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Subject: Society for Mathematical Biology Digest

SMB Digest  October 28, 2015  Volume 15  Issue 43
ISSN 1086-6566

Editor: Ray Mejía ray(at)smb(dot)org

Note:
Information about the Society for Mathematical Biology, including an
application for membership, may be found in the SMB Home Page,
http://www.smb.org/ .

Access the Bulletin of Mathematical Biology, the official journal of SMB, at
http://www.springer.com/11538 .

Inquiries about membership or BMB fulfillment should be sent to
membership(at)smb(dot)org .

Issue's Topics:
   Call for Contributed Talks & Posters: ECMTB/SMB 2016
   CfP: IJMSSC Special Issue on Agent-Directed Simulation
   PhD Studentship: Computational Cancer Biology, QUT, Queensland
   PhD Studentship: MRC Doctoral Training Partnership, U Manchester, UK
   PhD Studentships: Stochastic Modelling, U of Edinburgh
   Postdoctoral Position: Theoretical Ecology,  Klausmeier & Litchman Lab
   Postdoctoral Research Position: Influenza Lifecourse Epidemiology
   Postdoctoral Position: Infectious Disease Modeling, NCSU
   Multiple Postdoc Positions: Biomedical Informatics, Harvard Med School
   Funding Opportunity: 2016 NIH Director's Early Independence Awards
   iBiology Video by NIGMS Director; Nobel Prize to Grantees; Events ...
   SMBnet Reminders


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From: Markus Owen <Markus.Owen@nottingham.ac.uk>
Date: Fri, Oct 23, 2015 at 6:08 AM
Subject: Call for Contributed Talks & Posters: ECMTB/SMB 2016

ECMTB/SMB 2016 - www.ecmtb2016.org

Call for Contributed talks and posters - deadline, 14 Feb 2016

10th European Conference on Mathematical and Theoretical Biology / SMB
Annual Meeting

The joint meeting of the European Society for Mathematical and Theoretical
Biology (ESMTB) and the annual meeting of the Society for Mathematical
Biology (SMB) will be held in Nottingham, 11-15 July 2016.

We now invite abstracts for contributed talks and posters at the interface of
mathematics and biology, including all areas of the life and medical sciences.
Contributed talks will be for 20 minutes each (including time for questions
and changing speakers).

Please fill in the form at www.ecmtb2016.org/submissions/ to submit your
abstract.

Please note: The first submission associated with your email address
will create a user account, and a password will be emailed to that email
address. Each registered user may make a maximum of two submissions to
ECMTB 2016 (one as a minisymposium organiser; one for a minisymposium talk,
contributed talk or poster).

Confirmed plenary speakers include:
Ruth Baker (University of Oxford, UK)
Sander van Doorn (University of Groningen, Netherlands)
Julia Gog (University of Cambridge, UK)
Leah Keshet (University of British Columbia, Canada)
Johan van de Koppel (Royal Netherlands Institute for Sea Research)
Hisashi Ohtsuki (Kanagawa, Japan)
Johan Paulsson (Harvard University, USA)
and
John Rinzel (NYU, USA) - SMB Winfree Prize lecture


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From: Yu Zhang <yzhang@cs.trinity.edu>
Date: Wed, Oct 21, 2015 at 1:27 PM
Subject: CfP: IJMSSC Special Issue on Agent-Directed Simulation

International Journal of Modeling, Simulation, and Scientific Computing
http://www.worldscientific.com/worldscinet/ijmssc

Call for Papers
Special Issue on Agent-Directed Simulation

See: http://www.worldscientific.com/page/ijmssc/callforpapers01

Extended Deadline: 01/15/2016


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From: Graeme Pettet <g.pettet@qut.edu.au>
Date: Tue, Oct 20, 2015 at 2:25 AM
Subject: PhD Studentship: Computational Cancer Biology, QUT, Queensland

The Regenerative Medicine Group, Institute of Health and Biomedical Innovation
invites applications from interested students for the PhD project - A
Multi-scale, Physiologically-Based Computer Model to Simulate Ovarian Cancer.

