Subject: Society for Mathematical Biology Digest

SMB Digest  February 3, Volume 16  Issue 5
ISSN 1086-6566

Editor: Ray Mejía ray(at)smb(dot)org

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:
   Summer Undergraduate Research in Biology REU, May 8 - July 23
   3rd Annual UCSD-UiO-Simula Summer School: Computational Physiology
   Summer School: Computational Immunology, June 20-23, Yale University
   Conference: BAMM! Biology and Medicine through Mathematics, May 20-22
   West Australian Conference on Biological Structure Formation
   VectorBiTE Research Coordination Network Launched
   ToC: Bulletin of Mathematical Biology, Vol. 78, Issue 1
   ToC: BIOMATH, Volume 4, Issue 2
   PhD Position: Modelling Gait in People with Parkinson's Disease, Exeter
   Postdoctoral Research Associate: St. Jude Children's Research Hospital
   Postdoctoral Fellow: Mathematical Oncology, Moffitt Cancer Center
   Postdoc: Mathematical Biology, University of Sydney, Australia
   2-year Postdoc: Programme of Collaborative Mathematical Research
   Lecturer: Mathematical Biology, University of Birmingham
   Systems Biology Informatics Manager: Digital Salmon, NMBU, Ås, Norway
   NIH Update: Addressing rigor, transparency, and reproducibility ...
   SMBnet Reminders


From: Davis, Courtney L. <Courtney.Davis2@pepperdine.edu>
Date: Wed, Jan 27, 2016 at 2:10 PM
Subject: Summer Undergraduate Research in Biology REU, May 8 - July 23

We are seeking student applicants for a summer mathematical biology research
experience for undergraduates (REU). Please forward this to anyone who
might be interested! Thank you!

Summer Undergraduate Research in Biology (SURB) REU
Pepperdine University, Malibu, CA
Mathematical Modeling of Biological Systems: Models of Newt-Crayfish
Interactions in Southern California Streams
May 8 - July 23, 2016
Applications due February 15, 2016 at noon Pacific time

Program: In the summer of 2016, Pepperdine University will host the Summer
Undergraduate Research Program in Biology (SURB) REU developed specifically
for students who are interested in pursuing a career in biological
research, science education, environmental science, mathematical biology,
or biotechnology. Students will partner with a faculty member to develop
an individual research project in which they pose a quantitative biological
question and construct mathematical models to investigate it. Students also
travel to local field sites to observe the populations of interest. As
this mathematical modeling project is one tract of a larger biological
research program at Pepperdine, students in this program will have regular
opportunities throughout the summer to interact with laboratory and field
biology students, faculty, and visiting researchers. More information is
given below about the specific mathematical biology focus and application
information. See https://seaver.pepperdine.edu/surb/ for more details.

Research Focus: Ecologists at Pepperdine University have spent over twenty
years studying newt and crayfish populations in local Malibu streams. They
have observed the decline of local newt populations and explored the impact
of drought and invasive crayfish on the newt populations. With this rich data
set, we mathematically explore how rainfall and crayfish predation alter
newt reproduction and survivorship. We utilize a variety of mathematical
approaches to describe these population dynamics and species interactions,
including differential equations, discrete-time models, and agent-based
approaches. These mathematical models will be used to predict the long-term
effects of California's extreme drought on the local river ecosystem and to
mathematically explore how intervention methods such as crayfish trapping
affect newt populations long term.

Applications are due at noon PST on February 15, 2016. Please see
https://seaver.pepperdine.edu/surb/ for submission details. Please contact
Drs. Courtney Davis and Timothy Lucas at courtney.davis2@pepperdine.edu
and timothy.lucas@pepperdine.edu if you have questions.


From: Andy Edwards <andy@simula.no>
Date: Fri, Jan 29, 2016 at 10:06 AM
Subject: 3rd Annual UCSD-UiO-Simula Summer School: Computational Physiology

2016 UCSD-UiO-Simula Summer School in Computational Physiology of Excitable
Simula Research Laboratory, Oslo, Norway, June 13-24
University of California San Diego, La Jolla, CA, USA, August 4-12

Travel grants are available through Simula.

