SMB DIGEST
ISSN 1086-6566
VOLUME 17 ISSUE 12
March 22, 2017

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Issue's Topics:
† Stochasticity & Control in the Dynamics & Diversity of Immune ...
† Workshop on mathematical & Theoretical ecology
† International Summer school on deep learning, Bilbao, Spain
† Biofilm Models Special Issue European Journal of Applied Mathematics
† AAi Short Courses R Programming
† PhD scholarship, University of Edinburgh
† PhD thesis position at University of Lorrain, France
† Postdoc on modelling T cell response to malaria, University of Tennessee
† Positions on theoretical modeling
† SMBnet Reminders


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From: "Uri Hershberg" <uri.hershberg@gmail.com>
Date: Mar 14, 2017 1:45 PM
Resent-from: Ramit Mehr <prof.ramit.mehr@gmail.com>
Subject: Stochasticity & Control in the Dynamics & Diversity of Immune ...

We† would like to invite you to participate in a system immunology conference
that will take place from the 18th to the 23rd of June 2017 at the Israeli
Institute for Advanced Studies† (IIAS) in Jerusalem, Israel.
The meeting will focus on how stochasticity and control influence immune
dynamics and bring together leading experimental and computational
researchers.
Please submit abstracts for consideration by April 1
http://www.as.huji.ac.il/content/stochasticity-and-control-dynamics-and-diversity-immune-repertories?_ga=1.165900670.1197455970.1469238669
The conference will include tutorial sessions for graduate students and post
docs interested in novel methods of sequence analysis and modeling of immune
repertoires.


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From: Petrovskiy, Sergei (Prof.) <sp237@leicester.ac.uk>
Date: 2017-03-18 11:02 GMT-03:00
Subject: Workshop on mathematical & Theoretical ecology


One-day workshop:
"Uncertainty and predictability in ecology" (University of Leicester, April 6,
2017), organized by Sergei Petrovskii
Speakers & talks:
Robert Holt (University of Florida, USA): "Reflections on apparent
competition: a 40-year anniversary"
Ludek Berec (Institute of Entomology, Budejovice, Czech Republic): "Happy but
frustrated: Allee effects help control pests but are hard to estimate"
Axel Rossberg (Queen Mary University of London, UK): "What can we and what
can't we predict in community ecology?"
Max Souza (Universidade Federal Fluminense, Brazil): "Predator-prey dynamics:
mass action models, functional responses, and the PDE viewpoint"
Natalia Petrovskaya (University of Birmingham, UK): "`Heads or tails':
choosing between deterministic and probabilistic approaches to evaluation of
the population abundance from sparse data"
Sergei Petrovskii (University of Leicester, UK): "Catching ghosts with a
coarse net: use and abuse of spatial sampling data in detecting
synchronization"

This is the 6th of the META series of workshops (Mathematical Ecology: Theory
and Applications) co-organised by Natalia Petrovskaya, Edward Codling and
Sergei Petrovskii and supported by the London Mathematical Society.
Attendance is free and everybody is welcome. No pre-registration is required,
but expressions of interest and/or intention to attend are welcome.
For more details, please visit
http://www2.le.ac.uk/departments/mathematics/extranet/staff-material/staff-profiles/sp237/meta-research-group-workshop
or contact Sergei Petrovskii at†sp237@le.ac.uk


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From: GRLMC <grlmc@grlmc.com>
Date: 2017-03-18 17:39 GMT-03:00
Subject: International Summer school on deep learning, Bilbao, Spain


INTERNATIONAL SUMMER SCHOOL ON DEEP LEARNING
DeepLearn 2017
Bilbao, Spain
July 17-21, 2017

Organized by:
University of Deusto
Rovira i Virgili University

http://grammars.grlmc.com/DeepLearn2017/


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From: John Ward <John.Ward@lboro.ac.uk>
Date: 2017-03-21 13:40 GMT-03:00
Subject: Biofilm Models Special Issue European Journal of Applied Mathematics

