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2013

Bioinformatics Post Doctoral Fellow open

Laboratory for Public Health Informatics and Genomics 
niversity of Wisconsin-Milwaukee 

Job Title: Bioinformatics Post Doctoral Fellow 

Summary: The Laboratory for Public Health Informatics and Genomics (LPHIG) at the University of Wisconsin-Milwaukee has one postdoctoral research fellow position available for immediate appointment. The position is available for bioinformaticians who are interested in translational science in support of personalized medicine and public health by enhancing patient-centered outcomes through analyzing genomic data, extracting meaningful information from electronic heath/medical records and developing, conducting and simulating predictive models. 

The objective of LPHIG is to conduct research and seek translation of genetic discoveries into better understanding of disease prevention and health promotion. LPHIG conducts research and promotes collaborations with local, regional and international public health organizations to identify and test the use of genomics, genetics, electronic health records, and other environmental data sources to improve patient centered outcomes and achieve a reduction in inequalities in public health. We create approaches that bring the power of emerging computational technology together with biomedical and public health informatics techniques, tools and methods to create applicable public health information and evidence. Current projects include a pharmacogenetic patient-centered outcome research project to develop optimized treatment plans for segmented patient populations by conducting modeling, simulation and prediction studies based on large longitudinal comprehensive electronic medical records (EMR) complemented with genetic information and a molecular examination of the mechanisms of transgenerational disease inheritance. 

Role and Duties: As a member of LPHIG, the Fellow will assume important roles in prioritized LPHIG projects including: leading the computational efforts associated with LPHIG projects; work with the lab Director to identify and describe key pilot projects; participate in multidisciplinary project team projects to achieve research milestones; and participate in the training of graduate and undergraduate students. 

Qualifications: The ideal candidate has received their PhD in the computational science, bioinformatics, or related field of study within the last three years. Candidate must excel at modern bioinformatics skills such as python, perl, R, cluster computing or similar. Preference will be given to applicants with demonstrated research aptitude and a driving interest in improving medical research. The diversity of subject matter will require a creative mind and a candidate capable of deploying imaginative strategies and who is dedicated to solving complex and challenging problems. Applicants should be highly motivated and flexible, with excellent communication skills, and work well within an interdisciplinary 

How to apply: Email applications including curriculum vitae, summary statement of personal objective and research interests, PDFs of no more than three papers, and the names and email addresses of three references to: Peter J. Tonellato, Ph.D., ptone @ uwm.edu, 414-227-4019. 

For general interest in working at the LPHIG send CV, statement of objective and interests.

posted 2013.12.20

a postdoctoral fellowship or research fellowship position in the Bioinformatics and Systems Biology core open

Systems Biology Center 

Division of Intramural Research (DIR) 
National Heart, Lung and Blood Institute (NHLBI) 
ational Institutes of Health (NIH) 
Health and Human Services (HHS) 

Position Description: Applicants are invited to apply for a postdoctoral fellowship or research fellowship position in the Bioinformatics and Systems Biology core, systems biology center at the National Heart, Lung, and Blood Institute (NHLBI), the National Institute of Health (NIH) in Bethesda, Maryland. The core's mission is to collaborate with investigators to incorporate bioinformatics and systems biology synergistically in their research. The core focuses on research, methodology development, education, and applications in areas including but not limited to: network based analysis of Next-Gen sequence (NGS) data, integration of multiple types of Big Data, multi-scale modeling of emergent spatiotemporal orders in physiological systems. The initial appointment can be renewed annually for up to 5 years, dependent on performance. 2 positions are available. 

Requirements: We expect one position to be filled with a recent PhD in statistical genetics, mathematical genetics, biostatistics, or related disciplines providing solid training in statistics and knowledge of genetics/genomics; the second position to be filled with a recent PhD in mathematical biology or applied mathematics, statistical physics, biophysics, bioinformatics, computer science, or related disciplines providing training and experience in quantitative science, mathematical modeling, and appreciation of biological complexity. Individuals with experience in one of the following areas are preferred though not required: analysis and modeling of NGS data, graph theory and network modeling, data and mathematical model integration, time course data modeling, and dynamical systems. Programming skills in major programming languages R, Java, Python, and MatLab are desirable. Need to be a team worker with good communication skills. 

Applicants should submit the following: brief description of research interests and career goals, CV, and contact information for three references to Dr. Xujing Wang at xujing.wang @ nih.gov 

NIH offers highly competitive stipend and benefit, and rich resources for fellows to develop and transit into independent investigators. More information can be found from the office of intramural training and education: https://www.training.nih.gov/programs/postdoc_irp. The advertisement will remain open until the position is filled. 

HHS and NIH are Equal Opportunity Employers

posted 2013.12.05

Bioinformatics / Computational Systems Biology Postdoctoral Fellow open

We are looking for an exceptional and highly motivated post-doctoral researcher to develop multi-scale computational models, and algorithms and software tools to study biochemical networks involved in host-pathogen interactions. One of the main objectives of the project is the integration of biological data from various biological databases and across multiple scales into predictive computational and mathematical models. Using existing and newly developed computational models, the researcher will be responsible for identification of novel drug targets and development of biologically plausible disease models for experimental and clinical validations. 

Candidates must have a PhD in Bioinformatics, Computational Biology, Biophysics, Computer Science, Engineering or a closely related field. 

The researcher will work in collaboration with other members of the group, and will have the opportunity to work on multiple projects in an international and a highly interdisciplinary setting with laboratory scientists, computer scientists, engineers, and mathematicians. 

  • Experience with computational/mathematical modeling and simulations of networks is required. 
  • Strong computational skills (e.g., in the areas of Markov Models, machine learning, statistics, agent-based systems) 
  • Prior experience in network inference and analysis 
  • Experience with extracting and manipulating large data sets from various databases, and integration of these data into predictive computational models 
  • Strong programming skills in C/C++ and/or Java, as well as R 
  • Experience with algorithm design 

If interested, please send a cover letter, CV and contact information for three references to Dr. Tomas Helikar at thelikar2 at unl dot edu. 

The University of Nebraska has an active National Science Foundation ADVANCE gender equity program, and is committed to a pluralistic campus community through affirmative action, equal opportunity, work-life balance, and dual careers.

posted 2013.12.03

Research Scientist open

For our Strains Department in the Discovery team in Hørsholm we are looking for a theoretical biologist with a strong microbial physiology background within the field of Computational Systems Biology. Experimental biologists with computational biology experience are also invited to apply. 

The Discovery team is part of the Innovation organization within our biggest division, Cultures & Enzymes. In the CED-Discovery team we are currently 27 dedicated colleagues: 4 managers, 12 scientists and 11 technicians. Specifically, in the Strains Department we aim at gaining in-depth understanding of the physiology of Lactic Acid Bacteria for knowledge guided improvement of strains to be applied in new product development. Our ultimate goal is to develop new bacterial strains with improved functionalities and performance for the global fermented food industries, especially for dairy fermentations. Today's consumers demand natural, healthier, clean label foods with great organoleptic properties (flavor, texture, etc). In a science-based framework, we use microbial physiology insights to develop the cultures that can provide these solutions, thus satisfying the needs of the modern consumer. In addition, we place great research efforts in fulfilling the needs and requirements of our customers regarding phage robustness, shelf-life extension, waste reduction, and overall cost-effective fermentation processes. 

Your tasks 
our main focus will be on the generation of genome-scale biochemical reconstructions of our key Lactic Acid Bacteria. 
  • The work is part of cross organizational effort to establish a platform for -omics data integration and interpretation with the ability to predict behaviors and facilitate rational strain improvement and process design
  • Prediction of pathways for production of key functionalities in LAB and other microorganisms 
  • Collaboration with experimental biologists in analyzing experimental data and planning strategies for strain improvement
  • You will be responsible for research projects, including cross-organizational communication and coordination internally and with outside partners
  • You will engage in network building activities i.e. contact to and cooperation with specialists within different research fields at institutions, universities and other private companies 
 Your personal profile
  • You have a Ph.D. in Microbial Systems Biology, Computational Biology, Biology and Biochemistry (with computational biology experience)
  • You have a solid background in computational biology and a good understanding of microbial physiology
  • Experience in genome-scale biochemical reconstruction, constraint-based modeling and analysis
  • Experience in -omics data analysis e.g. genomics, transcriptomics, metabolomics
  • Good programming skills (e.g. R, Matlab or equivalent language) and experience with data integration platform applications is desirable
  • Previous experience in microbial physiology and strain development is a big plus
  • Experience in doing research in multidisciplinary environments 
  • Good communication skills in English are required
  • You are innovative and enthusiastic towards new ideas
  • You have a high degree of independence and responsibility, and you can be a driver for your area of work 

We offer 
A position with direct report to Department Manager of Strains, within the Cultures & Enzymes Division (CED). We offer a stimulating, international workplace within a professional organization focused on linking solid scientific research to business opportunities. 

