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Neurotechnology is a rapidly growing field of research, thriving to repair,
replace or
support physical functions affected by nervous system diseases by technical
means.
At the Bernstein Focus for Neurotechnology (BFNT) we exploit electrical
and chemical signals recorded in the brain to control external or implanted
devices.
The BFNT efforts are organized in projects on fundamental neurotechnological
research, the development of new techniques, clinical testing and
neuroethical considerations.
PhD-Positions are available in the following projects:
- Voluntary control of neuronal correlations for BMIs (Project A2)
- Co-Adaptivity of brain and computer: Interaction of two learning signals
(Project A3)
- Adaptive interception of epileptic events based on predictive network
dynamics (Project A4)
- Development, prototyping, fabrication and testing of individualized and
long-term safe electrode arrays (Project B1)
- Multielectrode arrays with adjustable stiffness (Project B2)
- Improving microelectrodes for single cell recordings in the human brain
(Project B3)
- NETCAD - An environment for 3D structural modeling of biological neuronal
networks (Project B5)
- Real time metabolite sensing for feedback control of behaviour in
neurological disorders (Project C4)
- Multicontact stimulation techniques for interventions in human focal
epilepsy (Project C5)
Further details on: www.bfnt.uni-freiburg.de/jobs
Contact:
Dr. Janina Kirsch
Coordinator for the BCCN Teaching & Training Programs
Bernstein Center for Computational Neuroscience
Albert-Ludwigs-University Freiburg
Hansastr. 9a
D - 79104 Freiburg
Germany
PhD position: Fully funded for 3 years, to begin in Spring/Summer 2009
(start date flexible).
Title of Research project: MODELLING GLOBAL ECOLOGICAL CHANGE OF THE BOREAL
FOREST: A MULTISCALE HIGH-PERFORMANCE COMPUTATIONAL SIMULATION APPROACH
Description of Research Project: Shifts in the geographical patterns
of vegetation are expected in coming decades as a result of climate
change. Biogeographical models based on current plant-climate relationships
predict that poleward expansion of biomes could reach 100 km in a
century (Emanuel et al. 1985, Prentice et al. 1992). These predictions,
emphasizing a primary control of climate on vegetation patterns have been
questioned by simulation based and empirical studies (Masek 2001, Gamache
and Payette 2005). Several authors have argued that climatic approaches
largely underestimate the importance of local processes (eg., dispersal
and competition) in ecological patterns.
Thus, one important issue is the interaction between local scale processes
and large scale ones that can limit predictions based only on species
requirements, as used in biogeographical models. Our aim is to study
how the boreal forest might respond to 1) climatic changes (changes in
temperature, disturbance regimes) and to 2) different harvesting options,
according to a simulation model approach. We will develop an individual-based
computational model of forest dynamics building upon previous work in our
lab (Caplat et al. 2008ab). A GIS based map will be used as background
for the simulations, allowing us to test what parameters best explain the
observed tree distribution. Then we will be able to forecast how changes
in these parameters could affect the forest structure, and to suggest
management options that counteract climate-induced effects.
The simulation of detailed ecological processes over large spatial scales
would not have been possible before the advent of high-performance computing
facilities and adapted software. There is some literature on parallelized
simulations of predator-prey models and some work on parallel computing
applied to agent-based spatial forest growth/dispersal models. Chave
(1999) implemented a spatially-explicit forest growth model, TROLL,
using a parallel implementation on 288 computer processors allowing
it to simulate plots of up 20 km^2 and 20x10^7 individuals. However,
there are no known parallel models to date designed to study impacts
of climate change on vegetation patterns using mechanistic models that
couple stochastic, individual-level interactions to community-level and
regional-level dynamics. The use of facilities such as Sharcnet to develop
such large-scale models may transform ecological modelling of vegetation
patterns in an era of climate change in the same way that high-performance
computing enabled development of whole-earth climate change models. The
outcomes will benefit fundamental ecological research as well as applied
land management. Improvement of modelling tools will also be beneficial
to Sharcnet users involved in biological or geographical research.
Research Methodology: The research will be based on computer simulation of
ecological processes across multiple scales, from individual to community
and regional levels. We will develop the simulation from our previous model
FORSITE, which was developed within the VisualWorks computing environment
(http://www.parcplace.com/vwnc/), through the CORMAS modelling platform
(http://cormas.cirad.fr/indexeng.htm). FORSITE is written in Smalltalk, a
flexible, powerful language. However, if necessary, the software platform
will be modified so that it may be accessible to a larger SHARCNET
user-group.
Within our modelling approach, trees are autonomous agents that follow
realistic life cycles. Land-use is simulated through a cellular automata
coupled with the spatial grid. Numerous studies have showed how stochastic
effects at the individual level in spatial systems can translate into
qualitatively different dynamics at the population level. However, as with
any agent-based model, simulation of detailed and realistic processes and/or
large populations is very difficult using only desktop computers, due to
their limited processing power and memory. At the large scales required to
simulate the effect of climate change on forest dynamics at the regional
level, it is necessary to simulate in excess of 100,000 trees, as well as
their interactions with one another and their environment. A simulation of
this magnitude requires high-performance computing. Moreover, sensitivity
analysis, which is crucial to understand the effects of uncertainties in
crucial model parameters, is also infeasible on desktop machines and hence
is often not performed.
According to our preliminary estimates, the computational requirement is
approximately 50,000 cpu hours. In the first phase of the project, the
existing CORMAS code will be rewritten in C and parallelized using Message
Passing Interface (MPI) to run on Sharcnet computers. Parallelization
will be particularly useful in in the earlier phases of developing and the
code, selecting a base case scenario, and developing a basic understanding
of model dynamics, since large populations can be simulated relatively
rapidly via parallelization. For univariate sensitivity analysis, multiple
realizations of the parallelized code will be run serially.
We will use data from GIS maps of Canadian boreal shield forests to create
realistic initial conditions for the simulations. Data will characterize
model outcomes at different levels of aggregation: individual tree
(growth rate, height), population (species composition, size) and landscape
(patchiness, connectivity). Data will exported and analyzed using spatial
analysis software (FRAGSTATS) and statistical software (R).
We expect to improve our model through a trial and error, evolutive approach
and thus to be able to share modeling tools specific to ecological analysis
(scaling methods, GIS-based applets) with the Sharcnet community. It is
expected that more ecological modellers will be brought into the Sharcnet
community as a result of this project.
This work will be done with collaborator Prof. Chris Bauch (Department of
Mathematics and Statistics, University of Guelph) who will contribute his
previous experience in spatial agent-based infectious disease simulations,
and parallelization of the simulation code via MPI and its implementation
on Sharcnet facilities.
Contact: Madhur Anand, Associate Professor & Canada Research Chair, Global
Ecological Change (GEC) Laboratory, Department of Environmental Biology,
University of Guelph, Guelph, Ontario; manand@uoguelph.ca
The Graduate Research Training Program PharMetrX: Pharmacometrics &
Computational Disease Modelling,
a joint graduate program of the Martin-Luther-Unversitaet Halle-Wittenberg
and the Freie Universitaet Berlin invites applications for the PhD program.
PharMetrX bridges pharmacy and mathematics. It offers its graduate students
a unique opportunity to experience research in the area of drug development
and optimising drug therapy jointly within academia and industry---the PhD
program is supported by the six research-driven pharmaceutical companies
Abbott, Bayer Schering Pharma, Bayer Technology Services, Boehringer
Ingelheim, Merck and Sanofi-Aventis.
The interdisciplinary PhD program is designed as a 3-year research program
including a structured research training curriculum of advanced academic
and industrial modules and a competitive research fellowship.
The PhD program is open for students holding a university degree in natural
sciences or medicine (e.g., 2. Staatsexamen of the Pharmacy curriculum or
a Masters degree in Bioinformatics or Mathematics).
In addition, external PhD students in their first PhD year are invited to
apply for participation in the curriculum component.
We are currently inviting applications to start the PhD program in March
2009. The closing date for applications is January 12th, 2009.
For further details and the online application procedure, please see
http://www.pharmacometrics.de
We would be grateful if you could communicate the announcement to interested
students.
Sincerely yours,
Charlotte Kloft & Wilhelm Huisinga (Program chairs)
PhD/Postdoc position: Comp. Biomechanics, U. Stuttgart, Germany
Opening for a PhD/Post-Doc position in Skeletal Muscle Modeling with
Applications to Lumbar Spine Mechanics
The PhD student/Post-Doc is supposed to work on a project focusing on
developing novel computational techniques to model skeletal muscles
mechanics. The goal is to overcome the computational challenge of
realistically modeling lumbar spine muscle mechanics while taking into
account the influence of a large number of muscles involved in complex
upper body movements. The skeletal muscles are modeled using the Finite
Element method in three dimensions and principles of nonlinear continuum
mechanics. For this purpose, a good background in computational continuum
mechanics, the Finite Element Method, and some programming skills are
desirable.
The PhD position is within the designated salary bracket TV-L 13 and has
a limited tenure of three years with a possible extension. The PhD student
will be part of the Graduate School Simulation Technology of the Cluster of
Excellence EXC 310 Simulation Technology (SimTech) at Universitaet Stuttgart
Applications with the usual documents (CV, degree certificates, references,
publication list, letter of motivation) should be sent directly to
Jun.-Prof. Oliver Roehrle (roehrle (_AT) simtech.uni-stuttgart.de),
Institute of Applied Mechanics (CE), Pfaffenwaldring 7, 70569 Stuttgart,
Germany. Applications will be accepted until the position is filled.
I would like to draw your attention to available stipends for PhD projects
in computational systems biology in Heidelberg, Germany. The stipends are
offered by the Heidelberg MathComp Graduate School and the VIROQUANT center.
Details about the projects are listed on the following page:
Specifically, in our group we are looking for applicants with a strong
mathematical background for projects involving the development of
computational methods for the analysis of stochastical models.
For further information about these projects you can contact
sven.sahle@bioquant.uni-heidelberg.de
Research Opportunities in High Performance Algorithms for Structural
Systems Biology
We have vacancies for two postdoctoral researchers, one graduate software
engineer, and one PhD student to work on exciting new projects to develop
high performance algorithms and knowledge-based approaches to advance the
state of the art in protein-protein docking, protein shape recognition,
and high throughput 3D virtual drug screening.
Location: LORIA, Nancy, France
Duration: Two years in the first instance
Starting date: January 1st 2009 (negotiable)
Remuneration: Standard INRIA rates
Candidates for the postdoc positions must have a PhD in one of the
mathematical or physical sciences, and must have strong and demonstrable
abilities and experience in programming using C or C++ on Unix/Linux or
Windows systems. Experience of scripting languages such as Python and
PHP would also be desirable. Experience of parallel programming, high
performance computing, and computer graphics would be desirable but is not
essential. Preference will be given to candidates with a strong interest or
background in structural biology, crystallography, computational chemistry,
molecular modelling, or related areas. Candidates should have a proven
research track record, demonstrated by publications in peer-reviewed
journals in one or more of the above areas.
