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2008

Junior Researcher in Computational Systems Biology open

CRS4 (Center for Advanced Studies, Research and Development in Sardinia) Italy-Sardinia-Pula

Position: Junior Researcher in Computational Systems Biology, 2-years renewable contract.

The Bioinformatics Laboratory of CRS4 (Center for Advanced Studies, Research and Development in Sardinia) has a Junior Researcher position available to work in the area of Computational Systems Biology in the RAGNO Group (Reverse-engineering and Analysis of Genome scale NetwOrks).

The Junior Researcher will be part of an ongoing project with focus on analysis of gene expression data in context of large scale Protein Signaling Networks. The aim is to discover dys-regulated signaling modules in cancers and neurological diseases, and discovery of general principles of gene expression (dys-)regulation of signaling systems.

Applications are invited from those interested in the computational aspects of Systems Biology and Functional Genomics. The suitable candidate has a PhD and strong experience in statistical analysis of gene expression data, systems biology and complex network analysis, and programming experience with C++, Matlab or R.

CRS4 Bioinformatica, established in the Sardinian Technological Park located in Pula (Ca), Italy, is an interdisciplinary research laboratory with focus on computational biology since 2006. CRS4 Bioinformatica currently harbors several groups that carry out fundamental research, develop computational tools and provide educational services for bio-medical research, in particular for personalized medicine. Our research activities are tightly integrated with an experimental laboratory providing exceptional facilities for high-throughput analysis. More than 20 people representing a wide range of expertise and experience in bioinformatics and related scientific disciplines are currently working in independent research groups fostering top quality interdisciplinary research.


CRS4 Bioinformatica
Alberto de la Fuente
http://www.bioinformatica.crs4.org/research/ragno-group

posted 2008.11.27

COMPUTATIONAL BIOLOGIST at Samuel Lunenfeld Research Institute closed

POSITION TITLE

COMPUTATIONAL BIOLOGIST

DEPARTMENT

Samuel Lunenfeld Research Institute

EMPLOYMENT TYPE

Regular Full Time

REPORTS TO

Drs Jeff Wrana, Laurence Pelletier and Daniel Durocher

 

A staff Scientist position is available for a highly motivated computer scientist with interests in the analysis of large biological datasets, in particular datasets that are based on images and functional genomic experimentation.

 

The successful applicant will hold a funded semi-independent position in a multi-disciplinary group headed by Drs Wrana, Pelletier and Durocher at the Centre for Systems Biology at the Samuel Lunenfeld Research Institute. The successful applicant will be expected to develop novel and innovative methods for the analysis, integration and representation of biological systems. The successful applicant will be encouraged to publish their work, either as part of collaborations or as a lead author.

 

We are seeking someone with a background in Physics, Mathematics or Computer Sciences. A university degree (Ph.D.) is essential. The successful candidate will be well versed in the computational and mathematical analysis of complex systems and demonstrate a strong interest in the development and application of machine learning, image analysis and graph theory.


The candidate needs to be self-motivated and have the ability to work well independently and in a team environment, and have excellent communication skills with desire to share knowledge and skills with others.

 

Please submit CV and cover letter to: application @ mshri.on.ca

Posting open until 12/24/2008.  

posted 2008.11.24

Computational Systems Biology Postdoctoral Fellowship at Boston University/HHMI open

Available immediately to develop and apply computational techniques to reverse engineer and analyze gene regulatory networks in bacteria and mammalian cells in the Collins lab at the HHMI and BU (www.bu.edu/abl).  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,
HHMI and Department of Biomedical Engineering,
Boston University, 44 Cummington St., Boston,
MA, 02215, jcollins @ bu.edu

posted 2008.11.13

Systems Biology modeling positions at Pfizer, Cambridge, MA closed

Applications are invited for two positions of Systems Biology Modeling Scientist (Job ID#: 929552), within the Systems Biology Group of the Biotherapeutics and Bioinnovation Center (BBC) at Cambridge, MA.

A summary of responsibilities for the two positions are listed below. For more information about the BBC and the roles and responsibilities, please visit the Pfizer Career site (http://www.pfizer.com/careers) and search for the job title "Systems Biology Modeler - 2 positions (R4/R5)" or by Job ID number (929552).

[1] Disease-level Modeler:

You will use your knowledge of biological systems at the physiological and molecular level combined with advanced applied mathematics to build complex models of health, disease and disease processes in the areas of diabetes, cancer, and inflammation. You will develop and apply methodologies for identifying how molecular level interventions will manifest as systemic and clinical effects.  Experience with PBPK modeling and/or modeling of immunology, metabolism or disease/physiology level modeling is preferred.

[2] Systems Analysis Modeler:

The systems modeler will use analytical techniques to expose and leverage biological phenomena to integrate biological information to cellular systems. You will conceptualize information flow within complex biological systems and implement quantitative models of said systems.   The ideal candidate will have the ability to apply a deep understanding of mathematical theory and physical systems in the context of biology. Experience applying a variety of mathematical approaches to biological systems including multi-scale modeling, translating from systems-level to cellular processes and vice versa in normal and diseased physiology is highly desirable.

 

posted 2008.11.08

Post-Doc and PhD positions: Computational Systems Biology, ETH Zurich open

Post-Doc and PhD positions: Computational Systems Biology, ETH ZurichApplications are invited for a PhD studentship and a Post-Doc position, within the Computational Biology Group at the Department of Biosystems Science and Engineering of ETH Zurich.
 
The group focuses on the development of detailed, predictive models for cellular signaling networks with a view to develop a comprehensive understanding of the dynamics and evolution of cellular signaling. All projects are carried out in close collaboration with experimental groups so that quantitative data is available and model predictions can be tested in experiments.
 
Applicants should have a strong background in mathematical and computational modeling, and demonstrated experience in nonlinear dynamics and numerical calculations. PhD candidates should hold or expect to obtain a degree in a numerate discipline (e.g. mathematics, computational science, computational biology, physics, biotechnology, chemical or bio- engineering, or related areas). Candidates are expected to engage in interdisciplinary research and to foster in-house collaborations with biologists and bioengineers.

The Department of Biosystems Science and Engineering of ETH Zurich is an integral part of SystemX.ch, the Swiss initiative in Systems Biology. It is located in Basel, a European hotspot for biomedical research, in close proximity of the Biozentrum of the University of Basel, the Friedrich Miescher Institute for Biomedical Research, and the pharmaceutical and biotech industry. ETH Zurich is a major research university, offering an excellent environment for innovative and collaborative research across disciplines.

For further information please visit our web page at
http://www.dbsse.ethz.ch/iber

posted 2008.11.05

Positions in joint experimental and theoretical systems biology projects open

The Division of Theoretical Bioinformatics at the German Cancer Research Center (DKFZ) is inviting applications from highly qualified candidates to work in interdisciplinary systems biology projects with a strong focus on medical/therapeutic applicability. The DKFZ is a world‐leading institution in the field of applied and basic cancer research. 
Within DKFZ, systems biology research plays a leading role and is carried out in close cooperation with BioQuant the Center for Systems Biology at the University of Heidelberg, where part of the positions will be localized.

