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SMB Digest September 9, 2015 Volume 15 Issue 36
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
Note:
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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
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Inquiries about membership or BMB fulfillment should be sent to
membership(at)smb(dot)org .
Issue's Topics:
Conference: LyonSysBio, Nov 18-20, Villeurbanne, France
ToC: BMB, Volume 77, Issue 7
ToC: Mathematical Biosciences & Engineering, Volume 12 Issue 6
PhD Position: Biomathematics Group, Imperial College London
Post-doc: Regulation of Autophagy, Los Alamos National Lab
Post-doc: Spatiotemporal Modeling of Cell Signaling, Los Alamos
Post-doc: Theoretical & Comp. Neuroscience, New York City area
SMBnet Reminders
----------------------------------------------------
From: François Briat <francois.briat@biosyl.org>
Date: September 7, 2015 at 9:49:41 AM
Subject: Conference: LyonSysBio, Nov 18-20, Villeurbanne, France
Lyon SysBio 2015
18-20 November 2015, Villeurbanne, France
LyonSysBio is the yearly international conference organized by the
Systems Biology Alliance of Lyon/ BioSyL.
Its goal is to promote exchanges between scientists from different
disciplines (biology, mathematics, computer sciences, physics, social
sciences,...) who are interested in the analysis of the wealth of data
generated by modern biology, as well as the construction of the
necessary modeling tools to gain system level thoughtful insights.
In 2014, this conference will be held from the 19th to the 21st of
November. It will be dedicated to discussions around the 4 following
themes: systems immunology, cell differentiation, microbial systems
biology and "A systems view on genotype-phenotype relationship."
Keynote lectures will be delivered by invited speakers, on
state-of-the-art advances on those themes. In addition, the conference
program will leave ample space for contributed talks and posters for
which proposals are welcome.
On November 18, Meet The Industry Day 2015, a satellite meeting jointly
organized with ECOFECT (http://ecofect.universite-lyon.fr/) will offer a
unique opportunity for private and public researchers to share ideas in
a stimulating environment. Register at
http://lyonsysbio2015.sciencesconf.org/.
CALL FOR PAPERS
We wish to favor works presenting results of a multidisciplinary
approach.
Please use the online system to submit a one-page abstract (maximum 500
words, in English) by October 5, 2015, indicating your choice of the
relevant session.
To register and to submit an abstract, you will have to create a
sciencesconf.org account by filling the on-line registration and
submission forms.
We are looking forward to welcoming you in Lyon for LyonSysBio 2015!
KEY DATES
October 5th 2015 - Deadline for submitting
October 26th 2015 - Notification to authors
November 6th 2015 - End of registrations
----------------------------------------------------
From: Springer <springer@alerts.springer.com>
Date: September 6, 2015 at 12:43:38 PM
Reply-To: Springer <onlineservice@springer.com>
Subject: ToC: BMB, Volume 77, Issue 7
Volume 77 Number 7 is now available at
http://link.springer.com/journal/11538/77/7?wt_mc=alerts.TOCjournals
In this issue
From Birds to Bacteria: Generalised Velocity Jump Processes with Resting
States
Jake P. Taylor-King, E. Emiel van Loon, Gabriel Rosser & S. Jon Chapman
An Epidemic Patchy Model with Entry?Exit Screening
Xinxin Wang, Shengqiang Liu, Lin Wang & Weiwei Zhang
A Model for Mountain Pine Beetle Outbreaks in an Age-Structured Forest:
Predicting Severity and Outbreak-Recovery Cycle Period
Jacob P. Duncan, James A. Powell, Luis F. Gordillo & Joseph Eason
Survival and Stationary Distribution Analysis of a Stochastic
Competitive Model of Three Species in a Polluted Environment
Yu Zhao, Sanling Yuan & Junling Ma
A Boundary Value Approach to Optimization with an Application to
Salmonella Competition
Glenn Young, Bard Ermentrout & Jonathan E. Rubin
A Multiscale Model of Cardiovascular System Including an Immersed Whole
Heart in the Cases of Normal and Ventricular Septal Defect (VSD)
Oscillations and Multiple Equilibria in Microvascular Blood Flow
Nathaniel J. Karst, Brian D. Storey & John B. Geddes
Extension and Justification of Quasi-Steady-State Approximation for
Reversible Bimolecular Binding
Richard Kollár & Katarína ?i?ková
