A portal site for systems biology.

Universitat Autonoma de Barcelona Dep of Genetics and Microbiology

We are looking for two students, preferably a biologists, to start two grants for two PhD in systems biology and/or evo-devo about:

- Gene network simulation in pattern formation, morphogenesis and morphological evolution.
                         or/and
- Compartive embryonic morphometrics

One of the current challenges of evolutionary biology is to understand how genetic variation leads to specific morphological variation (the g-p map) and how that process affects the direction of morphological change in evolution. Our group is devoted to address this question by using gene network models.

Programming skills or a willingness to acquire them is required.

The grants are provided by the Spanish ministry of science and innovation. One of them is for 4 years and the other is for 3 years extendable to an additional year.

The exact topic of the theses would be discussed in detail after interview.

For an outline of the groups research:
http://bioinf3.uab.cat/grupgbe/index.php?option=com_content&task=view&id=64&Itemid=104

For further inquiries:
isaac.salazar at uab.cat
Genomics, Bioinformatics and Evolution Group

Article exemple:
Salazar-Ciudad I, Jernvall J.A computational model of teeth and the developmental origins of morphological variation. Nature. 2010 Mar 25;464(7288):583-6.

The Autonomous University of Barcelona is a public university located 20 kms north of Barcelona centre. It has its own "green" campus. It is the university with more PhD students (in proportion of its size) in Spain.

Application Deadline: June 30th 2010

Background
In spite of the predicted global changes in climate, very little is known of how physiological temperature changes influence molecular signalling events that control key plant growth traits. To address this knowledge deficit the Halliday and Grima labs are combining molecular, genetic and theoretical approaches to establish how temperature regulates signalling in the light activated pathways: major regulators of plant development, growth rate and photosynthetic rate.

Project aim
To apply modelling approaches to understand how temperature alters the molecular behaviour of the light receptor signal transduction in the model plant Arabidopsis thaliana This project will use biological data, computational modelling and mathematical analysis, to understand the principles and molecular mechanisms that underlie temperature buffering or sensitivity in biological networks.

This is an opportunity to launch your career in interdisciplinary research: the biology of the future. We strongly encourage applicants with a background in any of the following areas: computational biology, bioinformatics, molecular biology, physics, mathematics or statistics.

For further information please contact:
vsparlin@ed.ac.uk and visit our websites:
http://www.biology.ed.ac.uk/research/groups/khalliday/
http://csbe.bio.ed.ac.uk/grima.php

This project will be supported by the Centre for Systems Biology at Edinburgh (CSBE)
http://csbe.bio.ed.ac.uk/

Related Scientific Papers

• Salazar et al., (2009) Prediction of photoperiodic regulators from quantitative gene circuit models. Cell, 139:1170-9.
  
• Gould, et al., (2006) The molecular basis of temperature compensation in the Arabidopsis circadian clock. Plant Cell, 18(5):1177-87.
  
• Locke et al., (2006) Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Mol. Syst. Biol., 2:59.
  
• Heggie L and Halliday KJ. (2005) The highs and lows of plant life: temperature and light interactions in development. Int J Dev Biol., 49:675-87. Review.

JACOBS UNIVERSITY BREMEN

Two PhD student positions are available in a project "Organization of excitable dynamics in hierarchical networks" supervised by Marc-­‐Thorsten Hütt and Claus Hilgetag at Jacobs University in Bremen/Germany.

Project Outline: We plan to characterize different types of hierarchical networks and identify the topological parameters that most strongly shape their functional dynamics. Moreover, we will determine which of the parameters are invariant to coarse-­ and fine-­ graining of the networks due to their hierarchical structure, and investigate how different excitable mechanisms at the node level affect the global network dynamics. For a large and biologically important class of excitable networks, we thus want to obtain a deep theoretical understanding of how network topology and dynamical processes interact.


For further information on the topic, see: Müller-­‐Linow, M., Hilgetag, C. and Hütt, M.-­‐Th. (2008) Organization of excitable dynamics in hierarchical biological networks. PLoS Computational Biology 4, e1000190.
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000190

Jacobs University Bremen is an international, private, independent research university offering accredited degree programs in engineering, the natural sciences, humanities and social sciences.

Successful candidates will have a background or strong interest in Computational Biology or Neuroscience and solid programming skills (e.g., Matlab/Mathematica/C++/Python).

Interested students are encouraged to submit a CV, contact details of two references and a short statement of research interest electronically to: m.huett [at] jacobs-­‐university.de or c.hilgetag [at] jacobs-­‐university.de
To be assured of full consideration, applications must arrive by April 16, 2010.
Please feel free to contact us for informal inquiries and additional information.

