SMB Digest June 3, 2015 Volume 15 Issue 22
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
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:
Conference: Models in Population..., Aug 24-28, Rio de Janeiro
Workshop: Quantitative Systems Pharmacology, Sep 14-17, UK
ToC: BMB, Volume 77, Issue 5
Books: New Books Alert, Springer
PhD Position: Projecting the..., Dutch National Institute of...
PhD Position: Computational Biology & Medicine, U Oslo
Post-doc: Yeast Systems Biology, U North Carolina
Post-doc: Cell Metabolism of Cancer Cells, U Southern Cal.
Post-doc: Computational Neuroscience, Louisiana State U
Lecturer: Applied Mathematics, U Manchester, UK
Position: Computational Biologist, ARA, Arlington, VA, US
NIH: Extramural Nexus
NIGMS: Division Director News, Council Summary, Funding...
Survey: Use of Math in Life Sciences
SMBnet Reminders
----------------------------------------------------
From: Petrovskiy, Sergei (Prof.) <sp237@leicester.ac.uk>
Date: June 2, 2015 at 8:22:48 AM
Subject: Conference: Models in Population..., Aug 24-28, Rio de Janeiro
Models in Population Dynamics & Ecology 2015: E^3 - bringing together
Ecology, Epidemiology and Evolution (Niteroi/Rio de Janeiro, Brazil,
Aug.24-28, 2015)
In order to accommodate an increasing number of inquiries and requests,
the registration deadline is now extended until July 1st.
For all the information about the conference, including the application
form, please visit the conference website at http://www.mpde15.uff.br/
or contact the conference organizers at max.souza@gmail.com (Max Souza)
or sp237@le.ac.uk (Sergei Petrovskii)
----------------------------------------------------
From: Marcus Tindall <m.tindall@reading.ac.uk>
Date: May 28, 2015 at 5:51:38 AM
Subject: Workshop: Quantitative Systems Pharmacology, Sep 14-17, UK
A UK Meeting & Problem Workshop on Quantitative Systems Pharmacology
14th to 17th September 2015
AstraZeneca, Alderley Park, Macclesfield, UK.
REGISTRATION OPEN -
http://www.personal.reading.ac.uk/~sas07mt/meetings.html
The emerging discipline of Quantitative Systems Pharmacology (QSP) - the
integration of biological mechanisms (from sub-cellular to patient
cohorts) in quantitative mechanistic models and their application in the
discovery and development of pharmaco-therapeutics, is an area of
growing research in academia and industry.
This 4 day meeting, kindly supported by AstraZeneca, Pfizer and
Unilever, will provide an introduction to QSP and a forum for
researchers in academia and industry to come together to discuss
developments in this emerging field of science in the UK and
internationally. The meeting will showcase current advances in the field
(Day 1) and provide the opportunity for mathematicians, engineers,
scientists and industrialists to exchange skills and knowledge by
working on problems brought by life scientists in industry and academia
(Days 2 to 4).
For any queries please e-mail m dot tindall at reading dot ac dot uk in
the first instance.
Marcus Tindall (on behalf of the Organising Committee)
----------------------------------------------------
From: Springer <springer@alerts.springer.com>
Date: June 1, 2015 at 8:15:17 PM
Reply-To: Springer <onlineservice@springer.com>
Subject: ToC: BMB, Volume 77, Issue 5
Volume 77 Number 5 is now available at
http://link.springer.com/journal/11538/77/5?wt_mc=alerts.TOCjournals
Special Issue: What Has Mathematics Done for Biology
In this issue
What Has Mathematics Done for Biology?
Michael C. Mackey & Philip K. Maini
Understanding, Treating and Avoiding Hematological Disease: Better
Medicine Through Mathematics?
