SMB Digest Volume 19 Issue 17

May 10, 2019
This issue’s editor:


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Issue’s Topics:
Tutorial Workshop: Parameter Estimation for Biol…., NCSU, US
Conference: Undergraduate Capstone, Aug 5-8, MBI, Ohio St, US
Workshop: Philip Maini’s 60th Birthday, 18-19 Sep, U Oxford
CfP: Symposium on Artificial Life, Dec 6-9, Xiamen, China
ToC: BMB: Volume 81, Issue 6
Newsletter: AIBS, April 2019
Newsletter: NIH Update: Cumulative Investigator Rate, Sample…
Post-doc: Understanding Complex Systems, McDonnell Foundation
Post-doc: Quantitative Biological…, Hong Kong Baptist U
Post-doc: Math Bio/Comp Neurosci, IUPUI, Indianapolis, US
Post-doc: Modeling Lassa Fever, U Idaho, US
Positions: Modeling Biological Systems, Novartis
SMBnet Reminders


from: Mette Olufsen <>
date: May 2, 2019, 2:35 PM
subject: Tutorial Workshop: Parameter Estimation for Biol…., NCSU, US

The NC State Research Training Group on Parameter Estimation for
Mechanistic Biological Models (, funded by NSF,
will run their fourth Tutorial Workshop on Parameter Estimation for
Biological Models between July 28th to August 1st, 2019.

Mathematical modeling of biological systems is a rapidly growing area of
research. Typically, some (and often many) of a model’s parameters and/
or states are unknown and have to be inferred from the available data.
However, for many systems only partial observations are available. Much
effort has been devoted to solving this problem. Some of the key
questions considered in this context are: How sensitive is a model’s
output to changes of its parameters (sensitivity analysis)? Which
parameters can be estimated uniquely from a model’s input and output
(identifiability analysis)? What are the uncertainties of parameters
estimated by fitting a model to data? How are predictions of a model
impacted by uncertainties in its parameters (and structure) (uncertainty

The workshop will cover these concepts at an introductory level with
special emphasis on illustrating their practical application. The
meeting will be in form of tutorial lectures combined with discussion.
In addition, participants will get the opportunity to use the methods on
concrete problems via hands-on computer practicals.

The workshop is aimed at graduate students, postdocs, and anyone
interested in learning basic techniques associated with modern methods
of identifiability theory, parameter estimation, and uncertainty
quantification in models arising in biology.

Further details about the workshop will appear at

Workshop 2019

Individuals wishing to participate should contact Mette Olufsen
( and fill out the Google Form at Recommendation letters and CVs
should be sent to Mette Olufsen. Full consideration will be given to
applications received by July 1st. Financial support is available to a
limited number of US students and postdocs (US citizens or US permanent
US residents or “green card” holders). If you wish to request financial
support, please send a copy of your CV and ask your advisor to email a
letter of recommendation to us.

On behalf of the co-organizers: Atanaska Dobreva, Alun Lloyd and
Mette Olufsen


from: Tony Nance <>
date: May 2, 2019, 9:59 AM
subject: Conference: Undergraduate Capstone, Aug 5-8, MBI, Ohio St, US

2019 MBI Undergraduate Capstone Conference
August 5-8, 2019, MBI, Ohio State University, Columbus, OH


The MBI Capstone Conference offers undergraduate student researchers in
the mathematical biosciences and related areas an opportunity to present
their work on the national stage. This student-centered conference
-Keynotes from prominent researchers
-Talks and posters by student researchers
-Panels on careers and fields of research
-A graduate studies recruitment event

Applications submitted by July 22, 2019 will receive full consideration.
There is no registration fee.
Limited funding will be available for some participants.

To apply, visit:


from: Ruth Baker <>
date: May 10, 2019, 7:52 AM
subject: Workshop: Philip Maini’s 60th Birthday, 18-19 Sep, U Oxford

On growth and pattern formation: a celebration of Philip Maini’s 60th
18th-19th September 2019
Mathematical Institute, University of Oxford

We are holding a two-day workshop to celebrate Professor Philip Maini’s
60th Birthday and his achievements and fundamental contributions in
Mathematical Biology.

Details of the meeting, and how to register can be found at

Invited speakers
David Sumpter, Uppsala University (Public Lecture)
Derek Moulton, University of Oxford
Hans Othmer, Minnesota University
Jim Murray, University of Washington
Jonathan Sherratt, Heriot-Watt University
Kevin Painter, Heriot-Watt University
Linus Schumacher, University of Edinburgh
Lucy Hutchinson, Roche
Mark Chaplain, University of St Andrews
Mark Lewis, University of Alberta
Mary Myerscough, University of Sydney
Natasha Martin, University of Bristol
Noemi Picco, Swansea University
Paul Kulesa, Stowers Institute for Medical Research
Ruth Baker, University of Oxford
Santiago Schnell, University of Michigan
Tim Pedley, University of Cambridge

There is funding available to support the attendance of ECRs at the
meeting. To apply, please send a CV and covering letter, including
estimated costs, to by 31st May 2019.

