Anschrift

Systems Biology and Mathematical Modeling

Dr. Georg Basler

Am Mühlenberg 1

14476 Potsdam

Germany

Dr. Georg Basler

Dr. Georg Basler

Dr. Georg Basler

Position:

Wissenschaftlicher Mitarbeiter

E-Mail:

Vita


Education & Employment

2015.07.16 – 2017.01.16

Postdoctoral researcher with a fellowship grant by the Max Kade Foundation and German Research Foundation (DFG)

University of California, Berkeley, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory

Supervisors: Jay Keasling, Danielle Tullman-Ercek

2013.06.01. – 2015.05.31

Postdoctoral researcher with a Marie Curie Intra-European Fellowship for Career Development (FP7-MC-IEF 2012, 329682) funded by the European Research Council

Estación Experimental del Zaidín (CSIC), Granada, Spain

Supervisors: Tino Krell, Juan Luis Ramos, Ana Segura

2013.06.17. – 2013.07.17

Research stay at the Center for Complex Network Research, Northeastern University, Boston

Supervisors: Albert-László Barabási, Yang-Yu Liu

2013.01.28 – 2013.03.27

Postdoctoral researcher with a Short-Term Fellowship by the Federation of European Biochemical Societies, Estación Experimental del Zaidín (CSIC), Granada, Spain

Supervisors: Juan Luis Ramos, Ana Segura

2012.10.11

PhD (“Dr. rer. nat.”) in Bioinformatics

Faculty of Science of the University of Potsdam, Germany

Thesis: “Mass-balanced randomization – a significance measure for metabolic networks”

Grade: magna cum laude

2008.06.12 – 2011.12.31

PhD student, University of Potsdam, Germany

International Max Planck Research School (IMPRS)

Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany

2007.12.01 – 2011.12.31

Software programmer, GoFORSYS project, University of Potsdam, Germany

2007.02.15 – 2007.11.30

Student assistant, Bioinformatics group,

Max Planck Institute for Molecular Plant Physiology

2000.10.01 – 2007.11.07

MSc Computer Science (“Diplom Informatik”)

Master’s thesis title: “Probenerfassung und Klassifikation von Massenspektren in der Metabolitanalyse“ (Eng.: „Sample acquisition and classification of mass spectra in metabolite profiling“)

Grade: excellent (“sehr gut”). Secondary graduate studies: Biology

Humboldt University of Berlin, Germany

Supervisors: Ulf Leser, Joachim Selbig

2004.04.01 – 2007.02.15

Software developer at Daimler AG (formerly DaimlerChrysler AG), Research & Technology, Berlin, Germany

Java development of a GUI-based classification tree editor (CTE XL/Testona) for the design of systematic tests

2002.09.01 – 2003.07.15

Exchange student within the Erasmus Programme of the European Commission
Escuela Técnica Superior de Informática, University of Granada, Spain

2000.01.10 – 2007.08.15

Software developer at IVU Traffic Technologies AG, Berlin, Germany

Main research interests

  • Computational Biology

  • Algorithm development

  • Metabolic Modelling

  • Plant-microbe interactions

  • Metabolic Engineering

  • Systems Biology

  • Retrosynthesis

  • Synthetic Biology

  • Network Analysis

Computational and modeling skills

  • Application and implementation of constraint-based approaches:
    Flux Balance Analysis, Flux Coupling Analysis, Flux Variability Analysis, Minimization of Metabolic Adjustment, Regulatory On/Off Minimization

  • Development of constraint-based approaches:
    Essential Reactions, Anti-Coupling, Inhibitive Coupling, Driver Reactions (see Basler et al. Genome Research 2016, 26(7):956-968), Modeling of Metabolic Engineering via Stoichiometric Capacitance (see Larhlimi, Basler et al. Bioinformatics 2012, 28(18): i502-i508)

  • Genome-scale metabolic network analysis (E. coli, P. putida, A. thaliana, S. cerevisiae, H. sapiens, and others)

  • Network analysis: graph theory, algorithms, randomization

  • Data integration: KEGG, Swiss-Prot/UniProt, BioCyc/MetaCyc, RegulonDB

  • Java software development (Classification Tree Editor, CTE XL/Testona)

  • Statistical Modeling of Metabolism

  • Graph theory, Complexity theory

Experimental skills

  • Lambda red based genome editing in E. coli

  • Genetic Engineering in E. coli and P. putida

  • Golden Gate Cloning

  • Gibson Assembly

  • Flow Cytometry

  • Fluorescence microscopy

  • Protein extraction and quantification

Programming languages

Java, Matlab, Tomlab, C#, C, C++, R, XML, SQL, PL/SQL (Oracle)