If you have any questions for the position, please feel free to contact Rute Neves by e-mail: dkruns @ chr-hansen or phone: +45 6034 1012. 
Please apply on-line, click here. Here you can enter your details into our CV-bank. 
Deadline for applications is 3 January 2014
Read more about working for Chr. Hansen at: www.chr-hansen.com/career


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posted 2013.12.03

Post-doctoral research position in biostatistics and high-throughput data open

In the Laboratory of Systems Tumor Immunology 
Dept. of Dermatology, University of Erlangen Nürnberg 

In the recently established laboratory of Systems Tumor Immunology we integrate mathematical modelling at different scales, network biology and biological high-throughput data analysis to investigate the interaction between a tumor and its microenvironment, with a special focus on the role of the immune system in tumor progression and metastasis. 

Our philosophy relies on tight collaborations with experimentalists and clinicians that work in biomedicine and translational medicine. We have established collaborations with several groups in the fields of tumor biology and immunology. The systems biology approach employed in our group uses mathematical modelling to construct and analyse regulatory networks and to test hypotheses concerning the structure and dynamics of these networks. Furthermore, we investigate their role in the emergence of cell phenotypes and tissue organization patterns. Now, we want to integrate high-throughput data and their analysis into our workflow. 

Job description 
We look for a junior post-doctoral scientist, with expertise in one or several fieldszx: 
  • biostatistics / biometry. 
  • processing, annotation, integration and analysis of biological high-throughput data (i.e., genomics, NGS, transcriptomics, proteomics or phospho-proteomics data). 
  • data analysis, data mining and data visualization (i.e., visualization of multidimensional data, (un-)supervised machine learning, reverse engineering...). 
  • computational methods for genome-wide association studies. 
  • analysis of biomedical data from pre-clinical and clinical studies. 

Requirements are a PhD in bioinformatics, biostatistics or computational data engineering, fluent English and/or German, advanced biostatistics and programming skills (i.e., Python, Matlab and/or R/Bioconductor), and strong interest in interdisciplinary research. The position may provide you the opportunity for teaching-related tasks. 
Salary: German E-13 scale, full position. 
Starting date: Immediately. Duration: up to 3 years. Deadline: 15th 
Submit your informal application to: Prof. Dr. Julio Vera-González, Laboratory of Systems Tumor Immunology, Department of Dermatology, University of Erlangen-Nürnberg (Germany). Email: julio.vera-gonzalez @ uk-erlangen.de

posted 2013.11.25

Assistant or Associate Professor for Computational Science Strategic Team open

Computational Sciences Strategic Team Hire - Assistant or Associate Professor University of Nebraska-Lincoln 

The Institute of Agriculture and Natural Resources (IANR) at the University of Nebraska-Lincoln (UNL) is seeking applicants for a tenured or tenure-earning professorial position to join a recent Strategic Team hiring initiative in the computational sciences. The successful candidate is expected to develop a nationally and internationally recognized research program integrating the methodological (e.g., machine learning, Bayesian nonparametrics, risk analysis, and multi-scale modeling) and the field specific (e.g., bioimaging, biomolecular, cellular signaling, remote sensing, and epidemiology) levels of computational biology. The program aims of the successful candidate may include one or more of the following focus areas: 

  1. At the Molecular Level - Development of statistical theory, algorithms, and software related to the design and analysis of high throughput data (e.g., high density genotypic, transcriptomic, proteomic, metabolomic, and sequence information) with the goal of predicting genetic and metabolic networks. 
  2. At the Organismal Level - Studies addressing plant and animal genomics, which will include the development of statistical theory, algorithms, and software related to the design and analysis of high throughput data sets with the goal of advancing new methodologies to correlate genetic traits in plant and animal systems with phenotypes (e.g., drought tolerance, enhanced nutritional value, or enhanced economic value of downstream products). 
  3. At the Systems Level - Studies addressing large empirical datasets from local to regional to continental scale relating to agricultural, environmental and natural resources, which will enable the development of computational approaches and model predictions at each scale -may include the use of Global Circulation Models and the development of statistical theory, algorithms, and software related to the design and analysis of large ecosystem data sets (e.g., water, carbon, methane, and nitrous oxide), with the goal of predicting complex ecosystem networks and climate forecasts. 

This position will have a 70% research, 28% teaching and 2% service appointment, and the tenure home for will be determined based on the expertise of the successful candidate. Potential homes include: Biochemistry, Biological Systems Engineering, Food Science and Technology, Animal Science, Agronomy and Horticulture, Nutrition and Health Science, School of Veterinary Medicine and Biomedical Sciences, Plant Pathology, Statistics, and the School of Natural Resources. The successful candidate will develop a national recognized research program and contribute to university-wide programs in areas that include statistics, biomarkers in disease and stress, quantitative genomics and phenotypes, proteomics, metabolomics, plant and animal genomics, mathematical biology, food safety or ecosystem modeling. 

A Ph.D. in Statistics, one of the Natural Sciences, Mathematics, Computational Sciences, Engineering, or a closely related field is required; for the Assistant Professor level two years (or equivalent) of postdoctoral experience is strongly preferred. For the Associate Professor level, an externally supported and nationally recognized research program in the broad area of Computational Biology is required. Preference will be given to candidates that have expertise in the development and implementation of models of large complex systems at the molecular, the organismal, or the systems levels. The successful candidates should have a strong commitment to undergraduate and graduate education and research, excellent communication skills, and the desire and abilities to work cooperatively on multi-disciplinary projects. 

To view the details and make application, go to http://employment.unl.edu. Search for position number F_ 130062. Click on "Apply to this job." Complete the application and attach a letter of interest, curriculum vitae, and a statement on areas of interest and career goals in computational science (Other Document). Arrange for three letters of reference to be sent to Joyce Ore at jore1@unl.edu. Review of applications will begin January 2, 2014, and continue until the position is filled or the search is closed. 

The University of Nebraska is committed to a pluralistic campus community through Affirmative Action, Equal Opportunity, work-life balance, and dual careers.

posted 2013.11.13

PhD Student - Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany open

We are looking for a highly motivated PhD student within a research project in the field of gene regulatory network inference funded by the Interdisciplinary Centre for Clinical Research, Erlangen. 

Applicants should have successfully completed their Master's/ Diploma degree in bioinformatics, bioengineering, applied mathematics, or a related discipline. Good programming skills, strong interest in the biological interpretation of results, and good working knowledge of English are a requirement. Competence in genomics data analysis and/or statistical modeling would be a plus. Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), with more than 35,000 students and over 550 professors, is the second largest university in Bavaria and has a research-intensive focus. Research at the Institute of Human Genetics aims at elucidating the molecular basis of both monogenic and complex diseases and its findings are translated into everyday patient care. The position is vacant immediately and the payment will be on the basis of 65% TV-L E13. FAU is an equal opportunities employer. 

Complete applications (including cover letter, CV, copies of degree certificates, and names of at least two references) should be submitted via mail or email to 
Dr. Fulvia Ferrazzi, 
Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany, 
email: fulvia.ferrazzi@uk-erlangen.de 
Application deadline: 10th December 2013 
Contact: Fulvia Ferrazzi, fulvia.ferrazzi@uk-erlangen.de

posted 2013.11.05

Graduate Student in the Systems Biology Research Group at UC Merced open

Postdoctoral Scholar
Area: Systems Biology
Position Title: Graduate Student
Position Code: QSB http://qsb.ucmerced.edu/grad-students/apply
Status:  Open
Description:  Multiple graduate student positions are available in the Systems Biology Research Groups at UC Merced.

In particular:
The Systems Biology and Cancer Metabolism Research Group uses computational systems biology tools, NMR spectroscopy, mass spectrometry, and network modeling to quantify changes in metabolism in human disease. The group is integrated into the Quantitative and Systems Biology Program as well as the Health Sciences Research Institute at UC Merced, providing a unique angle at today's health challenges.The University of California, Merced is an affirmative action/equal opportunity employer with a strong institutional commitment to the achievement of diversity among its faculty, staff, and students.

http://qsb.ucmerced.edu/grad-students/apply

The Quantitative and Systems Biology Graduate Group encourages applications from all students interested in dedicated graduate studies towards Ph.D. or M.S. degrees in this exciting field. Applications are invited from students with undergraduate degrees from any relevant discipline, including the life sciences, the physical sciences, engineering and mathematics. Please contact Fabian Filipp for more information.

All applicants should take the GRE general test (subject test optional). Applicants who are not native English speakers should go to the UC Merced Graduate Division website to see additional application requirements.

The admissions committee will make its decisions based on a comprehensive review of undergraduate coursework and GPA, GRE scores, research experience and recommendations in reaching a decision on admission. The deadline for receipt of applications is December 15 (although early applications are encouraged).


