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Subject: SMB Digest v13i16
SMB Digest April 19, 2013 Volume 13 Issue 16
ISSN 1086-6566
Editor: Amina Eladdadi eladdada(at)strose(dot)edu
Note:
Information about the Society for Mathematical Biology, including an
application for membership, may be found in the SMB Home Page,
Access the Bulletin of Mathematical Biology, the official journal of SMB, at
Inquiries about membership or BMB fulfillment should be sent to
membership(at)smb(dot)org .
Issue's Topics:
ToC: MBE Special Issue on Math. Methods in Sys.Bio...V10, No3, June 2013
Workshop: Stochastic....Approaches to Immunology, July 22-26, Edinburgh
Winter School: Giambiagi, Info. proc. in Bio. Sys.. July 15-19, Argentina
CfP: IEEE International Conference on Data Mining (ICDM) 2013
PhD: Mathematical Biology at the University of Adelaide, Australia
PhD: Retinal Hemodynamics at INRIA Paris, France
Postdoc: Epidemiological Modeling for Antimicrobial.., Canada
Postdoc: Computational and Systems Biology, Lille, France
NSF supported-Advanced Computational Infrastructure Open for Research
Job Opportunities - Co57 Systems
SMBnet Reminders
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Sent: Monday, April 15, 2013 9:06 PM
Subject: ToC: MBE Special Issue on Math. Methods in Sys.
Bio...V10, No3, June 2013
Mathematical Biosciences and Engineering (MBE):
Special Issue on Mathematical Methods in Systems Biology and
Population Dynamics is now available online.
Volume 10, Number 3, June 2013
From the guest editors
Urszula Ledzewicz, Avner Friedman, Jacek Banasiak, Heinz Schättler and
Edward M. Lungu
A singularly perturbed SIS model with age structure
Jacek Banasiak, Eddy Kimba Phongi and Miros?aw Lachowicz
Diffusion rate determines balance between extinction and proliferation in
birth-death processes
Hilla Behar, Alexandra Agranovich and Yoram Louzoun
Gompertz model with delays and treatment: Mathematical analysis
Marek Bodnar, Monika Joanna Piotrowska and Urszula Forys
Mathematical modeling of glioma therapy using oncolytic viruses
Baba Issa Camara, Houda Mokrani and Evans K. Afenya
Identifying preseizure state in intracranial EEG data using diffusion
kernels
Dominique Duncan, Ronen Talmon, Hitten P. Zaveri and Ronald R. Coifman
A partial differential equation model of metastasized prostatic cancer
Avner Friedman and Harsh Vardhan Jain
Can malaria parasite pathogenesis be prevented by treatment with tumor
necrosis factor-alpha?
Avner Friedman and Edward M. Lungu
Identifying requirements for the invasion of a tick species and tick-borne
pathogen through TICKSIM
Holly Gaff and Robyn Nadolny
Finite element approximation of a population spatial adaptation model
Gonzalo Galiano and Julian Velasco
Shear-thinning effects of hemodynamics in patient-specific cerebral
aneurysms
Alberto Gambaruto, João Janela, Alexandra Moura and Adélia Sequeira
On the sensitivity of feature ranked lists for large-scale biological data
Danuta Gawe? and Krzysztof Fujarewicz
An example from the world of tsetse flies
John Hargrove
Mathematical modeling of citrus groves infected by huanglongbing
Karly Jacobsen, Jillian Stupiansky and Sergei S. Pilyugin
Hybrid discrete-continuous model of invasive bladder cancer
Eugene Kashdan and Svetlana Bunimovich-Mendrazitsky
Calcium waves with mechano-chemical couplings
Bogdan Kazmierczak and Zbigniew Peradzynski
Spatial stochastic models of cancer: Fitness, migration, invasion
Natalia L. Komarova
Equilibrium solutions for microscopic stochastic systems in population
dynamics
Miros?aw Lachowicz and Tatiana Ryabukha
On optimal chemotherapy with a strongly targeted agent for a model of
tumor-immune system interactions with generalized logistic growth
Urszula Ledzewicz, Omeiza Olumoye and Heinz Schättler
On the MTD paradigm and optimal control for multi-drug cancer chemotherapy
Urszula Ledzewicz, Heinz Schättler, Mostafa Reisi Gahrooi and Siamak
Mahmoudian Dehkordi
Modeling bacterial attachment to surfaces as an early stage of biofilm
development
Fadoua El Moustaid, Amina Eladdadi and Lafras Uys
Modeling the role of drug barons on the prevalence of drug epidemics
John Boscoh H. Njagarah and Farai Nyabadza
