May 2018

Scalability and Validation of Big Data Bioinformatics Software.

Comput Struct Biotechnol J 2017 20;15:379-386. Epub 2017 Jul 20.

Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.

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http://dx.doi.org/10.1016/j.csbj.2017.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5537105PMC
July 2017

NAD Deficiency, Congenital Malformations, and Niacin Supplementation.

N Engl J Med 2017 08;377(6):544-552

From the Divisions of Developmental and Stem Cell Biology (H.S., A.E., M.R., E.M.M.A.M., R.W., J.M., J.O.S., E.I., K.S., J.H., K.K., G.C., D.B.S., S.L.D.), Vascular Biology (G.J.M., R.S.), and Molecular, Structural, and Computational Biology (D.T.H., J.W.K.H., E.G.), Victor Chang Cardiac Research Institute, the Faculties of Medicine and Science, University of New South Wales (H.S., A.E., J.O.S., E.I., D.T.H., G.J.M., J.W.K.H., K.K., R.S., E.G., G.C., D.B.S., S.L.D.), Liverpool Hospital, Department of Clinical Genetics (A.E., A.C.), the Department of Clinical Genetics (A.E., J.S., F.C., D.O.S.) and the Heart Centre for Children (D.S.W.), Children's Hospital at Westmead, the Discipline of Genetic Medicine (A.E., J.S., F.C., D.O.S.) and the Medical School (D.S.W.), University of Sydney, and the Faculty of Medicine and Health Sciences, Macquarie University (C.K.L., G.J.G.) - all in Sydney, the School of Biological Sciences, University of Adelaide, Adelaide, SA (J.N.H., P.Q.T.), and the Institute of Health and Biomedical Innovation, Queensland University of Technology (A.M.M.-L., P.J.L., M.A.B., E.L.D.), the Translational Research Institute (A.M.M.-L., P.J.L., M.A.B., E.L.D.), the Department of Endocrinology, Royal Brisbane and Women's Hospital (E.L.D.), and the University of Queensland School of Medicine (E.L.D.), Brisbane - all in Australia; and Spectrum Health Medical Group, Medical Genetics, Grand Rapids, MI (P.R.M.).

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http://dx.doi.org/10.1056/NEJMoa1616361DOI Listing
August 2017

Modelling, inference and big data in biophysics.

Biophys Rev 2017 Aug 30;9(4):297-298. Epub 2017 Jul 30.

School of Life Sciences, University of Bedfordshire, Park Square, Luton, LU1 3JU, UK.

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http://dx.doi.org/10.1007/s12551-017-0282-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578925PMC
August 2017

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data.

Genome Biol 2017 03 28;18(1):59. Epub 2017 Mar 28.

Victor Chang Cardiac Research Institute, Darlinghurst, 2010, NSW, Australia.

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http://dx.doi.org/10.1186/s13059-017-1188-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371246PMC
March 2017

PBrowse: a web-based platform for real-time collaborative exploration of genomic data.

Nucleic Acids Res 2017 May;45(9):e67

Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.

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http://dx.doi.org/10.1093/nar/gkw1358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5605237PMC
May 2017

Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud.

Bioinformatics 2017 03;33(5):767-769

Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btw732DOI Listing
March 2017

Male-lineage transmission of an acquired metabolic phenotype induced by grand-paternal obesity.

Mol Metab 2016 Aug 23;5(8):699-708. Epub 2016 Jun 23.

Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales, Kensington, NSW, 2052, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.molmet.2016.06.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021672PMC
August 2016

XGSA: A statistical method for cross-species gene set analysis.

Bioinformatics 2016 09;32(17):i620-i628

Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia, St Vincent's Clinical School, University of New South Wales Australia, Darlinghurst, NSW 2010, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btw428DOI Listing
September 2016

Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site.

Nucleic Acids Res 2016 Feb 17;44(3):1411-20. Epub 2015 Dec 17.

School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia

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http://dx.doi.org/10.1093/nar/gkv1466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756830PMC
February 2016

Crim1 regulates integrin signaling in murine lens development.

Development 2016 Jan 17;143(2):356-66. Epub 2015 Dec 17.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA

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http://dx.doi.org/10.1242/dev.125591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4725338PMC
January 2016

How to test bioinformatics software?

Biophys Rev 2015 Sep 13;7(3):343-352. Epub 2015 Aug 13.

Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.

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http://dx.doi.org/10.1007/s12551-015-0177-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425734PMC
September 2015

Efficient differentiation of steroidogenic and germ-like cells from epigenetically-related iPSCs derived from ovarian granulosa cells.

PLoS One 2015 9;10(3):e0119275. Epub 2015 Mar 9.

Division of Reproductive Endocrinology and Infertility, Department of Obstetrics, and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119275PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353623PMC
January 2016

hiHMM: Bayesian non-parametric joint inference of chromatin state maps.

Bioinformatics 2015 Jul 27;31(13):2066-74. Epub 2015 Feb 27.

Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481846PMC
July 2015

Decoding the complex genetic causes of heart diseases using systems biology.

Biophys Rev 2015 Mar 10;7(1):141-159. Epub 2014 Dec 10.

Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.

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http://dx.doi.org/10.1007/s12551-014-0145-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5418423PMC
March 2015

Targeted next-generation sequencing identifies pathogenic variants in familial congenital heart disease.

J Am Coll Cardiol 2014 Dec;64(23):2498-506

Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Sydney, Australia. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S07351097140657
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http://dx.doi.org/10.1016/j.jacc.2014.09.048DOI Listing
December 2014

How difficult is inference of mammalian causal gene regulatory networks?

