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Subject: SMB Digest v14i29
SMB Digest July 16, 2014 Volume 14 Issue 29
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
Note:
Information about the Society for Mathematical Biology, including an
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Access the Bulletin of Mathematical Biology, the official journal of
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Issue's Topics:
Seminar: Some Applications of Fractal Related..., UT Sydney
PhD Position: PharMetrX: Pharmacometrics..., Berlin/Potsdam
Post-doc: Microbial Ecology, France
Post-doc: Modeling...Mosquito-vectored Diseases, NC State U
SMBnet Reminders
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From: Advanced Analytics <AdvancedAnalytics@uts.edu.au>
Date: July 14, 2014 10:19:11 PM
Subject: Seminar: Some Applications of Fractal Related..., UT Sydney
AAi Seminar: Some Applications of Fractal Related Methods to
Bioinformatics - Tuesday 22 July 2014 at 2.00pm
Speaker: Zuguo Yu ? Professor at the School of Mathematics and
Computational Science, Xiangtan University, Hunan, China
Date: Tuesday 22 July 2014
Time: 2.00 pm to 3.00pm
Location: Blackfriars Campus, CB25.GC.03
Seminar Chairman: Assoc Professor Jinyan Li, Advanced Analytics
Institute (AAi), UTS
Abstract:
Fractal method was originally proposed in physics by Mandelbrot in
1970s. Since then it has been successfully used to study problems in
physics, mathematics, engineering, computer science, and biology etc.
DNA and protein sequences are of fundamental importance in understanding
living organisms, since all information of the hereditary and species
evolution is contained in these macromolecules. Retrieval of biological
information from complete genomes or protein sequences is of some
challenges in bioinformatics. Problems related to the classification and
phylogenetic relationship among species are also important. It is vital
and urgent that advanced computational and statistical methods be
developed and applied to support biological research and innovation
based on biological data. In this talk , I will show some applications
of fractal related methods to the study of bioinformatics problems, such
as DNA sequence analysis, prediction of protein structural classes and
functions, alignment-free methods for phylogenetic analysis.
Short Biography of the Speaker?
Professor Yu received his PhD degree in Mathematics in Fudan University
of China in 1997?then worked as a postdoctoral research fellow in
Chinese Academy of Science (1997-1999) and Queensland University of
Technology (QUT) (2000-2005), and a research fellow in QUT (2005-2009),
Professor in Xiangtan University (2002-current). Now he is a Lotus
Distinguished Professor of Hunan province, Deputy director of the Key
Laberatory of Intelligent Computation and Information Processing of
Ministry of Education, leader of Chinese Program for Changjiang Scholars
and Innovative Research Team In University (PCSIRT) in Xiangtan
University. He is also an adjunct professor of QUT, editor of Pac. J.
Appl. Math. Commun. Frac. Calc. Chin. J. Biol. and guest editor of
Current Bioinformatics.
Professor Yu has worked on fractal related methods, biological and
environmental information processing, complex networks since 1994. The
research has resulted in more than 100 peer-reviewed publications in
some well recognised international journals such as Mol. Biol. Evol.,
Mol. Ecol. Res., Fuzzy Sets and Systems, J. Chem. Phys., J. Geophys.
Res., PLoS ONE, BMC Bioinformatics, BMC Evol. Biol., J. Mol. Evol.,
Phys. Rev. E, J. Theor. Biol. etc. From 2003, Professor Yu is the first
chief investigator of 4 Natural Science Foundation of China (NSFC)
grants, 1 Fok Ying Tung Education Foundation of China. He is also a key
research member in 3 ARC grants, 1 NSFC grant and 2 Hong Kong ERC
grants.
Overview to AAI seminar series
The Advanced Analytics Seminar Series presents the latest theoretical
advancement and empirical experience in a broad range of
interdisciplinary and business-oriented analytics fields. It covers
topics related to data mining, machine learning, statistics,
bioinformatics, behavior informatics, marketing analytics and multimedia
analytics. It also provides a platform for the showcase of commercial
products in ubiquitous advanced analytics. Speakers are invited from
both academia and industry. It opens regularly on a week day at UTS. You
are warmly welcome to attend this seminar series. Inquiries go to the
seminar coordinator Associate Professor Jinyan Li Jinyan.Li@uts.edu.au
----------------------------------------------------
From: Cornelia Boehnstedt <cboehnstedt@zedat.fu-berlin.de>
Date: July 16, 2014 8:15:53 AM
Subject: PhD Position: PharMetrX: Pharmacometrics..., Berlin/Potsdam
PhD research fellowship: Pharmacometrics & Computational Disease
Modelling
The Graduate Research Training Program PharMetrX: Pharmacometrics &
Computational Disease Modelling is an interdisciplinary PhD program
bridging pharmacy and mathematics. PharMetrX offers its graduate
students a unique opportunity to experience research in drug development
and optimising drug therapy jointly within academia and industry.
