Simon Moxon | Personal homepage of Simon Moxon

University of East Anglia, Norwich, UK

PhD (2005-2008) “Computational detection and classification of small RNAs and their targets”

Advisors: Prof. Vincent Moulton and Dr. Tamas Dalmay

Research included:

Development of command line and online tools for the computational analysis of small RNAs (sRNAs) from high-throughput sequencing experiments (454 and Illumina data)

Development of a new algorithm for animal and plant miRNA target prediction

Development of an online toolkit for small RNA analysis

Analysis of high-throughput sRNA datasets leading to the discovery of novel regliatory sRNAs including a novel class of small non-coding RNA in Mucor circinelloides

Collaborations with wet-lab biologists from the Dalmay Lab and other groups within Europe resliting in several publications in high-impact journals

University of Liverpool, Liverpool UK

MSc Software Engineering (2000-2001)

BSc (Hons) Genetics (1996-1999)

Awards/Funding

2010: BBSRC Grant BB/H023895/1 – Deciphering the RNA degradome: A new tool for small RNA target discovery

Co-wrote successful application to create a new tool for finding sRNA targets in plants using degradome and sRNA datasets and uncovering networks of sRNA-target interactions

2010: BBSRC Grant BB/I00016X/1 – The sRNA Workbench

Co-wrote a successful Bioinformatics and Biological Resources Fund grant application to continue previous work on the UEA sRNA toolkit (http://srna-tools.cmp.uea.ac.uk)

2009: Nuffield Science Bursaries (REF: 36675) – Undergraduate Research Award

Successfully applied for funding for an undergraduate student to work on “Assessing the accuracy of de novo small RNA locus assembly from high-throughput sequencing data”.

2009: Centro de Ciencias de Benasque Pedro Pascual – Travel Grant.

Invitation and travel grant to attend “Computational methods for RNA analysis” workshop.

2008: BBSRC grant – BBG0080781 – Characterisation of tomato short RNAs involved in fruit development

Contributed to writing bioinformatics analysis section of the successful proposal

2007: BBSRC grant – BBE0040911 – A computational platform for the high-throughput identification of short RNAs and their targets in plants

Co-wrote successful grant application “A computational platform for the high-throughput identification of short RNAs and their targets in plants”.

2006: Wellcome Trust Sanger Institute

Award for largest contributor to the Pfam database at the 10 year anniversary.

2005: University of East Anglia, School of Computing Sciences

Awarded a three year Dean’s scholarship from the school to undertake my PhD

Education

My research interests involve the computational discovery and classification of non-coding RNAs, primarily focusing on analysis of regulatory small RNAs (sRNAs) from next generation sequencing data. During my PhD and postdoctoral training with Tamas Dalmay and Vincent Moulton at the University of East Anglia (Norwich, UK) I developed several computational tools and methods for the analysis of sRNAs from high-throughput sequencing data (e.g. UEA sRNA Tools). These tools are now widely used by the scientific community (around 80,000 visits per year) and have since received funding from two separate grants to maintain them and to extend their functionality. Before starting my PhD I worked as a Computational Biologist at the Wellcome Trust Sanger Institute (Cambridge, UK) where I worked for the Pfam, Rfam and miRBase databases, gaining an excellent grounding in biological sequence analysis of both proteins and non-coding RNAs.

I have a good knowledge of both biological and computer sciences gained through my undergraduate (BSc Genetics) and postgraduate education (MSc Software Engineering). I feel that this, along with my previous postdoctoral training, has provided me with the skills necessary to work well in interdisciplinary projects and communicate ideas and results effectively to other scientists from a variety of different backgrounds.

Yale University, New Haven, CT, USA – Postdoctoral Associate (April 2011-present)

Working as a computational biologist in the Giraldez Lab, studying the role of small regulatory RNAs during early zebrafish development.

University of East Anglia, Norwich, UK – Senior Research Associate (Jan 2010-Feb 2011)

Worked as a computational biologist to translate the UEA sRNA Toolkit into a downloadable, stand-alone tool and increase functionality by developing new algorithms and methods for the analysis of sRNA data generated using high-throughput sequencing techniques. Role involved supervision of PhD students and of postdoctoral researchers involved in developing software for the toolkit.

