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2010

Postdoctoral Fellow in Cancer Bioinformatics open

Department of Biomedical Informatics, Vanderbilt University Medical Center

One postdoctoral position is available immediately in Dr. Zhongming Zhao's Bioinformatics and Systems Biology Laboratory (BSBL, http://bioinfo.mc.vanderbilt.edu/) at Vanderbilt University Medical Center. The successful candidate is expected to join an established bioinformatics team, which currently comprises 11 members including seven postdocs in bioinformatics, one bioinformatics engineer, graduate students, and one program coordinator. The ongoing projects in our group use the data generated from platforms such as next generation sequencing (Illumina, 454, SOLiD) and microarrays (gene expression, GWAS, microRNA, CNVs, and methylation) to study cancer, neuropsychiatric disorders, or other complex diseases using bioinformatics and systems biology approaches. Integrative genomics approaches are often applied. The fund is available to support this position for up to three years. The candidate is expected to work in cancer bioinformatics and will have the opportunity to access many high throughput datasets and to interact with the investigators in Vanderbilt-Ingram Cancer Center.

Vanderbilt's Department of Biomedical Informatics is the largest academic department of biomedical informatics in the country, with more than 68 faculty members, a graduate training program, and a portfolio of research and development projects that spans from computational biology and bioinformatics applied to the understanding of biological molecules, through advanced clinical information systems that care for hundreds of thousands of patients at Vanderbilt, to regional health information projects that span many states. More information about the department can be found at http://dbmi.mc.vanderbilt.edu/ .

The qualified candidates should be highly motivated in research and have a Ph.D. in bioinformatics, computational biology, molecular biology, or related when the job starts. The successful candidate should have some experience in analyzing high-throughput genomic data, especially NGS data, and proved skills in at least one programming language (Perl, Java, or C/C++). Good understanding of molecular biology and familiarity with biostatistics are desirable. For more information, please visit our web site http://bioinfo.mc.vanderbilt.edu/ . Applicants should send a CV, brief statement of research interests, and reference to: Zhongming Zhao (zhongming.zhao @ vanderbilt.edu) Chief Bioinformatics Officer, Vanderbilt-Ingram Cancer Center

posted 2010.12.29

Post-Doctoral Position in Systems Biology: Analysis of the Host Cell Signaling Network Controlling Pathogen Entry into Human Cells closed

A Post-doctoral position is available in the research group of Prof. Christoph Dehio at the Biozentrum of the University of Basel (http://www.biozentrum.unibas.ch/dehio/index.html). This position is part of "InfectX" (http://www.systemsx.ch/projects/systemsxch-projects/research-technology-and-development-projects-rtd/infectx/), a collaborative project funded by SystemsX.ch - the Swiss Initiative in Systems Biology (http://www.systemsx.ch).

The aim of the InfectX project is to use a systems biology approach to decipher the host cell signaling network controlling entry of a diverse set of bacterial and viral pathogens in order to define novel drug targets for anti-infectives. In this context our laboratory will study the host cell signaling pathways controlling entry and intracellular replication of the related bacterial pathogens Bartonella and Brucella. Key technologies and methods applied by the successful candidates are genome-wide RNA interference (RNAi) screens, multi-dimensional fluorescence microscopy, surface- and phospho-proteomics, as well as conventional biochemical and cell biological methods, which in collaboration with computational modelers will facilitate signal transduction pathway reconstruction.

We are looking for highly motivated individuals with a degree in biology or biochemistry and solid knowledge and working experience in cell biology. Experiences in studying eukaryotic signal transduction and/or intracellular trafficking processes are an asset. The positions are funded for a maximum of 3 years. For questions please contact Prof. Christoph Dehio (christoph.dehio @ unibas.ch). Applications should include a letter of motivation, a full c.v., and the names of 2-3 references and be sent electronically to rachel.benzies @ unibas.ch.

Additional Information:
The Biozentrum is an internationally renowned institute for basic life science research. With over 400 employees from 30 countries, it is the largest natural science department of the University of Basel. About 30 research groups engage in interdisciplinary research, and are in close contact with local life sciences industry. The working language at the institution is English. SystemsX.ch is a Swiss research consortium with eight universities and three research institutions. More than 100 research groups devoted to Systems Biology collaborate in 14 Research-, Technology- and Development programs.

posted 2010.12.03

Personalized Medicine Research Fellowship open

The Department of Pathology, Beth Israel Deaconess Medical Hospital (BIDMC) and Center for Biomedical Informatics (CBMI), Harvard Medical School have one research fellowship available for immediate appointment. The position is part of the Laboratory for Personalized Medicine (LPM) 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 BIDMC initiative to bring the power of genetics to personalized, predictive medicine..

Role and Duties:
As a member of LPM, the Fellow is expected to assume important roles in prioritized LPM projects and work with LPM project leadership to identify and describe key pilot projects, participate in multidisciplinary project team projects to achieve research milestones, and support basic science, clinical researchers, and LPM's healthcare collaborations.

Qualifications:
The ideal candidate has received their PhD in a biomedical informatics, biomedical science or clinical informatics field and/or MD, Preference will be given to applicants with demonstrated research aptitude and a driving interest in improving the healthcare system. Scripting and programming skills (Perl/Python/Ruby, Java/C++) will be necessary, as well as familiarity with leading sequencing and variant databases, algorithms, and tools. 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: Dr. Michiyo Yamada, Michiyo_Yamada @ hms.harvard.edu

Equal Opportunity Employer

posted 2010.11.25

PhD fellowship funded by MRC at Imperial College London closed

Application Deadline: 15 December 2010

Systems biology of Calcineurin/NFAT signalling in adaptive immunity

A PhD fellowship is available to work in the Quantitative Systems Biology group, within the Clinical Sciences Centre of the Medical Research Council and the Faculty of Medicine of Imperial College in London (UK). The successful applicant will investigate the quantitative and systems-level properties of signalling, genetic and transcriptional networks in primary T lymphocytes, carrying out projects that integrate experimental measurements with data analysis and mathematical modelling.

Informal enquiries about the details of available research projects are particularly encouraged and should be made to Dr Alberto Polleri at polleri @ imperial.ac.uk

Additional information on the research carried out in the Quantitative Systems Biology group can be found on http://qsb.csc.mrc.ac.uk

For more information on the MRC Clinical Sciences Centre PhD program and to apply:
http://www.csc.mrc.ac.uk/Jobs/PhDStudentship/CSCPhD/

posted 2010.11.24

Faculty positions in Systems Biology at Nanyang Technological University (Singapore) open

School of Chemical & Biomedical Engineering at Nanyang Technological University (Singapore) is recruiting faculty members at Assistant/Associate/Full Professor level in systems biology and other biomedical related areas. If interested, we'd like to invite you to submit your CV to us (Email: H-BioE at ntu.edu.sg).

Our School hosts two Divisions: (a) the Division of Chemical and Biomolecular Engineering which offers degree programs in core chemical engineering disciplines with research emphasis on catalysis/ nano-support, pharmaceutical engineering, regenerative medicine, engineering biology, fundamental chemical engineering and process systems modeling/design and (b) the Division of Bioengineering which offers biomedical-related degree programs with emphasis on biomedical devices, nano-medicine, biomechanics, systems biology, and bioimaging.  The School of Chemical and Biomedical Engineering attracts top undergraduate students from Singapore and Asia, and is well-funded and equipped with state-of-the-art equipments.

posted 2010.11.24

PhD Student - Systems Biology of Small Molecules open

The Helmholtz Zentrum is a member of the Helmholtz Association of German Research Centres, a leading association Europe-wide, focusing on "Environmental Health".
The aim of its research is to proactively detect health risks for both humans and the environment, decoding the mechanisms of pathogenesis and developing concepts for prevention and therapy of diseases.
The new research group "Systems Biology of Small Molecules" has a Ph.D position open available immediately.