Project A:
  • 1 Junior Group Leader Ref‐No. 198/2008
  • 1 Postdoc Ref‐No. 199/2008
  • 1 PhD‐Position Ref‐No. 200/2008
(All positions are initially limited to three years with possibility for prolongation)

The goal is to develop and improve predictive multi‐scale (spatio‐)temporal models to incorporate biological mechanisms spanning different time‐ and length scales from protein signaling to multi‐cell communication and tissue/tumor development. The focus will be on elucidating cellular decisions and cell‐cell communication. Applications will range from understanding life‐death decisions in apoptosis/autophagy pathways, tumor‐stroma interactions in cancer, development of tumor progression markers to the understanding of wound healing processes in skin.
Candidates should hold a degree/PhD in physics, applied mathematics, engineering or biological sciences, having demonstrated expertise in interdisciplinary research, systems biology, biophysics and/or nonlinear dynamics.
Experienced applicants will have the opportunity to lead an established subgroup on systems biology including the supervision of Postdocs and PhD‐students.

Project B:
  • Central Data Management of experimental and clinical data: 1 IT‐professional Ref‐No. 201/2008
(initially limited to 2 year with possibility for prolongation)

The goal is to extend our Oracle based data management system for the maintenance of high dimensional experiments in the fields of biological and medical research.
The specific tasks are software development in Java with J2EE and J2SE Design, implementation and maintenance of multi‐tier‐solutions and GUI‐development of Web Frontends. Job experience with standard‐frameworks such as Spring or Hibernate and Tools (ANT, CVS, Eclipse) is desired, additional experience in Unix, Shell scripting, Tomcat WebServer, WebServices and XML‐Standards is preferable. Candidates should hold a degree in computer science.

Initial Deadline for applications is 1.12.2008 but further applications will be assessed until positions are filled.

posted 2008.10.31

SYSTEMS BIOLOGIST ASSISTANT PROFESSOR closed

IOWA STATE UNIVERSITY
Where you can become your best.

The Department of Genetics, Development and Cell Biology (http://www.gdcb.iastate.edu/) invites applications for a tenure-track faculty position at the level of Assistant Professor. We seek highly qualified applicants from all backgrounds relevant to Systems Biology. Specific areas of interest include, but are not limited to: analysis of developmental, neural, metabolic or regulatory networks, using experimental and computational or modeling approaches. The successful candidate will be expected to establish and maintain a vigorous, independent, extramurally funded research program, and to participate in undergraduate and graduate teaching. Qualified candidates must have a Ph.D. or other terminal degree, and demonstrated potential for excellence in research and teaching. The Department is sensitive to the needs of dual-career applicants and is committed to increasing diversity within the university community.

To view entire vacancy #080873 and apply, create an electronic application at http://www.iastatejobs.com that includes a cover letter briefly summarizing qualifications, curriculum vitae, a statement summarizing past, present and future research plans, and a brief statement of teaching interests and philosophy. Applicants should arrange for three letters of reference to be sent to:
Systems Biology Search Committee,
Iowa State University, Department of Genetics, Development and Cell Biology,
1210 Molecular Biology Building, Ames, IA 50011 or to GDCBsearch-SB @ iastate.edu .

To guarantee consideration the applications must be received by November 14, 2008.

posted 2008.10.28

Pathway database curator position at Gramene open

A full time 3-year pathway database curator position at the Research Associate or Postdoctoral Associate level is available immediately in Dr. Pankaj Jaiswal's group at the Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR (http://www.science.oregonstate.edu/bpp/). This position is required to develop a comprehensive catalog of rice and other cereal plant metabolic pathways and enzymes. The project expands the coverage of metabolic pathways from Rice (http://gramene.org/pathway/) to all known pathways in major cereal plants such as for maize, sorghum and wheat. The curator will be responsible for development, curation and maintenance of the Pathways section on Gramene Database (http://www.gramene.org) in following ways.

i)    Develop novel methods on annotating the metabolic and regulatory pathway associations to the genomic and genetic datasets.
ii)    Research new plant metabolic pathways and enzymes in the scientific literature, and to evaluate, extract, organize, and enter that information to the database;
iii)    Development /improvement of new or existing standard procedures and operation rules on curation methods and to the general development of the database, such as data integration, web page enhancement, and data exchange with database namely the www.reactome.org.
iv)    Communicating with the research community to improve the quality of the data, to train them in using the database and related tools, and to support user requests.
The successful candidates will work with Gramene database team that includes highly trained PhD. level bioinformatics specialists and software developers. The person will also work with collaborator databases such as Rice Genome Annotation Project, MaizeGDB, GrainGenes, MetaCyc, PlantCyc, AraCyc, SolCyc, and a number of pioneering plant biochemists from around the world.

Qualified candidates should have a Ph.D. degree or equivalent in biochemistry, biological chemistry, metabolomics, or related field preferably in plants, but not necessarily. The successful candidate should also have a demonstrated ability for independent and critical
thinking, excellent communication skills and enjoy teamwork. Experience with Lynx and Windows operating system, Perl, Java and HTML editing is desirable.

posted 2008.10.27

Postdoctoral Fellow and Software developer positions in Comparative Genomics and Systems Biology open

Jaiswal lab at Oregon State University (http://www.oregonstste.edu) is seeking talented and motivated  candidates for current and future job openings as postdoctoral fellows and software developers in the systems biology and bioinformatics. The successful candidates are expected to have either or both the experience of working in a biology wet lab and/or bioinformatics, computational biology lab. The successful candidate(s) will collaborate with researchers from Biochemistry, Molecular Biology, Plant Development, Genetics and Systems Biology programs. Postdoctoral applicants must have a Ph.D. (or equivalent degree) in biology, bioinformatics, molecular biology, biochemistry, genetics, computational biology or related fields, and some demonstrated experience in computer science/bioinformatics. For the computational biologists and software developer positions in addition to their experience and interest in biology, expertise in at least one scientific programming language and relational data management system is preferred.
Candidates with experience in network analysis methods are encouraged to apply. Candidates with BS/MS degrees are also encouraged to apply for future positions in the lab.

posted 2008.10.27

Assistant Professorships in Systems Biology at Harvard University closed

Harvard University has a large and growing systems biology community composed of faculty, fellows, and trainees, housed at several locations across the Boston area. This year, faculty positions are available in four locations. Applications for positions at the rank of assistant professor (tenure track) are especially encouraged, but exceptional candidates for associate professor (untenured) positions may also be considered.

 

1. The FAS Center for Systems Biology (http://sysbio.harvard.edu/csb/) on the Cambridge campus has two positions available and is particularly interested to hire in the field of microbial evolution & ecology and the field of physical properties of biological systems, but will consider outstanding candidates in other fields. Each new faculty member will hold an academic appointment in a participating department, such as Molecular and Cellular Biology or Organismic and Evolutionary Biology. Access to Harvard facilities including the Center's own Core Resource, the Center for Nanoscale Systems, the Center for Brain Science, and the Broad Institute will provide opportunities for collaborative research and technology development.

