----------------------------------------------------
Subject: SMB Digest v13i07
SMB Digest February 15 , 2013 Volume 13 Issue 7
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,
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:
ToC: Bulletin of Mathematical Biology, Vol. 75, Issue 2
ToC: DCDS-B Special Issue on Cancer Modeling... Vol. 18, no. 4
Workshop: Information, Probability,...in Sys. Bio. July 15-17, Edinburgh
EpiNet Advanced School: Modeling Epidemics..., 30 Sept-3 Oct, Catalonia
CfP: SIAM Conference on Geometric and Physical Modeling, Colorado
PhD Position: Math. Modelling for Inflammatory/Infectious Diseases, UK
PhD Position in Time-Frequency Analysis/Image Processing, Germany
Postdoc, Graduate student & Research Associate Positions, Northwestern U.
Postdoc: Researcher in Spatial Ecology, Univ. of Maryland
Postdoc Position: Regulatory Genomics, University of Chicago
Research Fellow in Modeling and Control of Socio-Motor Coordination, UK
SMBnet Reminders
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From: Springer <springeralerts@springer.delivery.net>
Date: Mon, Feb 11, 2013 at 8:26 AM
Subject: Bulletin of Mathematical Biology, Vol. 75, Issue 2
Volume 75 Number 2 is now available on SpringerLink
http://springer.r.delivery.net/r/r?2.1.Ee.2Tp.1gRqkl.C56agS..T.Zk7Y.4116.bW89MQ%5f%5fCdDSFOK0
========================================
Nominations solicited for 2013 Winfree and 2014 Okubo prize
The SMB is soliciting nominations for the 2013 Arthur T. Winfree Prize that
honors a theoretician whose research has inspired significant new biology,
and for the 2014 Akira Okubo Prize for the lifetime achievements of a
living senior scientist.
http://springer.r.delivery.net/r/r?2.1.Ee.2Tp.1gRqkl.C56agS..T.Zk7a.4116.bW89MQ%5f%5fCdeCFOS0
=========================================
*It pays to be a member of the SMB*
Learn more about the member benefits of the Society for Mathematical
Biology, including online access to the Bulletin of Mathematical
Biology. Join or renew today!
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=========================================
IN THIS ISSUE:
Comparing Neutral and Trade-off Community Models in Shaping the
Community Biomass-Diversity Relationship Under Different Disturbance
Levels
Sa Xiao, Liang Zhao, Jia-Lin Zhang, Xiang-Tai Wang & Shu-Yan Chen
Implicit Estimation of Ecological Model Parameters
Brad Weir, Robert N. Miller & Yvette H. Spitz
Fatal or Harmless: Extreme Bistability Induced by Sterilizing,
Sexually Transmitted Pathogens
Ludk Berec & Daniel Maxin
Numerical Simulation of the Inhibitory Effect of Angiostatin on
Metastatic Tumor Angiogenesis and Microenvironment
Gaiping Zhao, Wentao Yan, Eryun Chen, Xiaoli Yu & Wenjie Cai
Cell Migration with Multiple Pseudopodia: Temporal and Spatial
Sensing Models
Rachele Allena
Gene Expression in Self-repressing System with Multiple Gene Copies
Jacek Miekisz & Paulina Szymaska
Progressive Clustering Based Method for Protein Function Prediction
Ashish Saini & Jingyu Hou
Transcriptional Bursting Diversifies the Behaviour of a Toggle
Switch: Hybrid Simulation of Stochastic Gene Expression
Pavol Bokes, John R. King, Andrew T. A. Wood & Matthew Loose
----------------------------------------------------
From: Liwei Ning <editorial@aimsciences.org>
Date: Tue, Feb 5, 2013 at 8:20 PM
Subject: DCDS-B Special Issue on Cancer Modeling... Vol. 18, no. 4
DCDS-B Special issue on Cancer Modeling, Analysis and Control
Discrete and Continuous Dynamical Systems - Series B (DCDS-B)
Volume: 18, Number: 4 June 2013 is now availabe online:
http://www.aimsciences.org/journals/contentsListnew.jsp?pubID=580
>>Open Access<<
1. Preface: Special issue on cancer modeling, analysis and control
Amina Eladdadi, Noura Yousfi and Abdessamad Tridane
2. Modeling chemotaxis from L2--closure moments in kinetic theory of
active particles
Nicola Bellomo, Abdelghani Bellouquid, Juanjo Nieto and Juan Soler