Job Description
- Develop computational methods to integrate existing datasets from small molecules and proteins with new data generated in collaboration with experimental groups
- To understand better the mode of action of small molecules in biological systems, their phenotypic effects and to predict their impact on human diseases

Your Qualifications
- Diploma/Master or equivalent degree preferably in Computer Science, Bioinformatics, or Chemistry/Biology with a computational component
- Programming skills
- Interest on biology
- Highly motivated and team oriented

Our Offer
- Working in an innovative, well- equipped and scientifically stimulating surrounding
- Further training opportunities
- Initial short-term employment contract for three years and a standard public service salary (TVÖD)

We look forward to receiving your application via e-mail with a cover letter, CV
and names and contact information of three references to:
Monica Campillos
e-mail: monica.campillos @ helmholtz-muenchen.de

posted 2010.11.16

Position in Systems Biology at the University of Nebraska Medical Center open

Position in Systems Biology in the Department of Pharmacology and Experimental Neurosciences at the University of Nebraska Medical Center:

Postdoctoral Research Associate or Instructor depending on qualifications.

The successful candidate will use computational approaches and statistical analysis in parallel with gene/protein functional annotation tools to analyze proteomic and transcriptomic data relevant to neurodegenerative and/or infectious diseases. Individual will interact with investigators including neuroscientists, molecular biologists, virologists, statisticians and computer scientists both in our department at the College of Medicine at UNMC and our collaborators at the College of Information Science and Technology at the adjacent UN Omaha. A doctorate degree from an accredited college/university in a discipline related to biomedical research is required; productive postdoctoral experience is required for the Instructor-level position. Training or experience in bioinformatics is required, using tools such as R/BioConductor, Partek, GenePattern and Cytoscape to analyze and visualize large datasets. Entry or middle level knowledge of relevant programming languages is required.

Interested candidates should email a CV and contact information for 3 references to Dr. Howard Fox, c/o Gina Eide (rmeide @ unmc.edu). Individuals from diverse backgrounds are encouraged to apply.

posted 2010.11.04

Postdoctoral Position at the University of Texas at Dallas open

Applications are invited for an NIH funded Postdoctoral position in the University of Texas at Dallas within the research group of Prof. Leonidas Bleris. The project will be co-supervised by the Bleris Lab and the Ward/Ober Lab from the University of Texas, Southwestern Medical School.

The successful candidate will work towards modeling the behavior of engineered antibodies and subcellular trafficking in vivo. These models will be developed and extensively validated against experimental data that will be generated in the Ward/Ober Lab. The study aims to reveal important insights into the design of potential new therapeutic agents for the treatment of autoimmune diseases.

Candidates should have a Ph.D. with expertise in mathematical modeling.

The position is available immediately and all applications (including CV and references) should be sent to Prof. Leonidas Bleris (bleris @ utdallas.edu).

For further information about our research and the workplace environment (NSERL) please visit:
NSERL: http://ecs.utdallas.edu/nserl-slideshow.html
Bleris Lab: http://www.utdallas.edu/~bleris/
Ward/Ober Lab: http://www4.utsouthwestern.edu/wardlab/index.asp

posted 2010.10.28

University of California, Irvine Tenured or Tenure-track Faculty Position in Systems Biology open

The University of California, Irvine is renewing its recruiting initiative in Systems Biology.

Two positions are available this year, for which candidates will be considered from all areas of Systems Biology, including biological networks, regulatory dynamics and control, spatial dynamics and morphogenesis, synthetic biology, and mathematical and computational biology. Applications are being solicited at the Assistant Professor level, and appointment can be made in any of several departments, including Developmental and Cell Biology, Molecular Biology and Biochemistry, Ecology and Evolutionary Biology, Biomedical Engineering, Mathematics, Physics and Astronomy, Computer Science, and Statistics. Applications at the Associate and Full Professor level will also be considered, with appointment being subject to the availability of funds.

The successful applicant is expected to conduct a strong research program and to contribute to the teaching of undergraduate and graduate students. Systems Biology research and training at UCI is fostered by several interdisciplinary research units, an NIGMS National Center for Systems Biology, and Ph.D. training programs in Bioinformatics, and Mathematical and Computational Biology (for more information, see http://ccbs.bio.uci.edu). Applicants should submit a letter of application, curriculum vitae, bibliography, three letters of reference, and statements of research and teaching interests using the on-line recruitment system (see instructions at http://ccbs.bio.uci.edu or https://recruit.ap.uci.edu, under "Institutes and Centers"). To receive full consideration, material should be received by December 10, 2010.

The University of California, Irvine is an equal opportunity employer committed to excellence through diversity, and strongly encourages applications from all qualified applicants, including women and minorities. UCI is responsive to the needs of dual career couples, is dedicated to work-life balance through an array of family-friendly policies, and is the recipient of an NSF ADVANCE Award for gender equity.

posted 2010.10.22

PhD in evolutionary genomics (Geneva, Switzerland) closed

We are looking for a highly motivated and innovative PhD student to explore the evolution and patterns of selection acting on Conserved Non-Coding sequences (CNCs) using computational comparative genomics. It is estimated that about 4-7% of the human genome is under functional selection, yet only 2% encode proteins. This implies that there is a repertoire of functionally important elements at least as large as the repertoire of protein-coding genes, whose functions remain largely unknown. The project will develop our lead findings and will benefit from established collaborations.

The ideal candidate should have a strong background in bioinformatics including programming skills, and experience/background in molecular evolution. A Diploma or MSc degree in Biology or Bioinformatics, practical experience in the Unix environment, and fluency in English are required.
The project will be supervised by Prof. E. Zdobnov at the Department of Genetic Medicine and Development of the University of Geneva Medical School. We are also part of the renowned Swiss Institute of Bioinformatics, and offer a stimulating research environment with excellent facilities.

Closing date for applications: 15 November 2010.

To apply:
    send your full CV, statement of research interests,
    and names and contact details of at least two referees
    by e-mail to Evgeny.Zdobnov@isb-sib.ch with "phd job" subject.

The international city of Geneva, described as ʻthe smallest of the large capitalsʼ, offers a
vibrant city life within easy reach of the picturesque lake and stunning Alps.

posted 2010.10.19

PhD Student - Systems Biology of Small Molecules open

The Helmholtz Zentrum is a member of the Helmholtz Association of German Research Centres, a leading association Europe-wide, focusing on "Environmental Health".
The aim of its research is to proactively detect health risks for both humans and the environment, decoding the mechanisms of pathogenesis and developing concepts for prevention and therapy of diseases.
The new research group "Systems Biology of Small Molecules" has a Ph.D position open available immediately.

Job Description
- Develop computational methods to integrate existing datasets from small molecules and proteins with new data generated in collaboration with experimental groups
- To understand better the mode of action of small molecules in biological systems, their phenotypic effects and to predict their impact on human diseases

Your Qualifications
- Diploma/Master or equivalent degree preferably in Computer Science, Bioinformatics, or Chemistry/Biology with a computational component
- Programming skills
- Interest on biology
- Highly motivated and team oriented

Our Offer
- Working in an innovative, well- equipped and scientifically stimulating surrounding
- Further training opportunities
- Initial short-term employment contract for three years and a standard public service salary (TVÖD)

We look forward to receiving your application via e-mail with a cover letter, CV
and names and contact information of three references to:
Monica Campillos
e-mail: monica.campillos@helmholtz-muenchen.de

posted 2010.10.19

Postdoc in Computational and Evolutionary Modeling of Metabolic and Regulatory Networks open

This postdoc position is available immediately and will be advertised until filled.
Candidate will participate in the development of computational and systems biology methods to enable systems biology knowledgebase for DOE (joint proposal with Mark Gerstein from Yale U).  Applicant will work at the interface of physics and life sciences on computational analysis and mathematical modeling of metabolic and regulatory networks in bacteria. This includes: 1) developing new algorithms; 2) carrying out genomic, correlative, and topological analysis of integrated networks; and 3) performing dynamical and evolutionary modeling along the lines of PNAS, 106, 9743 (2009). Under the direction of Sergei Maslov .

Applicant will be expected to participate in lab meetings, and to help train, guide and mentor graduate students in Dr. Maslov's lab. The postdoctoral associate will also be expected to make presentations regarding his/her research, to publish the original results of research in peer-reviewed high-impact scientific journals, and to participate in grant proposal preparation.
A genuine interest in computational biology is required, as well as good interpersonal and communication skills and effective work habits. Background in mathematical modeling of biological systems and familiarity with MATLAB is a plus.
Applicants have to submit curriculum vitae, brief (less than one page) statement of research interests (in one document), and arrange for 3 recommendation letters to be sent to:
Dr. Sergei Maslov (E-mail: maslov@bnl.gov). Alternatively, applicants can apply online at: http://www.bnl.gov/HR/jobs/jobsCheck.asp (job #15503). BNL policy states that Research Associate appointments may be made to those who have received their doctoral degree within the past five years.
Starting salary of postdocs at Brookhaven is $50,000-$55,000/year.  Especially qualified candidates will be considered for Goldhaber Fellowship that will increase starting salary to $75,000/year. After three years Goldhaber Fellows are likely to be considered for tenure track (permanent staff) positions at BNL.