In conjunction with the University of California San Diego, Simula Research
Laboratory is pleased to announce the 3rd edition of our annual Summer School
in Computational Physiology. This year's school will focus on modelling
the physiology of excitable tissues and take in fundamental topics in
electrophysiology and mechanics of the heart, as well as related material
in computational neurophysiology and pharmacology.

We are currently seeking master's and early doctoral students to participate,
and will accept applications until March 1st 2015.

The initial series of lectures will be hosted by Simula Research Laboratory
in Oslo, Norway (June 13th-24th), followed by project work, a workshop in
scientific presentation skills, and final student presentations hosted by
the University of California San Diego from August 4th-12th.

The travel and accommodation expenses for successful applicants will be
covered by Simula. Details regarding scheduling, logistics, core scientific
material, and the application process can be found through our online call
for participation

Please contact Dr. Andy Edwards if you have any questions concerning the
scientific content:

For logistical questions, general inquiries, or to submit an application please
contact Elin Backe Christopherson


From: Kleinstein, Steven <steven.kleinstein@yale.edu>
Date: Fri, Jan 29, 2016 at 5:28 PM
Subject: Summer School: Computational Immunology, June 20-23, Yale University

Applications are now being accepted for: The 11th-annual Summer School in
Computational Immunology. The summer school is a part of the NIH-funded
Modeling Immunity for Biodefense program. This year the summer school
is organized by PRiME (Program for Research on Immune Modeling and
Experimentation http://tsb.mssm.edu/primeportal) at Yale University from
June 20-23, 2016. The summer school will be immediately followed by a 1
day research symposium on "Influenza Immunology: Data, Systems and Models"
on June 24, 2016. The summer school application and scholarship deadline
is March 25, 2016.

Please pass around this information to your colleagues and students.

School Overview

This 4-day summer school is intended for experimental immunologists who
desire an introduction to mathematical/computational modeling techniques and
their applications to problems in immunology. Computational biology graduate
students at the earliest stages of their studies are also welcome to apply.

With a focus on influenza virus immunology, the summer school provides a
hands-on introduction to:
* Metadata management and standards for large scale experiments
* R scripting approaches to data analysis techniques including PCA,
clustering, differential expression
* How to use experimentally motivated deterministic and stochastic models
to explore hypotheses
* Data mining, integration and network analysis

Each of these modules will combine a morning session composed of lectures,
with a hands-on computer lab in the afternoon. For more information and to
apply to the summer school please visit:
Note that travel/lodging scholarships are available.

When: June 20-23, 2016
Where: Yale School of Medicine, New Haven, CT
Application due date: March 25, 2016

Steven Kleinstein, Elena Zaslavsky and Stuart Sealfon


From: Rebecca Segal <rasegal@vcu.edu>
Date: Fri, Jan 29, 2016 at 1:30 PM
Subject: Conference: BAMM! Biology and Medicine through Mathematics, May 20-22

Conference Announcement: BAMM! Biology and Medicine through Mathematics!
May 20-22, 2016


This is a new Biomath conference that will be held at Virginia Commonwealth
University in Richmond, VA from Friday, May 20 to Sunday, May 22, 2016. The
conference will consist of plenary talks, break-out sessions, and a poster
session. We welcome participation from researchers at all academic levels
working in mathematical biology. Funding from NSF, SMB and MBI has been
secured for travel awards for junior researchers.

Confirmed plenary speakers:
Jim Cushing (The University of Arizona)
Leah Edelstein-Keshet (University of British Columbia)
Bard Ermentrout (University of Pittsburgh)
James Keener (University of Utah)

Important Dates:
Abstract Submissions Deadline 3/1/2016
Registration Deadline 4/10/2016

Organizing Committee:
David Chan, Laura Ellwein, Cheng Ly, Angela Reynolds, Suzanne Robertson, and
Rebecca Segal



From: Gerd Schröder-Turk <g.schroeder-turk@murdoch.edu.au>
Date: Mon, Feb 1, 2016 at 10:18 PM
Subject: West Australian Conference on Biological Structure Formation

The Boden Research conference 2016 entitled

Animal, Vegetal, Mineral? Emergence and function of complex nanostructures
in biological tissue and synthetic self-assembly.

will be held in Yallingup/WA from 19-23 Sept 2015. A list of topics and
speakers can be found on http://www.animal-vegetal-mineral.org/

Submissions for oral and poster presentations are invited from all relevant
disciplines, including in particular also the Mathematical Biology community.

