SMB Digest Volume 19 Issue 19

May 31, 2019
This issue’s editor:


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Issue’s Topics:
New textbook in nonlinear dynamics
Workshop on Complex Networks in the Life Sci., Madrid, Jul 25
Workshop on the Mechanics of Cell Aggregates, Turin, Sep 3-6
Threshold Networks Conference, Nottingham, Jul 22-24
3rd Exchange Workshop of UK QSP Network, Reading, Sep 9-10
AIBS May 2019 Newsletter
PhD Position: Precision oncology, Ghent University
PhD Position: Cell-matrix interactions, Maastricht University
RA: Prostate Cancer Research, Imperial College London
Postdoc: cell-matrix interactions, University of Grenoble
Postdoc: Eco-evolutionary modelling, University of Arizona
Postdoc: ComputatIonal biology, University of Edinburgh
Lecturer in Applied Mathematics, University of Liverpool
Dir & Prof. in School of Math. & Natural Sciences, ASU
Updated NSF funding opportunity: Research Experiences for…
Selected NIH Intramural Research & other job openings, May 2019
SMBnet Reminders


From: Roussel, Marc <>
Date: May 17, 2019, 8:46 PM
Subject: New textbook in nonlinear dynamics

I am happy to announce the publication of a new textbook in nonlinear
dynamics entitled Nonlinear Dynamics: A Hands-On Introductory Survey
in the IOP Concise Physics series. Details about this book can be
found here:

Many universities have a subscription to the IOP ebooks, so it is
quite possible that you may be able to download this book for free
through your library.


From: Saul Ares <>
Date: May 30, 2019, 6:51 PM
Subject: Workshop on Complex Networks in the Life Sci., Madrid, Jul 25

Workshop on Complex Networks in the Life Sciences
EBSA 2019 Satellite Meeting
Alcalá de Henares (Madrid, Spain) July 25th, 2019

The workshop will cover the application of network science to nature
at all scales, from genetic or metabolic networks to social networks,
ecology or climate. The plan is to join together people who work in
the frontier between biology or environmental sciences and complex
networks and discuss in a friendly environment about the present and
future of the discipline. The venue will be Alcalá de Henares, a
charming UNESCO World Heritage Site very close to Madrid.

More details at:

For more info write to or contact the
organisers Jacobo Aguirre or Saúl Ares


From: Davide Ambrosi <>
Date: Thu, May 2, 2019 at 4:05 AM
Subject: Workshop on the Mechanics of Cell Aggregates, Turin, Sep 3-6

A workshop on the Mechanics of Cell Aggregates will be held in Torino
(Italy) on September 3-6 2019.

The workshop will gather biophysicists and mathematicians who are
actively contributing in in understanding the mechanobiology of cell
aggregates. A non-exhaustive list of topics includes tumor spheroids,
embryos, single cell mechanics, monolayers and collective cell

More details at:


From: Stephen Coombes <>
Date: May 30, 2019, 12:25 PM
Subject: Threshold Networks Conference, Nottingham, Jul 22-24

This workshop will bring together a community of people interested in
both networks and dynamics, with an eye to both mathematical
tractability and applications to biology, engineering, physics, and
the social sciences. The emphasis will be on ‘thresholds’ in their
broadest sense as exemplified by node dynamics or interactions that
are described by simple, yet possibly non-smooth or discontinuous
switch-like processes. The workshop will cover both theory and

The meeting will have no parallel sessions, and it is expected to
involve around 60 participants (with 11 main speakers) and contributed
poster presentations.

More details at:

Scientific Organisers
Yi Ming Lai, Rüdiger Thul, and Stephen Coombes, University of Nottingham
Mason A. Porter, UCLA

Enquiries should be sent to:


From: Marcus Tindall <>
Date: May 23, 2019, 2:06 PM
Subject: 3rd Exchange Workshop of UK QSP Network, Reading, Sep 9-10

The 3rd Exchange Workshop of the UK QSP Network will be held on 9th
and 10th September 2019 at the University of Reading. The workshop is
focused on exploring the use of Artificial Intelligence (AI) and
mechanistic QSP modelling approaches in pharmacological research and
the synergy between them in tackling problems and questions in the
field. The meeting will combine talks from invited speakers, submitted
talk and poster abstract presentations with discussion sessions
focused on discussing AI and mechanistic modelling approaches and how
the two areas may be brought together to inform specific areas of
pharmacological research.

