SMB Digest     September 13, 2016   Volume 16 Issue 37
ISSN 1086-6566

Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com

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Issue's Topics:
         Conference: Systems Biology, Nov 16-18, Lyon, France
         Study Group: Multiscale Biology, Dec 12-15, U Birmingham, UK
         Conference: Bioinformatics & Com. Bio., March 20-22, Hawaii, US
         Conference: Math. Neuroscience, May 30-Jun 2, Boulder, CO, US
         Lecture Series: BD2K Guide to the Fundamentals of Data Sci....
         Springer: Japan Journal of Industrial and Applied Mathematics
         AIBS: Public Policy Report
         PhD Position: Comp. Approach to Psoriasis..., Newcastle U, UK
         Research Grant: DEB Estimation Development, MARETEC, Portugal
         Post-doc: Mod. Viral Hepatitis Dynamics, Loyola U Med, Chicago
         Post-doc: Comp. Mod.-Cancer Genetic Networks, Bar Harbor, US
         Post-doc: Control of Invasive Species, U Canterbury, NZ
         Tenure-track: Biomathematics, San Diego State U, US
         Tenure-track: Math Biology, Worcester Polytechnic Institute, US
         SMBnet Reminders


From: François Briat <>
Date: Mon, Sep 12, 2016 at 4:14 AM
Subject: Conference: Systems Biology, Nov 16-18, Lyon, France

LyonSysBio is the yearly international conference organized by BioSyL
the Systems Biology Alliance of Lyon (

Our goal is to promote exchanges between scientists from different
disciplines (biology, mathematics, computer sciences, physics, social
sciences) who are interested in the analysis of the wealth of data
generated by modern biology, as well as the construction of the
necessary modeling tools to gain system level thoughtful insights.

In 2016, the conference will be held from November 16th to 18th. Keynote
lectures will be delivered by invited speakers, on state-of-the-art
advances in various domains of Systems Biology (list available on the
conference website).

In addition, the conference program leaves ample space for contributed
talks and posters for which proposals are welcome. We wish to favor
results from truly multidisciplinary works.

Please use the online system to submit a one-page abstract (maximum 500
words, in English) by October 10th, 2016: To register and to submit an
abstract, you will have to create a account by filling
the on-line registration and submission forms.

Similarly to our previous editions, registration will be free but
mandatory for students. Registration fees for non-students will be of
100 euros. A Gala reception will be organized on November 17th.


From: Rosemary Dyson <>
Date: Tue, Sep 6, 2016 at 11:06 AM
Subject: Study Group: Multiscale Biology, Dec 12-15, U Birmingham, UK

The University of Birmingham, with funding from the POEMS network and
the UK Multi-Scale Biology Network, will host a Multiscale Biology Study
Group from 12th-15th December 2016. This event will bring together
biologists and clinicians with mathematicians to tackle research
questions posed by the experimentalists, following the successful
blueprint of the Mathematics in Medicine and Mathematics in the Plant
Sciences Study Groups (see and

Registration is free for UK-based researchers, and will cover
accommodation and subsistence for participants during the week. Limited
travel funding may be available on a case-by-case basis. Registration
will open shortly, further details will be posted at as they become
available, any queries should be directed to
Interested mathematics researchers at all levels are encouraged to

The call for problems will shortly go out - if you know of an
experimental researcher who may be interested please ask them to contact
Rosemary Dyson (


From: Nurit Haspel <>
Date: Sat, Sep 10, 2016 at 7:59 PM
Subject: Conference: Bioinformatics & Com. Bio., March 20-22, Hawaii, US

BICOB-2017 - Call for Papers
9h International Conference
on Bioinformatics and Computational Biology (BICOB)
March 20 - 22, 2017
Honolulu, HI, USA
(In Conjunction with CATA-2017)

Important Dates:
Paper Submission Deadline: October 31 2016
Notification of Acceptance: December 18, 2016
Pre-registration and Camera-ready Manuscripts: January 20, 2017
Paper submission site:

Most research areas of bioinformatics, computational biology and medical
informatics have experienced significant advances in recent years driven
by computational techniques in bioinformatics. The 9th International
Conference on Bioinformatics and Computational Biology (BICOB) will
provide an utmost venue for researchers and practitioners in
bioinformatics to present and publish their research results and
techniques. Bioinformatics and computational biology continue to be a
vibrant research area with broadening applications and new emerging
challenges. BICOB-2017 seeks original and high quality papers in the
fields of bioinformatics, computational biology, systems biology,
medical informatics and the related areas. The conference includes a
Best Paper Award to be given during the conference banquet. We also
encourage work in progress and research results in the emerging and
evolutionary computational areas. Work in the computational methods
related to, or with application in, bioinformatics is also encouraged
including: computational intelligence and its application in
bioinformatics, bio-data mining and text mining, evolutionary
algorithms, nature-inspired computation, machine learning and bio-NLP,
biomedical ontology, biomathematics, modeling and simulation, pattern
recognition, data visualization, biostatistics.

