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Sarah Pohl
My (research) interests are data analysis in Python and R with a focus on next generation sequencing data of bacteria; testing genome graph software for our bacterial samples; genotype-phenotype correlation using different tools; and database and website management.
I also compared data analysis programming approaches in Python and R for fun, and enjoy doing online courses to learn something new. In 2022, I’ve also started teaching others basic coding and data science skills as an Instructor and Maintainer with The Carpentries. I enjoy creative writing and proof reading in German and English, and I play the trombone when I can.
Despite working in bioinformatics/data science for several years now, I still use Windows-based systems (it’s what you get at my workplace), so I do know Microsoft Office tools and how to use Python and R on Windows machines (I curse Anaconda a lot of the time). Bigger data analysis takes place on our Ubuntu servers, though, and I know a little admin there as well.
Research Experience
PostDoc, Data Scientist
Twincore Centre for Experimental and Clinical Infection Research
Hannover, Germany
Nov 2016 - Present
Management and further development of the BACTOME database and support in data analysis and visualisation in the group Molecular Bacteriology of Prof. Dr. Susanne Häussler.
PhD Student, Data Science
Helmholtz Centre for Infection Research
Hannover, Germany
Sep 2012 - Nov 2016
PhD thesis on the ‘Transcriptional Profiling of Clinical Pseudomonas aeruginosa Isolates’ and support in data analysis and visualisation in the group Molecular Bacteriology of Prof. Dr. Susanne Häussler.
Research Assistant
Technical University Braunschweig
Braunschweig, Germany
Oct 2010 - Mar 2011
Manual curation of the plant-pathogen interaction database Pathoplant at the Institute of Genetics, in the Plant Genetics group of Prof. Dr. Reinhard Hehl.
Industry Experience
Sales & Marketing Assistant
geneXplain GmbH
Wolfenbüttel, Germany
Apr 2011 - Jul 2012
Management of social media accounts, customer acquisition and support, creation of advertising materials.
Gap Year
BUND Friends of the Earth
Braunschweig, Germany
Nov 2004 - Aug 2005
Office-related tasks, organisation of weekly biotope protection activities, establishment of a youth group.
Education
Dr. rer. nat.
Hannover Medical School
Hannover, Germany
Sep 2012 - Nov 2016
PhD thesis written at the Institute for Molecular Bacteriology, Twincore
Title: Transcriptional Profiling of Clinical Pseudomonas aeruginosa Isolates
Description: This cumulative thesis explores the transcriptomic landscape of 150 clinical
Pseudomonas aeruginosa isolates by applying a next-generation sequencing (RNA-Seq) approach.
Advisor: Prof. Dr. Susanne Häussler
M.Sc.
Technical University Braunschweig
Braunschweig, Germany
Oct 2008 - Oct 2010
Thesis written at the Institute for Genetics (Plant Genetics), Faculty of Life Sciences
Title: Functional Analysis of Two Receptor Kinases Up-Regulated by Fungal and Bacterial Pathogens
Description: This thesis analysed the influence of two potential resistance genes of Arabidopsis
thaliana in resistance to infections with bacterial and fungal pathogens by using knock-out
mutants and multiplex PCR.
Advisor: Prof. Dr. Reinhard Hehl
B.Sc.
Technical University Braunschweig
Braunschweig, Germany
Oct 2005 - Sep 2008
Thesis written at the Institute for Zoology (Cellular Neurobiology), Faculty of Life Sciences
Title: Konstruktion von miRNA-basierenden Vektorsystemen zum simultanen ‘Knock down’ der
Profilinisoformen 1 und 2 in primären Hühnerfibroblasten
Description: In this thesis a microRNA based vector system to knock down two profilin isoforms
was constructed.
Advisor: Dr. Martin Rothkegel
Other Education and Experience
I completed a number of online courses as well (I got into programming thanks to Codecademy’s Code Year 2012 in the first place): mostly on Codecademy (basic coding) and coursera (data science and management).