Confirmed invited speakers – Vincent Lemaire (GeneTech), Ben Macarthur
(University of Southampton), Marco Siccardi (University of Liverpool),
Ben Sidders (AstraZeneca), Joseph Standing and Ferran Hernandez
(University College London) and Jane White (University of Bath).

We welcome talk and poster abstracts which demonstrate the individual
or combined use of AI and mechanistic modelling QSP based approaches
in drug discovery and development, as well as biological and
biomedical modelling using these approaches. Abstracts should be half
an A4 page in length and consist of a title, contributors, contributor
affiliations, background to the work undertaken, methodology, results
and what has been achieved by undertaking the work.

More details at:


From: American Institute of Biological Sciences <>
Date: Fri, May 10, 2019 at 10:08 AM
Subject: AIBS May 2019 Newsletter

Please see


From: Ema Shollenberger <>
Date: May 23, 2019, 6:50 PM
Subject: PhD Position: Precision oncology, Ghent University

The cancer research teams at Ghent University supervised by prof. dr.
ir. Katleen De Preter (
and prof. dr. Karim Varmaelen (
have an open position for a highly motivated researcher with a keen
interest in translational cancer research and basic knowledge of

A new era of clinical care, so-called precision oncology is opening
unprecedented potential for developing novel therapeutic strategies
for cancer patients. The research of the translational bioinformatics
group of prof. dr. ir. Katleen De Preter at UGent-Center for Medical
Genetics ( is focused on the development of analytical and
bio-informatic pipelines for diagnostic, prognostic and predictive
analysis of tumors, enabling a more personalized and precise cancer
medicine. In collaboration with prof. dr. Karim Vermaelen (founder of
the ION network:, a
research project was recently started on the identification of new
biomarkers for immunotherapy sensitivity in lung cancer patients. For
this project, we are currently searching a highly motivated scientist.

More details at:


From: Carlier, Aurélie (MERLN) <>
Date: Sat, May 25, 2019 at 2:02 PM
Subject: PhD Position: Cell-matrix interactions, Maastricht University

Modeling life at the cell-matrix interface

The MERLN Institute for Technology-inspired Regenerative Medicine at
Maastricht University in the Netherlands invites applications for a
PhD position. The PhD student will perform cutting-edge research in
computational modeling methods applied to regenerative medicine and
more specifically, to cell-matrix interactions.

More details at:


From: Ema Shollenberger <>
Date: May 20, 2019, 1:21 AM
Subject: RA: Prostate Cancer Research, Imperial College London

The Prostate Cancer Research group, in the Division of Cancer, invite
applications for a Research Assistant position from highly-motivated
applicants with an enthusiastic interest in the roles of non-coding
RNAs as biomarkers of DNA damage and therapeutic response in prostate

You would be joining a dynamic and expanding group, undertaking
collaborative and multidisciplinary work with the aim of understanding
and combating resistance to therapy in advanced prostate cancer. The
role will involve liaison between laboratory and clinical teams. It
will also involve extensive collaboration with the Institute of Cancer
Research and will also other leading institutions in the UK and US,
offering excellent opportunities to develop skills and networks.

More details at:


From: Angélique Stéphanou <>
Date: May 20, 2019, 4:22 PM
Subject: Postdoc: cell-matrix interactions, University of Grenoble

A postdoc position is available in the TIMC-IMAG Laboratory in
Grenoble (, starting as soon as possible
and no later than 1st January 2020.

The project aims at investigating with a numerical model the
mechanochemical couplings between cells and the extracellular matrix
during the anastomosis process in angiogenesis. The project will be
realized in close collaboration with experimentalists.