David C. Dale & Michael C. Mackey
A Mathematical Model of Atherosclerosis with Reverse Cholesterol
Transport and Associated Risk Factors
Avner Friedman & Wenrui Hao
Functional Characterization of Oscillatory and Excitable Media
Leon Glass & Alvin Shrier
Bistability, Oscillations, and Traveling Waves in Frog Egg Extracts
John J. Tyson & Bela Novak
The Role of Mathematical Models in Understanding Pattern Formation in
Developmental Biology
David M. Umulis & Hans G. Othmer
Patient-Specific Mathematical Neuro-Oncology: Using a Simple
Proliferation and Invasion Tumor Model to Inform Clinical Practice
Pamela R. Jackson, Joseph Juliano, Andrea Hawkins-Daarud,
Russell C. Rockne & Kristin R. Swanson
Stochastic Dynamic Programming Illuminates the Link Between Environment,
Physiology, and Evolution
Marc Mangel
----------------------------------------------------
From: Springer <SpringerAlerts@springeronline.com>
Date: May 31, 2015 at 10:40:48 PM
Reply-To: Springer <onlineservice@springer.com>
Subject: Books: New Books Alert, Springer
NEW PRINT & EBOOKS
Mathematics
Mathematical and Computational Biology
Affine Diffusions and Related Processes: Simulation, Theory and
Applications
Book Series: Bocconi & Springer Series, Vol. 6
Alfonsi, Aurélien
http://www.springer.com/-/2/c246d4ed9d574ca2924a0401dbcf9697
Facets of Uncertainties and Applications
Book Series: Springer Proceedings in Mathematics & Statistics, Vol. 125
Editor/s: Chakraborty, Mihir; Skowron, Andrzej; Maiti, Manoranjan;
Kar, Samarjit
http://www.springer.com/-/3/c246d4ed9d574ca2924a0401dbcf9697
Molecular Dynamics
Book Series: Interdisciplinary Applied Mathematics, Vol. 39
Leimkuhler, Ben; Matthews, Charles
http://www.springer.com/-/4/c246d4ed9d574ca2924a0401dbcf9697
----------------------------------------------------
From: Hans Bogaards <hans.bogaards@rivm.nl>
Date: June 1, 2015 at 5:14:57 AM
Subject: PhD Position: Projecting the..., Dutch National Institute of...
PhD student: Projecting the effects of vaccination against multi-strain
pathogens, National Institute for Public Health and the Environment
(RIVM), Centre for Infectious Disease Control, Dept. Infectious Disease
Modelling
Project description: In order to prevent serious illness and disease
outbreaks, the Dutch government offers free vaccination against specific
infectious diseases to all children through the National Immunization
Programme. The most recent additions to this Programme are the vaccines
against pneumococcus, associated amongst others with meningitis, and
against papillomavirus, associated with various forms of cancer. Both
pneumococcus and papillomavirus are characterized by the existence of
various strains. The vaccines protect against a selected set of all
strains that can cause disease, being so-called polyvalent vaccines. An
anticipated effect of polyvalent vaccination is the elimination of
vaccine-specific strains from the population. A possible unwanted effect
is the take-over by other strains against which the vaccine is not
protective, such that the health benefit partly disappears. This
phenomenon is known as type-replacement and is caused by competition
between pathogenic strains. This project aims to deliver a better
assessment of type-replacement and its long-term consequences for the
effectiveness of polyvalent vaccination. Partners in this project are
the University Medical Centres of Utrecht (Paediatrics) and of Leiden
(Medical Statistics).
Your challenge: 1. Quantification of interactions between pathogenic
strains requires diverse statistical techniques (graphical models,
multi-state modelling, survival analysis) for a diversity of data
structures. The question is which techniques and which data are
informative for inferring competitive interactions, and which are
sensitive for the occurrence of type-replacement. To this end, you will
develop dynamic transmission models for multi-strain pathogens that can
incorporate a variety of interactions between strains. You will use
these models to simulate data for the joint occurrence of multiple
strains in epidemiological studies.
2. You will develop statistical techniques based on simulated data and
apply these to available data on pneumococcus and papillomavirus. You
will investigate indications for type-replacement and answer the
question how type-replacement may alter the expected health benefit of
vaccination. In the end, your research provides a consistent methodology
for multi-strain modelling that can be used to describe the
effectiveness of pneumococcal vaccination in an adequate way.
