Subject: Society for Mathematical Biology Digest

SMB Digest      May 25, 2016   Volume 16  Issue 21
ISSN 1086-6566

Editor: Alex Fletcher digest.alex(at)gmail(dot)com

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Issue's Topics:
    Workshop: Scientific Inference for Big Data, June 8-9, USA
    BioDynamics Workshop, Sept 7-9, UK
    Workshop: Multilayer and Interconnected Networks, July 28-31, Spain
    Guelph Biomathematics and Biostatistics Symposium, June 9, Canada
    ToC: Bulletin of Mathematical Biology, Vol. 78, Issue 3
    PhD: Evolutionary transitions, University of Adelaide, Australia
    Postdoc: Mathematical Epidemiology, University of Utah, USA
    Postdoc: Biomechanics, University of Manchester, UK
    Postdoc: Bacterial growth..., INRIA Grenoble - Rhône-Alpes, France
    Postdoc: Plant modelling, INRA Avignon, France
    Postdoctoral Fellow: Quantitative Systems Pharmacology, Pfizer, USA
    Quantitative Systems Pharmacologist, Merck, USA
    SMBnet Reminders


From: Lisa Dunnebacke <lisa.dunnebacke@NIH.GOV>
Date: Fri, 20 May 2016 21:57:00 +0000
Subject: Workshop: Scientific Inference for Big Data, June 8-9, USA

The Committee on Applied and Theoretical Statistics invites you to attend
a two-day workshop on the challenges of applying scientific inference to
big data. The workshop will bring together statisticians, data scientists
and domain researchers from different biomedical disciplines to explore
four key issues of scientific inference:

 * Inference about causal discoveries driven by large observational data
 * Inference about discoveries from data on large networks
 * Inference about discoveries based on integration of diverse datasets
 * Inference when regularization is used to simplify fitting of 
   high-dimensional models

The aim of the workshop is to identify new developments that hold significant
promise and to highlight potential research areas for the future. For more
information, including the preliminary program, check out the workshop
website. This workshop is sponsored by the NIH Big Data to Knowledge (BD2K)
Initiative and the National Science Foundation.  

Date: June 8-9, 2016
Location: Keck Center, Room 100, 500 Fifth St., N.W., Washington, D.C. 20001

This workshop will be professionally webcast. If you intend to join us in
person or online, please register by Monday, June 6th.
For questions about the workshop, please contact Michelle Schwalbe at


From: Jamie Walker <Jamie.Walker@exeter.ac.uk>
Date: Mon, May 16, 2016 at 4:15 PM
Subject: BioDynamics Workshop, Sept 7-9, UK

Dear Colleague
We would like to invite you to the next BioDynamics Workshop, which will 
take place in Exeter on 7-9 September 2016. This will be the third in a 
series of international workshops designed to bring together biologists, 
mathematicians, clinicians, physicists, and computer scientists who are 
interested in dynamics and networks in the biological and medical sciences. 
BioDynamics 2016 promises to provide an exciting opportunity for scientists 
to present both methods and data in a multidisciplinary forum and hear how 
interdisciplinary collaborations can provide major conceptual advances in 
our understanding of complex biomedical systems.

There will be a number of keynote presentations delivered by world-leading 
scientists, who will talk about their current research and highlight 
important future challenges within their field. Confirmed keynote speakers 
 * Professor Peter Hunter FRS, The University of Auckland, New Zealand
 * Professor Philip Ingham FRS, University of Exeter, United Kingdom
 * Professor Gareth Leng FRSE, University of Edinburgh, United Kingdom
 * Professor Angela McLean FRS, University of Oxford, United Kingdom
 * Professor Nick Talbot FRS, University of Exeter, United Kingdom
 * Dr Greg Worrell, Mayo Clinic, Rochester, Minnesota, United States

In addition to keynote presentations, the workshop will feature mini 
symposia, selected contributed talks, and poster sessions, for which we 
encourage abstract submissions from both students and post-docs (deadline 
for submission is 31 May 2016). There will be prizes awarded for the best 
posters from students and early-career scientists.
*Registration and abstract submission are now open*
Registration fees are as follows ("early bird" deadline is 31 May 2016):
 * "Early Bird" Registration (Lecturer and above) £200
 * "Early Bird" Registration (PhD and PostDoc) £150
 * Full Registration (Lecturer and above) £250
 * Full Registration (PhD and PostDoc) £200
 * Conference Dinner (optional) £25

*Deadline for abstract submission is 31 May 2016*

For more information about the workshop: 