 

2. The MGH Center for Systems Biology (http://csb.mgh.harvard.edu/) has one position available. This position is a joint appointment with the Department of Systems Biology at Harvard Medical School. The candidate will work in close proximity to MD and PhD scientists with strong research programs in human disease.  He/she will have the opportunity to establish collaborations with MGH clinicians, and with researchers and technology programs at the Broad Institute. Areas of special interest include: how disease-causing mutations perturb cellular networks to yield disease phenotypes; identification of network nodes that may be novel drug targets; epigenetics and disease; gene-environment interactions; using computational methods, quantitation, statistics, modeling and analysis of large data sets to understand mechanisms of complex disease, and to translate this understanding into new diagnostic methods, treatments, or prevention strategies. Expertise at analyzing (and/or generating) large data sets to investigate biological pathways and networks, using model organism or human samples, would be especially welcome.

 

3. The Department of Systems Biology at Harvard Medical School (http://sysbio.med.harvard.edu/) has two positions available. Special interests include systematic, quantitative and/or theoretical approaches to the following biological areas: variation in gene expression and function (such as variation in transcriptional control, translational control, protein degradation or protein modification); proteomics, particularly mass spectrometry; human genetics and population genetics; pharmacology, physiology and metabolism. 

 

4. The Harvard Institute for Biologically Inspired Engineering (http://hibie.harvard.edu/).  This position is a joint appointment with the Department of Systems Biology at Harvard Medical School. The special focus of this recruitment is Synthetic Biology, i.e. using genetic engineering and nanotechnology to build programmable self assembling materials, biological factories or integrated multifunctional living microdevices.  The successful candidate will become a member of a new interdisciplinary research institute composed of experimentalists, theoreticians and clinicians from Harvard University, its affiliated hospitals, and other academic institutions in the Boston/Cambridge area.  The Institute's central focus is research and advanced technology development and translation in the field of biologically inspired engineering.

 

Applications are due by December 1, 2008.

posted 2008.10.17

GROUP LEADER POSITION IN BIOPHYSICS open

Job Location: EML Research gGmbH, Heidelberg Germany

General Description:
EML Research gGmbH is a private non-profit research laboratory dedicated to basic and applied research in IT with a focus on bioinformatics and natural language processing. We offer a stimulating interdisciplinary environment, excellent computational facilities and support, and a competitive salary.

Job Description:
We are seeking outstanding candidates to establish an independent research group addressing fundamental questions in biophysics from a theoretical and/or computational perspective. The activities of the new research group should complement the existing groups at EML Research (see
www.eml-research.de) as well as related activities at the University of Heidelberg and other research organizations in the region. Through a collaboration agreement with the University of Heidelberg group leaders at EML Research can assume various academic responsibilities.
The successful candidate will be expected to develop an internationally recognized research program.
Group leaders at EML Research are encouraged to obtain additional funding through grant applications to national and international funding agencies.

Requirements:
Candidates must hold a doctorate in Physics, Biophysics, Chemistry or a related discipline. They should have at least 3 years of post-doctoral work experience in their scientific field. In addition they should have demonstrated independent research and leadership skills.

posted 2008.10.02

Postdoctoral positions in Computational Genomics open

Dr Olivier Elemento's computational biology group at the Weill Medical College of Cornell University in Manhattan, New York, has several openings for postdoctoral scientists. The group's research emphasis is on human regulatory genomics and proteomics. We develop innovative computational tools and approaches to generate testable hypotheses and discover fundamental principles in transcriptional, post-transcriptional and post-translational regulation of gene expression.

Our research is done in close collaboration with experimentalists at Weill and elsewhere and our ultimate goal is to develop translational research towards novel understanding and therapy for diseases such as cancer and neurodegenerative disorders.

For more details on the group's research, please consult :
http://physiology.med.cornell.edu/faculty/elemento/lab/

posted 2008.09.26

PostDoc Position in Berlin open

We are looking for a Postdoc (2 years, extension possible, start October 2008 or later) in our
group "Mathematical Modelling of Cellular Processes" at Max Delbrück Center for Moleculare Medicine (http://www.mdc-berlin.de/en/).

Our group develops and analyses mathematical models for signalling and gene-regulatory
networks. We are founded by the FORSYS Partner programme and are part of the Helmholtz
Alliance on Systems Biology.

In our NF-κB project which is done on close collaboration with the experimental group of
Prof. Claus Scheidereit at the MDC we are looking for a PostDoc for the development of a
logical model of the signalling pathway in normal cells and Hodgkin lymphoma. The aim is to
understand the network structure and its modification in disease states as a basis for the
prediction of effective inhibitors and rational therapies.

If you hold a PhD in bioinformatics, mathematical biology, biology or biophysics and have a
strong interest in mathematical modelling as well as molecular cell biology send your
application (including curriculum vitae, list of publications and the name and address of a
referee) to

posted 2008.09.17

Multiple Tenure Track Faculty Positions at Albert Einstein College of Medicine of Yeshiva University open

Department of Systems and Computation Biology
Albert Einstein College of Medicine of Yeshiva University

The Albert Einstein College of Medicine (www.aecom.yu.edu), one of the leading medical schools in New York City, is seeking to fill multiple tenure track faculty positions in the newly formed Department of Systems and Computational Biology. Established in April 2008, the main goal of the new department is to advance our understanding of living systems by developing theoretical, computational and experimental approaches to study complex biological systems.

The College has 750 medical students, 325 graduate students and 360 post-doctoral fellows in training and boasts a strong research faculty covering broad areas of experimental biology, offering outstanding opportunities for collaborative interactions. The 200,000 square foot Center for Genetic and Translational Medicine at Einstein, which opened in late 2007, locates computational, systems and experimental scientists in physical proximity to foster interdisciplinary communication and collaboration. Highly competitive start-up packages are available.

We seek outstanding scientists with broad experience and demonstrated collaborative interactions with experimental or clinical investigators. Candidates should have strength in a physical, mathematical or computational field at the Ph.D. or equivalent level. Experience applying these skills to a biological or biomedical area (demonstrated through publications or support) is also desirable. Areas of interest include, but are not limited to: Modeling cellular processes, such as signaling, transcriptional regulation and immune response; Pathway analysis; Genetic networks; Functional proteomics and genomics; Evolution of structure and function; Computational neuroscience; Mathematical and computational modeling of complex traits and diseases.

posted 2008.09.11

Research Associate / Research Assistant at the University of Rostock open

The Systems Biology & Bioinformatics group (www.sbi.uni-rostock.de) at the University of Rostock has an opening for a postdoctoral researcher and/or graduate student (aiming for a PhD).

The ideal candidate should have a background in mathematics or physics (with a strong interest in interdisciplinary research) or experience in the field of systems biology.