A Framework for Inferring Unobserved Multistrain Epidemic Subpopulations
Using Synchronization Dynamics
Eric Forgoston, Leah B. Shaw & Ira B. Schwartz
----------------------------------------------------
From: Liwei Ning <editorial@aimsciences.org>
Date: September 8, 2015 at 4:21:55 PM
Subject: ToC: Mathematical Biosciences & Engineering, Volume 12 Issue 6
Mathematical Biosciences and Engineering (MBE)
Volume: 12, Number: 6 December 2015
http://www.aimsciences.org/journals/contentsListnew.jsp?pubID=800
1. Application of ecological and mathematical theory to cancer: New
challenges
Yangjin Kim, Avner Friedman, Eugene Kashdan, Urszula Ledzewicz and
Chae-Ok Yun
2. Hybrid models of cell and tissue dynamics in tumor growth
Yangjin Kim and Hans G. Othmer
3. A data-motivated density-dependent diffusion model of in vitro
glioblastoma growth
Tracy L. Stepien, Erica M. Rutter and Yang Kuang
4. Mathematical model and its fast numerical method for the tumor growth
Hyun Geun Lee, Yangjin Kim and Junseok Kim
5. Synergistic effect of blocking cancer cell invasion revealed by
computer simulations
Kazuhisa Ichikawa
6. The role of the cytokines IL-27 and IL-35 in cancer
Avner Friedman and Kang-Ling Liao
7. An integrated cellular and sub-cellular model of cancer chemotherapy
and therapies that target cell survival
Alexis B. Cook, Daniel R. Ziazadeh, Jianfeng Lu and Trachette L. Jackson
8. Treatment strategies for combining immunostimulatory oncolytic virus
therapeutics with dendritic cell injections
Joanna R. Wares, Joseph J. Crivelli, Chae-Ok Yun, Il-Kyu Choi,
Jana L. Gevertz and Peter S. Kim
9. Dynamics and control of a mathematical model for metronomic
chemotherapy
Urszula Ledzewicz, Behrooz Amini and Heinz Schuttler
10. Oncogene-tumor suppressor gene feedback interactions and their
control
Baltazar D. Aguda, Ricardo C.H. del Rosario and Michael W.Y. Chan
11. Algebraic and topological indices of molecular pathway networks in
human cancers
Peter Hinow, Edward A. Rietman, Sara Ibrahim Omar and Jack A. Tuszynski
12. The performance of discrete models of low reynolds number swimmers
Qixuan Wang and Hans G. Othmer
13. Models, measurement and inference in epithelial tissue dynamics
Oliver J. Maclaren, Helen M. Byrne, Alexander G. Fletcher and
Philip K. Maini
----------------------------------------------------
From: Oyarzún, Diego A <d.oyarzun@imperial.ac.uk>
Date: September 7, 2015 at 11:59:32 AM
Subject: PhD Position: Biomathematics Group, Imperial College London
PhD Position in the Biomathematics Group, Dept. of Mathematics, Imperial
College London
We have a fully funded 3 year doctoral studentship in an exciting
project at the interface between Mathematics, Systems Biology and
Synthetic Biology. The position is available immediately and
applications will be reviewed on a rolling basis. Due to funding
regulations the position is available to UK/EU nationals only.
The primary goal of the project is to develop mathematical methods to
predict the dynamics of metabolic networks under feedback regulation.
The interplay between gene regulation and metabolism controls how cells
adapt to environmental perturbations. Some of the key topics in the area
are: to understand how asymptotic dynamics depend on feedback
architecture and parameters, and to quantify the propagation of
intracellular noise between gene expression and metabolism. Cutting-edge
progress in genetic engineering now allows synthetic biologists to build
intracellular feedback systems in microbes. This makes the study of
metabolic regulation ever more important, with diverse applications such
as the design of self-adaptive systems in metabolic engineering or the
identification of regulatory weak spots for future therapeutics. The
project is part of a multidisciplinary collaboration with Dr Fuzhong
Zhang's Synthetic Biology lab at the U Washington in St Louis. Through
our collaboration we will integrate theory and experiment to predict,
measure and modify the responses of E. coli to nutritional shocks.
The ideal candidate should have a strong interest in Mathematical
Biology, Systems & Synthetic Biology or Control Theory for Biological
Systems. We seek someone open-minded, creative and willing to explore
new ideas as part of a multidisciplinary team. The candidate should have
excellent theoretical and computational skills, and hold (or be near
completion of) a Masters-level degree in an area relevant to the
project. Experience with biochemical models would be advantageous.
