Subject: Society for Mathematical Biology Digest
SMB Digest  December 14, 2016  Volume 16  Issue 50
ISSN 1086-6566

Editor: Ray Mejía  digest.ray@gmail.com

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:
   Minisymposium submissions are open for SMB 2017
   New deadline for the SMB prize nominations
   Bi-Monthly News from NIMBioS
   Call for Applications: 2017 NIMBioS Summer Research Program
   Keystone Symposia Gender & Metabolism Meeting, Abstracts by Dec 19
   PhD Position, Modeling bacterial communities, Lausanne, Switzerland
   PhD scholarship available
   Postdoctoral Fellowships, social evolution theory, U Penn
   Postdoc, University of Kentucky
   Postdoc, Nonlinear dynamics of biological systems, University of Lille
   Tenure Track Assistant/Associate Professor, Evolutionary Life Sciences
   Assistant/Associate Professor, Data Science for Life Sciences
   Faculty Member: Dana-Farber Cancer Institute and Harvard Medical School
   Updated NSF funding opportunity: Software Infrastructure Sustained ...
   NIH Integrated Approaches funding opportunities
   SMBnet Reminders


From: Fred Adler <adler@math.utah.edu>
Date: Wed, Dec 14, 2016 at 12:40 PM
Subject: Minisymposium submissions are open for SMB 2017

Please consider submitting a proposal for a minisymposium for the annual
meeting of the Society for Mathematical Biology scheduled for July 17-20
on the campus of the University of Utah in Salt Lake City.
The deadline for submissions is February 10, 2017.

The details are on the conference website at

Briefly, each will consist of four or five 20-25 minute presentations on a
single topic of substantial current interest and importance in mathematics
and its application to biology and medicine. We seek proposals that are
diverse in topics and speakers.


From: Amina Eladdadi <eladdadi@gmail.com>
Date: Tue, Dec 13, 2016 at 10:06 AM
Subject: New deadline for the SMB prize nominations


 **Deadline extended to Sunday, Dec 18th.**


From: (NIMBioS) <newsletter@nimbios.org>
Date: Wed, Dec 7, 2016 at 12:14 PM
Subject: Bi-Monthly News from NIMBioS

Please see


From: Catherine Crawley <ccrawley@nimbios.org>
Date: Thu, Dec 8, 2016 at 11:37 AM
Subject: Call for Applications: 2017 NIMBioS Summer Research Program

The National Institute for Mathematical and Biological Synthesis (NIMBioS) is
now taking applications for its Summer Research Experiences for Undergraduates
and Teachers (SRE). The program will be held June 5 - July 28, 2017, on the
University of Tennessee, Knoxville, campus. Undergraduate majors in biology,
math, and related fields, as well as high school teachers in biology and
mathematics, will live on campus and work in teams with UT professors,
NIMBioS researchers, and collaborators to conduct research. This year's
research projects include modeling bird mating patterns, seasonality in
multi-host systems, La Crosse encephalitis spread, immune system response
in host-virus conflict, and a project to develop computer games for teaching
biology. Stipend and housing are provided along with some funding for travel.

Application Deadline: February 15, 2017

For more information, visit http://www.nimbios.org/sre/

For more information about NIMBioS, go to http://www.nimbios.org or
contact Kelly Sturner, NIMBioS Education and Outreach Coordinator, at
ksturner@nimbios.org or Suzanne Lenhart, NIMBioS Associate Director of
Education and Outreach, lenhart@math.utk.edu

Interested high or middle school math or science teachers should send an
email to Dr. Lenhart.


From: <keystonesymposia@keystonesymposia.org>
Date: Sat, Dec 10, 2016 at 6:31 PM
Subject: Keystone Symposia Gender & Metabolism Meeting, Abstracts by Dec 19



From: Sara Mitri <sara.mitri@unil.ch>
Date: Fri, Dec 9, 2016 at 9:55 AM
Subject: PhD Position, Modeling bacterial communities, Lausanne, Switzerland

I am looking to recruit a motivated and curious PhD student to work on
building mathematical and computational models of evolving multi-species
bacterial communities at the Department of Fundamental Microbiology in the
beautiful city of Lausanne in Switzerland. The position is fully funded
with a generous salary, and can start any time after May, 2017 (exceptions
can be made to start earlier).

The successful candidate will work within a multidisciplinary group
to construct models that capture interactions between five bacterial
species. These models will then be fit to data observed in the lab, and used
to make predictions that can later be validated again in the laboratory. The
work will include dynamical systems (differential equations), individual-based
models, and possibly control theory. A background in any of these areas is
not required but will be appreciated. A passion for the subject, programming
skills and a good command of written and spoken English are required.

