A portal site for systems biology.

PhD Student Position in Systems Biology - 2008
Systems Biology of Apoptotic Cell Death Signaling Networks

Applications are invited for a PhD studentship in Systems Biology in the Department of Physiology and Medical Physics/RCSI, Dublin, Ireland.

Candidates should have a background in computational biology, biophysics, or systems biology, and be experienced in numerical analysis/programming (e.g. C++, MATLAB, Mathematica or others). Good written and communication skills and a high level of motivation and commitment are required. The institute is located in the heart of Dublin city and offers an international and interdisciplinary working environment spanning the fields of systems biology, cancer and molecular biology, biophysics, and medical research.

Apoptotic cell death is regulated by complex signalling networks spanning several compartments within living cells. Impaired apoptosis can result in developmental disorders and cancer. In an industry collaboration with SIEMENS (Medical Division) the student will translate biological systems into novel computational models that allow the spatiotemporal and quantitative prediction of signalling events, and the identification of key regulatory factors or threshold mechanisms deciding on apoptotic cell death.

The applicant will work interactively with the experimentalists to discuss model validity and restrictions. Generated models will qualitatively and quantitatively be validated by experimentalists measuring the real time kinetics of key signalling events within living cells.

Applications should include CV, scans of relevant certificates and names and addresses of two referees and be sent (preferably by e-mail) to:

Dr. rer. nat. Markus Rehm
Lecturer in Physiology and Biophysics
Department of Physiology and Medical Physics
Royal College of Surgeons in Ireland
York Street Building Dublin 2 Ireland
email: mrehm at rcsi.ie Key

publications are available on request

posted 2008.03.25

Three research positions "Theoretical Systems Biology" at Dresden University of Technology, Germany

Applications from highly qualified candidates are invited for
* two full postdoctoral fellow positions for up to three years and
* one PhD position for three years in theoretical systems biology, mathematical biology and computational cell biology.

The goal is to discover, in close collaboration with experimental and medical partners, novel biophysical and biochemical mechanisms of information and material transport between subcellular compartments such as the plasma membrane, Golgi and nucleus as well as the spatio-temporal regulation of such mechanisms. The new members of our group will coordinate and conduct the above research and complement running projects which utilise a broad spectrum of theoretical tools with a focus on multi-scale modelling of spatio-temporal pattern formation.

The ideal postdoctoral candidate holds a Ph.D. in physics, applied mathematics or biology (or similar), has demonstrated expertise in systems biology, biophysics, nonlinear dynamics, stochastic methods or network analysis and has a strong interest in molecular cell biology. The Ph.D. candidate should possess a masters or diploma degree in physics or applied mathematics. A high level of motivation and commitment are required. Strong communication skills are important for the close collaborations with experimentalists and medical doctors.

The envisaged research will be conducted at the interdisciplinary Center for Information Services and High Performance Computing (ZIH), Dresden University of Technology, Germany, which hosts a department focusing on the mathematical modelling of biological systems (head: Andreas Deutsch). The Dresden campus is characterized by a vibrant international community of researchers that performs cross-disciplinary research at the highest level in state-of-the-art research centers. The city of Dresden and its surroundings are also rich in culture and impressive scenery. ZIH is an equal opportunity employer and strives to increase the number of women in research. We also encourage and invite applications from disabled individuals, who will be given priority if suitably qualified.

The positions are available from June 1, 2008. Deadline for applications
(by email, including contact details of two references): April 10, 2008.

Contact:
Andreas Deutsch
Center for Information Services and High Performance Computing (ZIH)
Dresden University of Technology, Germany
Tel.: +49 351 463-31943
Fax.: +49 351 463-38245
Email: andreas.deutsch at tu-dresden.de
WWW: http://theobio.mtbio.de/imc

posted 2008.03.25

Postdoctoral Fellowship: Mathematical Modeling of Viral Transcriptional Circuitry
U of California, San Diego

