Major Systems Biology
PhD Program
PhD Programme in Simulation Science
The Structured PhD Programme in Simulation Science is a new multi-institutional collaborative Ph.D. programme involving University College Dublin, Trinity College Dublin, Queen's University Belfast, Natioanl University of Ireland Galway and is supported by the Irish Centre for High End Computing.
Funded PhD Fellowships are currently available at NUI Galway in this programme. These SimSci Fellowships are fully funded for 4 years and include a stipend of 16,000 € per year together with an allowance for research travel and expenses and cover fees for EU studends.
Further information Simulation Science Phd Programme Nuig Lena
Recently established PhD program of Systems biology
The ViroQuant PhD program of Systems Biology is established in close collaboration with the Hartmut Hoffmann-Berling International Graduate School of Molecular & Cellular Biology and the Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences. Many of the core activities offered by the Graduate Schools have an emphasis on Systems Biology. Monthly held modeling clubs, workshops, lab rotations, a spring school as well as the BioQuant lecture series will give insights to recent topics and state-of-the-arts methods. The guidance and supervision of an interdisciplinary Thesis advisory committee (TAC) will help the PhD student to work with high efficiency and best possible outcome.
We have two open positions for PhD students in a collaborative research project on Systems Biology of Aging.
Applicants should have a a background in Bioinformatics or Systems Biology, or related fields. Both positions are in a collaborative research project within Heidelberg University, including both experimental and theoretical collaboration partners. The focus of the project is on systems biology of aging, and involves both high-throughput data analysis (for example deep sequencing or mutant screens), as well as modeling aspects. The ultimate aim is to develop computational models describing cellular processes in aging.
We are an international, young team, and offer an interdisciplinary working environment in an exciting and booming research area, and first-hand experience in collaborative research at an internationally competetive level. We are located in the BioQuant center, a leading center of Systems Biology research in Europe, located centrally on the Neuenheimer Feld Campus in Heidelberg.
Both position are paid according to the German TV-L salary scale (1/2 E-13), and are available immediately, for 3 years. The positions offer the possibility to obtain a PhD degree at Heidelberg University.
Applications will be accepted until the positions are filled. If interested in applying, please send your full application including CV,
list of publications if any, and transcripts of relevant certificates (Diploma / Master, Bachelor / Vordiplom, High School degree) preferably as one large pdf file by email to the address indicated below.
Dr. L. Kaderali
University of Heidelberg
Viroquant Research Group Modeling
Bioquant BQ0026
Im Neuenheimer Feld 267
69120 Heidelberg
Germany
e-mail lars.kaderali[at]bioquant.uni-heidelberg.de
http://hades1.bioquant.uni-heidelberg.de
Open Ph. D position: Multicellular Simulation.
In the frame of multiple systems biological projects funded by the German Ministry for Education and Research (BMBF: MEDSYS, FORSYS, Virtual Liver, GerontoSys) the Hamamatsu TIGA (Tissue Imaging and Analysis) Center of the University Hospital Heidelberg is looking for a PhD Systems Biology/ Bioinformatics: Multi-cellular Models, Networks & Simulation.
We have developed the foundations of a novel multi-cellular simulation environment based on multi-agent systems (Bioinformatics, 25(16):2057-63) for epithelial tissue, especially for the simulation of the rapid renewal process of human skin. In this simulation behavioral models of individual cells interact to form the emergent properties of epithelial tissue. Therefore, we are offering a PhD position in which novel strategies will be developed to integrate molecular network based models into cell behavioral models for subsequent simulation. Thereby logical or qualitative network models will drive the behavior of each cell. Experimental reference data are generated in our own lab from native tissue and in vitro experiments.
Environment:
The TIGA Center is a cooperative unit with multiple partners and is hosted in the internationally leading systems biological center BIOQUANT at the University Heidelberg. You will work in close collaboration with multiple research groups of the University Hospital (e.g. National Center for Tumor Diseases), German Cancer Research Center (DKFZ) and other groups. The open position therefore offers an exciting environment for interdisciplinary research with state-of-the-art modern systems biology. We offer a friendly but dynamic working atmosphere where you have the unique opportunity to daily work with experimentalists in our own and related groups to optimally continue your scientific career.
Position:
We are looking for a committed and integrating personality who values this special environment and would like to contribute his or her outstanding experience. Your background should be from computer science, bioinformatics or a related discipline. You should have experience in software developing/engineering (JAVA preferred). You will closely interact with biologists, therefore a general background in bioinformatics is expected for understanding the project needs. Also we expect a strong interest for multi-cellular systems biology, the ability to communicate in English in daily routine and the interest in contributing to scientific publications.
Your application should contain
a) a detailed CV
b) a description of previous scientific experiences (please select a representative publication)
c) your interests or method spectrum
d) two possible contacts for references.