Specialized courses

  • Biosystems Engineering: Bioreactors and Cell Factories (2014). Braunwald, Switzerland. Course directors: Elmar Heinzle, Saarland University, Germany, Matthias Reuss, University of Stuttgart, Germany, Christoph Wittmann, Saarland University, Germany, Athanasios Mantalaris, Imperial College London, United Kingdom (36 hours)

  • Intensive College Level Teaching Course (2015), Postdoc Teaching Opportunities Program, University of California, Berkeley. Course director: Natalia Caporale (13 hours)

  • Essential Molecular Biology – A hands on laboratory course (2015). Faculty of Medicine, University of Porto, Portugal. Course director: Carlos Reguenga (80 hours)

  • Intellectual Property Rights for Marie Curie Fellows (2013). Course director: Raimund Lutz (Vice President), European Patent Office, Munich, Germany (12 hours)

  • Junior Principal Investigator (2013), 12th European Conference on Computational Biology, Berlin, Germany, Course director: Jeroen de Ridder (8 hours)

  • Grant Proposal Writing (2011), Potsdam Graduate School, Potsdam, Germany, Course director: Iris Löhrmann (12 hours)

  • Networks – Theory and Practice in Biology (2008). 7th European Conference on Computational Biology, Cagliari, Italy. Course director: Sven Bergmann (6 hours)

Research collaborations

  • Jay Keasling, Hubbard Howe Jr. Distinguished Professor of Biochemical Engineering, University of California, Berkeley, USA

  • Danielle Tullman-Ercek, Associate Professor of Chemical and Biological Engineering, Northwestern University, Evanston, USA.

  • Hector García Martín, Director of Quantitative Metabolic Modeling, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, USA.

  • Albert-László Barabási, Distinguished University Professor and Director, Center for Complex Network Research, Northeastern University, Boston, USA.

  • Yang-Yu Liu, Assistant Professor, Harvard Medical School, Boston, USA.

  • Alisdair Fernie, Research Group Leader, Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany.

  • Abdelhalim Larhlimi, Associate Professor, Université de Nantes, France.

Languages

  • German (mother tongue)

  • English (proficient, C2/UNIcert IV in Academic Writing)

  • Spanish (proficient)

  • French (good)

PhD thesis

“Mass-balanced randomization – a significance measure for metabolic networks” (2012)

Universitätsbibliothek, Universität Potsdam, Germany

https://publishup.uni-potsdam.de/frontdoor/index/index/docId/5984

Book chapter

Georg Basler (2015). Computational prediction of essential metabolic genes using constraint-based approaches. L. J. Lu (Ed.), Gene Essentiality: Methods in Molecular Biology Vol. 1279 (pp. 183–204). New York; Springer. DOI:10.1007/978-1-4939-2398-4_12.

Peer-reviewed publications

  1. Jeanne M. O. Eloundou-Mbebi, Nooshin Omranian, Sabrina Kleessen, Jost Neigenfind, Georg Basler, Zoran Nikoloski (2016). A network property necessary for concentration robustness. Nature Communications 7, 13255. DOI:10.1038/ncomms13255.

  2. Georg Basler, Zoran Nikoloski, Abdelhalim Larhlimi, Albert-László Barabási, Yang-Yu Liu (2016) Control of fluxes in metabolic networks. Genome Research 26(7):956-968 (cover article). DOI:10.1101/gr.202648.115.

  3. Georg Basler, Anika Küken, Alisdair R. Fernie, Zoran Nikoloski (2016) Photorespiratory bypasses lead to increased growth in Arabidopsis thaliana: Are predictions consistent with experimental evidence? Frontiers in Bioengineering and Biotechnology 4:31. DOI:10.3389/fbioe.2016.00031.

  4. Nooshin Omranian, Sabrina Kleessen, Takayuki Tohge, Sebastian Klie, Georg Basler, Bernd Mueller-Roeber, Alisdair R. Fernie, Zoran Nikoloski (2015) Differential metabolic and coexpression networks of plant metabolism. Trends in Plant Science 20(5):266-268. DOI:10.1016/j.tplants.2015.02.002.

  5. Georg Basler, Evangelos Simeonidis (2015) Integrating food webs with metabolic networks: modeling contaminant degradation in marine ecosystems. Frontiers in Genetics 6:20. DOI:10.3389/fgene.2015.00020.

  6. Oriol Güell, Francesc Sagués, Georg Basler, Zoran Nikoloski, M. Ángeles Serrano (2012) Assessing the significance of knockout cascades in metabolic networks. Journal of Computational Interdisciplinary Science 3(1-2):45-53. DOI:10.6062/jcis.2012.03.01.0050.

  7. Abdelhalim Larhlimi, Georg Basler, Sergio Grimbs, Joachim Selbig, Zoran Nikoloski (2012) Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. Bioinformatics 28(18): i502-i508. DOI:10.1093/bioinformatics/bts381.

