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ESI Special Topic: Gene Silencing
Publication Date: December 2006

Gene Silencing

ESI Special Topics: February 2007
Citing URL:

An INTERVIEW with Dr. Sam Griffiths-Jones
Special Topics talks with Dr. Sam Griffiths-Jones about his paper, "The microRNA Registry," (Nucleic Acids Research 32: D109-11, 2004). This paper ranks at #9 on our list of gene silencing papers published in the past two years, with 170 total citations. In Essential Science Indicators, Dr. Griffiths-Jones’s record includes 22 papers, the bulk of which can be found in the field of Biology & Biochemistry, cited a total of 2,665 times to date. Formerly affiliated with the Sanger Institute, Dr. Griffiths-Jones recently took up the mantle of Fellow in the Faculty of Life Sciences at the University of Manchester.

ST: Please tell us a little about your educational background and early research.

My first degree was in Biochemistry and Biological Chemistry, from the University of Nottingham. I stayed in Nottingham to do a Ph.D. in the Chemistry department, in Mark Searle's group. We were interested in designing short peptides to fold into beta-sheet structures, and mainly used NMR to determine our success.

MicroRNAs were only recently identified as a major RNA class, and the fast-growing body of researchers determined a need for a centrally (and sensibly) managed nomenclature for these genes. ”

As a side project, I got interested in mining protein 3D structures bioinformatically—first to get some idea of propensities of different residues in proteins to adopt different conformations. At the end of my Ph.D., I thought I was probably pretty well suited to bioinformatics, and got a job at the Sanger Institute, working on the Pfam database of protein families (despite knowing embarrassingly little about genomics, the Sanger Institute, or bioinformatics!).

ST: What drew you to this field of study?

It became obvious to us that we could apply the techniques that Pfam used on proteins to families of structural RNA. We started the Rfam database in 2002. MicroRNAs were only recently identified as a major RNA class, and the fast-growing body of researchers determined a need for a centrally (and sensibly) managed nomenclature for these genes. We were happy to help out, without really realizing how important this was to become for the microRNA field.

ST: Your 2004 Nucleic Acids Research paper, "The microRNA Registry," has been singled out as a highly cited recent paper on gene silencing. Would you please sum up this paper and its significance for the field?

The paper principally describes a service to name novel microRNA genes. The primary aim is to ensure that different groups don't inadvertently use the same names to describe different microRNA sequences—the speed of growth of the field was and is so rapid that this is a real possibility. I therefore confidentially deal out names prior to publication of novel microRNAs.

The secondary aim is to make all microRNA sequence and annotation data available after it is published. The microRNA Registry (now rebranded the miRBase database) therefore became the central microRNA database. I guess most citations for the paper are for the "secondary" function of microRNA data resource. This has become more and more important as the quantity of data has increased, and the combination of a curated nomenclature and a sensible and clean database resource have really helped the microRNA field to grow at the incredible rate that it has.

ST: What is the process you use to amass a database such as the microRNA Registry? What is involved in keeping the project current?

Much of the primary data is submitted to us, so we rely largely on that. But of course, there is a considerable effort of curation: reading papers, and incorporating new data types. Some of this is in response to requests to be able to get data in a certain way, but the aim is to drive what it's possible to do with the data.

ST: If you are free to discuss them, please tell us about your current projects.

I currently manage Rfam and miRBase, and have research interests in the field of RNA computational biology. For example, I use these resources to annotate homologs of RNA genes in whole genomes, and to understand RNA gene evolution and function. In January 2007, I'm moving to the University of Manchester to start a research group there. I will continue to look after microRNA gene names, and will remain heavily involved with the Rfam project.End

Dr. Sam Griffiths-Jones
Faculty of Life Sciences
University of Manchester
Manchester, UK

Dr. Sam Griffiths-Jones's most-cited paper with 1,057 cites to date:
Bateman A, et al., "The PFAM protein families database," Nucl. Acid Res. 30(1): 276-80, 1 January 2002.

Source: Essential Science Indicators

ESI Special Topics: February 2007
Citing URL:

This special topic of Gene Silencing was originally featured in ESI Topics in December 2003. To view the archived Gene Silencing topic, click here.

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