SMB Digest Volume 18 Issue 46

November 1, 2018
This issue’s editor:



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Issue’s Topics:
Remembrance of Dr. Wilfrid Rall, November 9, NIH, Bethesda & via webcast
Upcoming Deadlines for Keystone Symposia 2019 Life Science Conferences
Two PhD Positions: Mathematical & Computational Biology, Edinburgh
PhD Position in cancer modelling, Royal College of Surgeons, Ireland
Postdoc: Integrated Mathematical Radiation Oncology, Moffitt
Postdoc Positions: Computational Systems Biology, UCI
Faculty Position: Applied Math, University of Wisconsin-La Crosse
Faculty Position: Applied Math/Stats, Shippensburg Univ, PA, USA
Assistant/Associate/Full Professor: UCSF BCHSI
SMBnet Reminders


from: Sherman, Arthur (NIH/NIDDK) [E] <>
date: Oct 30, 2018, 4:10 PM
subject: Remembrance of Dr. Wilfrid Rall, November 9, NIH, Bethesda & via webcast

On November 9, there will be a meeting at NIH, Bethesda, MD, USA, in
remembrance of Dr. Wilfrid Rall (1922-2018). Dr. Rall, who passed away in
April, was a pioneer in computational neuroscience and the developer of cable
theory for dendrites. He was a well-respected and successful neuroscientist at
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) from
1957 to 1994.

The event will be held from 10:00am-3:30pm in the Stone House (Building 16) on
the NIH Main Campus.

The list of speakers includes:
Idan Segev, Hebrew University
Gordon Shepherd, Yale University
Charlie Wilson, UT San Antonio
Nelson Spruston, Janelia Farms
Bill Holmes, Ohio University
John Rinzel, New York University

The full schedule can be downloaded from:

In addition to the scientific presentations, there will an open session for
remembrances by family, friends and other colleagues.

A scientific obituary was published in the journal Neuron:

Please note that the event will also be webcast live should you not be able to
attend in person and will be archived thereafter:

For more information or questions regarding the event please contact:
John Rinzel (, or Arthur Sherman ( or


date: Oct 29, 2018, 6:51 PM
subject: Upcoming Deadlines for Keystone Symposia 2019 Life Science Conferences



from: SCHUMACHER Linus <>
date: Oct 29, 2018, 7:28 AM
subject: Two PhD Positions: Mathematical & Computational Biology, Edinburgh

Two PhD positions in mathematical & computational biology are available at the
University of Edinburgh, UK, at the Centre for Regenerative Medicine.

One fully funded (incl. overseas) PhD position on mathematical modelling of
stem cells & regeneration:

One competitively funded position, involving theory & experiments, on stem cell

Application deadlines early December. See links above for application

For informal enquiries please contact

The University of Edinburgh is a charitable body, registered in Scotland, with
registration number SC005336.


from: Marc Sturrock <>
date: Oct 29, 2018, 4:56 PM
subject: PhD Position in cancer modelling, Royal College of Surgeons, Ireland

Project title: Predicting variability in glioblastoma proliferation and spread
using stochastic mathematical models and 3D cultures of patient-derived

Location: Royal College of Surgeons in Ireland (RCSI)

Supervisors: Dr Brona Murphy ( and Dr Marc Sturrock

Project Summary: The overarching research aim of this project is to develop
stochastic versions of the existing well-established deterministic mathematical
models of GBM growth and spread in order to understand the role of noise or
variability in tumour size. We also further aim to validate this platform as a
tool to predict individual GBM patient responsiveness to the current treatment
options of TMZ and the sensitizing co-treatment options of ABT-199 and TL32711,
that have entered clinical trials for other cancers and which may be of benefit
to patients suffering from GBM. In particular, the project involves developing,
simulating and analysing spatial stochastic mathematical models of glioma
proliferation and spread and performing image analysis of GBM patient-derived
neurospheres. The models will first be written down in their chemical master
equation form. From here, depending on the model complexity, the generating
function method or linear noise approximation will be used to find an
analytical solution for the noise in terms of model parameters where noise will
be defined as the Fano Factor or coefficient of variation squared. Failing
this, the stochastic simulation algorithm will be used to produce ensemble
simulations of glioma growth from which the noise can be calculated.

These mathematical results will be validated by image analysis of GBM
patient-derived neurospheres created from GBM patient samples. We currently
have ~20 patient derived neurosphere cell lines, derived from both
newly-diagnosed and recurrent tumours. As we have on-going collaborations with
research groups in Erasmus Medical Center, Rotterdam (Prof Martine Lamfers) and
the ICM (Brain & Spine Institute), Paris (Dr Ahmed Idbaih), this number can be
increased if needed. The neurosphere cell lines will be maintained in Corning
Ultra- Low Attachment flasks in neurosphere growth conditions containing EGF
and bFGF, to ensure their stem-like characteristics are propagated, at 37°C in
a 5% CO2 humidified incubator. The patient-derived neurospheres will be left
untreated or treated with TMZ alone and in combination with ABT-199 or TL3271.
The neurospheres will be visualised using an Eclipse TE 300 inverted microscope
(Nikon, Dusseldorf, Germany). These images of will be analysed to assess the
spatio-temporal noise in neurosphere size under different treatment conditions.
Dual staining with fluorescent Annexin V and propidium iodide (PI) will be used
to confirm whether the stem cell lines die by apoptosis following the varying