3. Designing proliferating cell population models with functional targets
for control by anti-cancer drugs
Frédérique Billy and Jean Clairambault
4. Recognition and learning in a mathematical model for immune response
against cancer
Marcello Delitala and Tommaso Lorenzi
5. Mathematical modeling of regulatory T cell effects on renal cell
carcinoma treatment
Lisette dePillis, Trevor Caldwell, Elizabeth Sarapata and Heather Williams
6. Modeling prostate cancer response to continuous versus intermittent
androgen ablation therapy
Harsh Vardhan Jain and Avner Friedman
7. A hybrid model for cell proliferation and migration in glioblastoma
Yangjin Kim and Soyeon Roh
8. A mathematical model for the immunotherapeutic control of the Th1/Th2
imbalance in melanoma
Yuri Kogan, Zvia Agur and Moran Elishmereni
9. Optimal controls for a mathematical model of tumor-immune interactions
under targeted chemotherapy with immune boost
Urszula Ledzewicz, Mozhdeh Sadat Faraji Mosalman and Heinz Schättler
10. B cell chronic lymphocytic leukemia - A model with immune response
Seema Nanda, Lisette de Pillis and Ami Radunskaya
11. Using fractal geometry and universal growth curves as diagnostics for
comparing tumor vasculature and metabolic rate with healthy tissue and
for predicting responses to drug therapies
Van M. Savage, Alexander B. Herman, Geoffrey B. West and Kevin Leu
12. A continuous model of angiogenesis: Initiation, extension, and
maturation of new blood vessels modulated by vascular endothelial
growth factor, angiopoietins, platelet-derived growth factor-B, and
pericytes
Xiaoming Zheng, Gou Young Koh and Trachette Jackson
----------------------------------------------------
From: Peter Swain <peter.swain@ed.ac.uk>
Date: Mon, Feb 11, 2013 at 10:41 AM
Subject: Workshop: Information, Probability, ...in Sys. Bio.
July 15-17, Edinburgh
We would like to announce a workshop on Information, Probability, and
Inference in Systems Biology to be held at the International Centre
for Mathematical Sciences in Edinburgh, Scotland, from 15-17 July
2013.
http://www.icms.org.uk/workshop.php?id=268
The workshop's aim is to bring experts in probability, information
theory, and stochastic systems alongside experimental systems
biologists to develop understanding of the principles underlying
cellular signalling and decision-making and to develop quantitative
techniques to investigate those principles experimentally.
Financial assistance is available for travel and accommodation costs
with priority given to early career researchers and PhD students.
Registration is on a first-come first-served basis.
Confirmed speakers and other information can be found on the workshop's
website: http://www.icms.org.uk/workshop.php?id=268
Organizers: Clive Bowsher, Caroline Colijn, Peter Swain
----------------------------------------------------
From: Joan Saldana <jsaldana@imae.udg.edu>
Date: Tue, Feb 12, 2013 at 5:56 AM
Subject: EpiNet Advanced School: Modeling Epidemics...,
30 Sept.-3 Oct., Catalonia
1st announcement of EpiNet Advanced School (Girona, 2013)
We are pleased to announce the school "EpiNet Advanced School:
Modelling epidemics on networks" that will be held in Girona
(Catalonia, Spain) from 30 September to 3 October, 2013.
The goal of the school is to introduce concepts, modelling approaches,
and tools that allow students and young researches to deal with
current research problems. Topics covered in the courses are:
Stochastic modelling of epidemic on networks
Epidemics on populations with different levels of mixing
Modelling human responses in epidemic dynamics
Deterministic approaches for epidemic modelling
Confirmed lecturers (in alphabetical order):
Tom Britton (University of Stockholm)
Istvan Z Kiss (University of Sussex)
Lorenzo Pellis (University of Warwick)
Caterina Scoglio (Kansas State University)
There will be room for short presentations by participants who wish to
present their current research.