Scholarships in Bioinformatics and Systems Biology funded by IRCSET are available in UCD and NUIG

New high-throughput technologies in biology have opened up exciting opportunities for numerate scientists to work in advanced areas of biological research. Our programme takes students from a variety of backgrounds (statistics, engineering, mathematics, computer science, biology, chemistry, physics) and gives them relevant courses during their PhD, tailored to their needs. There are several projects available in different areas such as systems biology, statistics, signalling and infection. Each project is jointly run by two supervisors, one with a background in modelling or computational analysis and one with an experimental research programme. The student is integrated into the research teams of both research groups. Studentships are based primarily in Dublin, and also in Galway.

EU STUDENTS ONLY

Each student receives:
• 4 year stipend of €18,000 per year, plus fees and travel expenses
• Budget for personal laptop/ PC
• lab consumables (up to €3,000 per year)
• Opportunity for work experience abroad

For the application procedure and further details visit our
website: http://bioinformatics.ucd.ie/PhD

Closing date : 31st March 2010

Unventional Computing and Cellular Automata

http://uncomp.uwe.ac.uk

A fully funded 3-year EPSRC DTA PhD studentship is availabl at the Unconvetional Computing Centre, University of the West of England, Bristol, UK. The Unconventional Computing Centre (UWE, Bristol) employs complex dynamics in physical, chemical and biological media to design computational techniques, architectures and working prototypes of novel and emerging computers.

The 3-year studentship includes tuition fees and an annual stipend of £13,200 (tax free) and is for UK (home) students only.

See more details and apply at

http://info.uwe.ac.uk/hr/vacancies/job_details.asp?ref=FET/AA

Structured PhD Programme in Bioinformatics and Computational Medicine

University College Dublin, Systems Biology Ireland, Dublin, Ireland

Applications are invited for PhD studentships, starting in October 2009 or later within the Bioinformatics and Computational Medicine Structured PhD Programme (http://bioinformatics.ucd.ie/PhD) at University College Dublin, to work on the following research projects focusing on computational and mathematical modeling of biochemical cellular pathways:

"Design principles of metabolic and regulatory pathways" (supervisors: Zoltan Neufeld, Denis Shields)

"Switches, oscillations and excitable behavior of signaling pathways" (supervisors: Boris Kholodenko, Zoltan Neufeld, Walter Kolch)

"High-dimensional and multiple time scale modeling of signaling networks" (supervisors: Boris Kholodenko, Walter Kolch)

For further details about these projects and the PhD program see http://bioinformatics.ucd.ie/PhD/)

The successful candidates will undertake a four-year research project on computational and mathematical modeling of biochemical cellular pathways in close collaboration with experimental research groups at Systems Biology Ireland.

Applicants should hold a degree in a numerate discipline, particularly with experience in mathematical and computational modeling (e.g. mathematics, physics, computational science, computational biology, chemical or bio-engineering or related areas) and have an interest in cell biology.

For further enquiries please contact: Zoltan Neufeld (zoltan.neufeld@ucd.ie).

The PhD positions are funded by the graduate education programme (GREP) of the Irish Research Council for Science, Engineering and Technology (IRCSET) and they are available for EU students only. The 4-year scholarship includes student stipend, fees, some consumables and travel budget to allow the student to obtain work experience abroad and industrial work experience in a company in Ireland or abroad. Applicants should send a CV, transcripts and names and addresses of two referees to bioinfo@ucd.ie before the closing date of August 21, 2009.

Contact Details: (bioinfo@ucd.ie) Closing date: 21st August 2009.

Are you interested in interdisciplinary research in mathematics, computing and biology?

New high-throughput technologies in biology have opened up exciting opportunities for numerate scientists to work in advanced areas of biological research. Our programme takes students from a variety of backgrounds (statistics, engineering, mathematics, computer science, biology, chemistry, physics) and gives them a structured training during their PhD, tailored to their needs. Each project is jointly run by two supervisors, one with a background in modelling or computational analysis and one with an experimental research programme. The student is integrated into the research teams of both research groups.

Applications are invited from EU students for 4-year PhD positions under the graduate education programme (GREP) of the Irish Research Council for Science, Engineering and Technology (IRCSET). Most studentships commence Oct 2009.

Projects currently available:

• Infection: Comparative genomics of pathogenic yeast
• Networks: Biological patterns in networks of protein and gene interactions
• Signalling: Spatio-Temporal Dynamics of Cell Signalling
• Cancer: Alternative Transcript Expression in Malignant Melanoma
• Infection: Functional genomics of mycobacteria-macrophage interactions in cattle
• Plant Systems Biology: The cis-regulatory code underlying plant development
• Health and disease: The Transcriptomic Phenotype of Human Adipose Tissue
• Statistics: Epigenetic/transcriptional integration from next generation sequencing
• Statistics: detecting alternate splice variants using next generation sequencing
• Modelling evolution: Modelling the evolution of protein interactions and motifs
• Thrombosis/signaling: Discovery of oligopeptides modulating platelet signalling
• Virology/signaling: Short linear protein motifs in HIV signalling in host cells
• Computational chemistry: Structurally constrained peptides as peptide mimetics
• Subcellular location: Determinants of protein localization in mammalian cells
• Systems Biology: Spatiotemporal code of signal specificity and pathway crosstalk
• Systems Biology: Design principles of regulatory and metabolic networks

Application procedure and further details: http://bioinformatics.ucd.ie/PhD

10 of these studentships are funded by IRCSET. They fund student stipend (€16,000), fees, some lab consumables ( up to €5,000 per year), and travel budget to allow the student to get work experience abroad and industrial work experience in a company in Ireland or abroad. 4 studentships are funded by SFI (Science Foundation Ireland).

