1 Research Experience

1.1 Current - The Epigenomics of Human Aging (PhD)

Supervisor Dr. Chris Bell C.G.Bell@soton.ac.uk

1.2 MSc Research Project – circRNAs in daf-2 and daf-2/16 mutant C. elegans Neurons.

This project sought to identify circRNA product with differential expression between the neurons of C. elegans with normal and extended lifespan mutants. I analysed RNA-seq data, performing QC with FASTQC and read trimming with Trimmomatic. I performed alignments with bowtie2 and bwa. Followed by circRNA discovery with two dedicated circRNA detection tools. I made an index of circRNA discovery tools. The tools I used in this analysis were find_circ and CIRI. I used the DESeq2 tool for differential expression analysis. We found very low levels of agreement in circRNA detection, even between biological replicates. I was not able to find differential expression in any of the circRNAs detected between the long-lived and normal lifespan worms.

Supervisor: Irilenia Nobeli i.nobeli@mail.cryst.bbk.ac.uk

1.3 4th year project – Working on the B methylase in the N6-methyladensine RNA modification system in Arabidopsis.

Gene knock out in Arabidopsis using CRISPR, involving designing guide RNAs and producing transfection vectors using PCR and Golden Gate cloning. Using agrobacterial floral dip transfection to produce Arabidopsis transformants. Screening Arabidopsis plants for antibiotic resistance markers. Extracting RNA, using reverse transcription PCR to assess expression levels of cas9 in putative transformant plants and using capillary electrophoresis to screen for small mutations.

Supervisor: Dr. Rupert Fray rupert.fray@nottingham.ac.uk

1.4 Summer Studentship 2014 (BBSRC REP [Research experience placement]) – Working on Bd1483 a Bdellovibrio bacteriovorus protein.

Restriction cloning to attempt to create bacterial two hybrid vectors. Attempted to create vectors to produce genomic deletion and GFP tagged Bd1483 mutants by recombination using Gibson assembly cloning. Bd1483 expression analysis using reverse transcription PCR on existing RNA samples. Basic bioinformatic and phylogenetic analysis of Bd1483 [Sockett Lab]. Produced and purified by nickel affinity chromatography quantities of His Tagged Bd1483 protein from an existing construct. Bd1483 was identified by molecular weight using Denaturing SDS-PAGE. Screened for metal cation binding using native PAGE. Prepared crystal trays for Bd1483, successfully producing X-ray diffracting crystals. Produced and attempted to purify DivIVA protein in solution containing surfactants [Lovering Lab].

Supervisors: Professor Liz Sockett liz.sockett@nottingham.ac.uk, Dr. Andy Lovering a.lovering@bham.ac.uk

1.5 3rd year project – Interactions of PilZ proteins of the Cyclic-dimeric-3’→5’-Guanosine Mono Phosphate (c-di-GMP) signalling system in Bdellovibrio bacteriovorus.

Restriction cloning to produce Bacterial two hybrid vectors and Screening for interactions with other Bdellovibrio Proteins. Involving preparative and analytic DNA agarose gel electrophoresis and the Miller Assay to assess β-galactosidase activity as semi-quantitative indicator of the extent of interaction.

Supervisor: Professor Liz Sockett liz.sockett@nottingham.ac.uk

1.6 Summer research placement – Identifying and expressing possible chlamydial effector protein genes in Human cell lines.

Examining a set of previously identified chlamydial effector proteins I noted that one contained a nuclear localisation sequence, and considered that searching for chlamydial genes with an NLS might be an effective method of identifying a sub-set of chlamydial effector proteins. Produced mammalian expression vectors containing fluorescently tagged possible chlamydial effector proteins using SLICE cloning; a recombination based cloning technique, this process involved custom primer design. Used high speed lithium borate DNA agarose gel electrophoresis. Transfected HeLa and U20s derived cell lines with the resulting vectors using lipotransfection. examined the subcellular localisation of proteins using wide-field fluorescence microscopy.

