SMB Digest Volume 18 Issue 11

SMB DIGEST ISSN 1086-6566
VOLUME 18 ISSUE 11
March 16, 2018

This issue’s editor:

Additional information about the Society for Mathematical Biology
may be found in the SMB Home Page, www.smb.org/.

Access the Bulletin of Mathematical Biology (BMB), the official journal
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From: Tony Nance <tony@mbi.osu.edu>
Date: Tue, Mar 13, 2018 at 5:14 PM
Subject: MBI Online Mathematical Biology Colloquium, March 21

MBI Online Mathematical Biology Colloquium
Wednesday March 21, 2018 at Noon Eastern Time

Philip Maini (Centre for Mathematical Biology, University of Oxford)

Modelling Collective Cell Motion in Biology

Details of how to participate can be found on the National Colloquium
webpage below. To view this live event you will need to register on the
event page. You may register at any time
mbi.osu.edu/go/n/colloquium

Next Online Colloquium:
April 18
Marc Suchard: High-dimensional Phenotypes on Evolutionary Trees:
Efficient Algorithms and New Models

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From: Kathleen Wilkie <kpwilkie@ryerson.ca>
Date: Wed, Mar 14, 2018 at 3:22 AM
Subject: CAIMS annual meeting, Toronto, June 4-7

The 2018 Annual Meeting of the Canadian Applied and Industrial
Mathematics Society (CAIMS) will be held on June 4-7 at Ryerson
University, Toronto, ON.

The website for this meeting is: www.caims2018.caims.ca/

Scientific Themes include:
* Combinatorial Optimization
* Computational Mathematics and Applications
* Financial Mathematics
* Fluid Dynamics
* Mathematics of Disease and Ecology

Plenary Speakers include:
* William J. Cook, University of Waterloo
* Linda Petzold, UC Santa Barbara
* Beatrice Acciaio, London School of Economics
* Bruce Sutherland, University of Alberta
* Caroline Colijn, Imperial College London / Simon Fraser University

Submission:
The call for abstracts is now open. Please submit your abstract for
contributed talks and poster presentations here:
www.caims2018.caims.ca/content/submissions

Abstract submission will close on April 15, 2018.

Registration:
The conference registration page is now open:
www.caims2018.caims.ca/content/registration-caims-2018

The early bird deadline is May 4, 2018, if you want to enjoy the
reduced rate.

We are looking forward to seeing you in Toronto!

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From: Ruediger Thul <Ruediger.Thul@nottingham.ac.uk>
Date: Tue, Mar 13, 2018 at 2:37 PM
Subject: Workshop: Spatial Cell signalling, Nottingham, May 30

The seventh Mathematics in Life Sciences (MiLS) meeting will focus on
“Spatial cell signalling” and will take place on the 30th of May 2018
from 11am to 5pm at the University of Nottingham.

The workshop will bring together researchers working at the interface
of mathematical, modelling, and biological aspects of
spatially-extended cell signalling. We are broadly interested in
models where signalling cascades are spatially distributed either at
the sub-cellular or cellular level. Studying these models naturally
requires techniques from multi-scale analysis to resolve the
biologically relevant scales and dynamics. Examples include the
formation of single-cell polarity, intracellular morphogenesis,
changes in cell shapes, membrane dynamics, and signalling
microdomains.

The meeting will consist of three review talks aimed at non-experts,
combined with several contributed research talks. The review talks
will be given by Andrew Goryachev (University of Edinburgh), Stan
Maree (John Innes Centre), and Claire Grierson (University of
Bristol).

We invite submissions for contributed talks, especially from early
career researchers and postgraduate students. If you are interested in
giving a talk, please send a title and abstract to Rüdiger Thul
(ruediger.thul@nottingham.ac.uk) and Daniele Avitabile
(daniele.avitabile@nottingham.ac.uk).

You can find out more about MiLS at mils.ghost.io.

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From: Marcus Tindall <m.tindall@reading.ac.uk>
Date: Thu, Mar 8, 2018 at 1:36 PM
Subject: UK QSP Network – 2nd Exchange Workshop, Reading, July 2-4

UK Quantitative Systems Pharmacology Network – 2nd Exchange Workshop
2nd to 4th July 2018
University of Reading, UK.

CALL FOR ABSTRACTS NOW OPEN!

Confirmed invited speakers: Richard Clayton (Sheffield), Richard
Currie (Syngenta), Adam Darwich (Manchester), Douglas Ferguson
(AstraZeneca), Steven Niederer (Kings College London)

Quantitative Systems Pharmacology (QSP) is a new emerging area of
science. It brings a systems approach to the development of
pharmaceuticals, using quantitative approaches such as mathematical
modelling and data analysis to integrate subcellular genetic and
protein-protein interaction networks with body scale information and
clinical data.