Ovarian cancer remains a major health problem due to its high lethality,
but despite extensive efforts to develop effective prevention and early
detection strategies, most patients are diagnosed at an advanced disease
stage. Designing improved therapies to achieve a long-term cure remains a
challenge as little is known about the underlying mechanisms promoting tumour
progression and its tumour-stroma microenvironment. Mathematical simulations
provide a means to improve our understanding of tumour progression, to
investigate biological hypotheses and to inform experimental design.

This research project will focus on discovering the mechano-biological
factors which influence the abnormal growth of ovarian cancer cells to
form ovarian tumours or multi-cellular spheroids. The PhD candidate will
apply innovative mathematical simulation methods to develop a computational
model which will be at the forefront of research in cancer biomechanics. The
model will represent the complex cellular communication which takes place
within multi-cellular ovarian cancer spheroids, at both the single cell and
multi-cellular scales. The research will involve implementing both finite
element modelling and mathematical modelling methods, in order to develop an
integrated simulation framework which replicates the mechanical and biological
factors associated with ovarian tumour development and progression. The
outcomes of this novel project will be integral in discovering key
mechano-biological factors associated with the progression of ovarian cancer.

The ideal candidate should hold a minimum of First Class Honours degree
(or equivalent) in Biomedical Engineering, Mathematical Science or a similar
field.  Demonstrated skills in the following would be an advantage: Computer
programming skills in Matlab, Python and C++. Prior research experience in
biomedical engineering, computational biology or biomechanics is desirable.

This exciting PhD studentship will provide the opportunity to work with
a wide collaborating group of leading international researchers in the
areas of mathematical sciences, biomedical engineering and regenerative
medicine.  Moreover, the position will bring with it the opportunity for
international travel and provide the candidate with a comprehensive set
of inter-disciplinary skills which will see them placed competitively for
future employment.

The research will be undertaken at Queensland University of Technology,
in Brisbane, Australia. The position includes a tax exempt living allowance
of AU$25,849 per annum for full time study. This stipend will be paid for
the duration of the 3 year, full time PhD candidature. 

To register your interest in this PhD position or for informal enquiries
contact Dr J Paige Little (j2.little@qut.edu.au) or Professor Dietmar
Hutmacher (dietmar.hutmacher@qut.edu.au). To apply send a copy of your full
CV, including undergraduate/postgraduate academic transcripts, the contact
details for two referees and other supporting information (eg. language
competency skills) to j2.little@qut.edu.au.


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From: Oliver Jensen <oliver.jensen@manchester.ac.uk>
Date: Wed, Oct 28, 2015 at 8:04 AM
Subject: PhD Studentship: MRC Doctoral Training Partnership, U Manchester, UK

Applications are invited for the following PhD project in the MRC Doctoral
Training Partnership at the University of Manchester, UK

Title: Feto-placental flow modelling from detailed vascular structural
image analysis

Outline: Exchange of oxygen and nutrients between maternal and fetal
blood takes place in the placenta, across a trophoblast interface having an
intricate geometric structure. Structural abnormalities of fetal blood vessels
are linked to some diseases of pregnancy and may lead to localised placental
insufficiency. We have used microCT technology to provide a unique detailed
structural image of the feto-placental vasculature. Mathematical, statistical
and computational approaches are now needed to characterise the vessel
network structure to assess the relationship between placental structure
and blood flow efficacy at the whole-organ level. This interdisciplinary
project involves the development of multi-scale mathematical models of the
feto-placental circulation, in normal and abnormal pregnancies, and validation
of model predictions using ex vivo placental perfusion experiments.   

This 3.5-year full-time MRC DTP studentship provides full support for tuition
fees, annual tax-free stipend at Research Council UK rates (currently £14,057)
and conference/travel allowance. The project is due to commence October
2016 and is open to UK/EU nationals only. Applicants should hold (or be
expected to obtain) a minimum upper-second class undergraduate degree in a
relevant area. A relevant Masters degree or equivalent research experience
would be an advantage. For details of the MRC DTP see
http://www.mhs.manchester.ac.uk/mrcdtp

Please direct enquiries to Dr Edward Johnstone (Institute of Human
Development, Edward.johnstone@manchester.ac.uk,
http://www.manchester.ac.uk/research/edward.johnstone/) or
Prof Oliver Jensen (School of Mathematics, Oliver.Jensen@manchester.ac.uk,
http://www.maths.manchester.ac.uk/~ojensen/)

Applications are invited up to and including 25 November 2015.