The European Journal of Applied Mathematics will be publishing† a special
issue centered on mathematical modeling of biofilm processes. Topics include
model formulation, analysis of biofilm models, numerial algorithms for biofilm
models, and model based study of biofilm phenomena.
Inquiries can be directed to the guest editors of the special issue, John Ward
[Loughborough,†John.Ward@lboro.ac.uk] and Hermann Eberl [Guelph,
heberl@uoguelph.ca]. In particular authors who plan to submit review articles
are encouraged to contact us beforehand.
Submitted mansucripts will undergo the usual EJAM peer review process. Target
date for submission is June 1, 2017.
To submit your manuscripts, please visit
http://www.edmgr.com/ejam/Default.aspx, and on submission select the special
issue ?Biofilms? link.


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From: Colin Wise <Colin.Wise@uts.edu.au>
Date: 2017-03-17 0:41 GMT-03:00
Subject: AAi Short Courses R Programming

AAi Short Courses ? ?R Programming - Stage 1 (Introduction)' ? on Thursday 23
March 2017 and ?R Programming - Stage 2 (Intermediate) ? on Friday 24 March
2017
http://www.uts.edu.au/research-and-teaching/our-research/advanced-analytics-institute/education-and-research-opportuniti-3

R Programming - Stage 1 (Introduction) is the basic R Programming one (1) day
short course for beginners and or those seeking refreshment in R Programming.

R Programming - Stage 2 (Intermediate) is the intermediate R Programming one
(1) day short course for those who have completed R Programming ? Stage 1 or
for those who consider themselves to have a working knowledge of R.
R is a very popular open source programming language that excels in
statistics, visualisation and data analysis. Its most significant advantage is
that there are now several thousand add-on packages that are available to
perform specific analysis tasks, and the whole ecosystem is free of charge.


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From: "Miguel O. Bernabeu" <miguel.bernabeu@ed.ac.uk>
Date: 15 March 2017 at 14:44:32 GMT
Subject: PhD scholarship, University of Edinburgh

PhD scholarship for the project: ?Developing new diabetic retinopathy
biomarkers through image processing, computational modelling, and machine
learning?. Deadline for application 5pm on 23 March 2017. Start date September
2017.
This is a collaboration with Prof. Andrew Morris, Dr Tom MacGillivray, and
Prof. Bal Dhillon from the University of Edinburgh and colleagues at Queen?s
University in Belfast.
More details can be found online at:
https://www.findaphd.com/search/ProjectDetails.aspx?PJID=81141


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From: Jean-NoŽl JAUBERT <Jean-Noel.Jaubert@univ-lorraine.fr>
Date: 2017-03-20 6:59 GMT-03:00
Subject: PhD thesis position at University of Lorrain, France

PhD candidate with ideally a strong background in chemical engineering
thermodynamics (equation of state, phase equilibria) and mathematics
(numerical methods).
Candidates with experience in (scientific) programming (especially ForTran)
will be preferred. Good communication skills are obviously necessary.
All information related to this position is recorded in the attached file.
Could you please be so kind to ask potential candidates to send me their C.V.
with a cover letter.
Do not hesitate to contact†jean-noel.Jaubert@univ-lorraine.fr†for further
information.


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From: Vitaly V. Ganusov <vitaly.ganusov@gmail.com>
Date: 2017-03-20 16:10 GMT-03:00
Subject: Postdoc on modelling T cell response to malaria, University of
Tennessee

A post-doctoral position is available in the laboratory of Vitaly
V. Ganusov in the Department of Microbiology at the University of
Tennessee in Knoxville in the area of modeling within-host dynamics of T cell
response to malaria infection.