3. You will publish your findings in scientific journals and present
your findings on international conferences. After four years, your
research is intended to result in an academic dissertation. An abroad
stay as part of your PhD research belongs to the possibilities.
Your profile: We seek a highly motivated, enthusiastic researcher with
an MSc or comparable degree in (applied) mathematics, physics,
biostatistics, theoretical biology or bioinformatics. Excellent verbal
and written command of English is required, programming experience in
C/C++ and R are welcome. We expect affinity with the promotion of public
health through prevention of infectious diseases.
Terms of employment: You will be stationed at the Dutch National
Institute of Public Health and the Environment (RIVM). Appointment takes
place based on 36 working hours a week for the initial term of one year.
Your contract will be prolonged in case of good performance. Salary is
in conformity with that of a PhD student (OIO) at a Dutch university.
More information: Dr. J.A. Bogaards, Project leader
(hans.bogaards@rivm.nl, tel 030-2744765), Dr. J. Wallinga, Head Dept.
Infectious Disease Modelling (jacco.wallinga@rivm.nl, tel. 030-2742553)
----------------------------------------------------
From: Lena Korsnes <lenako@simula.no>
Date: June 2, 2015 at 1:48:17 AM
Subject: PhD Position: Computational Biology & Medicine, U Oslo
PhD fellowships available through the SUURPh international training
programme
The Simula Research Laboratory and University of Oslo (UiO) welcome
applications for doctoral fellowships in computational biology and
medicine funded through the SUURPh programme. SUURPh fellows will be
enrolled through the faculty of Mathematics and Natural Sciences at UiO,
and conduct their work with advisors located primarily at Simula or UiO.
An important feature of these collaborative fellowships is that students
will also be supported (and required) to complete a portion of their
work at the University of California San Diego (USA). Typically this
period will last from 6 months to 1 year depending on the project. We
will accept applications from students of all backgrounds but recommend
that applicants possess a strong foundation in computational and
quantitative sciences. To be eligible, students must also have completed
a Masters in an appropriate field by the end of summer of 2015.
For more information and to submit your application, please visit the
SUURPh home page: www.simula.no/education/suurph-collaboration
----------------------------------------------------
From: Elston, Timothy C <timothy_elston@med.unc.edu>
Date: May 28, 2015 at 10:44:46 AM
Subject: Post-doc: Yeast Systems Biology, U North Carolina
Postdoctoral position in yeast systems biology - University of
North Carolina
We are seeking one or more postdoctoral fellows to develop computational
models and/or conduct live cell imaging analysis. The goal of the
project is to study the role of noise in cellular signal transduction
pathways (via G protein coupled receptors and MAPKs) and cell fate
transitions. This NIH-funded project is a collaborative effort between
the labs of Drs. Timothy Elston, Henrik Dohlman and Beverly Errede. The
successful candidate will have a PhD in computational biology,
biophysics, physics, applied mathematics, biochemistry, cell biology, or
a related field, a proven track record of research productivity, and
enjoy participating in interdisciplinary team science.
Project details: All intracellular processes are subject to large
amounts of molecular-level fluctuations. In certain contexts, this
"noise" may serve as a bet-hedging mechanism to diversify the response
of a population of otherwise identical cells, whereas in other contexts
noise suppression may be required to properly coordinate response
pathways when cells are faced with multiple competing stimuli. The yeast
Saccharomyces cerevisiae is the premier model system for studying
mechanisms of noise regulation. Planned investigations will combine
microfluidic devices and fluorescent imaging to follow single cells in
well controlled environments, quantitative image analysis to
characterize fluctuations in signaling and gene expression, and
stochastic modeling to suggest and test noise regulation mechanisms.
Lab websites:
http://www.med.unc.edu/~hdohlman/research.html
http://www.med.unc.edu/pharm/elstonlab/index.html
http://www.med.unc.edu/biochem/errede
Please email letter of interest, CV, and the names of three references
to Prof. Tim Elston at telston@med.unc.edu.