Registration is already open. Early registration fee (until 31 May): 150 Euros
For further information, please visit the school's website:
https://sites.google.com/site/epinetschool2013/home
----------------------------------------------------
From: Kirsten Wilden <Wilden@siam.org>
Date: Tue, Feb 12, 2013 at 9:37 AM
Subject: CfP- SIAM Conference on Geometric and Physical Modeling (GD/SPM13)
Conference Name: SIAM Conference on Geometric and Physical
Modeling (GD/SPM13)
Location: The Curtis, A DoubleTree by Hilton Hotel, Denver, Colorado, USA
Dates: November 11-14, 2013
The Call for Presentations for this conference is available at:
http://www.siam.org/meetings/gdspm13/
SUBMISSION DEADLINES:
Due date for abstract submissions for proceedings: April 8, 2013
Due date for full paper submissions for proceedings: April 15, 2013
Due date for minisymposium proposals: June 3, 2013
Due date for abstracts of all contributed and minisymposium
presentations: July 1, 2013
Please visit http://www.siam.org/meetings/gdspm13/submissions.php for
detailed submission information.
For additional information, contact the SIAM Conference Department
(meetings@siam.org).
----------------------------------------------------
From: Reiko Tanaka <r.tanaka@imperial.ac.uk>
Date: Mon, Feb 11, 2013 at 3:38 AM
Subject: PhD Position: Math. Modelling for Inflammatory/Infectious
Diseases, UK
PhD studentship in Imperial College London - Mathematical modelling
for inflammatory/infectious diseases
Department of Bioengineering, Imperial College London
Competitive funding available (home/EU fees + stipend)
We are looking for a prospective PhD student with strong background in
computational biology. The candidate should have research experiences
in computational biology with strong mathematical skills and good
Matlab skills. The Tanaka group develops mathematical models for
various biological systems ranging from cellular to behavioural levels
and reveals key mechanisms for efficient, flexible and robust
biological control across different levels. The students will develop
and analyse mathematical models to understand the regulatory
mechanisms for epithelium homeostasis and how its deregulation leads
to disease, such as atopic dermatitis and fungal infection, and will
design experiments that will be fed back into modelling.
More information on our research can be found at
http://www.bg.ic.ac.uk/research/r.tanaka. Interested candidates should
send both the CV and the research statement (max 2pages) to Dr Reiko
Tanaka by email (r.tanaka@imperial.ac.uk). Non-EU applicants should
confirm in the email that they can cover their PhD fees for oversea
students (http://www3.imperial.ac.uk/studentfinance/prospectivepgstudents).
----------------------------------------------------
From: Daniel J. Strauss <strauss@snn-unit.de>
Date: Sun, Feb 10, 2013 at 12:04 PM
Subject: PhD Position in Time-Frequency Analysis/Image Processing, Germany
A Ph.D. Position is available at the Faculty of Medicine (Systems
Neuroscience and Neurotechnology Unit), Saarland University,
Homburg/Saar, Germany, (www.snn-unit.de) in collaboration with the
Department of Mathematics (Mathematical Image Processing Group) of the
University of Kaiserslautern, Germany
(http://www.mathematik.uni-kl.de/~steidl/)
The position is within the project:
"Anisotropic analysis of electroencephalographic correlates of the sensory
and cognitive processing of single sweeps" promoted by the Deutsche
Forschungsgemeinschaft (DFG).
The ideal candidate will have a diploma/master in Mathematics with
extended knowledge in Applied Analysis as well as good programming
skills.
The contract is for three years. The earliest starting date is May, 2013.
Please send your application documents to Prof. Dr. Dr. Daniel J.Strauss
email: strauss@snn-unit.de
----------------------------------------------------
From: Kristin Rae Swanson <kristin.swanson@northwestern.edu>
Date: Mon, Feb 11, 2013 at 4:58 PM
Subject: Postdoc, Graduate Student & Research Associate
Positions at Northwestern U.