Candidates for the Software Engineering position must have a good Honours or
Masters degree in computing science or one of the mathematical or physical
sciences, and must have very good programming skills using C or C++.
Preference will be given to candidates with an interest or background in
structural biology, molecular modelling, or related areas. If progress is
good, the successful applicant will be encouraged to study for a PhD.
Candidates for the PhD Studentship should be qualified to Masters level
or equivalent in computing science or one of the physical or biological
sciences, and must have experience of programming using a procedural
language such as C or C++. Preference will be given to candidates with
a strong interest in the use of knowledge-based approaches and computer
graphics to help advance the state of the art in protein-protein docking.
This position could be filled initially by a student with a good Honours
degree who would register as a Masters intern before proceeding to undertake
a PhD.
Please send a detailed CV, which includes the names of two academic referees,
along with a brief statement of your research interests and motivation to:
Dave Ritchie: dave.ritchie@loria.fr cc: d.w.ritchie@abdn.ac.uk
Please indicate which post(s) you are applying for. Closing date: 31
December 2008.
PhD Student Position: Mathematical Modeling & Population Genomics
PhD Student Position - Mathematical Modeling and Population Genomics
A 3-year PhD student position in Mathematical Modeling and Population
Genomics is available in the newly formed lab of Dr. Oskar Hallatschek at the
Max-Planck-Institute for Dynamics and Self-Organization in Gottingen. The
student will join a young and interactive research group in evolutionary
dynamics and biophysics, including theoreticians and experimentalists. We
cultivate an international atmosphere and the everyday working language
is English. The Max-Planck-Institute for Dynamics and Self-Organization
is located close to the center of the medieval town of Gottingen. More
information about the group is available on the web at:
http://www.fas.harvard.edu/~ohallats/)
The goal of the PhD project is to quantify genetic footprints of natural
selection and demographic revolutions, and how they can be disentangled
from one another: Kimura's neutral theory dominated the field of population
genetics as long as sequence data was a rare commodity. The recent years
of whole genome sequencing revealed quite surprisingly that standard
neutral models rarely explain observed polymorphism data well. Many
researchers take these deviations as ubiquitous signatures of acting
natural selection. However, although standard neutral models seem to be a
poor null model, the new interpretation in terms of natural selection is
far from straight forward. Most models of natural selection make even more
stringent assumptions than neutral models, such as panmixia, demographic
equilibrium and negligible epistatic interactions. These simplifications
could well have dropped the baby with the bath water.
The situation clearly indicates that genetic data mining is ahead of our
theoretical understanding of the how molecular evolution works ("population
genetics was much more fun in lack of genetic data", Whitlock). What could
replace the neutral theory as a null model of molecular evolution? The PhD
student will join our group effort to develop a new null model, which could
well dependent on the species. Specifically, he or she will search for new
sensible ways to disentangle natural selection from a typically unsteady
demographic history. The project will pay attention to spatial aspects of
evolution, epistatic selection and the previously unseen types and amounts of
data of the coming years. Prior experience in population genetics modeling,
molecular evolution or comparative genomics is helpful but not necessary.
The appointment will be on a temporary basis for a maximum of 4 years. The
gross salary starts at approximately 1400,- per month depending on age and
experience (TV D 13/2, Stufe 1). The student will be enrolled in the
Gottingen Graduate School for Neurosciences and Molecular Biosciences (GGNB,
http://www.ggnb.uni-goettingen.de/). Applicants should have a master's
degree or equivalent in biology, math, physics, or related fields. If you
hold an excellent BSc (1st class honors) please contact us about possible
accession. German is not required but international students will be
offered opportunities to take German courses. Interested candidates should
send a cover letter summarizing their research background and interest in
the position, CV, and contact information of two potential referees as a
single PDF file to: oskar.hallatschek.applications@gmail.com
Applications will be reviewed beginning December 1, 2008. Interviews will
be held in January. Starting date is February 1 2009 or later. If you have
any specific questions (e.g. details of the project), feel free to email me.
The Max-Planck-Institute for Dynamics and Self-Organization is an Equal
Opportunity/Affirmative Action Employer and has an affirmative action
policy for the disabled.
Ph.D. Positions: Center for Biological Systems Analysis, Freiburg
The spindle assembly checkpoint (SAC) controls the onset of anaphase
dependent on the attachment state of the chromosomes to the mitotic
spindle. This checkpoint is essential in vertebrates, and its malfunction has
been implicated in tumor progression and birth defects. Despite the fact that
experimental knowledge has been growing over the past two decades only few
mathematical and computational studies aimed to understand the dynamical
aspects of the spindle assembly checkpoint. Mathematical modeling will
be crucial for a comprehensive understanding of the SAC. This is a joint
project with an experimental group at the MPI for Developmental Biology in
Tubingen. We will follow a twofold approach using differential equations
as well as computer simulations to exploit the advantages of both modeling
strategies. The goal is to enter a tight experiment-theory loop, in which
the mathematical analysis yields predictions that can be experimentally
tested. For this project we are looking for someone who wishes to work
theoretically but in close collaboration with biologists. The opportunity
to gain experimental experience as well is given.
Profile
Candidates ideally fulfill the following criteria:
- Master in theoretical biology, mathematics, physics or a related discipline
- able to communicate with scientists in biology and mathematics
- good programming skills
Direct requests for information or applications:
Dr. Christian Fleck
Center for Biological Systems Analysis
University of Freiburg
Habsburgerstrasse 49
79104 Freiburg, Germany
Tel: ++49-(0)761-203-97198
Email: Christian.Fleck@fdm.uni-freiburg.de
Web. http://www.fdm.uni-freiburg.de/~cfleck/
Applications should include a motivation letter, a curriculum vitae, list
of publications (if any), and the names and addresses of two persons that
can be approached to obtain further information.
2) Opening for a Ph.D. position.
Trichome patterning in Arabidopsis Thaliana
Trichomes are shoot epidermal hairs found in most plants. The functions
acriped to trichomes range from protecting the plant against insect
herbivores to reducing transpiration. They are regularly distributed over
the epidermis. This makes them an ideal candidate for the study of spatial
control of specific cell types in plants, since these structures arise by an
orchestrated interplay of many different components. In this joint project
together with an experimental group in Cologne we try to understand the
initiation of the trichome pattern using detailed information about the
molecular interactions. To this end we mainly employ non-linear partial
differential equations or, in a discrete formulation, systems of coupled
non-linear ordinary differential equations. Due to the complexity of
the equations one has in most cases to revert to numerical methods. In
this collaboration we have a very intense interaction between theory and
experiment. We are looking for someone who wishes to work theoretically
but in close collaboration with biologists.
Profile
Candidates ideally fulfill the following criteria:
- Master in theoretical biology, mathematics, physics or a related discipline
- able to communicate with scientists in biology and mathematics
- good programming skills
Direct requests for information or applications:
Dr. Christian Fleck
Center for Biological Systems Analysis
University of Freiburg
Habsburgerstrasse 49
79104 Freiburg, Germany
Tel: ++49-(0)761-203-97198
Email: Christian.Fleck@fdm.uni-freiburg.de
Web. http://www.fdm.uni-freiburg.de/~cfleck/
Applications should include a motivation letter, a curriculum vitae, list
of publications (if any), and the names and addresses of two persons that
can be approached to obtain further information.
Open PhD Positions: Simula Research Laboratory, Oslo
The Center for Biomedical Computing at Simula Research Laboratory has
two open PhD positions. The aim of the research is to develop efficient
computational methods and software for simulating biomedical processes,
with particular emphasis on adaptive finite element methods for biomedical
flow problems.
We are looking for candidates fulfilling one or more of the following
requirements:
* Candidates should have a strong background in numerical analysis and
scientific programming.
* A University degree in mathematics, physics, computer science,
informatics, mechanics, computational biology, or similar.
NEW GRADUATE PROGRAM IN APPLIED MATHEMATICS The University of Pennsylvania
The University of Pennsylvania has established a graduate group in Applied
Mathematics and Computational Science. We are now accepting applications
for PhD and Masters students, who will begin their graduate studies in Fall
of 2009. Students will be fully-funded for at least four years. The online
application form can be found at https://app.applyyourself.com/?id=UPENN-G
This is a highly interdisciplinary program, with a faculty drawn from
across the University. We are looking for students with an interest in,
and aptitude for mathematics, as well as some formal training beyond
a standard calculus sequence. Students need not have completed all the
usual course work required for a Bachelor's degree in Math, but they are
strongly encouraged to take a semester each of undergraduate analysis
(beyond calculus), linear algebra, probability, and complex analysis.
Interested students are also strongly encouraged to take the GRE Advanced
Math Subject Exam. Students with specific interest in applications of
mathematics are particularly encouraged to apply.
We are seeking mathematically talented students, interested in working in
any of the following fields:
Mathematical Biology
Bioinformatics and Genomics
Robotics, Machine Learning, and Computational Geometry
Analysis of Algorithms
Medical Imaging, Image Processing, and Analysis
Inverse Problems
Partial Differential Equations
Materials Science, and Nanoscience
Condensed Matter Physics, and Computational Chemistry
Mathematical Finance
Interested students can find further information at our website:
http://www.amcs.upenn.edu/AMCS/AMCSGrad.html
Vacancy
The Netherlands Institute for Systems Biology (NISB) and Centrum Wiskunde &
Informatica (CWI) invite applications for the position of a:
PhD student (OIO): Cell-based modeling of in vitro angiogenesis: role of
tip cell selection, cross-talk between diffusive and contact-dependent
signaling, and endothelial cell-matrix interactions.
The opening is a research position within the field of computational biology
Research background
Angiogenesis, the outgrowth of sprouts from existing blood vessels,
is essential for many biomedical phenomena, including tumor growth and
tissue engineering. A detailed understanding of its mechanisms will help
identify specific targets for therapeutical intervention. The key players
of angiogenesis are endothelial cells (ECs), the cells lining the inner
walls of mature blood vessels, and the surrounding matrix proteins. We
have previously built simple models of the ECs? self-organization into
angiogenic sprouts. In this project we aim to refine our understanding
of angiogenic sprouting, by including the selection of ?tip cells??the
leading cells of blood vessel sprouts?and the interactions between the
ECs and the protein matrix they live in. The final goal of this project
is to develop a multiscale, explanatory model of angiogenesis.
Job description
The PhD student will further develop and analyze cell-based models of
angiogenesis and, depending on interest, validate the cell-based models using
mean-field approaches. Techniques include ordinary differential equations
(ECs? regulatory networks), the Cellular Potts Model (cell behavior) and
PDEs (protein matrix). Model insights and predictions will be interpreted
and validated in close collaboration with our experimental collaborators.
