SMB Digest May 20, 2015 Volume 15 Issue 20
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
Note:
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Issue?s Topics:
NIMBioS: Support for Available for Activities at NIMBioS
Announcement: Letters in Biomathematics
PhD Position: Math Bio, Hemholtz Centre for Infection Research
PhD Position: Mechanics of Living Tissue During..., U Grenoble
PhD Position: Spatio-temporal Dynamic Model of the..., France
Position: Senior Health Econ./Modeller, Public Health England
SMBnet Reminders
----------------------------------------------------
From: Catherine Crawley <ccrawley@nimbios.org>
Date: May 19, 2015 at 10:10:29 AM
Subject: NIMBioS: Support for Available for Activities at NIMBioS
Support Available for Activities at the National Institute for
Mathematical and Biological Synthesis
September 1, 2015 is the deadline for requests for support for Working
Groups, Investigative Workshops, Sabbaticals, and Short-term Visitors
for activities beginning spring/summer 2016 at the National Institute
for Mathematical and Biological Synthesis (NIMBioS). All areas of
research at the interface of biology and mathematics will be considered,
but we are especially interested in activities expanding beyond the
areas of research supported to date. Potential organizers of activities
in areas of molecular biology, cell biology, network biology, immunology
and systems biology are particularly encouraged to submit requests for
support of Working Groups or Investigative Workshops. NIMBioS, located
at the University of Tennessee-Knoxville, is an NSF-sponsored initiative
to foster interdisciplinary research at the interface between
mathematical and biological sciences. The institute's mission is to
cultivate cross-disciplinary approaches in mathematical biology and to
develop a cadre of researchers who address fundamental and applied
biological problems in creative ways. Additional support for NIMBioS
comes from the University of Tennessee-Knoxville. More details are
posted at http://www.nimbios.org
Related Links:
NIMBioS Working Groups http://www.nimbios.org/workinggroups/
NIMBioS Investigative Workshops http://www.nimbios.org/workshops/
Postdoctoral Fellowships http://www.nimbios.org/postdocs/
Sabbaticals http://www.nimbios.org/visitors/sabbatical
Short-term Visits http://www.nimbios.org/visitors/
----------------------------------------------------
From: Callender, Hannah <callende@up.edu>
Date: May 13, 2015 at 12:29:55 PM
Subject: Announcement: Letters in Biomathematics
LETTERS IN BIOMATHEMATICS NOW TAYLOR AND FRANCIS JOURNAL
Letters in Biomathematics was introduced last year as a new,
peer-reviewed, open access journal for topics in both mathematical
biology research and undergraduate education in biomathematics. The
journal has already experienced great success in attracting high quality
manuscripts in both areas, and we are happy to announce that Letters in
Biomathematics will now be published through Taylor and Francis.
For further information, including access to journal issues, aim and
scope, and submission guidelines, please visit:
http://tandf.msgfocus.com/q/16vs5BQur5M/wv
----------------------------------------------------
From: School, Grad <HZIGrad.School@helmholtz-hzi.de>
Date: May 18, 2015 at 1:10:09 AM
Subject: PhD Position: Math Bio, Hemholtz Centre for Infection Research
The Helmholtz Centre for Infection Research (HZI) and the Braunschweig
Integrated Centre of Systems Biology (BRICS) offers a position as PhD
student in Mathematical Biology at the Department of Systems Immunology.
This position is offered in the context of a Human Frontier Science
Program (HFSP) research project on multiscale mathematical modelling of
the dynamics of antibody optimisation in germinal centres and of the
immunological synapse.
You will be embedded in a strong team of modellers headed by Michael
Meyer-Hermann with expertise in a wide range of quantitative modelling
methods, including spatio-temporal techniques and application to a large
range of biological problems. You will benefit from an environment with
long-standing experience in germinal centre modelling. You are expected
to actively shape the research with new ideas and will be supported by
strong team of experimental collaborators including Michael Dustin
(Oxford UK), Gabriel Victora (Cambridge MA USA), and Carola Vinuesa
(Canberra Australia). This team will generate quantitative data on the
immunological synapse, cell dynamics in germinal centres and
inter-germinal centre information processing.
The successful candidate will be educated in one of the following
disciplines: Theoretical Biology, Mathematical Biology, Computational
Biology, Physics, Mathematics, or other quantitative sciences. Severely
disabled applicants will be favoured if equally qualified.
Please submit your application until June 30, 2015 in our online
application tool at https://hzi.opencampus.net/ (after registration
choose "Application HZI Jobs" and select job no. 20/2015).
The HZI is a research centre under the roof of the Helmholtz Society,
which is a world leading and powerful institution funding basic and
applied research in natural sciences. HZI is narrowly connected to the
Technical University of Braunschweig and the University of Hannover and
is, thus, embedded in a dense environment of fundamental research in
Biology and Immunology. The HZI has proven in the past to provide
excellent support for the appointed scientists in order to promote their
career.
For further information please refer to www.systems-immunology.de or
contact Prof. Dr. Michael Meyer-Hermann by phone +49(0)531/6181-5400
or by e-mail michael.meyer-hermann@helmholtz-hzi.de.
----------------------------------------------------
From: Guy Blanchard <gb288@cam.ac.uk>
Date: May 19, 2015 at 5:12:58 AM
Subject: PhD Position: Mechanics of Living Tissue During..., U Grenoble
PhD position: Mechanics of living tissue during embryo development:
understanding biological observations with a mechanical model
Based in the Laboratoire Interdisciplinaire de Physique, Université
Grenoble Alpes, in collaboration with the Dept. of Physiology,
Development and Neuroscience, University of Cambridge.