Supervisor: Dr. Alan Huett Alan.Huett@nottingham.ac.uk

2 Programming Skills

I mostly use linux operating systems and am familiar with the Bourne shell, basic bash scripting and the composing of command line tools. I learned to code in perl 5 a language in which I am proficient, I also know some perl 6 a relatively new language with excellent support for parallelism, asynchrony and concurrency. I have experience using high performance computing clusters. I now spend most of my time using R for data analysis. I make extensive use of the ‘tidyverse’ libraries and am proficient at data manipulation with dplyr and static plotting with ggplot2, I have some familiarity with making dynamic plots using shiny. I do a lot of my work using Rnotebooks in R markdown with some use of LaTeX. I also have a passing familiarity with python along with its Matplotlib library as well as tools such as jupyter notebooks. In the area of web based tools I have basic javascript, PHP, HTML and CSS skills and well as knowledge of creating a querying databases with MySQL. I have experience of the ‘full stack’ of web services from front end to setting up Linux servers in very small scale contexts but have limited security and user management knowledge. I also have a passing familiarity with docker for the creation of fully reproducible data analyses. I have made some small contributions to R libraries on github and habitually use git for version management.

3 Education

3.1 Birkbeck University of London (2015-16)

MSc in Bioinformatics and Systems biology (Distinction). I undertook this degree to learn to program (a long-standing intention) and to extend my knowledge of statistics. Biology is increasingly a field to which data science is integral and in my experience the best wet work has a well-informed background in dry work and the best experimental design comes out a solid understanding of statistics.

3.2 Undergraduate (University of Nottingham 2011-15)

1st Class MSci with Honours in Biochemistry and Genetics from the University of Nottingham. (See 5.1 for detailed breakdown by module)

3.3 A-levels (The Sixth Form College Farnborough 2009-11)

Biology (A2)	Chemistry (A2)	Physics (A2)	Maths (A2)	Economics (AS)	General Studies (A2)
A	A	A	B	A	B

(See 5.2 for results by module)

3.4 GCSEs (Frensham Heights School 2005-2009)

Double Science	Maths	ICT	French	Photography	Design Tech(RM)	Art and Design 3D	Geography	English	English Literature
(A)A	A*	A*	A*	A*	A*	A*	A*	A	B

(Photography taken as an extra-curricular in 2007, French taken 1 year early in 2008)

3.5 Early life education

École Internationale de Genève (La Grande Boissière campus), from 2003-2005 (Switzerland, Geneva)
Cheddington Combined School 2000-2003 (UK)
Osgood Elementary 1999 – 2000 (USA, Massachusetts)
Cohasset Montessori 1997-1999 (USA, Massachusetts)
Bagshot Montessori 1996-1997 (UK)

4 Activities outside of core studies

4.1 During time at Birkbeck

Elected President of the National Federation of Atheist, Humanist and Secular Student Societies (AHS) in July 2015 and served a 1 year term. This role involved among other things working as a part of a 3 person executive team and managing a team of volunteers. The planning and execution of national events with several 10s to several hundred attendees and reporting our activities to our board.

4.2 During time at Nottingham

Website officer of the then Secular society for 1 year, President of the University of Nottingham Agnostics, Secularists and Humanists Society (UNASH) for 2 years. During my tenure the society or its members won 4 national awards including one for raising the highest total in the country (£1200) during our charity week, and one for organising the best regional convention.
Course representative providing feedback on the experience of students to staff for 3 years, during which time I won a silver award from the education network for my contribution.

