1. Matteo Ferla
Ribisvej 3, Gentofte, Denmark matteo.ferla@gmail.com 0044 7548849836
Contact Details
Links
Research Associate
July 2015 – October 2015 Institution: University of Bath
I was contracted by Prof. David Leak to analyse RNAseq data from Geobacillus thermoglucosida-
sius, set up an analysis pipeline and to teach his students. The task also involved extensive clean-
ing of poor genomic annotations. Lastly, in ordert to increase outreach of the research I built a
database website (http://www.geobacillus.com).
August 2014 – May 2015 Institution: University of Otago
I have done contracted bioinformatics jobs for two groups from my former department involv-
ing genome data mining (Dr. Alan Carne), molecular dynamics simulations and Matlab coding
(Dr. Sigurd Wilbanks) and various minor phylogenetic jobs for various researchers.
Research Scientist
November 2015 – Present Company: Biosyntia ApS
My major roles are as data analyst and as protein engineer. My tasks include extensive genome
mining, analysis of protemics and other complex large datasets (in order to devise changes to
improve the production strain), troubleshooting and optimisation of fluorescent genetic
biosensors, detailed experimental design for delegation, and scripting for Google Sheets, for
task automation and for data intregration.
Indicative Skills
▶ Exceptional understanding and insight into bacterial metabolic logic and chemistry
▶ NGS data analysis and genome data mining
▶ Phylogenetics, including ancestral sequence reconstruction
▶ Programming in Python, JavaScript and Perl
▶ MatLab, R, MS Office, Photoshop, Illustrator and Dreamweaver
▶ Web depelopment both serverside and clientside
▶ Familiarity with Unix environment and cluster computing
▶ General molecular biology wetlab skills
▶ Optimisation of protein expression and purification
▶ Biochemical analytical methods
▶ Enzyme mutagenesis
▶ E. coli genome manipulation (incl. MAGE)
GitHub https://github.com/matteoferla
A multitude of projects I have written throughout the years.
Science blog http://blog.matteoferla.com
My thought, analyses and findings about synthetic biology and biochemistry.
Homepage http://www.matteoferla.com
Links to several resources written by me.

2. MBiol (Hons) in Molecular Biology
Sept. 2004–July 2008 Mark: First class Institution: University of Bath
This was a combined Bachelors and Masters degree with a one-year internship.
Placement supervisor: Dr. Craig Tomlinson, Microarray Core, Dartmouth College (USA)
Role: I worked with mammalian cell lines, RNA, radioactivity and DNA hybridisations in
order to develop a technique to measure whole genome transcription rates.
Thesis supervisor: Dr. Matthew Wills, Department of Biology & Biochemistry, University of
Bath
Thesis: The phylogeny of the Malacostraca.
This resulted in a middle-author paper and the Oxford University Press prize in bioscience (Uni-
versity of Bath), 2008 award for best thesis in class.
Additional Research Experience
Sept. 2008–Dec. 2009 Supervisor: Prof. John Pickup Institution: King’s College London
I expressed, purified, fluorescently labelled and assayed glucose-binding protein mutants. I also
functionalised the ends of fibre optic cables with PEG hydrogels. This resulted in a middle-au-
thor paper.
PhD in Biochemistry
Febuary 2010 – August 2014 Institution: University of Otago
Supervisor: Dr. Wayne M. Patrick
Thesis: Catalytic multitasking in MetC: one enzyme, multiple reactions
(https://otago.ourarchive.ac.nz/handle/10523/4911)
Main project: I combined enzymology, bioinformatics and phylogenetics in order to identify and
investigate a set of multifunctional enzymes.
Side projects:
▶ Investigation of the phylogenetics of the Alphaproteobacteria.
▶ Collection of phylogenetic data for a paper in collaboration with Dr. Monica Gerth.
▶ Gaining an in-depth knowledge of microbial metabolism in order to investigate the
metabolism of certain species.
Ferla M.P., Mutanalyst, an online tool for assessing the mutational spectrum of epPCR
libraries with poor sampling. BMC bioinformatics, 2016, (17)152 (DOI:
10.1186/s12859-016-0996-7)
Details: Single author paper describing an online tool I developed indepedently:
http://www.mutanalyst.com. Journal impact factor: 2.6.
Ferla M.P., Patrick W.M., Bacterial methionine biosynthesis. Microbiology, 2014
160(8):1571–84. (DOI: 10.1099/mic.0.077826-0)
Details: A review of the litterature along with genome analyses in order to determine
pathway distribution. Accepted with no revisions. Cited twice. Journal impact
factor: 2.8.
Ferla M.P., Thrash J.C., Giovannoni S.J., Patrick W.M., New rRNA gene-based phylogenies of
the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and
phylogenetic instability. PLoSOne, 2013, 8(12):e83383. (DOI: 10.1371/journal.pone.0083383)
Details: The result of a collaboration with Prof. Giovannoni that I spearheaded. Several
different analyses were used to exclude the possibility of AT-richness driven
bias. Cited ten times, including by the latest edition of The Prokaryotes. Journal
impact factor: 3.5.
Publications

