A portal site for systems biology.

The Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital and the Ohio State University A postdoctoral position is available immediately at the Das Lab in the Battelle Center for Mathematical Medicine at The Research Institute at Nationwide Children's Hospital (www.nationwidechildrens.org/research). The Das Lab uses computational and theoretical tools based on stochastic methods, nonlinear dynamics and statistical mechanics. More details about the lab can be found at, http://openwetware.org/wiki/User:Jayajit_Das. All the projects are focused on understanding our immune system (innate and adaptive) at a mechanistic level and are carried out with synergistic collaborations with leading experimentalists in the area. Highly motivated and career oriented applicants with expertise in statistical physics, evolutionary dynamics, chemical engineering, bioengineering, systems biology or other areas of computational biology are particularly encouraged to apply.

We have a state of the art computer cluster with 96 INTEL processors. The resources at the Ohio State University campus are also available. The position will be for one year, renewable for a second year. Interested candidates should send (preferably by email), a brief cover letter stating your interest in our lab, a short CV and names and contact information of three referees to,

Jayajit Das
Assistant Professor
Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital and Department of Pediatrics and Physics, Ohio State University, Columbus, OH 43206
Email: das.70 @ osu.edu Ph: 614-355-4526 Fax: 614-355-2728

Please send a copy of the application to:
Alexis Phillips-Simmons
Admin. Assistant Phone # 614-722-3811
Email: Alexis.Phillips-Simmons @ nationwidechildrens.org

posted 2009.12.29

Department of Chemical and Biological Engineering
Colorado State University

A postdoctoral position is available immediately at the Prasad Lab in the Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado. The Prasad Lab uses computational and theoretical tools to study some key problems in biology. Main projects in the lab are focused on (i) understanding bone tissue regeneration mechanistically at a multiscale level (ii) modeling the human immune response, both at the level of individual cells and the organism. Other projects include studying the cytoskeleton and bacterial photosynthesis. Our projects are carried out in collaborations with experimental labs. Highly motivated applicants with expertise in statistical physics, chemical engineering, bioengineering, systems biology or other areas of computational biology are particularly encouraged to apply.
Some more details about the lab and current projects can be found at http://www.engr.colostate.edu/cheme/pages/Ashok_Prasad.html

We have a state of the art 96-core computer cluster with INTEL processors. The resources at the Colorado State University campus are also available. Fort Collins, CO is located along the foothills of the Rocky Mountains and is regarded as one of the best places to live in the USA. The position will be for one year, renewable for a second year. Interested candidates should send (preferably by email), a brief cover letter stating your interest in our lab, a short CV and names and contact information of three referees to,

Ashok Prasad
ashokp [at] engr.colostate.edu
Dept. of Chemical and Biological Engineering
Colorado State University
Campus Delivery 1370
Fort Collins, CO 80523

posted 2009.12.23

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:
•       Masters or 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
•       Candidates must be U.S. based and NO AGENCIES!

Please submit resumes or CVs to careers@immunetrics.com

Immunetrics, Inc.
2403 Sidney Street  Suite 271
Pittsburgh, PA 15203

posted 2009.12.15

A postdoctoral research position is available for a talented, creative and strongly motivated experimentalist with a recent PhD degree in Biology, Bioengineering or a related field. Successful candidate will join our efforts to investigate the survival of drug treatment and the development of drug resistance in Baker's yeast as a model organism. The project involves building synthetic gene circuits to regulate the expression of drug resistance genes, single cell imaging, flow cytometry, studying drug resistance, and experimental evolution under drug treatment. Individuals with a history of interdisciplinary collaboration and experience in yeast genetics, single cell imaging, and/or experimental evolution are especially encouraged to apply.

To apply, please email (i) a CV including list of peer-reviewed publications, (ii) the names and email addresses of three references, and (iii) a research statement (maximum 500 words) directly relevant to the above description to: <mdacc.job001@gmail.com>

Competitive salary and benefits will be commensurate with experience and qualification. The University of Texas M. D. Anderson Cancer Center is known as the leading cancer center in the world and has consistently been ranked and among the top 10 places to be a postdoctoral fellow based on surveys by The Scientist. We are located in the largest medical center of the continent, in close proximity to other degree granting universities and medical schools, with outstanding opportunities for research and development.

The University of Texas M. D. Anderson Cancer Center is an equal opportunity employer and does not discriminate on the basis of race, color, national origin, gender, sexual orientation, age, religion, disability, or veteran status except where such distinction is required by law. All positions at M. D. Anderson are security sensitive and subject to examination of criminal history record information. Smoke-free and drug-free environment.

Contact: Gabor Balazsi, PhD
Systems Biology - Unit 950
The University of Texas M. D. Anderson Cancer Center
P. O. Box 301429
Houston, TX 77230-1429
United States
Email: <mdacc.job001@gmail.com>

posted 2009.12.15

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

Postdoctoral positions are immediately available in the Theoretical Cellular Physics Section of
Computational Biology Laboratory at the National Heart, Lung and Blood Institute, National
Institutes of Health, Department of Health and Human Services, Bethesda, MD. Applicants
should have Ph.D. in theoretical chemistry, physics, applied math or engineering. Candidates
with strong computational skill and theoretical modeling experiences are highly desirable.
Projects would utilize sophisticated statistical mechanics techniques to investigate
mechanochemical couplings in various cellular processes, including membrane mechanics,
cytoskeleton dynamics and reaction networks. All the projects would be in extensive and close collaborations with experiments. For more information, see:
http://www.lobos.nih.gov/tcps/index.shtml

Appointment and salary are dependent on experience. Applicants should submit, in a PDF file, a letter of interest, curriculum vitae, and the names of three individuals willing to provide letters of reference to: Dr. Jian Liu at liuj7 [at] mail.nih.gov

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

posted 2009.12.12

PD017 - Systems Biologist, Sage Bionetworks, Seattle, WA

Sage is looking for exceptional candidates with strong biological backgrounds and interests in using high dimension genomic data to interpret disease processes.  In particular we are seeking individuals with a background in cancer biology. The successful candidate will have a background that includes hands on laboratory research as well as the generation and interpretation of genome-wide data. Research done in this position is inherently interdisciplinary and will involve mining data across organ systems and species to develop models of biology and prospectively test the utility of those models.  These models will be used to focus mechanistic experiments in many aspects of biology, including applications in therapeutic target and biomarker discovery as well as patient stratification for clinical outcome or pharmacological response.  A candidate will need to demonstrate the ability to lead complex projects and to work effectively in a team environment.

Qualifications:

·            PhD, MD, or equivalent in biological sciences and 3+ years of experience in an academic or corporate setting actively applying systems biology to experimental work, preferably relevant to cancer.

·            Expertise in one or more of the following: microarray expression analysis, genetics of gene expression analysis, deep sequencing data analysis, statistical methods development, network methods development or complex biological data mining.

·            Working knowledge of bioinformatics methods and database resources

·            Familiarity with relational databases (MySQL, SQL-Server, Access, etc.)

·            Basic statistical training

·            Programming and computing skills using R or Matlab

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

For information on Sage Bionetworks go to:  www.sagebase.org

Sage offers a comprehensive benefits package, including relocation benefits to bring the right talent to the team.

 

PD018 Network Biologist, Sage Bionetworks, Seattle, WA

Sage is looking for exceptional candidates with strong computational and analytical skills and an interest in applications relevant to the modeling of disease processes. A necessary pre-requisite for this position is hands on experience in developing network-based algorithms for representing high dimension genomic data.  This position will work in a multi-discipline team and contribute significantly to our efforts to systematically study complex human diseases through the integration of genetics, genomics, gene expression, transcription factor binding arrays, RNAi, clinical end-points, protein-protein interaction, literature data, etc.  The goal of the research is to identify causal relationships between pairs of traits, gene-gene or gene-clinical, and represent them in networks or probabilistic graphical models.  Such causal networks will be used to elucidate disease or drug mechanism, to aid target discovery and target prioritization.  This position will develop novel methods for integrating diverse data sources, comparing different networks (such as networks for human and mouse, or liver and adipose) and identify common features among networks or distinct pathways between normal networks and disease specific networks.  A successful candidate will need to demonstrate the ability to lead complex projects and to work effectively in a team environment.

Qualifications:

• Ph.D. or equivalent in physics, mathematics, statistics, computer science, electrical engineering, bioinformatics, or other relevant area.
• Solid programming skills and experience with large data sets.
• 3+ years of experience in an academic or corporate setting developing systems approaches.
• Expertise in one or more of the following: microarray expression analysis, genetics of gene expression analysis, deep sequencing data analysis, statistical methods development, dynamic systems, graph theory,  other network-based approaches to data analysis, or complex biological data mining.

 

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

For information on Sage Bionetworks go to:  www.sagebase.org

Sage offers a comprehensive benefits package, including relocation benefits to bring the right talent to the team.

 

PD019 Postdoctoral Fellow - Network Biologist, Sage Bionetworks, Seattle, WA

System biology is a fast moving area.  Many networks are proposed / constructed based on high throughput methods.  The challenges in the field are how to compare such networks, how to extract common information and how to combine them.  The answers to these important questions can guide decisions about which data to collect with limited resources and / or how to transfer knowledge from animal models to human disease.  

This Post-doctoral fellow will work in a multi-discipline environment and will be responsible for developing novel methods for comparing different networks (such as networks for human and mouse, or liver and adipose) and identifying common features among networks and / or distinct pathways between normal networks and disease specific networks.

Qualifications:

A Ph.D. or equivalent in physics, mathematics, statistics, computer science, electrical engineering, bioinformatics, or other relevant area is required.  Experience of analyzing large data sets is a plus. 

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

For information on Sage Bionetworks go to:  www.sagebase.org

 

PD020 - Postdoctoral Fellow, Sage Bionetworks, Seattle, WA

System biology is a fast moving area.  Network models derived from coherent sets of genome-wide data in populations provide an approach to building new models of biology that can be challenged, proofed, and refined in other populations and by experiments that perturb particular nodes or structures within molecular networks.  Many of the questions that arise in this research are highly-interdisciplinary and benefit from diverse perspective, analytical approaches, and experiment designs.  We seek postdoctoral fellows with strong cross-disciplinary training who are interested in leveraging the resources of the Sage Commons to develop a novel program of research.

Qualifications:

·         A Ph.D. or equivalent with strong experience and skills in both biology and computational research is required.  Experience of analyzing large data sets is a plus. 

 

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

For information on Sage Bionetworks go to:  www.sagebase.org

Sage offers a comprehensive benefits package, including relocation benefits to bring the right talent to the team.

posted 2009.12.08

Department of Health and Human Services National Institutes of Health National Cancer Institute

Postdoctoral research positions in SYSTEMS BIOLOGY/BIOINFORMATICS (deadline: open-ended)

The Neuro-Oncology Branch, a trans-institute program of the National Cancer Institute and the National Institute of Neurological Disorders and Stroke of the National Institutes of Health is seeking outstanding candidates to work in the area of cancer genomics, bioinformatics and systems biology, particularly on computational modeling of signaling and gene networks in cancer cells. Ongoing projects include the integration of -omics and clinical data in the exploration of signaling and transcriptional networks that govern cell differentiation, proliferation and migration in primary brain tumors, cancer tumor stem cells and normal embryonic neural stem cells and the translation of those discoveries to patients through the highly integrated clinical brain tumor research program. Applicants should have a strong background in mathematical and computational modeling and be expected to carry out an interdisciplinary project with experimental groups.

