SMB Digest July 15, 2015 Volume 15 Issue 28
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
Note:
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Issue's Topics:
Conference: Undergraduate Capstone, Aug 10-14, MBI, Ohio State
Summer School: Comp. Biol.-from Mole...., Sep 2-11, U Coimbra
Workshop: Cell Mechanics, Morphogen...., Sep 14-18, U Cambridge
Conference: Evolutionary Comp. in Robotics, Mar 30-Apr 1, Porto
ToC: Mathematical Biosciences & Engineering, Volume 12 Issue 5
PhD Position: Mathbio/Epid&Ecol/Network..., RMIT U, Melbourne
Post-doc: Computational Systems Biology, U Lille, France
Post-doc: Antibody Formulations, Pfizer, St. Louis
Post-doc: Systems Pharmacology, Bridgewater, NJ, USA
NSF/DMS & BD2K Partner to Encourage New Collaborations...
SMBnet Reminders
----------------------------------------------------
From: Tony Nance <tony@mbi.osu.edu>
Date: July 10, 2015 at 6:48:25 AM
Subject: Conference: Undergraduate Capstone, Aug 10-14, MBI, Ohio State
2015 MBI Undergraduate Capstone Conference
August 10 - 14, 2015, MBI, Ohio State University, Columbus, OH
NOW ACCEPTING APPLICATIONS!
MBI Undergraduate Capstone Conference, August 10-14
The MBI Capstone conference offers undergraduate student researchers in
the mathematical biosciences an opportunity to present their work on the
national stage.
This student centered conference features:
-Recruitment fair for graduate studies
-Panels on jobs and graduate opportunities
-Keynotes from prominent Math Biologist
-Social event at the Columbus Zoo/Aquarium
-Talks and posters by student researchers
Applications submitted by July 22, 2015 will receive full consideration.
To apply visit http://mbi.osu.edu/event/?id=902
----------------------------------------------------
From: Armindo Salvador <armindo.salvador@gmail.com>
Date: July 9, 2015 at 5:15:58 AM
Subject: Summer School: Comp. Biol.-from Mole...., Sep 2-11, U Coimbra
The Computational Biology network at the University of Coimbra
(http://www.uc.pt/en/iii/initiatives/cbuc) is pleased to announce the
2015 Summer School on Computational Biology - from molecules to tissues,
to be held in Coimbra (Portugal) on 2nd to 11th September 2015. This
will be an introductory course targeted to students from the M. Sc. to
post-doctoral levels with either biological or exact sciences
backgrounds who wish to acquire skills in Computational Biology. It will
include introductory lectures, courses on specialized Computational
Biology topics, seminars on recent developments, and mini-research
projects.
In order to apply, please send a CV and a short motivation paragraph
explaining why you are interested in participating in the summer school
to the email computational.biology@uc.pt, no later than July 25.
For further information please see http://www.uc.pt/go/summercompbiol
Poster to print:
http://www.uc.pt/en/iii/initiatives/cbuc/curso/poster#Poster
----------------------------------------------------
From: Sharon Lubkin <lubkin@ncsu.edu>
Date: July 9, 2015 at 11:23:14 AM
Subject: Workshop: Cell Mechanics, Morphogen...., Sep 14-18, U Cambridge
Workshop: Cell Mechanics, Morphogenetics and Pattern Formation:
perspectives from experimental and theoretical points of view
14-18 September, 2015, Isaac Newton Institute, University of
Cambridge, UK
Organisers: Till Bretschneider (Warwick), Damir Khismatullin (Tulane),
Sharon Lubkin (North Carolina State) and Christian Schmeiser (Vienna)
The mechanical characterisation of individual cells is complex and
dynamic. Nonetheless, great progress has been made in understanding how
the dynamics of subcellular structures leads to cell shape and motility.
Static tissues have also been well characterised. It is at the level of
morphogenesis where the bridging of scales between individual cell
dynamics and tissue dynamics is least understood. This workshop aims to
(1) present a framework for understanding what is already known about
cell-level and tissue-level mechanics, (2) identify gaps in our
understanding of how cells interact mechanically in tissues in order to
actuate morphogenesis, (3) propose new collaborations to increase our
understanding of the cell-tissue emergent dynamics. We will bring
together experts in development, microscopy, image analysis,
biomechanics, and modeling.