Patient-specific clinical-scale mathematical modeling of brain tumor
growth and response to therapy
Opportunities are available at Northwestern University in downtown
Chicago for research positions in the field of clinical scale brain
tumor computational and mathematical modeling at the postdoctoral,
graduate student and research scientist levels. Our lab is located on
the Feinberg School of Medicine campus in downtown Chicago, nestled
between Michigan Avenue and Lake Michigan.
We are seeking highly motivated people interested in applying
mathematical models, numerical methods and image analysis techniques
to clinical scale patient-specific data to provide novel insight into
brain tumor disease progression, invasion and response to treatment
using mathematical modeling. The appointed candidate(s) will work with
Dr. Kristin Swanson and senior research staff on one or more of the
following projects to answer a variety of questions focused on direct
clinical applications of mathematical modeling, such as:
-model implementation and comparison with experimental and/or clinical data
-the role of angiogenesis in tumor progression
-anti-angiogenic therapy and medical imaging
-the tumor microenvironment and histologic grading
-quantifying extent of tumor cell invasion and proliferation in
individual patients
-radiation therapy and regions of hypoxia induced focal resistance
The ideal candidate should have a strong background in applied
mathematics, bioenginering or computation, with biology a strong plus.
Experience with computational methods required to solve partial
differential equations and experience in computer programming and
visualization of results are highly desired. Excellent communication
skills and enthusiasm for communicating modeling results to a clinical
audience as well as working in an interdisciplinary team are
essential. The candidate will be expected to contribute to achieving
research grant goals and objectives as well as securing new sources of
funding. Depending on experience, the candidate may supervise junior
scientists, engineers or technicians on assigned work, mentor/train
staff in development of technical, project development skills, as well
as provide input into staffing of overall project teams by identifying
and evaluating candidates for open positions.
Applications will be accepted until positions are filled and are
contingent on continued research funding. To apply, visit:
http://MathematicalNeuroOncology.org/ and send a cv, cover letter and
contact information for three references to
----------------------------------------------------
From: Sharon Bewick <sharon_bewick@hotmail.com>
Date: Tue, Feb 12, 2013 at 12:03 PM
Subject: Postdoc Researcher in Spatial Ecology, U. of Maryland
Postdoctoral Researcher in Spatial Ecology:
Bill Fagan?s ecology lab at the University of Maryland in College
Park, MD, has a new opening for a Postdoctoral Researcher in Spatial
Ecology. This dynamic lab group, which currently includes two research
assistant scientists, three postdocs, six graduate students, and
numerous undergraduates, is pursuing a wide variety of research
efforts on spatial and theoretical topics that draw upon GIS,
mathematical modeling, and statistical analyses. For examples, see
http://www.clfs.umd.edu/biology/faganlab/
This advertisement is for a postdoctoral position in an NSF-funded
project focusing on the development and analysis of spatial models.
The candidate should have expertise in the analyses of animal
relocation data and mechanistic movement models. Experience in
multivariate stochastic processes, hierarchical spatial models, and/or
time series analyses is advantageous. In addition, good computational
skills with knowledge in various programming languages (e.g., R,
Python) are required. Experience in using remote sensing data for
habitat and species distribution models as well as handling of large
spatial databases & GIS software is desirable.
The successful candidate will have a PhD, likely in quantitative
ecology, geography, or a related field and a history of publishing in
top journals. Prior postdoctoral experience is beneficial, but not
required.
The initial appointment will be for one year, but funding is already
in place for up to two additional years pending good performance.
Efforts to secure substantial long-term support via collaborative
grant proposals would be encouraged and, when successful, could lead
to appointment at the level of research assistant scientist. Benefits
are included and pay will be commensurate with experience. The start
date is negotiable, but could be as early as June 2013.
