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PostDoc-Position/Scientific Coordinator

Computational Neuroscience and Statistical Signal Processing

The interdisciplinary research group Bio-inspired Communication Systems at Technische Universität Darmstadt invites applications for a

Postdoctoral position (E13 TV-H)

initially limited to two years, starting as soon as possible.

The position is dedicated to the development of robust signal processing methods for the processing of high-dimensional neuronal datasets stemming from voltage-sensitive dye recordings, calcium imaging and from multi-electrode arrays. In particular, methods that satisfy certain real-time constraints, enabling the experimenter to intervene in a closed loop manner should be developed. Additionally, those methods are required to be robust in a statistical sense, i.e., they should be able to cope with outliers and model mismatches.

The position is part of a collaborative research project spanning across three universities (Goethe University Frankfurt, Johannes Gutenberg University Mainz and Technische Universität Darmstadt) that recently formed the science cluster of Rhine-Main Universities (RMU). Apart from research, the position will be responsible for coordinating the common research activities among this group (organization of workshops, supporting novel collaborations, etc) and to direct the design of the joint research agenda of the research group for the following years. The position is ideal for a candidate seeking to combine research with gaining experience in managing collaborative research efforts. Participation in the neuroscience cluster RMN2 (www.rmn2.de) and the Centre for Cognitive Science (www.cogsci.tu-darmstadt.de) will be strongly supported.

Technische Universität Darmstadt provides the environment and support for publishing and presenting original research results at leading international conferences and in scientific journals. Technische Universität Darmstadt intends to increase the number of female researchers and encourages female candidates to apply. In case of equal qualifications applicants with a degree of disability of 50 or more will be given preference. Wages and salaries are according to the collective agreements on salary scales, which apply to the Technische Universität Darmstadt (TV-TU Darmstadt). Part-time employment is generally possible.

Your profile:
• Completed Ph.D. degree in computational neuroscience or signal processing/machine learning with neuroscience applications.
• Interest in scientific coordination of larger research programs and workshops.
• Appreciation for interdisciplinary work and proactive drive to connect people.

Application:
Your application must include:
• Cover letter explaining succinctly why you are interested in this position and why you believe you are the right candidate.
• CV
• List of passed courses and obtained grades
• Contact details of at least two references (academic advisors) of yours.

Please send your documents as one single PDF file to: indicating the application code within the subject line. Incomplete applications and applications in different file formats will be discarded.

Application code: RMU-2017-2

Ph.D.-Position in Biophysics and Fluorescence Microscopy

The interdisciplinary research group Bio-inspired Communication Systems at Technische Universitaet Darmstadt is inviting applications for a

PhD position (80% E13 TV-H)

initially limited for 3 years, starting as soon as possible.

The research position is dedicated to the development of novel single-cell and single-molecule techniques for the quantitative characterization of gene expression. In particular, already established in vivo nascent RNA labeling techniques should be further developed and combined with microfluidics in order to capture the transient, stochastic dynamics of gene expression. Practically, the project mostly involves molecular biology work in the wet-lab (i.e. genetic engineering of yeast and E. coli) and operation of a fully computer-controlled fluorescence microscope. Existing microfluidics designs for the accurate imaging of single cells will be further improved. Image processing algorithms will be adapted to robustly extract quantitative information from the fluorescence recordings that will then be used within the theory part of the group for computational modeling. Engaging into joint theoretical and experimental work within the group is highly encouraged and this opportunity for interdisciplinary research represents a unique feature of this position. Interest and skills to perform additional theoretical work is most welcome. The developed characterization techniques of gene expression should later be applied to simple gene regulatory networks, for instance, logic circuits as investigated in synthetic biology. Collaboration with the LOEWE Research Cluster CompuGene on synthetic biology (www.compugene.tu-darmstadt.de) is highly encouraged.

We provide the environment and support for publishing and presenting original research results at leading international conferences and in scientific journals. The fulfillment of the research and service requirements attached to this employment will equate to the academic requirements for the candidate's doctoral degree.

Technische Universitaet Darmstadt intends to increase the number of female researchers and encourages female candidates to apply. In case of equal qualifications applicants with a degree of disability of 50 or more will be given preference. Wages and salaries are according to the collective agreements on salary scales, which apply to the Technische Universitaet Darmstadt (TV-TU Darmstadt). Part-time employment is generally possible.

Your profile:
• Completed studies in physics, engineering, material science, chemistry or biology
• Experience with and passion for experimental laboratory work
• Appreciation for computational/theoretical work, basic programming skills
• Interest and proactive drive to learn about a new field (e.g. molecular biology) and work in an interdisciplinary team

Application: Your application must include
• a cover letter explaining succinctly why you are interested in this position and why you believe you are the right candidate
• a CV
• a list of passed courses and obtained grades
• and contact details of at least two references (academic advisors) of yours.

Please send your documents as one single PDF file to: indicating the application code number within the subject line. Incomplete applications and applications in different file formats will be discarded.

Application code: PhD-2017-11

4 x PhD Positions in Probabilistic Modeling for Synthetic Biology

Within the ERC project CONSYN “Contextualizing Biomolecular Circuits Models for Synthetic Biology” the Koeppl Lab at Technische Universität Darmstadt, Germany invites applications for

4 PhD positions (E13 TV-H)

initially limited for 3 years, starting as soon as possible.

