Rory Johnson

Rory Johnson

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Rory Johnson

Publications by authors named "Rory Johnson"

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Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.

Commun Biol 2020 Feb 5;3(1):56. Epub 2020 Feb 5.

Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010, Bern, Switzerland.

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http://dx.doi.org/10.1038/s42003-019-0741-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7002399PMC
February 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Nature 2020 02 5;578(7793):102-111. Epub 2020 Feb 5.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-020-1965-xDOI Listing
February 2020

CASPR, an analysis pipeline for single and paired guide RNA CRISPR screens, reveals optimal target selection for long noncoding RNAs.

Bioinformatics 2019 Nov 4. Epub 2019 Nov 4.

Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btz811DOI Listing
November 2019

LnCompare: gene set feature analysis for human long non-coding RNAs.

Nucleic Acids Res 2019 Jul;47(W1):W523-W529

Institute of Computational Medicine, School of Artificial Intelligence, Hebei University of Technology, Tianjin 300401, China.

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http://dx.doi.org/10.1093/nar/gkz410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602513PMC
July 2019

Hacking the Cancer Genome: Profiling Therapeutically Actionable Long Non-coding RNAs Using CRISPR-Cas9 Screening.

Cancer Cell 2019 04 28;35(4):545-557. Epub 2019 Feb 28.

Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2019.01.019DOI Listing
April 2019

Global Positioning System: Understanding Long Noncoding RNAs through Subcellular Localization.

Mol Cell 2019 03;73(5):869-883

Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.02.008DOI Listing
March 2019

Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs.

Genome Res 2019 02 26;29(2):208-222. Epub 2018 Dec 26.

Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.

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http://dx.doi.org/10.1101/gr.229922.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360812PMC
February 2019

Towards a complete map of the human long non-coding RNA transcriptome.

Nat Rev Genet 2018 09;19(9):535-548

Department of Medical Oncology, Inselspital, University Hospital and University of Bern, Bern, Switzerland.

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http://dx.doi.org/10.1038/s41576-018-0017-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451964PMC
September 2018

Capturing a Long Look at Our Genetic Library.

Cell Syst 2018 Feb;6(2):153-155

Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland; Department of Biomedical Research (DBMR), University of Bern, 3008 Bern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.02.003DOI Listing
February 2018

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.

Nat Genet 2017 Dec 6;49(12):1731-1740. Epub 2017 Nov 6.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1038/ng.3988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709232PMC
December 2017

CAIPIRINHA accelerated SPACE enables 10-min isotropic 3D TSE MRI of the ankle for optimized visualization of curved and oblique ligaments and tendons.

Eur Radiol 2017 Sep 23;27(9):3652-3661. Epub 2017 Jan 23.

Russell H. Morgan Department of Radiology and Radiological Science, Section of Musculoskeletal Radiology, Johns Hopkins University School of Medicine, 601 N. Caroline Street, JHOC 3140A, Baltimore, MD, 21287, USA.

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http://dx.doi.org/10.1007/s00330-017-4734-yDOI Listing
September 2017

LncATLAS database for subcellular localization of long noncoding RNAs.

RNA 2017 07 6;23(7):1080-1087. Epub 2017 Apr 6.

Department of Clinical Research, University of Bern, 3008 Bern, Switzerland.

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http://dx.doi.org/10.1261/rna.060814.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473142PMC
July 2017

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.

PLoS Comput Biol 2017 03 2;13(3):e1005341. Epub 2017 Mar 2.

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1005341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333799PMC
March 2017

Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features.

Sci Rep 2017 01 27;7:41544. Epub 2017 Jan 27.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.

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http://dx.doi.org/10.1038/srep41544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5269722PMC
January 2017

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells.

RNA 2016 06 18;22(6):867-82. Epub 2016 Apr 18.

Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain.

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http://dx.doi.org/10.1261/rna.053561.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878613PMC
June 2016

Erratum to: 'DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs'.

BMC Genomics 2016 Mar 9;17:215. Epub 2016 Mar 9.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.

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http://dx.doi.org/10.1186/s12864-016-2544-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784307PMC
March 2016

DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs.

BMC Genomics 2015 Oct 23;16:846. Epub 2015 Oct 23.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.

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http://dx.doi.org/10.1186/s12864-015-2086-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619085PMC
October 2015

Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization.

Genome Res 2015 Sep 20;25(9):1256-67. Epub 2015 Jul 20.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Catalonia, Spain; Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Catalonia, Spain;

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http://dx.doi.org/10.1101/gr.190538.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561486PMC
September 2015

Human genomics. The human transcriptome across tissues and individuals.

Science 2015 May;348(6235):660-5

Center for Genomic Regulation (CRG), Barcelona, Catalonia, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain. Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Catalonia, Spain. Joint CRG-Barcelona Super Computing Center (BSC)-Institut de Recerca Biomedica (IRB) Program in Computational Biology, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1126/science.aaa0355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547472PMC
May 2015

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs.

RNA 2014 Jul 21;20(7):959-76. Epub 2014 May 21.

Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain.

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http://dx.doi.org/10.1261/rna.044560.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114693PMC
July 2014

Neurodegeneration as an RNA disorder.

