Curriculum Vitae Richard Stephens

Full Name: Richard Huw Stephens

Date of Birth: 13th May 1966 Nationality: British Marital Status: Married

Personal StatementMy core values drive me to embrace excellence and to strive to enhance the experience of my clients. My focus has always been on timely delivery of accurate, appropriately formatted and accessible results that meet or exceed the needs of the end-users. My background is in clinical and life sciences research, bridging many disciplines including physiology, pharmacokinetics, genetics, computer modelling and epidemiology. I thrive in a cross-functional working environment, as an adaptable member of multiple research teams to anticipate, define, refine and finally meet the needs of stakeholders.

Summary of Key Skills:· DNA analysis using PCR, ABI Taqman, ABI SNaPShot, CE fragment analysis, Pyrosequencing,

Sequenom iPlex and Transgenomic WAVE.· Bioinformatic and genetic modeling/analysis with a range of tools including, but not limited to:

· BLAST, Clustal, GeoDIS, MrBayes, PowermarkerBiomart, Illumina Beadstudio, GoldenHelix SVS, CLC Genome Workbench, Geneious, Stata, R (packages including Ape, Geiger, Hierfstat, Corrsieve, Phangorn, PopGenome) and MatLab.

· Experience of forward and reverse-time population genetic data simulation and modeling using FFPopSim, Nemo, easyPOP, Bayesian Serial SimCoal, BEAST and SimuPOP (which requires intermediate knowledge of Python (2.7) and Biopython).

· Phylogenetic analyses using R, Network, Splitstree, Mesquite, Phylip, DnaSP, PhyML and MEGA.· DNA analysis using PCR, ABI Taqman, ABI SNaPShot, CE fragment analysis, Pyrosequencing,

Sequenom iPlex and Transgenomic WAVE.· A basic knowledge of Java and the bioinformatics applications of Perl and BioPerl.· Experience of OWL-based ontologies, Protégé and de novo genome annotation using tools such

as GO-Elite and DAVID.· Multi-omics analysis and annotation using ARACNE, Cytoscape, David.· Provision of bioinformatics and IT support and training to coworkers, students and

collaborators, including small group teaching.· Analytical pipeline automation using Taverna Workbench, Kepler, Rstudio and Galaxy.· Familiarity with NGS application platforms (DNA-SEQ, RNA-SEQ, ChIP-SEQ, methyl-SEQ).· Design, quality control and analysis of whole-genome and candidate gene studies.· Bio-repository management and construction, including the application and harmonization of

anonymised patient information databases and a bespoke LIMS under ISO 9001:2000 and local governance requirements.

· Liaison with diverse clinical and industrial stakeholder teams.· Working knowledge of Linux and OS virtualisation under Virtual box and VMware.· Able to apply skills across multiple OS platforms (Windows/Linux/MacOS).· Project management and fulfillment of stakeholder-defined deliverables. · Rapid extraction and dissemination of critical information from diverse literature and electronic

resources via ontologies, briefing notes and bespoke database records. · Experience with knowledge management tools such as Mendeley and Zotero.· Basic knowledge of version control using Git.

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Curriculum Vitae Richard Stephens

Most Recent Post:Postdoctoral Research Associate in Biomolecular ArchaeologyEvolutionary and Computational Biology GroupFaculty of Life SciencesThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchester M1 7DN

I was primarily responsible for the investigation of the evolution of agriculture using population genetics and phylogenetics approaches and analysis of crop plant genomic data obtained using next-generation sequencing and microsatellite/SSR typing. This project was funded under the EU Framework 7 programme. I developed mathematical modeling techniques and novel genetic analysis workflows using backward-time and forward-time simulation, employing Python, Perl, Java and R. I also undertook population genetic and phylogenetic analyses using a range of software including Matlab, BEAST, MEGA and Structure. In addition, I was responsible for the management of two technicians and acted as an advisor to three PhD students. Allied research areas included population genetic analysis of extant and ancient human mitochondrial and NRY inheritance and modeling of the impact of environmental factors on genetics, epigenomics and transcriptomics of selected non-model species at key points such as the Neolithic and Chalcolithic transitions. This contract ended on 30th April, 2015.Minimum Notice Period: N/A

Education:Postgraduate training in bioinformatics and Java development, 2011-2013.PhD, Paediatrics/Physiology, "An investigation into the development and regulation of water and solute transport mechanisms in the lung." University of London, 1997.BSc (Hons) Human Biology 2.1, Oxford Polytechnic, 19888 “O” levels, 4 “A” levels, Kingsthorpe Upper School, Northampton, 1979-1985

Other Courses Completed:Research Project Management - University of Manchester, 2007Introduction to Text-Mining – NaCTeM, 2009Introduction to Stata - University of Manchester, Sept 2009 to Jan 2010Fundamentals of Next Generation Sequencing – NowGen, October 2011Research Team Leadership - University of Manchester, Jan 2010 - March 2011Next Generation Sequencing Bioinformatics – NowGen, October 2011Reproducible Workflows for NGS Analysis – NowGen, January 2012Introduction to Application Development in Java - University of Manchester, 2011-2012Introduction to Biolinux – University of Sheffield, Jan 2013.Transcriptomic analysis using R and Big Data analysis using R and Cytoscape – University of Cardiff, September 2013.“Researchers into Management”; ILM level 5-accredited training in research management. University of Manchester, April-July 2014.NBAF Population Genomics Workshop, Liverpool, September 2014.