PLoS One 2014 4;9(11):e111661. Epub 2014 Nov 4.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111661PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4219746PMC
June 2015

Comparative analysis of metazoan chromatin organization.

Nature 2014 Aug;512(7515):449-52

1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/nature13415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227084PMC
August 2014

Impact of sequencing depth in ChIP-seq experiments.

Nucleic Acids Res 2014 May 5;42(9):e74. Epub 2014 Mar 5.

Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA Division of Genetics, Brigham and Women's Hospital & Harvard Medical School, Boston, MA 02115, USA Informatics Program, Children's Hospital, Boston, MA 02115, USA

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http://nar.oxfordjournals.org/content/42/9/e74.full.pdf
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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/gku178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027199PMC
May 2014

An antibody-based leukocyte-capture microarray for the diagnosis of systemic lupus erythematosus.

PLoS One 2013 13;8(3):e58199. Epub 2013 Mar 13.

Department of Clinical Immunology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058199PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596412PMC
September 2013

Application of a systems approach to study developmental gene regulation.

Authors:
Joshua W K Ho

Biophys Rev 2012 Sep 1;4(3):245-253. Epub 2012 Sep 1.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1007/s12551-012-0092-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5418408PMC
September 2012

iSyTE: integrated Systems Tool for Eye gene discovery.

Invest Ophthalmol Vis Sci 2012 Mar 21;53(3):1617-27. Epub 2012 Mar 21.

Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard edical School, Boston, Massachusetts, USA.

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http://iovs.arvojournals.org/article.aspx?doi=10.1167/iovs.1
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http://dx.doi.org/10.1167/iovs.11-8839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339920PMC
March 2012

A Wnt-bmp feedback circuit controls intertissue signaling dynamics in tooth organogenesis.

Sci Signal 2012 Jan 10;5(206):ra4. Epub 2012 Jan 10.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.

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http://stke.sciencemag.org/cgi/doi/10.1126/scisignal.2002414
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http://dx.doi.org/10.1126/scisignal.2002414DOI Listing
January 2012

Verification of phylogenetic inference programs using metamorphic testing.

J Bioinform Comput Biol 2011 Dec;9(6):729-47

Faculty of ICT, Swinburne University of Technology, VIC, Australia.

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http://dx.doi.org/10.1142/s021972001100563xDOI Listing
December 2011

Testing and Validating Machine Learning Classifiers by Metamorphic Testing.

J Syst Softw 2011 Apr;84(4):544-558

Centre for Software Analysis and Testing, Swinburne University of Technology, Hawthorn, Vic 3122 Australia.

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http://dx.doi.org/10.1016/j.jss.2010.11.920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3082144PMC
April 2011

ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.

BMC Genomics 2011 Feb 28;12:134. Epub 2011 Feb 28.

Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1186/1471-2164-12-134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3053263PMC
February 2011

Network modelling of gene regulation.

Biophys Rev 2011 Mar 23;3(1):1-13. Epub 2010 Dec 23.

School of Information Technologies, The University of Sydney, Sydney, NSW, 2006, Australia.

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http://dx.doi.org/10.1007/s12551-010-0041-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5418390PMC
March 2011

Customising an antibody leukocyte capture microarray for systemic lupus erythematosus: beyond biomarker discovery.

Proteomics Clin Appl 2010 Feb 2;4(2):179-89. Epub 2009 Dec 2.

Muscle Research Unit, Bosch Institute, The University of Sydney, Sydney, NSW, Australia.

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http://doi.wiley.com/10.1002/prca.200900165
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http://dx.doi.org/10.1002/prca.200900165DOI Listing
February 2010

A genetic ensemble approach for gene-gene interaction identification.

BMC Bioinformatics 2010 Oct 21;11:524. Epub 2010 Oct 21.

School of Information Technologies, University of Sydney, NSW 2006, Australia.

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http://dx.doi.org/10.1186/1471-2105-11-524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2973963PMC
October 2010

A voting approach to identify a small number of highly predictive genes using multiple classifiers.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S19. Epub 2009 Jan 30.

Department of Computer Science and Software Engineering, The University of Melbourne, Victoria 3010, Australia.

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http://dx.doi.org/10.1186/1471-2105-10-S1-S19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648737PMC
January 2009

An innovative approach for testing bioinformatics programs using metamorphic testing.

BMC Bioinformatics 2009 Jan 19;10:24. Epub 2009 Jan 19.

School of Information Technologies, The University of Sydney, Sydney, NSW 2006, Australia.

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http://dx.doi.org/10.1186/1471-2105-10-24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657898PMC
January 2009

Differential variability analysis of gene expression and its application to human diseases.

Bioinformatics 2008 Jul;24(13):i390-8

School of Information Technologies, The University of Sydney, Sydney, NSW 2006, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btn142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718620PMC
July 2008

Inferring differential leukocyte activity from antibody microarrays using a latent variable model.

Genome Inform 2008 ;21:126-37

School of Information Technologies, The University of Sydney, NSW, Australia.

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July 2009

A computer algorithm for the identification of protein interactions from the spectra of masses (PRISM).

J Am Soc Mass Spectrom 2007 Mar 11;18(3):563-6. Epub 2006 Dec 11.

School of Molecular and Microbial Biosciences, The University of Sydney, Sydney, NSW 2006, Australia.

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http://dx.doi.org/10.1016/j.jasms.2006.11.005DOI Listing
March 2007