----------------------------------------------------
From: Stacey Deleria Finley <sfinley@usc.edu>
Date: May 29, 2015 at 4:46:18 PM
Subject: Post-doc: Cell Metabolism of Cancer Cells, U Southern Cal.
The Computational Systems Biology Laboratory (CSBL) is seeking a
Postdoctoral Research Fellow interested in understanding the cellular
metabolism of cancer cells. The fellow will work to develop an
experiment-based, validated computational model of metabolism in
pancreatic cancer and apply the model to identify therapies that inhibit
tumor metabolism. Ultimately, the goal of this work is to impact the
development of therapeutics for treating pancreatic cancer by providing
a more in-depth understanding of the dynamics of altered metabolism and
how the metabolic pathways can be exploited to impede cancer
progression. The fellow will interact with experimental collaborators
and clinical consultants.
Required Knowledge, Skills, and Abilities: Research experience in
computational modeling of biochemical or metabolic reactions as
evidenced by publication record; Proficient knowledge of MATLAB; Desire
to identify and tackle new problems in cancer metabolism; Desire to work
in a multi-disciplinary research environment; Interpersonal skills to
communicate effectively with faculty, students, and staff; Experience
with any of the following techniques is particularly desirable: kinetic
modeling of metabolic pathways, parameter fitting, and stochastic
simulations.
Minimum Education: Doctorate degree in Biomedical Engineering,
Bioengineering, Chemical Engineering, or related field, from an
accredited institution.
Work Environment: The CSBL is located on the University Park campus of
the University of Southern California (USC). The position will involve
interactions with faculty, postdocs, and students both within and
outside of USC.
Salary: Commensurate with experience
Interested individuals should contact Professor Stacey Finley via email
(sfinley@usc.edu) and provide a cover letter, CV, and contact
information for three references that can affirm the applicant's
qualifications for this position.
----------------------------------------------------
From: Canavier, Carmen C. <ccanav@lsuhsc.edu>
Date: June 1, 2015 at 10:52:13 AM
Subject: Post-doc: Computational Neuroscience, Louisiana State U
Postdoctoral Researcher
Louisiana State University Health Sciences Center
A two (2) year Postdoctoral Researcher position is available in the lab
of Carmen Canavier in the School of Medicine, Department of Cell
Biology and Anatomy at LSU Health Sciences Center in New Orleans. The
focus of the lab is computational neuroscience. The main project is to
model bursting and tonic firing in midbrain dopamine neurons, in close
collaboration with experimentalists. Additional projects focus on
oscillations and synchrony in cortical and basal ganglia networks. The
primary duties will involve linear and non-linear analyses, writing
code, calibrating single neuron models, and generating predictions that
lead to additional experiments.
Candidates must have a Ph.D. in Engineering, Mathematics, Neuroscience,
Physics, Computer Science or a related field of study. Familiarity with
nonlinear dynamics, writing code, running the simulation package NEURON,
and modeling single neurons is preferred.
Qualified candidates may submit resume along with cover letter and
contact information for three references electronically to:
SOM-recruits@lsuhsc.edu; reference 00049561. This appointment is a two
(2) year assigned only. Applications should be received before July 1 to
ensure consideration for the position. LSUHSC is an Equal Opportunity
Employer for females, minorities, individuals with disabilities and
protected veterans.
----------------------------------------------------
From: Oliver Jensen <oliver.jensen@manchester.ac.uk>
Date: June 2, 2015 at 5:50:52 AM
Subject: Lecturer: Applied Mathematics, U Manchester, UK
Lecturer in Applied Mathematics
University of Manchester, UK
The School of Mathematics at the University of Manchester seeks a new
Lecturer in Applied Mathematics. Applications are welcome from
researchers whose interests complement and extend existing activity
within the School. Researchers with interests addressing data-driven or
interdisciplinary applications (for example in industry, medicine,
biology or geophysics) are particularly encouraged to apply. For
further details, see
https://www.jobs.manchester.ac.uk/universityofmanchesterinternal/displayjob.aspx?jobid=9845
Closing date: 31/07/2015
----------------------------------------------------
From: Jacqui Wentz <jwentz@ara.com>
Date: May 28, 2015 at 3:50:56 PM
Subject: Position: Computational Biologist, ARA, Arlington, VA, US
Applied Research Associates, Inc. (ARA) is seeking a scientist to help
develop mathematical models of the biological and physiological effects
of hazardous materials and the environments due to chemical, biological,
radiological and nuclear (CBRN) weapons.