From: Joan Saldana <joan.saldana@udg.edu>
Date: Wed, May 25, 2016 at 8:38 AM
Subject: Workshop: Multilayer and Interconnected Networks, July 28-31, Spain

The goal of the one-day workshop "Multilayer and Interconnected Networks: 
Epidemic Processes and Robustness" (MIN2016) is to bring together scientists 
working on the topic of multilayer and interconnected networks. The speakers 
will present their latest results and will carry out a discussion on the 
state of the art and current open challenges for this topic. We hope the 
meeting will provide an informal venue for encouraging interdisciplinary 

The workshop will be celebrated at the Universitat of Girona, Catalonia 
(Spain), June 8, 2016.  

Confirmed speakers (in alphabetical order):  

 * Marián Boguñá (Univ. de Barcelona)
 * Gregorio D?Agostino (ENEA, Italy)
 * Sergio Gómez (Univ. Rovira i Virgili) 
 * Robert Kooij (TNO & Delft Univ. of Technology)
 * Yamir Moreno (Univ. de Zaragoza)
 * Romualdo Pastor-Satorras (Univ. Politècnica de Catalunya)
 * Faryad Sahneh (Kansas State University)
 * Caterina Scoglio (Kansas State University)
 * Igor van Gemert (SIM-CI, The Netherlands) 

Attendance is free of cost but registration for audience members is required 
for organisational purposes (lecture room, coffees, lunch). 

Extended registration deadline: June 3, 2016.

For further information and registration, please visit the website of the 
workshop: https://sites.google.com/site/min2016girona/


From: Allan Willms <AWillms@uoguelph.ca>
Date: Tue, May 24, 2016 at 2:06 PM
Subject: Guelph Biomathematics and Biostatistics Symposium, June 9, Canada

The 12th Guelph Biomathematics and Biostatistics Symposium will take place 
on Thursday, June 9, 2016 at the University of Guelph. This year's theme is
Spatial Ecology: Applications of the Mathematical Sciences.

Register today at:

Spatial ecology deals with issues such as migration, environmental 
differences, quality of habitat, location of prey and predators, and 
breeding sites, and how all of these aspects affect the populations of 
various species. In recent years species distribution modelling has been a 
research area with intense international activity, with increasingly more 
sophisticated methods in spatial statistics being incorporated into the 
modelling approaches. These models have wide applicability in such areas as 
designing and managing nature reserve networks, and predicting the potential 
geographic spread and impact of invasive species. More recently climate 
change has become an issue of interest in spatial ecology since it can 
extend, reduce, or shift the suitable habitat.

Invited Speakers:

Mike Hutchinson, Emeritus Professor, Fenner School of Environment &
    Society, Australian National University
Dan McKenney, Chief, Landscape Analysis and Applications, Great Lakes
    Forestry Centre, Natural Resources Canada
Rebecca Tyson, Associate Professor, Mathematical Biology, University
    of British Columbia Okanagan
Ben Bolker, Professor, Dept. of Mathematics and Statistics, McMaster
John Fryxell, Professor and Chair, Dept. of Integrative Biology,
    University of Guelph
Madhur Anand, Professor, School of Environmental Sciences, University
    of Guelph


From: Springer <springer@alerts.springer.com>
Date: Sun, Apr 17, 2016 at 5:59 AM
Subject: ToC: Bulletin of Mathematical Biology, Vol. 78, Issue 3

Temperature- and Turbidity-Dependent Competitive Interactions Between Invasive Freshwater Mussels
Qihua Huang, Hao Wang, Anthony Ricciardi & Mark A. Lewis

Minimal Model of Plankton Systems Revisited with Spatial Diffusion and Maturation Delay
Jiantao Zhao, Jianjun Paul Tian & Junjie Wei

Alternative Stable States, Coral Reefs, and Smooth Dynamics with a Kick
Stephen Ippolito, Vincent Naudot & Erik G. Noonburg

Multicellular Mathematical Modelling of Mesendoderm Formation in Amphibians
L. E. Brown, A. M. Middleton, J. R. King & M. Loose

A Fractional Order Recovery SIR Model from a Stochastic Process
C. N. Angstmann, B. I. Henry & A. V. McGann

A Mathematical Model of T1D Acceleration and Delay by Viral Infection
James R. Moore & Fred Adler

Simulation of Yeast Cooperation in 2D
M. Wang, Y. Huang & Z. Wu

A Diffusion Approximation Based on Renewal Processes with Applications to Strongly Biased Run?Tumble Motion
Uffe Høgsbro Thygesen

Effective Rheological Properties in Semi-dilute Bacterial Suspensions
Mykhailo Potomkin, Shawn D. Ryan & Leonid Berlyand

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


From: Andrew Black <andrew.black@adelaide.edu.au>
Date: Thu, May 19, 2016 at 6:58 AM
Subject: PhD: Evolutionary transitions, University of Adelaide, Australia

PhD Scholarship: Mathematical modelling of evolutionary transitions.
School of Mathematical Sciences, University of Adelaide, Australia.