Although there are no pre-specified research objectives (details can be adjusted to the applicant's interests), the work should focus on either nonlinear dynamics, stochastic modelling, or system identification, relevant to applications in molecular & cell biology (cell signalling, gene expression, regulatory networks).

posted 2008.09.11

Permanent PI Scientific Position available in the Mass Spectrometry Group closed

Brazilian Synchrotron Light Laboratory (LNLS) has an opening for a motivated scientist with a strong background in protein/proteomics research using mass spectrometry. The activities associated to the position include to coordinate a multi-user mass spectrometry laboratory
and to conduct independent research, to supervise PhD students and post doctoral fellows.
The successful candidate is expected to have a PhD degree in biochemistry or related disciplines and a post-doctoral experience in protein/proteomics research using mass spectrometry.
Application letter and CV including the contacts of three referees should be sent to pesq.mas2008@lnls.br by October 30, 2008.

posted 2008.08.27

Post-doctoral position in Computational Systems Biology for the ANR Project "Skin TSLP", at Institut Curie, Paris, France open

The position is open in the frame of the ANR project « Role of the keratinocyte-derived cytokine Thymic Stromal Lymphopoietin (TSLP) in human skin inflammation ", coordinated by Dr Vassili Soumelis at Institut Curie, Department of Immunology.

The project:
This project aims at studying the role of the cytokine TSLP in skin inflammation in a global way: molecular regulation in specific systems and relative function within a complex inflammatory network reflecting the pathophysiology of atopic dermatitis and other skin inflammatory diseases. To address these challenging questions, we will use a combination of in vitro cellular and molecular immunology with systems biology approaches to dissect transcriptional profiles induced by complex stimuli. The project will be developed in an interdisciplinary way in collaboration with the Department of Bioinformatics and Computational Systems Biology of Cancer (Dr E. Barillot).

The post-doctoral fellow will develop and carry out computational systems biology approaches to identify the factors and molecular pathways leading to TSLP production by skin keratinocytes, reconstitute TSLP-driven networks relevant to atopic dermatitis, and characterize the function and dominance of TSLP within a complex inflammatory environment.

Requirements for the candidates:
We expect a candidate with a PhD in cell biology, immunology, computational biology, biostatistics or bioinformatics. The successful candidate will have a strong experience in computational data analysis and modeling in biology. Ideally, the candidate should be able to demonstrate some knowledge of the biological mechanisms involved in skin inflammation, and should have experience of interdisciplinary projects mixing, clinics and mathematics. Some programming skills will be useful (R, Perl). Good knowledge of English both spoken and written is required.

The position is open immediately and funded for 2 years with possible extension.
Please send CV, letter of motivation and references to bcsb23 @ curie.fr
For further information please contact Vassili.Soumelis @ curie.net and Emmanuel.Barillot @ curie.fr

posted 2008.08.27

Post-doc position in Computational Biology of Cancer at Institut Curie, Paris, France open

A postdoc position in Computational Biology of Cancer is open at Institut Curie, Paris, France, in the context of a project that join together bioinformaticians, biologists and clinicians.

The position is open immediately and created for 2 years with possible extension.

Context:

Institut Curie is one of the biggest European institutions for cancer research with strong and old interdisciplinary traditions. It also comprises a hospital specialized in cancer treatment, and therefore dispose of a continuum of expertise from fundamental research to patient care. It is located in the center of Paris in a both cultural and scientific rich environment (see http://www.curie.fr).

The Bioinformatics Laboratory of Institut Curie was created in 2003. In January 2008, it has become an INSERM mixed unit "Bioinformatics and Computational Systems Biology of Cancer" (unit 900 INSERM - Mines ParisTech - Institut Curie) involving about 50 researchers and students. It is a very active and growing interdisciplinary team of biologists, physicians, mathematicians, statisticians, physicists and computer scientists (see http://bioinfo.curie.fr).

posted 2008.08.05

Post-Doctoral Research Associate Position open

Department of Chemical Engineering
University of Massachusetts
Amherst, MA

Microbial Biofuels Production

A post-doctoral research position is available in the laboratory of Professor Michael A. Henson in the Chemical Engineering Department at the University of Massachusetts. The research involves the development of metabolic models for the conversion of cellulosic biomass to ethanol by the anaerobic bacterium Clostridium phytofermentans. This interdisciplinary systems biology project is funded by the Department of Energy through a subcontract from the startup company SunEthanol. Close interactions with microbiologists, biochemical engineers, and industrial collaborators will be required. Candidates with a Ph.D. in biology, engineering, or a related field and the following background are sought: (1) bacterial metabolism; (2) metabolic modeling; and (3) dynamic simulation and optimization.

posted 2008.07.31

R&D Scientist closed

   As a member of the scientific team, you will develop and validate cross application and cross product workflows, as well as test and validate new or existing Genomics products and technologies. As such, you will be part of a global development team that will work closely with other Scientists and R&D Engineers on a six month assignment in San Diego, CA.

  • Masters degree (with 5 years of post-graduate experience) or Ph.D., (with 2 years of experience) in Molecular Biology / Biochemistry / Genetics or a related Life Sciences field.
  • Extensive laboratory experience with various Genomics platforms and techniques such as microarrays, QRT-PCR, and DNA sequencing.
  • Experience in the development of microarray- and QPCR-based applications to address biological questions in the Gene Expression and miRNA spaces.
  • Strong problem solving skills and ability to analyze complex data.
  • Broad understanding of Life Sciences research, Molecular Biology, and the latest research developments in Genomics and related Bioinformatics tools and techniques.
  • Knowledge of intellectual property and industry experience.
  • Excellent communication skills, along with being a team player.
The successful candidate will have a combination of scientific expertise, strong customer focus, and communication skills.

posted 2008.07.11

A postdoctoral position open

A postdoctoral position is available dealing with nonlinear dynamics of the heart.
For additional details, see http://www.wm.edu/physics/DelosWeb/index.php

The preferred starting date is about January 1, 2009

Send application materials and letters of recommendation to jbdelo @ wm.edu (Put PDF on the subject line to get past the filters.)

posted 2008.07.08

Post-Doctoral Research Associate closed

Department of Engineering

University of Leicester 

Salary Grade 6 - £23,692 to £27,466 per annum

Available from September 2008

Fixed term contract for 32 Months

Applications are invited for a BBSRC-funded post-doctoral research associate to join a team of researchers working on an exciting interdisciplinary Systems Biology project, based jointly at the Universities of Leicester and Aberdeen.  The PDRA at Leicester will use mathematical modelling and techniques from control engineering to investigate the way in which yeast gene expression is regulated using highly complex robust feedback control mechanisms.  The overall aim of the joint project is to make fundamental breakthroughs in the understanding of how the essential polyamine synthesis metabolic pathway is regulated.  This pathway is central to the molecular biology of polyamine metabolism, and is a key pathway in DNA silencing, protein translation and the cell cycle.  Its components are also potential targets for cancer therapeutics.


