Scientific position

PhD or postdoctoral position in computational mass spectrometry

Group
Tomáš Pluskal Group
Biochemistry of Plant Specialized Metabolites

Job description

Our lab combines cutting-edge experimental (e.g., LC-MS, metabolomics, RNA-seq) and computational (e.g., bioinformatics, molecular networking, machine learning) approaches to develop rapid, generally applicable workflows for the discovery and utilization of bioactive molecules derived from plants. We are looking for talented and motivated computational researchers to join our team.

The successful candidate for this position will be developing the next generation of the MZmine platform for mass spectrometry data processing in metabolomics. Among other things, we are aiming to add full support for ion mobility spectroscopy (IMS) to MZmine, and to enhance its molecular networking capabilities.

The IOCB is one of the leading research institutes in central Europe with a vibrant international environment and excellent equipment and core facilities located in modern buildings close to the Prague city center.

References

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
T. Pluskal
S. Castillo
A. Villar-Briones
M. Orešič
BMC Bioinformatics 11: 395 (2010)
Metabolomics Data Analysis Using MZmine
T. Pluskal
A. Korf
A. Smirnov
R. Schmid
T. R. Fallon
X. Du
J. Weng
Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide (Robert Winkler Ed.), New Developments in Mass Spectrometry Series, 232 - 254, Royal Society of Chemistry (2020)
Feature-based molecular networking in the GNPS analysis environment
L. Nothias
D. Petras
R. Schmid
K. Dührkop
J. Rainer
A. Sarvepalli
I. Protsyuk
M. Ernst
H. Tsugawa
M. Fleischauer
F. Aicheler
A. A. Aksenov
O. Alka
P. Allard
A. Barsch
X. Cachet
A. M. Caraballo-Rodriguez
R. R. D. Silva
T. Dang
N. Garg
J. M. Gauglitz
A. Gurevich
G. Isaac
A. K. Jarmusch
Z. Kameník
K. B. Kang
N. Kessler
I. Koester
A. Korf
A. L. Gouellec
M. Ludwig
C. M. Martin
L. Mccall
J. Mcsayles
S. W. Meyer
H. Mohimani
M. Morsy
O. Moyne
S. Neumann
H. Neuweger
N. H. Nguyen
M. Nothias-Esposito
J. Paolini
V. V. Phelan
T. Pluskal
R. A. Quinn
S. Rogers
B. Shrestha
A. Tripathi
J. J. J. V. D. Hooft
F. Vargas
K. C. Weldon
M. Witting
H. Yang
Z. Zhang
F. Zubeil
O. Kohlbacher
S. Böcker
T. Alexandrov
N. Bandeira
M. Wang
P. C. Dorrestein
Nature Methods 17 (2020)

Requirements

  • MSc or PhD degree in the field of computer science, bioinformatics, or machine learning
  • Experience with Java programming
  • Good proficiency in spoken and written English
  • Passion for basic research and science

We offer

  • Competitive salary
  • Five weeks of vacation
  • Health insurance and full benefits package incl. contribution to pension, culture, and sport; lunch subsidy

How to apply

Please email your CV, a cover letter, and contact details of 2-3 references to Dr. Tomáš Pluskal.

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