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Ph.D positions Systems medicine of the liver

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A novel systems medicine network
Systems medicine of the liver
About five million individuals are affected by liver diseases in Germany, and the causes of these diseases often remain unknown. The Federal Ministry of Education and Research (BMBF) has recently funded a research network entitled ‘Systems Medicine of the Liver’ aimed at better understanding the etiology and progression of liver disease. Within this project, the PhD positions described below are available at the IFADO (Leibniz Research Centre) in Dortmund, Germany: http://www.ifado.de/toxikologie/. The successful candidates will work within an interdisciplinary network of molecular biologists, bioinformaticians, systems biologists and physicians. We are looking for highly motivated PhD candidates who are aiming for as successful career in science. The PhD students will be integrated into an international and successful research network. 

Example of publications with IFADO contributions:
Ghallab A, Cellière G, Henkel SG, Driesch D, Hoehme S, Hofmann U, Zellmer S, Godoy P, Sachinidis A, Blaszkewicz M, Reif R, Marchan R, Kuepfer L, Häussinger D, Drasdo D, Gebhardt R, Hengstler JG. Model-guided identification of a therapeutic strategy to reduce hyperammonemia in liver diseases. J Hepatol. 2016 Apr;64(4):860-71.
Godoy P, Schmidt-Heck W, Natarajan K, Lucendo-Villarin B, Szkolnicka D, Asplund A, Björquist P, Widera A, Stöber R, Campos G, Hammad S, Sachinidis A, Chaudhari U, Damm G, Weiss TS, Nüssler A, Synnergren J, Edlund K, Küppers-Munther B, Hay DC, Hengstler JG. Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells. J Hepatol. 2015 Oct;63(4):934-42.
Hoehme S, Brulport M, Bauer A, Bedawy E, Schormann W, Hermes M, Puppe V, Gebhardt R, Zellmer S, Schwarz M, Bockamp E, Timmel T, Hengstler JG, Drasdo D. Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10371-6.
Stewart JD, Marchan R, Lesjak MS, Lambert J, Hergenroeder R, Ellis JK, Lau CH, Keun HC, Schmitz G, Schiller J, Eibisch M, Hedberg C, Waldmann H, Lausch E, Tanner B, Sehouli J, Sagemueller J, Staude H, Steiner E, Hengstler JG. Choline-releasing lycerophosphodiesterase EDI3 drives tumor cell migration and metastasis. Proc Natl Acad Sci U S A. 2012 May 22;109(21):8155-60.
Vartak N, Damle-Vartak A, Richter B, Dirsch O, Dahmen U, Hammad S, Hengstler JG.Cholestasis-induced adaptive remodeling of interlobular bile ducts. Hepatology. 2016 Mar;63(3):951-64.
Zeigerer A, Gilleron J, Bogorad RL, Marsico G, Nonaka H, Seifert S, Epstein-Barash H, Kuchimanchi S, Peng CG, Ruda VM, Del Conte-Zerial P, Hengstler JG, Kalaidzidis Y, Koteliansky V, Zerial M. Rab5 is necessary for the biogenesis of the endolysosomal system in vivo. Nature. 2012 May 23;485(7399):465-70.
 
Our institute offers excellent research conditions, including well-equipped cell and molecular biology labs, confocal and two-photon based microscopy, flow cytometry facility, genome wide analyses, and a mouse facility with different reporter strains of liver cell types. Please send your applications to the project leaders, whose e-mail address is given after the descriptions of the individual PhD projects. Positions 1-3 are specifically for experimentalists with a background in cell or molecular biology, biochemistry, pharmacy or related fields. Positions 4-6 require a background in the theoretical sciences, such as computer science, bioinformatics, physics, engineering or related fields who will work closely together with a team of cell and molecular biologists and imaging experts at IFADO.
 
Ph.D positions
Position 1
The proposed study will focus on the small GTPase, Rab18, the activation of which is critical for lipid droplet formation. The goal is to develop a model that simulates the number, size and kinetics of lipid droplet formation as a function of Rab18 activity and localization. Intravital 2-photon fluorescence imaging of mouse livers and in vitro fluorescence imaging of hepatocytes will be used to study the relevance of Rab18 activation to the onset and progression of steatosis/steatohepatitis. The project entails work on different mouse models, in addition to in vivo and in vitro transfection and imaging expertise. Therefore, the successful candidate must be willing to work with animals. Experience with basic molecular biology- PCR, cloning and fluorescence imaging techniques is desirable. Due to the emphasis on in silico modeling and image processing, candidates with or willing to develop coding, image processing and quantification skills in MATLAB/Python/C/Java/ImageJ will be preferred. The successful candidate will be part of an international consortium of scientists and medical professionals working on liver diseases.
For further information contact: Dr. Nachiket Vartak (email: nash@ifado.de, Tel: +49-231-1084355).

