Sam Griffiths-Jones

Prof

Personal profile

Biography

Education and employment

2015-present Professor of Computational Biology, Faculty of Life Sciences, and Faculty of Biology, Medicine and Health, University of Manchester.

2011-2015 Senior Lecturer, Faculty of Life Sciences, University of Manchester.

2009-2011 Lecturer, Faculty of Life Sciences, University of Manchester.

2007-2009 Fellow, Faculty of Life Sciences, University of Manchester.

2003-2006 Project Leader, Rfam database of RNA families and the miRBase database of microRNA sequences, Wellcome Trust Sanger Institute.

2001-2002 Post-doctoral Researcher, Pfam database of protein families, Wellcome Trust Sanger Institute.

1997-2000 PhD Chemistry, Design and analysis of model beta-sheet systems — implications for protein folding, University of Nottingham.

1994-1997 BSc (Hons) First Class, Biochemistry and Biological Chemistry, University of Nottingham.

Research interests

RNA genes

The long-term aim of my research activities is to understand the complement of genomes that codes for functional RNA molecules, rather than translated proteins. Some classes of so-called non-coding RNA genes (ncRNAs) are well-known, for example, ribosomal RNAs, transfer RNAs and spliceosomal RNAs. Until recently, ncRNA genes have been essentially ignored by genome annotation projects, partly because many ncRNA genes conserve a base-paired secondary structure, without significant sequence conservation. Computational identification of such sequences is therefore extremely tough. However, comparative genomics and complementary experimental studies suggest that the number of ncRNAs in the eukaryotic genome may far out-strip previous expectations. Indeed, large and important classes of RNAs in eukaryotes have been discovered remarkably recently, including microRNAs (in 2001) and piwi-associated RNAs (in 2006).

Much of my work revolves around RNA database resources, and providing methods and models for computational ncRNA homologue detection. I co-founded and led the Rfam database of non-coding RNA families, and continue to collaborate in its development. I am also responsible for curating the nomenclature classification of microRNA genes, and run the miRBase database.

The solid database ground work means that the time is ripe for a wide range of ncRNA gene studies, their structure, function and evolution. I use the best available computational techniques and databases to address fundamental questions such as:

  • How many ncRNA genes are present in the eukaryotic genome?
  • What are their structures and functions?
  • How do ncRNA genes evolve?

The Rfam database provides a model for the computational identification of ncRNA homologues in complete genomes. Pushing these tools to their limits allows us to extend the taxonomic ranges of known ncRNA families, and inform on novel biology. For example, we recently identified homologues of the selenocysteine insertion machinery in apicomplexa (Mourier et al., 2004), for which selenocysteine incorporation was previously unknown. I also combine the large-scale use of computational tools, comparative genomics, and manual alignment and annotation to discover novel families of ncRNA genes, and to investigate novel RNA function. 

Positions available

Postdoctoral researchers: I have space in the lab for talented postdoctoral researchers interested in RNA computational biology. You are encouraged to seek monetary support in the form of a fellowship or other award. Please contact me informally for discussion.

 

More information

Please also see my research pages.

Overview

The most commonly understood role of RNA is as an intermediate in the decoding of genetic information in DNA into the proteins that carry out the majority of known structural and functional roles in the cell. A few other classes of functional RNA molecules, such as transfer RNAs, ribosomal RNAs and spliceosomal RNAs, are expressed from their own genes (so-called RNA genes), but were long assumed to be unusual specialised cases. However, in recent years it has become increasingly clear that RNA molecules are involved in essentially all cellular functions, including many that are linked directly to diseases. These RNAs can be tiny (just 20 or so bases in length in the case of a class called microRNAs) to extremely long (hundreds of thousands of bases). Current estimates suggest that there may be as many RNA genes as there are protein-coding genes in the human genome (i.e. tens of thousands), but we understand the functions of only a few hundred. My group is interested in the structure, function and evolution of functional RNAs. We employ mainly computational, genome-wide approaches to their analysis. We have particular interests in the class of microRNAs, and we manage the world-wide repository of microRNA data.

Teaching

I teach on a variety of undergraduate and Masters units, including Post-Genome Biology, 'Omics Technologies and Resources, Introduction to Bioinformatics, and Bioinformatics Tools and Resources.  In addition, I am the Academic Admissions Officer for all the biosciences undergraduate courses, and I have been a personal and academic advisor for Biochemists, Zoologists, and Life Scientists.

Expertise related to UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):

  • SDG 2 - Zero Hunger
  • SDG 3 - Good Health and Well-being

Research Beacons, Institutes and Platforms

  • Digital Futures
  • Lydia Becker Institute

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