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Dr Ryan Ames

Postdoctoral Research Fellow (LSI)

 Living Systems Institute S02.01

 

Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD

Overview

I am a EPSRC/BBSRC Innovation Research Fellow in the Living Systems Institute. My research uses computational approaches to gather, integrate and analyse biological big data, including working extensively with next-generation sequencing data. A major part of my work uses network approaches to study how phenotype arises from complex systems. Currently, I am using these approaches to study the evolution of pathogenicity in yeast in order to identify novel disease-associated pathways.

I am also affiliated with the Centre for Biomedical Modelling and Analysis. Where I have collaborated on a number of inter-disciplinary projects with researchers from Biosciences, the Medical School and Mathematics.

Broad research specialisms:

  • Next-generation sequence analysis
  • Network analysis
  • Systems biology

Qualifications

2007 – 2011  PhD Bioinformatics, University of Manchester
2006 – 2007  MSc Bioinformatics, University of Manchester
2003 – 2006  BSc Biology, University of Bristol

Career

2018 - Present EPSRC/BBSRC Innovation Fellow, University of Exeter

2015 - 2018 Research Fellow, University of Exeter

2012 - 2015 Research Associate, University of Manchester

Links

Research

Research interests

I am interested in understanding how phenotype arises from complex systems. I employ a variety of computational techniques and network approaches in my research. In particular I am interested in integrating genomic, transcriptomic and proteomic data to build network models that can be used to answer important biological questions. I apply these techniques to projects in my own research programme and a range of collaborative inter-disciplinary projects.

Currently, I am focused on identifying novel disease pathways in a range of pathogenic yeast including the human pathogen Candida albicans and the plant pathogen Magnaporthe oryzae. C. albicans is a human commensal and opportunistic pathogen that causes candidiasis and, in immumocomprimised patients, infection can be life threatening. M. oryzae is an important plant pathogen that infects a range of crops including rice and wheat. Losses of crops to this pathogen represent an important threat to global food security.

My work employs network biology techniques to integrate genomic, transcriptomic and proteomic data. These data are then interrogated to identify specific pathways. Ultimately, the identification of novel disease pathways may lead to new drug targets and new treatments for both humans and crops.

Research projects

Identifying new targets for antifungals in Magnaporthe oryzae

Magnaporthe oryzae is an important pathogen of plants and causes significant losses of crops each year. The pathogen, therefore, represent an important threat for food security. My EPSRC/BBSRC Innovation Fellowship will employ new network techniques to identify targets for antifungals. These targets will be validated using experimental studies. This fellowship includes an industry partnership with Syngenta.

Identifying novel disease pathways in Candida albicans
Candida albicans is a human pathogen that causes a high rate of mortality in immunocomprimised patients. Its genome is currently only partially annotated with many genes uncharacterized. I aim to employ a series of network techniques to integrate genomic, transcriptomic and proteomic data to identify novel disease pathways. These pathways will be used to identify new drug targets for medical intervention. This work benefits from collaboration with the MRC Medical Mycology Centre at the University of Aberdeen.