Qualifications:  Candidates must have a undergraduate degree in a related field like bioinformatics, bioengineering, systems biology, mathematics, physical or chemical sciences. A background in computational biology, analytical chemistry, lipodomics, NMR spectroscopy, mass spectrometry, chromatography; structural, chemical and/or computational biology is desireable. Candidates must also have the ability to work collaboratively with others.
 



 
Closing Date:  December 15th
 
To Apply:   http://qsb.ucmerced.edu/grad-students/apply
For more information: Please contact Fabian Filipp, Ph.D., M.Sc. 
filipp@ucmerced.edu or (858) 349-0349

http://www.ucmerced.edu/faculty/directory/fabian-v-filipp

posted 2013.10.30

Postdoctoral Scholar in the Systems Biology Research Group at UC Merced open

Postdoctoral Scholar
Area: Systems Biology / Cancer Metabolism
Position Title: Postdoctoral Scholar
Position Code: AHSRI4360A
Status: Open
Description: A postdoctoral scholar position is available in the Systems Biology Research Group at UC Merced.

The Systems Biology and Cancer Metabolism Research Group uses computational systems biology tools, NMR spectroscopy, mass spectrometry, and network modeling to quantify changes in metabolism in human disease. The group is integrated into the Quantitative and Systems Biology Program as well as the Health Sciences Research Institute at UC Merced, providing a unique angle at today's health challenges.The University of California, Merced is an affirmative action/equal opportunity employer with a strong institutional commitment to the achievement of diversity among its faculty, staff, and students. The University is supportive of dual career couples.
Qualifications: Candidates must have a Ph.D. in a related field with a strong background in analytical chemistry, lipodomics, NMR spectroscopy, mass spectrometry, chromatography; structural, chemical and/or computational biology. Candidates must also have the ability to work collaboratively with others.
 
Salary: Negotiated based on the University of California Pay Scale
 
Closing Date: Open until filled
 
To Apply: Interested applicants are required to submit 1) a cover letter 2) curriculum vitae 3) a list of three references with contact information including mailing address, phone number and e-mail address. 
For more information: Please contact Fabian Filipp, Ph.D., M.Sc. 
filipp @ ucmerced.edu or (858) 349-0349

http://www.ucmerced.edu/faculty/directory/fabian-v-filipp

posted 2013.10.30

Postdoctoral Researcher in Infection Biology open

Postdoctoral Researcher in Infection Biology
Basel, Switzerland 
 
Description: 
A Postdoctoral position is available in the Research group of Prof. Dirk Bumann at the Biozentrum, Basel. 

Infectious diseases are a major worldwide health concern. Current therapies have become increasingly inefficient because of emerging antimicrobial resistance, while the pipeline of new drugs is drying up. To avoid a public health emergency, the entire antibiotic research community must work together to reinvigorate research into new antibiotics. The available position will be part of the Innovative Medicines Initiative (http://www.imi.europa.eu/) project ND4BB-Translocation (http://www.imi.europa.eu/content/translocation) that will focus its efforts on identifying new ways of getting antibiotics into Gram-negative pathogens such as Pseudomonas aeruginosa and Klebsiella pneumoniae and preventing them from expelling the drugs before they can take effect. Our contribution to the project will be the determination of the composition of the bacterial cell wall envelope under in vivo conditions, and utilization of these data to build quantitative in silico models for Pseudomonas drug penetration and efflux. We collaborate with multi-national groups from academia and industry. 

The expertise in our group comprises multi-color high-speed FACS sorting, confocal microscopy, proteomics, metabolomics, microbial genetics, and in silico modeling (Nature 440, 303-7; Science 333,228-33). Group members include microbiologists, biochemists, chemists, pharmacologists, and software engineers. We are part of the Biozentrum that hosts numerous excellent labs with a wide and diverse range of interests and state-of-the art equipment (including FACSAria, FACS Fortessa, Leica SP5 and other confocal microscopes, automated microscopes, Orbitrap mass spec, etc). 

Basel offers an exciting international community with major pharmaceutical companies, an outstanding cultural life enhanced by the close proximity of France and Germany, and abundant out-door opportunities including the Alps at a ca. 60 min train ride. 

Qualification: 
You hold a PhD in one of the following disciplines: microbiology, biochemistry, bioinformatics, biophysics, chemistry, pharmacology, and software engineering. You have an interest in systems biology. The requirements are intentionally broad as there are a number of options available, depending on the candidates. 

Compensation Range: 
CHF 66'000 - 78'000 

How to Apply: 
Please send a pdf-file containing your C.V., letter of application, and contact info for three reference letters to Anne-Cécile Hiebel: bumannstelle @ unibas.ch

posted 2013.10.22

Tenure Track position in Molecular Systems Biology open

The Molecular Cell Biology unit and Quantitative and Systems Biology graduate group at UC Merced invite applications for an Assistant Professor (tenure-track) position from exceptional candidates in the field of Molecular Systems Biology. We seek experimental biologists who make technically innovative, theory-driven, high-dimensional measurements of whole cells and subcellular systems to explain fundamental biological processes. Theoretical biologists undertaking simulations at such scales are also invited to apply. Research areas of interest include macromolecular interaction networks, kinetic networks, regulatory networks, and multiplex single-molecule analysis. Applicants must have a Ph.D. in Molecular Systems Biology or allied field, a record of impact on the field of Molecular Systems Biology, and potential to maintain an extramurally-funded research program. The candidate will be expected to teach undergraduate and/or specialized graduate courses in quantitative and systems biology. For more information or to apply: http://jobs.ucmerced.edu/n/academic/position.jsf?positionId=4949. Fullest consideration will be given to applications received by December 15th. AA/EOE. 

UC Merced offers a unique academic atmosphere that fosters interdisciplinary research - connecting physical and mathematical sciences research to life sciences, materials sciences and engineering. We are committed to rapidly growing these collaborative research areas with allied and concurrent searches this year in Immunology, Biophysics, Applied Mathematics, Biomaterials, Bioengineering and Mechanical Engineering ( http://www.ucmerced.edu/careers ). Applicants are encouraged to apply separately for all positions that match their interests and qualifications. 

UC Merced is the newest campus in the UC system and currently serves more than 5000 undergraduate and graduate students. The University of California, Merced, is an affirmative action/equal opportunity employer with a strong institutional commitment to the achievement of diversity among its faculty, staff and students. The University is supportive of dual career couples. 

posted 2013.10.17

Senior Scientist Systems Biology at BASF Belgium open

We are the world's leading chemical company because we offer intelligent solutions for our customers and for a sustainable future. We link and develop people with diverse talents all over the world. For you, this means a variety of ways to advance. Not only your performance but also your personality matter to us. At BASF, careers develop from opportunities.

BASF Plant Science develops plant biotechnology solutions to increase the yield and quality of crop plants. CropDesign, the Belgian division of BASF Plant Science, focuses on rice as model crop. The company applies genomics, informatics and robotics technologies and employs over 150 employees in state-of-the-art laboratories and an automated greenhouse complex. www.cropdesign.com

What you can expect: 
As Senior Scientist Systems Biology you will be part of an international team of scientists, as
member of the Global Systems Biology team within the Crop Trait Knowledge function. There you will be the expert in gathering, integrating and mining of experimental data derived from multiple omics-platforms. You will participate in the biological interpretation of the data, and write and present reports on experiments and data analyses. As an experienced plant systems biologist, you will follow up on literature, connect with academics, and propose innovative approaches.

What we expect: 
You have a PhD in Systems Biology, Bioinformatics, Computational Biology or Biological
Sciences. You have experience in mining of biological data, in plant biology and in developing
and implementing research strategies. You combine your knowledge of the design and analysis of research experiments with hands-on experience with bioinformatic tools, databases and programming languages. Experience with R or equivalent statistical software is a plus. In addition to your excellent English skills, you are able to work in different multidisciplinary international teams.

We offer:
Responsibility from day one in a challenging work environment and "on-the-job" training as part of a committed team.

Competitive compensation including attractive benefits as well as excellent career opportunities in an international company.

Expect to be surprised by the exciting range of career opportunities at BASF.

Working area:
Research & Development

Location:
CropDesign N.V., Zwijnaarde

Working hours:
Full-time

Contract Type:
Permanent

Reference code
EN53267490_ONLE_8

Please apply online at 

or in writing to
BASF Belgium
Drève Richelle 161E/F
1410 Waterloo

For more information please contact:
Tel.: 00800 33 0000 33
 +32 (0)2 373 2222
E-Mail: jobs@basf.com

posted 2013.10.11

Doctoral Researcher Position at JSMC open

The Jena School for Microbial Communication (JSMC) is funded by the German Excellence Initiative. JSMC is an ambitious Graduate School with over 150 doctoral researchers who are educated in a structured, interdisciplinary training program based on top-level fundamental research. It conceptionally combines different research areas to a comprehensive picture of microbial communication (www.jsmc.uni-jena.de). Institutes at five faculties of the Friedrich Schiller University Jena, six non-university research institutes as well as 12 partner companies are participating in this cutting-edge research and training program.