3. Gerth M.L., Ferla M.P., Rainey P.B., The origin and ecological significance of multiple
branches for histidine utilization in Pseudomonas aeruginosa PAO1. Environ Microbiol. 2012,
14(8): 1929–40. (DOI: 10.1111/j.1462-2920.2011.02691.x)
Details: I performed the phylogenetic analyses to infer the evolutionary history of the
different branches of the pathway. Cited twice. Journal impact factor: 6.2.
Saxl T., Khan F., Ferla M.P., Birch D., Pickup J., A fluorescence lifetime-based fibre-optic
glucose sensor using glucose/galactose-binding protein. Analyst. 2011, 136(5): 968–72. (DOI:
10.1039/c0an00430h)
Details: I purified protein and performed chemical derivatisation. Cited 21 times.
Journal impact factor: 3.9.
Jenner, R.A., Nidhubhghaill, C., Ferla, M.P., Wills, M.A., Eumalacostracan phylogeny and
total evidence: limitations of the usual suspects. BMC Evol Biol, 2009, 9(1):21. (DOI:
10.1186/1471-2148-9-21)
Details: Some of the datasets and the resulting trees from my undergraduate thesis were
used in the paper. Cited 34 times. Journal impact factor: 3.4.
Publications (cont’d)
Ferla M.P., Hall K.R., Yosaatmadja Y., Comer N., Squire C., Patrick W.M., Phyloenzymology
uncovers primordial-like enzymes in bacteria with streamlined genomes.
Planned journal: Mol. Biol. Evol.
Details: This manuscript requires a prior lab paper to be submitted. It is based on my
main PhD project.
Ha M., Ferla M.P., McConnell M.A, Bekhit A.E.A., Carne A., In-depth characterization
of ruminant milk whey proteomes from biological and evolutionary
perspectives. Planned journal: Journal of proteomics
Details: I performed the data analysis comparison of the tissue-specific proteomes of the
three species investigated.
Future publications
Gronenberg L., Salomonsen B., Ferla M.P., Genee H.J., A genetically modified bacterial cell
factory for thiamine production, 2015, EU patent (15201200.1)
Patent
Oral presentations
Catalytic multitasking in MetC: one enzyme, multiple reactions. departmental seminar,
Department of Biochemistry. University of Otago, 2014.
MetC: A multitasking enzyme in three bacteria with streamlined genomes. Queenstown
Molecular Biology Meeting, Enzyme Evolution and Engineering Session, 2013.
The rise and fall of enzyme activities. Otago School Medical Sciences Postgraduate Symposium,
University of Otago, 2013.
Promiscuity, minimalism and redundancy. Institute of Natural Sciences Postgraduate
Symposium, Massey University (Auckland), 2012.

4. Dr. Wayne Patrick
Senior lecturer and PhD supervisor
Department of Biochemistry, University of Otago, Dunedin, NZ
wayne.patrick@otago.ac.nz
+64 3 479-7897
Prof. Kurt Krause
Head of Department during my PhD and thesis committee member
Department of Biochemistry, University of Otago, Dunedin, NZ
kurt.krause@otago.ac.nz
+64 3 479-5166
Dr. Monica Gerth
Research fellow and collaborator
Department of Biochemistry, University of Otago, Dunedin, NZ
monica.gerth@otago.ac.nz
+64 3 479-7836
Referees
Posters
Ferla M.P. and Patrick W.M. The rise and fall of enzyme activities. Presented at both Society
for Molecular Biology and Evolution Meeting 2012 (Dublin) and Gordon Research Conference
Biocatalysis 2012 (Rhode Island).
Ferla M.P. and Patrick W.M. Searching for prokaryotic amino acid sequences with too many
tandem repeats. NZ Structural Biology Meeting 2010 (Waiheke island, NZ).
Services
▶ Reviewer for the African Journal of Biotechnology and Nucleic Acid Research.
▶ Coordinator for the social club of University of Otago Deparment of Biochemistry for
two years (fortnightly event organisation, financial accounting, publicity etc.)