Our laboratory is currently focuses on studying the role of T cell responses,
mainly CD8 T cell
responses, in the control of pathogens in mammalian hosts.† Despite
great advances in biology and medicine in controlling infectious
diseases with antibiotics/antivirals and vaccines we still have a
limited understanding how pathogens cause the disease and how immune
responses control pathogen growth within the host. In our laboratory we adopt
a philosophy of data-driven mathematical modeling whereby we combine the use
of models and analysis of experimental data. This specific project will focus
on understanding how vaccine-induced CD8 T cells locate and eliminate
Plasmodium parasites, causing malaria, from murine livers. Experimental data
will come from intravital imaging experiments documenting movement of T cells
in the liver, localization of T cells around Plasmodium-infected hepatocytes,
and elimination of the parasite. The ultimate goal is to understand the number
and quality of vaccine-induced memory CD8 T cells needed to provide
sterilizing protection against Plasmodium infection. There will be also an
opportunity to work on questions related to other infections such as HIV and
Mycobacterium tuberculosis.

Requirements:
1) PhD (or equivalent) in mathematics, biology, physics or
similar area.
2) Previous documented experience in mathematical/computational
biology.
3) Solid knowledge of one of a higher level programming
languages (R, python, Matlab, Mathematica, or similar).
4) Good oral and written communication skills.

Basic understanding of infectious disease biology is a plus.
Position starts Aug 1st 2017 for 2 years with a possibility of extension given
adequate performance.
Salary is on the NIH scale with full University of Tennessee employee fringe
benefits.
To apply, please send your CV, 2-3 copies of your papers best representing
your contribution to science, and arrange for 2-3 letters of reference from
your previous advisers to be sent to†vitaly.ganusov@gmail.com.


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From: Ariel Weinberger <ariel@autonomous.bio>
Date: 2017-03-22 16:05 GMT-03:00
Subject: Positions on theoretical modeling

We have a number of positions open?this ad focuses on the theoretical modeling
positions (we?re also looking for bio and chemical engineers to help
genetically engineer and test the therapies).
An ideal modeling candidate has strong experience using and developing
deterministic and probabilistic approaches to analyze dynamical systems
(genetic evolution and disease transmission being two examples).† A Ph.D. is
preferred, but your research experience and passion are more important.
You?ll be working closely with experimentalists (at the company and at
universities) to probe whether our prototype therapies can safely control
fast-changing viruses.† We?ll build bioreactors to test your predictions.† So,
you?ll be developing (and publishing) new science, while helping optimize new
potential cures.
If your quantitative skills are exceptional and you?re passionate about
learning biology, we?ll train you in the biology.† We?d love to see some of
your work.

Benefits:
Our scientists are full-time employees with competitive salaries and stock
options in an early growth-stage company (with a number of first-in-class
drugs in the preclinical pipeline).
We also offer medical & dental insurance, 401(k) plans, commuter and fitness
benefits, and engaging places to work (e.g., New Lab in Brooklyn, UCSF campus
in San Francisco).
For the academic-minded, you will be able to publish, present at conferences,
attend DARPA workshops, and work closely with collaborators at seven academic
institutions.

About Us:
Our goal is to radically alter drug development and disease control?by
designing the first mutating, ?resistance-proof? therapeutics to target
rapidly evolving pathogens and cancers.
Current drugs are static biological or pharmaceutical compounds.† The problem
is that these non-evolving interventions are used to target evolving disease
targets that rapidly mutate across patients and populations.† The mismatch
between non-adaptive therapeutics and adaptive disease targets is the reason
that many pathogens and cancers emerge resistant to drug control and
untreatable.
We aim to obviate resistance by developing (the first) mutating therapeutics?
drugs that co-evolve with infectious diseases like HIV and Zika to maintain
lifelong control.† Imagine taking a drug (or flu vaccine) once in your life
and never needing to worry about that disease or any of its evolved variants
again.
More Info
A recent Bloomberg interview about us:

Print:
http://www.bloomberg.com/news/articles/2016-07-14/mutant-hiv-viruses-fight-new-infections-in-two-brothers-labs
Radio:
http://www.bloomberg.com/news/audio/2016-07-14/bay-state-biotech-report-brothers-mutant-hiv-fighting-viruses

Feel free to email us directly: ariel@autonomous.bio


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Subject: SMBnet Reminders

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