  8. Georg Basler, Sergio Grimbs, Zoran Nikoloski (2012) Optimizing metabolic pathways by screening for feasible synthetic reactions. Biosystems 109(2):186-191. DOI:10.1016/j.biosystems.2012.04.007.

  9. Georg Basler, Sergio Grimbs, Oliver Ebenhöh, Joachim Selbig, Zoran Nikoloski (2012) Evolutionary significance of metabolic network properties. Journal of the Royal Society Interface 9(71):1168-1176. DOI:10.1098/rsif.2011.0652.

  10. Georg Basler, Zoran Nikoloski (2011) JMassBalance: mass-balanced randomization and analysis of metabolic networks. Bioinformatics 27(19):2761-2762. DOI:10.1093/bioinformatics/btr448.

  11. Georg Basler, Oliver Ebenhöh, Joachim Selbig, Zoran Nikoloski (2011) Mass-balanced randomization of metabolic networks. Bioinformatics 27(10):1397-1403. DOI:10.1093/bioinformatics/btr145.

  12. Georg Basler, Sergio Grimbs, Joachim Selbig, Zoran Nikoloski (2010) Thermodynamic landscapes of randomized large-scale metabolic networks. In Proceedings of the 7th International Workshop on Computational Systems Biology (WCSB 2010). Tampere, Finland. Tampere International Center for Signal Processing. http://www.cs.tut.fi/wcsb10/proc_of_wcsb10.pdf.

  13. Georg Basler, Zoran Nikoloski, Oliver Ebenhöh, Thomas Handorf (2008) Biosynthetic potentials from species-specific metabolic networks. Genome Informatics 20:135-148. DOI:10.11234/gi1990.20.135.

  14. Karin I. Köhl, Georg Basler, Alexander Lüdemann, Joachim Selbig, Dirk Walther (2008) A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research. Plant Methods 2008, 4:11. DOI:10.1186/1746-4811-4-11.

Selected conference presentations

  • Peer-reviewed oral presentation: Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. 11th European Conference on Computational Biology (ECCB 2012). Basel, Switzerland, September 2012.

  • Invited presentation: Randomization of metabolic networks – a measure of evolutionary significance. BIT’s 2nd World DNA and Genome Day. Dalian, China, April 2011.

  • Invited presentation: Identifikation von signifikanten Grapheigenschaften in Stoffwechselnetzwerken (Eng.: “Identification of significant graph properties in metabolic networks”). Treffpunkt Bioinformatik. Berlin, Germany, September 2009.

  • Invited presentation: Functional evaluation of topological metabolic network properties. 11th International Conference on Molecular Systems Biology (ICMSB 2009). Shanghai, China, June 2009.

Award

Best Poster: Thermodynamic landscapes of randomized large-scale metabolic networks. 7th International Workshop on Computational Systems Biology (WCSB 2010) Luxembourg, Luxembourg, June 2010.

Independent third party funding

  • Max Kade Postdoctoral Research Grant. Max Kade Foundation and German Science Foundation (DFG) (July 2015-January 2017)

  • Estancias de Movilidad “José Castillejo” (CAS14/00348). Ministry of Education, Culture and Sports, Spain  (November 2014-April 2015)

  • Marie Curie Intra-European Fellowship for Career Development (PSEUDOMODEL 329682), 7th Framework Programme, European Commission (June 2013-May 2015)

  • FEBS Short-term fellowship. Federation of European Biochemical Societies (January-March 2013)

  • 11th European Conference on Computational Biology (ECCB 2012) Conference Fellowship, University of Basel (September 2012).

Participation in research projects

  • GoFORSYS: FORSYS Research Units for Systems Biology (2010-2011), University of Potsdam, Germany

  • Construcción de biosensores de nueva generación para detectar hidrocarburos aromáticos (EXPLORA BIO2011- 14589-E, 2012-2014), Estación Experimental del Zaidín, Spain

  • Comprensión de los mecanismos de traducción de señal que determinan la formación y dispersión de biofilm en bacterias (CVI-7335), Estación Experimental del Zaidín, Spain

Teaching

Tutorial for “Introduction to theoretical systems biology” (2009), University of Potsdam, Germany (28 hours)

Membership in scientific organizations

  • Marie Curie Alumni Association, Brussels, Belgium

  • International Society for Computational Biology, San Diego, USA

  • New York Academy of Sciences, New York, USA

Professional activities

Organisationseinheit (Abteilung, Gruppe, Einrichtung):

  • Abteilung 1 (Willmitzer)
  • PostDoc
  • Systems Biology and Mathematical Modelling

Weitere Informationen


 
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