The following skills and qualifications are required: 1) PhD in computer science, mathematics, bioinformatics, or related fields, and experience in machine learning and network generation algorithms; 2) basic knowledge of cell/molecular biology. Although not absolutely necessary, the ideal candidate will preferably have some experience in the analysis of genome-wide SNP and gene expression data.

Please send curriculum vitae, statement of research interests and two letters of reference to:
Howard A. Fine, Chief; Neuro-Oncology Branch, National Cancer Institute; MSC 8200, Room 225; 9030 Old Georgetown Road; Bethesda, MD 20892-8200 or to smithj9 [at] mail.nih.gov.
Candidates may be U.S. citizens, resident aliens, or nonresident aliens. DHHS, NIH, the National Cancer Institute and the National Institute of Neurological Disorders and Stroke are Equal Employment Opportunity and Affirmative Action employers that value and foster diversity throughout the entire organization.

posted 2009.12.02

Department of Health and Human Services National Institutes of Health National Cancer Institute

STAFF SCIENTIST research positions in SYSTEMS BIOLOGY/BIOINFORMATICS (deadline: open-ended)

The Neuro-Oncology Branch, a trans-institute program of the National Cancer Institute and the National Institute of Neurological Disorders and Stroke of the National Institutes of Health is seeking an outstanding candidate to work in the area of cancer genomics, bioinformatics and systems biology, particularly on computational modeling of signaling and gene networks in cancer cells. Ongoing projects include the integration of -omics and clinical data in the exploration of signaling and transcriptional networks that govern cell differentiation, proliferation and migration in primary brain tumors, cancer tumor stem cells and normal embryonic neural stem cells and the translation of those discoveries to patients through the highly integrated clinical brain tumor research program. Applicants should have a strong background in mathematical and computational modeling and be expected to carry out an interdisciplinary project with experimental groups.

The Staff Scientist candidate will take a lead role in the mentorship and scientific management of a team of bioinformatics research fellows. The following skills and qualifications are required: 1) PhD in computer science, mathematics, bioinformatics, or related fields, and at least 3 years of post-doctoral training in bioinformatics and/or systems biology; 2) experience in machine learning and network generation algorithms; 3) basic knowledge of cell/molecular biology; 4) experience in genome-wide genetic and gene expression data analysis.

Please send curriculum vitae, statement of research interests and two letters of reference to:
Howard A. Fine, Chief; Neuro-Oncology Branch, National Cancer Institute; MSC 8200, Room 225; 9030 Old Georgetown Road; Bethesda, MD 20892-8200 or to smithj9 [at] mail.nih.gov.
Candidates may be U.S. citizens, resident aliens, or nonresident aliens. DHHS, NIH, the National Cancer Institute and the National Institute of Neurological Disorders and Stroke are Equal Employment Opportunity and Affirmative Action employers that value and foster diversity throughout the entire organization.

posted 2009.12.02

EVOLUTION AND FUNCTION OF CYANOBACTERIAL GENES AND GENOMES

Supervisors:
Dr Daniel Barker, University of St Andrews, and Professor Geoffrey Codd, University of Dundee.

This project will improve knowledge of the evolution, metabolism, ecotoxicological status and biotechnological potential of cyanobacteria by the development and application of bioinformatics algorithms. Cyanobacteria are a metabolically diverse group of photosynthetic prokaryotes of global distribution. They play a crucial role in biogeochemical cycles (oxygen, carbon, nitrogen), produce toxins which present major health hazards to humans and animals, yet also contain metabolites with therapeutic and biotechnological applications, including biofuels. At least 48 cyanobacterial genomes have been sequenced. However, the function of many of the genes in their genomes remains unknown. This represents a major gap in biological knowledge which would be difficult to fill by traditional approaches. We have developed a comparative, bioinformatics procedure to delimit groups of genes which are functionally linked, on the basis of correlated gain and loss of those genes from genomes. This must be vastly improved, to also model gene-phenotype and gene-environment interactions, and applied to cyanobacteria. The project would involve research in computational comparative genomics. Results will be of interest to researchers in bioinformatics, environmental and health sciences and in biotechnology.

Informal enquiries to Daniel Barker, db60 [at] st-andrews.ac.uk

For further details, including how to apply, please see:

http://biology.st-and.ac.uk/projectProfile.aspx?psr=433&pid=168

IMPORTANT NOTE ON FUNDING

A successful candidate would receive funding (covering fees and stipend). Funding is ONLY possible for candiates who meet the Natural Environment Research Council's criteria:

http://www.nerc.ac.uk/funding/application/studentships/studentbook2008.pdf

In particular, please note the section "Residence" (pp. 3-6). If you do not meet these criteria, please only apply for this position if you have already obtained funding yourself.

posted 2009.11.24

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

The Quantitative Systems Biology group at the Clinical Sciences Centre of the Medical Research Council and the Faculty of Medicine of Imperial College in London (UK) is seeking postdoctoral candidates with an interest in interdisciplinary research aimed towards a quantitative understanding of the function of complex biological systems. The successful applicant will investigate the properties of signaling, genetic and transcriptional networks in mouse and human, carrying out projects that integrate experimental measurements with data analysis and mathematical modeling.
 
The successful candidate will have a Ph.D. in a biological discipline with a sound knowledge of the standard laboratory methods of molecular and cell biology and a strong publication record. Experience with flow cytometry analysis of primary cells and/or miRNAs and siRNA knockdown in an immunological context will be advantageous, as well as familiarity with mathematical and computational methods.  We are a recently established and expanding research lab seeking enthusiasm, flexibility and willingness to learn across disciplines.
 
Additional information can be found on our website http://qsb.csc.mrc.ac.uk Informal enquiries are highly encouraged and should be made directly to Dr Alberto Polleri, Group Head, at polleri@csc.mrc.ac.uk

This post is a Career Development Fellowship to support post-doctoral scientists in early or changed career training and help establish them as a successful research scientist in their chosen field. It is initially a 3-year training and development post, which incorporates both scientific and transferable skills training.
 
Applications for this role should be made online at http://jobs.mrc.ac.uk. If you do not have internet access or experience technical difficulties please call +44 (0)1793 301154 quoting the reference number CSC09/591. Please ensure you include a copy of your covering letter, CV, statement of research experience and goals and contact details for three professional referees within your application.

Closing date: 17 December 2009

posted 2009.11.17

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

posted 2009.11.17

The Computer Science Department (Dipartimento di Informatica) of the University of Torino seeks candidates for a post-doctoral position founded by the BioBITs Project (Converging Technologies 2007, area:Biotechnology-蜂CT), Regione Piemonte.

Title of research project:
Methods and tools for the analysis, design, validation, implementation and testing of biological systems.

Scientific direction:
Prof. Mario Coppo
Prof. Mariangiola Dezani-Ciancaglini
Dott. Angelo Troina

Related research interests:
Application of formal methods (logic, type theory, model checking, process algebras, automata theory, rewrite systems, etc.) in systems biology.

Qualification Requirements:
A PhD in Computer Science or a related field, preferably with some expertise in biology, formal methods for computer science, and quantitative (probabilistic or stochastic) analysis.

Languages required:
English spoken and written; spoken Italian is an asset. Working languages in the group are both Italian and English.

Salary:
May vary depending on qualifications and experience.

BioBITs Web site (under construction):
http://www.biobits.di.unipmn.it/

Submission deadline:
30 November 2009.

Starting date:
Negotiable, but we are especially interested in people available on short notice. In order to start in this position, the selected candidate will have to provide official university documents showing that they have completed all the requirements for their PhD degree.

Duration:
One year renewable.

Submission:
Applications for this role can be sent by email to the following address:
coppo [at] di.unito.it
dezani [at] di.unito.it

posted 2009.11.11

Description

Applications are invited for postdoctoral positions to work on mass spectrometry-based computational metabolomics/proteomics and the integration and modeling of -omics data. The successful candidate is expected to identify and formulate new mathematical problems and to apply applied mathematics, statistics, and machine learning to designing novel algorithms. This project is an integral part of our long-term goal to develop predictive models of biological systems based on heterogeneous types of -omics data.

Qualifications

• Recent Ph.D. in applied mathematics, statistics, bioinformatics, or related fields.
• Solid computer programming skills and quantitative data analysis capabilities.
• Research experience in bioinformatics or related fields.
• Track record of publishing scientific results.
• Creative independence.
• Highly motivated to work in close collaboration with biologists.
• Very good communication skills.

 

The Department of Bioinformatics & Genomics at the University of North Carolina at Charlotte is engaged in a multi-year expansion program encompassing two major sites. In addition to a new $35M state-of-the art bioinformatics building on the University's main campus, the Department has the leadership role in bioinformatics for the North Carolina Research Campus (NCRC) at Kannapolis. The NCRC is a $1.5B, 350-acre biotechnology research park that will be home to the research programs of seven North Carolina research universities and several health care organizations, as well as a large number of private biotechnology companies.

The interested applicants should email a CV, a description of research interest, and the name and contact information of three references to xiuxia.du [at] uncc.edu.

posted 2009.11.09

The Department of Statistics, Purdue University invites applications for a tenure-track position beginning August 2010 at the Assistant Professor level in the area of statistical bioinformatics. This hire will join an exciting and established group in statistical bioinformatics.

The Department of Statistics offers a stimulating and nurturing academic environment. More than 35 tenured and tenure-track faculty members direct research programs in a broad range of areas complementary to statistical bioinformatics. Further information about the department is available at

http://www.stat.purdue.edu

All applicants should hold a Ph.D. in Statistics or a related field, be committed to excellence in teaching, and have demonstrated strong potential for excellence in research. Salary and benefits are highly competitive. For all positions in Statistics, please visit

http://www.stat.purdue.edu/hiring/

to apply.

Review of applications will begin on December 1, 2009, and will continue until the position is filled. Purdue University is an Equal Opportunity/Equal Access/Affirmative Action employer fully committed to achieving a diverse workforce.

posted 2009.10.30

PhD position in computational evolutionary genomics We are looking for a highly motivated and innovative PhD student candidate (~4 years) to explore the wealth of genomic data from evolutionary perspectives using bioinformatics approaches. Our group has a broad range of interests related to the functional evolution of genomes, and actively contributes to international genome analysis consortia. The specific project aims and objectives will be developed together with the candidate to suit interests and skills.

The ideal candidate should have a strong background in bioinformatics, including programming skills (or the willingness and drive to acquire them), and a good understanding of molecular biology (preferably with some experience/background in molecular evolution). A Diploma or MSc degree in Biology or Bioinformatics, practical experience in the Unix environment, and fluency in English are required.

The project will be supervised by Prof. E. Zdobnov in the Department of Genetic Medicine and Development at the University of Geneva Medical School. We are also part of the renowned Swiss Institute of Bioinformatics, and offer a stimulating research environment with excellent facilities.

The international city of Geneva, described as 'the smallest of the large capitals', offers a vibrant city life within easy reach of the picturesque lake and stunning Alps.
 
Closing date for applications: 15 November 2009.
To apply: send your CV, statement of research interest, and names and contact details of at least two referees by e-mail to Evgeny.Zdobnov [at] isb-sib.ch

Further Information:
Computational Evolutionary Genomics Group, CEGG: http://cegg.unige.ch
Swiss Institute of Bioinformatics, SIB: www.isb-sib.ch
 
Online version of this advertisement: http://cegg.unige.ch/jobs/phd_2
Address: CEGG, CMU / 9022, Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland

posted 2009.10.19

Application instructions:

Candidates should email a SINGLE PDF or MS Word file containing a cover letter summarizing research interests, CV with information on academic/work experience, awards, publications, and names and contact information for 3 references. Applications will be reviewed as they are received.