CONSYN aims to provide a computer-aided design and analysis framework for synthetic biology. Key problems involve model calibration, model reduction and the composition of elementary models into novel biomolecular circuits. Considered models are mostly Markov and semi-Markov processes. Calibration requires the development of domain-specific machine learning methods to infer latent molecular states, to learn parameters and to discriminate model structures mainly based on time-lapsed single-cell microscopy data. Contextualizing circuit models to the molecular environment leads to large state-spaces and reduction techniques from the domain non-equilibrium statistical physics will be adapted and ultimately combined with the developed inference algorithms. Active learning/optimal experimental design problems will be addressed in order to minimize the experimental efforts for the characterization of novel synthetic circuits and for the screening of large panels of circuit variants. The Koeppl lab maintains its own experimental facilities and can generate dedicated data on large scale due to the use of custom-made parallelized microfluidic systems. The composition of stochastic models of elementary parts into larger circuit models raises several questions such as noise propagation across interfaces and we will investigate the use of formal methods for the automatic synthesis of hardware and software to tackle those problems.

Engaging into joint theoretical and experimental work within the group is highly encouraged. We also strongly support any collaboration with the ongoing LOEWE Research Cluster CompuGene on synthetic biology (www.compugene.tu-darmstadt.de). Technische Universität Darmstadt provides the environment and support for publishing and presenting original research results at leading international conferences and in scientific journals. The fulfillment of the research and service requirements attached to this employment will equate to the academic requirements for the candidate's doctoral degree.

Technische Universität Darmstadt intends to increase the number of female researchers and encourages female candidates to apply. In case of equal qualifications applicants with a degree of disability of 50 or more will be given preference. Wages and salaries are according to the collective agreements on salary scales, which apply to the Technische Universität Darmstadt (TV-TU Darmstadt). Part-time employment is generally possible.

Your profile:

• Completed studies in physics, mathematics, computer science or engineering

• Interested to work on theoretical/mathematical problems, good programming skills

• Appreciation for interdisciplinary work and proactive drive to collaborate with experimental people

Contact: Prof. Heinz Köppl, Rundeturmstrasse 12, 64283 Darmstadt, heinz.koeppl@bcs.tu-darmstadt.de

Application:

Your application must include

• a cover letter explaining succinctly why you are interested in this position and why you believe you are the right candidate

• a CV

• a list of passed courses and obtained grades

• and contact details of at least two references (academic advisors) of yours.

Please send your documents as one single PDF file to: application@bcs.tu-darmstadt.de indicating the application code number within the subject line. Incomplete applications and applications in different file formats will be discarded.

Application code: 2018-BCS-ERC1

2 x PostDoc Positions in Synthetic Biology and Biophysics

Within the ERC project CONSYN “Contextualizing Biomolecular Circuits Models for Synthetic Biology” the Koeppl Lab at Technische Universität Darmstadt, Germany invites applications for

2 Postdoctoral Positions (E13 TV-H)

initially limited for 3 years, starting as soon as possible.

CONSYN aims to discover general design principles for synthetic genetic circuits with the help of computational analysis. In collaboration with computational people within CONSYN, different synthetic circuits will be evaluated in a cell-free in-vitro setting and in-vivo based on the model organism yeast. In particular, the robustness of different circuit designs with respect to the molecular context, i.e., host loading and transcriptional cross-talk will be investigated and optimized. CONSYN aims to provide experimental characterization methods on the single-cell level for synthetic biology, hence contributing to the standardization and metrology efforts within synthetic biology. Novel methods based on microfluidics and fluorescent microscopy will be developed to characterize the dynamic response profile of synthetic circuits. In particular circuits realizing sequential logic circuits such as memories will be considered. The two postdoctoral fellows will work on the in-vitro and in-vivo implementation, analysis and optimization of synthetic circuits, respectively, and thus ample of opportunity to collaborate will exist. Fellows can resort to already established technology within the Koeppl Lab, such as microfluidic chemostats to run cell-free reactions at steady state conditions, droplet-based microfluidics to study cell-free reactions in batch mode and microfluidic single-cell traps to accurately track and quantify single yeast cells.

Engaging into joint theoretical and experimental work within the Koeppl Lab is highly encouraged. We also strongly support any collaboration with the ongoing LOEWE Research Cluster CompuGene on synthetic biology (www.compugene.tu-darmstadt.de). Fellows will be given the opportunity to participate in actively advising Ph.D. students that are involved in CONSYN. Ideal candidates already have experience with single-cell characterization in synthetic biology.

Technische Universität Darmstadt provides the environment and support for publishing and presenting original research results at leading international conferences and in scientific journals. The university intends to increase the number of female researchers and encourages female candidates to apply. In case of equal qualifications applicants with a degree of disability of 50 or more will be given preference. Wages and salaries are according to the collective agreements on salary scales, which apply to the Technische Universität Darmstadt (TV-TU Darmstadt). Part-time employment is generally possible.

Your profile:

• Completed Ph.D. studies in biophysics, biochemistry, biology or related field

• Wet-lab experience, in particular with genetic engineering and single-cell analysis

• Appreciation for interdisciplinary work and proactive drive to collaborate with modelers

Contact: Prof. Heinz Köppl, Rundeturmstrasse 12, 64283 Darmstadt, heinz.koeppl@bcs.tu-darmstadt.de

Application: Your application must include

• a cover letter explaining succinctly why you are interested in this position and why you believe you are the right candidate

• a CV

• and contact details of at least two references (academic advisors) of yours.

Please send your documents as one single PDF file to: indicating the application code number within the subject line. Incomplete applications and applications in different file formats will be discarded.

Application code: 2018-BCS-PD-ERC2

We are always looking for outstanding individuals for Ph.D. and postdoctoral research. Also internships for a few months at our Lab are possible.

Please send your application including motivation letter, CV and contact details of at least three references in one single PDF to