Location
The work will be embedded in the Biomodeling and Biosystems Analysis group
of the Netherlands Institute for Systems Biology (NISB) and within the Life
Sciences group of the Center for Mathematics and Computer Science (CWI)
in Amsterdam. As the ?core modeling group? of the Netherlands Consortium
for Systems Biology, the Biomodeling and Biosystems Analysis group develops
quantitative and predictive models and multiscale computer simulations in
collaboration with systems biology groups at participating institutes.
Profile
Candidates ideally fulfill the following criteria:
- M.Sc. in theoretical biology, computer science, mathematics or a related
discipline
- able to communicate with scientists in biology and mathematics
- good programming skills in C++ and Python or equivalent
Conditions of employment
The vacancy concerns a temporary research position for four years. The
salary and terms of employment are in accordance with the "CAO-
onderzoekinstellingen". Besides the salary, CWI offers attractive
and flexible terms of employment, like a collective health insurance,
pension-fund, and initial help with housing for foreigners.
Websites
http://www.sysbio.nl and http://www.cwi.nl
Applications and requests for information
Direct requests for information or applications before 1 December 2008 to:
Dr. Roeland Merks, Roeland.Merks@sysbio.nl
phone +31 20 592 4117, skype: roelandmerks
Centrum Wiskunde & Informatica (CWI) and Netherlands Institute for Systems
Biology (NISB)
Kruislaan 413, 1098SJ Amsterdam, The Netherlands
Applications should include a motivation letter, a curriculum vitae, list
of publications, and the names and addresses of at least two persons that
can be approached to obtain further information.
Closing time
1 December 2008
Literature
Roeland M. H. Merks, Sergey V. Brodsky, Michael S. Goligorksy, Stuart A.
Newman, James A. Glazier (2006). Cell elongation is key to in silico
replication of in vitro vasculogenesis and subsequent remodeling.
Developmental Biology 289, 44-54. doi:10.1016/j.ydbio.2005.10.003
Roeland M. H. Merks, Erica D Perryn, Abbas Shirinifard, James A
Glazier (2008). Contact-inhibited chemotaxis in de novo and sprouting
blood-vessel growth. PloS Computational Biology 4 (9), e1000163. doi:
10.1371/journal.pcbi.1000163
Graduate Study: Applied Math, University of Pennsylvania
The University of Pennsylvania has established a graduate group in
Applied Mathematics and Computational Science. We are now accepting
applications for PhD and Masters students, who will begin their graduate
studies in Fall of 2009. The online application form can be found at
https://app.applyyourself.com/?id=UPENN-G. Attached please find a pdf of a
poster advertising our program, which reproduces well on a greyscale printer.
This is a highly interdisciplinary program, with a faculty drawn from
across the University. We are looking for students with an interest in, and
aptitude for mathematics, as well as some formal training beyond a standard
calculus sequence. They need not have completed all the usual course work
required for a Bachelor's degree in Math, but are strongly encouraged to
take a semester each of undergraduate analysis (beyond calculus), linear
algebra, probability, and complex analysis. Interested students are also
strongly encouraged to take the GRE Advanced Math Subject Exam.
We are seeking mathematically talented students, interested in working in
the following fields:
Mathematical Biology
Bioinformatics and Genomics
Robotics, Machine Learning, and Computational Geometry
Analysis of Algorithms
Medical Imaging, Image Processing, and Analysis
Inverse Problems
Partial Differential Equations
Materials Science, and Nanoscience
Condensed Matter Physics, and Computational Chemistry
Mathematical Finance
It would be very helpful if you could forward this message to the
undergraduates in your institution, and direct interested students to
our web-site:
http://www.amcs.upenn.edu/AMCS/AMCSGrad.html
We are most grateful for your help in identifying good candidates for this
exciting new program.
Charles L. Epstein
Graduate Group Chair
Applied Mathematics and Computational Science
SCHOLARSHIP FOR A PhD STUDENT (Massey University, Auckland)
A PhD student is sought for a research project that aims at understanding
the complex behaviour of the respiratory neural network by using recently
developed numerical methods, called "equation free" (EF) techniques. The
student will work with Drs Alona Ben-Tal and Carlo Laing at the Institute
of Information and Mathematical Sciences at Massey University, Albany
campus, Auckland. The work is in collaboration with Prof Yannis Kevrekidis
(Princeton University, USA) and Dr Jeffrey Smith (National Institutes of
Health, USA), and the student will have the opportunity to visit the USA.
Salary (funded by the Marsden Fund): $25,000 pa scholarship (tax free)
for three years + tuition fees.
A good knowledge of nonlinear dynamics, scientific programming, and
physiology will be an advantage but is not necessary. To apply, please
send a CV, academic record and names of two referees to
Dr Alona Ben-Tal (E-mail: a.ben-tal@massey.ac.nz, Phone: 09-4140800 ext.
41050) or
Dr Carlo Laing (E-mail: c.r.laing@massey.ac.nz, Phone: 09-4140800 ext.
41038).
Postal address:
Institute of Information and Mathematical Sciences
Massey University
Private Bag 102-904 North Shore Mail Centre
Auckland, New Zealand
The position will remain open until a suitable candidate is found.
PhD Position: Mathematical Modelling, University of Heidelberg
PHD POSITION: CELL POLARISATION DURING EVAGINATION AND INVAGINATION,
University of Heidelberg
In many biological examples form often originates as a pattern of
curvature of cell sheets and its processes can be traced back to processes
of evagination or invagination at defined positions within originally
nearly flat cell sheets in the course of development. However, already the
basic processes of evagination or invagination of flat cell sheets is not
understood. The aim of this project is to unravel these basic mechanisms
of self-organisation leading to the emergence of form in two simple model
systems: Hydra and Xenopus.
It is widely accepted, that bending moments give rise to curvature, leading
to evagination or invagination. The bending moments themselves are typically
due to anisotropies caused by cell polarisation. Since the establishment of
symmetry breaking by cell polarity in developing tissues will be typically
determined by quantitative integration of multiple signals in a highly
dynamic and self-organised process, it can hardly be understood using
conventional molecular biology methods alone. Together with A. Kohler,
Ph. D. (http://www.zi2.uni-karlsruhe.de/index.html), Dr. F. Rossetti
(http://www.pci.uni-heidelberg.de/bpc2/members/rossetti.html) and Dr. M.
Zigman (http://www.zoo.uni-heidelberg.de/abt1.html) we want to harness
mathematical and modelling approaches with a novel biophysical method
using functionalised substrates to understand the formation of a symmetry
break in flat tissues from related model systems for developmental and
regenerative biology.
The project is funded by the WIN-programme of
the Heidelberg Academy of Sciences and Humanities
http://www.haw.baden-wuerttemberg.de/seiten/forschung/win_kolleg.php .
JOB DESCRIPTION:
- Mathematical modelling and simulation: individual based models and
partial differential equations
- Constant experiment-to-theory alignment
YOUR QUALIFICATIONS:
- Master in applied mathematics, physics, engineering or a related area
- Solid background in programming and numerical methods
- Good communication skills
- Authorisation to work in the EU
OUT OFFER:
- Working in an exciting interdisciplinary research project at one of the
leading German Universities
- Further training opportunities in the Heidelberg Graduate School
of Mathematical and Computational Methods for the Sciences
http:// www.mathcomp.uni-heidelberg.de
- Initial contract for three years (TVL-13/2, 1450 EUR/month) with the
possibility of prolongation for up to five years
Applicants should send a cover letter detailing motivation, training,
and work experience, a curriculum vitae, a publications list, and two
references to Dr. Dirk Hartmann (Dirk.Hartmann@iwr.uni-heidelberg.de). If
available, also include a copy of the master thesis, published articles
or similar relevant materials.
For further information please visit: http://www.hartmann.uni-hd.de
PhD Position: Computational Neuroscience, Georgia State University
Ph.D. position in computational neuroscience at Georgia State University,
Department of Mathematics and Statistics, Atlanta.
Earliest starting date: January 2009.
A new Ph.D. position in computational modeling and applied mathematics is
being funded by the NSF through the Emerging Models and Technologies program
(www.nsf.gov/pubs/2008/nsf08517/nsf08517.htm), as a grant awarded in the area
of Biological Systems Science and Engineering (BSSE). The Ph.D. student will
work in diverse topics associated with "complexity" in the life sciences,
and will explore the impact of computer-assisted data-driven modeling
on understanding of complex biophysical processes. The student will be
trained in a variety of techniques and have the opportunity to attend
national conferences. Georgia State University has a strong commitment
to computational neuroscience, and has an active community involved in
collaborative work between mathematics, physics, computer science and
neuroscience which extends to colleagues at Emory University and Georgia
Institute of Technology.
The project draws on a wide set of academic backgrounds, including
mathematics, computer science, biology, neuroscience, and physics. A
successful applicant will be highly motivated and have demonstrated
interests across more than one of these academic areas, but must be strong
in applied mathematics. Applicants must meet the basic requirements of the
Ph.D. program in the Department of Mathematics and Statistics, as described
at www2.gsu.edu/~wwwmat/students/grad/ph_d.html, and will be expected to
follow the Bioinformatics concentration. Previous experience in applied
mathematics research and scientific programming is desirable.
The application should include a statement of research interest, CV,
recent GRE scores and a transcript. Applicants from non-English speaking
countries must achieve a satisfactory score on the Test of English as a
Foreign Language (TOEFL). If available, also include a copy of the Master
thesis, published articles or similar relevant materials. Three letters
of recommendation should be sent under separate cover. The Ph.D. position
is for three years, but may be extended to a maximum of five years, and
will include teaching assistant duties at a level of at most 20%. Stipend
will be $18k-$22k depending on qualifications. Application details and
materials can be found at http://www.cas.gsu.edu/grad_admission.html
Further information about the department is available at
www2.gsu.edu/~wwwmat/index.html. The abstract for the project is available
at http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0829742, and
informal inquiries can be sent to rclewley[AT]gsu[DOT]edu.
Postdoc & PhD Positions: Computational Systems Biology, ETH Zurich
Post-Doc and PhD positions: Computational Systems Biology, ETH Zurich
Applications are invited for a PhD studentship and a Post-Doc position,
within the Computational Biology Group at the Department of Biosystems
Science and Engineering of ETH Zurich.
The group focuses on the development of detailed, predictive models
for cellular signaling networks with a view to develop a comprehensive
understanding of the dynamics and evolution of cellular signaling. All
projects are carried out in close collaboration with experimental groups
so that quantitative data is available and model predictions can be tested
in experiments.
Applicants should have a strong background in mathematical and computational
modeling, and demonstrated experience in nonlinear dynamics and numerical
calculations. PhD candidates should hold or expect to obtain a degree in a
numerate discipline (e.g. mathematics, computational science, computational
biology, physics, biotechnology, chemical or bio-engineering, or related
areas). Candidates are expected to engage in interdisciplinary research
and to foster in-house collaborations with biologists and bioengineers.