4.3 During A-levels

Elected president of the Student Association (an NUS affiliated Student’s union) at the Sixth Form College Farnborough an institution with >3000 students. During which time I lead a 12 person team who, among other things; started a network of Subject Reps to feed back to staff on student experience, broke the record for the most money raised for charity in our Raising and Giving Week, organised events with budgets of up to £30,000 and dramatically reduced the college paper use by having all printers set to duplex by default. During this time I also sat on the college’s board of governors, sharing responsibility for the oversight of the college’s major strategic decisions and ~£17M budget.
Winner of an award for outstanding contribution to college life.
Recipient of the Farnborough advanced level extend project award (analogous to the Extended Project Qualification: EPQ) for a project entitled: As advances in genomics and recombinant DNA technology become available what aspects of the human genome will be changed and when will we begin to effect these changes?
Participant in Computer Games Creation classes; creating simple games in basic.
Member of the Farnborough Debating Union, during which time I represented the college in a competition.
Royal Society of Chemistry - 43rd International Chemistry Olympiad 2011, 1st round, Bronze
Emergency First Aider at work.

4.4 Academic Society memberships

Member of the Biochemical Society
Member of the British society for research on ageing

5 Appendices

5.1 Birkbeck MSc Bioinformatics with Systems Biology - Results by Module

Code	Title	Credit (180/yr)	Mark/%
CRYS001H7	BioComputing I	15	88
CRYS002H7	Molecular Structure	15	80
CRYS003H7	Statistics	15	85
CRYS004H7	Data Management	15	83
CRYS005H7	Structural Bioinformatics	15	71
CRYS006H7	BioComputing II	15	80
CRYS007H7	Systems Biology	15	93
CRYS008H7	Sequence Analysis and Genomics	15	70
CRYS015D7	Project MSc Bioinformatics with Systems Biology	60	71

5.2 Nottingham MSci Biochemistry and Genetics - Results by Module

Code	Title	Credit (120/yr)	Semester	Mark/%
	4th Year (2014-15), 40% weighting
C14702	Cutting Edge Research Technologies and Ideas in Molecular Biology	10	Autumn	79
C14703	Advanced Experimental Design and Analysis	10	Autumn	73
C14705	Research Presentation Skills	20	Full Year	64
C14707	Project	80	Full Year	79
	4th year credit weighted average	76
	3rd Year (2013-14), 40% weighting
C13594	Gene Regulation	10	Autumn	69
C73510	Research Project BG	20	Autumn	74
C13698	Molecular Evolution: Constructing the Tree of Life	10	Spring	62
C43629	Ageing, Sex and DNA Repair	10	Spring	60
C43630	Cancer Biology	10	Spring	68
C73611	Research Project BG	20	Spring	74
C73ADB	Advanced Biochemistry	20	Full Year	59
C73B47	Biochemistry of Disease	10	Full Year	57
C73Y03	Data Analysis	10	Full Year	73
	3rd year credit weighted average	67
	2nd Year (2012-13), 20% weighting
C12341	Molecular and Developmental Neurobiology	10	Autumn	73
C12364	Genetics Dissertation II	10	Autumn	69
C12365	Medical Molecular Genetics	10	Autumn	76
C42324	Genes, Genomes and Chromosomes	10	Autumn	68
C72304	Laboratory Analysis of Proteins & Enzymes	10	Autumn	77
C72340	Proteins: Structure and Function	10	Autumn	70
C42418	Bacterial Genes and Development	10	Spring	66
C42443	Developmental Biology	10	Spring	74
C72445	Lipid Metabolism and Oxidative Phosphorylation	10	Spring	60
C72ISM	Introductory Signals and Metabolic Regulation	10	Spring	71
C72PAG	Principles and Analysis of Gene Function	20	Full Year	70
	2nd year credit weighted average	70
	1st Year (2011-12), 0% weighting
C11111	Experimental Design and Analysis 1	10	Autumn	76
C11120	Genetics, Ecology and Evolution	10	Autumn	78
C41105	Microbiology	10	Autumn	86
C71101	Cell Structure and Metabolism (L)	10	Autumn	79
C71102	Cell Structure and Metabolism (P)	10	Autumn	94
F11MSB	Molecular Structure and Bonding	10	Autumn	75
C11212	Introductory Human Physiology and Pharmacology 2	10	Spring	75
C41202	Genes and Cellular Control I (L)	10	Spring	96
C41204	Genes and Cellular Control I (P)	10	Spring	76
C71205	Fundamentals of Biochemistry	10	Spring	69
F11OMC	Reactivity of Organic Molecules and Coordination Chemistry	10	Spring	92
C11118	Biochemistry and Genetics Tutorial and Study Skills Module	10	Full Year	69
	1st year credit weighted average	80
	Weighted degree average	71