For more information on the type of work we do in the lab, please visit
our website: unil.ch/mitrilab. Please send questions and applications
(including a one-page motivation letter with your research interests,
a CV and evidence of a Master's degree) to sara.mitri@unil.ch.


From: BERNABEU LLINARES Miguel <Miguel.Bernabeu@ed.ac.uk>
Date: Fri, Dec 9, 2016 at 4:31 AM
Subject: PhD scholarship available

Dear colleagues,

I am currently advertising a PhD scholarship for a project entitled:
"Identifying new diabetic retinopathy biomarkers based on Optical Coherence
Tomography Angiography (OCT-A), advanced image processing, and computational
modelling" This is a collaboration with Prof. Andrew Morris, Dr Tom
MacGillivray, and Prof.  Bal Dhillon from the University of Edinburgh and
colleagues at Queen's University in Belfast.

More details can be found online at:

I would be extremely grateful if you could circulate this advert among
potential candidates at your institutions or elsewhere.


From: Akcay, Erol <eakcay@sas.upenn.edu>
Date: Thu, Dec 8, 2016 at 1:06 PM
Subject: Postdoctoral Fellowships, social evolution theory, U Penn

Multiple funded postdoctoral fellowships are available in the research
group of Erol Akcay at the University of Pennsylvania to work on the theory
of animal and human social behavior and social structure. We are seeking
enthusiastic and talented individuals to conduct original research on topics
related to the lab's interests. Specific potential topics include: dynamics
of social networks, evolution of social preferences and social norms, and
collective behavior. There will also be opportunity and encouragement to
develop own research questions within these broad areas.

The ideal candidate will have a strong background in mathematical or
computational theory in ecology, evolution, and/or social science (and a Ph.D.
in a related field), and will have demonstrated ability to conduct original
research. The fellow will join a vibrant research group working on diverse
questions in social evolutionary theory. Start date is flexible, from as
soon as possible to the Fall of 2017 at the latest. Funding is available
for multiple years, contingent on satisfactory progress.

More about the lab: The Akcay lab (http://erolakcay.wordpress.com/) is
based in the Department of Biology at the University of Pennsylvania in
Philadelphia, PA.  We study social evolution, broadly conceived, across
the tree of life. Work in the group addresses a range of questions at the
interface of ecology, evolution, and social dynamics, including: the evolution
of social behaviors and social systems of animals and humans, evolutionary
ecology of species interactions such as mutualisms, the interplay between
physiology and social behavior, dynamics of coupled natural and human systems,
and others. More information about the lab's research and links to recent
publications can be found at: http://erolakcay.wordpress.com/research and
http://erolakcay.wordpress.com/publications. The Biology Department and the
University of Pennsylvania provide a vibrant intellectual environment for
research in theoretical biology and social evolution, and ample opportunity
for cross-disciplinary collaborations. The University of Pennsylvania is
in an urban campus in the heart of Philadelphia, one of the most livable
big cities in the US.

To apply: send a CV, statement of research interests (2 pages max), two
representative papers (published or preprints), and contact information
for 3 references to Erol Akcay at eakcay@sas.upenn.edu. Applications will
be considered on a rolling basis; informal inquiries are welcome.

The University of Pennsylvania is an EOE/Affirmative Action Employer. Female,
underrepresented minority, and LGBT candidates are especially encouraged
to apply.


From: Qi, Zhen <zhen.qi@gatech.edu>
Date: Thu, Dec 8, 2016 at 2:46 PM
Subject: Postdoc, University of Kentucky

Candidates for a postdoctoral research position are sought for the Qi
Lab at the University of Kentucky located at the downtown of Lexington,
Kentucky. The successful applicant will develop computational models
and algorithms for modeling and analyzing metabolic dynamics in
the context of human cancer. This applicant will closely work with
collaborators on the campus, who will generate stable isotope-labeled
metabolomics data using a variety of analytical techniques, including MS
and NMR, from various samples including human tissues from cancer patients
(http://bioinformatics.cesb.uky.edu/bin/view/RCSIRM/).  Other high throughput
-omics data will also be available for analysis.  Furthermore, collaborators
also come from clinics, biology, biochemistry, pharmacology, computer science,
bioinformatics, and statistics.

Responsibilities Include:

 *  Build computational models of metabolism of key pathways, including
    glycolysis, the TCA cycle, nucleotide synthesis, amino acid metabolism,
    and lipid metabolism. Multiple systems are targeted for modeling,
    which may include cell lines, animals, human tissue slices, and in situ
    human tissues.
 *  Analyze stable isotope-labeled metabolomics data (and other -omics data if
    necessary) to gain mechanistic understanding of tumor metabolism during
    different stages and transitions between stages.
 *  Develop computational algorithms for data analysis and experimental design.
 *  Work with collaborators from various disciplines to relate the results of
    metabolic analysis to transcriptomics, proteomics, biophysical,
    physiological, and clinical experiments/observations.
 *  Help write manuscripts and grant proposals.