The Department of Biosystems Science and Engineering of ETH Zurich is an
integral part of SystemX.ch, the Swiss initiative in Systems Biology. It
is located in Basel, a European hotspot for biomedical research, in close
proximity of the Biozentrum of the University of Basel, the Friedrich
Miescher Institute for Biomedical Research, and the pharmaceutical and
biotech industry. ETH Zurich is a major research university, offering an
excellent environment for innovative and collaborative research across
disciplines.
Please send the usual application material, including at least two
references, as a single PDF file to dagmar.iber@bsse.ethz.ch (preferred),
or via surface mail to:
Prof. Dr. Dr. Dagmar Iber
ETH Zurich
D-BSSE
Mattenstrasse 26
4058 Basel
Switzerland
For further information please visit our web page at
http://www.dbsse.ethz.ch/research/group_iber
2 PhD Positions: Understand & Model Biomineralization, U Amsterdam
Within the Marie Curie Initial Training Network "Biomineralization:
understanding of basic mechanisms for the design of novel strategies
in nanobiotechnology (BIOMINTEC)" there are currently a number of PhD
positions available. The duration of each PhD position is 36 months. Being
part of a mobility program, PhD candidates will perform their work in two
of the partner institutions (18 months each, in two different countries)
which can not be the home country of the candidate. The University of
Amsterdam (The Informatics Institute) is one of the partners in the
BIOMINTEC project and involved in 2 PhD positions.
The first PhD (ESR2) will work on sponges and the title of the project is:
"Fractal mechanism of silicatein self-assembly and biosilicification
(Experimental studies and Modelling studies". The second PhD (ESR8)
will work on calcification, e.g., in scleractinian corals and molluscs,
the title of this project is "Biocalcification: Characterization of
crystal-shaping proteins of the molluscan shell and modelling gene
regulation". Candidates should have a master's degree (or equivalent)
in scientific computing or computational science, (computational) physics,
chemistry, molecular biology or a comparable expertise.
Details about both PhD positions are available at:
ESR2 (vacancy number 08-1057)
http://www.uva.nl/vacatures/vacatures.cfm/DDCC5833-1321-B0BE-A48DDAB8511F067D
ESR8 (vacancy number 08-1058)
http://www.uva.nl/vacatures/vacatures.cfm/DDDEE430-1321-B0BE-A4E8BE7F3E21A7E6
PhD Studentship: Theoretical marine ecology and biocomplexity
Theoretical marine ecology and biocomplexity: investigating the structure
and dynamics of marine-community interaction networks.
This PhD project in mathematical biology is part of a larger effort to
strengthen the theoretical basis of the 'Ecosystem Approach to Fisheries
Management' (EAFM), fully funded by the Irish Government (under the Beaufort
Marine Award Scheme). The prestigious 'Beaufort Research Scholarship'
will be based in the School of Biological Sciences at Queens University
Belfast in Northern Ireland; it will run for three years fully funded,
and is available without restrictions on nationality.
The aim is to develop recent theoretical advances (regarding food-webs
as dynamic, complex interaction-networks) into management-relevant
insights. This will involve adapting existing numerical models into forms
directly comparable with real marine ecosystems and generalising model
results by mathematical analyses to find the mechanisms determining system
structure and dynamics (we can be flexible about the ratio of analysis /
simulation types of study, to suite the individual student).
The 'scholar' will receive extensive training in marine ecology, food-web
theory and mathematical modelling and will benefit form our dedicated
high-performance computing facilities and collaborations with fisheries
scientists and ecologists in Denmark, Republic of Ireland and UK.
Suitable students will have a 1st class or 2.1 degree in a
mathematically-based discipline (e.g. physics) with excellent analytic
skills, an interest in stochastic methods and/or complex systems,
experience in scientific programming (e.g. Matlab) and a desire to use
maths and theory for practical ecological problems.
Applicants should send a letter outlining why they are suitable for the post,
along with a current CV to Dr Keith Farnsworth (k.farnsworth@qub.ac.uk)
by the 26th November 2008. We would hope the student can start early in,
or before 2009.
A cross-disciplinary research team studying the spread of Chronic Wasting
Disease (CWD) in the Canadian Prairies is seeking a postdoctoral fellow
to take the lead in creating mathematical models to inform understanding
as to how intervention strategies will affect spread of CWD and cervid
population dynamics. The modeler will work closely with established
researchers on infectious disease in the School of Public Health and
Department of Computer Science, and with researchers and students in the
Western College of Veterinary Medicine conducting an ongoing field studies
on the movement and health status of deer populations, investigating the
impact of intervention strategies and vaccination.
Applicants should have earned a doctoral degree in mathematics, Computer
Science, physics or engineering or other technical discipline, have past
experience in building or analyzing models of infectious disease spread,
familiarity with applied mathematics (including differential equations,
probability theory, and some knowledge of statistics), exposure to
programming and debugging in one or more object-oriented programming
languages, and an interest in applications of modeling to animal and
veterinary health. Exposure to epidemiology, and previous work with
ecological modeling or individual-based simulation models is desirable but
not required. Funding is currently available for a 1-year postdoctoral
positional position, with possible extension to 2 years, starting
immediately.
Applications will be considered until February 15, 2009.
Interested applicants should write to Dr. Cheryl Waldner at
cheryl.waldner@usask.ca to apply and for further information.
Postdoc Positions: Neurotechnology in Freiburg, Germany
Neurotechnology is a rapidly growing field of research, thriving to repair,
replace or support physical functions affected by nervous system diseases
by technical means.
At the Bernstein Focus for Neurotechnology (BFNT) we exploit electrical
and chemical signals recorded in the brain to control external or implanted
devices.
The BFNT efforts are organized in projects on fundamental neurotechnological
research, the development of new techniques, clinical testing and
neuroethical considerations.
Postdoc-Positions are available in the following projects:
- Co-Adaptivity of brain and computer: Interaction of two learning signals
(Project A3)
- Defined stimulus-response functions in active networks (Project A5)
- Improving microelectrodes for single cell recordings in the human brain
(Project B3)
- NEURONLINE - System for the on-site/on-line monitoring of neuronal
population activity (Project B4)
Postdoctoral Fellow in Mathematics of Collective Behaviour
Schools of Biological Sciences and of Mathematics and Statistics
Faculty of Science
Reference No. 145106
The Faculty of Science is a leading provider of education across the spectrum
of the sciences. It offers a diverse range of specialisations, research
programs and facilities, and an extensive liaison with international
institutions. The Schools of Biological Sciences and Mathematics and
Statistics are a core part of the Faculty dedicated to producing world-class
research teaching and research programs in Biology and Mathematics.
The Schools are currently seeking a results-driven Postdoctoral Fellow
to conduct research into a project that will investigate how different
nest-site requirements have shaped collective decision-making processes in
two species of honey bee. In recent years nest-site selection by colonies of
insects has served as a model system to study the speed-accuracy trade-off
in decentralised decision-making systems.
This project will investigate the speed-accuracy trade-off in the cavity
nesting western hive bee Apis mellifera and the open nesting red dwarf
bee A. florea. Both regularly need to select a new nest site and both
need to come to a decision quickly while selecting the most appropriate
site. However, due to their fundamentally different nest site requirements
(a cavity in a tree versus a shaded branch) natural selection has shaped
their respective speed-accuracy trade-offs in different ways to ensure
the best possible outcome for each species.
For more information about the position please visit:
http://positions.usyd.edu.au/steam145106email
For specific information about the position, please contact Associate
Professor Madeleine Beekman by email: mbeekman@bio.usyd.edu.au or Dr. Mary
Myerscough by email: m.myerscough@maths.usyd.edu.au
General enquiries can be directed to Fabrice Noel (+61 2) 9036 7295 or
by email: f.noel@usyd.edu.au
Topic:
Pathway-based tumour characterisation by alignment against cell panels
along multiple molecular dimensions.
Research:
Astra Zeneca Oncology has constructed large cell panels to serve as in
vitro models for drug response. These cell panels have been extensively
characterized by mutation analysis, mRNA expression, aCGH, response
to a wide variety of drugs, micro-RNA expression and phosphoprotein
characterization. In parallel, the same measurements are being performed
on a collection of colorectal samples. In this project two aims are
pursued. First, a comparative analysis will be performed between the cell
line data and the tumor data to determine the multi-dimensional molecular
states spanned by the cell lines and whether these states faithfully
recapitulate the space spanned by a representative and clinically relevant
selection of tumor samples. Guided by this mapping and by following a
pathway-based approach, integrative modeling will be applied on the cell
line panel data to construct models predictive of resistance.
Job description:
The successful candidate will be responsible for the bioinformatics analysis
of the cell line and tissue data. More specifically, these tasks include
1) constructing a comprehensive gene list of the PI3K and ERK network; 2)
Molecular characterisation of the colorectal cell panel and tumour samples
through integrative analysis of the various data sources within the space
spanned by the identified network genes and 3) Pathway-based alignment
of cell panel to tumours to determine the extent to which the cell panel
recapitulates the heterogeneity in the tissue set.
Location:
The position is embedded within the Bioinformatics and statistics group lead
by Dr Lodewyk Wessels (http://bioinformatics.nki.nl) at the Netherlands
Cancer Institute, Amsterdam and the Oncology Informatics group, Discovery
Medicine, Astra Zeneca, Alderley Park, UK lead by Dr Tim French. We plan
to have regular meetings, and the postdoc will also spend time at both
locations.
Requirements:
Candidates should fulfill the following criteria.
- MSc or PhD in one of the following areas: bioinformatics, engineering,
computer science, statistics, physics, biotechnology, or biology.
- Knowledge of fundamental aspects of cancer biology, especially signalling
pathways.
- Knowledge of fundamental aspects of computer science (algorithms and
data structures, programming languages).
- Knowledge or experience of informatics.
- Knowledge of statistics, artificial intelligence or bioinformatics is
highly desirable.
Conditions of Employment:
The successful candidate will be employed by the Netherlands Cancer
Institute. The employment conditions follow general employment rules
as laid down in the 'CAO' for hospitals. The salary will be determined
depending on education and experience.
Contact and Applications:
Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels@nki.nl or
Dr Tim French Discovery Medicine, Cancer Bioscience, tel. +44 1625-519922
or e-mail: Tim.French@AstraZeneca.com. Applicants should send a CV, list
of publications and the names and addresses of at least two persons that
can be approached to obtain further information.
Website:
http://bioinformatics.nki.nl
Closing date:
30 January 2009
Postdoc Position: Large-Scale Ecosystem Functioning, Stellenbosch U
Understanding the effects of climate change and land use on ecosystem
functioning is a challenging question addressed by the team of
environmental and biological scientists on the BIOTA-AFRICA project
(www.biota-africa.org). As part of the BIOTA-Southern Africa (Phase
III) project, this post-doctoral fellowship will entail analyzing the
long-term data collated over the past 8 years from 35 observatories and
800 sub-sites across the southern African transect (from Cape Point, South
Africa, to Caprivi, Namibia). Specific questions involved in the project
include (1) relationships between abiotic factors (e.g. soil nutrient
content and habitat heterogeneity) with ecosystem structure and community
composition (e.g. woody cover and species turnover); (2) the influence
of land use on soil respiration and therefore ecosystem productivity;
(3) spatial and scaling patterns of species and soil type distributions;
(4) spatiotemporal modelling of the plant-soil interactions under the
current climate change regime.