 

Related Web Site: http://biosci.umn.edu/plantbio/faculty/LibourelIgor/index.shtml

Job Contact: libourel(at)umn.edu

Job Type: Postdoctoral

 

Project description:

A postdoctoral position is available in the laboratory of Igor Libourel in the Department of Plant Biology at the University of Minnesota Twin Cities campus to reconstruct the metabolic networks of Ostreococcus species. Ostreococcus are common marine microalgae and are considered the most primitive members of the green lineage. Their small genome sizes (~12Mbp) give them excellent properties as plant systems biology model organisms. This project is an integral part of our long-range goal to develop mechanistic models that link individual metabolic components to the functional behavior of metabolic networks.

 

The position entails the genome-scale metabolic networks reconstruction of the two annotated Ostreococcus species O. tauri and O. lucimarinus. The postdoc will use existing software utilities to produce initial networks from the KEGG database. He/She will develop algorithms to iteratively refine these networks by gap analysis and dynamic orthology calls to the BLAST and KEGG databases. Because of the interdisciplinary character of systems biology, our group is dedicated to implement the common systems biology markup language (SBML) and the postdoc is expected to work extensively with the Matlab SBML toolbox. The postdoc should be receptive to advising students, and work closely with internal and external collaborators.  

 

Candidates should have a strong background in computational biology, systems biology, or related discipline. Candidates should have a solid background in mathematics, and have experience in software development.

 

posted 2009.10.16

A Postdoctoral Research Associate position in systems biology is immediately available as part of a collaborative project between St John's Institute of Dermatology (Professor Frank Nestle) and Centre for Bioinformatics at Kings College London.

The aim is to develop experimental data-driven mathematical (biophysically-detailed) models of the intra- and intercellular circuits for immune system responses. The models are expected to improve our mechanistic understanding of the immune system performance under normal and pathological conditions. The successful candidate will be highly motivated and have experience in either mathematical modelling, biophysics, bioinformatics or inflammation, a relevant Ph.D. and good communication skills.

This project is a part of ongoing collaboration between biomedical and systems modelling groups offers an exciting opportunity to apply modern developments in systems biology to current needs in translational medicine.

Applications are sought from highly ambitious individuals looking to work in interdisciplinary environment with education or experience in systems biology, bioinformatics, biophysics, control engineering or systems immunology. Applications from PhD candidates in the last year will be considered.

The post is available immediately for up to two years in the first instance.

The University offers an excellent remuneration package that will reflect the applicant's background and experience.

To apply email CV and covering letter to
Dr Najl Valeyev najl.valeyev [at] kcl.ac.uk

posted 2009.10.07

We are a trio of labs in Cambridge (UK), Trento (Italy) and Tokyo (Japan) about to undertake a collaborative and interdisciplinary project funded by the HFSP (http://www.cosbi.eu/index.php/research/projects/hfsp) to study systemic aspects of cell polarity regulation, using fission yeast as experimental model.
 
We will use a combination of state-of-the-art genetics, high-content and quantitative microscopy and computational modelling, to reconstruct how polarity regulators act in concert at the cell cortex to initiate, maintain or inactivate polarized cell growth.
 
We are seeking biologists with training in physics or computer science, and physicists/mathematicians/computer scientists interested in working on quantitative biology, to start immediately.
 
Candidates should be highly motivated, with a record of excellence, and experienced or able to work in an interdisciplinary environment. A strong background in at least one of the following areas is required: quantitative live microscopy, image processing and programming, yeast cell biology/genetics, computational modeling of biological systems.
 
If interested, please send your CV, a brief three-line description of motivation, and contact information for two references to:
 
rafael.carazosalas @ bc.biol.ethz.ch and csikasz @ cosbi.eu

posted 2009.10.01

Theoretical Modeling of the Dynamics of the Pacing Systems of Heart and Respiration of Infants in Neonatal Intensive Care Units

The pacing system of the heart is complex; a healthy heart is constantly integrating and responding to external and internal signals. However, in some pathological or age-related states, one finds that the dynamics can show reduced complexity. Such events provide an early, noninvasive warning of illness, and may also provide an opportunity to understand elements of the pacing system of the human heart.

Several years ago, Dr. Randall Moorman and his colleagues began collecting data on heart rates of infants in the neonatal intensive care unit at the University of Virginia. These infants are vulnerable to a variety of bacterial, viral or fungal infections (collectively called sepsis). The diagnosis of neonatal sepsis is difficult and time-consuming, so it would be good to have a continuous noninvasive monitor.

Moorman and colleagues showed that reduced variability of the heart rate is one warning sign of possible sepsis, and more recently we developed a pattern-recognition method proving that transient slowing of the heart rate is a second warning sign. In rare cases, these transient decelerations of the heart rate occur in a regular rhythm, with a period of about 15 seconds.

We have recently shown that the transition from low variability to periodic decelerations can be modeled by a Hopf bifurcation. We are seeking physiologically based models. It is known that models of the blood-pressure to heart-rate feedback loop can display a Hopf bifurcation; we need to test whether any such model fits the observations.

Also, the heart rate is controlled locally by a collection of cells called the sino-atrial node (SAN), which constitute the natural pacemaker of the heart. The SAN is governed internally by two coupled clocks, a transmembrane oscillator, and an internal calcium oscillator. A dynamical analysis of this pair of clocks is needed.

A new project deals with neonatal apnea, or apnea of prematurity. This is the most common serious disorder of premature infants in the neonatal intensive care unit (NICU). We have begun the collection of a huge database including EKG, respiration, oxygen saturation and in some cases blood pressure. We seek signals that will give early warning of apnea, and signals that indicate that the infant is safe.

This project is purely theoretical; it involves creation of pattern recognition software, statistical analysis of data streams, and dynamical analysis of mathematical models of the heart rate and respiration.

For related information see http://web.wm.edu/physics/DelosWeb/index.php
Send applications to jbdelo@wm.edu
John B Delos
Physics Department
College of William and Mary
Williamsburg, VA, 23187-8795
The College of William and Mary is a state supported university and an EEO/AA employer.

posted 2009.09.24

We are seeking a Senior Researcher with four or more years postdoctoral experience in biochemistry/pharmacology/physiology/cell biology or related disciplines. The successful candidate will have an excellent track record of publications in top quality international journals and demonstrable leadership skills. In addition to lab based studies, the candidate will be expected to take a lead role in the mentorship and support of postgraduate students.

The post will involve close collaboration with Prof. Cormac Taylor in a study aimed at using a systems biology approach to understanding how hypoxia impacts upon key decision making processes in stem cells. An in depth understanding of the biology of hypoxia and/or stem cell differentiation will be an advantage. The project is a component of Systems Biology Ireland, a multidisciplinary initiative which presents a unique opportunity for creative individuals who want to work at the cutting-edge of systems biology.

Benefits and salary commensurate with experience. Individuals with an interest in the utilisation of Systems Biology to understand basic physiologic processes are encouraged to apply.

Informal enquiries are welcome, please send them including CV to systemsbiology@ucd.ie

For formal applications use: http://www.ucd.ie/hr/jobvacancies/
Closing Date: 23.30 on Friday, 30 October 2009

NOTE:
Applications must be submitted by the closing date and time specified. UCD are unable to accept late applications Please note at this time UCD do not require assistance from Recruitment Agencies - Any CV's submitted by Recruitment Agencies will be returned. All current recruitment which is taking place within UCD is dependent on non-Exchequer, external and self-funding sources of finance.

posted 2009.09.24

A Bioinformatics Systems Programmer position is available in the Global Health Biotechnology Center's Bioinformatics Core facility at Seattle Biomedical Research Institute (SBRI).

Responsibilities
We are building a core service for the Institute and are looking for a bioinformatician to serve as the expert statistician within the team. The primary responsibility of this position is to provide a framework for the statistical analysis of genomics data from a variety of projects within the institute and as part of world-wide collaborations. On-going projects cover a broad spectrum of topics, from the analysis of whole genomes to target selection for structural genomics.

Requirements
Experience in the statistical analysis of large genomic datasets is essential. Familiarity with systems biology data and tool integration platforms is highly desirable. An interest in data management systems, data mining and/or semantic web would be of advantage.

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

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

Nearly 250 scientists and staff members strive to combat global infectious disease each day at SBRI.  By combining science and imagination, it is our goal to conquer the diseases (such as malaria, HIV) that are responsible for the majority of deaths worldwide.  SBRI (http://www.sbri.org<http://www.sbri.org/>) is an independent, non-profit research institute that is affiliated with the University of Washington.  SBRI occupies a new research facility that is in a fast developing Biotechnology hub in the South Lake Union area of Seattle that is home to many research organizations on the forefront of life sciences research.

If you are looking for an opportunity to make a difference, SBRI is the place for you.  In addition to an exciting work environment, we also offer a competitive benefits package that includes medical, dental, and vision coverage, as well as life insurance, disability insurance, retirement, vacation and sick pay.

Apply online directly to the SBRI Job Postings webpage by clicking or typing this link

http://www2.ultirecruit.com/sea1003/jobboard/NewCandidateExt.aspx?__JobID=285

SBRI is an Equal Opportunity Employer

posted 2009.09.16

Systems Biology Ireland, UCD, Dublin.

We seek outstanding candidates on junior and senior levels to work on computational modeling of signaling and gene networks in mammalian cells at Systems Biology Ireland, University College Dublin. Ongoing projects include the temporal and spatial dynamics of receptor tyrosine kinase signaling and transcriptional networks that govern cell proliferation, differentiation and motility (supported by a multi-PI grant to Profs. Boris Kholodenko, Walter Kolch and Zoltan Neufeld). The successful applicant will work closely with experimentalists at the interface between mathematics, engineering and biology in a multi disciplinary research community at Systems Biology Ireland. This presents a unique opportunity for creative individuals who want to work at the cutting-edge of systems biology.

You will be a part of an interdisciplinary team with national and international collaborations in the field of systems biology. The following skills and qualifications are required: 1) PhD in Biophysics, Chemical Engineering, Mathematics, or Biochemistry and evidence of practical work experience in the systems biology of signal transduction; 2) knowledge and experience of advanced mathematical modelling, including non-linear systems and non-linear dynamics, and 3) basic knowledge of cell/molecular biology. Understanding of probability theory and statistics is a plus. The complexity of the relevant problems requires at least a two years initial commitment.

Benefits and salary commensurate with experience. Individuals with an interest in Systems Biology are encouraged to apply.

Salary Scale: €40,000 - €50,000; for experienced researcher up to €76,000.

>Informal enquiries are welcome, please send them including CV to systemsbiology@ucd.ie For formal applications use http://www.ucd.ie/hr/jobvacancies/

Closing date: 23.30hrs on Wednesday, 23^rd October 2009

NOTE: Applications must be submitted by the closing date and time specified. UCD are unable to accept late applications

Please note at this time UCD do not require assistance from Recruitment Agencies - Any CV's submitted by Recruitment Agencies will be returned.

All current recruitment which is taking place within UCD is dependent on non-Exchequer, external and self-funding sources of finance.

UCD is an equal opportunities employer

posted 2009.09.15

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

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

Successful candidate shall have:
For software-centered positions

• Strong background in software development and biological model construction, 

For biology-centered positions

• Strong biological knowledge and experiences modeling of budding yeast as well as mammalian cells particularly on, but not limited to, signaling, cell cycle, and stem cell induction and differentiation pathways.
  