Keynote Speakers:
Professor Carl-Philipp Heisenberg (IST Austria)
Dr. Sean Megason (Harvard)
Professor Anne Ridley (King's College London)
Professor Stanislav Shvartsman (Princeton)
Professor Denis Wirtz (Johns Hopkins University and Johns Hopkins School
of Medicine)
Deadline for applications: 12 July 2015
https://www.newton.ac.uk/event/cgpw02
----------------------------------------------------
From: Evert Haasdijk <e.haasdijk@vu.nl>
Date: July 10, 2015 at 8:01:24 AM
Subject: Conference: Evolutionary Comp. in Robotics, Mar 30-Apr 1, Porto
EvoROBOT 2016
Porto, Portugal, 30 March - 1 April 2016
Call for Papers - Evolutionary Computation in Robotics
The EvoROBOT track is part of EvoApplications, the European Conference
on the Applications of Evolutionary Computation
(http://www.evostar.org/), to be held in Porto, Portugal.
The EvoROBOT track focusses on evolutionary robotics: the application of
evolutionary computation techniques to automatically design the
controllers and/or hardware of autonomous robots, real or simulated.
This is by nature a multi-faceted field that combines approaches from
other fields such as neuro-evolution, evolutionary design, artificial
life, robotics, et cetera.
We invite high quality contributions dealing with state-of-the-art
research in the area of evolutionary robotics.
Topics include but are not limited to:
-Evolution of (neural or otherwise) robot controllers;
-Evolution of modular robot morphology;
-Hardware/morphology and controller co-evolution;
-Open-ended evolution in robotics;
-Robotic evolutionary Artificial Life;
-Evolutionary self-assembly and self-replication;
-Evolution, development and learning;
-Evolutionary and co-evolutionary approaches.
Submission Deadline: 1 November 2015
----------------------------------------------------
From: Liwei Ning <editorial@aimsciences.org>
Date: July 8, 2015 at 3:47:55 PM
Subject: ToC: Mathematical Biosciences & Engineering, Volume 12 Issue 5
Mathematical Biosciences and Engineering (MBE)
Volume: 12, Number: 5 October 2015
http://www.aimsciences.org/journals/contentsListnew.jsp?pubID=784
1. Thermal detection of a prevascular tumor embedded in breast tissue
Ephraim Agyingi, Tamas Wiandt and Sophia A. Maggelakis
2. Parameters identification for a model of T cell homeostasis
Houssein Ayoub, Bedreddine Ainseba, Michel Langlais and
Rodolphe Thiébaut
3. Uncertainty quantification in modeling HIV viral mechanics
H. T. Banks, Robert Baraldi, Karissa Cross, Kevin Flores,
Christina McChesney, Laura Poag and Emma Thorpe
4. Stochastic modelling of PTEN regulation in brain tumors: A model for
glioblastoma multiforme
Margherita Carletti, Matteo Montani, Valentina Meschini, Marzia Bianchi
and Lucia Radici
5. Multi-host transmission dynamics of schistosomiasis and its optimal
control
Chunxiao Ding, Zhipeng Qiu and Huaiping Zhu
6. Order reduction for an RNA virus evolution model
Andrei Korobeinikov, Aleksei Archibasov and Vladimir Sobolev
7. Change detection in the dynamics of an intracellular protein
synthesis model using nonlinear Kalman filtering
Gerasimos G. Rigatos, Efthymia G. Rigatou and Jean Daniel Djida
8. Analysis of a cancer dormancy model and control of immuno-therapy
Ben Sheller and Domenico D'Alessandro
9. Ebola outbreak in West Africa: real-time estimation and multiple-wave
prediction
Xiang-Sheng Wang and Luoyi Zhong
10. Heteroclinic bifurcation for a general predator-prey model with
Allee effect and state feedback impulsive control strategy
Qizhen Xiao and Binxiang Dai
11. Global stability of a multi-group model with vaccination age,
distributed delay and random perturbation
Jinhu Xu and Yicang Zhou
12. Cilium height difference between strokes is more effective in
driving fluid transport in mucociliary clearance: A numerical study
Ling Xu and Yi Jiang
13. Combining robust state estimation with nonlinear model predictive
control to regulate the acute inflammatory response to pathogen
Gregory Zitelli, Seddik M. Djouadi and Judy D. Day
----------------------------------------------------
From: Lewi Stone <lewistone2@gmail.com>
Date: July 13, 2015 at 6:36:21 PM
Subject: PhD Position: Mathbio/Epid&Ecol/Network..., RMIT U, Melbourne
We invite applications for a PhD fellowship in the School of
Mathematical and Geospatial Sciences, RMIT University, Melbourne,
Australia, The applicants will have the opportunity to work on subjects
