Tim R Mercer

Tim R Mercer

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Tim R Mercer

Tim R Mercer

Publications by authors named "Tim R Mercer"

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Use of synthetic DNA spike-in controls (sequins) for human genome sequencing.

Nat Protoc 2019 07 19;14(7):2119-2151. Epub 2019 Jun 19.

Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, Australia.

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http://dx.doi.org/10.1038/s41596-019-0175-1DOI Listing
July 2019

Diagnosis of fusion genes using targeted RNA sequencing.

Nat Commun 2019 03 27;10(1):1388. Epub 2019 Mar 27.

Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.

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http://dx.doi.org/10.1038/s41467-019-09374-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437215PMC
March 2019

Machine learning annotation of human branchpoints.

Bioinformatics 2018 03;34(6):920-927

Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btx688DOI Listing
March 2018

Universal Alternative Splicing of Noncoding Exons.

Cell Syst 2018 Feb 24;6(2):245-255.e5. Epub 2018 Jan 24.

Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia; Altius Institute for Biomedical Sciences, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.12.005DOI Listing
February 2018

Reference standards for next-generation sequencing.

Nat Rev Genet 2017 08 19;18(8):473-484. Epub 2017 Jun 19.

Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.

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http://dx.doi.org/10.1038/nrg.2017.44DOI Listing
August 2017

The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome.

Trends Genet 2017 07 20;33(7):464-478. Epub 2017 May 20.

Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2017.04.004DOI Listing
July 2017

ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing.

Bioinformatics 2017 Jun;33(11):1723-1724

Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btx038DOI Listing
June 2017

Representing genetic variation with synthetic DNA standards.

Nat Methods 2016 09 8;13(9):784-91. Epub 2016 Aug 8.

Genomics and Epigenetics Division, Garvan Institute of Medical Research, New South Wales, Australia.

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http://dx.doi.org/10.1038/nmeth.3957DOI Listing
September 2016

Spliced synthetic genes as internal controls in RNA sequencing experiments.

Nat Methods 2016 09 8;13(9):792-8. Epub 2016 Aug 8.

Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.

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http://dx.doi.org/10.1038/nmeth.3958DOI Listing
September 2016

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.

Nat Methods 2015 Apr 9;12(4):339-42. Epub 2015 Mar 9.

1] Garvan Institute of Medical Research, Sydney, Australia. [2] St Vincents Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.

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http://dx.doi.org/10.1038/nmeth.3321DOI Listing
April 2015

Genome-wide discovery of human splicing branchpoints.

Genome Res 2015 Feb 5;25(2):290-303. Epub 2015 Jan 5.

Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia;

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http://genome.cshlp.org/lookup/doi/10.1101/gr.182899.114
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http://dx.doi.org/10.1101/gr.182899.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315302PMC
February 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells.

Mol Cell 2014 Oct 18;56(2):193-204. Epub 2014 Sep 18.

John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, and NIHR Biomedical Research Centre, University of Cambridge, CB2 0PY Cambridge, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge, UK. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.08.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578249PMC
October 2014

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq.

Nat Protoc 2014 May 3;9(5):989-1009. Epub 2014 Apr 3.

Garvan Institute of Medical Research, Sydney, New South Wales, Australia.

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http://www.nature.com/articles/nprot.2014.058
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http://dx.doi.org/10.1038/nprot.2014.058DOI Listing
May 2014

Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach.

BMC Genomics 2013 Oct 11;14:699. Epub 2013 Oct 11.

Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Qld 4072, Australia.

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http://dx.doi.org/10.1186/1471-2164-14-699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008361PMC
October 2013

Understanding the regulatory and transcriptional complexity of the genome through structure.

Genome Res 2013 Jul;23(7):1081-8

Garvan Institute of Medical Research, Sydney, New South Wales, Australia.

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http://dx.doi.org/10.1101/gr.156612.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698501PMC
July 2013

Structure and function of long noncoding RNAs in epigenetic regulation.

Nat Struct Mol Biol 2013 Mar;20(3):300-7

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.

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http://dx.doi.org/10.1038/nsmb.2480DOI Listing
March 2013

Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch.

BMC Genomics 2013 Jan 16;14:15. Epub 2013 Jan 16.

Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Qld 4072, Australia.