The Graduate School of Excellence 'JSMC' invites applications for a
Doctoral Researcher Position TV-L E13 65% (Ref.No. 100/2013) 
to conduct research on the project 
Exploring unbound human and mouse inflammatory defense mechanisms against bacterial and fungal infection employing bioinformatics/systems biology concepts 

Interested in exploring the communication between human immune cells and invading bacteria or fungi? Using gene expression datasets, we will explore the differences in immune cell regulation when responding to pathogens in the human blood. Immune cells respond to fungal and bacterial infections very different and such a response can get out of bounds. We will use mathematical models to (i) explain the different response mechanisms, and (ii) predict targets for therapy. More projects details: www.jsmc.uni-jena.de/phd-program/fellowship-application/vacant-projects/

We expect:
  • a Master's degree (or equivalent) in Natural Sciences (bioinformatics, biology, biotechnology, computer science, physics, mathematics or equivalent). Candidates about to earn their degree are welcome to apply.
  • desirable methodological skills: basic programming knowledge, basic knowledge about cell biology or genetics, basic statistics, good mathematical knowledge high motivation and interest to join one of the interdisciplinary research areas of JSMC 
  • creativity and interest to shape your own thesis project an integrative and cooperative personality with enthusiasm for actively participating in the lively JSMC Community
  • very good communication skills in English (instruction language at JSMC)
We offer:
  • a highly communicative atmosphere within a scientific network providing top-level research facilities
  • a doctoral researcher position (TV-L E13, 65%) funded for three years based on the regulations of the German Research Foundation as well as generous research funding
  • a comprehensive mentoring program with supervision by a team of advisors
  • a top-level PhD training program with courses in state-of-the-art research technologies and soft skills
  • Jena - the German City of Science 2008: a young and lively town with dynamic business activities, successful scientific centers of innovation and a vibrant cultural scene around the famous Friedrich Schiller University
Friedrich Schiller University Jena is an equal opportunity employer.

The application procedure takes place exclusively online via the JSMC website: www.jsmc.uni-jena.de 

Please acquaint yourself with the open PhD projects and the application process described on this website.
Selected applicants will be invited to the JSMC Recruitment Meeting in Jena, Germany, on December 4-6, 2013. Awarding decisions will be made shortly thereafter, allowing the projects to start immediately. 
Application deadline: October 20th, 2013 (12pm, CET)

posted 2013.10.08

Postdoctoral position for mathematical modelling of biological networks open

Postdoctoral position for mathematical modelling of biological networks
in a Computational Cancer Systems Biology project at Institut Curie (Paris, France)
(18 to 36 months temporary position)

A postdoctoral position for mathematical modelling of biological networks is open at Institut Curie, Paris (http://www.curie.fr), a major cancer research and treatment institute.

The successful candidate will work in the Department of "Bioinformatics and Computational Systems Biology of Cancer" (U900 Department, http://u900.curie.fr), joint Unit from institut Curie, INSERM and Mines ParisTech. The Department comprises 80 persons (biostatisticians, mathematicians, physicians, biologists, physicists and computer scientists) and deals with the integration and computational analysis of large scale data in projects devoted to improve our understanding of tumor progression and to develop new therapeutic strategies.
The position is open in the "Computational Systems Biology of Cancer team" (http://sysbio.curie.fr ).

The candidate will work in the frame of a computational systems biology project devoted to understanding molecular mechanisms involved in early invasion of breast cancer cells into the normal tissue epithelial to mesynchemal transition, regulation of cell adhesion and cell motility).
The project will be done in tight collaboration with a group of Institut Curie, performing tumor invasion experimental assays.

We expect the candidate to have a PhD in applied mathematics or bioinformatics.
He/she should have experience in modeling biological networks and understand the molecular biology of cell signalling. Excellent communication skills and team spirit, and a capacity to work in autonomy are essential.

The candidates should send a letter of motivation, a CV, reprints of their main publications and three references to bcsb64 @ curie.fr.

The position can start immediately.

posted 2013.09.11

Personalized Medicine Research Fellowship open

Laboratory for Personalized Medicine 
 
Job Title: Personalized Medicine Research Fellowship 

Summary: The Center for Biomedical Informatics (CBMI), Harvard Medical School has one research fellowship available for immediate appointment. The position is part of the Laboratory for Personalized Medicine (LPM, lpm.hms.harvard.edu) program to reengineer translational science and accelerate the migration of biomedical informatics methodology, analysis and applications into the clinical enterprise in support of personalized medicine. 

LPM's objective is to identify clinically impactful devices, procedures, and biomedical informatics resources; test the clinical validity of those items with likely impact in the personal medicine clinical enterprise; and to execute high priority projects that translate key technologies into the clinical IT enterprise in support of personalized, preventive health care. The long-term goal is to create a translational science method and environment that supports the continuous and systematic testing and translation of highest priority technologies and discoveries into the clinical enterprise. This objective is at the heart of translational science and will support the joint HMS and Harvard Affiliate CTSC efforts. 

Role and Duties: As a member of LPM, the Fellow is expected to assume important roles in prioritized LPM projects including: work with LPM project leadership to identify and describe key pilot projects, participate in multidisciplinary project team projects to achieve research milestones, provide teaching assistance to the Bioinformatics Track in the Master of Medical Sciences in Biomedical Informatics program at Harvard Medical School, and support basic science, clinical researchers, and LPM's healthcare collaborations. 

Qualifications: The ideal candidate has received their PhD in biomedical informatics, biomedical science or clinical informatics field and/or MD, RN, or related advance clinical degree within the last three years. Candidate must excel at modern bioinformatics skills such as python, pearl, R, cluster computing or similar. Preference will be given to applicants with demonstrated research aptitude and a driving interest in improving the healthcare system. The diversity of subject matter will require a creative mind, deploying imaginative strategies, dedicated to solving complex and challenging problems. Applicants should be highly motivated and flexible, with excellent communication skills, and work well within an interdisciplinary environment. 

How to apply: Email applications including curriculum vitae, summary statement of personal objective and research interests, PDFs of no more than three papers, and the names and email addresses of three references to: Peter J. Tonellato, Ph.D., peter_tonellato@hms.harvard.edu, 617-432-7185 

For general interest in working at the LPM send CV, statement of objective and interests. 

posted 2013.08.19

Bioinformatics and Systems Biology Core Facility open

Systems Biology Center 
Division of Intramural Research (DIR) 
National Heart, Lung and Blood Institute (NHLBI) 
Health and Human Services (HHS) 
National Institutes of Health (NIH) 

Position Description: Applicants are invited to apply for a postdoctoral or research fellowship position in the Bioinformatics and Systems Biology core at the National Heart, Lung, and Blood Institute (NHLBI) in Bethesda, Maryland. The core's mission is to collaborate with DIR investigators to incorporate bioinformatics and systems biology synergistically in their research. The core focuses on research, methodology development, education, and applications in areas including but not limited to: network based analysis of Next-Gen sequence (NGS) data, integration of multiple types of big data, multi-scale modeling of emergent spatiotemporal orders in physiological systems. The successful applicant will receive an initial 2-year appointment with the possibility of extension, dependent on performance. Up to 2 positions are available. 

Requirements: A recent PhD degree in statistical genetics, mathematical genetics, mathematical biology, bioinformatics, biostatistics, or related disciplines providing training and experience in quantitative science and understanding of biology. Individuals with experience in one of the following areas are preferred though not required: analysis and modeling of NGS data, network modeling, dynamical systems. Programming skills in major programming languages R, Java, Python, and MatLab are desirable. Need to be a team worker with good communication skills. 

Applicants should submit the following: brief description of research interests and career goals, CV and contact information for three references to 
Dr. Xujing Wang at xujing.wang@nih.gov 
The advertisement will remain open until the position is filled. 

HHS and NIH are Equal Opportunity Employers

posted 2013.08.16

Postdoctoral Position in Systems Biology of Small Molecules.

The Systems Biology of Small Molecules group at the IBIS institute of the Helmholtz Zentrum München is a young research group dedicated to study the function of small molecules in biological systems, their phenotypic effects, and their role in diseases. We develop computational methods to integrate and interrogate existing biological and chemical data. We would like to extend our research lines on areas including, among others, the molecular and phenotypic analysis of drug combination treatments and chemical perturbations in disease models.

We are seeking a motivated and talented postdoc to join the group. We welcome applications from individuals with a PhD in computational or life science disciplines with programming skills and interest on biology and multidisciplinary work. A proven record of publications is an asset.
Highly motivated candidates can apply by sending a motivation letter, names and contact information for three references, publication list, and CV to monica.campillos@helmholtzmuenchen.de.