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From: Ramon Grima <rgrima@staffmail.ed.ac.uk>
Date: Wed, Oct 28, 2015 at 8:16 AM
Subject: PhD Studentships: Stochastic Modelling, U of Edinburgh

Project 1: Development of novel approximation methods to study the stochastic
dynamics of biological systems

Supervisor: Dr Ramon Grima (Ramon.Grima@ed.ac.uk)

Description:

Biological dynamics is widespread in nature and occur at a multitude
of scales; for example intrinsic noise affects the time evolution of
the concentrations in biochemical systems, whilst demographic noise
plays an important role in the dynamics of a population of interacting
organisms. Master equations can be written down which describe the stochastic
dynamics of such systems, however they can rarely be exactly solved. Thus
the development of approximation methods is of paramount importance to
uncover some of the information contained in these master equations.

In this project the aim is to develop novel accurate approximations to
the master equation. Topics of interest include (but are not limited to)
the derivation of rigorous hybrid stochastic-deterministic descriptions,
stochastic model reduction in the absence of time scale separation and
approximations based on series expansions in relevant parameters. Some of
these methods may be based on approximation methods that we have derived
for biochemical systems in the past few years. The new methods will be
applied to model and yield insight into the dynamics of systems at various
spatial scales e.g. complex biochemical systems in single cells, cell-cell
interactions in a tissue and disease transmission in a population.

The ideal candidate will have at least an upper second-class honours degree
in Physics, Applied Mathematics or another quantitative discipline and a
desire to apply his/her skills to understanding biological systems. The
successful candidate will join the stochastic modelling group of Dr. Ramon
Grima in the Center for Systems and Synthetic Biology (SynthSys) at the
University of Edinburgh http://grimagroup.bio.ed.ac.uk/index.html

Interested individuals must follow Steps 1, 2 and 3 at this link on how
to apply
http://www.ed.ac.uk/schools-departments/biology/postgraduate/pgr/how-to-apply

Scholarships are available for EU and international students - you must
apply by 5.00pm on Monday 7 December 2015 at the latest.


Project 2: Stochastic modelling of intracellular reaction-diffusion processes

Supervisors: Dr Ramon Grima (Ramon.Grima@ed.ac.uk) and Dr Nacho Molina
(Nacho.Molina@ed.ac.uk)

Noise due to low copy number of molecules plays an important role in the
regulation of various intracellular processes. The effects of such noise in
well-mixed conditions has been the subject of a large number of theoretical
studies and is fairly well understood. However fact is that the cell is not
a well-mixed soup of chemicals; compartmentalisation and molecular crowding
imply that biochemical reactions occur in a structured and non-dilute
environment. The aim of this project is to (i) develop a computational
framework which can take into account these factors adequately and (ii) use
this framework to study analytically and numerically the effect of complex
intracellular geometry on the stochastic properties of various intracellular
pathways. The project is ideal for a candidate with a mathematics or physics
undergraduate degree and an interest in modelling biological systems.

The ideal candidate will have at least an upper second-class honours degree
in Physics, Applied Mathematics or another quantitative discipline and a
desire to apply his/her skills to understanding biological systems. The
successful candidate will join the stochastic modelling group of Dr. Ramon
Grima in the Center for Systems and Synthetic Biology (SynthSys) at the
University of Edinburgh http://grimagroup.bio.ed.ac.uk/index.html

This opportunity is ONLY open to UK nationals (or EU students
who have been resident in the UK for 3+ years immediately prior
to the programme start date) due to restrictions imposed by the
funding body. You must follow the instructions on the EASTBIO website
http://www.eastscotbiodtp.ac.uk/how-apply-0 for your application to be
considered. The deadline for applications is Monday 14 December 2015.


The University of Edinburgh is a charitable body, registered in Scotland,
with registration number SC005336.


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

From: Christopher Klausmeier <klausme1@msu.edu>
Date: Thu, Oct 22, 2015 at 7:38 AM
Subject: Postdoctoral Position: Theoretical Ecology,  Klausmeier & Litchman Lab

A postdoctoral position funded by a grant from the Simons Foundation is
available in the Klausmeier & Litchman lab at Michigan State University's
Kellogg Biological Station. The project is to develop and test trait-based
models in a metacommunity context to understand patterns of commonness and
rarity (species abundance distributions) as well as the temporal dynamics of
these patterns. Experience with ecological modeling is required; knowledge
of adaptive dynamics, metacommunities, variable environment theory, and
Mathematica are beneficial.