The candidate should have a background in computational biology or other
life science, and well-developed skills in mathematical modeling and
computer programming. The candidate should have an understanding of the
physiological effects associated with acute injuries (burns and trauma)
and exposure to radiation, hazardous materials and infectious organisms.
The individual must have good research, analysis, and model development
skills. The successful candidate will help develop and implement
physiologically-based mathematical models of human response to hazardous
exposures in support of consequence assessment and medical planning for
emergency response. The candidate will work in a team environment and
will assist in cultivating marketing opportunities.
Required Skills: The candidate must have a B.S. in computational biology
or a related science discipline, be proficient with mathematical or
statistical modeling, and have an understanding of human response from
the level of molecular biology to clinical presentation. The candidate
must have well-developed oral and written communication skills and be
able to work with little supervision, including setting and achieving
interim milestones that support higher task objectives. The candidate
must be able to obtain a U.S. government security clearance, which
includes U.S. citizenship.
Required Experience: Position requires two to four years of experience
in a relevant scientific discipline.
Desired Qualifications: A candidate with an advanced degree (Masters
or PhD) is preferred. Proficiency in programming languages such as
Python or MATLAB is highly desired; experience with Java or C++ is
considered a plus. Candidate should have strong research and analytical
skills.
Application Instructions: Please apply at www.careers.ara.com for the
Computational Biologist, (AD-2015-03) position. ARA is an EEO/AA
employer.
----------------------------------------------------
From: Dieffenbach, Ann (NIH/NIGMS) [E] <DIEFFENA@NIGMS.NIH.GOV>
Date: May 29, 2015 at 7:16:57 PM
Re-Sent From: Raymond Mejía <digest.ray@gmail.com>
Subject: NIH: Extramural Nexus
For an NIH Update on Considering Sex a Biological Variable; Delay in
Application Submission Due to Severe Weather; and New Reporting System
for Research Involving Chimpanzees, see
https://list.nih.gov/cgi-bin/wa.exe?A1=ind1505&L=extramuralnexus
----------------------------------------------------
From: Dieffenbach, Ann (NIH/NIGMS) [E] <DIEFFENA@NIGMS.NIH.GOV>
Date: May 28, 2015 at 8:45:12 AM
Subject: NIGMS: Division Director News, Council Summary, Funding...
For NIGMS information on Division Director news, Council Summary,
Funding Opportunity, see
https://list.nih.gov/cgi-bin/wa.exe?A1=ind1505&L=nigms_network
----------------------------------------------------
From: Pablo Duran <pduran@utexas.edu>
Date: May 28, 2015 at 2:50:00 PM
Subject: Survey: Use of Math in Life Sciences
USE OF MATH IN LIFE SCIENCES
As part of my dissertation, I am conducting a study on the main
mathematical and statistical tools currently used in life sciences. The
results of the study are intended to inform the graduate and
undergraduate curriculum in Biology and Mathematics--as well as the
curriculum of related training programs outside of academia--so that
they would better align to student needs at their future workplace.
The first part of the study consists of an online survey designed for
biologists from the areas of "developmental biology" and "ecology,
evolution, and behavior". This survey was piloted by faculty members and
students at UT Austin, with an average completion time of 9 minutes. I
can offer no compensation, but I would be happy to share the results of
the study, and make you eligible to win one of four $25 Amazon gift
cards. The online survey is completely anonymous; you will just need to
click on the link below to take it,
https://utexas.qualtrics.com/SE/?SID=SV_3sAsOBtAhu4R8BD
For more information please contact:
Pablo Duran
pduran@utexas.edu
Doctoral candidate in Mathematics Education
The University of Texas at Austin
----------------------------------------------------
Subject: SMBnet Reminders
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End of SMB Digest
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