Dr. Leor S Weinberger's laboratory (recently moved from Princeton) seeks applicants for a postdoctoral fellowship (2-3 years) exploring HIV and viral transcriptional regulation from a dynamical systems approach. The specific research project is flexible and can be tailored to the interests of the individual, but should fall under the broad fields of  transcriptional
regulation and circuitry. Our lab is a joint theoretical and experimental lab ( http://chem-faculty.ucsd.edu/weinberger) that stresses close interaction between theorists and experimentalists and houses all the computational resources and the wet-lab experimental infrastructure (including several confocal microscopes for measuring single-cell transcriptional dynamics in vivo) required for joint theoretical/experimental projects. Applicants will be considered from a diverse spectrum of backgrounds  (including PhDs in mathematics, statistics, physics, biology or related areas) but preference will be for highly
motivated applicants with excellent communication skills. The ideal candidate should also have training in dynamical systems (including computer simulation skills), good interaction capability with experimentalists and a proven record of independent research. The postdoctoral fellowship provides a competitive annual stipend plus benefits and health insurance. Start date and term are negotiable. Applications are welcome from candidates of any nationality, and will be reviewed on a rolling basis. UCSD offers an outstanding intellectual environmental with many top-five ranked scientific departments (including Biochemistry and Bioengineering), a highly regarded medical school, a Center for Theoretical Biological Physics (CTBP), and close proximity to the Salk and Scripps Institutes.  Highly motivated applicants are encouraged to email a statement of research interests, CV,
and contact details for three references to lsw (at) ucsd.edu. Informal inquiries are also welcome. Please see our website for further info:http://chem-faculty.ucsd.edu/weinberger

posted 2008.02.29

Centre for Integrative Systems Biology at Imperial College (CISBIC)

A PhD position in systems biology of plants is available at Imperial College, London from 1st October 2008. The position is funded by a joint Microsoft Research/BBSRC Dorothy Hodgkin Postgraduate Award, and will be jointly supervised by Dr Radhika Desikan (Biology) and Professor Jaroslav Stark (Mathematics/CISBIC). The award, for a total
amount of £90,000 will cover tuition fees and living expenses.

The project aims to build a mathematical model of the integrated signalling networks in plant cells called stomatal guard cells. These cells regulate water and gas exchange between the plant and the environment. Modelling of the signal integration processes is essential in order to understand better how plants may be able to survive adverse conditions, such as those caused by global warming. The project will develop a dynamical model to fit the existing data. The model will in turn inform the choice of further biological experiments, and their outcome will enable more complex modelling. Deterministic methods from linear and non-linear differential equations will be employed (such as bifurcation analysis) as well as stochastic differential equations.

A student with mathematics/computer science/computational biology background (with grades equivalent to a UK first class honours degree) of a nationality from those countries eligible for the DHPA (see www.rcuk.ac.uk/hodgkin/ ) will be eligible. The student will
interact with both biologists (in RD's lab) and mathematical modellers (in JS group/CISBIC) in order to further this project.

For further details contact Dr Radhika Desikan (r.desikan at ic.ac.uk) or Professor Jarsolav Stark (j.stark at ic.ac.uk). Closing date for applications is 30th April 2008. A PDF of this advertisement can be found at

http://www.ma.ic.ac.uk/~jstark/PDF/MSR%20Plant%20PhD.pdf

posted 2008.02.29

A postdoctoral position is available immediately in John Tyson's Research Group at Virginia Tech to conduct research in the area of mammalian cell cycle regulation. The work involves modeling molecular regulatory pathways using nonlinear ordinary differential equations.
Candidates must have a Ph.D. degree, experience in mathematical modeling, working knowledge of nonlinear dynamics as well as cell physiology and molecular biology, and an interest in applying models to problems in the molecular biology of cancer. Interested applicants must apply online at www.jobs.vt.edu, posting #080127. Complete the faculty
application and attach a cover letter, resume/vita and list of 3 references. Review of applications will begin on March 9, 2008. Virginia Tech is an Equal Opportunity / Affirmative Action Institution

posted 2008.02.20

We are currently recruiting to the large interdisciplinary Combinatorial Responses In Stress Pathways (CRISP) team which will be jointly based at the University of Aberdeen and at CISBIC, Imperial College London. are seeking ambitious and committed scientists to
join the CRISP team. This team will include four experimental biologists, four applied mathematicians, six PhD students supervised by the ten group leaders. The project will study the Systems Biology of stress responses in the medically important fungi Candida albicans and Candida glabrata. We will combine advanced modelling techniques
with state-of-the-art genomics, molecular biology, biochemistry and cell biology in these pathogens. This project is funded by the BBSRC under the SABR initiative for up to five years.

A PDF summary of the available posts can be found at

http://www.ma.ic.ac.uk/~jstark/PDF/SABR%20Advert%20Final.pdf

posted 2008.02.18

A key mission of US EPA's Office of Research and Development (ORD) is the development and implementation of robust and efficient methods to identify chemical hazards. Determining the mechanisms of action of toxic chemicals is a critical step toward improving our ability to achieve this mission.  A promising approach to this problem is to delineate toxicity pathways that are activated by chemicals. Toxicity pathways describe the key molecular level details of mechanisms of action and link chemical interactions at target sites with higher level adverse outcomes. The data that are required for pathway mapping come from assays that probe a system as it is perturbed by introduction of toxic chemicals. EPA researchers are generating large and diverse data sets that are ideal for use in mapping toxicity pathways. These include high throughput screening (HTS), high content screening (HCS) and genomics data from both in vitro and in vivo systems. A critical need is the development of robust analytical approaches that use these data sets to systematically map toxicity pathways.