To apply or for more information please contact Dr Diego Oyarzún
(d.oyarzun@imperial.ac.uk) or visit
http://www.imperial.ac.uk/people/d.oyarzun.
Applications should include a CV and the names of two referees.
----------------------------------------------------
From: Hlavacek, William Scott <wish@lanl.gov>
Date: September 3, 2015 at 4:15:05 PM
Subject: Post-doc: Regulation of Autophagy, Los Alamos National Lab
POSTDOCTORAL OPENING AVAILABLE
LOCATION: Theoretical Biology & Biophysics Group, Theoretical Division,
Los Alamos National Laboratory, Los Alamos, New Mexico, USA (near Santa
Fe and Taos)
CO-MENTORS:
William S. Hlavacek (http://www.t6.lanl.gov/wish/) and
Ruy M. Ribeiro (http://www.t6.lanl.gov/ruy/)
RESEARCH: The successful candidate will develop models to study the
regulation of autophagy in the context of influenza infection
SKILLS: Mathematical/computational modeling of complex biological
systems
COMPENSATION: Salary begins at $73,000 ($107,100 for a Feynman or
Oppenheimer Fellow)
http://www.lanl.gov/careers/career-options/postdoctoral-research/postdoc-program/postdoc-salary-guidelines.php
-Medical, dental, vision, legal and retirement plans
-Life, AD&D and disability insurance
-Paid sick and vacation days, federal holidays
The Postdoctoral Research Associate or Fellow 1) will gain experience in
mathematical modeling of viral dynamics (influenza) and computational
rule-based modeling of cell signaling, 2) will learn about regulation of
autophagy (a cellular recycling process) and the effects of influenza
infection on autophagy, and 3) will collaborate with local quantitative
experimentalists in the Laboratory?s Bioscience Division led by
Dr. Thomas C. Terwilliger (https://solve.lanl.gov/terwilliger/).
TO APPLY: Interested candidates should email Dr. Hlavacek
(wish@lanl.gov) and/or Dr. Ribeiro (ruy@lanl.gov). Please attach your CV
and a cover letter that highlights your unique skills and experiences
and explains your interests in the opening.
An ideal candidate would be:
-A modeler with experience in coordination of modeling and experimental
efforts
-A team player who shares knowledge with lab members
-A collaborator who is confident interacting with researchers from other
disciplines
-An effective communicator who will contribute to a fun and positive
work environment
-Creative, motivated, collaborative, and optimistic, with a strong
desire to impact human health
ENVIRONMENT: The Theoretical Biology & Biophysics Group was founded in
1974. The group played a key role in establishing GenBank and the HIV
databases and the rationale for combination therapy of HIV/AIDS and in
launching the Human Genome Project and the Annual q-bio Summer School
and Conference events. The staff includes members of the National
Academy of Sciences and the American Academy of Arts & Sciences and an
E.O. Lawrence Award winner. Opportunities exist to interact with
researchers in the Center for Nonlinear Studies
(http://cnls.lanl.gov/External/), the renowned Theoretical Division, and
the National Center for Systems Biology in New Mexico
(http://www.systemscenters.org, http://stmc.health.unm.edu). Outdoor
recreation (http://www.newmexico.org/true-outdoors/).
----------------------------------------------------
From: Hlavacek, William Scott <wish@lanl.gov>
Date: September 3, 2015 at 4:15:03 PM
Subject: Post-doc: Spatiotemporal Modeling of Cell Signaling, Los Alamos
POSTDOCTORAL OPENING AVAILABLE
LOCATION: Theoretical Biology & Biophysics Group, Theoretical Division,
Los Alamos National Laboratory, Los Alamos, New Mexico, USA (near Santa
Fe and Taos)
MENTOR: William S. Hlavacek (http://www.t6.lanl.gov/wish/)
RESEARCH: The successful candidate will work with
experimentalists in the Center for Spatiotemporal Modeling of Cell
Signaling (http://stmc.health.unm.edu), a National Center for Systems
Biology (http://www.systemscenters.org), to develop computational models
relevant for understanding immunoreceptor signaling, receptor tyrosine
kinase signaling and the interplay between receptor signaling and endocytic trafficking.