Preference will be given to candidates with strong skills in large-scale
data analysis using GIS and statistical multivariate methods. The candidates
will also be able to publish the output in peer-reviewed journals. The
German Federal Ministry of Education and Research is offering a commencing
fellowship of an amount of R120,000 for 2009, and the position will be based
in Stellenbosch University, South Africa. In addition to the fellowship,
the successful candidate will also be provided with a laptop computer and
other research equipment. Subsistence and transport costs during research
expeditions will be covered. The post-doc will work under the supervision
of Dr. Cang Hui (DST-NRF Centre of Excellence for Invasion Biology) and
Dr. Anthony J. Mills (Department of Soil Science).
A detailed CV, project outline (one-page maximum) and one/two publication
reprints, together with contact details of two references, should be sent
by email to chui@sun.ac.za and mills@sun.ac.za by the end of February
2009. The candidate should be able to start in the first quarter of 2009.
Postdoctoral Research Assistant: University of Oxford
Postdoctoral Research Assistant at the Control Engineering - Systems
Biology Interface
Department of Engineering Science, University of Oxford.
Applications are invited for the above post which is available for up to
8 months in the Department of Engineering Science at the University of
Oxford. This post will involve working in Systems Biology from a Control
Engineering perspective. The position suits a theoretician with a control
engineering, mathematical or computer science background. The aim is to
use control engineering tools to understand the design principles and
robustness properties of different feedback mechanisms in the chemotaxis
network of the bacterium R. sphaeroides. This signal transduction network
has an interesting feedback structure which can be understood from a control
engineering perspective. The successful candidate will become part of the
growing and flourishing inter-disciplinary environment in Oxford working in
Systems Biology. The work will be partly mathematical, partly computational
and will involve close interaction with researchers in Biochemistry.
You should have a good first degree and have completed or are about to
complete a doctorate in Engineering, Mathematics, Computer Science or a
related subject. A good publication record in internationally peer-reviewed
journals commensurate with stage of career is expected, and evidence of
previous research experience in Systems Biology is an advantage. The ability
to carry out independent research and to develop mathematical algorithms
and simulations in MATLAB is required. Experience of working in a team, a
demonstrated ability to write clear, correct, concise English and make clear,
well illustrated presentations of scientific material are all desirable.
The starting salary will be in Grade 7 28839 - 29704.
Further particulars (http://www.eng.ox.ac.uk/jobs/fp/DF08075fps.pdf)
and personal details form
(http://www.eng.ox.ac.uk/jobs/fp/personal_details_form.pdf)
may also be obtained by telephoning 01865 273013 or by email to
administrator@eng.ox.ac.uk to whom written applications should be made
enclosing a curriculum vitae and a fully completed personal details
form. Your letter should explain your interest in and relevant experience
for this job.
Please quote DF080075 in all correspondence.
The closing date for applications is noon 6th January 2009.
The University is committed to equality and valuing diversity
(http://www.admin.ox.ac.uk/eop/policy/cop.shtml).
UNIVERSITY OF DUNDEE
DIVISION OF Molecular and Environmental Microbiology
COLLEGE OF LIFE SCIENCES
Postdoctoral Position
For Mathematical Modelling of Cell Differentiation during Biofilm Formation
Grade 7 (28,839 - 35,469)
The bacterium Bacillus subtilis is a single celled Gram-positive soil
bacterium that can exist as part of an integrated, multicellular community
called a biofilm. Biofilm formation is a complex process that depends on cell
fate differentiation that occurs in spatio-temporal manner. Biofilms are
important in all sectors of our economy with examples ranging from human
health - they form the basis of chronic infections, to bioremediation ?
they are required for the effective treatment of sewage. B. subtilis has
advanced genetic and molecular biology tools ideal for studying the complex
development of biofilm communities.
The appointed postdoctoral scientist will be part of an interdisciplinary
team and will develop a multi-scale modelling approach to address, at the
systems biology level, how biofilm formation is controlled. This will lead
to a better understanding of microbial community dynamics with longer term
impact on applications to health and industry.
The overall aim of this work is to better understand how perturbations to
gene transcription pathways lead to changes in the macro-scale organisation
and function of the biofilm. Specific objectives of the proposed work are:
i) to model the interplay between key components of the gene transcription
network, using a combination of deterministic (ordinary differential
equations and dynamical systems theory) and stochastic techniques; ii)
model large scale sub-population interactions at the biofilm-scale using
partial differential equations. These modelling frameworks will ultimately
be used to inform the development of novel, multi-scale modelling approach
for the study of the collective behaviour of large numbers of distinct
(yet interacting) individual bacteria. The modelling framework will be
developed in tandem with state-of-the-art experimental techniques for
studying bacterial cell fate differentiation.
This project is funded as an initiation to pump-prime interdisciplinary
collaborations in Life Sciences at Dundee. It is planned to develop the
ideas formulated over this time period to establish a longer term programme
of funded research and suitable candidates would be well-placed to be part
of this longer term plan.
Candidates should have, or be about to obtain, a PhD at the interface of
mathematics and biology. The post is available for up to 12 months in the
first instance and is available immediately.
Informal enquiries can be made to Dr Fordyce Davidson (Division of
Mathematics) or Dr Nicola Stanley-Wall (College of Life Sciences), e-mail:
fdavidso@maths.dundee.ac.uk; n.r.stanleywall@dundee.ac.uk (applications
sent to either of these addresses alone will not be considered ? see below).
Applications in the form of a CV and covering letter, including the names
and addresses of 3 referees, should be sent to HR-LifeSciences@dundee.ac.uk
quoting LS/2505. Alternatively, please send 2 hard copies of your CV and
covering letter to Human Resources, College of Life Sciences, MSI/WTB/JBC
Complex, University of Dundee, DD1 5EH.
Applicants will only be contacted if invited for interview.
Closing Date: 16 January 2009
Postdoc Position: Centre for Plant Integrative Biology, Nottingham
School of Biosciences - Centre for Plant Integrative Biology
Postdoctoral Research Fellow (Applied Mathematician)
A five year programme within the Centre for Plant Integrative Biology
(CPIB) at the University of Nottingham aims to create a virtual root which
will serve as an exemplar for using Integrative Systems Biology to model
multi-cellular systems. CPIB is jointly funded by the BBSRC and EPSRC as
part of their Systems Biology Initiative to establish a number of Centres
for Integrative Systems Biology. This project brings together biologists,
engineers, mathematicians and computer scientists to generate new data,
biological resources and virtual models that will aid understanding of
how plant roots grow and develop.
Applications are invited for an applied mathematician on the above Virtual
Root project to undertake deterministic (differential-equation based)
modelling of gene and signalling networks involved in lateral root emergence.
Other duties include publication of this research in peer-reviewed journals
and presentations at national and international conferences.
Candidates must have a PhD in applied mathematics or a related area.
Research experience in mathematical modelling is essential and experience
of multidisciplinary research is desirable. This post will require the
person appointed to be able to work independently and as part of a team,
to be flexible and to have good communication and interpersonal skills.
Salary will be within the range 27,183 - 35,469 per annum, depending on
qualifications and experience (salary can progress to 38,757 per annum,
subject to performance). This post will be offered on a fixed-term contract
for a period of two years.
Informal enquiries may be addressed to Professor J King, School of
Mathematical Sciences, Email: John.King@Nottingham.ac.uk. For general
enquiries regarding CPIB contact Professor C Hodgman, School of Biosciences,
Email: Charlie.Hodgman@Nottingham.ac.uk. Further details are available at:
http://jobs.nottingham.ac.uk/.
Candidates should send a detailed CV, together with the names and addresses
of two referees, to Mrs M Axinte, School of Biosciences, The University
of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire,
LE12 5RD. Email: Mirela.Axinte@Nottingham.ac.uk.
Please quote ref. SCI/543X1. Closing date: 21 January 2009.
Postdoc Position: OCCAM, Mathematical Institute, Oxford
POST-DOCTORAL RESEARCH POSITION IN MATHEMATICAL MODELLING OF ION CHANNELS
Oxford Centre for Collaborative Applied Mathematics (OCCAM)
Mathematical Institute, University of Oxford
Closing Date: 9 January 2009
Appointment Term: 2 years
We invite applications for a Postdoctoral research position, funded by
the King Abdullah University of Science and Technology Global Research
Partnership [KAUST GRP], to work with Prof. S.J. Chapman and Dr R. Erban at
the newly established Oxford Centre for Collaborative Applied Mathematics
(OCCAM). This position is available from 1 April 2009.
OCCAM has been established with substantial funding from the KAUST GRP.
The Centre, which is part of the Mathematical Institute, is allied to a
global network of mathematicians. Aiming to meet the ever-increasing global
demand for quantitative understanding of complex scientific phenomena,
OCCAM has been built on the strength of four pre-existing groups of applied
and computational mathematicians working in Oxford: the Oxford Centre for
Industrial and Applied Mathematics, the Centre for Mathematical Biology,
the Numerical Analysis Group and the Computational Biology Group. It has
a symbiotic relationship with other scientific communities which have a
need for problem-solving mathematics both within the University of Oxford
and beyond. Over the first five years the centre will employ 40 new staff
and students.
Further details about the position, including the project description and
selection criteria, can be obtained at http://www.maths.ox.ac.uk/node/8183
Other current vacancies at OCCAM can be found at:
http://www.maths.ox.ac.uk/groups/occam/vacancies
Postdoc: Analysis of Signaling Networks, U of Luxembourg
Post Doc in Systems Biology (M/F)
Application End : 28 February 2009
The University of Luxembourg has a vacancy in its Faculty of Science,
Technology and Communication for a
Post Doc in Systems Biology
Fixed term contract (?Assistant-Chercheur?) 2 years, renewable
Reference: F1-080013
Research area: Analysis of Signaling Networks
Within the systems biology group mathematical models (mainly ODE based)
of different mammalian signaling pathways are developed. One main focus
currently lays on pro- and anti-apoptotic signaling. In addition projects
concentrating on JAK/STAT and PGDFR signaling will further characterize
their relevance in inflammation related diseases and cancer. Regarding
the analysis of the systemic characteristics of the underlying networks,
a key position of an ?Assistant-Chercheur? is open for application. This
theory-trained person shall provide a profound support of the necessary
analyses, e.g. focusing on global sensitivities, identifiability, robustness,
modularity and others. Based on the analyses results future experimental
strategies shall be suggested in close collaboration with the experimental
partners.