The scholarship is open to all international students, so this would be a 
great opportunity for someone to come and study in Australia for a few years. 

Details at: http://maths.adelaide.edu.au/andrew.black/phd_position.html


From: Damon Toth <toth@math.utah.edu>
Date: Fri, May 20, 2016 at 10:26 PM
Subject: Postdoc: Mathematical Epidemiology, University of Utah, USA

This position provides research support for mathematical and computer 
modeling projects in support of public health decision making for healthcare 
epidemiology, within the University of Utah Health Sciences Center. The 
postdoctoral fellow will work on one or more funded projects aimed at 
modeling interventions to reduce the incidence of healthcare associated 
infections in a regional network of hospitals and nursing homes. Within this 
scope, the postdoctoral fellow will have the opportunity to focus on 
theoretical and applied modeling topics of interest, including network 
epidemiology, antibiotic resistance and stewardship, strain competition, 
vaccine immunology, modes of transmission, and optimal intervention strategy.

Essential Functions:
 1. Provides support for scientific literature search and synthesis of 
    reviewed literature
 2. Assists in planning and executing models and computer simulations 
    according to project needs 
 3. Prepares and communicates research results in written and oral summary
 4. Works collaboratively with supervisor and other project team members in 
    supporting project needs

Minimum Qualifications:
This position requires expertise in mathematical modeling and computer 
programming with a minimum of a PhD degree, computer programming skills, an 
ability to manage deadlines, good writing and communication skills, and an 
ability to effectively work within a multi-disciplinary collaborative 

Interested candidates should apply online at 


From: Igor Chernyavsky <igor.chernyavsky@manchester.ac.uk>
Date: Fri, May 20, 2016 at 1:33 PM
Subject: Postdoc: Biomechanics, University of Manchester, UK

Applications are invited for a 2.5-year position focused on the biological 
physics and mechanics of the human placenta. The post is supported by a 
recently-awarded MRC Grant "Blood flow (dys)regulation and transfer function 
in the human placenta: an integrated in silico and ex vivo approach to fetal 
growth restriction".

You will join a rapidly expanding effort in biomechanics within the School 
of Mathematics, working directly with Dr I. L. Chernyavsky and Professor 
O. E. Jensen, in close collaboration with physiologists and clinicians from 
the Institute of Human Development and the University of Southampton. This 
position forms a part of a wider recruitment that will involve employment of 
a Research Associate in experimental placental physiology to support the 
mathematical modelling effort.

The theoretical part of the project lies at the interface between applied 
mathematics, continuum mechanics, multi-scale physics, spatial statistics 
and image analysis. The main aim of this project is in development of 
integrated analytical and computational techniques, informed by experimental 
data, for the study of flow and transport processes in the human placenta, a 
unique and critically important interface between the maternal and fetal 

You will hold (or be about to complete) a PhD in Applied Mathematics, 
Physics, Bioengineering, or a closely related field. You will have a solid 
track record of publications relevant to the project area, and a strong 
aptitude for interdisciplinary research. For further information and details 
of how to apply, please visit our web site 
or contact Dr Chernyavsky (Igor.Chernyavsky@manchester.ac.uk).

The closing date for applications is 16 June 2016


From: Hidde de Jong <Hidde.de-Jong@inria.fr>
Date: Thu, May 12, 2016 at 10:24 AM
Subject: Postdoc: Bacterial growth..., INRIA Grenoble - Rhône-Alpes, France

The IBIS group at INRIA Grenoble ­ Rhône­Alpes, in collaboration with the 
Laboratoire Interdisciplinaire de Physique of the Université Grenoble Alpes, 
is looking for a post­doctoral researcher to work on the mechanistic basis of 
growth rate control in bacteria. In particular, in the framework of the RESET 
project (https://project.inria.fr/reset/fr/project/), we are studying the 
relation between RNA polymerase expression and growth rate variability, under 
a variety of conditions, using single­cell time­series reporter gene data, 
image analysis, and mathematical modeling (Izard, Gomez Balderas et al., Mol. 
Syst. Biol., 11:840, 2015).