Submission Procedures
Papers will be accepted only by electronic submission (in PDF format). A
full paper, including title, author's name(s) and affiliation, mailing
address, telephone, fax and email of the principal author, should be
submitted by October 31, 2016 at the following web site: If you encounter any
difficulties during submission or if you require further information, please

Journal Publication:
Authors of selected papers in BICOB-2017 will be invited to submit
extended version of their papers for possible publication in the Journal
of Bioinformatics and Computational Biology (JBCB).


From: Zachary Kilpatrick <>
Date: Sun, Sep 11, 2016 at 10:43 PM
Subject: Conference: Math. Neuroscience, May 30-Jun 2, Boulder, CO, US

We are delighted to announce the 3rd International Conference on
Mathematical Neuroscience (ICMNS 2017), to be held at the Hotel
Boulderado in Boulder, Colorado from May 30 to June 2 (Tutorials:
May 30; Main Conference: May 31 - June 2).
*Abstract submission will open in October/November for both contributed
talks and posters.
*Student presenters can apply for travel awards funded by NSF, Burroughs
Wellcome, and SIAM.

Danielle Bassett (University of Pennsylvania)
Paul Bressloff (University of Utah)
Nicolas Brunel (University of Chicago)
Sophie Deneve (École Normale Supérieure)
Brent Doiron (University of Pittsburgh)
Ila Fiete (University of Texas)
Stefano Fusi (Columbia University)
Peter Thomas (Case Western Reserve University)
Taro Toyoizumi (Riken Brain Science Institute)
More TBA!

The conference will provide a forum for researchers to discuss current
mathematical innovations emerging in neuroscience. Tutorials will be
designed to attract and train young researchers on current methods in
mathematical neuroscience. The meeting will feature leaders in applied
mathematics and neuroscience that are developing new mathematical
techniques for understanding high-dimensional data sets, building models
to capture activity patterns and emergent computation, and working
closely with experimentalists to address targeted questions about brain


From: Dunnebacke, Lisa (NIH/OD) [C] <lisa.dunnebacke@NIH.GOV>

Date: Tue, Sep 6, 2016 at 10:32 PM
Resent-from: Raymond Mejía <>

Subject: Lecture Series: BD2K Guide to the Fundamentals of Data Sci....

The NIH Big Data to Knowledge (BD2K) program
( is pleased to announce The BD2K Guide
to the Fundamentals of Data Science, a series of online lectures given
by experts from across the country covering a range of diverse topics in
data science. This course is an introductory overview that assumes no
prior knowledge or understanding of data science.

This lecture series is a joint effort between the BD2K Training
Coordinating Center (BD2KTCC,, the BD2
Centers Coordination Center (BD2KCCC,, and the NIH
Office of the Associate Director of Data Science (ADDS, For up-to-date information about the
series and to view archived presentations, go to:

The series begins Friday, September 9th, and will run all year, once per
week, on Fridays from 12:00pm - 1:00pm ET. For additional event
information, contact Crystal Stewart (


From: Springer Mathematics <>
Date: Thu, Sep 8, 2016 at 3:40 AM
Reply-to: Springer <>
Subject: Springer: Japan Journal of Industrial and Applied Mathematics

Invitation to submit to the Japan Journal of Industrial and Applied

We invite you to take a closer look at the Japan Journal of Industrial
and Applied Mathematics

The Japan Journal of Industrial and Applied Mathematics is a Japan-based
international forum for the expression of new ideas and original
research across a range of mathematical topics.

The journal publishes articles offering new insight into mathematical
structures of phenomena in natural, social and industrial sciences,
content linking real-world phenomena and mathematics through modeling
and analysis, and research that impacts the development of mathematical


From: AIBS Public Policy Office <>
Date: Tue, Sep 6, 2016 at 11:23 AM
Subject: AIBS: Public Policy Report



From: Paolo Zuliani <>
Date: Thu, Sep 8, 2016 at 1:08 PM
Subject: PhD Position: Comp. Approach to Psoriasis..., Newcastle U, UK

A PhD studentship is available at Newcastle University, UK on "A
Computational Systems Biology Approach to Psoriasis Treatment".