Review of applications will begin 1 April 2013, and will continue
until the position has been filled. To apply for the position, please
email a CV and the names and email addresses of three references to:
Bill Fagan (bfagan@umd.edu)
----------------------------------------------------
From: Stranger, Barbara <bstranger@medicine.bsd.uchicago.edu>
Date: Wed, Feb 13, 2013 at 8:57 AM
Subject: Postdoc Position: Regulatory Genomics, University of Chicago
A position is available for a highly motivated postdoctoral researcher
in the group of Barbara Stranger at The University of Chicago, in the
Section of Genetic Medicine, and the Institute of Genomics and Systems
Biology. The researcher will be involved in analysis of a variety of
types of human genomics data, including DNA-Seq, RNA-Seq, SNPs, DNA
methylation, etc. Current research in the lab includes (1)
transcriptional network and pathway analysis; (2) comparative and
population genomics; (3) functional genomic data integration and data
mining; and (4) detection of disease susceptibility genes/networks.
Project topics include understanding the role of genetic and
epigenetic variation on transcriptional regulation in healthy human
cohorts, the contribution of that variation to higher order phenotypes
including immune-mediated diseases, adverse pregnancy outcomes, and
cancer, and elucidation of the evolutionary forces shaping functional
variation in humans.
MINIMUM QUALIFICATIONS:
-A Ph.D. in bioinformatics, computer science, genomics, population
genetics, or other relevant fields of statistical biology.
-Research experience (with strong first-author publications) in
computational genomics, molecular evolution, population genetics, or a
closely-related field
- Strong analytical, statistical, quantitative, and
computational/programming skills, ideally in C or C++ as well as in
scripting languages such as perl, matlab, or R. Should be comfortable
in a with large data sets, computer clusters, and databases.
- Creativity, curiousity, enthusiastiam, and ability to work independently.
PREFERRED QUALIFICATIONS:
-Experience in analysis of DNA-seq, RNA-seq, and/or CHiP-seq data, as
well as experience constructing complex biological networks.
-Background in genomics or population genetics.
-Candidates with a multidisciplinary background, spanning both life
sciences and quantitative sciences are especially encouraged to apply.
To formally apply, please send the following in PDF format to Barbara
Stranger (bstranger at uchicago dot edu):
1. A curriculum vitae, including names of 3 referees.
2. A brief statement describing current and future research goals
Our lab website is currently under construction, but informal
inquiries are welcome.
----------------------------------------------------
From: Krasi Tsaneva <K.Tsaneva-Atanasova@bristol.ac.uk>
Date: Fri, Feb 8, 2013 at 10:36 AM
Subject: Research Fellow in Modelling and Control of Socio-Motor Coordination
We seek to recruit a Research Fellow to undertake research into
mathematical modelling and control of human social interactions. You
will contribute to a joint venture between movement scientists from
Montpellier 1 University in France, computer science experts from the
DFKI centre (Germany), mathematicians from the University of Bristol
(UK), roboticists from the Ecole Polytechnique Fédérale de Lausanne
(CH), as well as clinicians, psychologists and psychiatrists from the
Academic Hospital of Montpellier (CHRU, FR).
You will have an excellent background in mathematics and/or
engineering, and should be committed to applying their research to
make real artificial agents? systems interacting with people in
challenging circumstances. You will possess a relevant PhD and be able
to demonstrate sufficient knowledge in mathematical modelling,
numerical bifurcation analysis and feedback control design in order to
work within the project. You are expected to produce reliable
mathematical models; feedback control strategies and numerical
algorithms that i) allow real-time adaptation of the coupled
human-artificial agent dynamics based on feedback control techniques
and ii) integrate all parts of the interactive cognitive architecture
together.
For informal enquires please contact:
Dr KT Tsaneva-Atanasova, Reader in Applied Mathematics
Email: K.Tsaneva-Atanasova@bristol.ac.uk
For further details and to apply please visit:
http://www.bris.ac.uk/jobs/find/list.html?keywords=&jobnum=ACAD100163&srcsubmit=Search&statlog=1&ID=Q50FK026203F3VBQBV7V77V83&mask=uobext&LG=UK
----------------------------------------------------
Subject: SMBnet Reminders
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The contents of this publication may be reproduced in whole or in part with
attribution.
End of SMB Digest
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