Tasks:
* Mainly research activities in the field of Systems Biology
* Teaching within the Master in Integrated Systems Biology
Profile:
* PhD degree in Systems Biology, Engineering, Life Sciences, (Bio-)
Informatics or comparable
* Experience in the analysis of signaling networks is desirable
Offer
* Opportunity to participate in a young and dynamic University
* International environment
* Competitive remuneration
For further information, please contact:
Prof. Thomas Sauter
University of Luxembourg
Life Sciences Research Unit
162a, avenue de la Faiencerie
L-1511 Luxembourg
Interested candidates are asked to send their full application (letter of
motivation, detailed CV, copies of diploma, photo) until February 28th,
2009 by e-mail to thomas.sauter@uni.lu .
The University of Luxembourg is an equal opportunity employer.
PhD/Postdoc position: Comp. Biomechanics, U. Stuttgart, Germany
Opening for a PhD/Post-Doc position in Skeletal Muscle Modeling with
Applications to Lumbar Spine Mechanics
The PhD student/Post-Doc is supposed to work on a project focusing on
developing novel computational techniques to model skeletal muscles
mechanics. The goal is to overcome the computational challenge of
realistically modeling lumbar spine muscle mechanics while taking into
account the influence of a large number of muscles involved in complex
upper body movements. The skeletal muscles are modeled using the Finite
Element method in three dimensions and principles of nonlinear continuum
mechanics. For this purpose, a good background in computational continuum
mechanics, the Finite Element Method, and some programming skills are
desirable.
The PhD position is within the designated salary bracket TV-L 13 and has
a limited tenure of three years with a possible extension. The PhD student
will be part of the Graduate School Simulation Technology of the Cluster of
Excellence EXC 310 Simulation Technology (SimTech) at Universitaet Stuttgart
Applications with the usual documents (CV, degree certificates, references,
publication list, letter of motivation) should be sent directly to
Jun.-Prof. Oliver Roehrle (roehrle (_AT) simtech.uni-stuttgart.de),
Institute of Applied Mechanics (CE), Pfaffenwaldring 7, 70569 Stuttgart,
Germany. Applications will be accepted until the position is filled.
Research Opportunities in High Performance Algorithms for Structural
Systems Biology
We have vacancies for two postdoctoral researchers, one graduate software
engineer, and one PhD student to work on exciting new projects to develop
high performance algorithms and knowledge-based approaches to advance the
state of the art in protein-protein docking, protein shape recognition,
and high throughput 3D virtual drug screening.
Location: LORIA, Nancy, France
Duration: Two years in the first instance
Starting date: January 1st 2009 (negotiable)
Remuneration: Standard INRIA rates
Candidates for the postdoc positions must have a PhD in one of the
mathematical or physical sciences, and must have strong and demonstrable
abilities and experience in programming using C or C++ on Unix/Linux or
Windows systems. Experience of scripting languages such as Python and
PHP would also be desirable. Experience of parallel programming, high
performance computing, and computer graphics would be desirable but is not
essential. Preference will be given to candidates with a strong interest or
background in structural biology, crystallography, computational chemistry,
molecular modelling, or related areas. Candidates should have a proven
research track record, demonstrated by publications in peer-reviewed
journals in one or more of the above areas.
Candidates for the Software Engineering position must have a good Honours or
Masters degree in computing science or one of the mathematical or physical
sciences, and must have very good programming skills using C or C++.
Preference will be given to candidates with an interest or background in
structural biology, molecular modelling, or related areas. If progress is
good, the successful applicant will be encouraged to study for a PhD.
Candidates for the PhD Studentship should be qualified to Masters level
or equivalent in computing science or one of the physical or biological
sciences, and must have experience of programming using a procedural
language such as C or C++. Preference will be given to candidates with
a strong interest in the use of knowledge-based approaches and computer
graphics to help advance the state of the art in protein-protein docking.
This position could be filled initially by a student with a good Honours
degree who would register as a Masters intern before proceeding to undertake
a PhD.
Please send a detailed CV, which includes the names of two academic referees,
along with a brief statement of your research interests and motivation to:
Dave Ritchie: dave.ritchie@loria.fr cc: d.w.ritchie@abdn.ac.uk
Please indicate which post(s) you are applying for. Closing date: 31
December 2008.
Postdoc: Infectious Disease Modeler, THETA, U Toronto & U Guelph
Infectious Disease Modeling and Health Economic Evaluation of
Pandemic Influenza Mitigation Strategies
A position for a postdoctoral fellow/infectious disease modeler is
available at THETA, the Toronto Health Economics and Technology Assessment
Collaborative - University of Toronto and the University of Guelph. The
postdoctoral fellow/infectious disease modeler will collaborate with
project investigators to address questions in the cost-effectiveness of
preventive and therapeutic pandemic influenza mitigation strategies,
including vaccination, targeted antiviral prophylaxis, treatment and
social distancing measures. The postdoctoral fellow/infectious disease
modeler will primarily develop, parameterize, and simulate an agent-based
model of influenza transmission that projects clinical effectiveness
and cost-effectiveness of mitigation strategies. The postdoctoral
fellow/infectious disease modeler will also co-author manuscripts and
interface with graduate students working on the project.
Major duties: In collaboration with project investigators, the postdoctoral
fellow/infectious disease modeler will
1. Assist in the development of the model under the supervision of the
study steering committee;
2. Assist in performing compiling data values for model parameters;
3. Assist in calibration and validation of the model
4. Assist in the design of the agent-based model;
5. Implement the agent-based model
6. Implement a stand-alone and web version of the model
7. Contribute to writing of project reports and manuscripts for publication.
Requirements: A master's (infectious disease modeler) or doctoral
degree (postdoctoral fellow) in a related quantitative field (such as
mathematics, computer science, statistics, epidemiology, biology, health
economics/decision science) with enthusiasm for applying these skills to
real-world, policy-relevant problems is required. Demonstrated skill for
programming and computing ability at a high level is required, and knowledge
of C, Fortran, Java, R, Netlogo, or AnyLogic is essential. Experience in
working with complex mathematical/agent-based models is highly desirable,
including some or all of: model construction, debugging, simulation,
validation and data collection, and policy applications. Excellent
organizational, written and verbal skills are essential to success in this
position, as is the ability to work independently.
We offer a competitive salary, appropriate to the level of qualifications
and experience required for this position. The position may be structured
as a one-year full-time or two-year part-time position, with job duties
to be specified accordingly.
To express interest or apply for this position, please send a cover letter,
CV, and the names and contact information for two referees to Beate Sander
(beate.sander@theta.utoronto.ca). Review of applications will begin 5
January 2009 and continue until the position is filled.
Postdoc Position: Odum School of Ecology, University of Georgia
POSTDOCTORAL RESEARCH ASSOCIATE
Odum School of Ecology, University of Georgia, USA
Applications are invited for a postdoctoral research fellowship in
Mathematical Epidemiology. The position will involve developing new
mathematical models and the analysis of data with a view to understanding
the persistence, transmission dynamics and evolution of whooping cough in
the US and UK.
A PhD in statistics, applied mathematics or a highly quantitative field
is essential. Previous experience in the analysis of ecological or
epidemiological systems would be desirable.
The position is for 2 years in the first instance, with a salary in the
range of $35-40,000 per year (depending on experience), plus fringe benefits.
For further information about these projects, contact Pej Rohani +1 706
542 9249, e-mail: rohani@uga.edu.
Applicants should send a detailed CV, together with a brief statement
of research interests and three references to Pej Rohani, Odum School of
Ecology, University of Georgia, Athens GA 30602. Electronic applications
are encouraged.
Review of applications will start on Jan 15 and will continue until the
post has been filled.
Postdoctoral Research Assistant and Career Development Fellow
Postdoctoral Research Assistant and Career Development Fellow Centre for
Mathematical Biology, University of Oxford and St Hugh's College, Oxford
Project: Multiscale modelling of cellular oscillators: applications to
vertebrate segmentation and hair follicle cycling.
The Centre for Mathematical Biology (CMB) is looking to recruit a post-
doctoral research assistant to work in the area of mathematical and
computational modelling of coupled oscillators in biological systems. The
position will be held in association with a Career Development Fellowship
at St Hugh's College. More specifically, the PDRA will work alongside Dr
Ruth Baker and Professor Philip Maini (CMB) and Professor Kevin Burrage
(University of Oxford Computing Laboratory) to develop multi-scale models
to describe the dynamics two paradigms of coupled biological oscillators:
the molecular clock involved in segmentation of the vertebrate body axis
and the hair follicle cycle. In either case, models consisting of systems
of non-linear differential equations will be developed on the level of the
individual oscillator, in tandem with phenomenological models to describe
events on the tissue level. Different types of oscillator coupling, the role
of noise and the integration of individual-level models into population-
level models will be addressed, and there may also be the opportunity to
visit experimental collaborators.
Candidates should have extensive experience in the following areas:
mathematical modelling and simulation of complex biological systems;
applied scientific computing; modelling coupled multi-scale systems. This
role would suit individuals who have a first degree in mathematics and
a PhD in mathematical modelling, show evidence of independent research,
enjoy working in a team and have a meticulous approach to their work. The
post-holder will be expected to carry out up to four hours teaching per
week for St Hugh's College during term-time.
Further particulars may be obtained from vacancies@maths.ox.ac.uk and at
http://www.maths.ox.ac.uk/notices/vacancies/.
If you have any questions or would like to discuss this position then
please do not hesitate to contact me via e-mail (ruth.baker@maths.ox.ac.uk).
Postdoc: Computational Neuroscience, LSUHSC Neuroscience Center
An NIH-funded postdoctoral position in computational neuroscience
is immediately available at the LSUHSC Neuroscience Center in New
Orleans. The project consists of modeling the generation of the firing
pattern in midbrain dopaminergic neurons in close collaboration with
electrophysiologists using patch clamp and dynamic clamp techniques.
The lab has an established research program in oscillations and synchrony,
and the dopaminergic neuron will be modeled as a system of coupled
oscillators.
Applicants should be fluent in spoken and written English and have a
PhD or equivalent in mathematics, engineering, physics, neuroscience or
a related field. Previous experience in some of the following areas is
recommended: the NEURON simulation package, C programming, Unix, and linear
and nonlinear systems theory, as is the ability and desire to acquire the
remaining skills. Candidates who are in a position to join the lab within
the next few months are particularly encouraged to apply.
Please send CV to Dr. Carmen Canavier at ccanav@lsuhsc.edu . LSUHSC/NO
is AA/EOE Employer.
Post Doctoral Position: Integrated Mathematical Oncology
Applications are sought for the position of post-doctoral research fellow
to work on an exciting inter-disciplinary research project concerning
the modeling of Cancer progression and development. We seek a talented
individual with a PhD and background in applied mathematics, physics or
a computational discipline to work in the unique research environment
of the Integrated Mathematical Oncology (IMO) division. The division
combines mathematicians, computer scientists, and imaging specialists as
well as clinical and experimental oncologists focused on developing novel
approaches for the treatment and understanding of cancer.