• Experiences in software development will be a plus. 

Communication skills, and capability to work relatively independently but collaboratively with other members of the project as well as in the context global collaboration is essential.
The official language of OIST is English.
 
Interested candidate shall contact Hiroaki Kitano (kitano # sbi.jp). Hiroaki Kitano is also present at ICSB-2009 so that quick interview can be set.

posted 2009.09.03

UNIVERSITY OF ARIZONA

The Department of Molecular and Cellular Biology (www.mcb.arizona.edu) as part of a new initiative in Systems Biology is seeking to hire 2 tenure-track Assistant Professors with expertise in Bioinformatics or Systems Biology for appointment in 2010. Successful candidates can become members of the interdisciplinary Bio5 institute (www.mcb.arizona.edu) and/or the Arizona Cancer Center and may apply for a joint appointment in Mathematics, Computer Sciences, Electrical and Computer Engineering, Physics, or other relevant departments. The appointed individuals will be expected to establish independent and collaborative research programs and contribute to undergraduate, graduate and/or medical education. Opportunities for interaction and collaboration are particularly strong in the areas of functional genomics, genetics, DNA repair, and cancer research.

To apply, submit an on-line faculty application for job number 43211 at www.uacareertrack.com. Applicants should be prepared to attach a curriculum vitae and a 1-2 page statement of research and teaching interests at the time of application. Separately, have at least three supporting letters sent via email to dslay@email.arizona.edu. To ensure consideration, complete applications should be received by September 15, 2009, although applications will be accepted until the positions are filled. The University of Arizona is an EEO/AA Employer/M/W/D/V and is seeking individuals who are able to work with diverse students and colleagues and who have experience with a variety of teaching methods and curricular perspectives.

posted 2009.09.03

UNIVERSITY OF OXFORD OXFORD CENTRE FOR INTEGRATIVE SYSTEMS BIOLOGY & DEPARTMENTS OF BIOCHEMISTRY, PHYSICS AND WEATHERALL INSTITUTE FOR MOLECULAR MEDICINE

Post-Doctoral Researcher - Modelling the origins & implications of global gene expression variation between cells

We are seeking to appoint a Post-Doctoral Researcher to investigate extrinsic noise in gene expression in mammalian cells and examine couplings to the cell cycle. The project aims to investigate the origins of the pronounced, global, variability observed between different cells in clonal populations and how variability might impact on other processes in both cell and organism. The PDRA will work with experimental data from the lab of Dr Francisco Iborra (Weatherall Institute of Molecular Medicine) and will develop theoretical treatments with Prof Bela Novak (Biochemistry) and Dr Nick Jones (Physics). The researcher will have a desk in the Jones lab but will have a principal base in the group of Prof Novak. This topic is approached by researchers in many fields so applications from across the disciplines will be considered. The appointment is of 2 years duration and would, desirably, start soon after a candidate is selected (though some flexibility is possible). Informal enquiries to sysbio-enquiries@bioch.ox.ac.uk

Applicants should possess a PhD or equivalent (or be about to receive one) and should have the following necessary and desirable experience:-

Essential: A good level of familiarity with master equations, generating functions, SDEs and ODEs; a high level of programming skills; enthusiasm to work with real biological data and to work with researchers from different backgrounds; experience modelling real systems from data, preferably in Biology and a strong, relevant, publication record and an ability to work independently if required
Desirable: Experience dealing with the parameters of large systems of equations; biological modelling especially of gene expression noise and familiarity with methods to simulate stochastic chemical processes.

The post is funded by BBSRC & EPSRC for 2 years (in the first instance) and is graded on the University's grade 7 scale, for which the salary range is £28,839 - £35,469 per annum. The actual starting salary offered will be based on qualifications and relevant skills acquired and will also be determined by the funding available.

For further general information, an application cover sheet and other application requirements please visit the Departmental website http://www.bioch.ox.ac.uk/jobs/instructions.html or phone (01865) 613204, quoting the reference number below

Applications, including 3 copies of the completed application cover sheet and recruitment monitoring form, three copies of a detailed CV, the names and addresses of two referees, (one of whom must be the current or most recent employer), and three copies of a letter setting out, with examples, how you meet the selection criteria for the post, should be sent to:
The Deputy Administrator
Department of Biochemistry
University of Oxford
South Parks Road
Oxford OX1 3QU

Please quote reference number: BR/399.

The closing date for applications is Friday, 25th September 2009

posted 2009.08.29

Three largest Latvian universities (Latvia University of Agriculture, University of Latvia and Riga Technical University) are forming an interdisciplinary team of 20-30 members to act in the field of Systems Biology.

Main scientific interest of the group is to combine metabolic engineering of microorganisms with modelling technologies to optimise biochemical processes for biotechnological purposes (biofuel production, optimisation of biotechnological features of organisms). Organisms we deal with are Saccharomyces cerevisiae and Zymomonas mobilis.

We succeeded to receive financing of European Social Fund within activity 1.1.1.2. „Attraction of Human Resources to Science" to establish an interdisciplinary systems biology group in Latvia. Currently we are looking for a scientist (PhD or Dr.sc.) to join our group in Latvia for time period from January 2010 till September 2012 (33 months).

The candidate has to satisfy following conditions:

• mathematical modelling of biochemical pathways and bioprocesses
• join the group in one of our locations in Latvia (cities Riga or Jelgava)
• good command of English language
• EU citizenship is mandatory

For further information please visit websites of groups that form the project
http://www2.llu.lv/homepg/biosystems/
http://www.lu.lv/instituti/mbi/bioenergetic.html
http://plantgenetics.lu.lv/
http://www.rtu.lv/index.php?option=com_content&task=view&id=886&Itemid=1113 http://www.latbiotech.lv/en/index.html
http://www.bioreactors.net/

Our offer is job in an interdisciplinary team of systems biology. Salary: circa €27,000 brutto (€19,000 netto) per annum. To apply, please email a cover letter, CV (in English) and contact information of three professional references quoting ref. "SB researcher" in the subject line, to: egils.stalidzans@llu.lv by the deadline 1-st November 2009.

posted 2009.08.28

Postdoctoral position: Mathematical modeling of human metabolism, University of Iceland

The Center of Systems Biology, University of Iceland (www.systemsbiology.is, CSB UoI) is looking to recruit a highly motivated postdoctoral fellow to join a growing effort focusing on systems biology of human metabolism. The research at the CSB UoI focuses on 1) human metabolism and 2) industrial biotechnology. The Center is an interdisciplinary center with the Schools of Medicine, Engineering and Natural Sciences participating.

The CSB UoI has been awarded an ERC grant to characterize human disease using a systems biology approach. The research effort focuses on 1) expanding the currently available human metabolic reconstruction, 2) discovery of new functions and pathways in human metabolism using computational and experimental techniques, 3) phenotyping of human cell lines using metabolomic techniques, 4) computational and experimental analysis of metabolic changes associated with disease, and 5) high-throughput drug screening. We use the state-of-the-art computational methods to guide and design human cell culturing experiments as well as metabolomic measurements. These technologies are embedded in a biologically driven research program that aims at systematic understanding of human metabolism, disease manifestation and drug target identification.

The successful candidate will be expected to work on expanding the human metabolic reconstruction and lead the computational gap filling effort. The postholder will also mine databases and genomic information, participate in protein annotation of this human metabolism project and will be expected to provide curation and quality control for the protein functional annotation framework. In addition, the postholder will be part of a team to develop quantitative tools required to expand mass spectrometry capabilities and integrative bioinformatics at the CSB UoI.

The ideal candidate will hold a PhD in Bioinformatics or related field and have a strong background in biology as well as computational modelling. All projects at the CSB UoI are interdisciplinary; therefore, a strong motivation to collaborate with experimental groups is required. Programming skills and knowledge of computational methods used in systems biology are required. Knowledge of human metabolism and drug metabolism will be advantage. Individuals with backgrounds in metabolic network reconstruction or metabolic engineering are especially encouraged to apply. Furthermore, the candidate must be fluent in English.

Additionally, the candidate must have excellent communication and interpersonal skills and be capable of working within a team of biologists and programmers.

All applications and inquires should be directed to Professor Ines Thiele (systemsbiology@hi.is) by the deadline of September 15th, 2009. All applications will be answered and applicants will be informed about the appointment when a decision has been made. Salary for the positions will be according to collective wage and salary agreement.

Appointments to the University of Iceland do take into account the Equal Rights Project of the University of Iceland.

Postdoctoral Position: Development of computational methods for human systems biology, University of Iceland

The Center of Systems Biology, University of Iceland (www.systemsbiology.is, CSB UoI) is looking to recruit a highly motivated postdoctoral fellow to join a growing effort focusing on systems biology of human metabolism. The research at the CSB UoI focuses on 1) human metabolism and 2) industrial biotechnology. The Center is an interdisciplinary center with the Schools of Medicine, Engineering and Natural Sciences participating.

The CSB UoI has been awarded an ERC grant to characterize human disease using a systems biology approach. The research effort focuses on 1) expanding the currently available human metabolic reconstruction, 2) discovery of new functions and pathways in human metabolism using computational and experimental techniques, 3) phenotyping of human cell lines using metabolomic techniques, 4) computational and experimental analysis of metabolic changes associated with disease, and 5) high-throughput drug screening. We use the state-of-the-art computational methods to guide and design human cell culturing experiments as well as metabolomic measurements. These technologies are embedded in a biologically driven research program that aims at systematic understanding of human metabolism, disease manifestation and drug target identification.

The successful candidate will be expected to process and employ high-throughput data (transcriptomic and metabolomic data) to generate cell- and tissue specific models, which will allow simulation of normal and disease states. The postholder will develop and improve computational methods based on operation research approaches. The project includes the interrogation of metabolic networks and translation of quantitative HT data as model constraints. Furthermore, the postholder will be involved in other projects in the group and at the CSB UoI requiring development of computational methods.

The ideal candidate will hold a PhD in Bioinformatics or related field and have a strong background in computational modelling, operation research, statistical analysis, high-throughput data analysis and biology. All projects at the CSB UoI are interdisciplinary; therefore, a strong motivation to collaborate with experimental groups is required. Excellent programming skills are required. Knowledge of human metabolism and drug metabolism is of benefit. Furthermore, the candidate must be fluent in English.

Additionally, the candidate must have excellent communication and interpersonal skills and be capable of working within a team of biologists and programmers. All applications and inquires should be directed to Professor Ines Thiele (systemsbiology@hi.is) by the deadline of September 15th, 2009.

All applications will be answered and applicants will be informed about the appointment when a decision has been made. Salary for the positions will be according to collective wage and salary agreement.

Appointments to the University of Iceland do take into account the Equal Rights Project of the University of Iceland.

posted 2009.08.25

Two Postdoc Fellows in Bioinformatics in BSBL
Two Postdoc Fellows in Bioinformatics in BSBL
Bioinformatics Engineer I
Bioinformatics Engineer II

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

Two Postdoc Fellows in Bioinformatics in BSBL

Department of Biomedical Informatics, Vanderbilt University Medical Center

Two postdoctoral positions are available immediately to join the Bioinformatics and Systems Biology Laboratory (BSBL, http://bioinfo.mc.vanderbilt.edu/) at Vanderbilt University Medical Center. The successful candidates are expected to join a diverse bioinformatics team and work on bioinformatics projects in cancer or other complex diseases using systems biology and other bioinformatics approaches. Analysis of genome-wide and high throughput data is expected. The fund is available for at least three years for each position.