This second Exchange Workshop of the UK QSP Network will focus on
drug absorption, clinical data & modelling, toxicology and adverse
events, validation & uncertainty quantification, and future
application areas for QSP. Further details, including important dates
and a draft programme, can be found at www.qsp-uk.net/reading-2018.html

Half page abstracts related to any of the above themes are invited.
Abstracts need to include a talk title, speaker name and
affiliation(s) and should be e-mailed to Marcus Tindall
(m dot tindall at reading dot ac dot uk) by 23RD MARCH. Speakers of
accepted abstracts will be advised by 16th April.

For further details on the UK QSP Network, please see www.qsp-uk.net

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From: German Enciso <enciso@uci.edu>
Date: Thu, Mar 8, 2018 at 7:02 PM
Subject: New Systems Biology Short Courses, UC Irvine, May 7-25

The Center for Complex Biological Systems at the University of
California, Irvine is excited to announce two new NIH-funded “short
courses” in Systems Biology:

1) Systems Biology: Foundation for Interdisciplinary Careers
2) Cancer Systems Biology

These are three week, on-site, intensive lecture- and laboratory-based
courses intended for graduate students, postdoctoral fellows, junior
and senior faculty, and industry scientists. Training will be provided
by UCI faculty and invited outside experts.

Both courses will be held from May 7th-May 25th, 2018, on the UCI
Campus in beautiful Southern California.

The courses have been designed to serve both individuals from
quantitative and computational disciplines who wish to apply their
training to biology, as well as individuals from biological and
biomedical science who wish to move their research in more
quantitative and computational directions.

The courses are supported by NIH grants and other sources that provide
financial support for course activities and a portion of trainee
expenses. Diverse, minority and disabled applicants are especially
encouraged to apply, and are eligible for additional financial support.

We hope you will consider attending one of these two courses, or would
be willing to share this email with individuals you think might be
interested.

Detailed information about both courses can be found on the Center for
Complex Biological Systems home page (ccbs.uci.edu).
In addition, please feel free to contact any one of us if you have any
specific questions.

German Enciso (enciso@uci.edu)
Arthur Lander (adlander@uci.edu)
Co-directors, Systems Biology: Foundation for Interdisciplinary Careers

John Lowengrub (jlowengr@uci.edu)
Marian Waterman (marian.waterman@uci.edu)
Co-directors, Cancer Systems Biology

Sohail Jahid (sjahid@uci.edu)
Academic Coordinator, Center for Complex Biological Systems

—————————————————-

From: Amina Eladdadi <eladdadi@gmail.com>
Date: Thu, Mar 8, 2018 at 5:06 PM
Subject: Graduate Program by the Intercollegiate Biomathematics Alliance

The Intercollegiate Biomathematics Alliance (IBA), a consortium of ten
universities and colleges, has just launched an exciting and a unique
one-year graduate certificate program in mathematical biology.

This new graduate certificate program is based on the IBA’s
community-curriculum initiative and is open to current undergraduate
and beginning graduate students nationwide. There are three possible
tracks: a completely online, a hybrid, and a completely offline, which
will all serve as a bridge to advanced studies in mathematical
biology.

More information, such as the details of each track, the course
catalog, cost of the program, as well as the application form can be
found by visiting www.biomathalliance.org

We are hoping that you will help us spread the word and advertise the
program to your students where applicable. Please don’t hesitate to
send your questions to biomath@ilstu.edu

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From: Philip Gerlee <gerlee@chalmers.se>
Date: Mon, Mar 12, 2018 at 8:24 AM
Subject: PhD Position: Brain tumour modelling, Chalmers

The Department of Mathematical Sciences at Chalmers University of
Technology is looking for a doctoral student in mathematical biology,
in particular, mathematical modelling of brain tumour growth. The
brain tumour glioblastoma multiforme (GBM) is characterised by a
diffuse morphology, which makes surgical intervention difficult and
invariably leads to tumour recurrence. The aim of this project is to
develop new stochastic models of glioblastoma growth which will be
used to quantify the impact of cancer cell properties on tumour
growth, and further to identify novel drug targets. The student will
be supervised by assistant professor Philip Gerlee and carried out in
collaboration with Sven Nelander’s group in Uppsala
(nelanderlab.org/).

More details can be found here:
www.chalmers.se/en/about-chalmers/vacancies/?rmpage=job&rmjob=6009

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From: Victor Matveev <matveev@njit.edu>
Date: Wed, Mar 14, 2018 at 10:27 PM
Subject: Postdoc: Mathematical biology, NJIT

Applications are invited for a postdoctoral position in the field of
mathematical and computational biology in the Department of
Mathematical Sciences at New Jersey Institute of Technology (NJIT).
The position is initially for one year  starting September 1, 2018,
with the possibility of renewal of one additional year, subject to
satisfactory performance.