The studentship is part of a recently awarded Rosetrees Trust grant on
computational modelling techniques for the development of personalised
psoriasis treatments. This interdisciplinary project will involve
collaboration with another PhD student and a clinical research fellow
based in the Institute of Cellular Medicine, and a post-doctoral
researcher based in Computing Science.

For more information and to apply, visit:


From: Gonçalo Marques <>
Date: Thu, Sep 8, 2016 at 4:22 AM
Subject: Research Grant: DEB Estimation Development, MARETEC, Portugal

In the framework Dynamic energy budget (DEB) theory the individual
organism can effectively be modelled in terms of a dynamical system and
is defined by a set of parameters. One of the crucial first steps when
using DEB is to estimate the parameters for the species of interest. A
call for a research grant to develop and test a new method for parameter
estimation to be included in the DEBtool package is now open. The
position is for one year at MARETEC - Marine, Environment and
Technology Center in IST, Lisbon. We are looking for someone with
interest in biology and mathematics/optimization (and Matlab

For more information please follow the link:


From: Dahari, Harel <>
Date: Thu, Sep 8, 2016 at 1:04 PM
Subject: Post-doc: Mod. Viral Hepatitis Dynamics, Loyola U Med, Chicago

In the Program for Experimental & Theoretical Modeling (PETM), Division
of Hepatology at Loyola University Chicago Medical Center, we conduct
research at the interface of experimental and theoretical biology with
an emphasis on viral infection dynamics and treatment response with a
particular focus on hepatitis viruses. We are looking for an
enthusiastic postdoctoral scientist with mathematical and statistical
skills and a strong interest in viral dynamics. Preference will be given
to candidates with research experience in the core areas of PETM; a
track record of publications; and commitment to work to the highest
standards. The candidate should have good programming skills, good
working knowledge of one or more mathematical, modeling or statistical
packages (e.g., Matlab, Monolix, R) and excellent English (both written
and oral). A PhD in applied mathematics, statistics, computer or
computational science, or mathematical biology is appropriate.
Interested?...please send your CV and names + email addresses of two
references to Dr. Harel Dahari (

Job posting:


From: Mingyang Lu <>
Date: Mon, Sep 5, 2016 at 7:57 PM
Subject: Post-doc: Comp. Mod.-Cancer Genetic Networks, Bar Harbor, US

Postdoctoral Position in Computational Modeling of Cancer Genetic

The Lu Lab at The Jackson Laboratory is currently seeking motivated and
innovative scientists for academic postdoctoral positions at the cutting
edge of computational systems biology. The Lu lab, in Bar Harbor, Maine,
is focused on the development and application of computational modeling
methods to study the operating mechanisms of cancer genetic networks.
The candidates will participate in a multidisciplinary environment and
have opportunities to interact with leaders of cancer biologists within
the Jackson Laboratory Cancer Center, the Jackson Laboratory for Genomic
Medicine at Farmington, Connecticut, and outside the institution.
Postdoctoral associates will have access to high-quality data measured
by state-of-the-art experimental techniques, high-performance computing
facilities and the largest repository of mouse resources in the world.

Applicants must have a Ph.D. (or equivalent degree) and a strong
background in quantitative biology, (bio)physics, systems biology or
related fields, expertise in a scientific programming language, and a
basic understanding of cancer genomics. Applicants must have a
commitment to solving biological problems and good communication skills.
Preference will be given to self-motivated and career-oriented
individuals. Exceptional candidates will have the opportunity to apply
to become a JAX Postdoctoral Scholar, a selective award addressing the
national need for research scientists who are accomplished in the
broadly defined fields of genetics and genomics. The award includes an
independent research budget, travel funds, and a salary above standard
postdoctoral scale (check
for details)

The Jackson Laboratory in Bar Harbor, Maine, USA, is recognized
internationally for its excellence in research, unparalleled mouse
resources, outstanding training environment characterized by scientific
collaboration and exceptional core services - all within a spectacular
setting adjacent to Acadia National Park. The Jackson Laboratory was
voted among the top 15 "Best Places to Work in Academia" in the United
States in a poll conducted by The Scientist magazine. The Jackson
Laboratory Cancer Center (JAXCC) is one of seven NCI-designated Cancer
Centers with a focus on basic cancer research.