The qualified candidates should be highly motivated in research and have a Ph.D. in bioinformatics, computational biology, molecular biology, or related when the job starts. The successful candidate should have some experience in analyzing high-throughput genomic data and proved skills in one programming language (Perl, Java, or C/C++). Good understanding of molecular biology and familiarity with biostatistics are desirable.
Applicants should send a CV, brief statement of research interests, and reference to: Zhongming Zhao (zhongming.zhao@vanderbilt.edu), Chief Bioinformatics Officer, Vanderbilt-Ingram Cancer Center. Please specify the position "Bioinformatics Postdoc in BSBL" in the application.

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

Two Postdoc Fellows in Bioinformatics in FGSR

Functional Genomics Shared Resource (FGSR), Vanderbilt University Medical Center

Two postdoctoral positions are available immediately to join the Vanderbilt Microarray Shared Resource (VMSR, http://array.mc.vanderbilt.edu/). The VMSR is currently under expansion and in the transition to Functional Genomics Shared Resource (FGSR). The successful candidates are expected to join the Informatics Group which includes bioinformatics engineers and post-doctoral fellows and is under the leadership of Dr. Zhongming Zhao, Chief Bioinformatics Officer in Vanderbilt-Ingram Cancer Center. The candidates will perform advanced analysis of the data generated from the collaborative projects in FGSR. Currently, data generated and analyzed by VMSR has been published in many high profiling journals including Nature series and Science. The positions are supported by the Vanderbilt-Ingram Cancer Center and NIH grants.

The qualified candidates should be highly motivated and have a Ph.D. in bioinformatics, computational biology, molecular biology, or related when the job starts. The successful candidates should have experience in analyzing high-throughput genomic data derived from microarray and some other high throughput technologies (e.g., GWAS, CNVs) and proved skills in at least one programming language (Perl, Java, or C/C++). Good understanding of molecular biology and familiarity with biostatistics are desirable. Applicants should send a CV, brief statement of research interests, and reference to: Zhongming Zhao (zhongming.zhao@vanderbilt.edu), Chief Bioinformatics Officer, Vanderbilt-Ingram Cancer Center. Please specify the position "Bioinformatics Postdoc in FGSR" in the application.

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

Bioinformatics Engineer I

Functional Genomics Shared Resource (FGSR), Vanderbilt University Medical Center

One Bioinformatics Engineer I position is available immediately to join the Vanderbilt Microarray Shared Resource (VMSR, http://array.mc.vanderbilt.edu/). The VMSR is currently under expansion and in the transition to Functional Genomics Shared Resource (FGSR). The successful candidate is expected to join the Informatics Group which includes bioinformatics engineers and post-doctoral fellows and is under the leadership of Dr. Zhongming Zhao, Chief Bioinformatics Officer in Vanderbilt-Ingram Cancer Center. The position is supported by the Vanderbilt-Ingram Cancer Center.

Job Responsibilities:

1. Data process and transfer and computer support for the Vanderbilt Microarray Shared Resource (VMSR).
• 1a. Data process, quality control, data transfer, and basic analysis for microarrays.
• 1b. Provide software and hardware installation and maintenance for the various computers in the VMSR.
2. Database development and software design
• 2a. Develop web-based tools to access data contained in the databases maintained by the VMSR.
• 2b Develop software tools to automate the transfer of data from internal databases.
• 2c. Develop custom software to assist users in data analysis to present information for publication and grant submission.
3. Web development
• 3a. Assist with design and maintenance of web-based resources including web pages.
• 3b. Develop web pages for online submission of sample information and handling.
4. Assist with training and educational support to users of shared resource lab
5. Actively identify and participate in training, education, and development activities to improve own knowledge and performance to sustain and enhance professional development

Requirements

• a. Require some experience in processing high-throughput genomic datasets derived from microarray and some other high throughput technologies as well as familiarity with available third party software packages useful to analyzing these data.
• b. Effective communication skills are required.
• c. Those candidates having experience in basic quality control and analysis in Affymetrix, Agilent, and NimbleGen arrays are strongly encouraged to apply.

Applicants should send a CV and reference to: Zhongming Zhao (zhongming.zhao@vanderbilt.edu), Chief Bioinformatics Officer, Vanderbilt-Ingram Cancer Center. Please specify the position "Bioinformatics Engineer I in FGSR" in the application.

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

Bioinformatics Engineer II

Functional Genomics Shared Resource (FGSR), Vanderbilt University Medical Center

One Bioinformatics Engineer II position is available immediately to join the Vanderbilt Microarray Shared Resource (VMSR, http://array.mc.vanderbilt.edu/). The VMSR is currently under expansion and in the transition to Functional Genomics Shared Resource (FGSR). The successful candidate is expected to join the Informatics Group which includes bioinformatics engineers and post-doctoral fellows and is under the leadership of Dr. Zhongming Zhao, Chief Bioinformatics Officer in Vanderbilt-Ingram Cancer Center. The position is supported by the Vanderbilt-Ingram Cancer Center.

Job Responsibilities:

1.  Data process and transfer and computer support for the Vanderbilt Microarray Shared Resource (VMSR).
• 1a. Data process, quality control, data transfer, basic analysis and some advanced analysis for microarrays.
• 1b. Provide software and hardware installation and maintenance for the various computers in the VMSR.
2. Database development and software design
• 2a. Develop web-based tools to access data contained in the databases maintained by the VMSR.
• 2b Develop software tools to automate the transfer of data from internal databases.
• 2c. Develop custom software to assist users in data analysis to present information for publication and grant submission.
3. Web development
• 3a. Assist with design and maintenance of web-based resources including web pages.
• 3b. Develop web pages for online submission of sample information and handling.
4. Provide training and educational support to users of shared resource lab
• 4a. Develop manuals and detailed documentation for training sessions.
• 4b. Develop and lead monthly training to the resource users on the various informatic and analysis software packages supported by the area.
5.   Serve as a leader to ensure objectives are met
• 5a. Provide bioinformatics leadership for the lab core, staff, and students.
• 5b. Instruct in methods and procedures using effective teaching techniques.
• 5c. Handle employee problems. 5d. Hire, terminate and discipline according to institutional policies.
6.   Actively identify and participate in training, education, and development activities to improve own knowledge and performance to sustain and enhance professional development

Requirements

• a. Experience in processing and analyzing high-throughput genomic datasets derived from microarray and some other high throughput technologies as well as familiarity with available third party software packages useful to analyzing these data.
  
• b. Effective communication skills are required.
  
• c. Those candidates having significant experience in basic quality control and analysis as well as advanced analysis of data generated by Affymetrix, Agilent, and NimbleGen arrays are strongly encouraged to apply.

Applicants should send a CV and reference to: Zhongming Zhao (zhongming.zhao@vanderbilt.edu), Chief Bioinformatics Officer, Vanderbilt-Ingram Cancer Center. Please specify the position "Bioinformatics Engineer II in FGSR" in the application.

posted 2009.08.24

Molecular Systems Biology has a vacancy for an in-house research Editor.

This exciting position involves working together with the existing editorial team on all aspects of the editorial process including critically reading submitted research, organizing peer-review, commissioning and editing reviews, and developing the content and editorial policies of the journal.

Molecular Systems Biology was launched by Nature Publishing Group and EMBO in March 2005, and has rapidly become the premier journal in the fields of systems biology, synthetic biology and systems Medicine.

This is a great opportunity to continue to work in science and to be intensively exposed to high quality research in the rapidly developing disciplines of systems biology

To meet the challenging tasks of this role, the ideal candidate will have a strong research background, a PhD in molecular biology and a deep interest in systems biology. Other essential attributes include a broad knowledge in cell and molecular biology, excellent written and verbal communication skills and a commitment to the communication of scientific ideas. An important aspect of the job is interaction with the scientific community and attending international conferences. Successful candidates must therefore be dynamic and outgoing, be prepared to travel, and have excellent interpersonal skills.

An initial contract of 3 years will be offered to the successful candidate. This can be renewed, depending on circumstances at the time of review.

For further information please visit http://www.embo.org and http://www.nature.com/msb

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.

To apply, please email a cover letter, CV (in English) and contact information of three professional references quoting ref. no. SB/09/066 in the subject line, to: application@embl.de

posted 2009.08.20

We seek outstanding candidates to work on computational modeling of signaling and gene networks in mammalian cells at Systems Biology Ireland, University College Dublin. Ongoing projects include the temporal and spatial dynamics of receptor tyrosine kinase signaling and transcriptional networks that govern cell proliferation, differentiation and motility (supported by a multi-PI grant to Profs. Boris Kholodenko, Walter Kolch and Zoltan Neufeld). The successful applicant will work closely with experimentalists at the interface between mathematics, engineering and biology in a multi disciplinary research community at Systems Biology Ireland. This presents a unique opportunity for creative individuals who want to work at the cutting-edge of systems biology.

You will be a part of an interdisciplinary team with national and international collaborations in the field of systems biology. The following skills and qualifications are required: 1) PhD in Biophysics, Chemical Engineering, Mathematics, or Biochemistry and evidence of practical work experience in the systems biology of signal transduction; 2) knowledge and experience of advanced mathematical modelling, including non-linear systems and non-linear dynamics, and 3) basic knowledge of cell/molecular biology. Understanding of probability theory and statistics is a plus. The complexity of the relevant problems requires at least a two year initial commitment.

Benefits and salary commensurate with experience. Individuals with an interest in Systems Biology are encouraged to apply.

To apply on line: http://www.ucd.ie/hr/jobvacancies/ Informal enquiries are welcome, please send them to systemsbiology@ucd.ie.

Salary: circa €45,000 per annum NOTE: Applications must be submitted by the closing date and time specified. UCD are unable to accept late applications / agency applications. Such applications will be returned.

Closing date: 23.30hrs on Friday 28th August 2009

Please note: All current recruitment which is taking place within UCD is dependent on non-Exchequer, external and self-funding sources of finance.
UCD is an equal opportunities employer

posted 2009.08.19

A position is available for a bioinformatics specialist to support the development of a database that integrates a variety of clinical and molecular information for a rare form of cancer called Adenoid Cystic Carcinoma (ACC). We would like to make this resource available online so that the larger ACC research community can take advantage of existing resources. This project is supported by a grant from the ACC Research Foundation (see http://www.accrf.org/) as part of a collaboration with Dr. Chris Moskaluk in the Department of Pathology.
In addition to strong undergraduate training in biology/medicine and engineering/computation, applicants for the position should have web development and web security skills, as well as experience with designing relational databases, SQL, and PHP or Perl.

The position has funding for one year, with a possibility for longer-term support. To apply, please send a CV to Dr. Jason Papin (papin@virginia.edu).

posted 2009.08.11

RESEARCH ASSOCIATE POSITIONS (2 POSTDOCTORAL FELLOWS AND 1 BIOINFORMATICIAN) AVAILABLE IN TRANSLATIONAL BIOINFORMATICS AND COMPUTATIONAL BIOLOGY AT THE UNIVERSITY OF MARYLAND

Several research positions are available immediately in Dr. Maricel Kann's Laboratory at the University of Maryland UMBC (http://umbc.edu/biosci/general/user/mkann) to develop computational approaches for the detection of protein domains and their interactions and to understand the molecular basis of diseases.