The conference is organised by Stephen Hyde (ANU), Gerd Schröder-Turk
(Murdoch), Charlotte Conn (RMIT), Myfanwy Evans (TU Berlin) and Bodo Wilts
(Adolphe Merkle Institute).


From: VectorBiTE RCN <vectorbitercn@gmail.com>
Date: Fri, Jan 29, 2016 at 10:58 AM
Subject: VectorBiTE Research Coordination Network Launched

Dear colleagues,

We are very pleased to announce the launch of a new NIH/BBSRC funded Research
Coordination Network on the role of Vector Behaviour in Transmission Ecology:

Over the next 5 years, this RCN will support annual meetings and workshops
to promote collaborative research and training in order to improve our
understanding of how the behavioral ecology of vectors impacts disease
transmission. Additionally, a key component of this effort will be the
creation of a global databases on vector traits, population dynamics and
transmission rates. For more information on our network goals please see:

Our first meeting will take place at in Clearwater, FL from March 23-25,
2016. During this first meeting we will prioritize themes for the RCN's
focus, develop strategies for building the global databases, and organize
participants into working groups. Please register for the RCN on the website
and apply for the meeting at http://vectorbite.org/. We plan to provide
travel support for approximately 40 participants to attend. Applications
received by February 1 will receive full consideration, although will
continue to evaluate applications on a rolling basis until all spaces have
been filled. We are pleased to begin this new adventure and look forward
to providing a new platform for interaction in this important area.

Exciting times ahead!

Best wishes,
Leah Johnson, Lauren Cator, Erin Mordecai, Samraat Pawar, and Pete Hudson


From: Springer <springer@alerts.springer.com>
Date: Fri, Jan 29, 2016 at 11:09 AM
Subject: ToC: Bulletin of Mathematical Biology, Vol. 78, Issue 1

Reinhard Laubenbacher & Alan Hastings

The Dynamics of HPV Infection and Cervical Cancer Cells
Tri Sri Noor Asih, Suzanne Lenhart, Steven Wise, Lina Aryati, F. Adi-Kusumo,
Mardiah S. Hardianti & Jonathan Forde

Algebraic Systems Biology: A Case Study for the Wnt Pathway
Elizabeth Gross, Heather A. Harrington, Zvi Rosen & Bernd Sturmfels

An Image-Based Model of Fluid Flow Through Lymph Nodes
Laura J. Cooper, James P. Heppell, Geraldine F. Clough,
Bharathram Ganapathisubramani & Tiina Roose

Approximating the Critical Domain Size of Integrodifference Equations
Jody R. Reimer, Michael B. Bonsall & Philip K. Maini

Protein Synthesis Driven by Dynamical Stochastic Transcription
Guilherme C. P. Innocentini, Michael Forger, Ovidiu Radulescu &
Fernando Antoneli

Phylogenetic Networks with Every Embedded Phylogenetic Tree a Base Tree
Charles Semple

Impact of Spring Bird Migration on the Range Expansion of Ixodes scapularis
Tick Population
Xiaotian Wu, Gergely Röst & Xingfu Zou

Zoonotic Transmission of Waterborne Disease: A Mathematical Model
Edward K. Waters, Andrew J. Hamilton, Harvinder S. Sidhu, Leesa A. Sidhu &
Michelle Dunbar

Do you want to publish your article in this journal?