The position is currently limited for 2 years. Salary is according to TV-L 13/2.
The University of Heidelberg is an equal opportunity employer.
Please send your application exclusively by e-mail to: tiga.jobs@googlemail.com
PD Dr. Niels Grabe,
Institute for Medical Biometry and Informatics, University Hospital Heidelberg.
http://tigacenter.bioquant.uni-heidelberg.de/
Open Ph. D position: Mathematical modeling of the regulation of cell migration.
PhD student at Gothenburg University, Sweden
Project Title: Experimental Investigation of the yeast Hxk2/Snf1/Mig1 network
Research Objectives: To understand the dynamic control of the Hxk2/Snf1/Mig1 glucose signaling pathway employing single cell technology developed in this network
Requested Background: Yeast biology, yeast genetics, glucose signaling, use of microfluidic devices, microscopy, Image analysis, application of nano-sensor technology, "systems" tinking
Contact: Prof. Stefan Hohmann
stefan.hohmann[at]gu.se
PhD student at Gothenburg University, Sweden
Project Title: Theoretical investigation of the yeast Hxk2/Snf1/Mig1 network
Research Objectives: To understand the dynamic control of the Hxk2/Snf1/Mig1 glucose signaling pathway employing single cell technology developed in this network
Requested Background: Yeast biology, yeast genetics, glucose signaling, use of microfluidic devices, microscopy, Image analysis, application of nano-sensor technology, "systems" tinking
Contact: Prof. Stefan Hohmann
stefan.hohmann[at]gu.se
PhD student at Gothenburg University, Sweden
Project Title: Development of (microfluidic) systems for improved single cell analysis.
Research Objectives: to generate an advanced experimental system with holographic optical tweezers based cell positioning and with improved imaging.
Requested Background: Development of microfluidic devices, control of microscopy hardware, high-end image analysis, yeast biology, usage of confocal microscope
Contact: Dr. Mattias Goksör
mattias.goksor[at]physics.gu.se
PhD student at Rijksuniversiteit Groningen, Netherlands
Project Title: Investigation of fast metabolic system behaviour.
Research Objectives: To understand fast complex metabolic behaviour in single yeast cells using the technology developed in this network.
Requested Background: Usage of microfluidic devices, microscopy, yeast biology, glucose metabolism, development of mathematical models.
Contact: Prof. Matthias Heinemann
m.heinemann[at]rug.nl
PhD student at Rijksuniversiteit Groningen, Netherlands
Project Title: Investigation of slow metabolic system behaviour.
Research Objectives: To understand complex metabolic behaviour in single yeast cells using the technology developed in this network.
Requested Background: Usage of microfluidic devices, yeast biology, glucose metabolism and signalling, application of nano-sensors, image analysis, development of mathematical models.
Contact: Prof. Matthias Heinemann
m.heinemann[at]rug.nl
PhD student at ETH Zürich, Switzerland
Project Title: Development of an array-based microfluid system
Research Objectives: To develop a microfluidic device, in which cells can be cultivated in an array-based format and from which single can be released in an addressable manner.
Requested Background: Microfabrication and clean room work, development of microfluidic system, microelectronics, basics of yeast biology and mass-spectrometry
Contact: Prof. Andreas Hierlemann
andreas.hierlemann[at]bsse.ethz.ch
PhD student at ETH Zürich, Switzerland
Project Title: Development of mass-spectrometry based single cell metabolomics.
Research Objectives: To develop a technology for simultaneous detection of numerous cellular metabolites from single cells using mass sprctrometry (MS) with high-throughput capability.
Requested Background: Mass-spectrometry, metabolomics, application of metabolite nano-sensors, usage of microfluidic devices, insight into material sciences
Contact: Prof. Renato Zenobi
zenobi[at]org.chem.ethz.ch
PhD student at University of Oxford, United Kingdom
Project Title: Development of novel imaging techniques
Research Objectives: To develop an ultrasensitive single molecule fluorescence microscope capable of millisecond time scale imaging of proteins in single cells, and designing advanced bespoke imaging analysis software catered for in vivo single-molecule single-cell microscopy.
Requested Background: Microscopy, imaging hard- and software, yeast biology, modeling, application of nano-sensors
Contact: Dr. Mark Leake
m.leake1[at]physics.ox.ac.uk
PhD student at Syddansk Universitet, Denmark
Project Title: Development of aptamer-based nano-sensors for single cell metabolite analysis
Research Objectives: To develop aptamer-based nano-sensors to visualize metabolites and dynamically on the single cell level
Requested Background: Biochemistry, development of aptamer-based nano-sensors, imaging, basics of mass spectrometry and microfluidic devices
Contact: Dr. Lars Folke Olsen
lfo[at]bmb.sdu.dk
