SMB Digest January 21, 2014 Volume 14 Issue 4
ISSN 1086-6566
Editor: Wandi Ding wding1(at)gmail(dot)com
Note:
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application for membership, may be found in the SMB Home Page,
Access the Bulletin of Mathematical Biology, the official journal
Inquiries about membership or BMB fulfillment should be sent to
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Issue's Topics:
2014 MBI Undergraduate Summer Research Program
Adaptive dynamics workshop in Milano, May 26-30
JEEP 2014 - Lyon March 26-28
Santorini 2014 conference
Journal of Mathematical Neuroscience - recent articles
Bulletin of Mathematical Biology, Vol. 76, Issue 1
NIH Big Data to Knowledge Training FOAs (K01 and R25s)
EMBL course and conference memorabilia
PhD in Mathematical Demography and Ecology, U of Amsterdam
PhD in computational modelling, U of Groningen
Postdoc position - Biological Engineering - MIT
Postdoc position - University of Oldenburg, Germany
Postdoc position - U of Michigan Medical School
Postdoc position - Computational Biology, Ryerson U, Canada
SMBnet Reminders
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Date: Wed, Jan 15, 2014 at 3:50 PM
Subject: 2014 MBI Undergraduate Summer Research Program
2014 MBI Undergraduate Summer Research Program
(June 2 - August 15, 2014)
This program introduces students to exciting new areas of mathematical
biology and involves them in collaborative research with their peers
and faculty mentors. For full consideration, completed applications
must be received by Monday, January 27, 2014. The program consists
of three parts:
-Two-week Introduction (June 2-13, 2014): Tutorials, computer labs,
and team efforts designed to introduce students to a variety of
topics in mathematical biology. Applications for the TWO-WEEK
INTRODUCTION ONLY will be due in April.
-Eight week REU Program (June 16 - August 8, 2014): An
individualized research experience as part of a research team
at a participating institution. There are 14 projects to choose
from.
-Capstone Conference (August 11-15, 2014): A student centered
conference featuring talks and posters by student researchers
in math biology, keynotes by prominent math biologists, and a
graduate studies recruitment fair. Applications for CAPSTONE
CONFERENCE ONLY will be due in June.
A complete application will require:
-Two letters of reference
-A ranked list of the three projects that you want to participate
in (see above)
-A statement indicating your reasons for wanting to participate
in this program
For full consideration, completed applications must be received
by Monday, January 27, 2014.
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Date: Mon, Jan 13, 2014 at 1:44 PM
Subject: Adaptive dynamics workshop in Milano, May 26-30
9th SICC International School Topics in Nonlinear Dynamics
MODELLING AND ANALYSIS OF INNOVATION AND COMPETITION PROCESSES
May 26-30, 2014, Politecnico di Milano, Milano, Italy
The aim of the course is to present adaptive dynamics (AD), a
mathematical framework to model long-term evolution of coevolving
multi-species communities, with special emphasis on the generation
of diversity through evolutionary branching. Evolutionary
branching takes place when a resident and a similar mutant type
coexist in the same environment and natural selection favors
further differentiation between the two types. The evolutionary
dynamics are described as a random walk in the space of the
coexisting strategies, a space with variable dimension according to
evolutionary branching and extinction. Evolution proceeds in the
direction of the local fitness gradient and can be approximated
by deterministic continuous dynamics ruled by the AD canonical
equation. Applications to relevant biological communities, as
well as to social and economic sciences, where innovations and
competition play the role of mutations and natural selection,
will be presented.
The course is part of the teaching activities organized by the
PhD Program in Information Technology at Politecnico di Milano,
yet it is not only addressed to PhD students, but to all
researchers working in any areas of science and engineering and
interested in modelling innovation and competition processes.
Advanced theoretical topics and cutting-edge applications of AD
will be presented in the workshop by the leading scientists in
the field.
All presentations will be given in English.