The position is available immediately, initially for one year with a standard public service salary (TVöD EG 13). During this period, the successful candidate is expected to apply for external funding.

Group web page: http://www.helmholtz-muenchen.de/en/new-ibis/institute/groups/systemsbiology-of-small-molecules/about-us/index.html

posted 2013.07.31

Computational Systems Biology Postdoctoral Position in Methods Development open

Postdoctoral applicants are sought in Computational Systems Biology to work with Professor Jeffrey Skolnick in the Center for the Study of Systems Biology at the Georgia Institute of Technology. Specific areas include the development and application of novel algorithms for the: 

  • Prediction of protein-protein, protein-DNA and protein-RNA interactions. 
  • Development of the tertiary structure of multidomain proteins. 
  • Development of network models for the prediction of subcellular dynamics and biological function. 
  • Development of multiscale modeling approaches for the simulation of virtual cells. 

Highly creative and outstanding individuals are sought with the following qualifications: 
  • Extensive experience in developing computer code in languages such as Fortran, C, C++, Perl. 
  • Previous experience doing international quality research in structural modeling, virtual ligand screening, large scale biological simulations, 
  • Brownian or Stokesian Dynamics, bioinformatics, or computational genomics would be major advantages. 
  • A track record of publication in high quality, international journals. 
  • Ability to work in a team, yet think independently. 

To apply, please email your CV to: skolnick @ gatech.edu 
Center for the study of Systems Biology Georgia Institute of Technology 
250 14th Street, NW Atlanta, GA 30318 

posted 2013.07.25

PhD Positions: Berlin, Germany open

The Berlin Institute for Medical Systems Biology at the Max-Delbrück Center for Molecular Medicine (MDC) offers an exceptional PhD Exchange Program to support interdisciplinary research projects and international PhD education.

PhD topics are structured as collaborative projects between the Center for Genomics and Systems Biology at New York University (NYU) and the Berlin Institute for Medical Systems Biology at the MDC. A Principal Investigator from each institution supervises each student, students who are expected to divide their time between Berlin and New York, taking advantage of complimentary research and training expertise. Resources are available for travel from Berlin to New York for both short and long term working periods as well as for course and conference participation. The regular guidance of an international PhD Committee supports the creation of individual research and training portfolios.

We offer projects in the areas:

  • Systems Biology and Molecular Networks
  • Gene Regulation: microRNAs, Epigenetics, Transcription, RNA Biology
  • Bioinformatics, Computational Biology and Mathematical Modeling
  • Genomics, Proteomics, Metabolomics, Single Cell Analysis and Imaging
  • Cell Fate Conversion, Neuronal Differentiation, Reprogramming and Signaling

  • Further information on the Institute and its mission to decipher the post-transcriptional regulatory code here: www.mdc-berlin.de/en/bimsb

    The program is embedded into the research and training activities of the Helmholtz Graduate School Molecular Cell Biology (MDC) and the Department of Biology (NYU).

    Online registration/application is now activated.

    Application deadline is August 26th 2013.

    For more information please refer to: www.mdc-berlin.de/application

    posted 2013.07.17

    2 Post-doc positions for computational systems biology open

    We are looking for enthusiastic candidates for postdoctoral positions in reverse engineering as well as pplying and developing methods for the analysis and integration of heterogeneous high-throughput data. These are required and to be applied to a portfolio of international research projects. The candidates will be involved in reverse engineering of regulatory networks of the corresponding target systems; and analysis and integration of large experimental datasets obtained from project collaborators using appropriate computational platform. These positions require extensive communication and collaboration with computational modelers, bioinformaticians, biologists, microbiologists, engineers, and clinicians. 

    Requirements 
    For these positions we request a solid background in computational biology and a good understanding of molecular biology. In addition, you are characterized by a high degree of independence and responsibility. Dedication, teamwork and persuasiveness complete your profile. Due to our international orientation, good knowledge of English is essential. 
    In particular: 
    • Knowledge in pattern recognition, machine learning, multivariate statistics and large-scale 
    data mining; 
    • Experience in inference of the underlying regulatory networks of prokaryotes, yeast, algae, 
    and/or mammalian cells using transcriptomics and proteomics data; 
    • Good programming skills (e.g. C, C++, Python, Perl, Matlab or equivalent) and experience 
    with data integration platform development; 
    • Ability to collaborate independently with other project members to implement, develop, and 
    refine relevant computational tools; 
    • Experience in doing research in a multi-disciplinary team; 
    • High interest in biological challenges and in combining different scientific disciplines to 
    develop new insights and skills; 
    • Willingness to learn new skills to support other computational tasks when necessary; 
    • Willingness to travel to our European partners is prerequisite. Depending on your qualification 
    a 2-4 week stay in the Netherlands may be required during the familiarization phase. 

    Qualifications
    • PhD degree in Computational Life Science, Bioinformatics, Physics or an equivalent discipline; 
    • Practical experience dealing with gene ontology, annotations notions, and public repositories 
    of omics data; 
    • Extensive experience in C, C++, Python, Perl, or equivalent plus ability to work with other 
    programming languages; 
    • Fluency in written and spoken English. 

    We offer 2 post-doc positions with an average working time of 40 hours per week for each position for a period of 2 years with possibility of extension. 
    The payment will correspond to the fare of the public service (TVL 14) depending on your qualification. 

    Please apply electronically to info@lifeglimmer.com with your CV, cover letter, and supporting 
    information in a single document (max. 3MB). The application deadline is July, 10th 2013.

    LifeGlimmer GmbH
    Markelstr.. 38
    12163 Berlin
    Handelsregister Amtsgericht Charlottenburg 
    Steuernummer: DE 282 940 451

    posted 2013.07.07

    Wissenschaftliche Mitarbeiter/innen: Systems Tumor Immunology (Hautklinik) open

    Der Arbeitsgruppe Arbeitsgruppe Systems Tumor Immunology (Hautklinik) sucht mehrere

    Wissenschaftliche Mitarbeiter/innen 

    Das Aufgabengebiet umfasst u. a.: 
     • Entwicklung eines Workflows zur computergestützten Konstruktion von miRNARegulationsnetzwerken 
    • Entwicklung einer Methode zur Indentifikation möglicher miRNA-assozierter Regelungstrukturen 
     • Entwicklung einer Webapplikation und Software zur Konstruktion und Analyse von miRNANetzwerken 

    Notwendige Qualifikation: 
    • MA-Abschluss in Bioinformatik oder Biomathematik. 
    • Promotion in Bioinformatik, Netzwerk Biologie oder Biostatistik. 
    • Programming Languages: Java, C, Python/BioPython, Perl, R/Bioconductor, MATLAB 
    • Beherrschen Medizinische und/oder Biologische Online-Datenbanken 
    • Beherrschen die deutsche und/oder die englische Sprache 
    • Wir erwarten Kooperationsbereitschaft und die Fähigkeit zu interdisziplinärer Arbeit im Team Bemerkungen: Stellenbeschreibung: 
    • Beabsichtigte Eingruppierung je nach Qualifikation und persönlichen Voraussetzungen:
      Entgelt-/Bes.Gr.: E13 
    • Die Stelle ist befristet. • Es handelt sich um eine Vollzeitstelle. 
    • Sonstiges: • Voraussichtlicher Einstellungstermin: nächstmöglich. 

    Die Bewerbungsfrist endet zum: 31.8.2013. 

    Für Auskünfte steht Ihnen zur Verfügung: 
    Prof. Dr. Julio Vera-González 
    Arbeitsgruppe Systems Tumor Immunology 
    Email: julio.vera-gonzalez@uk-erlangen.de 

    Die Bewerbungen sind zu richten an: 
    Prof. Dr. Julio Vera-González 
    Arbeitsgruppe Systems Tumor Immunology 
    Hautklinik, Universitätsklinikum Erlangen Hartmannstraße 14 
    91052 Erlangen

    posted 2013.06.18

    EPSRC CASE Studentship in Systems Physiology open

    Project title:"Using systems biology methods to optimize human nutrition

    Proposed start date: 1/10/2013 
    Duration of project: 3.5 Years 
    Primary supervisor:Dr Lindsay Edwards, King's College London, UK. 