Places are limited, so please do sign up sooner rather than later!


from: Hiroki Sayama <>
date: May 6, 2019, 9:00 AM
subject: CfP: Symposium on Artificial Life, Dec 6-9, Xiamen, China

Call for Papers:
IEEE ALIFE 2019: 2019 IEEE Symposium on Artificial Life

as part of
2019 IEEE Symposium Series on Computational Intelligence (IEEE SSCI
Xiamen, China December 6-9, 2019

IEEE ALIFE 2019 brings together researchers working on the emerging
areas of Artificial Life and Complex Adaptive Systems, aiming to
understand and synthesize life-like systems and applying bio-inspired
synthetic methods to other science/engineering disciplines, including
Biology, Robotics, Social Sciences, among others.

Important dates
Paper Submissions: July 10, 2019
Notification to Authors: Sep. 1, 2019
Final Submission: Oct. 1, 2019
Early Registration: Oct. 1, 2019

Fore more details, please visit the symposium website:


from: Springer <>
date: Jan 26, 2019, 5:07 PM
reply-to: Springer <>
subject: ToC: BMB: Volume 81, Issue 6

We are pleased to deliver the table of contents alert for the Bulletin
of Mathematical Biology. Volume 81 Number 6 is now available at


from: American Institute of Biological Sciences <>
date: Apr 18, 2019, 12:31 PM
subject: Newsletter: AIBS, April 2019

Please see .


from: NIH Extramural Nexus (NIH/OD) <>
date: May 7, 2019, 9:31 AM
subject: Newsletter: NIH Update: Cumulative Investigator Rate, Sample…

Please see


from: Brent Dolezalek <>
date: May 2, 2019, 11:12 AM
re-sent from: Santiago Schnell <>
subject: Post-doc: Understanding Complex Systems, McDonnell Foundation

We want to share with you an opportunity that may be of interest to your
doctoral students or others at your institution. The James S. McDonnell
Foundation has posted updated guidelines for the 2019 Postdoctoral
Fellowship Award program in Understanding Dynamic and Multi-scale

The JSMF Fellowship is a unique opportunity for students with an
interest in and an aptitude for complexity science who are in the final
stages of completing their Ph.D. and looking to make a significant
change in direction for their first postdoctoral fellowship (field of
study, model organism, theory vs experimental, etc.) that will either be
difficult or impossible without an external source of funding. Students
should anticipate activating the Fellowship between June 2020 and
February 28, 2021.

This Fellowship is not intended for individuals that already have
completed a Ph.D. or students that have already identified a
postdoctoral position and a postdoctoral mentor as traditional funding
mechanisms are better suited to these students. Such applications are
ineligible for consideration.

The total amount of the JSMF Fellowship is $200,000 USD to be expended
in no less than 2 and no more than 3 years. Typically JSMF can support
up to 10 Fellowships each year. The deadline to apply is June 13, 2019
15:59 CDT (20:59 UTC).

We encourage you to share this opportunity with students you believe fit
the goals of the program and will be completing their Ph.D. and ready to
start their first fellowship between June 2020 and February 2021.
Detailed information can be found on our website


from: Pan-Jun Kim <>
date: Apr 28, 2019, 7:53 PM
subject: Post-doc: Quantitative Biological…, Hong Kong Baptist U

Postdoctoral Research Fellows / PhD Students in Quantitative Biological
Modeling, Systems Biology, and Biomedical Informatics

The research group led by Dr. Pan-Jun Kim at Hong Kong Baptist
University (Department of Biology) invites applications for postdoctoral
research fellows and PhD students (research postgraduate students) in
the areas of quantitative biological modeling, systems biology, and/or
biomedical informatics. Hong Kong Baptist University is a public
institution funded by the Hong Kong SAR Government, promoting academic
excellence and innovation. Information on Pan-Jun Kim’s group can be
found from

The research will focus on the predictive computational modeling of
(i) global microbial ecosystems inside human body and (ii) various
metabolic, regulatory, and signaling networks inside/between cells, and
(iii) large-scale analysis of multi-omics and medical data. Screening of
applications begins immediately and will continue until the positions
are filled.

1. Applicants for postdoctoral research fellows should satisfy at least
one of the following conditions (i)-(iii): (i) trained in mathematics,
physics, or other computational sciences, with strong backgrounds in
computer simulations with programing languages such as Python and C++,
(ii) familiar with various machine learning algorithms, or
(iii) familiar with statistics and high-throughput -omics data. To
apply, please send your cover letter and curriculum vitae (including the
contact information of at least three references) to Dr. Pan-Jun Kim
through the email address: panjunkim (AT) hkbu (DOT) edu (DOT) hk.