Employer:
Located on Long Island, New York, Brookhaven National Laboratory (BNL) is a multi-program national laboratory operated by Brookhaven Science Associates for the U.S. Department of Energy (DOE). Brookhaven has a staff of approximately 3,000 scientists, engineers, technicians and support staff and over 4,000 guest researchers annually. Brookhaven campus encompasses 5000 acres in close proximity to beaches on both the Atlantic Ocean and the Long Island Sound. It is located about 1 hour east from New York City to which it is connected by regular train service from nearby stations. There are no citizenship restrictions for employment. Non-US citizens typically work on H-1B or J-1 visas.

posted 2010.10.01

Bioinformatics Scientist, Novartis Vaccines and Diagnostics srl open

A Bioinformatics Scientist position is available at Novartis Vaccines and Diagnostics srl Research Center in Siena, Italy.

Responsibilities
We are building a core service for molecular epidemiology of bacterial pathogens at the Novartis Research Center and we are looking for a bioinformatician to serve as the expert database developer and data manager within the team. The primary responsibility of this position is to provide a framework for the statistical analysis of genomics data from a variety of projects within the institute and as part of world-wide collaborations. On-going projects cover a broad spectrum of topics, from the analysis of whole genomes to epidemiology of selected antigens for vaccines development.

Requirements
PhD in bioinformatics, mathematics, physics, computer science or related field and familiarity with biological research problems. Experience in statistical analysis of large genomic datasets is essential, in particular molecular evolution and phylogeny methods. Familiarity with systems biology data and tool integration platforms is highly desirable.

Required skills:
* Solid understanding of computational techniques associated with whole genome sequences
* In-depth knowledge of public biological sequence databases
* Fluency with Perl and R
* Good programming skills in at least one OO language: Java, C++
* Experience with a mainstream RDBMS: PostgreSQL, Oracle or MySQL

Knowledge of computational methods for molecular epidemiology and population genetics are a plus.

The successful candidate will join a team of bioinformaticians and software engineers. We value highly the ability to react quickly to evolving requirements and implement creative solutions using existing open-source software. The initial appointment will be one year.

Please send a CV and two reference letters to the following address: claudio.donati @ novartis.com

posted 2010.09.29

Post-Doc Image Processing (open) open

In the frame of multiple systems biological projects funded by the German Ministry for Education and Research (BMBF: MEDSYS, FORSYS, Virtual Liver, GerontoSys) the Hamamatsu TIGA (Tissue Imaging and Analysis) Center of the University Hospital Heidelberg is looking for a

Post-Doc in Applied Image Processing (Virtual Microscopy)

The TIGA is collaborating with many research groups of the Heidelberg University Hospital (e.g. Institute of Pathology, National Center for Tumor Diseases), the German Cancer Research Center (DKFZ), international companies and BMBF-project partners from different universities. The TIGA is running manifold research projects covering clinically relevant questions in terms of the semi-automatic and automatic processing of tissues by using high-throughput microscopy, particularly virtual microscopy. More precisely e.g. diagnostic
approaches using histological tissue sections are developed as well as methods to extract relevant data for systems biological tissue simulations out of the images. Your task is to plan projects together with our partners within the given research framework and to develop and finally publish novel image processing algorithms.

Environment: The TIGA Center is a cooperative unit with multiple partners and is hosted in the internationally leading systems biological center BIOQUANT at the University Heidelberg. You will work in close collaboration with multiple research groups of the University Hospital (e.g. National Center for Tumor Diseases), German Cancer Research Center (DKFZ) and other groups. The open position therefore offers an exciting environment for interdisciplinary research at the pulse of modern systems biology. We offer a friendly but dynamic working
atmosphere where you have the unique opportunity to daily work with experimentalists in our own and related groups to optimally continue your scientific career.

Position: We are looking for a committed and integrating personality who values this special environment and would like to contribute his or her outstanding experience in developing image processing algorithms. Particularly, the existing image processing platform should be used and further developed within the scope of the various research projects. Also we expect a strong interest for systems biology, the ability to communicate in English in daily routine and to write scientific publications. Participation in teaching is welcomed.

Your application should contain
a) a detailed CV
b) description of previous scientific experiences (please select a representative publication)
c) your interests or method spectrum
d) two possible contacts for references

The position is currently limited for 2 years. Salary is according to TV-L 13.
The University of Heidelberg is an equal opportunity employer.

Please send your application exclusively by e-mail to: tiga.jobs @ googlemail.com
PD Dr. Niels Grabe,
Institute for Medical Biometry and Informatics,
University Hospital Heidelberg.

posted 2010.09.29

Post-Doc Systems Biology Large-Scale Networks (open) open

In the frame of multiple systems biological projects funded by the German Ministry for Education and Research (BMBF: MEDSYS, FORSYS, Virtual Liver, GERONTOSYS) the Hamamatsu TIGA (Tissue Imaging and Analysis) Center of the University Hospital Heidelberg is looking for a

Post-Doc Systems Biology / Bioinformatics: Qualitative Large-Scale Networks and Simulation.

Topic: You will work in close collaboration with multiple research groups of the University Hospital (e.g. National Center for Tumor Diseases), German Cancer Research Center (DKFZ) as well as international companies on multiple clinically relevant questions. Goal of the works is the development of algorithms for modeling and simulation of qualitative large-scale networks. The logical or qualitative networks are to be constructed from different gene and protein databases and used for interpreting experimental high-throughput data from our own lab or partners. Logical or qualitative reasoning and simulation approaches will be used for
deriving predictions from the networks. Together with the project partners and other team members you will structure the projects, implement apply novel algorithms and publish the results.

Environment: The TIGA Center is a cooperative unit with multiple partners and is hosted in the internationally leading systems biological center BIOQUANT at the University Heidelberg. The open position therefore offers an exciting environment for interdisciplinary research with state-of-the art experimental and theoretical techniques. We offer a friendly but dynamic working atmosphere where you have the unique opportunity to daily work with experimentalists in our own and related groups to optimally continue your scientific career.

Position: We are looking for a committed and integrating personality who values this special environment and would like to contribute his or her outstanding experience. Your background could from bioinformatics or a related discipline. You should have demonstrated experience in developing theoretical methods for handling large-scale networks, should have sufficient software development experience and be acquainted with the according databases. Experience in dealing with microarray data is expected. We expect a demonstrated interest for systems biology and the ability to communicate in English in daily routine. Participation in teaching is welcomed.

Your application should contain
a) a detailed CV
b) description of previous scientific experiences (please select a representative publication)
c) your interests or method spectrum
d) two possible contacts for references

The position is currently limited for 2 years. Salary is according to TV-L 13.
The University of Heidelberg is an equal opportunity employer.

Please send your application exclusively by e-mail to: tiga.jobs @ googlemail.com
PD Dr. Niels Grabe,
Institute for Medical Biometry and Informatics,
University Hospital Heidelberg.

posted 2010.09.29

Post-Doc Systems Biology Multi-Cellular Simulation (open) open

In the frame of multiple systems biological projects funded by the German Ministry for Education and Research BMBF: MEDSYS, FORSYS, Virtual Liver, GerontoSys) the Hamamatsu TIGA (Tissue Imaging and Analysis) Center of the University Hospital Heidelberg is looking for a

Post-Doc in Multi-Cellular Simulation (in Bioinformatics, Software Engineering, Visualization)

We have developed the foundations of a novel multi-cellular simulation environment based on multi-agent systems (Bioinformatics, 25(16):2057-63) for epithelial tissue, especially for the simulation of the rapid renewal process of human skin. In this simulation behavioral models of individual cells interact to form the emergent properties of epithelial tissue. We are now aiming at further developing the simulation towards a more realistic histomorphological behavior and integrating gene functions (molecular networks) into the cell behavioral models. We are looking for a skilled scientist, with experiences in software development, simulation, visualization with knowledge in bioinformatics or related disciplines. Experimental (e.g. histological) reference data are generated in our own lab from native tissue and in vitro experiments. The molecular networks to be integrated are constructed by cooperating team members and will be implemented in close collaboration.