Please visit the homepage of Bulletin of Mathematical Biology
for full details on:
 *  aims and scope
 *  editorial policy
 *  article submission

Impact Factor: 1.389 (2014)
Journal Citation Reports®, Thomson Reuters


From: Roumen Anguelov, roumen.anguelov@up.ac.za
Date: 2 February 2016
Subject: ToC: BIOMATH, Volume 4, Issue 2
Biomath 4/2, Table of Contents

On the Approximation of the Cut and Step Functions by Logistic and Gompertz
Anton Iliev Iliev, Nikolay Kyurkchiev, Svetoslav Markov

Modeling of Community- and Hospital-acquired Methicillin-resistant
Staphylococcus Aureus Transmission in Hospital Settings
F.B. Agusto, K.N. Knight, M. Jones

Identification of HIV Dynamic System in the Case of Incomplete Experimental
Peter Mathye, Igor Fedotov, Michael Shatalov

Which Matrices Show Perfect Nestedness or the Absence of Nestedness? An
Analytical Study on the Performance of NODF and WNODF
Nicholas Britton, Mario Almeida Neto, Gilberto Corso

Efficient Implicit Runge-Kutta Methods for Fast-Responding Ligand-Gated
Neuroreceptor Kinetic Models
Edward Dougherty

Coupling Within-Host and Between-Host Infectious Diseases Models
Maia Martcheva, Necibe Tuncer, Colette St Mary


From: Tsaneva-Atanasova, Krasimira <K.Tsaneva-Atanasova@exeter.ac.uk>
Date: Tue, Feb 2, 2016 at 2:16 PM
Subject: PhD Position: Modelling Gait in People with Parkinson's Disease, Exeter

Based within the EPSRC Centre for Predictive Modelling in Healthcare, a £2M
initiative bringing together mathematicians, statisticians and clinicians,
you will work on a project aiming to develop a data-driven mathematical
modeling framework in order to study gait impairments in patients with
Parkinson's under the supervision of Prof Krasimira Tsaneva-Atanasova.

To Apply: Candidates with strong quantitative training (e.g. a BSc or MSc
in Physics, Mathematics, Computational Neuroscience, Computer Science,
or Engineering) and evidence of scientific achievement are invited to
apply. Knowledge of biomechanics and/or neuroscience is a plus. Please
apply using the following link:



From: Panetta, Carl <Carl.Panetta@stjude.org>
Date: Wed, Jan 27, 2016 at 3:20 PM
Subject: Postdoctoral Research Associate: St. Jude Children's Research Hospital

Job Title: Postdoctoral Research Associate (Pharmacometrician/Systems Modeler)
Department: Pharmaceutical Sciences
Faculty Member: Clinton F. Stewart

A Postdoctoral Research Fellow position is available in the laboratory of Dr.
Clinton Stewart at St. Jude Children's Research Hospital. Our laboratory
uses contemporary mathematical methodologies applicable to pharmacokinetic
(PK) and pharmacodynamic (PD) modeling to address clinically relevant
problems encountered in the therapy of children with solid malignancies or
brain tumors.

Specifically, we have embarked on a comprehensive series of pharmacokinetic,
pharmacogenetic, and pharmacodynamic studies to understand how developmental
changes in infants and young children affect the disposition and toxicities
of anticancer drugs used in the treatment of infants with malignant brain
tumors.  In addition, using in vitro, in vivo, and clinical data we develop
and analyze mathematical models that lead to a better understanding of how
to dose and schedule anticancer drugs to treat children with cancer. 

The laboratory is highly collaborative, working with many basic and
clinical scientists, which enhances the opportunity of the post-doc to
translate findings from the lab directly into the clinic. We are seeking an
ambitious postdoctoral fellow with a track record of productivity, a strong
interest in translational pharmacology research, and strong oral and written
communication skills. Ideal candidates will possess a strong background
in applied mathematics, computer modeling, or pharmacology. In addition,
candidates with knowledge of clinical oncology are strongly encouraged
to apply.