Prog Neurobiol 2012 Dec 10;99(3):293-315. Epub 2012 Oct 10.

Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader, 88, 08003 Barcelona, Catalunya, Spain.

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http://dx.doi.org/10.1016/j.pneurobio.2012.09.006DOI Listing
December 2012

The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter".

Front Genet 2011 9;2:107. Epub 2012 Jan 9.

Bioinformatics and Genomics, Centre for Genomic Regulation, Universitat Pompeu Fabra Barcelona, Spain.

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http://dx.doi.org/10.3389/fgene.2011.00107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266617PMC
October 2012

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

Long non-coding RNAs in Huntington's disease neurodegeneration.

Authors:
Rory Johnson

Neurobiol Dis 2012 May 14;46(2):245-54. Epub 2011 Dec 14.

Bioinformatics and Genomics Group, Centre for Genomic Regulation and UPF, C Dr Aiguader, 88 Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1016/j.nbd.2011.12.006DOI Listing
May 2012

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors.

EMBO J 2012 Feb 23;31(3):522-33. Epub 2011 Dec 23.

Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1038/emboj.2011.459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273385PMC
February 2012

New insights into non-coding RNA networks in Huntington's disease.

Exp Neurol 2011 Oct 30;231(2):191-4. Epub 2011 Jul 30.

Centre for the Cellular Basis of Behaviour, The James Black Centre, King's College London, Institute of Psychiatry, 125 Coldharbour Lane, London SE5 9NU, UK.

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http://dx.doi.org/10.1016/j.expneurol.2011.07.005DOI Listing
October 2011

Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells.

Genome Res 2011 Aug 1;21(8):1284-93. Epub 2011 Jun 1.

Stem Cell and Developmental Biology, Genome Institute of Singapore, 138672 Singapore.

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http://dx.doi.org/10.1101/gr.114488.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149495PMC
August 2011

MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA.

Biochim Biophys Acta 2010 Sep 14;1799(9):597-615. Epub 2010 Oct 14.

Department of Neurology, Wayne State University, Detroit, MI, USA.

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http://dx.doi.org/10.1016/j.bbagrm.2010.10.001DOI Listing
September 2010

Genome-wide computational identification and manual annotation of human long noncoding RNA genes.

RNA 2010 Aug 29;16(8):1478-87. Epub 2010 Jun 29.

Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MO 48202, USA.

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http://rnajournal.cshlp.org/cgi/doi/10.1261/rna.1951310
Publisher Site
http://dx.doi.org/10.1261/rna.1951310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905748PMC
August 2010

The role of REST in transcriptional and epigenetic dysregulation in Huntington's disease.

Neurobiol Dis 2010 Jul 17;39(1):28-39. Epub 2010 Feb 17.

King's College London, Institute of Psychiatry, Centre for the Cellular Basis of Behaviour, James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK.

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http://dx.doi.org/10.1016/j.nbd.2010.02.003DOI Listing
July 2010

Human accelerated region 1 noncoding RNA is repressed by REST in Huntington's disease.

Physiol Genomics 2010 May 23;41(3):269-74. Epub 2010 Feb 23.

Stem Cell and Developmental Biology Group.

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http://dx.doi.org/10.1152/physiolgenomics.00019.2010DOI Listing
May 2010

Gene dysregulation in Huntington's disease: REST, microRNAs and beyond.

Neuromolecular Med 2009 21;11(3):183-99. Epub 2009 May 21.

Stem Cell and Developmental Biology Group, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore.

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http://dx.doi.org/10.1007/s12017-009-8063-4DOI Listing
December 2009

Transcriptional dysregulation of coding and non-coding genes in cellular models of Huntington's disease.

Biochem Soc Trans 2009 Dec;37(Pt 6):1270-5

Department of Neuroscience, Institute of Psychiatry, King's College London, CCBB, London SE5 9JU, UK.

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http://dx.doi.org/10.1042/BST0371270DOI Listing
December 2009

Evolution of the vertebrate gene regulatory network controlled by the transcriptional repressor REST.

Mol Biol Evol 2009 Jul 24;26(7):1491-507. Epub 2009 Mar 24.

Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1093/molbev/msp058DOI Listing
July 2009

Is REST a regulator of pluripotency?

Nature 2009 Feb;457(7233):E5-6; discussion E7

King's College London, Institute of Psychiatry, Centre for the Cellular Basis of Behaviour, James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK.

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http://dx.doi.org/10.1038/nature07784DOI Listing
February 2009

A microRNA-based gene dysregulation pathway in Huntington's disease.

Neurobiol Dis 2008 Mar 13;29(3):438-45. Epub 2007 Nov 13.

Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore.

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http://dx.doi.org/10.1016/j.nbd.2007.11.001DOI Listing
March 2008

Distinct profiles of REST interactions with its target genes at different stages of neuronal development.

Mol Biol Cell 2005 Dec 29;16(12):5630-8. Epub 2005 Sep 29.

School of Biochemistry and Microbiology, University of Leeds, Leeds LS2 9JT, United Kingdom.

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http://dx.doi.org/10.1091/mbc.e05-07-0687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1289408PMC
December 2005