posted 2008.07.03

Post-Doctoral Research Associate closed

Department of Engineering

University of Leicester 

Salary Grade 6 - £23,692 to £27,466 per annum

Available from September 2008

Fixed Term Contract for 30 Months 

The Research Associate will join the University of Leicester Systems Biology Lab (www.SBLab.org), based in the internationally leading Control and Instrumentation Research Group, to work on this EPSRC funded project.  The research project aims to apply a systems approach to the problem of mechanical ventilation of the lungs.  We will use advanced control theory to "close the loop" between diagnostic measurements derived from computer-based simulations and adjustment of parameters in a functioning ventilation system, with the ultimate ain of significantly reducing ventilation-associated lung injury in critically ill patients.  The Research Associate at Leicester will work closely with a second Research Associate funded on this project, based at the University of Nottingham and supervised by Dr. Jonathan Hardman (http://www.jghardman.co.uk/).  This is an exciting opportunity to join a genuinely multidisciplinary team of researchers working at the Life Sciences Interface.  Applications are welcome from candidates holding (or about to complete) a PhD in control or Systems Engineering, Physics and Mathematics.

posted 2008.07.03

Post-Doctoral Research Associate Position open

Department of Chemical Engineering
University of Massachusetts
Amherst, MA

A post-doctoral research position is available in the laboratory of Professor Michael A. Henson in the Chemical Engineering Department at the University of Massachusetts. The research involves the development of molecular and multicellular models of intercellular synchronization and rhythm generation in the mammalian circadian system. This interdisciplinary systems biology project is funded by the National Institute of General Medical Sciences. Close interactions with circadian biologists, bioengineers, computer scientists, and applied mathematicians will be required. Candidates with a Ph.D. in biology, engineering, or a related field and the following background are sought: (1) circadian biology; (2) biological systems modeling; and (3) complex systems dynamics.

posted 2008.07.02

Postdoctoral Fellow in Computational Biology open

A postdoctoral research position is available in the Computational Biology and Machine Learning group at Queen's University Belfast (UK). The Computational Biology and Machine Learning group is in the Center for Cancer Research and Cell Biology and studies molecular biological questions on a pathway level by designing and developing computational and statistical methods. We are especially interested in network based analysis. (For more information visit www.bio-complexity.com)

For inquiries please email a short statement of research and your curriculum vitae to Frank Emmert-Streib:  v @ bio-complexity.com

posted 2008.06.16

Postdoctoral Associate Position open

Rutgers University, Department of Physics & Astronomy and BioMaPS Institute for Quantitative Biology.

Dr. Morozov invites applications from highly motivated individuals for a postdoctoral associate position in the area of computational and theoretical biological physics. Current research projects in Dr. Morozov's lab involve computational studies of chromatin structure and gene regulation, biophysical models of protein evolution, and predictions of protein-DNA interactions. More information about Dr.Morozov's research interests can be found at http://www.physics.rutgers.edu/~morozov.

The postdoctoral position is available for two years, with extension contingent upon research progress and funding. Interested candidates should have a Ph.D. in physics, astrophysics, computational biology and bioinformatics, or statistics. Working knowledge of C/C++, Perl, Python, or similar is preferred. Knowledge of biology, although not required, is a plus.

posted 2008.06.12

Senior Scientist - Gene Synthesis Program Manager open

Biosearch Technologies, Inc. helped launch the market for synthetic oligonucleotides,  and continues to advance nucleic acid technologies - now in the area of commercial manufacture of synthetic genes.  To join our team of scientists we are seeking a program manager for this exciting new field on the vanguard of biotechnology--an individual with an accomplished academic or industrial record in the fields of molecular biology, synthetic biology or  biochemistry. Efficient and meticulous development is needed to advance gene synthesis as an automated, high-throughput, production process; preferred candidate has previous experience in a similar environment.

posted 2008.06.06

Research Associate - Gene Synthesis Specialist on a track toward open

Biosearch Technologies, Inc. helped launch the market for synthetic oligonucleotides,  and continues to advance nucleic acid technologies
- now in the area of commercial manufacture of synthetic genes.  We are seeking a motivated researcher to join our R&D team and contribute to this exciting new field on the vanguard of  biotechnology.  Position will require the design, testing, and evaluation of new production methods alongside the routine manufacture of large constructs for commercial sale.  Excellent writing ability, professional communication, and detailed record keeping are essential.  Preferred candidate has previously operated automated instruments in a high-throughput lab, remains efficient under minimal supervision, and is highly effective at collaborating with others.

posted 2008.06.06

Intership/Student project: PARTICLE SIMULATION OF ANTIBODY - TARGET INTERACTION open

Description:

To design a new generation of monoclonal antibody (mAb) drugs we are applying novel modeling and simulation approaches. An accurate modeling of antibody-target interaction is critical for reliable predictions which directly feed into the drug development process. The current project aims to study the fundamentals of antibody-target interaction. Commonly this system is modeled with ordinary differential equations. For a one-to-one partner binding system this model is an accurate description. However, for the case of cell surface targets or where the target has multiple binding sites it is unclear how the interactions must be modeled in an ODE framework. The idea is to develop a particle simulation tool that can be used to study the fundamentals of antibody dynamics and derive the appropriate ODEs. This study is  also expected to impact the design of more complex biological constructs and is therefore at the leading edge of modeling and simulation in drug development.

posted 2008.05.07

Position for plant-related Systems Biology open

Job Description:
The Dow Chemical Company is making strategic investments to enable new product development in the BioSciences arena. This emerging market space targets R&D in new biotechnology-derived products ranging from agricultural commodities, to biomaterials, biomimetics, and biofuels. Computational modeling and biological systems analysis are foundational competencies for this field of research and development. Dow is building a Bioanalytical Center of Expertise located at the Dow AgroSciences facility in Indianapolis, IN. As a member of this Bioanalytical Center you will be accountable for leading the development and implementation of plant-related Systems Biology capabilities for Dow AgroSciences and Dow BioSciences projects and product platforms. 

Key responsibilities will include:
  • Advance our computational biology capability and apply biological modeling approaches to enable or accelerate R&D projects
  • Act as an internal technical expert to develop a robust infrastructure for computational modeling in biology, and lead efforts that utilize external collaborations in this arena
  • Apply relevant computational tools for the analysis of plant metabolic networks
  • Assess, implement and document various bioinformatics and Systems Biology tools to streamline data management, data analysis and experimental design

posted 2008.05.07

PhD Scholarship in B-Cell Autoreactivity and its Role in Solid Organ Transplantation closed

Applications are invited for a 3-year PhD scholarship at DTU Nanotech with starting date soon, but negotiable.  The project is part of a larger collaboration between DTU Nanotech, Technical University of Denmark (DTU), Copenhagen University Hospital (Rigshospitalet), Denmark, and the Weizmann Institute of Science, Israel, and is funded by the Danish Agency for Science, Technology and Innovation and DTU through DTU's Graduate Programme in Medicine and Technology.