Submit applications to:

Contact Information
J. Carl Panetta, Ph.D.
Department of Pharmaceutical Sciences
St. Jude Children's Research Hospital
262 Danny Thomas Place
Memphis, TN 38105
Office: (901) 595-3172
Mobile: (901) 921-3740
Fax: (901) 595-3125


From: Alexander Anderson <alexander.ra.anderson@gmail.com>
Date: Thu, Jan 28, 2016 at 5:38 PM
Subject: Postdoctoral Fellow: Mathematical Oncology, Moffitt Cancer Center

Postdoctoral Fellow in Mathematical Oncology

Applications are sought for the position of Postdoctoral Research Fellow to
work under the supervision of Dr. Alexander R. A. Anderson on an exciting
inter-disciplinary research project focussed on tumour-immune interactions.
This project will be part of our recently award Physical Sciences Oncology
Centre http://physics.cancer.gov/network/ and will connect the successful
candidate with the greater PSOC community. We seek a talented individual
with a PhD and background in applied mathematics, physics or a computational
discipline to work in the unique research environment of the Moffitt Cancer
Centre Integrated Mathematical Oncology (IMO) Department.

The successful candidate will have experience in mathematical and/ or
computational modeling, as well as demonstrated creativity, high motivation,
good communication skills. A desire to work closely with experimentalists
and clinicians is also necessary. Preference will be given to candidates
with the ability to code (C++/Java/Python), visualize and analyse
numerical/experimental data.

The IMO is housed within the H. Lee Moffitt Comprehensive Cancer Center
which is a modern facility on the University of South Florida Campus that
conducts research on various aspects of Cancer Biology with emphasis on
translational research. IMO integrates mathematicians, computer scientists,
and physicists together with imaging specialists as well as clinical and
experimental oncologists to develop novel approaches for the treatment and
understanding of cancer.

Further details on the type of research being carried out in the Anderson
lab can be found at http://labpages.moffitt.org/andersona/. Please send CV
and cover letter directly to Alexander.Anderson@Moffitt.org. You can also
apply online through the Moffitt recruitment system: Req ID Number 18657


From: Mary Myerscough <mary.myerscough@sydney.edu.au>
Date: Tue, Feb 2, 2016 at 2:12 AM
Subject: Postdoc: Mathematical Biology, University of Sydney, Australia

Postdoctoral position in Mathematical Biology, University of Sydney, Australia

The University of Sydney is Australia's first university and has an
outstanding global reputation for academic and research excellence. It
employs over 7500 permanent staff, supporting over 52,000 students.

The School of Mathematics and Statistics at the University of Sydney is a
leading centre for mathematical research and education in Australia. The
School attracts outstanding undergraduate students, including many who are
particularly talented in the mathematical sciences, and has a large cohort
of postgraduate research students. It regularly hosts overseas visitors
and offers a diverse and world class research environment. 

We currently seek a Postdoctoral Research Associate position in Mathematical
Biology to work on a project, funded by the Australian Research Council on
"Dynamics of atherosclerotic plaque formation, growth and regression". The
Chief Investigators on this project are Professor Mary Myerscough
http://sydney.edu.au/science/people/mary.myerscough.php, Associate Professor
Charlie Macaskill http://www.maths.usyd.edu.au/ut/people?who=C_Macaskill
(both at School of Mathematics and Statistics,
University of Sydney) and Dr Christina Bursill
(at the Heart Research Institute, Newtown, which is a short walk away from
campus). This project is funded for the period 2016-2018.

In this role you will:
 *  undertake the development, analysis and numerical solution of differential
    equation models for immunological events in the artery wall that lead to
    the formation of atherosclerotic plaques and the consequent development
    of cardio-vascular disease and strokes
 *  engage with the scientific literature and medical science community
    as part of model construction and evaluation
 *  participate in all aspects of the project, as well as presenting research
    results at seminars and conferences
 *  be part of the research team which includes, not only the grant
    holders, but also graduate students and overseas visitors
 *  and write scholarly papers for publication in academic journals

For further information:
Postdoctoral position in Mathematical Biology, University of Sydney
or contact Professor Mary Myerscough, mary.myerscough@sydney.edu.au


From: Andrei Korobeinikov <akorobeinikov@crm.cat>
Date: Mon, Feb 1, 2016 at 10:30 AM
Subject: 2-year Postdoc: Programme of Collaborative Mathematical Research

The CRM welcomes applications for one 2-years postdoctoral position
within the programme of Collaborative Mathematical Research.
The collaborative projects proposed in this call are in one of the following
Complex Systems
Industrial Mathematics
Mathematical Epidemiology
Computational and Mathematical Biology
Computational Neuroscience
Financial Mathematics and Risk Control

To apply for a position, please send to crmcalls@crm.cat an email with 
the following information: name, personal address, email and phone number
The application package should include a CV, academic records,
incorporating, if possible, the computation of the average grade and a
motivation letter.
A minimum of one and a maximum of three hosting CRM research groups have to
be chosen, indicating preferences in the motivation letter, if any.