Lecturers
-Fabio Della Rossa, Department of Electronics, Information, and
Bioengineering, Politecnico di Milano
-Fabio Dercole, Department of Electronics, Information, and
Bioengineering, Politecnico di Milano
-Ulf Dieckmann, Evolution and Ecology Program, International
Institute for Applied Systems Analysis (to be confirmed)
-Stefan Geritz, Department of Mathematics and Statistics,
University of Helsinki
-Mats Gyllenberg, Department of Mathematics and Statistics,
University of Helsinki
-Christopher Klausmeier, W. K. Kellogg Biological Station,
Michigan State University
-Pietro Landi, Department of Electronics, Information and
Bioengineering, Politecnico di Milano
-Géza Meszéna, Department of Biological Physics, Eötvös
University, Budapest
-Hans Metz, Mathematisch Instituut, Universitet Leiden
-Kalle Parvinen, Department of Mathematics and Statistics,
University of Turku
-Tadeas Priklopil, Department of Mathematics and Statistics,
University of Helsinki
-Sergio Rinaldi, Department of Electronics, Information and
Bioengineering, Politecnico di Milano
For information and application visit
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Date: Tue, Jan 14, 2014 at 10:42 AM
Subject: JEEP 2014 - Lyon March 26-28
Deadline to submit lecture abstract: 17 January 2014!
The procedure is detailed on the dedicated page of the conference
We also remind you the deadline for registration with negociated
fees is the 16th of february. The deadline is near, do not wait to
We remain at your disposal for any complementary information, and
are waiting for you in Lyon for this anniversary edition.
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Date: Fri, Jan 17, 2014 at 6:36 AM
Subject: Santorini 2014 conference
You are kindly invited to participate and possibly contribute an
abstract (until end of February) to the upcoming Santorini 2014
conference on systems biology and applications to personalized
health and therapy (be it pharmaceutical or nutritional).
The Santorini Conferences are bringing together scientists from
various origins interested in genetics and biochemical variations
in man and its impact on the origin, prediction, prevention,
diagnosis and therapy of human multifactorial disorders.
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Date: Fri, Jan 17, 2014 at 6:25 AM
Subject: Journal of Mathematical Neuroscience - recent articles
The Journal of Mathematical Neuroscience publishes research
articles on the mathematical modeling and analysis of all areas
of neuroscience. The current list of journal articles is
Stabilization of Memory States by Stochastic Facilitating
Synapses Miller P
Analysis of a Scenario for Chaotic Quantal Slowing Down of
Inspiration Baesens C and MacKay RS
Mechanisms of Intermittent State Transitions in a Coupled
Heterogeneous Oscillator Model of Epilepsy Goodfellow M
and Glendinning P
Analytical Insights on Theta-Gamma Coupled Neural Oscillators
Fontolan L, Krupa M, Hyafil A and Gutkin B
Gap Junctions, Dendrites and Resonances: A Recipe for Tuning
Network Dynamics Timofeeva Y, Coombes S and Michieletto D
All articles are Open Access.
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Date: Sat, Jan 18, 2014 at 12:41 PM
Subject: Bulletin of Mathematical Biology, Vol. 76, Issue 1
Volume 76 Number 1 is now available on SpringerLink
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Date: Fri, Jan 17, 2014 at 9:04 AM
Subject: NIH Big Data to Knowledge Training FOAs (K01 and R25s)
The NIH Big Data to Knowledge (BD2K) initiative aims to enable
biomedical scientists to extract full value from biomedical big
data. BD2K is developing programs to facilitate the use of big
data, develop new software tools, enhance training, and discover
and disseminate advances in data science. We are pleased to
announce the release of three FOAs focused on training.
1)RFA-HG-14-007 Mentored Career Development Award in Biomedical
Big Data Science for Clinicians and Doctorally Prepared
Scientists(K01)
2)RFA-HG-14-008 Courses for Skills Development in Biomedical
Big Data Science (R25)
3)RFA-HG-14-009 Open Educational Resources for Biomedical
Big Data (R25)
The deadline for submission is April 1, 2014.
Additional information may be obtained by contacting
interested colleagues.
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Date: Sat, Jan 18, 2014 at 10:03 AM
Subject: EMBL course and conference memorabilia
This year the European Molecular Biology Laboratory is celebrating
its 40th anniversary!
As part of the anniversary celebrations, the EMBL Course and
Conference Office is planning an exhibition showcasing training
at EMBL over the years. The exhibition will be open throughout the
year in the Advanced Training Centre at EMBL Heidelberg, Germany
and will be available to all visitors of our training activities.
We are currently in the process of putting together the exhibition,
and would like to ask for your help in acquiring EMBL course and
conference memorabilia.
By submitting a memorabilia you will have the chance to win a
Kindle Paperwhite!
Items we are looking for include:
-Images taken between 1976 - 2010 at EMBL training events
(lectures, poster sessions, lab practicals, parties, etc )
-Venue images (MPI, Operon, Poster session in the EMBL tent)
-Abstract books and event posters pre 1995
-Any other memorabilia you might have! (eg. bags, pens, lanyards,
registration badges)
-Testimonials / memories / stories from past courses and conferences
We would be very happy if you could help us with this project, and
would be grateful if you could send us your memorabilia by 7 February 2014.