EPA has an immediate opening at the postdoctoral level to develop new approaches to use HTS, HCS, genomics and whole animal toxicology data sets to map out toxicity pathways. This project will requires skills in bioinformatics (required to manage and manipulate large, multi-domain data sets and to link these with other related data); in statistics (required to mine the data sets for correlations that are indicative of true interactions); and in computational sciences (required to build the requisite software and databases). Novel tools will be tested on data being generated by mission critical EPA programs. The position is at the EPA campus in Research Triangle Park, NC, but will involve significant interactions with EPA researchers at other sites.

The ideal candidate would have experience in one or more of the areas of computational modeling, computer science, data mining and statistical analysis, combined with a background in bioinformatics, systems biology, molecular biology, cell biology, physiology or genomics. Because the position requires both the conceptual development and the implementation of this system, both biological knowledge and software development experience are critical.

Benefits: Salary range of $54,494 - $84,913; Full four-year appointments; Paid relocation to EPA duty location; Vacation and sick leave; Federal health benefits, life insurance, and retirement program; Travel to professional and scientific meetings; Flexible start date in 2008

Application Deadline: March 14, 2008

For more information, please contact
Richard Judson
judson.richard @ epa.gov
(919) 541-3085

posted 2008.02.13

Mathematical Modeler Job Posting

Company Overview

Immunetrics is a bio-simulation company that specializes in in-silico modeling. Immunetrics modeling technology is intended to provide critical information to drug developers to accelerate and improve the drug discovery and development process by providing clinically predictive models of disease. Immunetrics' bio-simulation technology enables drug discovery and development firms to gain comprehensive insights into the potential problems facing a compound before investing significant resources into time-intensive and costly animal testing and human clinical trials. The Immunetrics models are based on dynamical systems modeling, i.e. systems of differential and algebraic equations, which represent the actual biological mechanisms that drive components of the system.

Mathematical Modeler

Primary Responsibilities:

Function as part of a team of mathematical modelers to design and develop cell-based mechanistic models of complex biological systems
Research biological literature and understand biological pathways and physiological processes
Analyze clinical data and work with statisticians to perform data analysis
Develop and test new models using Immunetrics proprietary platform
Perform fits of mathematical models to experimental/clinical data
Design and perform clinical trial simulations on Immunetrics proprietary platform
Perform routine presentations of recent research and findings
Regular meetings with physicians and investigators
 
Qualifications:

PhD in Bioengineering, Chemical, Mathematics, Physics or related field
Experience with the development of mechanistic models of biological systems is required
Knowledge of biology is essential
Strong background in computation, especially differential equations and parameter estimation
Familiarity with researching biological literature using available tools
Experience with large mathematical systems is preferred, but not essential
Some knowledge of statistics is preferred, but not essential
Strong communication skills and ability to communicate with physicians and investigators.
 
Please submit resumes or CVs to careers @ immunetrics.com

posted 2008.02.01

The U.S. Department of Health and Human Services, Food and Drug Administration (FDA), National Center for Toxicological Research (NCTR), Office of Research is seeking to hire a highly qualified scientific leader for the position of Director, Division of Systems Toxicology (DST). The successful candidate will be expected to lead the DST scientists in multi-disciplinary teams of six Centers of Excellence including Centers for Functional Genomics, Proteomics, Metabolomics, Hepatotoxicity, Toxicoinformatics and Chemistry. The successful applicant will be expected to provide research leadership, technical expertise and functional area mentorship for the inclusion of OMICs (genomic, transcriptomic, proteomic, and metabolomic), bio-imaging techniques, nanotechnology and informatic tools to support regulatory decisions including use in studies for the development of safe and effective drugs, veterinary medicines, medical devices and foods associated with the FDA's Critical Path Initiative. The fundamental idea of the Critical Path Initiative is to reduce the uncertainty about product performance throughout the product life cycle through scientific research.

The incumbent will address agency Critical Path scientific issues using a systems approach that links data from "OMICs" technologies with in vivo data to provide a comprehensive mechanistic assessment to predict and evaluate the safety of FDA regulated products.