Research grants

  • 2018 EPSRC
    New bioinformatics tools for novel fungicide target discovery

Links


Publications

Key publications | Publications by category | Publications by year

Publications by category


Journal articles

Ames RM, Talavera D, Williams SG, Robertson DL, Lovell SC (In Press). Binding interface change and cryptic variation in the evolution of protein-protein interactions. BMC Evolutionary Biology Abstract.  Full text.
Stoney RA, Ames RM, Nenadic G, Robertson DL, Schwartz JM (In Press). Disentangling the multigenic and pleiotropic nature of molecular function. BMC Systems Biology, 9(Suppl 6). Abstract.  Full text.
Tyrrell J, Wood AR, Ames RM, Yaghootkar H, Beaumont RN, Jones SE, Tuke MA, Ruth KS, Freathy RM, Davey Smith G, et al (In Press). Gene-obesogenic environment interactions in the UK Biobank study. Int J Epidemiol, 46(2), 559-575. Abstract.  Author URL.  Full text.
Naseeb S, Ames RM, Delneri D, Lovell SC (2017). Rapid functional and evolutionary changes follow gene duplication in yeast. Proceedings of the Royal Society B: Biological Sciences, 284(1861). Abstract.  Full text.
Ames R (2017). Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae. Microorganisms, 5(1), 3-3. Full text.
Ames RM, Lovell SC (2014). DupliPHY-Web: a web server for DupliPHY and DupliPHY-ML. Bioinformatics, 31(3), 416-417.
Ames RM, Money D, Lovell SC (2014). Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions. PLoS ONE, 9(6), e99480-e99480. Full text.
Ames RM, MacPherson JI, Pinney JW, Lovell SC, Robertson DL (2013). Modular Biological Function is Most Effectively Captured by Combining Molecular Interaction Data Types. PLoS ONE, 8(5), e62670-e62670. Full text.
Ames RM, Money D, Ghatge VP, Whelan S, Lovell SC (2011). Determining the evolutionary history of gene families. Bioinformatics, 28(1), 48-55. Full text.
Ames RM, Lovell SC (2011). Diversification at Transcription Factor Binding Sites within a Species and the Implications for Environmental Adaptation. Molecular Biology and Evolution, 28(12), 3331-3344. Full text.
Ames RM, Rash BM, Hentges KE, Robertson DL, Delneri D, Lovell SC (2010). Gene Duplication and Environmental Adaptation within Yeast Populations. Genome Biology and Evolution, 2, 591-601. Full text.

Conferences

Tyrrell J, Yaghootkar H, Beaumont R, Jones SE, Ames RM, Tuke MA, Ruth KS, Kutalik Z, Freathy RM, Murray A, et al (2016). Gene-obesogenic environment interactions in the UK Biobank study.  Author URL.  Full text.

Publications by year


In Press

Ames RM, Talavera D, Williams SG, Robertson DL, Lovell SC (In Press). Binding interface change and cryptic variation in the evolution of protein-protein interactions. BMC Evolutionary Biology Abstract.  Full text.
Stoney RA, Ames RM, Nenadic G, Robertson DL, Schwartz JM (In Press). Disentangling the multigenic and pleiotropic nature of molecular function. BMC Systems Biology, 9(Suppl 6). Abstract.  Full text.
Tyrrell J, Wood AR, Ames RM, Yaghootkar H, Beaumont RN, Jones SE, Tuke MA, Ruth KS, Freathy RM, Davey Smith G, et al (In Press). Gene-obesogenic environment interactions in the UK Biobank study. Int J Epidemiol, 46(2), 559-575. Abstract.  Author URL.  Full text.

2017

Naseeb S, Ames RM, Delneri D, Lovell SC (2017). Rapid functional and evolutionary changes follow gene duplication in yeast. Proceedings of the Royal Society B: Biological Sciences, 284(1861). Abstract.  Full text.
Ames R (2017). Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae. Microorganisms, 5(1), 3-3. Full text.

2016

Tyrrell J, Yaghootkar H, Beaumont R, Jones SE, Ames RM, Tuke MA, Ruth KS, Kutalik Z, Freathy RM, Murray A, et al (2016). Gene-obesogenic environment interactions in the UK Biobank study.  Author URL.  Full text.

2014

Ames RM, Lovell SC (2014). DupliPHY-Web: a web server for DupliPHY and DupliPHY-ML. Bioinformatics, 31(3), 416-417.
Ames RM, Money D, Lovell SC (2014). Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions. PLoS ONE, 9(6), e99480-e99480. Full text.

2013

Ames RM, MacPherson JI, Pinney JW, Lovell SC, Robertson DL (2013). Modular Biological Function is Most Effectively Captured by Combining Molecular Interaction Data Types. PLoS ONE, 8(5), e62670-e62670. Full text.

2011

Ames RM, Money D, Ghatge VP, Whelan S, Lovell SC (2011). Determining the evolutionary history of gene families. Bioinformatics, 28(1), 48-55. Full text.
Ames RM, Lovell SC (2011). Diversification at Transcription Factor Binding Sites within a Species and the Implications for Environmental Adaptation. Molecular Biology and Evolution, 28(12), 3331-3344. Full text.

2010

Ames RM, Rash BM, Hentges KE, Robertson DL, Delneri D, Lovell SC (2010). Gene Duplication and Environmental Adaptation within Yeast Populations. Genome Biology and Evolution, 2, 591-601. Full text.

Ryan_Ames Details from cache as at 2018-12-09 09:25:43

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Teaching

I currently run the RNA-Seq workshop for the Biomedical Informatics Hub. This workshop aims to teach a comprehensive pipeline for RNA-Seq analysis.

Supervision / Group

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