    The central goal of this project is to use cutting-edge computational methods to design candidate nutritional strategies for humans that i) support healthy muscle regeneration and growth, ii) support optimal muscle performance and iii) minimize fat deposition

    Systems biology uses mathematical and computational methods to describe and explore complex biological networks. An important recent trend in systems biology has been the development and application of constraint-based modelling 1. Briefly, this approach applies progressive physical, chemical and experimental inequalities (constraints) to the fluxes through a biochemical network, leading to sets of feasible solutions (called the solution space) rather than a single set of values. This process can be applied to very large network models and has proved particularly successful in analysing genome and proteome-scale models of metabolism 2,3. Given that these models are built from genomic and proteomic datasets4, the subsequent computation provides a theoretical framework whereby an organism's phenotypic space may be connected to its genotype1. Once built, they can be deployed and analysed to a variety of ends. For example, constraint-based modelling has been used to successfully predict the metabolic signatures of human inherited diseases5-7 and, intriguingly, to design an effective metabolic anti-cancer drug8. We recently showed that a genome-scale model of human cardiac mitochondrial metabolism was able to predict the effects of the fatty acid uptake inhibitor, perhexiline, with great accuracy and detail9. A similar model recapitulated many features of hypoxic exposure (and even allowed us to predict genes under pressure in humans living in the persistent hypoxia of high altitude)10,11. These latter two examples are pertinent here, because they demonstrate that constraint-based modelling can accurately predict physiological responses to alterations in nutrient supply. 

     Although good exercise nutrition is both event- and client-specific, the broader aims of exercise nutrition include i) to support (or even promote) muscle cell growth (or recovery), while minimizing fat deposition (adipogenesis and lipogenesis) and ii) to support muscle performance.A wealth of research has been conducted into human muscle and adipose cell metabolism under a variety of conditions. However, a fully quantitative dissection of the effects of varying the supply of all known nutrients on the metabolism of specific cell types in healthy humans has not been attempted, perhaps because, until recently, viable tools to answer these questions were not available.Genome-scale models, analysed using constraint-based methods, provide the ideal platform to quantitatively analyze the effect of nutrient supply on muscle and adipose cell metabolic function, both individually and together. Indeed, a multi-cell (muscleadipocyte-liver) genome-scale model of human metabolism was recently reported to have recapitulated key features of human metabolic interaction (for example, the Cori cycle)12

    We seek an outstanding graduate with a background in systems biology, applied mathematics or computing (or a biologist with excellent mathematics) to undertake a 3.5-year program of research designed to harness the power of genome-scale models and apply them to key questions in exercise nutrition. This work will, to our knowledge, comprise the first fully quantitative examination of the effects of nutrient availability on muscle and adipose cell metabolic function, and their interactions. 

    First, we will build and analyze two, related, genome-scale models of muscle cell metabolism. One will be of mouse C2C12 myotubes and will be used in conjunction with cell culture experiments aimed at refining our computational methods and testing the quality of our experimental predictions quickly, easily and cheaply. The other muscle model will be of mature human skeletal muscle and will ultimately be used for predicting the effect of nutrient manipulation of muscle metabolism (and designing strategies for use in humans). These models will be hand-curated (using standard operating procedures 4) and analysed, using constraint-based methods. This will allow us to systematically analyze the effects of manipulating the supply of every metabolite and small molecule that muscles can exchange with their environment.Thus we will be able to computationally determine optimal patterns of nutrient supply, under a range of conditions and with a number of objectives (to include muscle growth, both hypertrophy and hyperplasia, and performance). We will test our predictions (as well as continually validating our model) by culturing human and mouse muscle cells and making a range of measurements (for example, we will use metabolomic profiling to measure actual metabolite uptake and excretion under various conditions). 

    Having analysed muscle cell metabolism quantitatively in this way we will carry out a similar process to study adipose cells. We will use existing 'banked' data to build genome-scale models of human and mouse adipocyte metabolism. Once the models have been built and validated, we will analyze the effects of varying nutrient supply on adipocyte growth and lipogenesis. We will validate our model and test our predictions using cultured adipocytes. Finally, we will build a twotissue model by combining the myocyte and adipocyte models (connected by a blood compartment). This two-cell model will allow us to quantitatively analyze interactions between the two cell types, and to design nutrient supply strategies that optimize muscle cell growth and performance while limiting adipocyte growth and lipogenesis (for example, by minimizing lipid 'overspill').

    For more details or for an informal discussion please contact Dr Lindsay Edwards: 
    Email: lindsay.edwards@kcl.ac.uk 
    Tel: +44 (0)20 7848 6978

    1. Lewis NE, et al.(2012) "Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods" Nat Rev Microbiol. 10(4):291-305
    2. Oberhardt MA, et al.(2009) "Applications of genome-scale metabolic reconstructions" Mol Syst Biol. 5:320
    3. Feist AM, et al.(2008) "The growing scope of applications of genomescale metabolic reconstructions using Escherichia coli" Nat Biotechnol. 26(6):659-667
    4. Thiele I, et al.(2010) "A protocol for generating a high-quality genomescale metabolic reconstruction" Nat Protoc. 5(1):93-121
    5. Sigurdsson MI, et al.(2009) "Genome-scale network analysis of imprinted human metabolic genes" Epigenetics. 4(1):43-46
    6. Smith AC, et al.(2011) "A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle" BMC Syst Biol. 5:102
    7. Shlomi T, et al.(2009) "Predicting metabolic biomarkers of human inborn errors of metabolism" Mol Syst Biol. 5:263
    8. Frezza C, et al.(2011) "Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase" Nature. 477(7363):225-228
    9. Yin X, et al.(2013) "Effects of perhexiline-induced fuel switch on the cardiac proteome and metabolome" J Mol Cell Cardiol. 55:27-30
    10. Edwards LM, et al.(2013) "The effect of hypoxia on human mitochondrial genetics and metabolism: studies using a genome-scale network reconstruction"- submitted. 
    11. Edwards LM, et al.(2011) "Studying the effects of hypoxia on mitochondrial metabolism in human heart using a genome-wide metabolic network model" Proc Aus Phys Soc. 42:33P
    12. Bordbar A, et al.(2011) "A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology" BMC Syst Biol. 5:180

    posted 2013.06.08

    Metabolic Engineering Scientist open

    Job Description
    Arzeda is seeking a creative and motivated metabolic engineering scientist who likes to work in an innovative and extensively multi-disciplinary team environment. Arzeda is a oung and dynamic biotech start-up at the forefront of the "green" chemistry revolution, eveloping transformational products and inspired solutions to a sustainable future everaging our core expertise in computational protein design, experimental iochemistry and synthetic biology, we design novel enzymes and metabolic pathways to ferment renewable feedstock into bio-based chemicals. Arzeda has developed its own roprietary product portfolio. Following an Open Innovation model, Arzeda is also nvolved in select industrial collaborations with leading chemical and agricultural multinational companies.

    The successful candidate will be leading the development of Arzeda's fermentation strains that incorporate novel designed pathways. At the research scientist level, she/he will:
    • be responsible for procurement and set-up of research tools required for the metabolic engineering of E. coli and Yeast strains
    • perform construction of strains harboring Arzeda's novel enzymatic pathways including multiple variants)
    • perform strain optimization to reach productivity levels consistent with industrial rocesses
    • report to upper management

    Job Requirements
    The ideal candidate will have Ph.D. and at least 3 years of practical industrial experience in E coli and preferably Yeast metabolic engineering. Candidates with a Ph.D. and a significant postdoctoral experience in the field will also be considered. A thorough nowledge of molecular biology, biochemistry, genetics and metabolic strategies and xperimental techniques is required. Previous experience with low-pH industrial ermentation as well as with computational metabolic engineering/system biology tools is uge plus.

    The successful candidate must be willing to work autonomously in a small, driven environment. In addition, she/he will have excellent interpersonal skills while exhibiting eadership. Finally, Arzeda seeks and greatly values a strong desire to learn, innovate nd be continuously challenged.

    Contact
    For further information about this position and to apply please send your CV and a cover letter to 
    jobs @ arzeda.com.

    Arzeda Corp. (www.arzeda.com) is an equal opportunity employer promoting diversity
    and inclusion in the workspace.

    posted 2013.05.21

    Doctorale Candidate (PhD student) in computational modeling of host-microbe interactions open

    The University of Luxembourg has the following vacancy in the Luxembourg Centre for Systems Biomedicine (LCSB):

    Doctorale Candidate (PhD student) in computational modeling of host-microbe interactions (m/f)


    • Fixed-term contract 3 years, 40h/week
    • Employee and student status (start date: as soon as possible)
    • Ref.: I1R-MSP-COM-120000
    Area: Constraint-based modeling (COBRA) of host-microbe interactions

    Your Role
    • Computational modeling of host metabolism and its metabolic interactions with selected microbes.
    • Reconstruction and validation against published data of the microbial metabolic reconstruction using established protocols.
    • Integration and analysis of experimental data in the microbial and host metabolic model.
    • Databases and literature mining for genomic information.
    • The project will thus include key technologies used in computational systems biology and bioinformatics.
    Your Profile
    • Master´s degree (or equivalent) in Biochemistry, Medicine, (Molecular) Biology, Microbiology, or Biotechnology.
    • Strong interest in metabolism, biochemistry, and computational modeling.
    • Basic skills/ experience in programming and statistical data analysis.
    • Excellent communication skills are required.
    • Excellent working knowledge of English is required.
    We offer
    • Fully funded position.
    • Working in a scientifically stimulating, innovative, dynamic, well-equipped, and international surrounding.
    • Opportunity to participate in the development of the newly created LCSB and to work closely with worldwide academic partners.
    • In-depth training in cutting edge technologies used in systems biology.
    • Numerous training opportunities in (molecular) biology, systems biology, and bioinformatics.
    The University offers highly competitive salaries based on the candidate's experience and is an equal opportunity employer.