 One postdoctoral position is focused on translational bioinformatics. Candidates will be expected to develop computational methodologies for the classification and clustering of molecular data related to human diseases. The ideal candidate is a highly motivated individual with a Ph.D. in computer science, mathematics, bioinformatics, or related fields. The position involves interaction with clinicians and experimental biologists in the field of cancer and pharmacogenomics. Background on structural biology and familiarity with clinical data are strong assets for this position. Non-US citizen applicants are encouraged to apply. The position is available immediately. Selection of candidates and interviews will be performed starting on August 15th and will continue until the position is filled. To apply, send an email to mkann@umbc.edu with CV, 3 publication or programming samples, a brief research interest statement, and the name of 3 references. Please use "postdoc_tbio position" in the subject.

 The second postdoctoral position on computational biology requires expertise in the analysis of protein networks. Candidates will be expected to develop computational techniques for the prediction of protein interactions and analysis of protein interaction networks. The ideal candidate is a highly motivated individual with a Ph.D. in computer science, mathematics, bioinformatics, or related fields. The candidate will work in close collaboration with biophysicists and experimental biologists from several institutions. Non-US citizen applicants are encouraged to apply. The position is available immediately. Selection of candidates and interviews will be performed starting on August 15th and will continue until the position is filled. To apply, send an email to mkann@umbc.edu with CV, 3 publication or programming samples, a brief research interest statement, and the name of 3 references. Please use "postdoc_cbio position" in the subject.

 
Bioinformatician. This position requires a BS or MS in Bioinformatics or related field with experience in bioinformatics projects. The ideal candidate should have strong scientific programming skills and experience in data mining of biological and clinical data. The candidate will work in close collaboration with a team of researchers from several institutions. Non-US citizen applicants are encouraged to apply. The position is available immediately. Selection of candidates and interviews will be performed starting on August 15th and will continue until the position is filled. To apply, send an email to mkann@umbc.edu with CV, publication or programming samples, and the name of 3 references. Please use "biotech position" in the subject.
 

posted 2009.07.27

posted 2009.07.18

The German Cancer Research Center Heidelberg (DKFZ) and the Medical Faculty of the University of Heidelberg invite applications from scientists for a group leader position to establish an independent

Junior Research Group on Translational Systems Biology

The successful candidate should have an outstanding scientific track record in experimental systems biology in the context of a highly relevant medical topic. In particular, the applicant should have successfully worked on projects bridging modern molecular cell biology with theoretical modeling in the context of a medically relevant application. The group is structurally integrated into the Helmholtz Alliance on Systems Biology, in particular into the network SBCancer on systems biology of signal transduction in cancer (http://www.dkfz.de/en/sbcancer/) led by DKFZ. The junior group will be localized in the BioQuant Systems Biology Center at the University of Heidelberg. The establishment of this new research group should enforce the link between fundamental systems biology research at DKFZ and clinically relevant topics of tumor formation, progression and therapy. The future research program of the group is expected to be closely linked to the European Pancreas Center of the Medical Faculty of Heidelberg.

Besides the group leader position (Ref-No. 69/2009), the junior research group will be endowed with 1 position for a post-doc, 1 position for a PhD student and 1 position for a technical assistant. Funds are available for up to five years with an external review held after three years. The DKFZ has a policy of raising the proportion of women in academic positions and therefore specifically invites the application of women with the necessary qualifications. Under German law disabled applicants with full qualifications are to be preferred.

Please send your application including CV, publication record, planned research program (max. 5 pages A4) and two letters of recommendation by July 31st, 2009.

Please address informal inquiries to the scientific coordinator of the Helmholtz Alliance on Systems Biology, Prof. Dr. Roland Eils (r.eils@dkfz.de), or to the project management of the alliance (Dr. Jan Eufinger, j.eufinger@dkfz.de , Phone +49 6221 42-3623).

The German Cancer Research Center is committed to increase the percentage of female scientists and encourages female applicants to apply. Among candidates of equal aptitude and qualifications, a person with disabilities will be given preference.

Please send your significant application to

Deutsches Krebsforschungszentrum
Personalabteilung
Im Neuenheimer Feld 280
D-69120 Heidelberg
Or apply preferably online: http://www.dkfz.de

posted 2009.07.18

A postdoctoral position is available in the Systems Biology Research Group at the University of Rostock, Germany (Olaf Wolkenhauer, www.sbi.uni-rostock.de).

Photorespiration represents one of the major elements in plant primary metabolism, constituting the second-most important process in the land-based biosphere. In light of the importance of this process a DFG funded research network PROMICS is to take a systems biology approach to understand the dynamics of photorespiration.  The DFG research unit involves three groups from the University of Rostock (H.Bauwe, M.Hagemann) and six other leading experimentalists from Institutes across Germany.

Applicants should have a strong background in mathematical and computational modeling and motivation to carry out an interdisciplinary project with experimental groups. Individuals with backgrounds in metabolic network reconstruction or metabolic engineering are especially encouraged to apply. Excellent communication skills are required for the candidate to lead the modeling activity within PROMICS.

The project is funded for an initial period of three years, with a possible extension for three more years. The salary is according to the German University payment scheme (E14) for an experienced postdoc (equivalent to a research group leader).

The Wolkenhauer Group (www.sbi.uni-rostock.de) provides a vibrant research environment, with a number of active research projects in the areas of bioinformatics and systems biology. The group moved in July 2009 into a new building and provides excellent facilities. The University of Rostock (founded in 1419) is one of the oldest in Europe and the north-east of Germany is one of the most attractive tourist regions of Germany.

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

olaf.wolkenhauer@uni-rostock.de

posted 2009.07.15

Postdoctoral positions are available immediately in the  area of Systems Biology of Human Diseases at Rice University (Houston, Texas) for motivated researchers. Candidates are sought to join a collaborative effort between Rice University, Baylor College of Medicine and MD Anderson, Texas in studying the metabolism of cancer and stem cells. The focus of the research will be (1) to elucidate the metabolism of cancer in knockout and overexpressed cell lines and (2) to understand the changes in metabolite profile of embryonic stem cells and induced pluripotent stem cells during differentiation into various lineages. Early career scientists with a background in molecular and cell biology, who are seeking an interdisciplinary adventure are encouraged to apply. Strong background in stem cells is desirable. Interested candidates should electronically apply by sending their CV to clinicalsysbio@gmail.com

posted 2009.07.07

Applications are invited for PhD fellowships within the Synthetic Biology Lab at the Department of Electrical Engineering of the University of Texas in Dallas.

The successful candidates will model, design, experimentally implement and characterize synthetic mammalian gene networks. Applicants should have a strong background in mathematical and computational modeling and motivation to carry out experimental research. Experience in standard molecular and mammalian cell biology techniques is an advantage.
Candidates will be expected to engage in interdisciplinary research and to foster in-house
collaborations with current nanotechnology and biomedical engineering expertise of NSERL. For further information about NSERL, please visit the web site: http://ecs.utdallas.edu/nserl-slideshow.html.

Please send your application including CV and academic transcript to: leonidas.bleris@gmail.com

posted 2009.07.06

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:

• Masters or 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

Immunetrics, Inc.
2403 Sidney Street  Suite 271
Pittsburgh, PA 15203

posted 2009.06.18

A postdoctoral position is available for a highly motivated and creative individual with a strong quantitative background. The main project will be associated to the development, integration and implementation of novel techniques to analyze electronic health records and biomedical literature, working in an interdisciplinary environment. The project is a collaboration between Carol Friedman, Geroge Hripcsak and Raul Rabadan at Columbia University, New York.

Applicants must have a PhD degree in any quantitative science  (preferably physics, astrophysics, computer science, computational biology, statistics or mathematics). Medical/biological knowledge is not expected but highly valued. The candidate should have a working knowledge of programming with demonstrated experience in problem solving. Excellent organizational and communication skills are a must.

Interested applicants should submit a letter of interest, CV, and name and contact information of three references by e-mail (preferred) to *rabadan@dbmi.columbia.edu
*  or by mail to Raul Rabadan, PhD, Assistant Professor, Department of  
Biomedical Informatics, Columbia University, 622 West 168th Street,  
VC-5, New York, NY 10032, USA. Deadline: 15th June 2009.

Columbia University is an affirmative action/equal opportunity employer and encourages applications from women and underrepresented minorities.

Raul Rabadan, PhD

Assistant Professor
Department of Biomedical Informatics
Center for Computational Biology and Bioinformatics

Columbia University College of Physicians and Surgeons
1130 St. Nicholas Ave
ICRC Bldg 8th Floor, Office 803B
New York, NY 10032

posted 2009.06.03

A position is available for an individual with an interest in computational systems biology and/or metabolic engineering. A major focus of the project will be to refine the genome-scale metabolic network reconstruction of Chlamydomonas reinhardtii, an alga of interest for its ability to produce hydrogen and other biofuel targets. There is also substantial interest in applying the metabolic network to pursue novel metabolic engineering hypotheses. This work is being done in collaboration with Dr. Kourosh Salehi-Ashtiani and other experimental researchers at the Center for Cancer Systems Biology at the Dana Farber Cancer Institute, Harvard Medical School.

Excellent communication skills and a Ph.D. in bioengineering, bioinformatics, biochemistry, molecular biology, or a suitable quantitative field with strong experience working on biological applications are required. Individuals with backgrounds in metabolic network reconstruction or metabolic engineering are especially encouraged to apply. The position will remain open until filled. The Computational Systems Biology Laboratory maintains a vibrant research environment, with active research in reconstruction of metabolic, regulatory and signaling networks which are applied toward probing network structure, host-pathogen interaction, and engineering of novel therapeutic targets.

To apply, please send a CV, brief statement of research accomplishments and career goals, and contact information for three references to Dr. Jason Papin (papin@virginia.edu).

posted 2009.05.21

POSTDOCTORAL POSITION:
A postdoctoral position in quantitative biology is available immediately.  The successful candidate will develop predictive rule-based models for signal-transduction systems in collaboration with theoretical and experimental researchers in the Center for Spatiotemporal Modeling of Cell Signaling, which is comprised of research groups at Los Alamos National Laboratory, the University of New Mexico Cancer Center, and other institutions. 
The position is a two-year appointment with the possibility of an extension to a third year.  Salary starts at $69,800. 

To apply, send CV and names of three references to Dr. William S. Hlavacek via email (wish@lanl.gov).

posted 2009.05.14

Postdoctoral applications are sought to work with Professor Jeffrey Skolnick in the Center for the Study of Systems Biology at the Georgia Institute of Technology. Specific areas include the Molecular and Cell Biology of Cancer with an emphasis on Cancer Metabolomics, large-scale biological simulations and the automated assignment of proteins to biological pathways using novel algorithms and the integration and systematization of high-throughput data into regulatory, signalling, metabolic and interaction networks.

Highly creative individuals are sought with the following qualifications:

• Very strong background in Cell Biology, Cancer Biology, Molecular Biology or Biochemistry.
• Interest in large-scale analysis and integration of biodata to understand specific biological processes.
• Extensive experience in developing computer code in languages such as C++, Perl or Phyton.
• Previous experience doing international quality research in Biomedical Informatics, Bioinformatics or Computational Genomics applied to concrete biological problems, as evidenced by a track record of publication in high quality international journals.