Contact Details: (bioinfo@ucd.ie) Closing date: 30th March 2009

Oxford Bioinformatics Programme
Want to study part-time at the University of Oxford? 
Find out more at our Virtual Open Day on Friday 25th April 2008

Visit http://bioinfomsc.stats.ox.ac.uk

Interested in studying bioinformatics on a part-time basis at one of the world's most famous universities?  Half of the people studying with the Oxford Bioinformatics Programme do not reside or work in the UK. Our Postgraduate Certificate in Bioinformatics only requires students to be in Oxford for two weeks in a year.  We also have a part-time Master's and a selection of online and one-week face-to-face courses.

Our Online Open Day on Friday 25th April will provide you with an invaluable insight into studying bioinformatics at the University of Oxford.  Between 9am and 11am (Pacific Daylight Saving Time) / 12 midday and 2pm (Eastern Daylight Saving Time) online discussion forums will take place with the Academic Director, Dr Andrew Dalby, the course administrative team, as well as current and past students. 

In addition to these discussion forums, throughout the day you will be able to view and download course content as well as application packs and other student resources.

All participants will be entered in to a prize draw to win a £100 discount on a module.  There are five prizes available.

For more information contact mathews@stats.ox.ac.uk .

This Ph.D Programme is for Graduate Students in Biology, Mathematics, Chemistry, Physics and Medicine. Prospective students should have an excellent score in their previous classes, a strong undergraduate science background, a strong commitment to research and they should accept the challenge posed by a new interdisciplinary science. Indeed the present Programme is specifically interested in recruiting students with broad scientific interests and a taste for collaboration.

The Programme is designed to offer scientific training, research projects and perspectives in the area of post-genomic biology by using combined computational, engineering and experimental approaches with theoretical modelling, rooted in theoretical physics and mathematics. The biological interests include cell differentiation and development, cell signalling, cell growth and motility, cancer progression, cancer cell genetics, protein folding, gene-expression.

Further information on the web site or by contacting the Chair, Professor Federico Bussolino: federico.bussolino @ unito.it
http://www.bioinformatica.unito.it/phD.complexity/

The Integrative Biology Graduate Program fosters training in research areas focused on understanding the molecular and cellular basis of integrated biological systems. The Integrative Biology Graduate Program (IBGP) promotes effective cross-disciplinary research involving approximately sixty faculty members in basic science and clinical departments with the goal of training students for careers as independent investigators. Some areas of research interests in this program include response and adaptation to physiological (exercise, microgravity, and pregnancy), and pathological (hypertension inflammatory and immune diseases, diabetes, sepsis, and cancer) stresses. Specific areas of investigation address cell-cell signaling, including the basis of fertilization, exocrine secretion, renal tubular transport, gene regulation in development and differentiation, regulation of cardiovascular function and metabolism, regulation of muscle contraction and protein turnover, sensory regulation of behavior, carbohydrate and lipid metabolism, and tumor biology.
http://www.utsouthwestern.edu/utsw/home/education/integrativebiology/

The Lewis-Sigler Institute for Integrative Genomics, housed in the Carl Icahn Laboratory at Princeton University, was established to innovate in research and teaching at the interface of modern biology and the more quantitative sciences. The Institute is the hub of the Center for Quantitative Biology, funded by the the National Institute of General Medical Sciences (NIGMS), one of the National Institutes of Health (NIH).
http://www.genomics.princeton.edu/

The Tri-Institutional Program in Computational Biology & Medicine (CBM) is a collaboration between three outstanding research and educational institutions: Cornell University (both the Ithaca campus and the Weill Graduate School of Medical Sciences), The Rockefeller University, and Sloan-Kettering Institute. This highly selective program offers Ph.D. degrees in the newly emerging field of Computational Biology and Medicine, at the interface between biology, mathematics, and computer science. The combined resources of these world-leading institutions create an unparalleled interdisciplinary environment for excellence in CBM. The program strongly encourages collaboration among the campuses and the different disciplines.
http://www.triiprograms.org/cbm/about.html

Plants are crucial for mankind. As an established institute at the forefront of Plant Sciences, our mission is to use systems biology approaches combining bioinformatics, computational biology, functional genomics and classical biology to further explore the potential of plants to help build a sustainable economy. Our activities
are rooted in fundamental research and oriented towards applications for the benefit of society.
http://www.psb.ugent.be/

http://www.sbi.uni-rostock.de/index2.html

http://www.sysbio.de/

http://itb.biologie.hu-berlin.de/