Applicants are expected to have a background in biophysics, mathematical 
biology, or bioinformatics, with a strong interest in the application of 
quantitative methods to the study of biological systems. We offer a one­-year 
contract in an interdisciplinary and international environment in our 
research centre located in the French Alps (https://team.inria.fr/ibis/). 

For more information on the position and for applications, please contact 
Hidde de Jong (Hidde.de-Jong@inria.fr). Applications should be accompanied 
by a CV and a motivation letter.


From: Valentina Baldazzi <valentina.baldazzi@paca.inra.fr>
Date: Fri, May 20, 2016 at 8:34 AM
Subject: Postdoc: Plant modelling, INRA Avignon, France

The INRA GAFL and PSH units are seeking a highly-qualified post-doctoral 
researcher to work on a project on genotype-phenotype kinetic modelling, in 
France. The successful candidate should hold a PhD with a background in 
modelling, and also have experience in parameter estimation, optimization 
and sensitivity analysis. The appointment is for 2 years, with a start date 
by the end 2016 or early 2017.

The objective of this project is to integrate the genetic control of sugar 
metabolism in an existing kinetic model (Desnoues et al, in preparation) and 
to use it for ideotype design. At term, an improved optimisation strategy 
together with the mechanistic nature of the model have the potential to 
facilitate the discovery of new genes of interest for the modification of 
sugar metabolism.

The position depends on the success of the project proposed to AgreenSkills/

For details and application, candidates can contact Dr. QUILOT-TURION 
Bénédicte at benedicte.quilot@avignon.inra.fr.


From: Mark Majewski <Mark.Majewski@pfizer.com>
Date: Wed, May 18, 2016 at 3:56 PM
Subject: Postdoctoral Fellow: Quantitative Systems Pharmacology, Pfizer, USA

Job Title: Postdoctoral Fellow - Cardiovascular and Metabolic Diseases 
Research Unit, Quantitative Systems Pharmacology, 1026494
Location: United States-Massachusetts-Cambridge

The Quantitative Systems Pharmacology (QSP) Lab in Pfizer's Cardiovascular 
and Metabolic Diseases (CVMET) Research Unit is responsible for developing 
insights to help advance CVMET clinical candidates and identifying and 
evaluating promising new therapeutic targets through physiologically-based 
modeling and simulation, and analysis and interpretation of preclinical and 
clinical data. We seek a highly motivated postdoctoral candidate to develop 
and analyze mechanistic, mathematical models of cardiomyocyte biophysics to 
enable the in silico testing of mechanistic hypotheses and improve the 
identification and evaluation of therapeutic targets for the treatment of 
heart failure (HF).

The successful candidate will apply quantitative systems modeling and 
simulation methods to develop a validated mathematical model that couples 
cellular electrophysiology and ion transients to cellular metabolism, 
mitochondrial function, and contractile force generation in human 
cardiomyocytes. In addition to enabling in silico identification and 
assessment of HF drug targets, the successful candidate will pursue new 
avenues for scientific development in areas of QSP modeling, cellular 
biophysics, data analysis, and uncertainty quantification. The mechanistic 
insights gained from detailed analyses of the in silico model will generate 
physiological hypotheses that may be tested experimentally and/or in the 
clinic. The expectation is that the resulting findings will lead to improved 
confidence in rationale for the pursuit of novel agents for the treatment of 
heart failure.

To be considered for this position, please apply at www.pfizercareers.com by 
searching Job ID 1026494.


From: Sachs, Jeff <jeff_sachs@merck.com>
Date: Thu, May 19, 2016 at 2:08 PM
Subject: Quantitative Systems Pharmacologist, Merck, USA

The Quantitative Pharmacology and Pharmacometrics (QP2) group at Merck is 
now hiring at 3 levels: Senior Scientist, Associate Principal Scientist, and 
Principal Scientist. Qualified candidates will be hired at the level 
commensurate with their experience. We sponsor work visas for qualified 
candidates. Please see below for job description and forward to potential 
candidates. Thank you for your consideration.
Location: West Point, PA; Upper Gwynedd, PA; Kenilworth, NJ; Rahway, NJ; 
Boston, MA.
Fo further details and to apply online, please visit 
 * Senior Scientist, R3 (QUA004740)
 * Associate Principal Scientist, R4 (QUA004739)
 * Principal Scientist, R5 (QUA004336)


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