Should you have any questions at all, please don?t hesitate to contact
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Date: Wed, Jan 8, 2014 at 5:46 AM
Subject: PhD in Mathematical Demography and Ecology, U of Amsterdam
A funded PhD position is available with Dr. Hal Caswell, in the
Theoretical Ecology Research Group within the Institute for
Biodiversity and Ecosystem Dynamics at the University of Amsterdam.
This position is part of a research program on Individual
Stochasticity and Population Heterogeneity in Plant and Animal
Populations, which is funded by an ERC Advanced Grant.
Variation among individuals in reproduction, longevity, and
other demographic traits, is universal. It has two potential
sources: heterogeneity (biological differences among
individuals in their properties) and individual stochasticity
(random differences resulting from vital rates applied to
identical individuals). The goal of this research program is to
develop a comprehensive theory for incorporating individual
stochasticity and heterogeneity into demographic models for
plants, animals, and humans.
This Ph.D. project will involve both theoretical development
and application of matrix population models, Markov chain models,
and perturbation analysis to explore variation in longevity,
lifetime reproduction, and other demographic properties.
Applications may include populations of conservation and
management concern, evolutionary questions related to
senescence and resource allocation, and measures of health
status and health expectancy in human and non-human populations.
The Theoretical Ecology group at UvA currently comprises 2
professors, 3 assistant professors, 1 post-doc, and 4 PhD students,
and currently hosts two ERC Advanced Grants. It has active
research programs in structured population modelling,
resource-consumer interactions, epidemiology, demography,
and evolutionary and eco-evolutionary theory.
The candidate should have:
-A Master?s degree, with strong quantitative skills, in ecology,
population biology, or demography, or a degree in applied
mathematics or statistics with experience in population biology.
-Interest in developing new theory in population biology.
-Good computer skills, including programming in Matlab or R.
-Willingness to work in a multidisciplinary environment.
To apply, please visit the University of Amsterdam web page at:
Applications should be sent before 28 January 2014, via email, to:
Please quote the vacancy number in the subject field. Interviews,
possibly via Skype, will be held after 28 January 2014.
For additional information, please contact Hal Caswell at
The project starts early 2014. The full-time appointment will be on
a temporary basis for a maximum period of four years (18 months plus
a further 30 months after a positive evaluation) and should lead to
a dissertation (PhD thesis). An educational plan will be drafted
that includes attendance of courses and (international) meetings.
The PhD Student is also expected to assist in teaching of
undergraduates. The full-time gross monthly salary will range from
? 2,083 in the first year to ? 2,664 in the final year, according
to the Dutch salary scales for PhD students. The Collective Labour
Agreement Dutch Universities is applicable. The annual salary
will be increased by 8 % holiday allowance and 8,3 % end-of-year
bonus.
Applications should include a detailed CV including educational
experience, a list of publications, a letter describing research
interests, and the names and contact addresses of two academic
references from which information about the candidate can be
obtained. Combine these materials into a single PDF file.
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Date: Fri, Jan 17, 2014 at 4:53 AM
Subject: PhD in computational modelling, U of Groningen
PhD(4 years) position in computational modelling of biological systems
The behavioural Ecology and Self-organization Group at the University
of Groningen is seeking to recruit a PhD student to strengthen its
research team on Self-organization of Social systems. The position
is full-time and available immediately.
Research environment:
The position is part of the project ??Optimisation of navigation
for intercepting prey during aerial hunting by birds?, funded
by a Grant (ALW) from the Netherlands Science Foundation (NWO) to
Prof. dr. Charlotte Hemelrijk. Key objective of this project is
to understand how the hunting strategy of a raptor has been
shaped by evolution: whether evolution has optimised the guidance
of the raptor for hunting as a specialist or as generalist and hat
the robustness is of the optimised prey-targeting system in
relation to the behaviour of the prey, whether it is unwary or
trying to escape, it is flying solitarily or is flocking. Daily
supervision will come from Prof. dr. Hemelrijk and Dr. Hanno
Hildenbrandt. Dr. Graham Tayler (Oxford Flight Group, UK)
will co-supervise the project.
Requirements:
The successful candidate will have previous research experience
in theoretical modeling, be in good command of the English
language (oral and written) and possess excellent communication
skills. (indicated by the ability to write scientific papers and
deliver presentations). Since studies on self-organisation are
highly interdisciplinary, successful candidates are expected to
demonstrate an active and supportive approach to inter-disciplinary
research and collaborate with other group members. Suitable
candidates can be either individuals with a background in the
computational (life-) sciences, with interest in evolutionary
and biological questions, or evolutionary biologists with
experience in computational modeling.