The successful candidate will have experience in modeling biological
systems, with a preference for medical applications using a variety of
modeling techniques. As well as demonstrated creativity, high motivation,
good communication skills and importantly, experience in developing/writing
publications in peer reviewed high impact scientific journals. They
should possess the ability to work independently and within the research
group. A good understanding of biology and the desire to work closely
with experimentalists and clinicians is also necessary. Preference will
be given to candidates with the ability to program (C/C++/Java/Matlab),
visualise and analyse numerical/experimental data.
The IMO is housed within the H. Lee Moffitt Comprehensive Cancer Center
which is a modern facility on the University of South Florida Campus that
conducts research on various aspects of Cancer Biology with emphasis on
translational research. Research environment includes state of the art
modern core facilities and access to experimental and clinical data.
Please navigate to the IMO website (http://www.moffitt.org/imo) and click on
Jobs for further information on how to apply. If you have any questions or
would like to discuss this position then please do not hesitate to contact
me via email (alexander.anderson@moffitt.org)
POSTDOCTORAL POSITION IN MATHEMATICAL / COMPUTATIONAL BIOLOGY University
of New South Wales, Sydney, Australia
The Complex Systems in Biology Group at the University of new South Wales
is seeking applicants for two positions as post-doctoral fellow. The group
works in INFECTION and IMMUNITY, and the projects offer a variety of areas
from ODE modelling, simulation, biostatistics, bioinformatics etc. The
applicant should have a PhD in mathematics / physics / computer science /
engineering or related discipline.
The Complex Systems in Biology Group is within the Faculty of Medicine,
and currently comprises two post-docs, four PhD students, and two research
assistants. It works closely with experimental collaborators to analyse and
model experimental data in infection and immunity. The group has a strong
history of retraining physicists / mathematicians to work in mathematical
biology, and welcomes applicants with no background in biology if they have
a strong publication record in their own discipline. The group currently
holds seven grants and has published 14 papers in 2008, and is looking for
enthusiastic post-docs to join the team. The University is well situated
close to the city and within 1 km of the beaches. The positions are
available to 31 December 2010, pending further funding. Further details
of the group are available at: http://www.cvr.net.au/research/complex.htm
Full details of the position will be published on the UNSW website
http://www.unsw.edu.au/ , and formal applications must be through this site.
Postdoc Opportunity: Pacific Biological Station, British Columbia
I'm posting this for a colleague (though I'm also interested in helping
develop the models).
Genomics Tools for Fisheries Management
Applications are invited for an exciting, multidisciplinary postdoctoral
fellowship to develop novel, quantitative approaches for integrating
genomics, physiology, environmental and fisheries data into Pacific salmon
management models.
The successful candidate must hold a PhD in quantitative fisheries or
ecological modeling, and have a strong background in parameter estimation,
Bayesian statistics, and programming with ADMB, R, or an equivalent
language. Applicants should be creative and demonstrate how their previous
research has helped develop or refine conceptual or applied fisheries
management tools. In addition, valuable assets include previous experience
with stock assessment of Pacific salmon; knowledge of epidemiology, salmon
life histories, fish physiology, oceanography, climate change impacts
in the northeast Pacific, or the socio-economic dimensions of fisheries
management; and experience with bioinformatics or database management.
The researcher must have a demonstrated ability to work effectively within a
multidisciplinary team, and communicate their research through publications
and oral presentations to audiences with a quantitative fisheries or ecology
background. This Genome BC-funded project "Genomics Tools for Fisheries
Management"
http://www.genomebc.ca/genomics_programs/research_projects/agip/fisheries_management.htm
is led by a highly collaborative team based at the Pacific Biological Station
(Kristi-Miller Saunders, Janelle Curtis) and the University of British
Columbia (Anthony Farrell, Scott Hinch, Paul Pavlidis, Paul Wood). Our
team also works closely with colleagues at the Pacific Salmon Commission,
Fisheries and Oceans Canada (DFO), Carleton University and the National
Oceanic and Atmospheric Administration (NOAA). Responsibilities of the
postdoctoral fellow will include developing and evaluating novel approaches
for incorporating genomics information into pre-season forecast and in-season
management adjustment models for wild Pacific salmon stocks. The postdoctoral
fellow will have opportunities to work closely with several other
postdoctoral fellows and PhD students working on the genomics, physiology,
bioinformatics, and social sciences aspects of this 3-year project. For
some background on this long-term collaborative research program, see
Cooke SJ, Hinch SG, Farrell AP, et al. 2008. Developing a mechanistic
understanding of fish migrations by linking telemetry with physiology,
behaviour, genomics and experimental biology: an interdisciplinary case
study on adult Fraser River sockeye salmon. Fisheries 33: 321-338.
Funding for this position is available for 2 years, starting in June
2008. Qualified applicants will be invited to submit applications for
a Visiting Fellowship (VF) from the Natural Sciences and Engineering
Research Council of Canada (NSERC). For more information on eligibility
and the NSERC VF application process, please visit the following websites:
To express interest or apply for this position, please send a cover letter,
CV, and the names and contact information for three referees to Janelle
Curtis (email: janelle.curtis@dfo-mpo.gc.ca; fax: 250-756-7053). Review of
applications will begin 30 November 2008 and continue until the position
is filled.
Please feel free to circulate this job posting widely.
Postdoc: Systems Biology (M/F), University of Luxembourg
Post Doc in Systems Biology (M/F) at the University of Luxembourg
Application End: 7 December 2008
The University of Luxembourg has a vacancy in its Faculty of Science,
Technology and Communication for a
Post Doc in Systems Biology / Life Sciences
3-years contract
starting January 2009 (or later)
Research area: Systems Biology - Life Sciences
Within systems biology detailed mathematical (ODE) models based on
molecular interactions are widely used to analyze mammalian signalling
networks. Sensitivity analysis methods allow for rating of the influence of
model parameters on the dynamic and static behaviour of the model states
(e.g. concentrations). This information can be used to get deeper insight
into the system under investigation by identification of key mechanisms and
sensitive or fragile network points. In this project global sensitivity
methods (variance based) shall be implemented and applied to analyze the
pro- and anti-apoptotic signalling in mammalian cells. The focus will be
on different published or currently developed detailed mathematical models
which describe various aspects of pro- and anti-apoptotic processes. This
will help to identify the hub proteins within this network which will be
promising targets for pharmaceutical strategies.
Tasks:
* Mainly research activities in the field of Systems Biology, with
special focus on global sensitivity analysis
Profile:
* PhD degree in Systems Biology, Engineering, Life Sciences (Biology),
Biotechnology or comparable
* Good written and oral English skills are obligatory, working knowledge
in German and/or French is an advantage.
Offer
* research within an up-to-date field
* exciting interdisciplinary environment
* competitive remuneration
For further information, please contact:
Prof. Thomas Sauter
University of Luxembourg
Life Sciences Research Unit
162a, avenue de la Faiencerie
L-1511 Luxembourg
Interested candidates are asked to send their full application (letter
of motivation, detailed CV, copies of diploma, photo) until December 7th,
2008 by e-mail to thomas.sauter@uni.lu .
The University of Luxembourg is an equal opportunity employer.
The Department of Engineering Sciences and Applied Mathematics at
Northwestern University expects to recruit one Postdoctoral Fellow
for appointment beginning in fall, 2009 as part of an NSF sponsored
Research Training Grant project. This project will provide support for
the Postdoctoral Fellow for a period of up to three years. The successful
candidate will teach an average of one course per quarter and will have
the opportunity to work in interdisciplinary research teams on cutting
edge applied mathematics research in the life sciences and mechanics.
Applicants will be considered until the position is filled. This position
is restricted to U.S. citizens and permanent residents.
Please contact Alvin Bayliss (a-bayliss@northwestern.edu) for further
details.
Northwestern University is an Affirmative Action/Equal Opportunity Employer.
Applications from women and under-represented minorities are encouraged.
Postdoc Position: Modeling Complex Microbial Systems, U Guelph
We invite applications for a Postdoc Position at the University of Guelph in
"Mathematical modeling of complex microbial communities"
as part of an interdisciplinary research project with government scientists
(Health Canada; Agriculture and Agrifood Research Canada), pending on final
approval of funds. The begin of the project is to some extent negotiable,
with a preference on early 2009.
The incumbent should possess
(+) a PhD in a relevant discipline (Mathematics, Engineering, etc)
(+) prior experience in modeling complex microbial systems (e.g. anaerobic
digestion, activated sludge, complex populations in a chomestat/gradostat,
intestinal microflora, microbial population genetics etc), nutrition
modeling, and/or a good understanding of microbial ecology
(+) the communication skills necessary to interact in an interdisciplinary
team.
The postdoctoral fellow will join the Computational Biomathematics Laboratory
(lead by Dr Hermann J Eberl, Assoc. Prof and Canada Research Chair)
within the Department of Mathematics and Statistics. The research group
currently is composed of one faculty, one postdoctoral fellow, and eight
graduate students. The main research area of the group is mathematical
modeling of microbial systems; other currently active research areas are
modeling in apiculture, forest dynamics, and social dynamics. For more
information see http://www.uoguelph.ca/~heberl
Guelph is located centrally in Southern Ontario, about one hour west of
Toronto. The University of Guelph is Canada's leading comprehensive research
university with a long tradition in the Life Sciences. Biomathematics and
Statistics is the largest research area in the Dept. of Mathematics and
Statistics with currently about 10 research active faculty and 25 grad
students.
Interested individuals are invited to send their electronic application (pdf
or ps format preferred) to Dr. Hermann J Eberl at heberl@uoguelph.ca, to
whom also informal inquiries can be directed. An application should include:
(+) academic curriculum vitae/resume
(+) a brief statement (1-2 pages) outlining (i) prior experience in
modeling microbial systems and microbial ecology, (ii) experience in
interdisciplinary research, (iii) computational skills.
(+) the names and contact details for at least two academic or professional
references
Initial screening of applications will start December 15. Applications
are accepted until the position is filled.
Postdoctoral Position: Mathematical Biology, UC Davis
POSTDOCTORAL POSITION IN MATHEMATICAL BIOLOGY AT UNIVERSITY OF CALIFORNIA,
DAVIS
The Mathematics department at the University of California Davis is
accepting applications for a postdoctoral position in Mathematical Biology.
The position will involve research, teaching, and active participation
in the Math Biology group. Preference will be given to applicants with
mathematical/biological research interests that are compatible with those
of the faculty. The initial appointment will be for one year, with the
possibility of renewal for up to three years.
Applications will be accepted until the position is filled. The review
of applications will begin on December 1st, 2008. Apply to the postdoc
position in the mathematics department at UC Davis by submitting the
AMS Cover Sheet and supporting documentation electronically through
http://www.mathjobs.org . Please list mathematical biology as your
primary research interest. For further information, contact Tim Lewis
(tjlewis@ucdavis.edu) or Bob Guy (guy@math.ucdavis.edu).
UC Davis is an affirmative action/equal employment opportunity employer
and is dedicated to recruiting a diverse faculty community.