A simple model of carcinogenic mutations with time delay and diffusion
Monika Joanna Piotrowska, Urszula Fory?, Marek Bodnar and Jan Poleszczuk
Application of evolutionary games to modeling carcinogenesis
Andrzej Swierniak and Michal Krzeslak
A flexible multivariable model for Phytoplankton growth
Mohammad A. Tabatabai, Wayne M. Eby, Sejong Bae and Karan P. Singh
T model of growth and its application in systems of tumor-immune dynamics
Mohammad A. Tabatabai, Wayne M. Eby, Karan P. Singh and Sejong Bae
Computational modeling approaches to studying the dynamics of oncolytic
viruses
Dominik Wodarz
----------------------------------------------------
Date: Fri, Apr 12, 2013 at 10:38 AM
Subject: Workshop: Stochastic... Approaches to Immunology,
July 22-26, Edinburgh
Stochastic, Statistical and Computational Approaches to Immunology
Jul 22, 2013 - Jul 26, 2013
ICMS, 15 South College Street, Edinburgh, EH8 9AA
The primary objective of this workshop is to continue the current
effort in Mathematical Immunology that has been initiated by a series
of international meetings.
For further details and registration, please visit
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Sent: Friday, April 12, 2013 11:07 AM
Subject: Winter School: Giambiagi, Info. proc. in
Bio. Sys.. July 15-19, Argentina
XV Giambiagi Winter School
Information processing in Biological Systems: From cells to equations,
and back.
Buenos Aires, Argentina
July 15-19, 2013
The central theme of the meeting is information processing in biological
systems. The meeting includes a one week school of several mini-courses,
and a short workshop where young participants will be able to interact among
themselves and with the lecturers. Courses will cover different key aspects of
the proposed theme, such as gene regulatory networks, dynamical aspects
of signaling pathways, molecular noise, the quantification of information in
cellular processes and the physics of the cell.
Confirmed short courses:
Cellular response to conflictive inputs.
Small regulatory networks and motifs. James Ferrell (Stanford)
Noise in gene regulatory networks. Ivo Sbalzarini (MPI-CBG)
Transition to multicellularity. Ray Goldstein (Cambridge)
Information processing in tissues. Marcos González-Gaitán (Geneva)
Financial Support and registration fees:
There are no registration fees to attend the School. Partial financial support will be
available for a limited number of students covering transportation and lodging.
More information
----------------------------------------------------
Date: Mon, Apr 15, 2013 at 7:56 PM
Subject: CfP: IEEE International Conference on Data
Mining (ICDM) 2013
ICDM '13: The 13th IEEE International Conference on Data Mining
Sponsored by the IEEE Computer Society
Dallas, Texas, US
8-11 December 2013.
Important Dates
Workshop proposals: April 2
Workshop notification: April 30
ICDM contest proposals: April 30
Full paper submissions: June 21
Demo and tutorial proposals: August 3
Workshop paper submissions: August 3
Conference paper, tutorial, demo notifications: September 20
Workshop paper notifications: September 24
Conference dates: December 8-11 (Sunday-Wednesday)
All paper submissions will be handled electronically. Detailed
instructions are provided on the conference home page at
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Date: Thu, Apr 18, 2013 at 3:50 AM
Subject: PhD: Mathematical Biology at the University of Adelaide, Australia
A fully funded PhD studentship is available in the School of
Mathematical Sciences, University of Adelaide from July 2013. The
studentship is associated with the recent grant of an ARC Discovery
Early Career Researcher Award to Dr Edward Green. Potential topics
include:
* Mathematical modeling of the mechanics of complex biological
materials, with applications in tissue engineering and the mechanics
of the intervertebral disc
* Mathematical modeling of the role of cell-cell and
cell-extracellular matrix interactions in tissue development
These projects will involve the development of continuum models
(PDEs), with scope for also investigating individual-based modeling
approaches, depending on the interests of the student.