Candidates for the PhD position should have:
-MSc in mathematical biology, a MSc in computational science
with focus on biology or an MSc in computational physics with
specialization in biology, MSc in Artificial Intelligence with
a specialization in an area of computational or mathematical
biology or a MSc in Biology, with a specialization in an
area of computational or mathematical biology.
-Experience with developing computer simulation code and a
sufficient background in mathematics.
-A strong interest in biomechanics of flight and attack,
interest in collective, swarming behavior. Candidates with
research experience in these areas are particularly encouraged
to apply.
Conditions of employment:
The University of Groningen offers a salary of ? 2,042 (salary
scale 50.0) gross per month in the first year, up to a maximum of
? 2,612 (scale 50.3) gross per month in the final year, based on
a full-time position. The position requires residence in
Groningen and must result in a PhD thesis within the 4-year
contract period. A PhD training program is part of the
agreement and the successful candidate will be enrolled in
the Graduate School of Science. The successful candidate
will first be offered a temporary position of one year with the
option of renewal for another three years. Prolongation of
the contract is contingent on sufficient progress in the
first year to indicate that a successful completion of
the PhD thesis within the next three years is to be expected.
How to apply:
Applications, including a letter of motivation, a curriculum
vitae, a list of publications (if any), a list of examination
marks, and the contact information of three academic referees,
must be submitted online through the website
The position will remain open until filled. All applications
received by February 15, 2014 will be given full consideration.
For further information, please consult
Informal enquiries can be made to prof. dr. Charlotte K Hemelrijk
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Date: Tue, Jan 14, 2014 at 10:20 AM
Subject: Postdoc position - Biological Engineering - MIT
POSTDOCTORAL ASSOCIATE, Biological Engineering, to join a $32M,
five-year project funded by DARPA and the NIH that was launched
last summer with the aim of creating a game-changing paradigm for
drug discovery and development. The project includes teams at
Massachusetts Institute of Technology, Draper Laboratory, as well
as tissue engineering/device/pharma/biotech companies and is aimed
at creating a platform that supports ten interacting micro-organ
systems and associated sensors for assessing cellular responses to
inflammatory cues and therapeutic interventions. Will work on a
project involving computational analysis of how therapeutic agents,
including biomolecules like cytokines, distribute throughout the
system and act at the micro-organ. Will be responsible for
mechanism-based models relating in vitro data to human in vivo data
using mechanistic PKPD and systems pharmacology models. The project
involves very close interaction with analytical chemists, biologists,
and the platform hardware design team. Position is located at MIT,
Cambridge, MA.
REQUIRED: a Ph.D. or postdoctoral experience modeling complex
biological systems at the cellular and molecular scale; ability
to link clinical data to data-driven computational models;
demonstrated ability to interact in a highly collaborative way
with other modelers and experimentalists; and hands-on knowledge
of state-of-the-art modeling and simulation and data fitting with
MATLAB. Experience in physiology-based pharmacokinetic modeling
(PBPK) and in-vitro in-vivo correlation (IVIVC) is highly desirable.
Experience with inflammation models and quantitative structure
and activity relationship (QSAR) is also desired. Job #10784
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Date: Wed, Jan 15, 2014 at 3:39 AM
Subject: Postdoc position - University of Oldenburg, Germany
Postdoc position (Theoretical Ecology): Functional consequences
of spatial biodiversity patterns.
Institute for Chemistry and Biology of the Ocean (ICBM)
University of Oldenburg, Germany
within the project "Biodiversity ? Ecosystem Functioning across
marine and terrestrial ecosystems (BEFmate)"
BEFmate is a joint project by the University of Oldenburg and the
Georg-August University of Göttingen. It addresses biodiversity-
ecosystem function relationships across marine and terrestrial
ecosystems employing meta-analyses, syntheses, ecological modeling
and empirical experiments. A particular focus of the subproject B2
is the relationship between biodiversity and ecosystem function
in spatially structured ecosystems. To explore the functional
consequences of spatial biodiversity patterns, we will establish
mathematical models that describe the meta-community dynamics,
biodiversity, ecosystem function, and species turnover in networks
of interconnected habitat patches. Using these models we will
study the hypothesis whether increasing spatial complexity alters
the relationship between biodiversity and ecosystem function
and if self-organized spatial heterogeneity can be a significant
driver of biodiversity. The models will further be used to closely
accompany the planed field experiments on artificial islands in BEFmate.
