SMB Digest     July 12, 2016   Volume 16 Issue 28
ISSN 1086-6566

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

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Issue's Topics:
         Workshop: COMBINE 2016, Sep 19-23, deadline extended
         Workshop: EMBnet and NETTAB 2016, Oct 25-26, deadline extended
         Conference: Computational Science, SIAM, Feb 27-Mar 3, Atlanta
         PhD Position: Disease Modelling, PharMetrX, Germany
         Post-doc: Infectious Disease Modeling, North Carolina State U
         Post-doc: Whole-cell Modeling, Mt Sinai, New York City
         Post-doc: Computational Epidemiology, Simon Fraser U, Canada
         Lecturer/Senior Lecturer: Systems Genomics, U Melbourne
         Tenured/Tenure-track: Math Biology, Virginia Commonwealth U
         NSF: Funding Opportunity, Quantum Information Science
         NSF: Funding Opportunity, Security and Trustworthy Cyberspace
         SMBnet Reminders


From: Paolo Zuliani <>
Date: Mon, Jul 11, 2016 at 9:48 AM
Subject: Workshop: COMBINE 2016, Sep 19-23, deadline extended

COMBINE 2016: 7th Computational Modeling in Biology Network Workshop
19-23 September 2016, Newcastle upon Tyne, UK

The deadline for the submission of abstracts and scholarship
applications has been extended until July 15, 2016.

For additional information, see


From: Paolo Romano <>
Date: Wed, Jul 6, 2016 at 5:25 AM
Subject: Workshop: EMBnet and NETTAB 2016, Oct 25-26, deadline extended

Reproducibility, standards and SOP in Bioinformatics
A combined CHARME, EMBnet and NETTAB 2016 Workshop
October 25-26, 2016, Rome, Italy

The deadline for the submission of abstracts for oral communications has
been extended until July 15, 2016.

For additional information, see


From: Jan S Hesthaven <>
Date: Mon, Jul 11, 2016 at 12:38 AM
Subject: Conference: Computational Science, SIAM, Feb 27-Mar 3, Atlanta

SIAM Conference on Computational Science (SIAM CSE'17)
Location: Atlanta, Georgia, USA
Dates: February 27-March 3, 2017

The call for participation for this conference is now available. Please
visit for more information.

August 1, 2016: Minisymposium proposals
August 29, 2016: Abstracts for contributed and mini symposium speakers
August 29, 2016: Abstracts for contributed posters and minisymposterium
posters (thematic groups)
August 19, 2016: SIAM Student Travel Award and Post-doc/Early Career
Travel Award Applications
Detailed guidelines for the preparation of abstract, minisymposia and
poster submissions are available at

We especially encourage submissions of posters to CSE17, where we will
have expanded poster sessions, including demos and thematic groups of
posters (or poster minisymposia), as well as poster prizes. CSE17 poster
sessions will be great opportunities for networking and interacting in
depth about research topics. More details are below and on the call for

Contact SIAM Conference Department at with any
questions about the conference.


From: Cornelia Boehnstedt <>
Date: Mon, Jul 11, 2016 at 7:53 AM
Subject: PhD Position: Disease Modelling, PharMetrX, Germany

PhD research fellowship: Pharmacometrics & Computational Disease

The Graduate Research Training Program PharMetrX: Pharmacometrics &
Computational Disease Modelling is an interdisciplinary PhD program
bridging pharmacy and mathematics. PharMetrX provides its graduate
students a unique opportunity to experience research in drug development
and optimising drug therapy.

PharMetrX offers:
- a transdisciplinary research environment and research program
- a competitive 3.5 years research fellowship
- a structured research training curriculum of specifically designed
academic and industrial modules
- a joint supervision of the scientific progress by both program chairs
- an individual research and development plan
- an individual mentorship from one of the industry partners

We are currently inviting applications to start the PharMetrX PhD
program in March 2017. PharMetrX is open to candidates with a university
degree in pharmacy, mathematics/statistics, natural sciences or

Deadline for applications: September 15th, 2016.
For details see

PharMetrX is a joint program of the Freie Universität Berlin and the
Universität Potsdam, supported by several global research-driven
pharmaceutical companies.


From: Cristina Lanzas <>
Date: Wed, Jul 6, 2016 at 3:39 PM
Subject: Post-doc: Infectious Disease Modeling, North Carolina State U

One postdoctoral associate position on infectious disease modeling is
available in Cristina Lanzas' group (Department of Population Health and
Pathobiology, North Carolina State University). Applicants with a
background in mathematical modeling of infectious diseases and/or
population biology are highly encouraged to apply.