Environment: The TIGA Center is a cooperative unit with multiple partners and is hosted in the internationally leading systems biological center BIOQUANT at the University Heidelberg. You will work in close collaboration with multiple research groups of the University Hospital (e.g. National Center for Tumor Diseases), German Cancer Research Center (DKFZ) and other groups. The open position therefore offers an exciting environment for interdisciplinary research at the pulse of modern systems biology. We offer a friendly but dynamic working atmosphere where you have the unique opportunity to daily work with experimentalists in our own and related groups to optimally continue your scientific career.

Position: We are looking for a committed and integrating personality who values this special environment and would like to contribute his or her outstanding experience. Your background could be from computer science, bioinformatics or a related discipline. The existing software package has been developed using state-of-the art software engineering techniques in JAVA. Therefore we expect according knowledge in working on larger software packages. Experience in visualization would be beneficial. Also we expect a strong interest for multi-cellular systems biology, the ability to communicate in English in daily routine and to write scientific publications. Participation in teaching is welcomed.

Your application should contain
a) a detailed CV
b) description of previous scientific experiences (please select a representative publication)
c) your interests or method spectrum
d) two possible contacts for references

The position is currently limited for 2 years. Salary is according to TV-L 13.
The University of Heidelberg is an equal opportunity employer.

Please send your application exclusively by e-mail to: tiga.jobs @ googlemail.com
PD Dr. Niels Grabe,
Institute for Medical Biometry and Informatics,
University Hospital Heidelberg.

posted 2010.09.29

PhD Systems Biology Multi-Cellular Simulation (open) open

In the frame of multiple systems biological projects funded by the German Ministry for Education and Research (BMBF: MEDSYS, FORSYS, Virtual Liver, GerontoSys) the Hamamatsu TIGA (Tissue Imaging and Analysis) Center f the University Hospital Heidelberg is looking for a

PhD Systems Biology / Bioinformatics: Multi-cellular Models, Networks & Simulation.

We have developed the foundations of a novel multi-cellular simulation environment based on multi-agent ystems (Bioinformatics, 25(16):2057-63) for epithelial tissue, especially for the simulation of the rapid renewal rocess of human skin. In this simulation behavioral models of individual cells interact to form the emergent roperties of epithelial tissue. Therefore, we are offering a PhD position in which novel strategies will be eveloped to integrate molecular network based models into cell behavioral models for subsequent simulation.
Thereby logical or qualitative network models will drive the behavior of each cell. Experimental reference data re generated in our own lab from native tissue and in vitro experiments.

Environment: The TIGA Center is a cooperative unit with multiple partners and is hosted in the internationally eading systems biological center BIOQUANT at the University Heidelberg. You will work in close collaboration ith multiple research groups of the University Hospital (e.g. National Center for Tumor Diseases), German ancer Research Center (DKFZ) and other groups. The open position therefore offers an exciting environment or interdisciplinary research with state-of-the art modern systems biology. We offer a friendly but dynamic orking atmosphere where you have the unique opportunity to daily work with experimentalists in our own and related groups to optimally continue your scientific career.

Position: We are looking for a committed and integrating personality who values this special environment and would like to contribute his or her outstanding experience. Your background should be from computer cience, bioinformatics or a related discipline. You should have experience in software developing/engineering JAVA preferred). You will closely interact with biologists, therefore a general background in bioinformatics s expected for understanding the project needs. Also we expect a strong interest for multi-cellular systems iology, the ability to communicate in English in daily routine and the interest in contributing to scientific publications.

Your application should contain
a) a detailed CV
b) a description of previous scientific experiences (please select a representative publication)
c) your interests or method spectrum
d) two possible contacts for references

The position is currently limited for 2 years. Salary is according to TV-L 13/2.
The University of Heidelberg is an equal opportunity employer.

Please send your application exclusively by e-mail to: tiga.jobs@googlemail.com
PD Dr. Niels Grabe,
Institute for Medical Biometry and Informatics,
University Hospital Heidelberg.

posted 2010.09.29

Postdoctoral Position in Complex Biological Networks open

The group of Professor Adilson E. Motter at the Department of Physics and Astronomy, Northwestern University, has an opening for a postdoctoral position in the area of systems biology. The research will focus on the predictive modeling of dynamical processes in intracellular networks, with emphasis on the analysis of network perturbations and its applications to the study of cancer. The ideal candidate will have experience in the areas of systems biology, computer simulations, and complex networks. Previous experience with cancer biology, nonlinear dynamics, and/or data analysis would be a plus.  Competitive candidates will also have good writing skills and a demonstrated ability to conduct independent high-impact research. This project will interact synergistically with ongoing projects on epigenetics and gene regulation mechanisms relevant to cancer development at the Northwestern University's Physical Sciences-Oncology Center.

The appointment is available immediately. Salary is competitive, depending on qualifications and experience. To apply, please e-mail curriculum vitae along with a brief statement of how your research interests are related to this position to Adilson E. Motter at motter@northwestern.edu, and arrange to have two letters of recommendation e-mailed to the same address. Applications received before October 15, 2010 will receive full consideration. For more information about The Motter Group, please go to http://www.physics.northwestern.edu/people/personalpages/amotter.html.

The Department of Physics and Astronomy at Northwestern University is located in Evanston, Illinois, which is situated along the shores of Lake Michigan only 30 minutes north of downtown Chicago. Northwestern University is an Affirmative Action/Equal Opportunity Employer. Applications from women and under-represented minorities are encouraged. Hiring is contingent upon eligibility to work in the US.

posted 2010.09.24

Postdoctoral Researcher in Systems Biology open

NATURE AND SCOPE OF JOB
The Global Security Computing Applications Division (GS-CAD) at Lawrence Livermore National Laboratory has an opening for a postdoctoral researcher in Bioinformatics and Systems Biology. The successful applicant will contribute to the research and development of systems biology tools integrated within the Protein Function Prediction Platform project, supported by DTRA's Transformational Medical Technology Initiative, to enable rapid genome-scale analysis of newly sequenced pathogens, provide a higher-level context for the biological function of proteins and pathways of interest, and support research to identify and analyze potential target genes for countermeasure development. The candidate will develop methods to predict and analyze pathway modularity and pathway membership based on protein structure-to-function and protein-protein interaction predictions generated by other modules of the project. The successful candidate will work as part of a computational and systems biology team, and will have the opportunity to interact with molecular biologists, geneticists, immunologists, biochemists, chemists, engineers, physicists and computer scientists. Will also have the opportunity to pursue independent (but complementary) research activities. Will report programmatically to the principal investigator and administratively to GS-CAD's Computational Biology & Bioinformatics Group Leader.

NOTE: This is a one-year term appointment with the possibility of extension to a maximum of three years. Eligible candidates are recent Ph.D.s within five years of the month of the degree award at time of the employment offer.
 
ESSENTIAL DUTIES
- Integrate systems biology tools into the larger platform, and to develop novel ways to bridge between high level systems-based insights and low-level protein structure and structure-to-function analyses working closely with other members of the Protein Function Prediction Platform project.
- Develop and implement methods to predict and analyze pathway modularity and pathway membership based on protein structure-to-function and protein-protein interaction predictions
- Develop strong, mutually beneficial scientific collaborations interacting with other staff members within GS-CAD and the Biosciences and Biotechnology Division.
- Present results at group meetings, workshops, scientific conferences, and sponsor meetings.
- Prepare research results for publication in scientific journals.
- Prepare monthly progress reports to support project needs and deadlines.
- Identify and pursue complementary research problems.
- Perform all assignments in accordance with ESH&Q, Security, and business practice requirements and policies.

ESSENTIAL SKILLS, KNOWLEDGE AND ABILITIES

- Recent Ph.D. in Computer Science, Mathematics, Statistics, or Biological Sciences with significant bioinformatics experience.
- Candidates must show significant achievement in computational biology, and a strong background in genomics, systems biology, or protein structure.
- Demonstrated competency in a broad range of bioinformatics tools and databases (e.g., BLAST, CLUSTALW, HMMER, Pfam, NCBI databases, PDB, Uni-Prot, Gene Ontology).
- High-level analytical and programming skills, preferably in Perl or Python, as well as first-hand experience with the analysis of large-scale biological data sets.
- Advanced technical writing skills with a publication record in peer-reviewed literature and experience presenting research results to a large audience.
- Demonstrated initiative, leadership, and communication skills with desire and ability to work in a collaborative, multidisciplinary team environment.