To apply please email your CV to: skolnick@gatech.edu

posted 2009.05.05

Postdoctoral applications are sought in Bioinformatics to work with Professor Jeffrey Skolnick. Available projects include the development and application of novel algorithms to predict protein structure and function on a genomic scale. Specific areas include:

• Structure prediction of GPCRs followed by virtual ligand screening
• Prediction of protein-protein and protein-DNA interactions
• Proteome scale virtual ligand screening
• Development of algorithms to minimize drug side effects
• Development of multiscale modeling approaches for the simulation of virtual cells

• Extensive experience in developing computer code in languages such as Fortran, C, C++, Perl.
• Previous experience doing international quality research in structural modeling, virtual ligand screening, bioinformatics, or computational genomics would be major advantages
• A track record of publication in high quality international journals.
• Ability to work in a team, yet think independently.

To apply please send your CV to skolnick@gatech.edu.

posted 2009.05.05

We are looking for a highly motivated, innovative and independent individuals to work at the
exciting interface of bioinformatics and genomics. You will report to Prof. E. Zdobnov, heading
the Computational Evolutionary Genomics group. We are also part of the renowned Swiss
Institute of Bioinformatics, and offer a stimulating research environment with excellent facilities.
The international city of Geneva, described as 'the smallest of the large capitals', offers a
vibrant city life within easy reach of the picturesque lake and stunning Alps.

• UNIX administrator / IT manager
Candidates must have extensive UNIX system administration experience with a clear evidence
of successful work in a multidisciplinary research environment. Good knowledge of French and English is essential. A strong background in software engineering and hands-on experience in building and managing large-scale data management pipelines is a plus.
• Postdoc / Research Associate position
(Systems genetics and evolution of animal molecular systems)
Candidates must have a PhD and demonstrate clear evidence of successful work in computational biology, including a thorough understanding of evolutionary concepts, genomics and genetics. Practical programming experience in the Unix environment and fluency in English are required. Experience in a multidisciplinary research environment, familiarity with graph and data analysis algorithms, Bayesian statistics, and MATLAB is a plus.
• Scientific Programmer
(Bioinformatics infrastructure development and data mining)
Candidates must demonstrate clear evidence of successful work, and have at least 3 years experience in a multidisciplinary research environment. Practical programming experience in the Unix environment, SQL databases, and fluency in English are required. Knowledge of Web technologies (Web 2.0, AJAX, CSS, PHP) or statistical data analysis is a plus.
• PhD position
(Exploring Conserved Non-Coding sequences using comparative genomics)
The ideal candidates should have a strong background in bioinformatics, including programming skills, and a good understanding of molecular biology and evolution. A Diploma or MSc degree in Biology or Bioinformatics, practical experience in the Unix environment, and fluency in English are required.

Closing date for applications: 31 May 2009.
To apply: send your CV, motivation letter, and the names and contact details of at least two
referees by e-mail to Evgeny.Zdobnov@isb-sib.ch

posted 2009.04.22

The Pulmonomics laboratory at Boston University School of Medicine (http://pulmonomics.org) is seeking a creative and motivated postdoctoral fellow to join the laboratory and participate in our active and well-funded research program aimed at gaining insights into the physiological responses to tobacco-smoke exposure and how variability in these responses contributes to tobacco-related diseases such as lung cancer and COPD.  These aims are pursued primarily using genome-wide gene-expression data.  Current areas of interest include using high-throughput sequencing technology to discover tobacco-smoke-exposure- and disease-associated novel small RNAs and transcript variants, using network reconstruction algorithms to discover potential regulatory mechanisms underlying disease-associated gene-expression patterns, understanding how small regulatory RNAs such as microRNAs contribute to this process, and developing sensitive and specific biomarkers able to diagnose disease and/or predict therapeutic outcome.   Candidates should have or be close to obtaining a Ph.D. or equivalent degree in bioinformatics, computational biology, biostatistics, computer science, or a closely related field. Applicants must possess good communication skills and be fluent in both spoken and written English. Critical thinking, problem-solving abilities, and the ability to work semi-independently are required. Prior successful experience working with and developing statistical algorithms for analyzing high dimensional datasets is required. Experience analyzing genome-wide gene-expression data is strongly desired. Experience programming with Perl and the R statistical language, as well as experience with databases such as MySQL is preferred. The postdoctoral position is a temporary appointment, the chief objective being to qualify the selected candidate for work in senior positions in their disciplines. Grants to the laboratory provide funding for the position through September 2012, and the selected candidate will be encouraged to seek independent fellowship funding. The selected candidate will be jointly supervised by Dr. Avrum Spira and Dr. Marc Lenburg, have access to the robust bioinformatics infrastructure at Boston University, and will receive a competitive salary and benefits package.

Interested individuals should send or email a letter of intent/cover letter, a CV with contact info for three references, and a 1-2 page description of relevant previous accomplishments to Ms. Erika Langer; pulmonomics@gmail.com; The Pulmonary Center, Boston University School of Medicine, 715 Albany Street, R-304, Boston, MA 02118.  The closing date for receipt of applications for this position is May 25^th, 2009.

posted 2009.04.04

The Microsoft Research - University of Trento Centre for Computational and Systems Biology (CoSBi) invites applications for:

• 1 Researcher position in the field of Metabolic and gene regulation networks

The ideal candidate has a PhD in biology, chemical/physical sciences, or computer sciences with a strong background in systems biology, has at least 4 years post-doctoral experience in both fields of metabolic and gene regulation, and has a thorough understanding of modeling approaches and tools for quantitative and qualitative evaluation of biological systems. The candidate must have a demonstrated ability to conduct and lead independent research lines, with a non-decreasing curve of publications in the last three years, no decrement of the average impact factor over the last three years, successful coordination of a local group within an international project, successful organization of at least 1 international event and participation in at least 1 international program committee. Invited talks at relevant scientific events and seminars in highly-ranked institutions or presentations at top-quality conferences will also be considered in the evaluation of applications.

Good programming skills, knowledge of methods and approaches for inference of biological networks, and ability to perform analysis of dynamical systems will constitute an asset.

• 1 Junior Researcher position in the field of Tumor formation and cell growth modeling

The ideal candidate has a PhD in biology, chemical/physical/mathematical or computer sciences with a background in systems biology, and has 1-2 years post-doctoral experience in computational/mathematical/ theoretical modeling of biological systems. The candidate must have an impressive publication record, good scientific communication and writing skills, including capability to interact with researchers from various disciplines. The candidate's research work will focus on spatial, temporal and hierarchical modeling of cell cycle and cell growth regulation in the cellular and tissue level to investigate tumor formation. Experience with any of these topics is an asset, as well as good programming skills, knowledge of methods and approaches for inference of biological networks, and ability to perform analysis of dynamical systems.

• 1 Junior Researcher position in the field of Compilation of concurrent languages on parallel architectures

The ideal candidate has a PhD in computer sciences and consolidated experience with parallel algorithms, parallel and multi-core architectures, multi-thread programming and compiler technology. The candidate's research work will focus on the design of optimized execution schemes for systems biology application to exploit the computational power of grid computing and multi-core architectures.

A background in systems biology will constitute an asset.

• 1 Junior Researcher position in the field of Quantitative evaluation of computing and telecommunication systems

The ideal candidate has a PhD in computer sciences and consolidated experience in stochastic modeling for performance and dependability quantitative evaluation. The candidate's research work will focus on the formulation of models of computing systems and telecommunication networks based on conceptual tools developed in the systems biology domain, as well as on their adaptation and extension to handle the specific aspects of the quantitative evaluation of artificial systems.

Good programming skills and a background in systems biology will constitute an asset.

• 1 Junior Researcher position in the field of Stochastic reaction-diffusion models for intra-cellular kinetics

The ideal candidate has a PhD in biology, chemical/physical sciences, or computer sciences with a strong background in systems biology, and has consolidated experience in stochastic modeling of intracellular kinetics. The candidate's research work will focus on the formulation of models of stochastic protein diffusion and diffusion-driven reactions kinetics in intra-cellular medium, as well as in the design of computational tools implementing the numerical procedures for simulating a realistic biochemical reaction-diffusion system.

Good programming skills, knowledge of methods and approaches for inference of biological networks, and ability to perform analysis of dynamical systems will constitute an asset.

• 1 Junior Researcher position in the field of Quantitative model checking and analysis of interactive systems

The ideal candidate has a PhD in computer science and 1-2 years post-doctoral experience in modeling of concurrent systems. The candidate must have an impressive publication record, good scientific communication and writing skills, including capability to interact  with researchers from various disciplines and a strong interest in systems biology. The candidate's research work will focus on the definition, development and implementation of algorithms and techniques to analyze biological properties of complex dynamic and  interactive systems. The candidate must have good programming skills, knowledge of the semantics of process calculi and the ability to perform analysis of dynamical systems. Experience with biological networks is an asset.

• 1 PhD fellowship position in the field of Benchmarking of systems biology modeling tools

The ideal candidate has a Master's degree in computer sciences or computer science engineering, is skilled in discrete/continuous, deterministic/stochastic modeling formalisms for biological systems, programming language theory, concurrency theory and is knowledgeable with tools for computational biology. S/he will work primarily on the comparative evaluation of usability and performance of systems biology tools, identifying areas of improvement and designing them. Background knowledge on discrete-event simulation is highly desirable.

• 1 PhD fellowship position in the field of Compositional modeling of interacting biological networks

The ideal candidate has a Master's degree in computer sciences or computer science engineering, is skilled in programming language theory, concurrency theory and is knowledgeable regarding tools for computational biology. S/he will work primarily on the definition and prototypal implementation of approaches for compositional modeling of complex biological networks consisting of interacting sub-networks. Background knowledge on discrete-event simulation is highly desirable.

1 PhD fellowship position in the field of Hierarchical modeling, analysis and simulation of biological systems

The ideal candidate has a Master's degree in computer sciences or computer science engineering, is skilled in modeling formalisms and is knowledgeable regarding the application of stochastic processes for quantitative evaluation of computing and telecommunication networks. S/he will work primarily on the definition of hierarchical modeling approaches and abstractions for the modeling of multi-scale and multi-level biological systems. Background knowledge on programming language theory, concurrency theory, discrete-event simulation and computational biology is highly desirable.

• 1 PhD fellowship position in the field of Polarized cell growth

The ideal candidate has a Master's degree in biology, computer science, chemistry, mathematics or physics and a deep interest and background knowledge in biology (especially in cell and molecular biology). Basic training in computer science and mathematics is expected. Experience with computational modeling of biological systems is desirable, but not a must. The candidate will work on the spatial and temporal interactions that are responsible for the polarized growth in wild-type and mutant fission yeast cells. Experience in investigating this or related biological topics is an asset. The applicant will work with the CoSBi Lab platform on the biological systems described in Csikasz-Nagy et al. (2008) Yeast, 25(1):59-69 and Csikasz-Nagy (2009) Brief Bioinform, advance online.

• 1 PhD fellowship position in the field of Regulation of p53 induced transcription

The ideal candidate has a Master's degree in biology, computer science, chemistry, mathematics or physics and a deep interest and background knowledge in biology (especially in cell and molecular biology). Basic training in computer science and mathematics is expected. Experience with computational modeling of biological systems is desirable, but not a must. The candidate will work on how p53 can achieve selective binding and differential transactivation of target genes in response to various stress conditions. Experience in investigating this or related biological topics is an asset. The applicant will work with the CoSBi Lab platform on the biological systems described in Tomso, Inga et al. (2005) PNAS 102: 6431-6436 and on the computational side in Csikasz-Nagy (2009) Brief Bioinform, advance online.

• 1 Research Software Developer position

The ideal candidate has a Master's (laurea magistrale) or bachelor's (laurea triennale) degree in computer science plus equivalent work experience (2/3 years). The candidate must have real-world experience in software development, an academic background and/or practical experience in construction of compilers and programming languages, concurrency and complex data structure manipulation. Very good programming and problem-solving skills, as well as willingness to explore and acquire new skills, are a must.