To apply, please submit a cover letter, a current CV, a statement of
research interests and the names of three references online. Select link
for Bar Harbor position #5717 at

The Jackson Laboratory is an EOE/AA Employer. All qualified applicants
will receive consideration for employment without regard to race, color,
religion, sex, national origin, disability or protected veteran status.


From: Samantha Malcolm <>
Date: Sun, Sep 11, 2016 at 11:59 PM
Subject: Post-doc: Control of Invasive Species, U Canterbury, NZ

Postdoctoral Fellow - Large-scale control of invasive predators

Geospatial Research Institute
-Full-time (37.5 hours per week)
-3 year fixed-term position

The Geospatial Research Institute, in partnership with Te Punaha
Matatini, seeks a postdoctoral research fellow to work on
socio-ecological models of large-scale predator control. The New Zealand
government recently announced the ambitious goal of completely
eradicating exotic predators by 2050. To achieve this goal will require
a massive coordinated effort across the country's publicly and privately
owned land areas. Key stakeholders in this effort include the Department
of Conservation, regional councils, NGOs and private landowners. The
current "Cape-to-City" (C2C) predator control programme in Hawkes Bay
and its potential extension across four regions in the lower North
Island are the first steps towards predator-free New Zealand.

The aim of this research project is to use socio-ecological models to
assess the feasibility of scaling-up predator control outside
traditional conservation areas and to inform decisions about resource
allocation. These models will be combine ecological population dynamics
models with geospatial information on land ownership and data on
landowner attitudes to participation in pest control programmes.

As the successful candidate, you will be based in the Geospatial
Research Institute at the University of Canterbury in Christchurch, and
will also be part of Te Punaha Matatini via its early career researcher
network. You will have a PhD in mathematics, statistics or related
subject, as well as advanced skills in Geospatial Sciences, excellent
communication skills and experience in collaborating with researchers
from different disciplines. A formal background in biology or sociology
is not necessary, but an interest in these subjects is essential.

The Geospatial Research Institute Toi Hangarau, is a broadly-conceived
research institute at the University of Canterbury that conducts
innovative research across the geospatial research spectrum. Our mission
is to provide a national centre of gravity for geospatial research, to
provide the underpinning research that enables New Zealand to more fully
realize the benefits of spatial information technology.

For information about the Geospatial Research Institute Toi Hangarau
please visit us online at:

The closing date for this position is: Friday, 7 October 2016.

Applications for this position should include a cover letter, resume and
any additional attachments combined into one document and submitted

Should you wish to e-mail any additional attachments or have queries in
relation to the application process, please forward these to Nikki
Gibbs, Recruitment Coordinator,

Enquiries of an academic nature may be made to Associate Professor
Michael Plank (

For information about the range of benefits in joining UC please visit
us online at:

Internal candidates should apply via the Careers option in Employee

The University of Canterbury is an EEO employer and actively seeks to
meet its obligation under the Treaty of Waitangi.


From: Amy Gonsalves <>
Date: Fri, Sep 2, 2016 at 3:47 PM
Subject: Tenure-track: Biomathematics, San Diego State U, US

Assistant Professor of Biomathematics at San Diego State University
The Department of Mathematics and Statistics at SDSU has an open
position in Biomathematics at the assistant professor level. Exceptional
candidates may be considered for higher rank. The successful candidate
will develop original research in mathematical biology, which
complements SDSU areas of excellence in quantitative biology. The area
of specialty is open and may include complex biological systems,
theoretical and computational biophysics, computational biology,
population dynamics, epidemiology, or mathematical physiology to name a
few. He/She will have a strong record of research accomplishments,
employ state-of-the-art approaches in biomathematics, have experience
collaborating with researchers in other disciplines, show a strong
ability writing grants, have a solid plan for extramural funding. He/She
is also expected to demonstrate an ability to teach a wide variety of
courses at the undergraduate and graduate level in mathematics and
applied mathematics.

New techniques in biophysics and molecular biology are transforming
biology and biomedicine into stronger quantitative disciplines. The
complexity of biological systems, however, requires new mathematical and
computational approaches to accurate analyze, predict, and understand
the rapid growth of biological data. In recent years, SDSU has pursued
an ambitious expansion in several research areas of excellence that rely
on quantitative biology. To sustain and reinforce the lead in these
disciplines, SDSU aims to incorporate new talented faculty with a
strategic vision in modern applications of Biomathematics.