that cross the interface of mathematical biology, theoretical
epidemiology and ecology, network theory, and BigData. The Department
has a vibrant group of active researchers in these areas, and intends to
build this group further. Please contact Prof. Lewi Stone, in the first
instance by emailing: lewistone2@gmail.com
----------------------------------------------------
From: Pfeuty Benjamin <Benjamin.Pfeuty@univ-lille1.fr>
Date: July 10, 2015 at 7:13:41 AM
Subject: Post-doc: Computational Systems Biology, U Lille, France
A Postdoctoral Position in Computational Systems Biology at the
University of Lille, France
Topic: Computational modeling of stress response in normal and cancer
cells
Our team combines experimental and computational modeling techniques to
study the response of mammalian cells to various stresses such as
oxidative, thermal and metabolic stresses. The goal of this project is
to characterize the main differences between non-cancerous and cancerous
cells in their sensitivity (survival/death rates) to stress signals, with
the long-term objective to develop novel anti-cancer therapeutic
strategies. The fact that cancer cells typically show aberrant
metabolism and proliferation and our experimental ability to induce
various types, intensities and durations of stresses motivate the study
of several related issues: What are the relevant timescales involved in
stress responses? Are there non-trivial effects in combining stress
signals? How do cells coordinate stress response, metabolism and cell
cycle?
The postdoctoral position is dedicated to working on the computational
modeling aspect of this stress response project. Models will be useful
to provide both quantitative and qualitative insights into the dynamics
of stress-response factors and of cell fate decisions under various
stress conditions. Modeling work will mainly consist in (i) identifying
the known cellular pathways involved in stress-specific responses,
(ii) translating these signaling, regulatory and metabolic networks into
ordinary differential equation models, (iii) simulating and analyzing
the model behavior under various settings, and (iv) comparing with
experimental data.
CANDIDATE PROFILE
The candidate should have: (i) a strong background in applied
mathematics or physics, especially computational and theoretical skills
in working with systems of differential equations; (ii) basic notions of
cell biology and biophysics gained from previous research experience;
(iii) ability to work within a team environment.
POSITION AND APPLICATION DETAILS
The position is for one year renewable, and would start between October
2015 and January 2016. Net annual salary is about 28000 euros and
includes a benefits package (health insurance, retirement and
unemployment benefits). The laboratory
(http://www.phlam.univ-lille1.fr/) is located on the Villeneuve d'Ascq
campus of the University of Lille. Lille is a lively city connected by
highspeed train to Brussel (30mn), Paris (1h) and London (1h30).
Applicants should send a letter of motivation, a CV including a complete
list of publication and at least 2 letters of recommendation to:
quentin.thommen@univ-lille1.fr and Benjamin.pfeuty@univ-lille1.fr
For more informations:
http://www.phlam.univ-lille1.fr/spip.php?article1066
----------------------------------------------------
From: Charest, Jenifer <Jenifer.Charest@pfizer.com>
Date: July 8, 2015 at 10:12:37 AM
Subject: Post-doc: Antibody Formulations, Pfizer, St. Louis
Job Title: Postdoctoral Fellow, Antibody Formulations
Job Id: 1014595
Target Openings: 1
Locations: United States-Missouri-Saint Louis
Responsibilities
A postdoctoral researcher is sought to conduct fundamental computational
research towards understanding solution behavior of highly concentrated
antibody formulations. The research shall involve an inter-disciplinary
mix of multi-scale molecular modeling and dynamics simulations, and high
performance computing to advance our understanding of inter-molecular
interactions (protein:protein and protein: cosolutes) in highly
concentrated biologic drug solutions. The researcher will be expected to
discover/design novel viscosity reducing excipients, and contribute
toward development of novel approaches focused at early detection of
develop-ability challenged therapeutic candidates.
Other duties as assigned time to time by research supervisor.