Position 2
This study investigates the role of the glycerophosphodiesterase, GPCPD1 (EDI3, GDE5) in tumour development and progression in vivo. GPCPD1 has been shown to be relevant in lipid and choline metabolism, as well as cell adhesion and migration in in vitro analyses. In the present study, both orthotopic tumour and transgenic mouse models of cancer will be used, together with in vivo and in vitro fluorescence imaging, NMR, and LC/MS to study GPCPD1’s role in vivo. Initially, cell models with altered and mutated expression of GPCPD1 will be created and characterized in vitro. Therefore, in addition to a willingness to work with animals, candidates with a background in cellular and molecular biology techniques will be preferred. Experience with murine cancer models and microscopy is highly desirable.
For further information contact: Dr. Rosemarie Marchan (email: marchan@ifado.de, Tel: +49-231-1084213).

Position 3
The project focuses on the role of the matricellular protein WISP1 in liver pathophysiology. The study entails analysis of transcriptional regulatory networks associated with stress, inflammation and proliferation, using mouse models of liver damage and inflammation. In addition, a strong focus on immunophenotyping will be applied using FACS analysis on liver leukocytes. Finally, in vitro assays will be established to study in detail the molecular mechanisms involving WISP1 action in liver cells. Experience with animal experiments, cloning and recombinant protein production is highly desirable.
For further information contact: Dr. Patricio Godoy (email: godoy@ifado.de, Tel: +49-231-1084370).

Position 4
Aim is the quantitative agent-based modeling of regeneration after drug-induced liver damage in healthy and chronic disease in mouse and human based on confocal and bright field micrographs (J Hepatol. 2014 Oct;61(4):951-6). The candidate should implement model components in the tool TiSim/Cellsys and run extensive simulations and collaborate with image processing experts and experimentalists. Background in physics, mathematics, computer science or engineering is expected.
For further information contact: Dr. habil. Dirk Drasdo (dirk.drasdo@inria.fr, Phone: +33-1 80 49 43 18).
 
Postdoc positions:
Position 5:
Image processing and analysis. Aim is the quantification of liver disease, degeneration and regeneration processes at a histological tissue level in liver. The candidate is expected to develop algorithms, design image processing chains and perform image analysis of bright field and confocal laser scanning micrographs. The image analysis software TiQuant (Bioinformatics, 2015) already used for this purpose should be extended accordingly. The candidate is expected to collaborate with experimentalists and modellers. A background in computer science, mathematics, mathematics or engineering with extensive experience in image processing is required.
For further information contact: Dr. habil. Dirk Drasdo (dirk.drasdo@inria.fr, Phone: +33-1 80 49 43 18).
 
Position 6:
Mathematical multiscale modelling: Aim is the multi-scale quantitative modelling of disease, degeneration and regeneration processes at histological tissue level in liver. The candidate is expected to set up and develop model components, as metabolic and signal transduction path way models in each cell, implement them on the computer (into our modelling tool TiSim/CellSys designed for this purpose, Bioinformatics 2010) and run simulations to be directly validated against experimental data. The candidate is expected to collaborate with experimentalists and image analysis people. A background in computer science, mathematics or engineering with extensive experience in mathematical modelling, ideally numeric or agent-based system modelling is required.
For further information contact: Dr. habil. Dirk Drasdo (dirk.drasdo@inria.fr, Phone: +33-1 80 49 43 18).

All positions are financed for three years according to the German public wage law (TVL-E13 (50 %) for PhD students, and TVL-E13 or E14 for post docs). IFADO is an equal opportunity employer, and does not discriminate on gender, race, colour, religion, national origin, disability, or age in its programs and activities. 
 

Contact detail


How to apply:
All positions are immediately available. Please send your application with reference to the appropriate project, including a CV, a letter of motivation, and the name and contact information of two referees to the project leaders whose E-mail addresses are given after the description of the individual positions or additionally to Ms. Silke Hankinson at hankinson@ifado.de or by post to the following address:
Leibniz-Institut für Arbeitsforschung
an der TU Dortmund (IFADO)
Ms. Silke Hankinson
Ardeystr. 67
D-44139 Dortmund
 
Deadline closes May 10, 2016
Send application to
to E-mail addresses are given after the description of the individual positions or additionally to Ms. Silke Hankinson

 hankinson@ifado.de

or by post to the following address:
Leibniz-Institut für Arbeitsforschung
an der TU Dortmund (IFADO)
Ms. Silke Hankinson
Ardeystr. 67
D-44139 Dortmund

Job profile


Working hours
Part-Time
Contract duration
Temporary
Type of job
Postdoc
Work experience
job experience is not required
Region
Germany (Nordrhein-Westfalen)
Working place
44139 Dortmund
Area of expertise
Biology & Life Sciences
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