The NCTR, located approximately 30 miles south of Little Rock, Arkansas, conducts FDA mission-related research that is of critical importance for the Agency to develop a scientifically sound basis for regulatory decisions. Over 110 Ph.D. scientists and 400 support scientists, on-site-contractors and administrative staff make up a dynamic group of professionals in the NCTR organization. Undergraduate and graduate students, post-doctoral fellows and visiting scientists also pursue education and research opportunities in a multi-disciplinary team atmosphere. For more information on NCTR research and training activities, visit http://www.fda.gov/NCTR.

In the Division Director-level position, the incumbent will be expected to be a visionary leader and to establish a nationally recognized research program in systems toxicology to support the Agency's mission. The appointee will represent, manage and provide leadership to DST multi-disciplinary teams of toxicologists, biologists, chemists, molecular biologists and toxicoinformatics scientists.

The Division Director will perform the full range of administrative duties required to manage and supervise a diverse staff of professional research scientists and technical support staff with expertise in areas including, but not limited to, biology, chemistry, molecular biology, toxicoinformatics, and computational chemistry. The incumbent is responsible for recruiting new senior, support, and postdoctoral staff to maintain a state-of the art systems toxicology research program. The Director will participate in the development of intermediate and long-range research plans and goals, evaluates specific research proposals, conducts employee appraisals, and identify budget and facility needs and critiques manuscripts and abstracts. The incumbent will be responsible for furthering the goals of equal employment opportunity by adhering to nondiscriminatory employee practices.

The position requires a Ph.D., M.D. or equivalent with demonstrated success in leading a multi-disciplinary team, a strong publication record in peer reviewed journals, relevant administrative experience, and a strong independent research program. Preference will be given to individuals with a demonstrated record of accomplishments in proteomics, metabolomics, functional genomics, or toxicoinformatics. Evidence of effective planning, organization and decision-making capabilities and excellent interpersonal and communication skills is required.

This is an excepted civil service position under Title 42 USC 209(f) with the salary negotiable and commensurate with experience and qualifications (range of $130,000 - $190,000). The candidate must be a U.S. citizen or permanent resident. Benefits include health and life insurance options, retirement, paid holidays, vacation and sick leave. Relocation expenses may or may not be paid in accordance with FDA policy.
Interested individuals should send a letter of application with a curriculum vitae, statement of proposed and current research plans, copies of up to five peer reviewed publications, and names with complete contact information of three references to the attention of Mary Ann Hutchison, Office of Management Services, NCTR, 3900 NCTR Road, Jefferson, AR 72079.

Applications must be postmarked no later than February 15, 2008. FDA is an Equal Opportunity Employer. FDA/NCTR is a smoke free environment.

posted 2008.01.25

Computational Systems Biology Postdoctoral Fellowship at Boston University

Available immediately to develop and apply computational techniques to reverse engineer and analyze gene regulatory networks in bacteria and mammalian cells. Expertise in computational techniques and algorithm development in required. Applicants must have a PhD in physics, engineering, bioinformatics or a related discipline. Applicants should send a brief statement of research interests, a CV and names of three references to: Dr. J.J. Collins, Department of Biomedical Engineering, Boston University, 44 Cummington St., Boston, MA, 02215, jcollins @ bu.edu

posted 2008.01.15

Post-doctoral Openings in Systems Biology (starting in 2008)

We are advancing new technologies to better understand the growth, spread and evolution of viruses. Active and new NIH-supported projects are in three areas: (1) flow-enhanced spread and characterization of infections in microfluidic devices, (2) phenotype distributions from measurements and models of infections initiated by single virus particles, (3) dynamics of virus populations in anti-viral environments. Systems of current interest are influenza virus and vesicular stomatitis virus. The most competitive applicants will be exceptionally creative, highly-motivated individuals with significant experience in:

Engineering or physical sciences: modeling or simulation of reactive systems, fluid and particle dynamics, and/or microfluidics
     or
Quantitative biology: live-cell reporting of gene expression, RNA and protein quantification, microscopy, imaging and analysis, and/or flow cytometry

Madison, Wisconsin is an attractive and affordable city surrounded by beautiful lakes. It routinely ranks as a 'best place to live,' and residents thrive on its rich diversity of outdoor and cultural opportunities. All researchers in our laboratory develop and maintain
standards of institutionally-approved biosafety (BSL 2) protocols.

Forward your CV with cover letter, and have three letters of reference sent to John Yin by e-mail (yin @ engr.wisc.edu), fax (608/262-5434) or regular mail: Department of Chemical and Biological Engineering, University of Wisconsin, Madison, WI 53706-1607 USA.

posted 2008.01.09