The applicant should arrange for two referees familiar with her/his 
work to send a reference letter to crmcalls@crm.cat before the deadline
The deadline to submit an application is February 26, 2016

Applicants should be available for interviews (possibly via Skype) from 
March 7 onwards.

Details and How to apply:


From: David Smith (School of Mathematics) <D.J.Smith.2@bham.ac.uk>
Date: Tue, Feb 2, 2016 at 8:53 AM
Subject: Lecturer: Mathematical Biology, University of Birmingham

Lectureship in Mathematical Biology
University of Birmingham - School of Mathematics

Location: Birmingham
Salary: £38,896 to £52,219
Hours: Full Time
Contract Type: Permanent

Placed on: 21st January 2016
Closes: 22nd February 2016
Job Ref: 43152

Applications are invited for a Lectureship position in the School of
Mathematics, in the area of Mathematical Biology.

The School of Mathematics is looking for someone to join the Mathematical
Biology Research Group. The successful candidate will join an energetic
and outward-facing group with internationally-recognised strengths in
plant biomechanics, microbiology, biological fluid dynamics and healthcare
applications. Excellent candidates working in any area of mathematical
biology are encouraged to apply.

The successful candidate will have PhD (or equivalent level) training
in mathematical modelling, a first-class research record in mathematical
biology, including active multidisciplinary collaboration, and a commitment
to teaching, along with excellent communication skills. 

The appointee will be expected to expand or complement present research
areas in the School, develop research collaboration inside and outside the
School and University, and assist in the design, development and delivery
of teaching in Mathematics.

Informal enquiries should be directed to Dr David Smith (tel. +44 121 414
7374, email d.j.smith.2@bham.ac.uk) or the Head of School, Prof Paul Flavell
(tel. +44 121 414 3740, email p.j.flavell@bham.ac.uk).

Reference: 43152


From: Jon Olav Vik <jonovik@gmail.com>
Date: Fri, Jan 29, 2016 at 10:10 AM
Subject: Systems Biology Informatics Manager: Digital Salmon, NMBU, Ås, Norway

Dear list,

The Department of Animal and Aquacultural Sciences seeks a bioinformatician or
systems biologist with skills or interest in ontological annotation, semantic
interoperability or knowledge management, for the systems biology of salmon
farming. This is a Researcher position of 3 years (with possibility of
extension) at the Norwegian University of Life Sciences, Ås, Norway.

The project "Towards the Digital Salmon: From a reactive
to a pre-emptive research strategy in aquaculture (DigiSal
is part of Digital Life, Norway's first call dedicated to systems
biology. Effective management of data and model resources is key in this
endeavour, and DigiSal will initiate The Digital Salmon: A knowledge base
of salmon genetics and physiology, interfacing closely with complementary
databases, repositories, and research infrastructures such as ELIXIR. This
knowledge base is a key deliverable of the DigiSal project, and the long-term
ambition is that it will enable aquaculture industry to quickly address
emerging challenges, quickly reanalysing existing data and identifying
knowledge gaps to rapidly acquire required new data.

Full advertisement:

Application deadline: Thursday 2016-02-25. Email enquiries welcome: Jon Olav
Vik, jonovik@gmail.com.

Please forward this announcement to anyone you think might be interested!


From: NIH Extramural Nexus (NIH/OD) <ExtramuralNexus@mail.nih.gov>
Date: Mon, Feb 1, 2016 at 6:17 PM
Subject: NIH Update: Addressing rigor, transparency, and reproducibility ...



Subject: SMBnet Reminders

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