I am looking for a job that allows me to pursue data analysis combined with biological interpretation of results. My academic background has allowed me to explore several very different biological fields, all of which have required handling of large datasets and have given me significant wet lab and field-work experience. I have a passion for problem solving and enjoy learning new techniques that help me develop as a data scientist.

I finished my PhD studies at the National Oceanography Centre in Southampton (NOCS), UK with the focus of my research being the characterisation of the Pleuromamma copepod gut microbiome. I had the opportunity to join several research cruises while at NOCS, including two Atlantic Meridional Transect cruises, during which I gained experience in sample collection and working at sea. I then used a variety of traditional molecular (e.g. fluorescence in situ hybridisation) and next generation sequencing techniques (e.g. 16S amplicon sequencing and analysis) to gain an understanding of this fascinating host-microbe association.

I continued my Postdoctoral research in the Department of Symbiosis at the Max Planck Institute for Marine Microbiology, in Bremen, Germany. I worked on further characterising the copepod gut microbiome and understanding the metabolic potential of the association using genomics and transcriptomics.

I am currently employed as a Bioinformatics Programmer at the Alkek Center for Metagenomics and Microbiome Research within Baylor College of Medicine, Houston, Texas. Our goal is to understand the human microbiome and its impact on health and disease.

Education and Work experience

May 2016 – Nov 2017: Postdoctoral Researcher
Department of Symbiosis, Max Planck Institute for Marine Microbiology, Bremen, Germany
Project: Further characterising the Pleuromamma copepod gut microbiome and understanding the metabolic potential of the association using genomics and transcriptomics.

Oct 2011 – May 2016: PhD Ocean & Earth Science
(title awarded Nov 2016)
National Oceanography Centre, University of Southampton, UK
Supervisory team: Mikhail Zubkov, Douglas Connelly and Duncan Purdie
Thesis title: “Microbiota of dominant copepods from the Atlantic: Pleuromamma species host betaproteobacterial symbionts

Jan 2014 – Jul 2014 & Jan 2015 – Apr 2016:
Visiting PhD researcher at the Department of Molecular Ecology, Max-Planck Institute for Marine Microbiology (Bremen), working with Bernhard Fuchs and Rudolf Amann.

Sep 2010 – Sep 2011: MSc in Marine and Fisheries Ecology (with Commendation)
University of Aberdeen, College of Life Sciences and Medicine, School of Biological Sciences
Supervisor: Stuart Piertney
Thesis title: “Population genetic structure of deep-sea grenadier (Coryphaenoides armatus Hector 1875) from the Mid- Atlantic Ridge

1 Oct 2005 – 6 July 2010: Univerzitetni diplomirani biolog (MSc equivalent, academic study programme in biology)
University of Ljubljana, Biotechnical Faculty, Department of Biology
Supervisory team: Jernej Jakse and Sebastjan Radisek
Thesis title: “Differential gene expression in hop after infection with Verticillium albo-atrum

Feb 2006-Apr 2007 & Aug 2007-Sep 2010 :
Worked as Undergraduate Researcher on different projects within the Centre for Plant Biotechnology and Breeding, Biotechnical Faculty. These included “Molecular marker in figs and olives” and “Differential gene expression in hop”.


Knap, T., Jakse, J., Cregeen, S., Javornik, B., Hladnik, M., Bandelj, D. Characterization and defining of a core set of novel microsatellite markers for use in genotyping and diversity study of Adriatic fig (Ficus carica L.) germplasm. Braz. J. Bot. (2016). doi:10.1007/s40415-016-0299-2

Cregeen, S., Radisek, S., Mandelc, S., Turk, B., Stajner, N., Jakse, J., Javornik, B. Different Gene Expressions of Resistant and Susceptible Hop Cultivars in Response to Infection with a Highly Aggressive Strain of Verticillium albo-atrum. Plant Mol. Biol. Report. (2014). doi:10.1007/s11105-014-0767-4.

Stajner, N., Cregeen, S., Javornik, B. Evaluation of Reference Genes for RT-qPCR Expression Studies in Hop (Humulus lupulus L.) during Infection with Vascular Pathogen Verticillium albo-atrum. PLoS One. 8 (7), 1-13 (e68228). (2013).

Ritchie, H., Cousins, N. J., Cregeen, S. J. & Piertney, S. B. Population genetic structure of the abyssal grenadier (Coryphaenoides armatus) around the mid-Atlantic ridge. Deep Sea Res. Part II Top. Stud. Oceanogr. 98, 431–437 (2013).

Attendance at scientific meetings

18-24 Jun 2016
GRS Marine Microbes – talk & GRC Marine Microbes – poster presentation (Changes in microflora associated with marine pelagic Pleuromamma copepods along an Atlantic Meridional Transect)

21-26 Jun 2015
GRC Animal-Micorbe Symbioses – poster presentation (Changes in microflora associated with marine pelagic Pleuromamma copepods along an Atlantic Meridional Transect)

6 -7 Nov 2013
Postgraduate Research in Marine and Earth Science 2013 at National Oceanography Centre, Southampton – talk (Do microbial communities in marine zooplankton reveal important biogeochemical processes in the water column?)

20 – 23 Sep 2009
Joint Congress Slovene Biochemical Society and Slovene Genetics Society Otocec 2009 – poster presentation (cDNA-AFLP analysis reveals differential gene expression in response to Verticillium wilt infection in hop)

20 – 23 Mar 2007
International Natural Sciences Students` Conference BioCoin 2007 in Vilnius, Lithuania – short lecture (Analysis of DNA microsatellite sequences)

Research cruises

22 Sep – 03 Nov 2014
RRS James Clark Ross JR303 (Atlantic Meridional Transect Cruise – AMT24) – Microplankton communities and copepod gut microflora

10 Oct – 24 Nov 2012
RRS James Cook JC079 (Atlantic Meridional Transect Cruise – AMT22) – Microplankton communities and copepod gut microflora

29 Apr – 12 May 2012
RRS James Cook Cruise 71 (Porcupine Abyssal Plain: sustained ocean observation) – Prokaryotic community structure


Awarded the Lindsay Laird Prize for the best student in MSc Marine and Fisheries Science course.

Graduation thesis “Differential gene expression in hop after infection with Verticillium albo-atrum” won the top student award presented by the University of Ljubljana for excellent research work.


Field work

  • Preparation for research cruises
  • Plankton collection using vertical and horizontal net tows
  • Microplankton and mesozooplankton taxonomy and sample sorting
  • Sample fixation

Molecular biology

  • Extraction of DNA and RNA
  • Polymerase Chain Reaction
  • Sanger sequencing
  • qRT-PCR
  • Fluorescence in situ hybridisation
  • Agarose and polyacrilamide gel electrophoresis
  • Preparation of media for bacterial growth
  • Gene cloning
  • Histological embedding, sectioning and staining
  • Epifluorescence and confocal microscopy
  • Preparation of samples for Stable Isotope Analysis

Data analysis

  • Sanger sequence processing
  • Phylogenetic analysis
  • Population genetics
    • Microsatellite marker development and analysis
  • Next generation sequencing
    • Quality control and read processing
    • Amplicon library analysis
    • Metagenome and metatransciptome analysis
  • Statistical analysis: uni- and multivariate statistics


  • Proficient in Linux, Mac OS and Windows environments
  • Image analysis and processing (Zeiss software, Adobe suite, ImageJ, FlowCAM)
  • R (proficient)
  • BASH (user)
  • Python (learner)