The PhD program is designed as a 3-year research program including a
structured research training curriculum of advanced academic and
industrial modules and a competitive research fellowship.
We are currently inviting applications to start the PharMetrX PhD
program in March 2015. Deadline for applications: September 15th, 2014.
For details see https://www.PharMetrX.de.
PharMetrX is a joint program of the Freie Universität Berlin and the
Universität Potsdam, supported by several research-driven pharmaceutical
companies.
Charlotte Kloft & Wilhelm Huisinga
Program Chairs
----------------------------------------------------
From: Judith Legrand <jlegrand@moulon.inra.fr>
Date: July 15, 2014 11:06:16 AM
Subject: Post-doc: Microbial Ecology, France
A post-doctoral position is available for two years, on the following
project, "Dynamics of yeasts and lactic acid bacteria interactions in
sourdoughs ecosystems". The postdoctoral researcher will work in
collaboration with two research groups, one located in Montpellier, the
other in Gif-sur-Yvette, France.
Project
The community dynamics of an ecological niche is driven both by
selection and by complementation interaction between organisms. These
interactions have been studied extensively for social organisms, or
host-parasites interactions. Microbial species interactions in
food-processing systems have drawn less attention. Sourdough, which
includes less than ten species according to published studies, appears
as a relatively simple model for studying positive and negative
interactions. In sourdoughs, Lactic Acid Bacteria (LAB) and yeasts are
always found together suggesting ecological facilitation between these
prokayotes and eukaryotes. By contrast, within LAB and within yeasts,
we observe a dominant species suggesting that competition drives the
dynamics of the species diversity. The post-doctoral fellow will conduct
experimental and mathematical modeling studies to understand: i) how
yeast species and LAB species interact during the fermentation process;
and ii) whether yeasts and LAB associations enhance the resilience of
the sourdough community to the colonization by the commercial yeast
Saccharomyces cerevisiae. The dynamics of sourdough ecosystems and its
resilience to commercial yeast will be analysed both experimentally by
microbial community monitoring and mathematically by modelling
population dynamics in sourdough microbial community.
Requirements
The successful candidate will have a PhD in ecology or microbiology and
will demonstrate interest and abilities for both experimental and
theoretical work. Ideally, the candidate will have skills in
microbiology, mathematical modeling of systems dynamics, statistical
analysis and R programming. He/she will also show enthusiasm for
interdisciplinary research and ability to communicate effectively with
other scientists at the interface of empirical and theoretical studies.
Research environment
The position is funded by a French interdisciplinary project untitled
"Diversity and interactions in a low-input 'Wheat/Human/Sourdough'
agro-food ecosystem: toward a better understanding of bakery
sustainability" (Project ANR BAKERY, 2014-2018). This project includes
eight academic partners with complementary skills (bio-mathematics,
plant genetics, microbiology, sociology, centre for genetic resources
managements) as well as bakers and farmers/bakers.
The experimental part of the post-doctoral project will be carried out
in the research group "Yeasts diversity and adaptation to anthropic
environment" on the Supagro campus in Montpellier
(http://www6.montpellier.inra.fr/spo_eng/Presentation) and the modeling
part will be done in the research group "Fundamental Quantitative
Genetics" in Gif-sur-Yvette
(http://moulon.inra.fr/index.php/en/team/genetique-quantitative-fondamentale).
The candidate will share his/her time between both locations according
to personal convenience and scientific queries.
Terms
Full time contract for 24 months. The salary varies depending on the
candidate experience. Starting date: from October 2014
Application and Contacts
For application, please send a short CV including a description of past
and present research activities, a motivation letter and the contact
details of at least two referees. Application and informal enquiries
should be sent to Delphine Sicard (sicard@supagro.inra.fr) and Judith
Legrand (judith.legrand@moulon.inra.fr).