DESIRED SKILLS, KNOWLEDGE AND ABILITIES
- Hands-on experience with SRI International's Pathway Tools platform and the BioCyc collection of pathway genome databases.
- Expertise in metabolic modeling, protein structure modeling, molecular dynamics, protein function prediction, protein annotation, pathogen biology, or immunology.
- Expertise in Machine Learning, including HMM, SVM, Bayesian methods, etc.
- Knowledge of Matlab, R, SQL, Lisp.

Please apply via http://jobs.llnl.gov, job# 008779

https://jobs.llnl.gov/psc/jobs/EMPLOYEE/HRMS/s/WEBLIB_LL.VIEW_JOBS_LL.FieldFormula.IScript_View_Jobs_LL?KEYWORD=008779&x=0&y=0&

For more information, contact Dr. Patrik D'haeseleer, patrikd at llnl.gov

posted 2010.09.01

Biology/Mathematical Modeler (Scientist/Sr. Scientist) open

At Pfizer BioTherapeutics Division, Applied Quantitative Genotherapeutics (AQG) group, we are dedicated to developing and implementing investigative approaches focused on evaluating potential drug candidates and identifying new targets in preclinical models of disease. We use the latest scientific knowledge and apply novel approaches to discover new ways of treating disease. We encourage cooperation and support a high level of scientific freedom to find the best answers to biological questions. Located in South San Francisco, AQG provides the feel of a small start-up company with the resources of a large pharmaceutical company in the heart of the biotech capital of the world.


Responsibilities:

As part of the Applied Quantitative Genotherapeutics group, you will be working with a multi-disciplinary team which utilizes both bench biology and computational skills.  You will use your understanding of biology and computational expertise to partner with, and support, project teams and individuals in research, clinical or business units.

A desirable candidate is someone with a strong mathematical background (for example - physics, chemical or electrical engineering, etc.) who is willing to apply these skills to biological and physiological systems in order to aid in generation and optimization of biotherapeutics.  It is required that this person have some general awareness of biological systems.  Another desirable candidate is someone with a multi-disciplinary biological background (for example - biology, biochemistry, immunology etc.) who would be willing to learn the mathematical skills necessary to model the systems described above.  An ideal candidate would possess all of the above qualifications.  This position will be located in South San Francisco, with the group being split between Cambridge MA and South San Francisco.


Qualifications:

BS, MS, or PhD in the biomedical or physical sciences (or equivalent) required with a minimum of 2-3 years experience in the biotechnology, pharmaceutical or chemical industry.  Awareness of current modeling techniques or a strong background in biology is preferred.  The successful candidate should be willing to learn new areas of science and be a superior written and oral communicator.

Please submit resumes for Requisition #942863 to www.pfizer.com

posted 2010.08.26

FACULTY POSITION at UCSB open

FACULTY POSITION
MELLICHAMP CHAIR IN SYSTEMS BIOLOGY
DEPARTMENTS OF MECHANICAL ENGINEERING &
ELECTRICAL AND COMPUTER ENGINEERING
UNIVERSITY OF CALIFORNIA, SANTA BARBARA


The Departments of Mechanical and Electrical/Computer Engineering at the University
of California, Santa Barbara seek to hire a highly creative and productive individual
to fill a Mellichamp Chair in Systems Biology, made possible by a generous gift by Duncan
and Suzanne Mellichamp. Candidates at all levels and in all areas of Systems Biology will
be considered, with preference given to candidates who incorporate an experimental element
to their research.

UCSB is emerging as a leader in the field of Systems Biology. Current efforts focus on
the computational modeling, simulation, analysis, and mechanical manipulation of biological
networks, bio-image informatics, as well as the development of new sensors/devices for
biomolecular analysis. A number of important biological processes are under investigation,
including gene regulation, protein translocation, bioadhesion, and cellular mechanosensation.

The Systems Biology program is supported by superb interdisciplinary research and education
centers on campus, including the Center for Control Dynamical Systems and Computation,
the ARO-sponsored Institute for Collaborative Biotechnologies, the California NanoSystems
Institute, the Center for Stem Cell Biology and Engineering, the Neuroscience Research
Institute, the Materials Research Laboratory, Center for Bio-image Informatics, and the
Kavli Institute for Theoretical Physics.

UCSB College of Engineering has an outstanding record of multidisciplinary recruiting.
Highly qualified individuals from all relevant disciplines are encouraged to apply.
Primary and/or Joint appointments in related departments are possible. The University is
especially interested in candidates who can contribute to the diversity and excellence
of the academic community through research, teaching, and service.

Applications must be submitted electronically at: http://me.ucsb.edu/position/mellichamp

Applications should contain a letter briefly outlining career plans, a statement of research
and teaching interests, curriculum vitae, and names and contact information for 3 - 5 references.
Although the position will remain open until filled, applicants are encouraged to submit their
applications by November 30, 2010 for priority consideration. Please note this is a new search;
prior applicants must reapply.

Questions regarding this position should be directed to the Chair of the Search Committee,
Professor Megan Valentine, at: sysbio at engineering.ucsb.edu.

The University of California is an equal opportunity, affirmative action employer.

posted 2010.08.25

Software Developer, Sage Bionetworks, Seattle, WA open

Sage Bionetworks is recruiting for a Software Developer to assist in the building and deployment of the Network Data Management Component (NDMC) or other components of the Sage Commons, providing scalable access to biological network data. The NDMC is the core repository for network models in the Sage Commons and is fundamental to the transition of data and practices to a scalable platform that can serve a broader community of scientists interested in aggregating, sharing and collaboratively improving our understanding of the biological networks that underlie human health and disease.

This position will be part of a newly-formed team responsible for the development and non-user testing of the NDMC. 

Specific responsibilities include:

  • Designing and implementing user interface software solutions, data driven middle-layer software components and storage layer software components
  • Developing system interface specifications and implementing code to meet these specifications
  • Deploying developed software
  • Troubleshooting code defects, and implementing and deploying timely fixes
  • Identifying areas for optimization and improvement
  • Interacting directly with stakeholders to understand their needs
  • Analyzing new requirements and providing accurate effort assessments and delivery estimates
  • Participating in design and code reviews
  • Creating and maintaining technical documentation

Qualifications:

  • Bachelors degree or higher in Computer Science, Software Engineering or equivalent required. Biology related coursework or work experience preferred.
  • At least four years experience in the software industry shipping enterprise and / or web-scale software systems
  • Versatile and strong programming skills in a variety of computer languages, including:
    • Working knowledge of C++ and enterprise-level Java
    • Knowledge of .NET languages, including C#/Mono
  • Experience in building web user interfaces and data transfer applications
  • Strong understanding of, and experience utilizing, object oriented design and programming, and design patterns
  • Experience designing software APIs used by other software development teams. 
  • Ability to rapidly assess and integrate new software technologies into a complete solution
  • Experience with and strong understanding of an SDLC methodology
  • Solid understanding of database fundamentals and knowledge of SQL
  • Excellent verbal and written communication skills
  • Ability to balance concurrent tasks
  • Experience in Bioinformatics preferred

Sage Bionetworks, www.sagebase.org, is a medical research organization building advanced predictive models of disease.  Sage offers a comprehensive benefits package, including relocation benefits to bring the right talent to the team.

To apply for this position, please contact: sw.jobs at sagebase.org

posted 2010.08.23

Postdoctoral Research Associate, Systems Biology of Ageing open

Postdoctoral Research Associate,
Systems Biology of Ageing (2 posts)
at the University of Rostock, Department of Systems Biology & Bioinformatics

Applications are invited from highly motivated individuals to work in an interdisciplinary environment, combining mathematical modeling with molecular cell biology.