In addition to research duties, the candidate is expected to teach one
course per academic year. Currently, research interests of the NJIT
mathematical biology group are focused on mathematical and
computational neuroscience, perception of timing and rhythm, cell
physiology, circadian rhythms, cell calcium dynamics, and biofluids,
emphasizing the applications of parameter estimation techniques,
stochastic analysis and the theory of dynamical systems and partial
differential equations to problems in mathematical biology.

More details can be found here:
njit.csod.com/ats/careersite/JobDetails.aspx?site=1&id=243

Inquires can be sent to Dr. Victor Matveev at matveev@njit.edu.

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From: Holger Perfahl <holger.perfahl@gmail.com>
Date: Tue, Feb 20, 2018 at 2:23 PM
Subject: Postdoc: Systems medicine, Stuttgart

Post-doc position in Systems-Medicine: Agent-based Modelling of
Vascular Tumour Growth and Comparison to Imaging Data (Stuttgart,
Germany)

A postdoctoral position is available at the Stuttgart Research Center
Systems Biology (SRCSB) in Germany. The successful candidate will work
in the development and implementation of agent-based models of
vascular tumour growth and their comparison to experimental imaging
data from the medical hospital in Tübingen. Therefore, candidates from
the fields of mathematical modelling and image analysis are welcome to
apply. The fellowship is part of the Federal Ministry of Education and
Research (BMBF) funded e:Med initiative and the salary will be in
group TVöD 13.

Applicants should possess a Ph.D. degree in Engineering, Physics,
Computer Science, Mathematics, or a related field. The candidate
should have a strong knowledge in mathematical modelling, image
analysis and Fortran / C++ programming.

Prof. Dr.-Ing. Dr.h.c. Matthias Reuss
Universität Stuttgart
Stuttgart Research Center Systems Biology (SRCSB)
matthias.reuss@ibvt.uni-stuttgart.de

—————————————————-

From: Leonid Chindelevitch <leonid@sfu.ca>
Date: Thu, Mar 8, 2018 at 9:17 PM
Subject: Postdoc: Statistical methods for pathogen genomics, Vancouver

Pathogenic microbial organisms cause a significant burden of disease
not only in low-resource countries, but also in high-income countries,
especially in hospital settings. One challenge that is particularly
relevant today is the problem of drug resistance, whereby a pathogen
no longer responds to treatment by one or more available drugs.
Additionally, the frequency of pathogen outbreaks requires the
development of surveillance tools to rapidly track, prevent, and
ultimately disrupt the chain of transmissions. The availability of
fast, reliable and affordable whole-genome sequencing (WGS) methods
has the potential to be a major boon for public health authorities
attempting to control the development of drug resistance and the
spread of epidemic outbreaks. However, in order to fully harness the
power of these methods, there is an urgent need for novel statistical
and algorithmic techniques for microbial WGS data. These methods are
still in their infancy, and developing them further could lead to a
significant impact.

The successful applicant for this position will extend
state-of-the-art computational statistics methodology to address key
challenges from fields such as pathogen genome-wide association
studies; phylodynamics, for example, methodological developments
related to Approximate Bayesian Computation (ABC) or Sequential Monte
Carlo (SMC); and molecular epidemiology. The specific focus will
depend on the background of the successful candidate. The ideal
candidate will have a Ph.D. in computational biology, statistics,
applied mathematics, or a related field. The candidate should be a s
elf-starter, able to work independently and assist in supervising MSc
or Ph.D. students. Experience working with genomic data, and a
knowledge of phylodynamics, GWAS, ABC and/or SMC methodologies is an
asset.

The position will be based in Vancouver, BC, jointly hosted by Leonid
Chindelevitch (Simon Fraser University, Computer Science Department)
and Alexandre Bouchard-Côté (University of British Columbia,
Statistics Department) and funded by a Collaborative Research Team
Project from the Canadian Statistical Sciences Institute. The
applicant will also have the opportunity to collaborate with
researchers in the life sciences and clinical departments. The
applicant will be expected to travel within Canada and internationally
for collaboration and presentation of research results; our
collaborators on this project are based in Montreal, Halifax, Toronto,
Ottawa, London, and Boston, MA.

The position will come with a competitive postdoctoral-level
compensation for one year, with a possibility of extension.
Applications will be considered on a rolling basis.