The position is for one year initially, renewable depending on performance
and continued funding. Start date is as soon as possible. Interested
applicants should email a CV, a brief statement of research interests and
accomplishments, and the names and contact information of two references
to Christopher Klausmeier (klausme1@msu.edu). Review of applications will
begin November 16, 2015 and continue until filled.

See <http://preston.kbs.msu.edu> and <http://www.kbs.msu.edu> for more info
on the lab and KBS, and email if you have questions.


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

From: Qifang Bi <qbi1@jhu.edu>
Date: Thu, Oct 22, 2015 at 11:14 AM
Subject: Postdoctoral Research Position: Influenza Lifecourse Epidemiology

Postdoctoral Research Position in Influenza Lifecourse Epidemiology

Our group in the Department of Epidemiology at the Johns Hopkins Bloomberg
School of Public Health is looking for a research fellow to work on a project
investigating serologic responses to influenza virus exposure over the
lifespan. This position is an excellent opportunity for an individual with
a mathematical modeling/applied mathematics background to gain hands-on
experience analyzing empirical data, or an individual with a laboratory
background to gain experience with infectious disease dynamics. Importantly,
the applicant must be proficient in advanced statistical analysis, ideally
with experience in serologic data translation between the laboratory
and population levels. The applicant will also be expected to maintain
an organized, timeline-driven approach to ensure completion of research 
objectives, liaise with international collaborators, manage data for analysis,
assist with manuscript preparation, and contribute to the development of
subsequent research activities.

Applicants with a strong analytic background and master's degree will be
considered; a PhD in epidemiology, biostatistics, or a related quantitative
field (e.g., computer science, infectious disease modeling, ecology)
is preferred.

The successful applicant will work with Dr. Justin Lessler and colleagues on
a project funded by the National Institutes of Health that aims to measure
and explain the complex, varying patterns of influenza immunity over a
lifetime and better understand how broad, cross-strain immunity affects 
health outcomes in two cohort studies from China. You would be joining a
highly collaborative group who work on projects ranging from empirical
data collection to theoretical modeling of disease dynamics, and there
will be potential to work on cross-cutting projects focused on issues in
infectious disease transmission and control. Depending on an applicant's
exact interests and skill sets, some of the time on this project may be
spent working on-location in China.

Interested candidates should contact Justin Lessler (justin@jhu.edu) with a
CV, brief statement of interest, and two references. Interested individuals
should apply by November 30, 2015.


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From: Cristina Lanzas <clanzas@ncsu.edu>
Date: Tue, Oct 27, 2015 at 9:58 PM
Subject: Postdoctoral Position: Infectious Disease Modeling, NCSU

One postdoctoral associate position on infectious disease modeling is
available in Cristina Lanzas' group (Department of Population Health
and Pathobiology, College of Veterinary Medicine, North Carolina State
University). Applicants with a background in mathematical modeling of
infectious diseases and/or population biology are highly encouraged to
apply. Our research combines data, epidemiological analysis and mathematical
models to study transmission and disease control and it is currently
supported by NIH.

The research focus will be the transmission and control of infectious
diseases caused by enteric pathogens (specifically Clostridium difficile,
Enterohaemorrhagic E. coli, and Salmonella), the use of mathematical modeling
to study the antimicrobial resistance dissemination at multiple scales,
and the effect of intestinal microbial disruption by treatments such as
antibiotics on host susceptibility and pathogen transmission. A number of
potential research projects are available and so the research focus may be
tailored to the interests and skills of the individual.

The postdoctoral associates shall have a Ph.D. degree in a relevant
quantitative discipline (ecology, epidemiology, engineering, applied
mathematics, statistics and related fields) and have a deep interest in
interdisciplinary collaboration, strong quantitative skills and good oral and
writing skills are expected. The applicants must have experience in R and/or
MATLAB. Experience developing and implementing agent-based models and/or
multi-scale models is desirable. The salary will be commensurate with the
qualifications and experience of the individuals. Review of applications will
begin immediately and will continue until suitable candidates are identified.

Interested applicants should submit a letter of intent, curriculum vitae and
the names and contact information for three references to clanzas@ncsu.edu.