The applicant will work in the mathematical modelling group of Prof.
Dr. Bernd Blasius.
Applicants must have an above-average doctoral or PhD degree in
theoretical ecology, applied mathematics, physics, or related
discipline. Applicants experienced in biodiversity research or
one of the relevant disciplines (theoretical biology, mathematical
modeling, statistical physics) are particularly encouraged to apply.
Applicants should have a strong interest to work in an
interdisciplinary team and must have good knowledge of English.
Salary will be according to TVL E13 (100%).
The position is for three years. Start date: March 1, 2014.
The Carl von Ossietzky University of Oldenburg is an equal
opportunity/affirmative action employer. In order to increase the
percentage of female staff members, qualified women are especially
encouraged to apply. Applicants with disabilities will be
preferentially considered in case of equal qualification.
The deadline for applications is January 30, 2014. Application
documents must include the following: the reference number: PD.B2,
a curriculum vitae, a list of publications, talks and posters,
copies of certificates, letter(s) of reference. Please send your
application as a single PDF document to: Prof. Helmut Hillebrand,
Dr. Helmut Hillebrand, Universität Oldenburg, Postfach 2503;
26111 Oldenburg)
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Date: Thu, Jan 16, 2014 at 10:07 PM
Subject: Postdoc position - U of Michigan Medical School
Dr. Santiago Schnell is announcing an opening for a postdoctoral
position to work in the area of mathematical and computational
biology at his research group. The postdoctoral fellow will
specifically work in investigating how to control, influence
and inhibit the aggregation of amyloid proteins in protein
folding diseases. The research fellow will also interact with
our experimental collaborators in this area at the University
of Michigan.
Candidates should have experience in the mathematical modeling
and numerical solutions of differential equations, and an
understanding of chemical dynamics, biochemical kinetics,
biochemistry and cell biology. This position would suit
individuals who have a first degree in mathematics, physics,
engineering or biomedical sciences, and a PhD in applied
mathematics, systems biology, biophysics, theoretical physical-
chemistry, biomedical or chemical engineering. Candidates must
enjoy working in a team and have a meticulous approach to their
work. They must have experience writing publications and very
good communication skills. This position is available immediately
for a period of five years. It will be renewed yearly subject to
satisfactory performance. Salary level is determined by the
number of full years of relevant postdoctoral experience at
the NIH NRSA scale.
Applications, including a full CV, a covering letter explaining
suitability for the position and how the candidate satisfies
the selection criteria, and the names and addresses of two
referees should be sent to Dr. Santiago Schnell, University of
Michigan Medical School, Department of Molecular & Integrative
Physiology, Brehm Center 5132, 1000 Wall Street, Ann Arbor, MI
Candidates must arrange for their referees to send references
direct to Dr. Santiago Schnell (fax or email is sufficient).
Review of applications will continue until the position is filled.
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Date: Sun, Jan 19, 2014 at 7:58 AM
Subject: Postdoc position - Computational Biology, Ryerson U, Canada
A postdoctoral position is available in Computational Biology in
Toronto, Canada. This position provides an opportunity to engage
in research in Applied Mathematics, with a limited amount of teaching.
The salary is competitive, with funding provided for one year.
We are seeking qualified and motivated applicants in Applied
Mathematics, to work on interdisciplinary projects aimed at
developing stochastic modelling and simulation tools for studying
biological systems. The ideal candidate would have a strong
background in Applied Mathematics (Numerical Analysis and Probability)
and/or Computer Science. Strong programming skills in Matlab are
mandatory. Experience with dynamical systems is expected. In
addition, knowledge of biological/chemical reaction modelling
and stochastic simulation is considered an asset.
The fellowship is open to candidates of any nationality and
selection will be based upon the candidate's research potential
and teaching ability. Ideally the job will begin as early as
May 1, 2014, however there is some flexibility in the starting
date. The research will be led jointly by Dr. Silvana Ilie and
Dr. Katrin Rohlf.
The screening process will start on February 17, 2014, and
continue until the position is filled. Applicants should
submit a curriculum vitae and three letters of recommendation.
At least one of these letters should report on the candidate's
teaching abilities. Application material and reference letters
We appreciate all replies to this advertisement, but only
applicants under consideration will be contacted. Ryerson
University has an Employment Equity Program and encourages
applications from all qualified candidates, including aboriginal
peoples, persons with disabilities, members of visible
minorities, and women.
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