Applicants should have a Masters degree (or, in the case of Australian
applicants, a good Honours degree) in mathematics, physics,
engineering or a related subject, and must satisfy the entry
requirements of the Adelaide Graduate Centre
background in mathematical modeling, partial differential equations,
and programming in Matlab would be an advantage. Some knowledge of
biology would be helpful, but is not essential.
The studentship provides a stipend of AU$ $24,653 per year. A fee
waiver for international applicants has been agreed in principle.
Potential applicants should contact Dr Edward Green
----------------------------------------------------
Date: Mon, Apr 15, 2013 at 3:48 PM
Subject: PhD: Retinal Hemodynamics at INRIA Paris, France
PhD position on Retinal Hemodynamics at INRIA Paris, France
This research will be conducted under the supervision of Jean-Frederic
Gerbeau at INRIA Paris-Rocquencourt and Université Pierre et Marie
Curie Paris 6, France, and in the framework of a European-funded
four-year Marie Curie Initial Training Network Project REVAMMAD.
Topic: This PhD thesis will address the mathematical modeling and the
numerical simulation of various phenomena taking place in the retina.
A multiscale mathematical model of the hemodynamics will be proposed.
Numerical simulations will be based on the data obtained from retinal
imaging modalities used in the REVAMMAD network. Data assimilation
techniques recently developed at INRIA will be used in order to adapt
the model to measurements. Two questions could be considered during
the project: modeling of the neovascularization under the action of
vascular endothelium growth factor and modeling of the interaction
between neural cells and microcirculation. The work will be in
particular motivated by the modeling of diseases like the Retinopathy
Of Prematurity (ROP), which is a common cause of blindness in
children, or the Age Related Macular Degeneration (ARMD), which causes
loss of central vision in the ageing population.
Prerequisite: The PhD candidate must have a strong background in
mathematical modeling and numerical methods for partial differential
equations. The numerical method will be based on the finite element
method and the software will be developped in C++.
Eligibility rules: PhD students can be nationals of any country but
must not have resided or carried out their main activity in France for
more than 12 months in the 3 years immediately prior to their
recruitment.
Salary: about 2800 euros/month if the PhD candidate is single, about
3150 euros/month if the PhD candidate comes in France with a family.
The official starting of the PhD can be anytime from now to April
2014. It is possible to start working as an intern or as a master
student.
and Jean-Frederic.Gerbeau
than the end of May 2013.
----------------------------------------------------
Date: Mon, Apr 15, 2013 at 12:38 PM
Subject: Postdoc: Epidemiological Modeling for Antimicrobial.., Canada
Postdoctoral Fellowship ?Epidemiological Modelling for Antimicrobial
Stewardship?, at Mount Sinai Hospital, York University and Memorial
University of Newfoundland
Applicants are invited for a postdoctoral position in epidemiological
modeling for antimicrobial stewardship. The postdoctoral fellow will
be expected to play an important role in a Collaborative Health
Research Project (CHRP) on quantifying antimicrobial resistance in
Canadian hospitals, and will join an accomplished team of researchers
representing both the health and natural sciences.
The postdoctoral fellow will be expected to interact with the team,
and be responsible for the epidemiological model development and
analysis: model concept design, data retrieval from published
literature as well as from the datasets available to the team;
mathematical analysis and computer simulations; testing and validating
models; performing sensitivity and uncertainty analysis and addressing
the issues related to antimicrobial stewardship and infection control
strategies.
The fellowship will be jointly supervised by Dr. Andrew Morris (Mount
Sinai Hospital, Toronto), Dr. Jianhong Wu (York University) and Dr.
Amy Hurford (Memorial University of Newfoundland). This fellow will
initially be placed at the Centre for Disease Modelling (CDM) in York
University and then moved to Memorial University of Newfoundland.