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

From: Haskell, Catherine G. <Catherine_Haskell@hms.harvard.edu>
Date: Mon, Oct 26, 2015 at 9:54 AM
Subject: Multiple Postdoc Positions: Biomedical Informatics, Harvard Med School

Multiple Postdoc positions available at Harvard Medical School, Dept. of
Biomedical Informatics:

http://dbmi.hms.harvard.edu/careers/postdoctoral-fellows


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From: "Murcia, Ellie (NIH/OD) [E]" <murciae@OD.NIH.GOV>
Date: Fri, 23 Oct 2015 19:28:38 +0000
Resent-from: Raymond Mejía <mejiar@helix.nih.gov>
Subject: Funding Opportunity: 2016 NIH Director's Early Independence Awards

Funding Opportunity Announcement:
2016 NIH Director's Early Independence Awards

The National Institutes of Health Common Fund announces the FY 2016
funding opportunity for the NIH Director's Early Independence Awards (EIA)
<http://commonfund.nih.gov/earlyindependence/index.aspx>. The EIA initiative
allows exceptional junior scientists to accelerate their transition to
an independent research career by "skipping" the traditional postdoctoral
training. To be eligible, candidates at time of application must be within
one year (before or after) of completion of their terminal degree or
clinical residency. In addition, at time of application, candidates must
not be in an independent position (as defined in the FOA). Each institution
(designated by a unique DUNS identifier) may submit up to two applications in
response to this FOA. Letters of intent are due Dec. 29, 2015 Applications
are due January 29, 2016. See the instructions in the Funding Opportunity
Announcement <http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-15-006.html>
(RFA-RM-15-006).

To facilitate the "matching" of prospective candidates with potential
host institutions, the NIH Common Fund has created a matching portal
website <https://commonfund.nih.gov/ei/matchingportal/index.aspx> in
which institutions may indicate their interest in hosting EIA awardees
and provide pertinent information. Prospective candidates will be able
to use this portal to identify potential host institutions. Institutions
are invited to provide information as soon as they are able. The portal
will be updated on a continuing basis. Note that while registration by
institutions is encouraged, it is not required and candidates may identify
host institutions through other means.

Responses to Frequently Asked Questions about the Early Independence Awards
initiative are available at http://commonfund.nih.gov/earlyindependence/faq.
The NIH Common Fund (formerly the NIH Roadmap) encourages collaboration and
supports a series of exceptionally high impact, trans-NIH programs. These
programs are supported by the Common Fund, and managed by the NIH Office
of the Director in partnership with the various NIH Institutes, Centers
and Offices. Additional information about the NIH Common Fund can be found
at http://commonfund.nih.gov.

The National Institutes of Health (NIH) "The Nation's Medical Research
Agency" includes 27 Institutes and Centers and is a component of the
U. S. Department of Health and Human Services. It is the primary federal
agency for conducting and supporting basic, clinical and translational
medical research, and it investigates the causes, treatments and cures
for both common and rare diseases. For more information about NIH and its
programs, visit http://www.nih.gov.


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From: Dieffenbach, Ann (NIH/NIGMS) [E] <DIEFFENA@nigms.nih.gov>
Date: Wed, Oct 21, 2015 at 12:40 PM
Subject: iBiology Video by NIGMS Director; Nobel Prize to Grantees; Events ...

Contents

--iBiology Video by NIGMS Director

--Nobel Prize to Long-Time NIGMS Grantees

--Watch Stetten Lecture and PRAT Symposium Live or Later

--NIH Announces Upcoming Changes to Policies, Instructions, and Forms

See: https://list.nih.gov/cgi-bin/wa.exe?A2=nigms_network;bf128e44.1510


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Subject: SMBnet Reminders

To subscribe to the SMB Digest please point your browser at
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After you subscribe, you will receive a greeting with additional information.

Submissions to appear in the SMB Digest should be sent to
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Items of interest to the mathematical biology community may be submitted
for inclusion in the SMBnet archive.  See instructions at
    http://smb.org/publications/SMBnet/pubs/fyi .

The SMB Digest is also available on the SMB Home Page at
    http://smb.org/publications/SMBnet/digest/ .

The contents of this publication may be reproduced in whole or in part with
attribution.

End of SMB Digest
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