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Curriculum Vitae Richard Stephens

NERC workshop ‘Computational approaches to study biological mechanisms’, Liverpool, September 2014.

Home Address:40 Chelmer WayElyCambridgeshireCB6 2WS

Tel: 01353 361250Mobile: 0758 4296396Email: mdmmsrhs1@gmail.com

http://uk.linkedin.com/pub/richard-stephens/14/445/664

http://www.researchgate.net/profile/Richard_Stephens4/

Hobbies and Interests:

I am interested in computer programming and data visualization/digital art, particularly the applications of Python and Processing. I also enjoy industrial archaeology, urban and military history, linguistics, paleoanthropology and paleoclimatology and current technology affairs. Other interests include Major League Baseball, sabermetrics, long walks in the countryside, Warhammer 40,000, electronic, alternative rock and classical music, modern fiction including Douglas Coupland, William Gibson and Neal Stephenson and stand-up comedy.

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Curriculum Vitae Richard Stephens

Appendix 1: Employment History:Mar 2003-Jan 2012

School of Cancer & Enabling SciencesThe University of ManchesterStopford BuildingOxford RoadManchester M13 9PT

Post: Research Associate in Diabetes GenomicsProject: Lead post-doctoral researcher on a genetic epidemiology study of the causes and complications of diabetes in the population of Salford.

Sept 1998-Feb 2003

Gut Barrier GroupUniversity of ManchesterClinical Sciences Building Hope HospitalSalford M6 8HD

Post: Postdoctoral Research AssociateProject: Investigation of intestinal drug efflux in collaboration with a major pharmaceutical company.

Feb-Aug 1998

School of Biomedical SciencesWorsley Medical and Dental BuildingUniversity of Leeds Leeds LS2 9JT

Post: Research Fellow in Physiology. Project: Molecular biology of O2-sensing K+ channels in neuro-epithelial bodies.

April1994-Jan 1998

Department of Child HealthSt George’s Hospital Medical SchoolCranmer TerraceLondon SW17 0RE

Post: Research Assistant.Project: In utero and postnatal control of lung liquid homeostatic mechanisms, continuing work begun at UCL.

Feb 1991-Mar1994

Department of PaediatricsUCL Medical SchoolThe Rayne Institute5 University StreetLondon WC1E 6JJ

Post: Research Assistant. Project: Fetal and postnatal regulation of lung liquid homeostatis

April 1990-Jan 1991

Derwent Publications LtdLiterature DivisionBerkshire HouseHigh HolbornLondon WC1V 7AA

Post: Biomedical indexerDuties: Rapidly summarising published scientific information and assigning searchable index terms for online databases.

Oct 1988-Dec 1989

MRC Clinical Research CentreSection of Surgical ResearchNorthwick Park HospitalWatford RoadHarrow HA1 3UJ

Post: Scientific Officer. Project: Acute aetiology of neuropathy in non freezing cold injury (trench foot). Funded by Institute of Naval Medicine.

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Curriculum Vitae Richard Stephens

Appendix 2: Refereed Publications:

Bouwman AS, Kennedy SL, Muller R, Stephens RH, Holst M, Caffell AC, Roberts CA and Brown TA (2012) The genotype of a historic strain of Mycobacterium tuberculosis. Proc. Nat. Acad. Sci. USA. 109(45), 18511-18516.

Collett A, Stephens RH, Harwood M, Humphrey M, Dallman L, Bennett J, Davis J, Carlson G and Warhurst G (2008) Investigation of regional mechanisms responsible for poor oral absorption in humans of a modified release preparation of the alpha-adrenoreceptor antagonist, 4-amino-6,7-dimethoxy-2-(5-methanesulfonamido-1,2,3,4 tetrahydroisoquinol-2-yl)-5-(2-pyridyl)quinazoline (UK-338,003): the rational use of ex vivo intestine to predict in vivo absorption. Drug Metab Dispos. 36(1), 87-94.

Salonen JT, Uimari1 P, Aalto1 J-M, Pirskanen M, Kaikkonen J, Todorova B, Hyppönen J, Korhonen V-P, Asikainen J, Devine C, Tuomainen T-P, Nyyssönen K, Luedemann J, Nauck M, Kerner W, Stephens RH, New JP, Ollier WE, Gibson JM, Payton A, Horan MA, Pendleton N, Mahoney W, Meyre D, Delplanque J, Froguel P, Luzzatto O, Yakir B and Darvasi A (2007) Type 2 diabetes whole genome association study in four populations: the DiaGen consortium. Am J Hum Genet 81, 338-345.