For application and further information: http://ukjobs.uky.edu/postings/126437


From: Benjamin Pfeuty <Benjamin.Pfeuty@univ-lille1.fr>
Date: Fri, Dec 9, 2016 at 8:55 AM
Subject: Postdoc, Nonlinear dynamics of biological systems, University of Lille

A Postdoctoral Position in "Nonlinear dynamics of biological systems" at the
University of Lille, France.

"Topic: Nonlinear dynamics of small biochemical network -
Theoretical investigations of stress-induced cell death decisions".

A challenge in biology is to understand the design principles of complex
biochemical networks that are required to execute sophisticated regulatory
functions in the cell. A theoretical framework to study this issue consists
in comprehensively investigating the dynamical properties of small biochemical
circuits combining a few elemental feed forward and feedback loop motifs.

Our team is investigating, computationally and experimentally, the
stress-induced cellular response - adaptation or death - depending on
the type, intensity and duration of the stress. The adaptation process
relies on negative feedback or incoherent feed forward loops while the death
decision relies on positive feedback loops. In addition, cellular response
shows significant cell-to-cell variability. These features motivate us to
investigate the nonlinear and stochastic dynamics of minimal biochemical
circuits that combine these motifs.

This theoretical project requires to perform extensive dynamical system
analysis of a broad class of low-dimensional differential equation biochemical
models, by using and combining various approaches (linear stability,
bifurcation, phase-space, control theory and stochastic approaches). This
project is closely related with other experimental and systems-biology
projects in our team.

The candidate should have (i) a strong background in applied mathematics
or physics, especially in the field of nonlinear dynamical systems; (ii)
some interest for biology.

The position is for one year renewable, and would start anytime in
the first semester of 2017. Net annual salary is about 28000EU and
includes a benefits package (health insurance, retirement and unemployment
benefits). The laboratory (http://www.phlam.univ-lille1.fr/) is located on
the Villeneuve d'Ascq campus of the University of Lille. Lille is a lively
city connected by high-speed train to Brussels (30mn), Paris (1h) and London
(1h30). Applicants should send a letter of motivation, a CV including a
complete list of publication and at least 2 letters of recommendation to:
quentin.thommen@univ-lille1.fr and Benjamin.pfeuty@univ-lille1.fr.

For more information: http://www.phlam.univ-lille1.fr/spip.php?article1066


From: Rampal S. Etienne <r.s.etienne@rug.nl>
Date: Wed, Dec 14, 2016 at 8:57 AM
Subject: Tenure Track Assistant/Associate Professor, Evolutionary Life Sciences

The University of Groningen offers 5 Tenure Track Assistant or Associate
Professor positions in Evolutionary Life Sciences

The Groningen Institute for Evolutionary Life Sciences (GELIFES)
was established in 2015 and is the largest institute of the Faculty of
Mathematics and Natural Sciences (FMNS) of the University of Groningen.

GELIFES fills a special niche in the life sciences by covering and integrating
mechanistic, evolutionary and ecological approaches.  GELIFES' main aim is
to integrate proximate and ultimate approaches in the Life Sciences. This
strategy generates better understanding of fundamental biological processes
and contributes to the solution of societal problems. Our research fields
include behavioural biology, chronobiology, ecology and conservation biology,
evolutionary biology, genetics and genomics, neurobiology, physiology and
theoretical biology, using a wide array of research tools from molecular,
through the whole organism, to population and community level, under
laboratory, semi-natural and field conditions. We study a wide array of
species, from microbes, algae, plants and insects to vertebrates such
as fish, birds, rodents, marine mammals and humans. Our institute is the
driving force of the Adaptive Life Programme, one of four integrative focus
research areas of the FMNS.

To further strengthen Adaptive Life, the University of Groningen and FMNS
enabled us to hire for 5 new faculty and 25 PhD scholarship positions,
as well as to invest in large scale new facilities. This support also
facilitated the establishment of the Sustainable Landscape Competence Centre
and the Brain and Behavioural Competence Centre, in order to attract external
research funds and further organize our outreach.

GELIFES has the following vacancies for Tenure Track or Associate Professor
positions, depending on career stage of the candidate:

 - a position in Evolutionary Ecology of Marine Animals
 - a position in Chronobiology
 - a position in Microbial Ecology and Evolution
 - 2 positions in Evolutionary Medicine

Candidates are expected to set up an independent research line within one of
these fields, complementary to ongoing research within the institute. The
candidates are expected to have an interest in strengthening the research
program and faculty theme called Adaptive Life in which biological adaptation
is studied by integrating mechanistic with evolutionary approaches. Candidates
are expected to attract funding for new PhD projects and attain a leading
international position in the field. They are excellent teachers who can
attract students of different disciplines and have an interest in teaching
at both the bachelor, master and PhD level.