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http://dx.doi.org/10.1186/1471-2164-14-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610266PMC
January 2013

Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins.

RNA 2011 Dec 25;17(12):2085-93. Epub 2011 Oct 25.

Western Australian Institute for Medical Research and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia.

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http://rnajournal.cshlp.org/cgi/doi/10.1261/rna.029405.111
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http://dx.doi.org/10.1261/rna.029405.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222122PMC
December 2011

Targeted RNA sequencing reveals the deep complexity of the human transcriptome.

Nat Biotechnol 2011 Nov 13;30(1):99-104. Epub 2011 Nov 13.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.

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http://dx.doi.org/10.1038/nbt.2024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710462PMC
November 2011

RNA processing in human mitochondria.

Cell Cycle 2011 Sep 1;10(17):2904-16. Epub 2011 Sep 1.

Western Australian Institute for Medical Research and Centre for Medical Research, The University of Western Australia, Perth, WA Australia.

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http://dx.doi.org/10.4161/cc.10.17.17060DOI Listing
September 2011

Expression of distinct RNAs from 3' untranslated regions.

Nucleic Acids Res 2011 Mar 12;39(6):2393-403. Epub 2010 Nov 12.

Institute for Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.

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http://dx.doi.org/10.1093/nar/gkq1158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064787PMC
March 2011

A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells.

RNA 2010 Jun 20;16(6):1156-66. Epub 2010 Apr 20.

Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology and Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia.

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http://rnajournal.cshlp.org/cgi/doi/10.1261/rna.2019810
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http://dx.doi.org/10.1261/rna.2019810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874168PMC
June 2010

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation.

BMC Neurosci 2010 Feb 5;11:14. Epub 2010 Feb 5.

Institute for Molecular Bioscience, University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia.

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http://dx.doi.org/10.1186/1471-2202-11-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829031PMC
February 2010

Genome-wide identification of long noncoding RNAs in CD8+ T cells.

J Immunol 2009 Jun;182(12):7738-48

Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.

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http://dx.doi.org/10.4049/jimmunol.0900603DOI Listing
June 2009

Long non-coding RNAs: insights into functions.

Nat Rev Genet 2009 Mar;10(3):155-9

Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1038/nrg2521DOI Listing
March 2009

NRED: a database of long noncoding RNA expression.

Nucleic Acids Res 2009 Jan 1;37(Database issue):D122-6. Epub 2008 Oct 1.

ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia.

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http://nar.oxfordjournals.org/content/early/2008/10/01/nar.g
Web Search
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkn617
Publisher Site
http://dx.doi.org/10.1093/nar/gkn617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686506PMC
January 2009

RNA regulation of epigenetic processes.

Bioessays 2009 Jan;31(1):51-9

Australian Research Council Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, the University of Queensland, St. Lucia, Australia.

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http://dx.doi.org/10.1002/bies.080099DOI Listing
January 2009

Differentiating protein-coding and noncoding RNA: challenges and ambiguities.

PLoS Comput Biol 2008 Nov 28;4(11):e1000176. Epub 2008 Nov 28.

ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia.

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http://dx.doi.org/10.1371/journal.pcbi.1000176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518207PMC
November 2008

Noncoding RNAs in Long-Term Memory Formation.

Neuroscientist 2008 Oct;14(5):434-45

Institute for Molecular Biosciences, University of Queensland, Brisbane, Australia.

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http://dx.doi.org/10.1177/1073858408319187DOI Listing
October 2008

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation.

Genome Res 2008 Sep 18;18(9):1433-45. Epub 2008 Jun 18.

ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia.

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http://dx.doi.org/10.1101/gr.078378.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527704PMC
September 2008

The eukaryotic genome as an RNA machine.

Science 2008 Mar;319(5871):1787-9

Institute for Molecular Bioscience, University of Queensland, St. Lucia QLD 4072, Australia.

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http://dx.doi.org/10.1126/science.1155472DOI Listing
March 2008

Specific expression of long noncoding RNAs in the mouse brain.

Proc Natl Acad Sci U S A 2008 Jan 9;105(2):716-21. Epub 2008 Jan 9.

Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD 4072, Australia.

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http://dx.doi.org/10.1073/pnas.0706729105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2206602PMC
January 2008