    Further Information

    Applications (in English) need to contain the following documents:
    • Cover letter mentioning the reference number
    • Detailed curriculum vitae
    • Description of past research experience and future interests
    • Name and addresses of three referees
    For further information, please contact: Prof. Ines Thiele Ines.thiele@gmail.com
    Please apply online by 20th May 2013 here: http://emea3.mrted.ly/5yr1
    Relevant recent publications:
    • Thiele, I. et al.,''A community-driven global reconstruction of human metabolism'', Nat Biotech, doi:10.1038/nbt.2488 (2013). Heinken, A., Sahoo, S., Fleming, R. M. T., Thiele, I., "Systems-level characterization of the host-microbe metabolic symbiosis in the mammalian gut", Gut Microbes, 4(1):1-13 (2013).
    • Thiele, I., Heinken, A., Fleming, R.M.T. "A systems biology approach to studying the role of microbes in human health, Curr Opin Biotech, 24(1):4-12 (2013).
    • Thiele, I. and Palsson, B. O.,"''A protocol for generating a high-quality genome-scale metabolic reconstruction'', Nat Prot, 5(1): 93 - 121(2010).

    posted 2013.05.07

    PhD Student Positions at International Leibniz Research School (ILRS Jena) open

    The graduate school „Jena School for Microbial Communication (JSMC)" invites applications for 12 doctoral researcher fellowships on several topics in Natural and Life Sciences. 
     Please check the website for details: 

    Deadline for application: May 1, 2013 
    Selected applicants will be invited to attend the JSMC Recruitment Meeting in Jena (scheduled for the end of June/beginning of July).

    posted 2013.04.17

    Postdoctoral position in computational and systems biology available in Lille, France open

    A postdoctoral position is available in the department of Physics of Université Lille 1, France, to work on the dynamics of regulatory etworks underlying circadian clocks and their design principles. The esearch will be focused on the mathematical modeling of the circadian lock of the microscopic green alga Ostreococcus tauri and will e conducted in close collaboration with the group of biologists at bservatoire Océanologique de Banyuls who have first identified streococcus clock genes.

    Candidates are expected to have a strong background in nonlinear ynamics as well as in computational or systems biology, in the ontext of! cellular regulatory networks. A significant programming xperience is also required (preferably C/C++ or Fortran under a linux nvironment). The post-doctoral researcher will base its research on n extensive set of experimental time series recorded in Banyuls to xtend the current knowledge about the molecular networks of streococcus clock. The results obtained in this project will be of igh significance for the circadian biology field, because : (1) streococcus clock appears to be closely related to that of rabidopsis thaliana but with a simpler architecture, (2) previous athematical modeling of this clock has revealed a very interesting trategy to buffer fluctuations in daylight intensity. A complete mathematical model of the clock would therefore provide a simple xample of a robust clock network.

    The contract is for one year, extendable for 10 additional months. The onthly net salary is! about 2200 euros. Candidates should send as soon s possible a cover letter stating their motivations and CV to Marc efranc (marc.lefranc@univ-lille1.fr), preferably before June 1st, 013. They should also arrange for two reference persons to send simultaneously recommendation letters to the same address. Before applying, candidates are advised to check whether the position is till available at http://www-phlam.univ-lille1.fr/perso/lefranc/postdoc.html where they will also find more information.

    The ``Dynamics of Biological Networks'' team comprises three permanent esearchers (Marc Lefranc, Quentin Thommen and Benjamin Pfeuty). The esearch aims at understanding the dynamical behavior and design rinciples of biological networks, in particular signaling cascades nd genetic oscillators (circadian clocks, cell cycle,...), using the ools of nonlinear dynamical systems theory and statistic! al physics.

    posted 2013.04.17

    Scientific programmer for constraint-based modeling (m/f) open

    The University of Luxembourg has the following vacancy in the Luxembourg Centre for Systems Biomedicine (LCSB):

    Scientific programmer for constraint-based modeling (m/f)

    • Fixed-term contract 2 years, 40h/week
    • Employee status (start date: as soon as possible)
    • Ref.: I1R-MSP-PFN-12ATHU


    Area: Constraint-based modeling (COBRA) of human metabolism

    Your Role
    • Design and implement efficient computational workflows.
    • Develop and maintain an in-house database.
    • Assist researchers with their programming needs.
    • Assist with data pre-processing and data analysis.
    • Maintain programming code.
    Your Profile
    • An MSc or PhD in computer science, bioinformatics, systems biology, or related fields with an interest in biological and medical problems.
    • Proven ability to program COBRA methods in Matlab are required.
    • Strong computer programming skills (R, C/C++, Python/Perl, MySQL) are desired.
    • Excellent communication skills are required.
    • Excellent working knowledge of English is required.
    We offer
    • Competitive salary.
    • The opportunity to participate in the development of the newly created LCSB and to work closely with worldwide academic partners.
    • Exciting, interdisciplinary, international environment.


    The University is an equal opportunity employer.

    Further Information

    Applications (in English) should contain the following documents:

    • A detailed curriculum vitae
    • Cover letter mentioning the reference number
    • List of publications, if applicable.
    • Description of past research experience and future interests 
    • Name and addresses of three referees


    For further information, please contact:
    Prof. Ines Thiele
    Ines.thiele@uni.lu



    Please apply online by 30th April 2013 here: http://emea3.mrted.ly/5qot

    posted 2013.04.17

    postdoctoral position advertisement in Systems Developmental Biology open

    A postdoctoral position is available in the Department of Genetics at Albert Einstein Medical College in New York City to study the dynamics of gene expression oscillations underlying the vertebral segmentation process by using zebrafish as the model organism. 

    Interested candidates must have a PhD degree and a strong record of accomplishment and experience in the following areas: genetics, systems biology, imaging and computational biology. 

    The applicants must have proficiency in English, at least one first author publication in a reputed international journal from their Ph.D. work, enthusiasm in pursuing research in systems developmental biology. Developmental Biology experience is preferred, but not necessary. We are looking for a colleague who is collegial, highly motivated and independent. 

    Please send applications, which should include a cover letter detailing your past research accomplishments and future research goals, and a complete CV (with bibliography) by email to:  

    Ertuğrul M. Özbudak 
    Department of Genetics 
    Albert Einstein College of Medicine 
    Email: ertugrul.ozbudak @ einstein.yu.edu 

    Salary support will be based on research experience and accomplishments.

    posted 2013.03.29

    Synthetic Biology/Citizen Science Post-doctoral position open

    The Evolutionary Systems Biology Team, INSERM
    Synthetic Biology/Citizen Science Post-doctoral position 

    We seek an autonomous post-doc to join us in developing novel synthetic biology projects through crowd-sourcing, DIY approaches and gamification as part of a new Europeanfunded project, Citizen CyberLab - a three-year project to study and enhance the opportunities for learning and creativity available to participants in citizen science projects.The post-doc will join the extended CRI lab that includes synthetic and systems biology researchers as well as coders and game designers. 

    Our team from diverse backgrounds and nationalities is embedded within the Centre for Research and Interdisciplinarity (The CRI). The CRI harbors international interdisciplinary English-speaking undergrad and graduate programs and is a hub for challenging exchanges amongst faculty and top-notch students. Team members may directly benefit from this environment by participating in the teaching experience at the CRI. The CRIbased iGEM team trophy path started in 2007 with the foundational advance award and includes the 2012 world's 2nd runner-up and best environment project prizes. 

    Candidates should have relevant scientific background, an excellent track record (including at least one publication as 1st author), pertinent view on synthetic biology human practice issues as well as motivation to work in a collaborative framework. 

    Fellowship is available for a 12 month period, with potential extension. In parallel, our postdocs are strongly encouraged and supported to apply for their independent fundings. http://www.citizencyberlab.eu

    Apply by sending your CV and detailed motivation to ariel.lindner @ inserm.fr 

    Citizen CyberLab: www.citizencyberlab.eu _____________________________________________________________________________ 
    The Evolutionary Systems Biology team 
    (head: F. Taddei; senior researcher: A. Lindner), 
    INSERM U1001 Centre for Research and Interdisciplinarity (CRI), 
    Faculty of Medicine, Paris Descartes University. 
    24 rue du Fbg St Jacques, Paris 14, France. 
    Websites (new release soon!): www.necker.fr/tamara www.cri-paris.org

    posted 2013.03.21

    Bacterial Systems Biology Post-doctoral positions open

    The Evolutionary Systems Biology Team, INSERM

    We seek autonomous post-docs with backgrounds in systems biology, synthetic biology, Molecular Biology, Physics or Computer Sciences to enlarge our interdisciplinary group.