Postdoctoral or Research Scientist Position: Stanford University
Postdoctoral or Research Scientist Position: Stanford University,
Fred Hutchinson Cancer Research Center, Canary Foundation
The Canary Foundation, Stanford University, and the Fred Hutchinson Cancer
Research Center are jointly seeking a highly qualified post-doctoral
fellow or research scientist with an interest in applying various modeling
approaches to represent disease management strategies. The ideal candidate
would have a Ph.D. or M.S. in a field related to quantitative modeling
(decision modeling or game theory, biomathematics or biostatistics)
or a substantive field that includes training in statistical modeling
(health-outcomes research, economics, epidemiology, or computational
biology). The ideal candidate should have experience in developing models
related to a medical management problem including a detailed analysis of
the literature. Experience in computer programming is essential. The ideal
candidate will apply analysis expertise to extend and develop models of
cancer natural history and cancer screening in order to answer important
questions related to alternate screening strategies, cost-effectiveness,
and other key parameters. Excellent verbal and written communication skills
are key. This two-year position (possibly extendable to three years) will be
funded by Canary Foundation, a non-profit organization focused on the early
detection of cancer. Canary Foundation has assembled a team of scientists
from several institutions (including Stanford University and the Fred
Hutchison Cancer Research Center) to focus on in vitro diagnostics (e.g.,
blood biomarkers) and in vivo diagnostics (e.g., molecular imaging). As
an integral part of this team, the position will receive mentorship from
several participating investigators, including Drs. Sanjiv Gambhir,
Nicole Urban, Sylvia Plevritis, and Patrick Brown.
For further information or to apply for the position, please submit a
cover letter and CV to hiring@canaryfoundation.org.
The Netherlands Institute for Systems Biology (NISB) and Centrum Wiskunde &
Informatica (CWI) invite applications for the position of a
Postdoc (two years, with possibility for extension): Computational modeling
of structural genomic variation in hierarchically-regulated gene networks
The opening is a research position within the field of computational biology
Research background
Structural variation of the genome, including translocation of DNA chunks
across chromosomes, inversions, and deletions can have enormous impact
on gene expression and consequently on cell function. Hierarchical
regulation mechanisms, including conditional DNA folding and nuclear
lamina interactions, can switch gene clusters between a state rendering
the genes inaccessible to transcription and a ?permissive? state in which
gene transcription is possible.
The consequences of hierarchical network organization for the dynamics
and evolution of gene networks are poorly understood. The project will
develop computational and mathematical modeling approaches to explore the
effects that structural genomic variation can have on gene expression in
hierarchically-structured gene networks at single-organism and evolutionary
time scales.
Job description
The postdoc will develop and analyze theoretical, evolutionary models
of hierarchical gene network regulation using discrete and/or continuous
modeling approaches. Model insights and predictions based on artificial
and actual regulatory networks will be interpreted in close collaboration
with two functional genomics groups that participate in the NCSB: the
Edwin Cuppen group at the Hubrecht laboratory, Utrecht and the Lodewyk
Wessels group at the Netherlands Cancer Institute in Amsterdam.
Location
The work will be embedded in the Biomodeling and Biosystems Analysis group
of the Netherlands Institute for Systems Biology (NISB; www.sysbio.nl) and
within the Life Sciences group of the Center for Mathematics and Computer
Science (CWI) in Amsterdam. As the ?core modeling group? of the Netherlands
Consortium for Systems Biology, the Biomodeling and Biosystems Analysis
group develops quantitative and predictive models and multiscale computer
simulations in collaboration with systems biology groups at participating
institutes.
Profile
Candidates ideally fulfill the following criteria:
- Ph.D. theoretical biology, computer science, mathematics or a related
discipline
- able to communicate with scientists in biology and mathematics
- good programming skills in C++ or equivalent
Conditions of employment
The vacancy concerns a temporary research position for two years,
with possibility of extension. The salary and terms of employment are
in accordance with the "CAO-onderzoekinstellingen" and are based on
qualifications. Besides the salary and excellent working conditions, CWI
offers attractive and flexible terms of employment, like a collective health
insurance, pension-fund, and initial help with housing for foreigners. The
position is at postdoc level for 38 hrs/week.
Websites
http://www.sysbio.nl and http://www.cwi.nl
Applications and requests for information
Direct requests for information or applications before 1 December 2008 to:
Dr. Roeland Merks, Roeland.Merks@sysbio.nl
phone +31 20 592 4117, skype: roelandmerks
Centrum Wiskunde & Informatica (CWI) and Netherlands Institute for Systems
Biology (NISB)
Kruislaan 413, 1098SJ Amsterdam, The Netherlands
Applications should include a motivation letter, a curriculum vitae, list
of publications, and the names and addresses of at least two persons that
can be approached to obtain further information.
POSTDOCTORAL POSITION: SALIVARY GLAND BRANCHING MORPHOGENESIS
University of Heidelberg
During its development, the submandibular salivary gland undergoes branching
morphogenesis, which is a common strategy used by many organisms and
mammalian organs to maximise the amount of surface area in contact with
the environment. Existing approaches for engineering salivary glands have
been unable to recreate the complex in vivo 3D structure, nor have they
been able to successfully differentiate cells into saliva-secreting acinar
cells. In order to engineer branched tissues, we need to understand how this
process occurs during development and how signalling pathways translate into
physical changes. While many signalling pathways and structural components
have been identified that play a role in branching morphogenesis, there
is so far no comprehensive model that incorporates all of these components
into an integrated model.
Together with Dr. Melinda Larsen (http://www.albany.edu/faculty/mlarsen) we
want to investigate the dynamics of salivary gland branching morphogenesis
from a mechanical as well as chemical point of view using mathematical
modelling (discrete and continuum models) in connection with experiments.
The project "Modeling Dynamics of Salivary Gland Branching Morphogenesis"
is funded by the National Institute of Dental and Craniofacial Research
(http://www.nidcr.nih.gov).
JOB DESCRIPTION:
- Mathematical modelling and simulation: individual based models and
partial differential equations
- Image analysis preprocessing experimental results
- Constant experiment-to-theory alignment
YOUR QUALIFICATIONS:
- PhD in applied mathematics, physics, engineering or a related area
- Solid background in programming and numerical methods
- Good communication skills
- Authorisation to work in the EU
OUR OFFER:
- Working in an exciting interdisciplinary research project at one of the
leading German Universities
- Further training opportunities
- Initial contract for one year (TVL-13, 2900 EUR/month) with the possibility
of prolongation for up to five years
Applicants should send a cover letter detailing motivation, training, and
work experience, a curriculum vitae, a publications list, and two references
to Dr. Dirk Hartmann (Dirk.Hartmann@iwr.uni-heidelberg.de). If available,
also include a copy of the PhD and master thesis, published articles or
similar relevant materials.
For further information please visit: http://www.hartmann.uni-hd.de
Postdoc & PhD Positions: Computational Systems Biology, ETH Zurich
Post-Doc and PhD positions: Computational Systems Biology, ETH Zurich
Applications are invited for a PhD studentship and a Post-Doc position,
within the Computational Biology Group at the Department of Biosystems
Science and Engineering of ETH Zurich.
The group focuses on the development of detailed, predictive models
for cellular signaling networks with a view to develop a comprehensive
understanding of the dynamics and evolution of cellular signaling. All
projects are carried out in close collaboration with experimental groups
so that quantitative data is available and model predictions can be tested
in experiments.
Applicants should have a strong background in mathematical and computational
modeling, and demonstrated experience in nonlinear dynamics and numerical
calculations. PhD candidates should hold or expect to obtain a degree in a
numerate discipline (e.g. mathematics, computational science, computational
biology, physics, biotechnology, chemical or bio-engineering, or related
areas). Candidates are expected to engage in interdisciplinary research
and to foster in-house collaborations with biologists and bioengineers.
The Department of Biosystems Science and Engineering of ETH Zurich is an
integral part of SystemX.ch, the Swiss initiative in Systems Biology. It
is located in Basel, a European hotspot for biomedical research, in close
proximity of the Biozentrum of the University of Basel, the Friedrich
Miescher Institute for Biomedical Research, and the pharmaceutical and
biotech industry. ETH Zurich is a major research university, offering an
excellent environment for innovative and collaborative research across
disciplines.
Please send the usual application material, including at least two
references, as a single PDF file to dagmar.iber@bsse.ethz.ch (preferred),
or via surface mail to:
Prof. Dr. Dr. Dagmar Iber
ETH Zurich
D-BSSE
Mattenstrasse 26
4058 Basel
Switzerland
For further information please visit our web page at
http://www.dbsse.ethz.ch/research/group_iber
Postdoctoral Positions: Quantitative Systems Biology, UC Irvine
Postdoctoral Positions, Quantitative Systems Biology, U. of
California, Irvine
The Center for Mathematical and Computational Biology (CMCB) at University
of California, Irvine, is looking for two to three postdoctoral fellows.
The successful candidates are expected to work in an inter-disciplinary
research environment on projects in systems biology funded by NIH.
Appointments will be effective on July 1, 2009. Please refer to UCI-MATH/QSB
#4241 on MathJobs.org: https://www.mathjobs.org/jobs/165/1433
for instructions on the electronic application process.
For further inquiry on the positions, please contact Qing Nie
(qnie@math.uci.edu).
Centre for Immunity, Infection and Evolution
"A Wellcome Trust-funded Centre-in-Development"
The University of Edinburgh has recently established the Centre for Immunity,
Infection and Evolution, as a new initiative in infectious disease research
with funding from The Wellcome Trust. The Centre combines over 20 Principal
Investigators with established research funding. Full details on constituent
laboratories of the Centre are available on http://sbsweb2.bio.ed.ac.uk/iie/.
The Centre offers an innovative Fellowship Programme, for which we are
now inviting applications.
Two Advanced Fellowships are available for 3 years, extendable with
University support to tenure-track status. Fellows will be emerging leaders
in their fields, able to bring further interdisciplinary strengths to the
Centre. Fellows will be expected to propose their own research programme
complementary to, and consonant with, the new Centre.
Three 2-year Research Fellowships will also be appointed. Fellows
will have, typically, up to 4 years? postdoctoral experience and may
take up one of the collaborative projects outlined on the web site
http://sbsweb2.bio.ed.ac.uk/iie/fellowships. Alternatively, candidates
may propose their own research plan in conjunction with two different
Centre laboratories. Fellows will be encouraged to continue their work at
the Centre beyond this time through competitive applications for external
Fellowship funding.
The deadline for applications for 2-year Fellowships is 13 November 2008,
and for the Advanced Fellowships 27 November 2008.
Postdoctoral Teaching Fellowship in Biomathematics
The Swarthmore Departments of Mathematics/Statistics and Biology invite
applications for a 3-year position, beginning with the fall semester 2009.
We anticipate the post-doctoral fellow will help shape a program in
mathematical biology at Swarthmore College. Responsibilities will likely
include two semester-long courses each year, the nature and level of
which the fellow will help determine. In addition, the position involves
the development of materials that