More details at:


From: Regis Ferriere <>
Date: Sat, May 25, 2019 at 8:22 PM
Subject: Postdoc: Eco-evolutionary modelling, University of Arizona

A post-doctoral fellowship is available to work on an NSF Dimensions
of Biodiversity-funded project to develop statistical inference tools
for eco-evolutionary dynamics, and apply these tools to analyze the
eco-evolutionary drivers of toxic algal blooms. The post-doc will work
under the supervision of Dr. Regis Ferriere to (1) develop general
methods for inferring eco-evolutionary feedbacks using eco-evolutionary
dynamics models and statistical methods such as particle MCMC and
Approximate Bayesian Computation, (2) develop eco-evolutionary models
specifically targetting the empirical system (blooms of the toxic
haptophyte alga Prymnesium parvum in Eastern U.S. lakes), (3) apply
the newly developed models and statistical inference tools using
ecological time series, ‘omics data and phylogenies from natural lakes
and laboratory mesocosm experiments. The work will be done in close
collaboration with Principal Investigator Dr. Jennifer Wisecaver
(Purdue University) and Collaborator Dr. William Driscoll (Penn State
University at Harrisburg).

More details at:


From: FENG Yi <>
Date: May 27, 2019, 12:26 PM
Subject: Postdoc: Computaitonal biology, University of Edinburgh

We are recruiting a highly motivated post-doctoral researcher who will
focus on the application and development of cutting-edge computational
methods in the area of integrated multi-Omic analysis of metabolomics
and single-cell RNA sequencing. The successful candidate will join Dr
Feng’s group in the Centre for Inflammation Research (CIR), and will
link closely with Professor Ponting’s group based at the Institute of
Genetics and Molecular Medicine (IGMM) and Dr Campbell’s group in the
school of chemistry.

The Feng lab has developed a zebrafish model for in vivo live imaging
and genetic analysis of pre-neoplastic cells (PNCs) in its initiating
niche in vivo. One of the goals of the lab is to dissect mechanisms
that regulate how host cells interact with the initial PNCs in its
niche, by fully characterising details of lineage development and the
cell-cell interaction network using scRNAseq analysis. The single cell
RNAseq data will also be integrated with metabolomic data generated
through Imaging Mass Spectrometry (IMS) on intact zebrafish PNC niche.

More details at:


From: Bearon, Rachel <>
Date: May 28, 2019, 1:25 PM
Subject: Lecturer in Applied Mathematics, University of Liverpool

We are seeking to appoint a Lecturer initially for 3 years with the
possibility to become permanent after competitive evaluation after 2+1
years in the area of Applied Mathematics. The posts will be held in
the Department of Mathematical Sciences, which is part of the School
of Physical Sciences at the University of Liverpool.

More details at:
Job Ref: 011688

Informal enquiries regarding mathematical biology at Liverpool welcome
– please contact Prof Rachel Bearon


From: Sara Cutrone <>
Date: May 28, 2019, 5:56 PM
Subject: Dir & Prof. in School of Math. & Natural Sciences, ASU

The School of Mathematical and Natural Sciences (SMNS) in the New
College of Interdisciplinary Arts & Sciences at Arizona State
University (ASU) invites applications for School Director. This is an
opportunity to take a leadership role in a rapidly growing School; one
embedded in the truly interdisciplinary and innovative environment of
New College.

More details at:


From: Henry Warchall <>
Date: May 22, 2019, 6:30 PM
Subject: Updated NSF funding opportunity: Research Experiences for…

Dear Colleagues,

An updated NSF program solicitation (NSF 19-582) is now available:
Research Experiences for Undergraduates (REU)

Please see for

Full Proposal Deadline Date: August 28, 2019


From: Owens, Roland (NIH/OD) [E] <>
Date: Fri, May 17, 2019 at 6:18 PM
Resent-from: Mejia, Raymond (NIH/NHLBI) [E] <>
Subject: Selected NIH Intramural Research & other job openings, May 2019

Senior Scientist
Epidemiology and Biostatistics Program, DCEG-NCI
(deadline: May 24)

The Division of Cancer Epidemiology and Genetics (DCEG), National
Cancer Institute (NCI), National Institutes of Health (NIH) is
recruiting an accomplished Senior Scientist in the Epidemiology and
Biostatistics Program (EBP). DCEG’s epidemiologists, geneticists, and
biostatisticians conduct population and multidisciplinary research to
discover the genetic and environmental determinants of cancer and new
approaches to cancer prevention. The Division’s research has an impact
on public health policy in the United States and around the world.

More details at:

The NIH Intramural Research Program:

Link to Fellowships and Positions of Interest to fellows:


Subject: SMBnet Reminders

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