The positions are available from early 2011 for a period of up to three years and are paid according to the German academic pay scale (E13 100%), which varies with age and experience. The research is conducted as part of a research network, involving six experimental groups in the Faculty of Medicine at the University of Rostock, two industrial partners and two external academic partners in Leipzig and Lübeck.  Mitochondria and ROS production are key elements in the pathogenesis of degenerative diseases which ultimately determines the overall process of ageing. The experimental partners in the network will generate data from the subcellular level, in different experimental systems and for different organs. One of the posts will focus on mathematical modeling of ROS production, while the other focuses on ROS induced DNA damage and p53 signaling and inflammatory response. The modeling work is embedded in an iterative cycle of quantitative cell biology, mathematical modeling, parameter estimation, study of patterns in transient dynamics and sensitivity analysis, design of refined experiments and experimental validation of model predictions to understand ROS effects and induced downstream responses at the subcellular level.

The Department of Systems Biology & Bioinformatics provides a vibrant research environment, with extensive experience in interdisciplinary collaborations, covering a wide range of methodologies and technologies. The group moved in July 2009 into a new building and provides excellent facilities. The University of Rostock, founded in 1419, is one of the oldest in Europe. Rostock is located in the north-east of Germany with road and train connections to Berlin and Hamburg, as well short ferry links to Denmark, Sweden and other Baltic states. The area around Rostock is one of the most popular tourist regions in Germany.

Applications, including a full CV, copies of certificates and contact information of three referees should be send to Prof. Olaf Wolkenhauer in PDF format by Email: peggy.sterling at uni-rostock.de (Subject: "ROSage"). Candidates should demonstrate their experience in applied mathematical modeling and interest in systems biology of ageing by providing a one page overview of their main achievements; providing pdfs of their most important publications, with a short description of the method(s) used and his/her contribution to the paper; and a one page description of goals and objectives related to the new post.

posted 2010.08.19

Postdoctoral Research Associate, Systems Biology of Cell Signaling Networks open

Applications are invited from highly motivated individuals interested in integrating quantitative experimentation and computational modeling in the field of molecular cell biology.

The successful applicant will join a dynamic team engaged in a multidisciplinary effort combining an array of experimental and computational approaches to understand the dynamic co-regulation of signaling pathways in normal cells and their dysfunctional regulation in cancer cells.

The position is available immediately, and funding for the project is available for up to four years. Salary will be offered commensurate with current NIH postdoctoral fellowship stipend levels.

The successful candidate will hold a Ph.D. in bioengineering, biophysics, chemical engineering, cell biology, or a related field.
Applications including full CV and contact information of three references should be sent to Prof. Haugh by email:

Jason M. Haugh
Professor of Chemical & Biomolecular Engineering
North Carolina State University
jason_haugh @ ncsu.edu

posted 2010.08.04

A research associate position in the Systems Biology Research Group at the University of Rostock open

A research associate position is available in the Systems Biology Research Group at the University of Rostock (Olaf Wolkenhauer, www.sbi.uni-rostock.de) for a duration of 3 years and which could lead to a PhD.

Candidates should have a Masters degree or diploma in either mathematics, physics, engineering or computer science and demonstrate the ability to do independent research in an interdisciplinary environment.

They are expected to support the group leader in administrative and teaching matters. A solid mathematical background and excellent English language skills are required.

The salary is according to the German University payment scheme (E13).

The Wolkenhauer Group provides a vibrant research environment, with a number of active research projects in the areas of bioinformatics and systems biology. The group moved in July 2009 into a new building and provides excellent facilities.

The University of Rostock (founded in 1419) is one of the oldest in Europe and the north-east of Germany is one of the most attractive tourist regions of Germany.

Interested candidates should send their CV and documents in pdf format to:

olaf.wolkenhauer @ uni-rostock.de

posted 2010.08.04

BioInformatics Scientist open

AVEO Pharmaceuticals, Inc.
75 Sidney Street, 4th Floor
Cambridge, MA  02139
www.aveopharma.com
 
BioInformatics Scientist
Reports to: Manager Bioinformatics

Job Code: 10-TR25
Department: Translational Research
Location: Cambridge, MA

Description
We are seeking a highly motivated, independent bioinformatics scientist to join a group of scientists, analysts and programmers to develop tools and methodologies for large-scale gene expression data analysis.  The group supports a variety of research projects in target and drug discovery as well as biomarker development for AVEO's growing pipeline of novel anti-cancer drugs,

AVEO's Translational Research program utilizes a novel platform combining proprietary, inducible tumor models and bioinformatics approaches to discover, validate and generate therapeutics against molecular targets in oncology.  We have generated large populations of tumors that exhibit inter-tumor heterogeneity similar to that seen in human tumor populations. Each tumor has been characterized by microarray, array CGH, histology, key signaling pathways as well as sensitivity to a variety of cancer therapeutics, including AVEO's clinical stage drug candidates.  This well-characterized tumor population model system enables the correlation of gene expression and DNA copy number with drug efficacy, providing an attractive platform for the creative innovative bioinformatics scientist to develop and test translational hypotheses. Our goal is  to use the platform to inform clinical trial design regarding tumor, tumor subtype and patient selection for AVEO's own clinical stage oncology drug candidates.

Responsibilities
The candidate will:
*    Participate in generating, processing and evaluating large oncology-related datasets. 
*    Work on a variety of high-dimensional data projects largely centered on biomarker discovery and develop biomarkers for response to therapy and disease subtype classification
*    Execute a wide range of computational and analytical tasks, including developing and implementing algorithms for target identification and biomarker discovery.
*    Integrate publicly or commercially available genomic data with novel experimental data.
*    Identify and execute innovations (computational, statistical, and strategic) that will quantifiably improve Projects
*    Identify new datasets and data mining techniques relevant to cancer target and drug discovery
*    Develop and test novel methods and algorithms, working with academic collaborators where opportunities arise

Qualifications & Requirements
*         PhD in Biology, Bioinformatics, or equivalent, as well as 2+years of full time experience in an academic or biotechnology industry lab, or equivalent experience.
*         Interest in, and working knowledge of cancer biology,
*         A solid understanding of statistics. Have experience with a broad range of statistical methods for classification and prediction, e.g., linear models, machine learning, and other multivariate analysis methods.
*         Programming experience and ability to write R and Perl script.
*         The candidate will have experience with large-scale genomics data and a solid understanding of bioinformatics data bases (eg: GenBank, RefSeq, dbSNP etc)
*         Experience with some bioinformatics software such as: Spotfire, Partek, Ingenuity, GeneGo, Balst, and Blat.
*         The candidate will have the ability and interest in learning new techniques and skills in accordance with evolving research program needs.
*         Candidates with a proven ability to work efficiently in a team setting, and excellent communication skills are preferred. 

About AVEO
AVEO Pharmaceuticals (NASDAQ: AVEO) integrates a proprietary cancer biology platform with drug development and commercial expertise in its efforts to discover and develop targeted cancer therapeutics. The company's lead product, Tivozanib, is an oral, triple VEGF receptor inhibitor with potential for a best-in-class profile. Tivozanib is currently being investigated in a global, randomized Phase 3 clinical trial called TIVO-1  comparing Tivozanib to Sorafenib in advanced kidney cancer, as well as additional clinical studies in other solid tumor types. AVEO's proprietary, integrated cancer biology platform offers the company a unique advantage in oncology drug development that both increases the probability of clinical success and provides a discovery engine for high-value targets.
This approach has resulted in a promising pipeline of monoclonal antibodies against novel targets including HGF, ErbB3, RON, Notch and FGFR.
For more information, please visit the company's website at www.aveopharma.com.

Please forward resumes to hr at aveopharma.com
<mailto:hr@aveopharma.com?subject=Research%20Associate%20Drug%20Discover
y%20(DD1206M)>.

AVEO is an Equal Employment Opportunity employer that values the strength diversity brings to the workplace.

posted 2010.07.20

Faulty positions/Postdoctoral positions in Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences open

Faulty positions/Postdoctoral positions in Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

BACKGROUND:
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (SIBS, www.sibs.ac.cn), is an exciting hub of several outstanding institutes, centers and laboratories working on different disciplines. Key Laboratory of Systems Biology is one of the leading research institutes for the area of systems biology, computational biology and bioinformatics ( www.sysbio.ac.cn) in China. Shanghai is also a beautiful city to live, having many attractions and diverse culture. The successful candidates for full professors, associate professors, assistant professors, postdoctoral fellows will work with other scientists in Key Lab of Systems Biology.