Application Due: July 1, 2008

posted 2008.05.01

Post-doc position for the European Project "APO-SYS - Apoptosis systems biology applied to cancer and AIDS", at Institut Curie, Paris, France open

This position is created to support participation of Institut Curie to the EU-FP7-HEALTH-2007-2.1.2-4 project "Apoptosis systems biology applied to cancer and AIDS: An integrated approach of experimental biology, data mining, mathematical modeling, biostatistics and molecular medicine". One of the goal of Institut Curie in the project is the creation of a generic mathematical model of apoptosis pathways, based on quantitative (using ODEs) and qualitative (using logical formalism developed by R. Thomas) approaches. The final model should recapitulate existing models of different aspects of apoptosis and integrate data that will be provided by molecular biologists involved in the project. The mathematical model will be formally analyzed (robustness, parameter sensitivity study, bifurcation analysis, model-checking). Finally the model will be used to facilitate experimental design and make predictions for the biological systems under study.

...

posted 2008.04.30

Two Post-Doctoral Positions open

1. Biological Modeling Post-Doctoral Position.
2. Metabolic Modeling Post-Doctoral Position.

Jennifer Reed
University of Wisconsin-Madison
Dept of Chemical and Biological Engineering
1415 Engineering Dr, 3639 Engineering Hall Madison, WI 53706
jlreed @ wisc.edu

posted 2008.04.22

PhD-studentship or Postdoctoral position in Systems Biology closed

The department of Systemic Cell Biology at the Max Planck Institute of Molecular Physiology in Dortmund, Germany, invites applications for a PhD-studentship or a Postdoctoral researcher

posted 2008.04.21

Senior Electron Microscopy Technician & Postdoctoral Fellow open

POSITION AVAILABLE Senior Electron Microscopy Technician & Postdoctoral Fellow

A Senior Electron Microscopy Technician and a Postdoctoral Fellow are sought to carry out research work on the structure of actin filament complexes that (1) are associated with cardiac and skeletal muscle regulatory proteins to control muscle activity and (2) interact with smooth muscle actin-binding proteins to modulate the assembly of the smooth muscle cytoskeleton. Applicants must have experience in high-resolution EM work and first-rate facility with computer-assisted image analysis. Prior familiarity with preserving and recording macromolecular assemblies in negative stain and by cryo-EM methods would be invaluable. Experience in supervising research students would also be important.

Interested applicants should contact Dr. William Lehman at the meeting or send their CV with three references to:

Dr. William Lehman
Professor of Physiology & Biophysics Department of Physiology & Biophysics
Boston University School of Medicine
715 Albany Street Boston, MA 02118 Or
Email: wlehman @ bu.edu
Dr. Lehman's research is summarized on his home page: http://biophysics.bumc.bu.edu/faculty/lehman/index.html

posted 2008.04.18

PhD student researcher closed

FORSYS Junior Research Group
Systems biology of pancreatic cancer

Systems Biology and Bioinformatics group
University of Rostock
www.sbi.uni-rostock.de

Job description:
  • Research in systems biology of pancreatic cancer in an interdisciplinary junior research team working in collaboration with the Department of Gastroenterology at the Medical Faculty
  • Mathematical modelling of chemical kinetics and transport processes of cellular signal transduction pathways in pancreatic cancer on basis of quantitative experimental data
  • Analyzing model properties using methods from dynamical systems theory
  • Development of mathematical tools for experimental design
  • Statistical analysis of QTPCR and western blot data

Requirements:

  • Degree in Systems Biology, Physics, Mathematics, Engineering or Biochemistry
  • Experiences in the above research fields
  • Interest in interdisciplinary research in the life sciences
Salary: E13, full time job
Starting date: June-September 2008
Project duration: 2 years, with the possibility for extension (five years maximally)
Deadline: May 20, 2008.

Further information: Dr. Katja Rateitschak Tel. +49 381 498 7573

Application expenses cannot be reimbursed.
Submit your application (CV, certificates, etc.) in pdf format to:

Dr. Katja Rateitschak
FORSYS Nachwuchsgruppe
LS Systembiologie und Bioinformatik
Institut fuer Informatik Universitaet Rostock
D-18051 Rostock Germany
katja.rateitschak @ uni-rostock.de

posted 2008.04.16

Tenure Track/Tenure Investigator Positions in Systems Immunology and Infectious Disease Modeling closed

The National Institute of Allergy and Infectious Diseases (NIAID), Division of Intramural Research (DIR) is seeking several outstanding individuals for its new Program in Systems Immunology and Infectious Disease Modeling (PSIIM).

Modern technology allows the analysis of immune responses and hostpathogen interactions at multiple levels - from intracellular signaling networks, to individual cell behavior, to the functioning of a tissue, organ, and even the whole organism. The challenge is not only to collect the large amounts of data, but also to organize it in a manner that enhances our understanding of how the immune system operates or how pathogens affect their hosts. To do this, it is necessary to develop detailed quantitative models that can be used to predict the behavior of a complex biological system. These models can help explain the mechanisms underlying physiological and pathological responses to infection or vaccination, which can then be employed to design better therapies or vaccines.

Achieving these goals requires an interdisciplinary effort and for this reason the PSIIM is organized as an integrated team of scientists and support staff. Within the PSIIM, there will be groups with expertise in the areas of computational biology, bioinformatics, proteomics, genomics, cell biology, immunology, and infectious diseases. These teams will have access to the latest technology for gene expression profiling, high content screening of RNAi libraries for the discovery of pathway components, imaging tools, genomic and proteomic analysis, cores for the genetic manipulation of animals, and a substantial computer infrastructure. They will also have access to BSL3 facilities for working with infectious agents of high priority for human health and biodefense. Although the PSIIM has been established within NIAID and has an immune / infectious disease focus, it is also expected to play a major role in fostering the growth of systems biology efforts throughout the NIH and involving diverse biomedical areas.

Current teams in the PSIIM include Immunology, Computational Biology - Modeling and Simulation, and Molecular / Cell Biology - High-throughput screening. The PSIIM is now recruiting for tenure track or tenure level team leader appointments in the following areas:

Bioinformatics / Biostatistics:
the incumbent will lead a group focused on developing and implementing computational tools and statistical methods for the analysis of genomic and proteomic data. The ideal candidate will have a strong background in statistics, mathematics, programming, and modeling biological systems as well as a strong interest in collaboration with biologists for the elucidation of biological mechanisms. The group will include expertise in software development (C++, Java, Perl, SQL etc.), knowledge of bioinformatic tools, databases and algorithms, and experience with heterogeneous computer environments (UNIX, Windows, Mac).

Proteomics: the incumbent will lead a group involved in the development and application of new methods for the determination of protein number, binding affinities, post-translational modification, and other qualitative and quantitative aspects of protein expression and behavior that are necessary for computer modeling and simulation. Tools such as mass spectrometry and microfluidic-based multiplexed binding assays are expected to be key elements in the efforts of this group. A strong background in protein biochemistry and the relevant instrumentation needed for high-throughput, high-sensitivity analysis is required.