The fellowship can start anytime, initially for one year but can be
renewed for up to a total of 3 years. The salary/stipend is in the
range of $40,000~48,000 per year (including benefits).
Applicants should have significant experience in mathematical biology.
Experience in modeling biodiversity and manipulating large datasets
will be an asset.
Applicants should submit a cover letter, curriculum vitae along with
complete contact information, some representative research and arrange
for two letters of recommendation to be sent directly to Katya
immediately, and only short listed applicants will be contacted.
----------------------------------------------------
Date: Wed, Apr 17, 2013 at 5:45 AM
Subject: Postdoc: Computational and Systems Biology, Lille, France
Postdoctoral position in computational and systems biology available
in Lille, France
A postdoctoral position is available in the department of Physics of
University Lille 1, France, to work on the dynamics of regulatory
networks underlying circadian clocks and their design principles. The
research will be focused on the mathematical modeling of the circadian
clock of the microscopic green alga Ostreococcus tauri and will
be conducted in close collaboration with the group of biologists at
Observatoire Océanologique de Banyuls who have first identified
Ostreococcus clock genes.
Candidates are expected to have a strong background in nonlinear
dynamics as wel! l as in computational or systems biology, in the
context of cellular regulatory networks. A significant programming
experience is also required (preferably C/C++ or Fortran under a linux
environment). The post-doctoral researcher will base its research on
an extensive set of experimental time series recorded in Banyuls to
extend the current knowledge about the molecular networks of
Ostreococcus clock. The results obtained in this project will be of
high significance for the circadian biology field, because : (1)
Ostreococcus clock appears to be closely related to that of
Arabidopsis thaliana but with a simpler architecture, (2) previous
mathematical modeling of this clock has revealed a very interesting
strategy to buffer fluctuations in daylight intensity. A complete
mathematical model of the clock would therefore provide a simple
example of a robust clock network.
The contract is for one year, ext! endable for 10 additional months. The
monthly net salary is about 2200 euros. Candidates should send as soon
as possible a cover letter stating their motivations and CV to Marc
2013. They should also arrange for two reference persons to send
simultaneously recommendation letters to the same address. Before
applying, candidates are advised to check whether the position is
still available at
will also find more information.
The Dynamics of Biological Networks team comprises three permanent
researchers (Marc Lefranc, Quentin Thommen and Benjamin Pfeuty). The
research aims at understanding the dynamical behavior and design
principles of biological networks, in particular signaling cascades
and genetic oscillators (circadian clocks, cell cycle,...), using the
tools of nonlinear dynamical systems theory and statistical physics.
----------------------------------------------------
Date: Mon, Apr 15, 2013 at 10:39 AM
Subject: NSF supported-Advanced Computational Infrastructure
Open for Research
Two NSF-supported advanced computational infrastructure facilities
were recently formally declared open for use by the science and
engineering research community at-large. Stampede at the University
of Texas at Austin's Texas Advanced Computing Center (TACC) was
dedicated on Wednesday, March 27, 2013, and Blue Waters at the
NationalCenter for Supercomputing Applications at the University of
Illinois at Urbana-Champaign was dedicated on Thursday, March 28,
2013.
More information about these dedications is available from the
NSF new releases:
NSF-Supported Stampede Opens the Gates of Advanced Computation to
Thousands of Research Teams
NSF-Supported Blue Waters, One of the World's Most Powerful Computers,
Is Open for Research
These two major facilities are part of the NSF's comprehensive
strategy for advanced computing infrastructure to enable
transformative foundational research in computational and
data-intensive science and engineering across all disciplines.
To apply to use these facilities, please see:
Stampede and other resources:
Blue Waters:
----------------------------------------------------
Date: Tue, Apr 16, 2013 at 12:15 PM
Subject: Job Opportunities - Co57 Systems
Building Visual Intelligence
Co57 designs cognitive architectures for artificial vision systems,
enabling them to perceive and interact with the world.
Research and Development- Open Positions
For more information on these and other positions, please check out the
----------------------------------------------------
Subject: SMBnet Reminders
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