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From: Reinhard C. Laubenbacher <laubenbacher@uchc.edu>
Date: Fri, Mar 9, 2018 at 5:13 PM
Subject: Postdocs: (1) Biofilms (2) Disease, UConn Health

POSTDOCTORAL RESEARCH POSITION IN AGENT-BASED
MODELING OF MULTISPECIES MICROBIAL BIOFILMS
The Laubenbacher and Mendes Research Groups at the Center for
Quantitative Medicine at UConn Health have an immediate opening for a
postdoctoral researcher to join an interdisciplinary team focused on
an NIH-funded project to develop novel approaches to the control of
heterogeneous multispecies microbial biofilms. The project team
combines expertise in mathematical modeling and control, biochemistry,
and microbial ecology. The team includes the laboratory of Dr.
Dongari-Bagtzoglou in the UConn School of Dental Medicine. For more
details see health.uconn.edu/laubenbacher/research/projects/
The position is for two years, with the possibility of an extension.
The researcher to fill this position will play an important leadership
role in the development of the mathematical modeling and control
component of the project. Required expertise for the position includes
a Ph.D. in mathematics, computer science, or computational biology,
knowledge of one programming language, a solid understanding of the
mathematics underlying dynamic models, interest in developing a new
agent-based model of multi-species microbial biofilms, and prior
experience with at least one type of computational modeling. Desired
expertise includes good knowledge of the Java programming language,
prior experience with agent-based models, knowledge/experience in
microbiology, and experience with the software package IDynoMiCS.

POSTDOCTORAL RESEARCH POSITION IN MULTISCALE
MODELING OF DISEASE
The Laubenbacher Research Group at UConn Health and the Jackson
Laboratory for Genomic Medicine has an immediate opening for a
postdoctoral researcher to join an interdisciplinary team focused on
an NIH-funded project to develop new software design approaches to
multiscale computational modeling. The application area is the innate
immune response to fungal infections in the lung. For more details see
health.uconn.edu/laubenbacher/research/projects/
The project team combines expertise in mathematical modeling,
pulmonary immunology, and scientific visualization. The position is
for two years, with the possibility of an extension. The researcher to
fill this position will play an important leadership role in the
development of innovative approaches to disease models in biomedicine.
The Laubenbacher Group has several other ongoing and planned
multiscale disease modeling projects that will also benefit from this
research. An important focus of the project is on the design of novel
software architectures for multiscale models, combining a strongly
modular design with Dockerization to build models that are easily
extendable, modifiable, shareable, and whose output is reproducible.
Innovative visualization techniques will make the models usable by
non-modelers. We are looking for a researcher who has experience with
up-to-date software design approaches in the context of multiscale
mathematical and computational modeling, the use of Docker containers,
and familiarity with popular programming languages, such as Java,
Python, and C++. Previous experience in implementing parallel and
multithreaded applications is required. A strong mathematical
background related to various aspects of dynamic models would be a
great plus.

Please direct inquiries to Dr. Reinhard Laubenbacher:
laubenbacher@uchc.edu

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From: Ryan Chisholm <ryan.chis@gmail.com>
Date: Fri, Mar 9, 2018 at 3:11 AM
Subject: Postdoc: Theoretical ecology, National University of Singapore

I am seeking a post-doctoral fellow with expertise in theoretical
ecology for an exciting collaborative project modelling the effects of
temporal environmental variance on the diversity of ecological
communities. The project will involve a combination of mathematical
work, computer simulations, and data analysis. The ideal candidate
will have experience with analysis of dynamical systems and Markov
chain models.

The project is funded by a collaborative grant between the National
Research Foundation of Singapore and the Israeli Science Foundation.
The Singapore Principal Investigator is me (Ryan Chisholm, National
University of Singapore) and the Israeli Principal Investigator is
Nadav Shnerb (Bar-Ilan University). The post-doctoral fellow will be
based in Singapore but will travel to Israel for collaborations.

Singapore is a dynamic, tropical, multicultural, highly developed city
state with great food in the heart of Southeast Asia. The National
University of Singapore is consistently ranked among the world’s top
universities, and our lab in the Department of Biological Sciences is
a thriving lab with high research output.

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From: Kapitanov, Georgi <Georgi.Kapitanov@pfizer.com>
Date: Tue, Mar 13, 2018 at 1:48 PM
Subject: Senior Scientist: Modeling & Simulation, Pfizer, Cambridge MA

For more details, see here:
pfizer.wd1.myworkdayjobs.com/en-US/PfizerCareers/job/United-States—Massachusetts—Cambridge/Senior-Scientist–Modeling—Simulation_4692408-2

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From: NIH Extramural Nexus (NIH/OD) <ExtramuralNexus@mail.nih.gov>
Date: Mon, Mar 12, 2018 at 1:51 PM
Subject: NIH Update: Funding Rates, Fy17 Numbers, Draft Strategic Plan…

NIH Update: Funding Rates, Fy17 Numbers, Draft Strategic Plan for
Data Science

Subject: SMBnet Reminders

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