SKILLS: Mathematical/computational modeling of complex biological
systems
COMPENSATION: Salary begins at $73,000 ($107,100 for a Feynman or
Oppenheimer Fellow)
http://www.lanl.gov/careers/career-options/postdoctoral-research/postdoc-program/postdoc-salary-guidelines.php
-Medical, dental, vision, legal, and retirement plans
-Life, AD&D, and disability insurance
-Paid sick and vacation days, federal holidays
The Postdoctoral Research Associate or Fellow 1) will gain experience in
computational rule-based modeling of cell signaling; 2) will work
closely with quantitative experimentalists who are dedicated to
predictive understanding of cellular regulatory systems and who are
affiliated with the University of New Mexico Cancer Center, an
NCI-designated comprehensive cancer center; and 3) will learn about
antigen recognition receptors, receptor tyrosine kinases, and the
regulation of endocytic trafficking.
TO APPLY: Interested candidates should email Dr. Hlavacek
(wish@lanl.gov). Please attach your CV and a cover letter that
highlights your unique skills and experiences and explains your
interests in the opening.
An ideal candidate would be:
-A modeler with experience in coordination of modeling and experimental
efforts
-A team player who shares knowledge with lab members
-A collaborator who is confident interacting with researchers from other
disciplines
-An effective communicator who will contribute to a fun and positive
work environment
-Creative, motivated, collaborative, and optimistic, with a strong
desire to impact human health
ENVIRONMENT: The Theoretical Biology & Biophysics Group was founded in
974. The group played a key role in establishing GenBank and the HIV
databases and the rationale for combination therapy of HIV/AIDS and in
launching the Human Genome Project and the Annual q-bio Summer School
and Conference events. The staff includes members of the National
Academy of Sciences and the American Academy of Arts & Sciences and an
E.O. Lawrence Award winner. Opportunities exist to interact with
theoretical/computational researchers in the Center for Nonlinear
Studies (http://cnls.lanl.gov/External/) and the renowned Theoretical
Division. Outdoor recreation (http://www.newmexico.org/true-outdoors/).
----------------------------------------------------
From: Horacio G. Rotstein <horacio@njit.edu>
Date: September 4, 2015 at 10:59:21 AM
Subject: Post-doc: Theoretical & Comp. Neuroscience, New York City area
NIH funded Postdoctoral Fellowship in Theoretical & Computational
Neuroscience to explore Axonal Coding at NJIT/Rutgers (NYC metropolitan
area) - Nadim lab
This is an ideal position for a candidate with a PhD and a strong
background in the quantitative sciences (Math, Physics, Computer
Science, Computational Biology) and a genuine interest in developing and
using biophysically plausible mathematical models to explore neuronal
coding questions using electrophysiological data. Although performing
experimental recordings is not a requirement, it is a potential
opportunity depending on the interest of the applicant. Appropriate
training will be provided for postdocs interested in exploring this
opportunity who do not have previous experimental experience. The
applicant should also have a genuine interest in and willingness to
interact with other experimentalists and theoreticians. The NJIT/Rutgers
Newark campuses have a vibrant interdisciplinary Neuroscience
community including the Federated Department of Biological Sciences, the
Mathematical Biology group and the Center for Behavioral and
Computational Neuroscience (CMBN).
The Nadim lab is located in the Federated Department of Biological
Science of the New Jersey Institute of Technology and Rutgers University
in Newark, New Jersey (20 min train ride from New York City). The
position is supported by an NIH grant on The Role of Axons in Neural
Coding. The project makes use of the well-defined temporal patterns of
activity in the crustacean stomatogastric nervous system to define
neuromodulator- and activity-dependent changes in axonal excitability
and their impact on the temporal fidelity of action potential
propagation. History-dependence of action potential propagation is an
understudied form of neural plasticity that is important for neural
coding and has become a recent subject of extensive interest. This
position is specifically intended for a computational neuroscientist who
will do computational and theoretical exploration of axonal activity and
its consequences for neural coding.
The potential start date is at any time within the next 6 months. The
salary will be based on experience and is competitive with all
international standards. The initial appointment is for one year with
the possibility of renewal contingent to performance.
Required documents include CV, cover letter, names and emails of three
references. Applications must be submitted on the NJIT HR website
(njit.jobs posting number 0602785).
Please contact Farzan Nadim (farzan@njit.edu) with any questions.
----------------------------------------------------
Subject: SMBnet Reminders
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