Genomics:
the incumbent will be responsible for developing novel approaches to the systems-wide analysis of such issues as transcription factor and epigenetic control of gene expression, the effects of allelic polymorphism on gene expression and function, quantitative measurement of gene expression, and the role of non-coding regions and transcripts such as miRNAs in regulating gene/gene product expression patterns.

Knowledge of modern methods in high-throughput analysis of gene transcription, transcription factor binding site identification, analysis of epigenetic modifications, and analysis of gene regulatory circuits is required; bioinformatics experience is desirable. These positions and the research activities they conduct are fully funded by the intramural research program of NIAID. Each team leader is expected to build a working group consisting of postdoctoral fellows, students, technicians, and staff scientists. The team leaders will work with the Program Director to help set the goals for the PSIIM and to determine how best to reach these goals as an integrated group. To ensure appropriate career trajectories for those joining the PSIIM team effort, the NIH has modified its tenure policies to take specific account of contributions made in such a team science setting. Applicants should be seeking a difficult
challenge in which creativity, technical expertise, and a strong desire to achieve in a team setting will be critical for success.

Interested candidates may contact Dr. Ronald Germain, Program Director, PSIIM, DIR, NIAID at (301) 496-1904 or email (rgermain @ niaid.nih.gov) for additional information about these positions.

To apply, submit your curriculum vitae, bibliography, and a detailed statement of how your expertise can contribute to the success of the PSIIM program, to Wanda Jackson at NIAID.DIR.Search @ niaid.nih.gov.
In addition, three letters of reference must be sent directly from your three referees to Dr. Robert Hohman, Chair, NIAID Search Committee, c/o Wanda Jackson at NIAID.DIR.Search @ niaid.nih.gov or 10 Center Drive, MSC 1356, Building 10, Room 4A22, Bethesda, Maryland 20892-1356.
Email is preferred. Completed applications MUST be received by Friday, May 23rd.
Please refer to ad #019 for bioinformatics/biostatistics, #020 for proteomics, and #021 for genomics on all correspondence.
Further information regarding the DIR laboratories is available at:http://www3.niaid.nih.gov/about/organization/dir/default.htm and information on working at NIAID is available on our website at: http://healthresearch.niaid.nih.gov

For more information about the NIAID systems biology program, please visit http://www.nih.gov/catalyst/2006/06.09.01/page1.html

posted 2008.04.14

Group leader biomodeling and biosystems analysis closed

Netherlands Institute for Systems Biology (NISB, www.sysbio.nl)
Amsterdam, The Netherlands

The Netherlands Institute for Systems Biology (NISB, www.sysbio.nl) is a joint venture of the two Amsterdam universities (the Vrije Universiteit and the University of Amsterdam) and two national research institutes in Amsterdam (the CWI (Netherlands research institute for mathematics and computer science) and AMOLF (FOM Institute for Atomic and Molecular Physics)).

The Netherlands Genomics Initiative (NGI, www.genomics.nl) has recently initiated the Netherlands Consortium for Systems Biology (NCSB), a 15 million Euro national research program to implement systems biology in ongoing research lines of seven high ranking Dutch research groups in the fields of biomedical and biotechnological research. As part of this investment a Biomodeling and Biosystems Analysis Group will be set up in the Netherlands Institute for Systems Biology (NISB) in Amsterdam.

The task of the Biomodeling and Biosystems Analysis Group is to develop generic as well as
specific tools and approaches for modeling and analysis of complex biological systems, specifically those that are addressed in the context of the NCSB program. The group will be housed in Amsterdam in the premises of one of the four parties that constitute the NISB (two universities and two national research institutes in Amsterdam). The group leader has a budget of 1.5 million Euro for a period of five years. A tenure position can be negotiated for this function.

In addition to the postdocs, PhD students and other personnel in the group, the group leader will be responsible for the modeling and system analysis activities of about twelve investigators (postdocs and PhD students) that are positioned in the different biomedical and biotechnological research groups that participate in the NCSB program. In this, the Biomodeling and Biosystems Analysis Group plays a central role in the NCSB program.

Candidates should fulfill the following criteria.
  • Strong track record in modeling and analysis of complex biological systems based on experimental data sets.
  • Able to build bridges between mathematicians/physicists/informaticians and experimental biologists
  • Proven leadership.
  • Able to communicate with researchers in the fields of biomedical and biotechnological research.
Application should be send to the director of the Netherlands Institute for Systems Biology (NISB): prof. Dr Roel van Driel, c/o University of Amsterdam, Kruislaan 318, 1098SM Amsterdam, the Netherlands. Information can be obtained from the same person (office: +31 (0)20 525 5150; home: +31 (0)251 657 356; mail: van.driel @ science.uva.nl).
Deadline May 1st, 2008.

posted 2008.04.11

Senior/Research Associate (Bioinformatician - Network Analysis) closed

Newcastle University, Centre for the Integrative Systems Biology of Ageing and Nutrition
Senior/Research Associate (Bioinformatician - Network Analysis)

Ref                        A1090R
Faculty/Services     Medical Sciences
Department            Institute for Ageing & Health
Job Type                Research
Hours of Work        Full time
 
Salary: Level F: £25,134 - £32,796
           Level G: £33,779 - £40,335
 
Closing date: 15 April 2008

We seek an experienced bioinformatician or computing scientist with a strong research background in biological networks and their analysis, and a sound understanding of molecular biology. Ideally, you will also have a detailed knowledge of high-throughput post-genomic technology.

The development and use of functional integrated networks are an important focus of CISBAN and your role will be to continue to progress this area of research taking responsibility for the continued research and development of the CISBAN integrated networks database CID.

You will also research and develop novel methods of representing and integrating molecular and cellular data as networks and to apply this methodology to the characterisation of novel proteins, and elucidation of novel pathways, involved in the process of cellular ageing and senescence.

You will also interact closely with the other bioinformaticians, computing scientists, biostaticians, mathematical and computational modellers on the CISBAN project and therefore good communication skills are required.

This post is for a research associate to join our existing expert team and is available immediately.

Tenable until 30 September 2010.

Informal enquiries may be made to Dr. Anil Wipat, anil.wipat @ ncl.ac.uk

Please apply online at
http://www.ncl.ac.uk/vacancies/jobs/


posted 2008.04.10

PhD student researcher on Systems Biology in CALSYS closed

PhD student researcher on Systems Biology
(computer scientists, physicists, mathematicians or engineers)
In the FORSYS Junior Research Group for Cancer and Aging (CALSYS)
UNIVERSITÄT ROSTOCK
Systems Biology and Bioinformatics Group
(University of Rostock)
www.sbi.uni-rostock.de
In CALSYS we investigate the role that the p53-p21-pRB, p16-pRB and other signalling
pathways have in the induction and maintenance of senescence growth arrest and how their
responses are combined to decide whether the cell must undergo cell cycle arrest, senescence or apoptosis in response to (cancer or aging related) DNA damage or stress signals. The aim of the project is to improve our understanding of the relation between cancer and aging using a systems biology approach. The project includes two main scientific parts: i) the investigation of the signalling pathways linking cancer with aging, and ii) the development of methodologies for the qualitative global analysis of cell signalling models based on ordinary diffrential equations.