RESPONSIBILITIES:
Key lab of Systems Biology will have at least three faculty openings at Assistant Professor, Associate Professor, and Full Professor levels. There are also two postdoctoral fellow (PF) positions in systems biology, bioinformatics, and computational biology. A faculty or PF in this position will collaborate with the researchers in studies conducted using genomics, proteomics, and metabolomics as well as high throughput sequencing technologies.

REQUIREMENTS:
We are looking for faculty candidates with interests in multidisciplinary research areas related to systems biology, computational biology and bioinformatics. Strong candidates in molecular biology, computer science, mathematics/statistics and related research areas will be considered. An applicant at Full, Associate, or Assistant Professor level should have a PhD degree and demonstrated research ability. Requirements for the PF position include programming skills, familiarity with data analysis software, and experience in processing various omics data.

PREFERENCES:
Preference will be given to candidates who have excellent written and oral communication skills, an in depth understanding of the biological questions, modeling and programming abilities and are good team players.

TERMS:
The position is available immediately. For appointment at Assistant Professor, Associate, Professor and Full Professor level, initial appointment will normally be on a three year contract, renewable subject to mutual agreement. PF position is on a two-year contract.

SALARY & BENEFITS:
Salary is highly competitive and will be commensurate with qualifications and experience.

HOW TO APPLY:
Applications, including curriculum vitae and bibliography, cover letter with summary of past accomplishments, as well as three letters of recommendation (sent separately) to ywu01 at sibs.ac.cn.

posted 2010.06.28

Postdoc position in modeling the development of the Drosophila wing

A postdoctoral position is available to model the development of the Drosophila wing.  This is part of a larger project to understand the relationship between genetic and phenotypic variation and evolutionary change using the Drosophila wing as a model organ.  The position is part of a collaborative project involving David Houle (Florida State University), Isaac Salazar-Ciudad (Universitat Autonoma de Barcelona) and Ian Dworkin (Michigan State University).   Primary responsibility of this position is construction of a cell-based model  of morphogenesis, differentiation and growth that will interface with sub-cellular models of gene interactions.  The winning candidate will also collaborate with a larger team to compare model to empirical results, to test and refine the model, and use the model to make evolutionary predictions.  Preference will be given to candidates  with experience in computational and analytical modeling , and a desire to fuse developmental, genetic and evolutionary approaches to fundamental questions about the relationship between genotype and phenotype.

The position is for an initial period of two years, and may be extended for an additional two years.   It will be supervised by Houle and Salazar-Ciudad.   Applications should be submitted as a single pdf file and include a curriculum vitae, a summary of research accomplishments and future research objectives, and the names and contact information for at least one professional reference (and preferably three).  Review of applications will begin July 15, 2010 and continue until a suitable candidate is identified.  Application materials should be sent electronically to David Houle (dhoule at bio.fsu.edu).  Florida State University is an Affirmative Action / Equal Opportunity Employer.

Candidates who are attending the Society for the Study of Evolution meeting are  encouraged to contact Houle (dhoule at bio.fsu.edu) to arrange an interview.  Candidates who are attending the European Evo Devo meeting are encouraged to contact Salazar-Ciudad (Isaac.Salazar at uab.cat) to arrange an interview.

posted 2010.06.23

Postdoctoral positions in computational biology at the Joint Bioenergy Institute and Lawrence Livermore National Laboratory open

The following three postdoctoral positions in computational biology, at the Joint Bioenergy Institute and Lawrence Livermore National Laboratory.

All candidates should apply through http://jobs.llnl.gov, and need to have received their Ph.D. within the past five years.

--------------------------------------------

We are looking for a Postdoctoral Researcher in Metagenomics and Bioinformatics, to develop computational analysis methods for the discovery of new enzymes and metabolic pathways isolated from biomass-degrading microbial communities. The successful candidate will be an integral part of the Microbial Communities team in the Deconstruction Division of JBEI, a large multidisciplinary team of microbiologists, microbial ecologists, biochemists, and computational biologists. The postdoc will provide the computational backbone to process and integrate the various types of experimental data generated by the team, and develop cutting-edge analysis methods to achieve a functional understanding of the metabolic processes and interactions involved. Applicants should have a strong background in bioinformatics, experience dealing with large scale sequence data / metagenomics, and a commitment to collaborative research.

Note that this postdoc will be located at the Joint Bioenergy Institute in Emeryville, CA.

Please apply via http://jobs.llnl.gov, job# 008910

--------------------------------------------

We are looking for a Postdoctoral Researcher in Systems Biology, to contribute to the research and development of systems biology tools integrated within the Protein Function Prediction Platform project, to enable rapid genome-scale analysis of newly sequenced pathogens, provide a higher-level context for the biological function of proteins and pathways of interest, and support research to identify and analyze potential target genes for countermeasure development. The postdoc will develop methods to predict and analyze pathway modularity and pathway membership based on protein structure-to-function and protein-protein interaction predictions generated by other modules of the project. Applicants must show significant achievement in computational biology, and a strong background in systems biology, machine learning, or protein function prediction.

Please apply via http://jobs.llnl.gov, job# 008779

--------------------------------------------

We are looking for a Postdoctoral Researcher in Protein Structure to Function Analysis (computer scientist, bioinformatics scientist) with strong scientific interest and experience in protein sequence analysis, protein structure analysis, and protein function annotation.
The selected candidate will contribute to the research and methods development, data integration, and application of bioinformatics tools for the needs of the Protein Function Prediction Platform project. Will provide support for all phases of the platform development life cycle including design, application development, testing, and validation of created predictions. Will design and develop approaches to solutions, explore a variety of approaches within established practices and procedures, and recommend improvements to processes as
appropriate.

Please apply via http://jobs.llnl.gov, job# 008696

--------------------------------------------

posted 2010.05.17

FACULTY POSITIONS : SYSTEMS BIOLOGY THEME at the UNIVERSITY OF WISCONSIN-MADISON open

THE WISCONSIN INSTITUTE FOR DISCOVERY (WID)- SYSTEMS BIOLOGY THEME at the UNIVERSITY OF WISCONSIN-MADISON seeks three outstanding individuals with a Ph.D. and a strong background relevant to systems biology.

The Mission of the Systems Biology Theme is to advance the frontiers of knowledge by promoting synergistic research and education at the interfaces of quantitative, computational and evolutionary biology. The successful candidate will contribute to collaborative efforts combining these approaches.

Quantitative Experimental Biology

Development and application of new measures of biological entities (e.g. molecules, viruses, microbes), including their levels, functions, activities and interactions.

Computational Biology

Integration of diverse data to advance predictive models of how biomolecular networks, viruses, cells, or whole organisms function and interact.

Evolutionary Biology

Development of new experimental, mathematical or computational approaches to better understand how viruses, cells or organisms evolve and co-evolve. 

Areas of special interest for the Systems Biology Theme include: virus-host and microbe-host interactions (beneficial or pathogenic), innate and adaptive immunity, and ecological and evolutionary dynamics.

Details about the position and the application process are available at the website listed below. These tenure track positions will be at a rank commensurate with the qualifications and background of the successful candidates. Candidates should have a distinguished academic record, exceptional potential for creative research, and a commitment to both undergraduate and graduate instruction. For more senior applicants, an outstanding reputation in the field of specialty is a prime requirement. ;

Applications should be submitted via https://newfac.sysbio.discovery.wisc.edu/.

The University of Wisconsin is an equal opportunity affirmative action employer.

posted 2010.04.16

POST-DOCTORAL RESEARCH FELLOW closed

A post-doctoral research fellowship in system biology is available at the European Centre for Living Technology, Ca' Foscari University of Venice, Venice Italy. The appointment is for one year, with possibility for extension.

A one-year postdoctoral research fellowship funded within the framework of the EuroTranBio
Project ProTuMa, is available in the group of System and Synthetic Biology. The research
project focuses primarily on unraveling the interactome network of 4 membrane biomarkers
related to the onset and progression of melanoma tumors. A broad range of experimental
strategies will be used to characterize the interaction network of candidate biomarkers aided
with cutting-edge computational techniques.

We are seeking a highly motivated and skilled postdoctoral fellow with broad experience within one or more of the following areas: molecular biology, cell biology, biochemistry, protein
chemistry. Previous experience with one or more of the following techniques is required: phage display, Yeast 2-hybrid screening, BacterioMatch. Applicants must hold a degree equivalent to an Italian PhD/doctoral degree.