Successful candidates are expected to develop an active relationship
with members in the Department of Mathematics and Statistics as well as
the Computational Science Research Center. He/She should also establish
collaborations across campus, which may include SDSU centers of
excellence like the Viral Information Institute
(, Center for Clinical and Cognitive
Neuroscience (, Center for Sensorimotor
Neural Engineering (, or Center for Human
Dynamics in the Mobile Age ( The
candidate is expected to mentor students in interdisciplinary Master and
PhD programs such as Mathematics, Biology, Bioengineering, Computational
Science, and Statistics.

SDSU is a large, diverse, urban university and Hispanic-Serving
Institution with a commitment to diversity, equity, and inclusive
excellence. Our campus community is diverse in many ways, including
race, religion, color, sex, age, disability, marital status, sexual
orientation, gender identity and expression, national origin, pregnancy,
medical condition, and covered veteran status. We strive to build and
sustain a welcoming environment for all. SDSU is seeking applicants with
demonstrated experience in and/or commitment to teaching and working
effectively with individuals from diverse backgrounds and members of
underrepresented groups.

This position may also be eligible for the SDSU Building on Inclusive
Excellence (BIE) hiring program that creates additional faculty lines
for candidates who meet two or more of the criteria listed in To be considered for one of these
additional BIE hires, candidates should identify in their letter of
application how they meet two or more of the criteria.

The person holding this position is considered a "mandated reporter"
under the California Child Abuse and Neglect Reporting Act and is
required to comply with the requirements set forth in CSU Executive
Order 1083 as a condition of employment.

SDSU is a Title IX, equal opportunity employer and does not discriminate
against persons on the basis of race, religion, national origin, sexual
orientation, gender, gender identity and expression, marital status,
age, disability, pregnancy, medical condition, or covered veteran

Applicants should apply via Interfolio at Review of applications will begin
November 7, 2016 and will continue until the position is filled.
Incomplete applications are not guaranteed full consideration. Please
direct any questions to the Search Committee Chair, Vadim Ponomarenko,
at The appointment will start in Fall 2017.


From: Olson, Sarah D <>
Date: Sat, Sep 10, 2016 at 1:51 PM
Subject: Tenure-track: Math Biology, Worcester Polytechnic Institute, US

Position: Tenure Track Assistant Professor in the Department of
Mathematical Sciences at Worcester Polytechnic Institute to begin in
Fall 2017. The Department webpage can be found at
The broad focus is in those areas of applied mathematics that develop
and study models describing biological processes. In particular, we seek
candidates that are working to develop multiscale models that connect
several components to understand biological mechanisms. Application
areas of particular interest include but are not limited to cell
motility (related to cancer progression or tissue engineering),
neuromodulation or transduction, biomechanics, and biofluids dynamics.
We seek candidates who show mathematical strength as well as great
promise to contribute to WPI's growing interdisciplinary programs (e.g.,
Bioinformatics and Computational Biology). The successful applicant is
expected to lead a high quality research program and contribute to the
teaching mission of the department both at the undergraduate and
graduate levels.

Qualifications: Applicants must have a Ph.D. in Mathematics, or in a
related area. A degree or background in the biological sciences is a
plus. Teaching and postdoctoral research experience is preferred.

Salary, benefits and start-up funding are competitive and commensurate
with research experience and accomplishments. Qualified applicants
should submit a detailed curriculum vitae, a statement of specific
teaching and research objectives, and four letters of recommendation at
least one of which addresses teaching experience or potential, via math

Review of applications will begin on October 1, 2016 and will continue
until the position is filled. We encourage interested candidates to send
in their applications even if they cannot meet the October 1, 2016
proposed target. Founded in 1865, WPI is one of the nation's first
technological universities. A highly selective private university
located within an hour of Boston, WPI is consistently ranked among the
top 70 research institutions by US News & World Report. The university
is home to an innovative and intensive project-based curriculum that
empowers students with the knowledge and skills to address real world
problems around the globe. The Mathematical Sciences Department
currently has 28 tenured/tenure-track faculty members, 10 postdoctoral
scholars, and features an active Ph.D. program in Mathematical Sciences.
The department offers bachelor's degrees in Mathematical Sciences and in
Actuarial Mathematics, and master's degrees in Applied Statistics,
Applied Mathematics, Financial Mathematics, and Industrial Mathematics
(see The department has a strong reputation
for its cutting-edge interdisciplinary research and for its successful
programs addressing mathematical and statistical problems in industry.
Located in the heart of New England, WPI is surrounded by cultural and
recreational opportunities. The UMass Medical Center, a large number of
technology companies and many colleges and universities are located in
the immediate area making it ideal for two career families.


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