University of East Anglia, Norwich, UK – Senior Research Associate (2008-2010)

Worked as a computational biologist on the BBSRC funded project to characterise sRNAs involved in fruit development in tomato. Role included close collaboration with experimental biologists in the Dalmay group, supervision of both undergraduate and PhD students and writing grant applications.

The Wellcome Trust Sanger Institute, Hinxton, UK – Computer Biologist (2002-2005)

Made significant contributions to Pfam and Rfam groups to annotate new protein and non-coding RNA families, assist with new releases and develop in-house software and analysis pipelines to improve quality control and productivity.

Conferences/Workshops Attended

Keystone Meeting: “Gene Silencing by Small RNAs” 2011, Vancouver Canada

Poster presentation “Dissecting small RNA Pathways During Zebrafish Development”

EMBL Non-Coding Genome Symposium 2010, Heidelberg Germany

Poster presentation on the UEA Plant sRNA Toolkit

SIROCCO Meeting 2010

Invited to present my work on the UEA sRNA tools website

RNA Sequence Database Workshop. 2010, WTSI, Hinxton

Invited to attend a meeting to draft an outline for a white paper on a federated non-coding RNA database with other members of the RNA community

Plant Short RNA Workshop. 2010, University of East Anglia, Norwich

Talk on the UEA Plant sRNA Toolkit

Computational methods for RNA analysis. 2009, Benasque, Spain

Invited speaker – talk entitled “Computational analysis of high-throughput sRNA data”

MicroRNAs Europe 2007 & 2008, Cambridge

Poster presentations on the UEA Plant sRNA Toolkit

SIROCCO Bioinformatics Day. 2008. Genome Campus, Hinxton

Talk/tutorial on the UEA Plant sRNA Toolkit

ISMB/ECCB 12th International Conference on Intelligent Systems for Molecular Biology, 2004. Glasgow

Poster presentation on the Rfam database

Research

Academic Skills

Excellent communication and team working skills: I’ve been involved with many local, national and international collaborations during my PhD and postdoc positions which have led to successful publications and feel that I can communicate well with biologists and computer scientists to create solutions to understand biological data generated using next generation sequencing technologies

Strong computer skills including Perl (expert), Linux/UNIX (advanced), R (working knowledge), MySQL & PHP

Solid background in molecular biology, genetics and some laboratory techniques allowing a good understanding of biological problems and communication of complex ideas in a cross-disciplinary environment

Good written skills evidenced by several publications and successful grant applications

Expert knowledge of non-coding RNA alignment, homology searching and annotation

Several years of protein domain family building, annotation and homology searching

Expert knowledge of standard bioinformatics search, alignment and visualisation tools

Several years experience in working with data from high-throughput sequencing experiments (including sRNA and metatranscriptome data)

Excellent time management and project planning skills: during my PhD and postdoc position I’ve had the opportunity to work on multiple projects simultaneously and have had to carefully plan and prioritise my workload in order to efficiently complete tasks

Exceptional problem solving and analytical skills evidenced through my publication record

Reviewed articles for the following journals & conferences: Bioinformatics, PLoS Computational Biology, BMC Bioinformatics, Nucleic Acids Research, BMC Genomics, BMC Evolutionary Biology, BMC Plant Biology, Functional & Integrative Genomics, Plant Biotechnology Journal, IEEE International Conference on Bioinformatics and Bioengineering, IEEE European Conference on Computational Biology, Workshop on Algorithms in Bioinformatics

Skills

Publications

1. Moxon, S.*; Folkes, L.*; Woolfenden, H. C; Stocks, M. B.; Szittya, G.; Dalmay, T.; Moulton, V. PAREsnip: A tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucl. Acids Res. 2012 10.1093/nar/gks277
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2. Bateman, A.; Moxon, S; et al. RNAcentral: a vision for an international database of RNA sequences. RNA Journal. doi: 10.1261/rna.2750811
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3. Mohorianu, I.; Schwach, F.; Jing, R.; Lopez-Gomollon, S.; Szittya, G.; Moxon, S.; Sorefan, K.; Moulton, V.; Dalmay, T. Integration of short RNA, mRNA and degradome profiles during fleshy fruit development reveals components of regulatory networks and widespread positive correlation between microRNA and target mRNA expression. Plant Journal. doi: 10.1111/j.1365-313X.2011.04586.x Download pdf

