I am a Staff Scientist at the Centre for Genomic Regulation (CRG) in Barcelona, in the Bioinformatics and Genomics group of Professor Roderic Guigó. 

Here is the Group's homepage:

http://big.crg.cat/bioinformatics_and_genomics

My current research interests involve the combination of experimental and computational approaches to understanding LONG NONCODING RNAs in the human genome.

I studied Physics at Imperial College, London. After travelling and working, I studied for my PhD (2002-2006) on the Wellcome Trust 4-Year Programme in Noel Buckley's group, then at the University of Leeds (UK). You can find a downloadable version of my thesis below. After graduation I spent 3 years at the Genome Institute of Singapore in the group of Lawrence W. Stanton, studying the genomics of stem cells.

I am fortunate to collaborate with many excellent researchers, including Noel Buckley (King's College), Ian Wood (University of Leeds), Lezanne Ooi (University of Leeds), Efthimios Motakis (Bioinformatics Institute of Singapore), Ralf Jauch (Genome Institute of Singapore), Mathijs Voorhoeve (Duke NUS School Singapore), Ray Dunn (Institute of Medical Biology), Leonard Lipovich (Wayne State University).

Selected research publications  (*Corresponding Author)

Click on the PDF symbol to download...

10. Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L.

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

9. Johnson R, Richter N, Jauch R, Gaughwin PM, Zuccato C, Cattaneo E, Stanton LW. The Human Accelerated Region 1 noncoding RNA is repressed by REST in Huntington's disease. Physiol Genomics. 2010 41: 269-274

8. Johnson R* and Buckley NJ*. Gene Dysregulation in Huntington's disease: REST, microRNAs and Beyond. Neurobiol Dis. 2010 Jul;39(1):28-39.

 

7. Johnson R*, Samuel J, Ng C, Jauch R, Stanton LW, Wood IC*. Evolution of the vertebrate gene regulatory network controlled by the transcriptional repressor REST. Mol Biol Evol. 2009 Jul;26(7):1491-507.

Check out media coverage of this paper:

http://www.yorkshirepost.co.uk/news/Breakthrough-in-understanding-evolution.5369504.jp

And a podcast:

http://www.genengnews.com/articles/chitem.aspx?aid=3030

 

6. Buckley NJ, Johnson R, Sun YM, Stanton LW. Is REST a regulator of pluripotency? Nature. 2009 Feb 26;457(7233).

See the write up about this exchange in Epigenie:

http://epigenie.com/article/39/ESC+Pluripotency+Players+Take+To+REST.html

5. Johnson R*, Teh CH, Jia H, Vanisri RR, Pandey T, Lu ZH, Buckley NJ, Stanton LW, Lipovich L*. Regulation of neural macroRNAs by the transcriptional repressor REST. RNA 2009 Jan;15(1):85-96

  4. Johnson R, Teh CH, Kunarso G, Wong KY, Srinivasan G, Cooper ML, Volta M, Chan SS, Lipovich L, Pollard SM, Karuturi RK, Wei CL, Buckley NJ, Stanton LW.  REST regulates distinct transcriptional networks in embryonic and neural stem cells. PLoS Biol. 2008 Oct 28;6(10):e256.

  3. Johnson R*, Zuccato C, Belyaev ND, Guest DJ, Cattaneo E, Buckley NJ. A microRNA-based gene dysregulation pathway in Huntington's disease.Neurobiol Dis. 2008 Mar;29(3):438-45

2. Johnson R*, Gamblin RJ, Ooi L, Bruce AW, Donaldson IJ, Westhead DR, Wood IC, Jackson RM, Buckley NJ. Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Nucleic Acids Res. 2006;34(14):3862-77.

1. Sun YM, Greenway DJ, Johnson R, Street M, Belyaev ND, Deuchars J, Bee T, Wilde S, Buckley NJ. Distinct profiles of REST interactions with its target genes at different stages of neuronal development. Mol Biol Cell. 2005 Dec;16(12):5630-8.

Download 

I defended my PhD in November 2006. You can download my thesis HERE

An updated version (September 2008) version of my Curriculum Vitae / Resume can be found HERE

You can download a copy of my publication list HERE

Project Students

If you are a highly motivated student and are interested in doing a project in our group, please contact me! We offer exciting experimental (wet lab) or computational (bioinformatics) projects. See the advertisement HERE. Information about my former and current project students can be found HERE

Contact Details

You can reach me at the following email addresses:

rory.johnson@crg.eu

Postal address

Links 

The Stem Cell and Developmental Biology Group at the Genome Institute of Singapore 

Find my LinkedIn profile.

LUUSAC, my former diving club and an infamous rain-lashed trip to Bridlington: http://www.luusac.co.uk/trip_reports.html?trip_id=159

Emphasis English Academy, run by my friend Ronan O'Carroll, Malaysia http://www.emphasis.edu.my

Check out Ben Kienewicz's (see photo) excellent site at www.benspage.co.uk

Here is Efthimios Motakis' homepage at the Singapore Bioinformatics Institute: 

http://web.bii.a-star.edu.sg/~efthimiosm/

Friendship Guesthouse in the beautiful Gunung Leuser National Park, Sumatra: http://www.ketambe.com/

Handy Awk One Liners: http://www.ee.ucl.ac.uk/~hamed/misc/awk1line.txt 

Online Contingency Tables: http://statpages.org/ctab2x2.html

R Graph Gallery: http://addictedtor.free.fr/graphiques/

Colour Schemes: http://www.colorschemedesigner.com/ 

Rensselaer: http://mfold.bioinfo.rpi.edu/

Softpanorama: http://www.softpanorama.org/Tools/index.shtml 

CPC Protein Coding Calculator: http://cpc.cbi.pku.edu.cn/ 

Galaxy: http://main.g2.bx.psu.edu/

Protocol Online: http://www.protocol-online.org/ 

More Awk One Liners: http://www.catonmat.net/blog/awk-one-liners-explained-part-one/

Rasterbator: http://homokaasu.org/

R Reference Card: http://cran.r-project.org/doc/contrib/Short-refcard.pdf

Last updated 6/7/2011