Specific Requirements:
-1st class or equivalent BSc in Applied Mathematics/Mathematical
Biology/Systems Biology/Computational Biology/Biophysics/Computer Science with
preference given to those candidates with experience in cancer modelling
-Experience with fitting models to data e.g. using Bayesian parameter
estimation techniques (MCMC, ABC etc.)
-Experience with agent based models or stochastic simulation algorithms would
be beneficial
-Some cell culture and/or image analysis experience would also be beneficial
-Scientific computing skills in C / Python / Julia

Further details can be found here (where it is listed as project 8):


from: Enderling, Heiko <>
date: Oct 29, 2018, 8:07 PM
subject: Postdoc: Integrated Mathematical Radiation Oncology, Moffitt

Postdoctoral Fellow – Integrated Mathematical Radiation Oncology

Applications are sought for a postdoc position under the mentorship of Dr.
Heiko Enderling ( on inter-disciplinary
research projects on cancer radiotherapy.

We seek a talented individual to work in the unique research environment of the
Integrated Mathematical Oncology (IMO) department at Moffitt Cancer Center on
the University of South Florida campus in Tampa. IMO integrates mathematicians,
computer scientists, and physicists together with imaging specialists as well
as clinical and experimental oncologists to develop novel approaches for the
understanding, treatment and prevention of cancer.

Position Highlight:

At Moffitt Cancer Center we created the Future of Radiation Therapy (FoRT)
program, in which mathematical modeling of patient-specific treatment responses
to dynamically adapt treatment plays a central role.

The Ideal Candidate:

• has a desire to work closely with experimentalists and clinicians
• has experience in modeling biological systems, with a preference for those
with knowledge of cancer and or radiation therapy
• experience in developing/writing publications in quality peer reviewed
scientific journals
• ability to develop mathematical models and to program (Matlab, Python, R, C,
Java, etc.), visualize and analyze numerical/experimental data
• demonstrated creativity, high motivation, and good communication skills


• Communicate clearly and openly, present research results on local and
national platforms
• Perform independent research
• Meet with team leader and members frequently
• Build relationships across research disciplines to promote a collaborative
research environment

Credentials and Qualifications:

• MD or PhD and background in applied mathematics, physics or a computational

A competitive salary and benefits package will be offered to the successful

How to Apply: Interested applicants should send a cover letter and C.V.
directly to<> and
formally apply through the online recruitment system to


from: Qing Nie <>
date: Oct 30, 2018, 12:11 PM
subject: Postdoc Positions: Computational Systems Biology, UCI

Applications are invited for multiple postdoctoral fellow positions at
University of California Irvine in the area of Computational Systems Biology.
The successful candidates will be working with Professor Qing Nie on various
topics related to cell fate dynamics. More information on the position and the
application submission link can be found at:


from: James Peirce <>
date: Oct 30, 2018, 2:43 PM
subject: Faculty Position: Applied Math, University of Wisconsin-La Crosse

The Mathematics & Statistics Department at the University of Wisconsin-La
Crosse invites applications for a tenure-track assistant professor position in
Applied Mathematics beginning August 26, 2019. The department is particularly
interested in receiving applications from candidates that can provide our
students with the interdisciplinary skills necessary to further enhance
Wisconsin’s workforce in high-demand STEM fields.

We welcome applicants with traditional mathematical modeling experience, as
well as those interested in applying the methods of data science, machine
learning, mathematical biology, and/or topological data analysis. Our
department recognizes that interdisciplinary skills can be learned in various
environments. Preference will be given to candidates whose training and
research can enhance and expand the department’s collaborative STEM activities,
including partnerships with faculty across campus and scientists and medical
professionals in the La Crosse area.

Note: Electronic submission of application materials is required. For
additional information about this position and to apply, please visit

Please contact the chair of the Search and Screen Committee, Dr. James Peirce
(, if you have a special need/accommodation to aid your
participation in our hiring process.


from: Melara, Luis <>
date: Oct 30, 2018, 12:45 PM
subject: Faculty Position: Applied Math/Stats, Shippensburg Univ, PA, USA

Tenure-Track Position in Applied Mathematics/Statistics at
Shippensburg University of Pennsylvania

The Mathematics Department at Shippensburg University is looking to expand its
offerings in applied mathematics, statistics, actuarial science, and/or data
science. One tenure-track position is available. Applications will begin to be
reviewed on Nov. 30, 2018.

Please contact Prof. Kate McGivney at with any inquiries.

For more information on this position, please go to


from: Jessica Godoy <>
date: Oct 30, 2018, 3:28 PM
subject: Assistant/Associate/Full Professor: UCSF BCHSI

Assistant, Associate, Full Professor (basic science)
UCSF Bakar Computational Health Sciences Institute and Gladstone Institutes

Please apply online and submit CV, cover letter, statement of contributions to
diversity, statement of research, statement of teaching, and 3 references at


subject: SMBnet Reminders

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