The Carpentries Instructor Training
The Carpentries
online
Jul 2021 - Apr 2022
qualified as Carpentries Instructor to teach official Software/Data/Library Carpentries workshops
CPANG19 participant
Instituto Gulbenkian de Ciência (IGC)
Oeiras, Portugal
Sep 2019
Practical course on Computational PANgenomics, taught by Erik Garrison and Mikko Rautiainen
Introduction to SQL participant
Leibnitz Universität IT Services
Hannover, Germany
Jul 2017
Practical introductory course to SQL using PostgreSQL, taught by Anja Aue
R User Group organiser
Twincore/Hannover Medical School
Hannover, Germany
2015 - 2016
Organiser of an R user group (R-Club) with weekly meetings and an introductory R course, together with Dr. Peter Braubach
EMBO practical course participant
European Bioinformatics Institute
Hinxton, UK
Jul 2014
Practical course on genotype to phenotype mapping of complex traits, organised by Laura Emery, Oliver Stegle, and Christoph Lippert
Publications
Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype
npj Biofilms and Microbiomes, 6 (1), 2, 10.1038/s41522-019-0113-6
N/A
2020
Janne G. Thöming, Jürgen Tomasch, Matthias Preusse, Michal Koska, Nora Grahl, Sarah Pohl, Sven D. Willger, Volkhard Kaever, Mathias Müsken, Susanne Häussler
The Core Proteome of Biofilm-Grown Clinical Pseudomonas aeruginosa Isolates
Cells, 8 (10), 1129, 10.3390/cells8101129
N/A
2019
Jelena Erdmann, Janne G. Thöming, Sarah Pohl, Andreas Pich, Christof Lenz, Susanne Häussler
BACTOME—a reference database to explore the sequence- and gene expression-variation landscape of Pseudomonas aeruginosa clinical isolates
Nucleic Acids Research, 47 (D1), D716–D720, 10.1093/nar/gky895
N/A
2019
Klaus Hornischer, Ariane Khaledi, Sarah Pohl, Monika Schniederjans, Lorena Pezoldt, Fiordiligie Casilag, Uthayakumar Muthukumarasamy, Sebastian Bruchmann, Janne Thöming, Adrian Kordes, Susanne Häussler
Transcriptome Profiling of Antimicrobial Resistance in Pseudomonas aeruginosa
Antimicrobial Agents and Chemotherapy, 60 (8), 4722–4733, 10.1128/AAC.00075-16
N/A
2016
Ariane Khaledi, Monika Schniederjans, Sarah Pohl, Roman Rainer, Ulrich Bodenhofer, Boyang Xia, Frank Klawonn, Sebastian Bruchmann, Matthias Preusse, Denitsa Eckweiler, Andreas Dötsch, Susanne Häussler
Unravelling post-transcriptional PrmC-dependent regulatory mechanisms in Pseudomonas aeruginosa
Environmental Microbiology, 18 (10), 3583–3592, 10.1111/1462-2920.13435
N/A
2016
Jonas Krueger, Sarah Pohl, Matthias Preusse, Adrian Kordes, Nils Rugen, Monika Schniederjans, Andreas Pich, Susanne Häussler
Deep transcriptome profiling of clinical K lebsiella pneumoniae isolates reveals strain and sequence type-specific adaptation
Environmental Microbiology, 17 (11), 4690–4710, 10.1111/1462-2920.13016
N/A
2015
Sebastian Bruchmann, Uthayakumar Muthukumarasamy, Sarah Pohl, Matthias Preusse, Agata Bielecka, Tanja Nicolai, Isabell Hamann, Roger Hillert, Axel Kola, Petra Gastmeier, Denitsa Eckweiler, Susanne Häussler
The Pseudomonas aeruginosa Transcriptional Landscape Is Shaped by Environmental Heterogeneity and Genetic Variation
mBio, 6 (4), e00749, 10.1128/mBio.00749-15
N/A
2015
Andreas Dötsch, Monika Schniederjans, Ariane Khaledi, Klaus Hornischer, Sebastian Schulz, Agata Bielecka, Denitsa Eckweiler, Sarah Pohl, Susanne Häussler
The extensive set of accessory Pseudomonas aeruginosa genomic components
FEMS Microbiology Letters, 356 (2), 235–241, 10.1111/1574-6968.12445
N/A
2014
Sarah Pohl, Jens Klockgether, Denitsa Eckweiler, Ariane Khaledi, Monika Schniederjans, Philippe Chouvarine, Burkhard Tümmler, Susanne Häussler
In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles.
mBio, 5 (4), e01075–14, 10.1128/mBio.01075-14
N/A
2014
Piotr Bielecki, Uthayakumar Muthukumarasamy, Denitsa Eckweiler, Agata Bielecka, Sarah Pohl, Ansgar Schanz, Ute Niemeyer, Tonio Oumeraci, Nils von Neuhoff, Jean-Marc Ghigo, Susanne Häussler