----------------------------------------------------
From: Alun Lloyd <alun_lloyd@ncsu.edu>
Date: July 16, 2014 3:01:12 AM
Subject: Post-doc: Modeling...Mosquito-vectored Diseases, NC State U
Postdoc: Modeling Population Dynamics and Genetics of Mosquito-vectored
diseases
North Carolina State University, with Fred Gould and Alun Lloyd
PROJECT DESCRIPTION: Dengue is a mosquito-vectored disease that affects
over 100 million people each year. With funding from the NIH and Gates
Foundation, we have developed a set of mathematical models ranging from
simple to complex, aimed at assisting the design and deployment of novel
approaches for suppressing transmission of dengue by its major mosquito
vector, Aedes aegypti. We are especially interested in evaluating the
potential utility of, as well as risks associated with, using
genetically engineered, selfish genetic elements to drive genes into
mosquito populations that render them incapable of transmitting dengue
fever. Our work also extends to models relevant to suppressing malaria.
Our most detailed model simulates the population dynamics and population
genetics of Ae. aegypti in a city on the Amazon river, Iquitos, for
which there are rich data sets on both mosquito dynamics and dengue
epidemiology. An accompanying epidemiological model is currently under
development. Both are coded in C++.
We are just completing a large-scale experiment in Iquitos to both test
the model and collect data that can be used to improve the
parameterization of all Ae. aegypti models. In the experiment, the
mosquito population in one area of the city is suppressed and then
allowed to return to normal densities. Although our population dynamics
model and many others have been tested to determine if they predict
equilibrium dynamics, a much more stringent test is to determine if they
can predict response to a perturbation. Following a transition period
interfacing with our current postdoc, the new postdoc will assume
responsibility for leading the analysis of these data and will further
develop the model to examine the dynamic behavior and efficacy of a set
of novel transgenic and non-transgenic approaches for manipulating the
mosquito population. These innovative technologies and strategies are
being developed by our colleagues, so empirical data on small field
tests will be available. We are also building simple spatial and
non-spatial, deterministic models as heuristic tools for better
understanding basic principles.
In addition to working on model development and analysis, and on
comparisons between model and data, the person in this position will
collaborate in an interdisciplinary research group composed of mosquito
ecologists, disease epidemiologists, molecular biologists,
biomathematicians, ethicists, and scientists from disease-endemic
countries, in efforts to develop novel transgenic strategies for disease
reduction. The person in this position will have the opportunity to
spend time in Iquitos to better understand the system being modeled.
Desirable skills include the ability to program in C++ or knowledge of a
related programming language, statistical experience, particularly in
parameter estimation and evaluation of performance of mechanistic
models.
For more details on the project see the following publications:
Magori, K., M. Legros, M. Puente, D. A. Focks, T. W. Scott, A. Lloyd,
F. Gould. 2009. Skeeter Buster: a stochastic, spatially-explicit
modeling tool for studying Aedes aegypti population replacement and
population suppression strategies. PLoS Negl Trop Dis 3(9): e508.
doi:10.1371/journal.pntd.0000508
Gould, F., Huang, Y., Legros, M., Lloyd, A. L. 2008. A killer-rescue
system for self-limiting gene drive of anti-pathogen constructs.
Proc. Royal. Soc. Lond. B. 275:2823-2829.
Xu, C., Legros, M., Gould, F, Lloyd, A. L. 2010. Understanding
Uncertainties in Model-Based Predictions of Aedes aegypti Population
Dynamics. PLoS Negl. Trop. Dis. 4(9): e830.
doi:10.1371/journal.pntd.0000830
Huang, Y., Lloyd, A.L., Legros, M., Gould, F. 2010. Gene-drive into
insect populations with age and spatial structure: a theoretical
assessment. Evol. Appl. ISSN 1752-4571.
Okamoto K. W., M. A. Robert, A. L. Lloyd, F. Gould. 2013. A reduce and
replace strategy for suppressing vector-borne diseases: Insights from a
stochastic, spatial model. PLoS ONE 8(12): e81860.
doi:10.1371/journal.pone.0081860
To apply: email a cover letter and CV to Fred_Gould@ncsu.edu and
Alun_Lloyd@ncsu.edu
----------------------------------------------------
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