Heald A, Stephens R and Gibson JM (2006) The insulin-like growth factor system and diabetes – an overview. Diabetic Medicine 23 Suppl 1, 19-24.

Stephens RH, McElduff P, Heald AH, New JP, Worthington J, Ollier WE, Gibson JM (2005). Polymorphisms in Insulin-Like Growth Factor-Binding Protein 1 (IGFBP1) are Associated With Impaired Renal Function In Type-2 Diabetes mellitus. Diabetes 54, 3547-3543.

Stephens RH, Tanianis-Hughes J, Higgs N.B., Bennett, J, Humphrey M. and G. Warhurst (2002). Region-dependent modulation of intestinal permeability by drug efflux transporters: in vitro studies in mdr1a (-/-) mouse intestine. J. Pharmacol. Exp. Ther. 303(3), 1095-1101.

Stephens RH, O’Neill CA, Bennett J, Humphries M, Henry B, Rowland M and Warhurst, G. (2002) Use of the isolated wild type and mdr1a (-/-) mouse intestine in the study of drug transport mechanisms in vitro. Br. J. Pharmacol. 135, 2038-2046.

Stephens RH, O’Neill CA, Warhurst A, Carlson GL, Rowland M and Warhurst G. Kinetic profiling of P-glycoprotein mediated drug efflux in rat and human intestinal epithelia. (2001) J. Pharmacol. Exp. Ther. 296 (2), 584-591.

O'Kelly I, Stephens RH, Peers C and Kemp PJ. (1999) Potential identification of the O2-sensitive K+

current in a human neuroepithelial body-derived cell line. Am. J. Physiol. 276, L96-L104.

Stephens RH, Benjamin AR and Walters DV (1998) The regulation of lung liquid absorption by endogenous cAMP in postnatal sheep lungs perfused in situ. J. Physiol. (London) 511, 587-597.

Stephens R.H, Benjamin A.R, Walters D.V (1996) Liquid absorption in juvenile postnatal sheep lungs, perfused in situ, is mediated by cyclic adenosine-3',5'-monophosphate (cAMP) from cellular sources other thanβ-adrenergic stimulation. Early Hum. Devel. 45(1):142-143.

Stephens RH, Benjamin, AR, Walters DV. (1996) Volume and protein concentration of epithelial lining liquid in perfused in situ postnatal sheep lungs. J. Appl. Physiol. 80, 1911-20.

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Curriculum Vitae Richard Stephens

More than 10 Abstracts presented at international meetings, including:

Polymorphisms in human AHSG (Fetuin-A) gene are associated with risk of nephropathy in type 2 diabetes. RH Stephens, XX Pan, RM Middleton, PA Kalra, DJ O’Donaghue WER Ollier and JM Gibson. The Endocrine Society, San Diego CA, June 2010.

RH Stephens, RL Oliver, JP New, WER Ollier and JM Gibson. Insertion/deletion (indel) polymorphisms in the IGFBP1 Promoter: influence on circulating IGFBP-1 and BMI in a cohort of type-2 diabetes (T2DM) patients. Diabetes UK, Liverpool March 2010.

RH Stephens, R Middleton, R Hoefield, JP New, P Kalra, D O’Donoghue, N Pendleton, MA Horan, A Payton, WER Ollier and JM Gibson. Polymorphism downstream of IGFBP1 gene is associated with Type 2 Diabetes (T2DM) prevalence in a population sample from North West England. Diabetes UK, Liverpool March 2010.

Stephens RH, New JP, Ollier WE & Gibson JM. Single Nucleotide Polymorphisms (SNPs) in the Insulin (INS)/IGF2 gene region associated with altered risk of nephropathy in Type-2 Diabetes mellitus (T2DM). The Endocrine Society, Boston MA, June 2006.

Stephens RH, Heald AH, McElduff P, New JP, Ollier WE and Gibson JM. Polymorphisms in insulin-like growth factor-binding protein-1 (IGFBP-1) are associated with increased type 2 diabetes mellitus prevalence. Diabetes UK Professional Meeting, Birmingham, March 2006.

Stephens RH, McElduff P, Worthington J, Ollier WE, New JP, Payton A, Pendeleton N, Horan MA, Cruickshank JK and Gibson JM (2005) Single-Nucleotide Polymorphisms (SNPs) in the IGFBP1 gene are associated with diabetes risk and nephropathy in a cohort of type 2 Diabetes mellitus patients. Diabetes 54, Suppl. 1, A293 (65th Scientific Sessions of the American Diabetes Association, San Diego CA, 2005).

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