    Open projects target the causes and consequences of natural patterns of phenotypic variability, of aging and death at single-cell level within the context of bacterial lineages. To this end, we unite powerful bacterial genetics, systems and synthetic biology approaches together with state-of-the-art microfluidics, microscopy, robotics, image analysis and modeling to tackle such fundamental questions relevant to all living systems.

    Our team from diverse backgrounds and nationalities is embedded within the Centre for Research and Interdisciplinarity (The CRI). The CRI harbors international interdisciplinary English-speaking undergrad and graduate programs and is a hub for challenging exchanges amongst faculty and top-notch students. Team members may directly benefit from this environment by participating in the teaching experience at the CRI.

    Candidates should have relevant scientific background, an excellent track record (including at least one publication as 1st author) and motivation to work in a collaborative interdisciplinary research and teaching environment.

    Fellowship is available for a 12 month period, with potential extension. In parallel, our postdocs are strongly encouraged and supported to apply for their independent fundings.

    Apply by sending your CV and detailed motivation to ariel.lindner @ inserm

    Recent relevant publications
    [1] Ni M. et al. (2012) Pre-disposition and epigenetics govern variation in bacterial survival upon stress. PLoS Genet.
    2012 Dec;8(12):e1003148.
    [2] Delebecque CJ et al. (2011) Organization of intracellular reactions with rationally designed RNA assemblies.
    Science. 333(6041):470-4
    [3] Robert L. et al (2010) Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable
    switch. Mol Syst Biol. 6:357.
    [4] Lindner AB et al. (2009) Protein aggregation as a paradigm of aging, Biochim Biophys Acta 1790 980-96.
    [5] Lindner AB et al. (2008) Asymmetric segregation of protein aggregates is associated with cellular aging and
    rejuvenation, Proc Natl Acad Sci U S A 105 (2008) 3076-81.


    The Evolutionary Systems Biology team (head: F. Taddei; senior researcher: A. Lindner), INSERM U1001
    Centre for Research and Interdisciplinarity (CRI),
    Faculty of Medicine, Paris Descartes University.
    24 rue du Fbg St Jacques, Paris 14, France. Websites (new release soon!): www.necker.fr/tamara   www.cri-paris.org

    posted 2013.03.15

    Post-doctoral fellowship in molecular systems biology open

    ​The Molecular Systems Biology Group at the Center for Neuroscience and Cell Biology (CNCB) - University of Coimbra, is seeking highly motivated candidates for a post‐doctoral fellowship under the project FCOMP‐01‐0124‐FEDER‐020978 (FCT ref.: PTDC/QUI‐BIQ/119657/2010) "Finding the naturally evolved design principles of prevalent metabolic circuits". Applicants of any nationality must have a Ph. D. degree by the application deadline, a documented strong mathematical and computational background, and a strong publication record in bioinformatics, computational systems biology or related areas. Documented experience in bioinformatics or mathematical modeling of biochemical processes is a preferential condition.

    The object of activity will be the characterization of principles of quantitative design of metabolic network motifs through mathematical modeling, systems analysis and analysis of experimental data.

    The fellowship will have the duration of 12 months and start May 2013 (negotiable date). Eventual renewal will be based on merit and availability of funds. The monthly salary will be €1495.

    Applications can be submitted by email to armindo.salvador@gmail.com, from March 6th to April 6th 2013. They must indicate reference BPD2/PTDC/QUI‐BIQ/119657/2010 and include all the following documents: motivation letter, curriculum vitae, publications list, copy of Ph. D. diploma/certificate, and contact information (email and phone) of at least three references.

    For further information please see http://www.eracareers.pt/opportunities/index.aspx?task=global&jobId=34466​​

    posted 2013.03.15

    Postdoctoral Research Fellow in Computational Toxicology

    Job description :
    The Johns Hopkins Center for Alternatives to Animal Testing is involved in several scientific projects implementing the vision of Toxicity Testing in the 21st Century as formulated by the National Research Council report in 2007. The center is leading the NIEHS -funded Human Toxome Project, which is collaborative effort between CAAT, Georgetown University, Hamner Institute, Agilent and the US Environmental Protection Agency (EPA) to map pathways of toxicity. We are seeking a post-doctoral researcher to analyze and integrate multiple different data streams including, high-throughput screening data from the EPA ToxCast project (http://www.epa.gov/ncct/toxcast).

    Experience:
    The candidate will develop/use computational tools to identify and evaluate putative predictors of toxic effects due to endocrine disruption. Required skills include empirical analysis of using HTS, metabolomics and proteomics data using machine learning methods, and pathway analysis using in-house and publicly available tools. Demonstrated experience with computer programming using open-source tools (R and/or Python) is a must.

    Posted Qualifications:
    Ph.D. in computational biology/toxicology, bioinformatics, physics, computer science, mathematics or related field. Have some knowledge of pathway analysis approaches and experience in applying machine learning techniques to noisy data sets. Highly motivated and a self-starter, with the ability to work efficiently with minimal supervision. Additional education may substitute for required experience and additional related experience may substitute for required education, to the extent permitted by the JHU equivalency formula.

    Location:
    The position is located in Research Triangle Park, North Carolina at the National Center for Computational Toxicology of the US Environmental Protection Agency EPA and partly at the Johns Hopkins Center for Alternatives to Animal Testing, Baltimore MD.

    Contact Information:
    Dr. rer. hum. biol. Andre Kleensang
    Research Associate
    Johns Hopkins Center for Alternatives to Animal Testing (CAAT)
    Johns Hopkins University Bloomberg School of Public Health
    615 N. Wolfe St., W7032 Baltimore, MD, 21205
    phone: +1 410 614 4971 fax: +1 410 614 2871

    posted 2013.02.20

    Research Associate in the Department of Bioengineering at Imperial College open

    Applications are invited for the post of Research Associate in the Department of Bioengineering at Imperial College working under the supervision of Dr Reiko Tanaka.

    This post is for a project aimed at understanding regulatory mechanisms leading to skin inflammation. We will employ a diverse range of theoretical/engineering methodologies to model and elucidate the regulatory mechanisms for skin barrier homeostasis and inflammatory signalling. The project will include collaboration with experimentalists and clinicians. The main responsibilities of this post will include development of mathematical models for skin barrier homeostasis and inflammation, proposition of the experiments, coordination, integration and analysis of experimental data, and the statistical analysis and reformulations of these models in light of the collected data. More information on research activities in Dr Tanaka's group is found in http://www.bg.ic.ac.uk/research/r.tanaka.

    Applicants should hold a PhD or equivalent in a relevant area (Computational Biology, Applied Mathematics, or closely aligned disciplines) to undertake this project. You should also have experience in modelling and analysis of biological systems, expertise in modelling with differential equations and numerical methods, and strong interest in biology. We look for highly motivated applicants with excellent interpersonal, written and oral communication skills and enthusiasm for exposure to a diversity of scientific projects.

    Interested candidates should send CV and the research statement directly to Dr Reiko Tanaka (r.tanaka @ imperial.ac.uk). Applications will be assessed on the rolling basis, until the post is filled.

    posted 2013.02.19

    POSTDOCTORAL POSITIONS IN THEORETICAL BIOPHYSICS open

    Department of Health and Human Services
    National Institutes of Health
    National Heart, Lung and Blood Institute

    POSTDOCTORAL POSITIONS IN THEORETICAL BIOPHYSICS

    Multiple postdoctoral positions are available in the Theoretical Cellular Physics Section of Biochemistry and Biophysics Center at the National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD. Applicants should have Ph.D. in theoretical chemistry, physics, applied mathematics, or engineering. Candidates are expected to have open mind, theoretical modeling experiences in biophysics, and strong computational skills. Projects would utilize different statistical mechanics techniques to investigate mechanochemical couplings in various cellular processes, including membrane mechanics, cytoskeleton dynamics, and reaction networks. All the projects would be in extensive and close collaborations with experiments. For more information, see: http://www.nhlbi.nih.gov/research/intramural/researchers/pi/liu-jian/liu-jian.html

    Appointment and salary are dependent on experience. Review of applications will commence as early as February 15th, 2013, and will continue until filled. Applicants should submit, in a PDF file, a letter of interest, curriculum vitae, and three letters of reference to: Dr. Jian Liu at jian.liu @ nih.gov

    HHS and NIH are Equal Opportunity Employers. Applications from women, minorities and persons with disabilities are strongly encouraged.

    posted 2013.01.11