2. Applicants for PhD students should be trained in mathematics,
physics, or other computational sciences, and should be highly
motivated, cooperative, and responsible. The candidates are expected to
have some computer programing experience (e.g., Python or C++), and good
communication skills in English. Prior research experience would be a
plus. To apply, please send your cover letter, curriculum vitae
(including the contact information of at least three references), and
English-translated copies of transcripts to Dr. Pan-Jun Kim through the
email address: panjunkim (AT) hkbu (DOT) edu (DOT) hk. Non-English
native applicants are encouraged to send their scores in TOEFL, IELTS,
or CET to the same email address.


from: Rubchinsky, Leonid L <>
date: May 1, 2019, 12:33 PM
subject: Post-doc: Math Bio/Comp Neurosci, IUPUI, Indianapolis, US

NSF-supported postdoctoral position in mathematical biology/
computational neuroscience in my group in the Department of
Mathematical Sciences at Indiana University-Purdue University
Indianapolis (IUPUI).

This position involves research in the mechanisms and properties of
intermittent synchronization in neural and other living systems
including collaboration with experimentalists. The position offers
excellent interdisciplinary training possibilities in computational
neuroscience and mathematical biology.

Applicants should have (or expected to get in a near future) Ph.D. in
mathematics, physics, neuroscience, biomedical engineering, computer
science, or another related field. Applicants should have strong
quantitative skills, some experience in dynamical modeling and data
analysis, and a strong interest in life sciences applications.
Experience in nonlinear dynamics, computational neuroscience, and
mathematical biology is a plus.

Please apply via at Screening of applications
will continue until position is filled.

Please address informal inquires to Leonid Rubchinsky via e-mail:


from: Remien, Christopher <>
date: May 1, 2019, 12:51 PM
subject: Post-doc: Modeling Lassa Fever, U Idaho, US

Postdoctoral position: Modeling the evolutionary dynamics of Lassa fever

We have a postdoctoral position developing mathematical and
computational models predicting the evolutionary dynamics of Lassa virus
available in my group ( starting in October 2019. The
specific goal of this project is to predict genetic variation and
sequence diversity of Lassa virus in its natural reservoir, M.
natalensis, within Sierra Leone. Exciting opportunities exist to
evaluate and refine model performance using viral sequence data being
collected from natural reservoir populations within Sierra Leone and
experimental infection studies conducted at Rocky Mountain Laboratories.
This project is part of an international collaborative effort to
forecast the spillover of Lassa virus into the human population and
develop a transmissible vaccine to eliminate it from its animal
reservoir The post-doc work
directly with the University of Idaho group including Chris Remien and
Jim Bull, but also have opportunities to work with our international
collaborators and some flexibility to develop side-projects that work
toward overall project goals.

This position will be based at the University of Idaho and anticipated
to be available starting October 1 of 2019. The University of Idaho
boasts an outstanding program in evolutionary biology supported by a
number of interdisciplinary programs including the Institute for
Bioinformatics and Evolutionary Studies (,
the Center for Modeling Complex Interactions
( and a vibrant graduate program in
Bioinformatics and Computational Biology
( The university is located at the
interface of the Palouse Prairie and Rocky Mountains and offers
excellent access to outdoor activities including mountain biking,
whitewater rafting and kayaking, rock climbing, fly fishing, and
backpacking. Moscow, the home of the University of Idaho, is a small but
dynamic community with a diversity of cultural activities.

Applicants should have a PhD in evolutionary biology, genetics,
mathematics, or a related field and a demonstrated ability to develop,
analyze, and publish mathematical models of biological processes.
Familiarity with sequence data and phylodynamic approaches is a plus. To
apply, e-mail a CV and the names and contact information of three
references to Scott L. Nuismer ( The initial
appointment will be for one year with the possibility of renewal for an
additional year. Review of applications will begin immediately and
continue until the position is filled.


from: Ramprasad Ramakrishna <>
date: May 1, 2019, 9:09 AM
subject: Positions: Modeling Biological Systems, Novartis

Novartis is looking for talented individuals with strong backgrounds in
mathematical and statistical modeling and being able to apply this in
biological systems. These positions are across discovery to clinical
development and can be located in East Hanover, NJ, Cambridge, MA and
Basel, Switzerland.

Many of the key questions that modelers address in these areas try to
derive biological/pharmacological insights of pre-clinical and clinical
data in order to understand drug dosing, identification of patterns in
drug concentration and responses (biomarker, efficacy, safety) and
finding the right subsets of patients who may respond to treatment for
an experimental therapy. The work involves collaboration with many
different groups across different disease areas and Novartis is
committed to providing an environment to promote learning in drug
development and the realization of everybody’s full potential to
developing new medicines.

Please write to me for further details and if possible please attach a

Thank you very much.

Prasad Ramakrishna


Subject: SMBnet Reminders

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