L=Lecture, P=Practical

5.3 A-level Results By module

Exam Session	Module Code	Module Description	Exam Board	UMS	Max	Grade
Biology
Jan-10	107101	BY1: BASIC BIOCHEMISTRY AND ORGANISATION	WJEC	110	120	A
Jun-10	107201	BY2: BIODIVERSITY AND PHYSIOLOGY OF BODY SYSTEMS	WJEC	120	120	A
Jun-10	107301	BY3: PRACTICAL ASSESSMENT	WJEC	36	60	C
Jan-11	107401	BY4: METABOLISM, MICROBIOLOGY AND HOMEOSTASIS	WJEC	110	120	A
Jun-11	107501	BY5: ENVIRONMENT, GENETICS AND EVOLUTION	WJEC	96	120	A
Jun-11	107601	BY6: PRACTICAL ASSESSMENT	WJEC	39	60	C
		Subject Score and Grade		511	600	A
Chemistry
Jan-10	F321	ATOMS, BONDS AND GROUPS	OCR	78	90	A
Jun-10	F322	CHAINS, ENERGY AND RESOURCES	OCR	122	150	A
Jun-10	F323	PRACTICAL SKILLS IN CHEMISTRY 1	OCR	54	60	A
Jan-11	F325	EQUILIBRIA, ENERGETICS AND ELEMENTS	OCR	114	150	B
Jun-11	F324	RINGS, POLYMERS AND ANALYSIS	OCR	61	90	C
Jun-11	F326	PRACTICAL SKILLS IN CHEMISTRY 2	OCR	51	60	A
		Subject Score and Grade		480	600	A
Economics
Jan-10	F581	MARKETS IN ACTION	OCR	92	100	A
Jun-10	F582	THE NATIONAL AND INTERNATIONAL ECONOMY	OCR	76	100	B
		Subject Score and Grade		168	200	A
General Studies
Jan-10	GENA1	CULTURE AND SOCIETY	AQA	78	100	B
Jun-10	GENA2	SCIENCE AND SOCIETY	AQA	73	100	B
Jan-11	GENA4	SCIENCE AND SOCIETY	AQA	72	100	B
Jun-11	GENA3	CULTURE AND SOCIETY	AQA	74	100	B
		Subject Score and Grade		297	400	B
Mathematics
Jan-10	MPC1	PURE CORE 1	AQA	86	100	A
Jun-10	MM1B	MECHANICS 1B	AQA	91	100	A
Jun-10	MPC2	PURE CORE 2	AQA	81	100	A
Jan-11	MPC3	PURE CORE 3	AQA	86	100	A
Jun-11	MM2B	MECHANICS 2B	AQA	61	100	C
Jun-11	MPC4	PURE CORE 4	AQA	72	100	B
		Subject Score and Grade		477	600	B
Physics
Jan-10	G491	PHYSICS IN ACTION	OCR	70	90	B
Jun-10	G492	UNDERSTANDING PROCESSES, EXPERIMENTATION AND DATA HANDLING	OCR	139	150	A
Jun-10	G493	PHYSICS IN PRACTICE	OCR	58	60	A
Jan-11	G494	RISE AND FALL OF THE CLOCKWORK UNIVERSE	OCR	54	90	C
Jun-11	G495	FIELD PARTICLE PICTURES	OCR	137	150	A
Jun-11	G496	ADVANCES IN PHYSICS	OCR	58	60	A
		Subject Score and Grade		516	600	A