The successful candidate shall be highly motivated, hardworking, and
intellectually productive team player. He/she shall be expected to
publish in high impact scientific journals and contribute towards
Pfizer's expertise on biopharmaceutical drug development. Fluency in
oral and written English is required. Good inter-personal and
communication skills are required.
Qualifications
EDUCATIONAL BACKGROUND: Ph.D. in Computational Molecular Biophysics,
Chemical Engineering or related fields
DESIRABLE: One or two years of postdoctoral research experience. Record
of first class scientific research productivity as demonstrated by
publications in high impact journals
WORK EXPERIENCE/SKILLS: Advanced understanding of antibody
structure-function, Protein: Protein interactions, and viscosity issues
in highly concentrated antibody solutions is essential. Expertise in
computer programming, molecular modeling, coarse-grained and all atom
MD simulations of large macromolecules is required. Expertise with MOE,
Discovery Studio, Schrodinger, VMD, MATLAB and modern programming
languages is required.
Equal Employment Opportunity
Pfizer is committed to equal opportunity in the terms and conditions of
employment for all employees and job applicants without regard to race,
color, religion, sex, sexual orientation, age, gender identity or gender
expression, national origin, disability or veteran status. Pfizer also
complies with all applicable national, state and local laws governing
nondiscrimination in employment as well as work authorization and
employment eligibility verification requirements of the Immigration and
Nationality Act and IRCA. Pfizer is an E-Verify employer.
----------------------------------------------------
From: Karim Azer <Karim.Azer@sanofi.com>
Date: July 15, 2015 at 7:19:20 AM
Subject: Post-doc: Systems Pharmacology, Bridgewater, NJ, USA
Job Description:
This is a postdoctoral position in the area of systems pharmacology. The
individual will be based in the Department of Clinical and Exploratory
Pharmacology in Bridgewater NJ, and will be a member of the
Interdisciplinary Program in Pharmacometrics which links pharmacometric
experts across the Scientific Core Platforms. The individual will
primarily be involved with the development of systems pharmacology
models, working as part of a modeling team. The models will aim to
quantitatively integrate pathway biology, physiology and clinical
pharmacology, i.e. systems pharmacology.
-Major Duties & Responsibilities: Develop computational systems models
working with internal and external collaborators, Communicate with
clarity the results of modeling in presentations to key stakeholders.
Qualifications
-Formal Education And Experience Required: PhD with a track record of
productivity in the areas of systems pharmacology, computational biology
or related field, as manifested in publications and presentations.
-Basic experience in Pharmacometrics or Clinical Pharmacology. Knowledge
And Skills: Extensive knowledge of biological pathways relevant to
disease. Superb skill in communicating both highly technical material as
well as the distilled take-home messages.
Knowledge And Skills Desirable: Expert knowledge in at least one area
(e.g. rare diseases, cardiovascular) highly desirable.
-Modeling and computational experience, Excellent scientific computing
and programming skills in a variety of computational tools such as
MATLAB, Monolix, NONMEM, Mathematica, R and excellent working knowledge
of Linux and Windows environments
Please email karim.azer@sanofi.com to inquire about the position.
----------------------------------------------------
From: Beth Russell <beth.russell@nih.gov>
Date: July 13, 2015 at 8:02:58 AM
Resent-From: Raymond Mejía <mejiar@helix.nih.gov>
Subject: NSF/DMS & BD2K Partner to Encourage New Collaborations...
The National Science Foundation's (NSF) Division of Mathematical Sciences
(DMS https://www.nsf.gov/div/index.jsp?div=DMS ), Directorate for
Mathematical and Physical Sciences and the National Institutes of
Health's (NIH) Big Data to Knowledge (BD2K
https://datascience.nih.gov/bd2k ) Initiative are working together to
support collaborations that build effective teams to tackle biomedical
data science problems. NSF/DMS and NIH/BD2K are jointly sponsoring small
one-year planning grants for new teams of investigators that include
mathematicians, statisticians, and biomedical researchers. These
planning grants aim to foster inter- and multi-disciplinary, exploratory
collaborations by encouraging the submission of unsolicited proposals.
Proposals will be accepted until August 6, 2015 in response to the Dear
Colleague Letter: Unsolicited Proposals for Quantitative Approaches to
Biomedical Big Data (QuBBD) posted at:
http://www.nsf.gov/pubs/2015/nsf15093/nsf15093.pdf.
----------------------------------------------------
Subject: SMBnet Reminders
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