The successful candidate will join an interdisciplinary group modeling
Clostridium difficile dynamics in health-care settings. Clostridium
difficile is one of the most common health-care associated pathogens.
The group is developing mean-field and agent-based models. The
postdoctoral fellow will ideally work in expanding existent models to
integrate multiple scales and data sources (e.g. omic, clinical and
epidemiological data), linking C. difficile within host dynamics and

The postdoctoral associates shall have a Ph.D. degree in a relevant
quantitative discipline (ecology, epidemiology, engineering, applied
mathematics, statistics and related fields) and have a deep interest in
interdisciplinary collaboration, strong quantitative skills and good
oral and writing skills are expected. The applicants must have
experience in R and/or MATLAB. Previous experience developing and
implementing agent-based models and/or multi-scale models is desirable.
The salary will be commensurate with the qualifications and experience
of the individuals. Review of applications will begin July 11th and will
continue until a suitable candidate is identified.

Interested applicants should submit a letter of intent, curriculum vitae
and the names and contact information for three references to


From: Jonathan Karr <>
Date: Mon, Jul 11, 2016 at 3:38 PM
Subject: Post-doc: Whole-cell Modeling, Mt Sinai, New York City

The Karr Lab at the Institute for Genomics & Multiscale Biology at the
Icahn School of Medicine at Mount Sinai is seeking talented, ambitious
researchers to develop cutting-edge whole-cell computational models of
individual cells, as well as new technologies to enable larger and more
accurate whole-cell models. Despite the explosion of experimental data,
we do not understand the details of how phenotype arises from genotype
and the environment. We are developing whole-cell computational models
which comprehensively predict how behavior emerges from the molecular
level by representing all of the biochemical activity inside cells. Our
goal is to use whole-cell models to transform bioengineering and
medicine into rigorous, quantitative disciplines. For example, we
believe that whole-cell models could enable bioengineers to design
microbial genomes for a variety of industrial applications, as well as
enable physicians to tailor medical therapy to individual patients. Our
research is highly interdisciplinary, involving systems biology,
genomics, bioinformatics, data integration, parallel simulation,
optimization, software engineering, and data visualization, and highly

We are currently looking for team members in three areas:
-Human whole-cell modeling. The candidate will develop a whole-cell
model of human embryonic stem cells and use the model to gain insights
into pluripotency maintenance among other fundamental cell behaviors.
This will include aggregating and organizing experimental data,
designing submodels, integrating submodels, fitting models, validating
models, analyzing simulations, and using models to generate new
hypotheses. There are also many opportunities to contribute to the
development of new whole-cell modeling methods and tools. The candidate
will work closely with our team at Mount Sinai, including our
experimental collaborators.
-Bacterial whole-cell modeling. The candidate will lead the development
a whole-cell model of the reduced bacterium Mycoplasma pneumoniae and
use the model to design more predictable, faster-growing, and
non-virulent strains that could serve as chassis for future
bioengineering such as a bacterial-based drug synthesis and delivery
system. This includes expanding the scope of whole-cell models;
improving the accuracy of whole-cell models; using new types of genomic
data to train whole-cell models; systemizing the construction,
representation, and simulation of whole-cell models; and developing new
methods to use whole-cell models to design genomes. The candidate will
work closely with our team at Mount Sinai, as well as our Minicell
consortium experimental collaborators: Maria Lluch-Senar and Luis
Serrano at the Center for Regulatory Genomics in Spain; Yonaton Arfi,
Alain Blanchard, Carole Lartigue, and Pascal Sirand at the National
Institute for Agricultural Research in France; and Jörg Stülke at the
University of Göttingen in Germany. This project is supported by the NSF
and ERASynBio.
-Whole-cell modeling methods and technology development. To enable
larger whole-cell models, including models of human cells, the
Postdoctoral Fellow/Engineer will develop new methods for simulating
large, multi-algorithmic whole-cell models. This will include developing
a new algorithm for concurrently integrating mathematically
heterogeneous submodels that share state and implementing this as a
high-performance, parallel simulation software system. The Postdoctoral
Fellow/Engineer would work closely with our team at Mount Sinai, as well
as our parallel simulation collaborators Drs. Peter Barnes and David
Jefferson at Lawrence Livermore National Laboratory and our broader
international team of collaborators. The Postdoctoral Fellow/Engineer
would also have many opportunities to work with our team to build and
analyze whole-cell models.

Desired skills/experience
Whole-cell modeling is a highly interdisciplinary problem. Consequently,
we're looking for people with a broad range of skills and experience.
The ideal candidate has the following skills. Applicants with related
experience are also encouraged to apply.
-PhD in computational biology or related field;
-Strong experience in dynamical and/or genome-scale modeling;
-Broad knowledge of cell biology, genomics, mathematics, and computer
-Deep commitment to innovation and desire to tackle the most challenging
-Abilities to solve challenging problems by thinking creatively,
integrating diverse concepts, and pushing through barriers;
-Passion for transforming bioengineering and medicine;
-Excellent oral and written communication skills; and
-Abilities to work independently and within a team.