Job description
We look for a doctoral student with a Master Degree in Computer Sciences, Mathematics,
Physics or Engineering interested on getting experience in Systems Biology of cell signalling
systems. Tasks to be performed include:
  • Mathematical modelling of signalling pathways in cancer and aging.
  • Development of methodologies for global qualitative analysis of ODE models, models in cell signalling. Design of a software tool.
  • Design and administration of a webpage.
Requirements:
Degree in Computer Sciences, Mathematics, Physics or Engineering.
Interest in interdisciplinary research in the life sciences.
Fluent English and/or German.
Matlab programming, Java.
Proficient in Computational Biology.
Previous experience in systems biology and in design and implementation of
numerical algorithms and software will be very positively valued.
Willing to travel across Europe.

Salary: E13, full time job (approx. 2.600 Euro/month gross income).
Project starting date: June-July 2008.
Deadline: 25th april 2008
Project duration: 1 years, a possible extension for three more years.

Submit your application (CV, certificates) to:
Dr. Julio Vera Gonzalez
FORSYS Junior Research Group in Cancer and Aging.
Systems Biology and Bioinformatics Group.
Institute for Informatics, University of Rostock.
D-18051 Rostock Germany.
e-Mail: julio.vera @ uni-rostock.de
http://www.uni-rostock.de/Stellen/st-einzel.asp?ID=3028

posted 2008.04.09

A Five years post-doctoral position at CEB-UM closed

A Five years post-doctoral position is open at the Institute for Biotechnology and Bioengineering - Centre of Biological Engineering in Braga (Portugal) for Systems Biology.

The CEB-UM < www.ceb.uminho.pt > is part of the IBB - Institute for Biotechnology and Bioengineering a R&D unit founded in October 2006 aiming to be a strategic infrastructure for the development of the Portuguese R&D and innovation policies in the areas of Biotechnology, Bioengineering, Biomaterials and Life, Biomedical and Agricultural Sciences.

Job summary:

Systems Biology profile covering the integration of information obtained from genome sequencing projects and data-mining of genome-scale analytical techniques and subsequent development of rational metabolic engineering strategies.

Job description:
The activities associated with development and application of Systems Biology tools to R&D in Biotechnology at CEB-UM cover 3 main vectors:
  • Integration of information obtained from genome sequencing projects in metabolic and biological engineering projects;
  • Development and application of algorithms to the treatment and interpretation of data resulting from the application of genome-scale analytical techniques and subsequent development of rational metabolic engineering strategies;
  • Development and application of algorithms to support technologies and projects in molecular biology.
The candidate should have:
  • PhD in Bioinformatics, Biotechnology, Biochemical Engineering or Computer Science;
  • Extensive knowledge on Bioinformatics and Systems Biology, including several applications and techniques like database search, sequence analysis, construction and simulation of biological models and high-throughput data integration and analysis;
  • Programming skills in Perl and/or Java and in R and/or MATLAB.
Applicants should also display evidence of managerial skills, independent research and significant scientific accomplishments. The successful candidate should have a strong publication record and propose an innovative research project relevant to the Research Unit that he/she wants to integrate.

Application procedure:
To apply, please send your complete CV (with photo), in English, a covering letter (1 page A4) outlining the qualifications, skills and experience in relation to this position, two reference letters, as well as other information considered relevant. All the elements should be sent to the "CEB
-  Centro de Engenharia Biológica" to the following e-mail address: Dr. Eugénio Ferreira -  ecferreira @ deb.uminho.pt The deadline for application is 29 May 2008.

More details:
http://www.eracareers.pt/opportunities/index.aspx?task=global&jobId=9025 
 

posted 2008.04.08

PhD position on evolutionary dynamics - Simula Research Laboratory closed

Simula Research Laboratory conducts basic research in the fields of  communication technology, software engineering and scientific computing.  The research in the Scientific Computing (SC) department is focused on the development of numerical methods, algorithms and software, and large scale biomedical and systems biology oriented simulation studies applying these methods. In recent years, the main application area for computational research studies has been the simulation of the electrical and mechanical activity of the heart. Currently, we plan to extend our computational research to simulations of the evolutionary dynamics of genetic networks controlling the properties of organisms.

The aim of the research project is to study key evolutionary processes such as the adaptation of organisms to their environment, the splitting up of a species into multiple species and the 
development of multicellular organisms from a single fertilized cells. A key aspect of the research will be to study how the architecture and dynamics of genome organization and gene regulatory network structure influence the properties of organisms and hence how they influence the above mentioned evolutionary processes and how this contrasts with findings from more classical population genetics models.

Our understanding of genome organization and gene regulatory networks has changed dramatically over the last decade. A large part of DNA that was previously considered junk turns out the be functional after all, coding for RNAs that are however not translated into proteins. These RNAs in turn are often involved in regulating the expression of genes, which were previously thought to be exclusively regulated by proteins. Incorporating these new insights into our models is another key aspect of the research project.

Modeling formalisms used will typically be discrete, individual-based, event-based, and often
spatially extended and will involve the explicit modeling of the evolution of genes, genomes and gene regulatory networks determining the properties of simulated agents. The project will be supervised by a new member of our research group, Dr. Kirsten ten Tusscher (http://
www-binf.bio.uu.nl/khwjtuss/
).

Simula offers excellent opportunities for doing high quality research, generous support for travels and equipment, and competitive salary (around 47.000,- Euro/69.000,- USD for a Ph.D. position)

We are looking for candidates who fulfill one or more of the following requirements:

  • a strong interest in evolutionary biological  research
  • a University degree in computational biology, systems biology, biomedical engineering, artificial life, artificial intelligence, computer science, physics or applied mathematics
  • experience with computational modeling, simulation and analysis of complex (biological)systems.

The position requires excellent English writing skills and high marks from the BSc and MSc degree. Women are encouraged to apply. For more information contact Joakim Sundnes (sundnes@simula.no) or Kirsten ten Tusscher(tentussc@simula.no). To apply, email a short application letter, curriculum vitae, copies of transcripts and grades, and a publication list to jobs@simula.no. The subject of the email must contain 0830 Scientific Computing.

Application deadline: May 16, 2008

posted 2008.04.03

PhD Student Position in Systems Biology - 2008 open

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" closed

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

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

posted 2008.03.25

Postdoctoral Fellowship: Mathematical Modeling of Viral Transcriptional Circuitry open

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) closed

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 at Virginia Tech closed

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

Systems Biology Posts at Aberdeen and CISBIC open

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

Environmental Protection Agency Cross-ORD Postdoctoral Program Mapping Toxicity Pathways for Environmental Chemicals closed

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 open

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

Director, Division of Systems Toxicology closed

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 open

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) closed

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