University Ca' Foscati of Venice is an equal opportunity employer, women and minorities
are therefore particularly encouraged to apply.

Ref. No: ECLT2010/Bio10
The application (labelled with Ref. No. ECLT2010/Bio10) can be submitted electronically
(Please include the ref.no. in the "subject" field of the email) by e-mail to
info @ ecltech.org.
The electronic application must contain the following documents as pdf-files:
i. application letter,
ii. CV,
iii. publication list,
iv. certificates,
v. and up to five key scientific papers.

Applicants may be called in for an interview.
Application Deadline: 16 March 2010

For further information please contact:
Dr. Elena Lynch
Phone: +390412347594
e-mail: info @ ecltech.org

posted 2010.03.06

Junior Researcher Position at The Microsoft Research - University of Trento Centre for Computational and Systems Biology (CoSBi) closed

The Microsoft Research - University of Trento
Centre for Computational and Systems Biology (CoSBi)
invites applications for:
· 1 Junior Researcher position in the field of Compilation of concurrent languages on
parallel architectures

The ideal candidate has a PhD in computer sciences and consolidated experience with
parallel algorithms, parallel and multi-core architectures, multi-thread programming and
compiler technology. The candidate must have an impressive publication record, good
scientific communication and writing skills, including capability to interact with researchers
from various disciplines. The candidate's research work will focus on the design of optimized
execution schemes for systems biology application to exploit the computational power of grid
computing and multi-core architectures.
A background in systems biology will constitute an asset.
Applicants must be prepared to work in a highly multidisciplinary
and dynamic field at the forefront of converging sciences.

For more information and applications, please go to:
www.cosbi.eu

posted 2010.02.27

Postdoctoral Research Fellow in Quantitative Systems Biology closed

Postdoctoral Research Fellow in Quantitative Systems Biology
(3 Year fixed term)

MRC Band 4 Salary £29,663 - £35,399 pa inclusive London W12

The Quantitative Systems Biology group, within the Clinical Sciences Centre of the Medical Research Council and the Faculty of Medicine of Imperial College in London (UK), is seeking postdoctoral candidates with a motivated interest in interdisciplinary research, aimed towards a quantitative understanding of the function of complex biological systems. The successful applicant will investigate the quantitative and systems-level properties of signalling, genetic and transcriptional networks in mouse and human T lymphocytes, carrying out projects that integrate experimental measurements with data analysis and mathematical modelling.

The successful candidate will have recently completed a Ph.D. in a biological discipline with a strong publication record. In addition, a sound knowledge of the standard laboratory techniques of molecular and cell biology is expected, as well as experience with immunoassays, flow cytometry and handing of primary cells. Familiarity with high-throughput methods for the analysis of genomes, transcriptomes or proteomes and a working knowledge of mathematical and computational methods will be advantageous.  We are a recently established and expanding research lab seeking enthusiasm, flexibility and willingness to learn across disciplines.

Additional information can be found on our website http://qsb.csc.mrc.ac.uk. Informal enquiries about the research projects are particularly encouraged and should be made to Dr Alberto Polleri, Group Head, at polleri [at] csc.mrc.ac.uk

This post is a Career Development Fellowship to support post-doctoral scientists in early or changed career training and help establish them as a successful and independent research scientist in their chosen field. It is a 3-year training and development post, which incorporates both scientific and transferable skills training.

Applications for this role should be made online at http://jobs.mrc.ac.uk. If you do not have internet access or experience technical difficulties please call +44 (0)1793 301154 quoting the reference number CSC10/061. Please ensure you include a copy of your covering letter, CV, statement of research experience and goals and contact details for three professional referees within your application.


Closing date: Thursday, 18 March 2010

posted 2010.02.27

Postdoctoral Fellowship Position at Metrum Institute open

Metrum Institute is seeking a qualified and motivated candidate for a postdoctoral fellowship position.  The fellow will apply modeling and simulation methodologies to continue the development of a systems biology model relating calcium homeostasis and bone remodeling. The purpose of this multiscale model is to simultaneously describesub-cellular mechanisms, multi-organ interactions, and clinical outcomes.  The goal of this model is to provide a workbench to evaluate the ramifications of system perturbations caused by disease state(s),
genetic abnormalities, and therapeutic intervention(s).  Skills to be applied and developed include physiologic modeling, clinical pharmacology, Bayesian methodologies, and various low- and high-level programming languages.

Founded in 2005, Metrum Institute is a nonprofit organization dedicated to the advancement of quantitative modeling and simulation in biomedical research, with particular emphasis on problems in clinical pharmacology and therapeutics. Our efforts include training courses in modeling & simulation techniques/methods, development of quantitative tools and software,
publications, methods and applied research, symposia, and collaboration with the academic community in research and training of fellows and graduate students.  Metrum Institute is dedicated to the promotion, advancement, and dissemination of knowledge through research,
education, and training in quantitative modeling and simulation applied to biomedical research.

The successful candidate will work alongside and interact with the world-class scientific staff of Metrum Institute. Participation in weekly lab meetings and journal clubs will add to the breadth of experiences during the fellowship.

The fellowship appointment is for one year with the possibility of an additional year with mutual agreement. A doctoral degree (Ph.D., PharmD, or M.D.) is required in pharmacokinetics, pharmaceutical sciences, biostatistics, bioengineering or related discipline at the time of appointment. Prior experience with Bayesian and other modeling and simulation tools, programming and statistical training, and an understanding of biological processes is desirable. Applicants must be eligible to work in the United States. Metrum Institute is an equal opportunity employer.

For further information, or to apply (CV / cover letter), please contact:

William R. Gillespie, Ph.D.
Research and Development Director
Metrum Institute
2 Tunxis Road,  Suite 112
Tariffville, CT 06081 USA
billg [at] metruminstitute.org

posted 2010.01.20

Postdoctoral Opportunity in cancer systems biology open

A NIH-funded postdoctoral fellowship in cancer systems biology is available immediately in the laboratory of Dr. Helene McMurray in the Department of Biomedical Genetics, University of Rochester. The successful candidate will explore the role of recently discovered 'cooperation response genes' (McMurray et al., Nature, 2008) in breast and prostate cancer. Genomic analysis, in vitro cell culture and in vivo animal models will be used to identify and test the importance of this gene class in transformed breast and prostate cells.

The laboratory is located at the University of Rochester Medical Center, in Rochester, NY, USA, which offers a stimulating research environment and excellent opportunities for integrated training in cancer genetics, genomics and systems biology.

Candidates must hold a Ph.D. in a life science discipline, such as genetics, or systems, molecular, or cell biology and possess strong independent research abilities, excellent verbal and written communication skills, be self-motivated, and able to work well in a team. Experience with mammalian cell culture, xeno-transplantation in mice, and standard molecular biology methods are highly desirable. Ability to program in R a plus.

To apply, please e-mail CV, statement of research interests and names of three references to gensys @ ur.rochester.edu.

posted 2010.01.14

POST-DOC and RESEARCHER for OPEN BIOLOGY UNIT open

POST-DOC and RESEARCHER for OPEN BIOLOGY UNIT at Okinawa Institute of Science and Technology, Japan

Open Biology Unit (PI: Hiroaki Kitano) of Okinawa Institute of Science and Technology (President: Sydney Brenner) is now looking for candidates to fill its post-doctoral fellows and researchers to work on novel systems biology software platforms as well as large-scale interaction network development and analysis. The project aims at development of "open-flow" systems biology modeling platform based on established platforms such as CellDesigner
(developed by SBI), SBML, SBGN, and Payao (developed jointly by OIST and SBI). In addition, the project aim to carry out a large-scale model integration of budding yeast as well as key networks of mammalian cells.

Successful candidate shall have:
For software-centered positions
- Strong background in software development and biological model
construction,
For biology-centered positions
- Strong biological knowledge and experiences modeling of budding yeast as well as mammalian cells particularly on, but not limited to, signaling, cell cycle, and stem cell induction and differentiation pathways.
Experiences in software development will be a plus.
Communication skills, and capability to work relatively independently but collaboratively with other members of the project as well as in the context global collaboration is essential.
The official language of OIST is English.

Interested candidate shall contact Hiroaki Kitano (kitano # oist.jp : Replace # with @ ).

posted 2010.01.07