4. Surridge, A. K.; Lopez-Gomollon, S.; Moxon, S.; Maroja, L. S.; Rathjen, T.; Nadeau, N. J.; Dalmay, T.; Jiggins, C. D. Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene. BMC Genomics. 12(1):62
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5. Moxon, S.*; Nicolas, F.*; de Haro, J.; Calo, S.; Grigoriev, I.; Torres-Martínez, S.; Moulton, V.; Ruiz-Vázquez, R.; Dalmay, T. Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Research. 2010 38(16):5535-41 Download pdf

6. Pantaleo, V.; Saldarelli, P.; Miozzi, L.; Giampetruzzi, A.; Gisel, A.; Moxon, S.; Dalmay, T.; Bisztray, G.; Burgyan, J. Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology. 408(1):49-56. Download pdf

7. Szittya, G.; Moxon, S.; Pantaleo, V.; Toth, G.; Rusholme-Pilcher, R.; Moulton, V.; Burgyan, J.; Dalmay, T. Structural and Functional Analysis of Viral siRNAs. PLoS Pathogens. 2010 6(4):e1000838.
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8. Pantaleo, V.; Szittya, G.; Moxon, S.; Miozzi, L.; Moulton, V.; Dalmay, T.; Burgyan, J. Identification of grapevine microRNAs and their targets using high throughput sequencing and degradome analysis. The Plant Journal. 2010 62(6):960-76. Download pdf

9. Navarro, B.; Pantaleo, V.; Gisel, A.; Moxon, S.; Dalmay, T.; Bisztray, G.; Di Serio, F.; Burgyán, J. Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS One. 2009 4(11):e7686.
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10. Schwach, F.; Moxon, S.; Moulton, V. & Dalmay, T. Deciphering the diversity of small RNAs in plants: the long and short of it. Briefings in Functional Genomics & Proteomics. 2009, 8(6):472-81.
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11. Moxon, S.*; Szittya, G.*; Santos, D.M.; Jing, R.; Fevereiro, M.P.S; Moulton, V.; Dalmay, T. High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics. 2008, 9:593. Download pdf

12. Moxon, S.*; Runchun, J.*; Szittya, G.*; Schwach, F.; Rusholme Pilcher, R.L.; Moulton, V.; & Dalmay, T. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Research. 2008, 18:1602-1609.
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13. Moxon, S.*; Schwach, F.*; Studholme, D.; Dalmay, T.; MacLean, D. & Moulton, V. A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics. 2008, 24(19):2252-3.
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14. Bagnall, A. J.; Moxon, S. & Studholme, D. J., Moulton, V. Time Series Data Mining Algorithms for Identifying Short RNA in Arabidopsis Thaliana. BIOCOMP’08 – The 2008 International Conference on Bioinformatics & Computational Biology. 2008.
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15. Moxon, S.; Moulton, V. & Kim, J. T. A scoring matrix approach to detecting miRNA target sites. Algorithms for Molecular Biology. 2008, 3:3. Download pdf

16. Pilcher, R. L. R.; Moxon, S.; Pakseresht, N.; Moulton, V.; Manning, K.; Seymour, G. & Dalmay, T. Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta. 2007, 226:709-717.
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17. Finn, R. D.; Mistry, J.; Schuster-Böckler B.; Griffiths-Jones, S.; Hollich, V.; Lassmann, T.; Moxon, S.; Marshall, M.; Khanna, A.; Durbin, R.; Eddy, S. R.; Sonnhammer, E. L. L. & Bateman, A. Pfam: clans, web tools and services. Nucleic Acids Research. 2006, 34:D247-D251.
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18. Griffiths-Jones, S.; Moxon, S.; Marshall, M.; Khanna, A.; Eddy, S. R. & Bateman, A. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Research. 2005, 33:D121-D124.
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19. Bateman, A.; Coin, L.; Durbin, R.; Finn, R. D.; Hollich, V.; Griffiths-Jones, S.; Khanna, A.; Marshall, M.; Moxon, S.; Sonnhammer, E. L. L.; Studholme, D. J.; Yeats, C. & Eddy, S. R. The Pfam protein families database. Nucleic Acids Research. 2004, 32:D138-D141.
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* Authors contributed equally to this work

Book Chapters

1. Pais, H.; Moxon, S.; Dalmay, T.; Moulton, V.; Small RNA Discovery and Characterisation in Eukaryotes Using High-Throughput Approaches in RNA infrastructure: RNA processing and regulatory networks. ISBN 978-1-4614-0331-9. Abstract

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