The University of Groningen has adopted an active policy to increase the
number of female scientists across all disciplines of the university.
Therefore, female candidates are especially encouraged to apply.

For more information on this position, qualifications and conditions of
employment, please check the vacancy website:
http://www.rug.nl/about-us/work-with-us/job-opportunities/overview. The
deadline for application is January 25th 2017.

For more information on GELIFES, its staff and research, please visit:

For more information on the Adaptive Life Programme, please visit:


From: Mark van Rossum <mvanross@inf.ed.ac.uk>
Date: Fri, Dec 9, 2016 at 6:11 AM
Subject: Assistant/Associate Professor, Data Science for Life Sciences

Applications are invited for a Lecturer, Senior Lecturer or Reader in Data
Science for the Life Sciences to join the School of Informatics, at the
University of Edinburgh.

We seek candidates that combine research in the Life Sciences with innovative
computational data analysis approaches. Candidates are particularly sought
with research interests in areas complementing, or reinforcing, existing
strengths in the Institute for Adaptive and Neural Computation, including
Computational Biology, Bioinformatics, and Computational Neuroscience. The
University of Edinburgh hosts the largest academic informatics research
faculty in Europe. We also benefit from extensive links to world leading
biological, biomedical and clinical research institutes and companies both
locally and internationally.



From: Laura Kleiman <kleiman@jimmy.harvard.edu>
Date: Wed, Dec 14, 2016 at 11:01 AM
Subject: Faculty Member: Dana-Farber Cancer Institute and Harvard Medical School

Computational Biology
Assistant/Associate Professor
Dana-Farber Cancer Institute

The Dana-Farber Cancer Institute (DFCI) and Harvard Medical School (HMS)
seek an accomplished and innovative research faculty member to join the
newly formed cBio Center at DFCI. The Center is an open and collaborative
environment with a focus on computational biomedicine and cancer systems
biology and is headed by Chris Sander. We provide an opportunity to pursue
basic and translational research with an emphasis on solving biological
problems using computational and data science methods, and to collaborate with
cancer researchers and clinicians to impact clinical trials and cancer care
in the age of genomically informed personalized medicine. The primary position
will be in the Department of Biostatistics and Computational Biology at DFCI,
with an academic appointment in the Department of Biomedical Informatics
at HMS.

Particular areas of interest include:
 *  machine learning and big data sciences
 *  biomedical image analysis
 *  phenotypic heterogeneity & single cell profiling
 *  computational immunology
We also encourage strong applications in other areas of quantitative biology.

Requirements: a Ph.D. or M.D./Ph.D. degree and a significant record
of asking good questions, advancing technology, making discoveries, and
reporting these in peer-reviewed publications. Academic rank at Assistant or
Associate Professor will be according to experience and productivity. Please
send the following to chair@jimmy.harvard.edu, best by January 10, 2017: 1)
a letter of application including a concise statement of past, current, and
future research, 2) a curriculum vitae (preferably using the IMPACT format,
see http://sanderlab.org/associateprofessor.html), 3) PDFs of your key
publications (max four), and 4) contact information for four references. In
addition, please ask your references to send letters of support to Giovanni
Parmigiani, chair@jimmy.harvard.edu. Applications will be reviewed once
the application package is complete.

We are an equal opportunity employer and all qualified applicants will receive
consideration for employment without regard to race, color, religion, sex,
sexual orientation, gender identity, national origin, disability status,
protected veteran status, or any other characteristic protected by law. We
especially encourage women to apply.


From: Henry Warchall <hwarchal@nsf.gov>
Date: Wed, Dec 7, 2016 at 6:59 PM
Subject: Updated NSF funding opportunity: Software Infrastructure Sustained ...

Dear Colleagues,

An updated NSF program solicitation (NSF 17-526) is now available:

  Software Infrastructure for Sustained Innovation (SSE, SSI, S2I2)

Please see


for details.


From: Whang, Kenneth C. <kwhang@nsf.gov>
Date: Sun, Dec 11, 2016 at 3:28 PM
Subject: NIH Integrated Approaches funding opportunities

NIH BRAIN is now offering a family of "Integrated Approaches" NIH BRAIN FOAs
that range from small or exploratory, targeted brain circuits projects with
specific research deliverables (R21, R01) to large, team-research projects
with extensive and elaborated goals and a 5-plus year horizon of discovery
(U19). Potential applicants are encouraged to visit the NIH BRAIN Initiative
website for information and guidance


Subject: SMBnet Reminders

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