Advisors: Dr Jocelyn Étienne (Grenoble) & Dr Guy Blanchard (Cambridge)
During the development of living organisms, large-scale movements of
tissues occur to sculpt the adult form from a single fertilized egg. The
mechanics of these deformations is poorly understood, although their
driving forces are known to originate in the subcellular dynamics of
filaments of actin proteins, which are contracted by the action of
myosin, a motor-molecule. Understanding the self-organizing capacity of
networks of actin and myosin and how this is controlled during
development to generate appropriate form is one of the great current
challenges at the interface between physics and biology. The objective
of this PhD project is to work on physical models of the subcellular
dynamics of these filaments, and of the resulting tissue-scale dynamics
of cells, in order to understand how the molecular processes give rise
to the correct morphogenetic movements.
Full advert and details:
http://www-liphy.ujf-grenoble.fr/pagesperso/etienne/droso_en/
Deadline: 24th May 2015
----------------------------------------------------
From: Benoit Sarels <benoit.sarels@ljll.math.upmc.fr>
Date: May 19, 2015 at 5:14:46 AM
Subject: PhD Position: Spatio-temporal Dynamic Model of the..., France
PhD topic
Spatio-temporal dynamic model of the translation repressor 4E-BP
regulation network
In this project, we aim to study three levels of the dynamics of the
translation repressor 4E-BP.
1. We will study the impact of numerous and hierarchical phosphorylation
sites found in 4E-BP on the ultra-sensitivity of conformation
modifications and association with eIF4E. The proteins that are
activated only through the phosphorylation of several sites may have a
ultra-sensitive response and lead to a sigmoid-type functional response
(Ferrell & Ha, 2014a; Ferrell & Ha, 2014b). First, we want to integrate
in the existing model the different conformations that the proteins may
have (no folding, partial or full folding), and thus the different
reaction rates that they may have, and the different degradation rates.
One can think that the model would need to be either compartmented into
a finite (small) number of possible conformations or structured through
a (continuous) phosphorylation variable (similar to a methylation
variable). This question needs to be addressed during the course of the
PhD studies.
Keywords : compartmented vs structured models, conformational
structuration
2. We will also extend the current ordinary differential equations model
and take into account the aforementioned delay happening between
fertilization and activation of protein synthesis. This will be done
through a partial differential equations model involving active and
passive transport (diffusion). Appropriate interaction with the
biologists in the lab will allow to weigh the relative importance of
these phenomena.
Keywords : spatial structuration, (active) transport, diffusion
3. We then want to analyze the spatio-temporal dynamics of the TORC1
pathway and its impact on the protein synthesis. The model will be made
as realistic as possible by taking into account the form on the cell in
vivo. The quasi-spherical shape and the constant volume of the sea
urchin egg offer a simple model to begin with. The spatial repartition
of the organelles (such as the vesicles) can be acutely determined
through interaction with the biologists in the lab and then be included
in the model (Elias & Clairambault, 2014).
Keywords : 3D models, spatial heterogeneity
The PhD project comes with a standard 3-year-contract called ?contrat
doctoral?. The selected candidate will work in the Roscoff marine
station under the supervision of Patrick Cormier (biologist) and Benoît
Sarels (mathematician). The candidate will be encouraged to actively
collaborate with the mathematicians in the LJLL in Paris.
The candidate should have obtained or be about to complete a master's
degree in applied mathematics. Other profiles may be considered if the
candidate demonstrates a strong ability either in applied mathematics or
modeling. Prior knowledge of transport-reaction-diffusion PDE would be
a plus. The candidate must master a numerical computing software or
programming language, and be able to use and further develop numerical
schemes. The candidate will have to demonstrate a strong interest for
system biology approaches that aim at modeling, analyzing and simulating
complex biological systems. It is critical for the candidate to be
willing to work in a strongly multidisciplinary environment. An
outstanding candidate would have the opportunity to take part in the
creation of an emerging team of mathematical modeling in the Roscoff
marine station. No knowledge of French is required as both supervisors
are fluent in English. Please note however that the work language in the
lab is French.
Applications should be sent by email with the string "MoDyST" in the
subject to patrick.cormier@sb-roscoff.fr and
benoit.sarels@ljll.math.upmc.fr. Please send in a CV, a student
certificate, a transcript with the grades obtained during the current
and the last years and a cover letter. Applications will be reviewed as
soon as they are received. We expect to interview candidates in Roscoff
in June 2015. The PhD contract will start between September 1st and
December 1st. The candidate will have the opportunity to teach classes
over the course of the PhD studies. The teaching load is then of 64
hours per year with an additional salary of approximately 300 euros per
month. The teaching would consist of supervisions sessions in the
"double major biology - mathematics" UPMC bachelor program in Roscoff.
----------------------------------------------------
From: Julie Robotham <Julie.Robotham@phe.gov.uk>
Date: May 18, 2015 at 8:27:06 AM
Subject: Position: Senior Health Econ./Modeller, Public Health England
A job opportunity with Public Health England:
https://www.jobs.nhs.uk/xi/vacancy/4dafbe0f901c45b52eac303f8df19212/?vac_ref=913768624
----------------------------------------------------
Subject: SMBnet Reminders
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