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

posted 2009.03.23

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

The Bioinformatics Laboratory of CRS4 (Center for Advanced Studies, Research and evelopment 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 position will be in either one of two main projects of the group.

Project 1:
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. The suitable candidate has a PhD, expertise in statistical analysis of gene-expression data and programming in R, and experience or strong interest in systems biology and complex network analysis.

Project 2:
The Junior Researcher will be the part of an ongoing project with focus on analysis of Genetical Genomics data (gene expression and genotyping). The Junior Researcher will work on a data simulator aiming to generate Genetical Genomics data using large network models with non-linear ordinary differential equations. This project combines numerical analysis, complex network science and genetics. The suitable candidate has a PhD, expertise in programming with Fortran/C++, Matlab and numerical methods, and experience or strong interest in systems biology and complex network analysis.

---

CRS4, 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

How To Apply:

Interested candidates are encouraged to apply as soon as possible. Send your cover letter, curriculum vitae, list of publications and the names of at least two references to job_bioinfo@crs4.it. Please send all documents in pdf format and use as subject line "Junior Researcher in Computational Systems Biology".

posted 2009.03.17

The Chair of Chemical Biology at the Dortmund University of Technology invites applications for a Postdoctoral position in　Systems Biology. The position is available immediately (initially limited to 2　years with the possibility to extend the contract). Salaries are according to E13 TV-L.

Environment:

The position is available in a Junior Research Group associated with the TU Dortmund and the Department for Systemic Cell Biology at the Max-Planck-Institute for molecular Physiology. The project is funded by the project "Subsystem Interactions in Neuromorphogenesis", which is financed by the FORSYS initiative for supporting systems biology in Germany.

Project:

Our group is studying the mechanisms, by which neurons develop their complex shape. We are particularly interested in the role of the cytoskeleton and how it interacts with other cellular components. Through iterative cycles of experimentation and mathematical modeling, we aim to gain a better understanding about this complex, dynamic biological system.

You will be responsible for spearheading the development of dynamic mathematical models of the neuronal cytoskeleton that will complement the cutting-edge microscopy-based techniques employed by the lab. To develop and extend such models, you will work closely with highly motivated experimentalists and theorists at the TU Dortmund and the associated Max-Planck-Institute.

Requirements:

We are seeking a highly motivated candidate with excellent scientific and interpersonal skills. Applicants must hold a Ph.D. level degree in life sciences, mathematics, physics or computer sciences, should have basic experience in modeling of molecular systems and a strong interest in studying the neuronal cytoskeleton via mathematical models and physical simulations.

Please note that applications from women are particularly welcome. The same applies to qualified disabled people.

Please send your cover letter, CV and 2 references to: TU Dortmund, Faculty of Chemistry, Chair for Chemical Biology, Dr. Leif Dehmelt, Otto-Hahn-Str. 6, D-44221 Dortmund, Germany or directly to leif.dehmelt@mpi-dortmund.mpg.de.

Website: http://www.mpi-dortmund.mpg.de/forschungProjekte/AGs/Dehmelt/index.html

posted 2009.03.06

For two multi-institution projects funded by the Federal Ministry of Science and Education (BMBF: MEDSYS,FORSYS)the University Hospital Heidelberg is seeking highly-motivated team members with an interest in interdisciplinary research to establish new computational and experimental approaches in cell based medical systems biology. All positions are located at the Hamamatsu Tissue Imaging and Analysis (TIGA) Center in the central systems biological BIOQUANT building which is the key stone Systems Biology at University Heidelberg. The projects pursue a systems biological approach towards the cell based modeling of human skin using an integrated computational and cell biological approach. Successful candidates will join a diverse team of scientists working together to facilitate cutting-edge research. Post-doctoral fellows will actively participate in coordination, multi-disciplinary team building, designing and implementing state-of-the art approaches of the relevant fields.

In detail we offer the following positions:

1 Post-Doc and 3 PhD in Computational Multi-Scale Modelling of Human Skin 

Tasks: Creation of systems biological models, automatic reconstruction of genetic networks from time series data, integration of genetic networks in the computational skin model, mining of networks from databases, software development
Expected Know-How: Background in systems biology, computational or biophysical modelling of biological systems, bioinformatics

1 Post-Doc and 1 PhD in Organotypic Skin Models For Studying Wound Healing

Tasks: Treatment of wounded human organotypic co-cultures of keratinocytes and fibroblasts (growth factors), RNA/Protein isolation, functional analysis of regulation of epidermal homeostasis on RNA and protein level, review of literature data, specification of computational models of genetic networks
Expected Know-How: Experimental cell biology, molecular biology, primary cell culture, in situ hybridisation, understanding of systems biology

1 Post-Doc in Applied Computational Image Processing

Tasks: Participation/coordination of virtual microscopy related projects, reconstruction of systems biological models from microscopic images, classification algorithms based on morphological cell and tissue parameters extracted from histological sections (fluroescence and brightfield)
Required Know-How: Computer science, image processing, bioinformatics, microscopy, software development, understanding of systems biology

For all positions please contact: Dr. Niels Grabe: tiga.jobs@gmail.com (www.tiga.uni-hd.de)

How to apply

Salary and benefits are according to a public service position in Germany (TV-L E13 with 50% position for Ph.Ds). The University Hospital and German Cancer Research enter are Equal Opportunity Employers. All positions are available immediately and for 3 years. Applications will be assessed directly and successful applicants can start as soon as possible. Applications including a CV, and contact details (e-mail, phone), previous research experience, a list of eventual publications, as well as two references should be sent via e-mail only to the specified address.

posted 2009.03.05

University College Dublin is seeking to appoint a Lecturer in Applied and Computational Mathematics in the School of Mathematical Sciences.

UCD School of Mathematical Sciences is committed to research and teaching across the mathematical sciences, including mathematics, applied and computational mathematics, and statistics and actuarial science, and their connections with other fields. The advertised position concerns the discipline of applied and computational mathematics.

The successful candidate will be expected to engage in research in some aspect of Applied and Computational Mathematics, including supervision of research students and projects, and to contribute to the School's wide-ranging programme of undergraduate and postgraduate teaching. Applications from excellent candidates with interests in all areas of Applied and Computational Mathematics will be considered.

Salary: € 37,411 - € 87,724 pa (95 Lecturer Scale)
Appointment on scale will be made commensurate with qualification and experience

NOTE:Applications must be submitted by the closing date and time specified. (04 March 2009) UCD are unable to accept late applications.

http://www.ucd.ie/vacancies

posted 2009.02.23

A postdoctoral position is available for a highly motivated individual. The main project will be associated to the development and implementation of techniques to detect, reconstruct and classify emerging pathogens using High Throughput Sequencing Technologies. The project is a collaboration between the Lipkin's and Rabadan's Laboratories at Columbia University, New York.

Applicants must have a PhD degree in any quantitative science (preferably physics, astrophysics, computer science, biomedical informatics, statistics or mathematics). Medical/biological knowledge is not expected but highly valued. The candidate should have a working knowledge of programming with demonstrated experience in problem solving. Excellent organizational and communication skills are a must.

Interested applicants should submit a letter of interest, CV, and name and contact information of three references by e-mail (preferred) to rabadan [at] dbmi.columbia.edu or
by mail to Raul Rabadan, PhD, Assistant Professor, Department of Biomedical Informatics, Columbia University, 622 West 168th Street, VC-5, New York, NY 10032, USA.
Deadline: 24th February 2009.

Columbia University is an affirmative action/equal opportunity employer and encourages applications from women and underrepresented minorities.

posted 2009.02.18

The Computational Biology & Biological Physics Division (http://cbbp.thep.lu.se) at the Department of Theoretical Physics pursues a broad spectrum of research activities within Life Sciences. Current research topics include:

• Structure and dynamical aspects of folding and interactions of macromolecules, in particular proteins, including protein-ligand binding, mechanical unfolding, and misfolding and aggregation of disease-related proteins.
• Multiscale systems biology modeling of pathways and assemblies of cells, ranging from intra- and intercellular molecular interactions to cell-cell interactions.  Applications include stem cells and cancer cells as well as plant development.
• Analysis of high-throughput genomics and proteomics data, including mapping results onto high-level functional categories, e.g., pathways and ontologies.
• Topological and dynamical properties of random graphs and complex networks, with some emphasis on transcriptional networks.
• Machine learning with some focus on biomedical information processing, in particular for ECG analysis, image processing and medical decision support for heart related diseases.
  

We will have 3 PhD position openings during the spring of 2009 and are at this time searching for potential high quality candidates. Interested applicants are asked to supply a letter-of-intent to phd_2009 [at] thep.lu.se together with a CV. Academic background may vary from Physics, Mathematics, Computer Science to Biomedical Sciences.

We expect to begin deciding on PhD appointments on May 1, 2009, although the search will continue until the positions are filled.

Principal Investigators:
Anders Irbäck
Mattias Ohlson
Stefan Wallin
Patrik Edén
Bo Söderberg
Henrik Jönsson
Carsten Peterson

For additional information on current research, see our individual websites http://cbbp.thep.lu.se/people .

posted 2009.02.10

The Research Institute at Nationwide Children's Hospital
The Battelle Center for Mathematical Medicine

A postdoctoral position is available immediately at the Das Lab in the Battelle Center for Mathematical Medicine at The Research Institute at Nationwide Children's Hospital (www.nationwidechildrens.org/research). The Das Lab uses computational and theoretical tools based on stochastic methods, nonlinear dynamics and statistical mechanics. More details about the lab can be found at, http://openwetware.org/wiki/User:Jayajit_Das. All the projects are focused on understanding our immune system (innate and adaptive) at a mechanistic level and are carried out with synergistic collaborations with leading experimentalists in the area.
Highly motivated and career oriented applicants with expertise in statistical physics, chemical engineering, bioengineering, systems biology or other areas of computational biology are particularly encouraged to apply.
We have a state of the art computer cluster with 96 INTEL processors. The resources at the Ohio State University campus are also available. The position will be for one year, renewable for a second year. Interested candidates should send (preferably by email), a brief cover letter stating your interest in our lab, a short CV and names and contact information of three referees to,

Jayajit Das
Assistant Professor
Battelle Center for Mathematical Medicine, The Research Institute at Nationwide
Children's Hospital and Department of Pediatrics, Biophysics Graduate Group, Ohio

posted 2009.02.04

Position Title:  Research Associate/Research Fellow
                      Computational modeling of biological systems
Level: Level A or B (depending upon qualifications and experience)
Position Number: 308230
Where:  The University of Western Australia, Perth Australia

Description:
The role of the position is to develop computational/mathematical models of biological systems. Models will be developed to integrate a wide range of biological processes, including: tissue deformation, fluid-tissue interactions, cell population dynamics, inter and
intra-cellular communication (systems biology), and protein synthesis. Projects cover aspects of cancer biology (specifically colorectal and prostate cancer), regenerative medicine and osteoarthritis, and glaucoma surgery. Close collaboration with key experimentalists in these fields is expected. Typically models will involve a combination of partial differential equations, ordinary differential equations and discrete methods (e.g. molecular dynamics, cellular automata). Researchers will be matched to projects based on expressed interests and background experience. Work on other research and consulting projects may be required from time to time.   Several positions are available.

For more information go to:
https://www.his.admin.uwa.edu.au/jobvacs/external/academic/doc/doc1316580.RTF

posted 2009.01.28