Commensurate with experience and education.

All employees are eligible for medical, dental, and health insurance.
Subsidized housing is available for postdoctoral fellows.

About the Institute for Genomics & Multiscale Biology and the Icahn
School of Medicine at Mount Sinai
The Icahn Institute for Genomics & Multiscale Biology is a leader in
basic and translational genomic and computational biology research. The
institute's multidisciplinary researchers bring state-of-the-art genomic
technologies together with advanced computational analyses to discover
new disease mechanisms, develop new diagnostics, and identify new drug
targets. The institute is a highly collaborative and interdisciplinary
environment. Please see the institute's website for more information.

The Icahn School of Medicine at Mount Sinai is a world leader in
translational medicine. The school's multidisciplinary research
institutes foster collaboration along a seamless continuum from the
laboratory to patient care. State-of-the-art laboratories support
groundbreaking research, and abundant clinical venues offer superb
patient care and training.

More information
Please see our website ( or contact
Jonathan Karr (

How to apply
Please email a cover letter outlining your research interests and a CV
to Jonathan Karr (


From: Leonid Chindelevitch <>
Date: Mon, Jul 11, 2016 at 9:29 PM
Subject: Post-doc: Computational Epidemiology, Simon Fraser U, Canada

Are you a creative, motivated, and talented researcher with a background
in mathematics, computer science, quantitative biology or operations
research? Do you have an interest in making a difference in infectious
disease research? Then this is the opportunity for you!

Our group explores a range of problems centred around the study of
infectious disease genomes. Our projects straddle computational and
systems biology, epidemiology, and public health policy; our current
projects include:
-an integrative analysis of genomic markers (SNPs, copy numbers, MLST,
rearrangements), with the goal of identifying epidemiologically-related
strains during a bacterial outbreak
-analysis and visualization of genetic, geographic and temporal patterns
in an outbreak, with the goal of identifying transmission hotspots and
risk factors for tuberculosis
-identification and dynamical modelling of bacterial diversity within
ticks, with the goal of understanding the ecological processes driving
the evolution of Lyme disease pathogens

Our North American collaborators include the British Columbia Centre for
Disease Control (BC CDC), the British Columbia Centre for Excellence in
HIV/AIDS (BC-CfE), and the New York City Department of Health and Mental
Hygiene (NYC DOHMH). We also collaborate internationally with groups in
the United Kingdom, France, Germany, India, China and South Africa.

The ideal candidate for this position will have:
-a PhD in a quantitative discipline (mathematics or computer science
preferred) by August 2016
-a strong publication record (at least two published papers and one
other in preparation)
-an interest in designing models and algorithms for solving biological
or epidemiological problems
-advanced knowledge of at least one of: C++, Java, MATLAB, Python, R
-expertise in discrete mathematics, combinatorial optimization, machine
learning or statistics
-experience in designing and building robust computational pipelines in
a Unix-like environment

A complete application should include a statement of interest, a CV, the
names of 2 references, and a link to the repository of a programming
project you took part in. Please submit applications to Leonid
Chindelevitch,, with "Postdoctoral fellowship" in the
subject line. All applications will be considered; preference is given
to Canadian citizens or permanent residents. The starting date is
September 1, 2016, and the position will remain open until filled.


From: advertising-hr <>
Date: Sun, Jul 10, 2016 at 8:33 PM
Subject: Lecturer/Senior Lecturer: Systems Genomics, U Melbourne


School of BioSciences, Faculty of Science, The University of Melbourne

Salary: AUD95,434 - AUD113,323 p.a. (Level B) or AUD116,901 -
AUD134,792 p.a. (Level C), plus 17% superannuation. Level of appointment
is subject to qualifications and experience.

The School of BioSciences is seeking to recruit an excellent researcher,
with a commitment to teaching and other academic duties, in the area of
systems genomics, defined broadly to include a range of
computation/statistics-based research on any aspects of the processes
leading from genotype to phenotype. The new post is associated with the
appointment of Professor D Balding, who is Professor of Statistical
Genetics jointly in the Schools of BioSciences and of Mathematics &
Statistics, and Director of the University's Centre for Systems
Genomics. The successful applicant will be expected to join the Centre,
which has an interdisciplinary focus on the application of
maths/stats/computing techniques to genomic profiling data to help
understand genotype-to-phenotype processes in humans and other
organisms, including microbes and the host-microbe interaction, as well
as the roles of other factors in the cellular, tissue and external

The successful applicant will be expected to undertake research and
student supervision in cutting-edge methods using large-scale datasets
to help understand the functions of genomes, especially at a systems
level. The successful applicant will have the opportunity to contribute
to and benefit from the development of the Centre, have use of research
data generated by collaborators, and have access to the Centre's
computing resources and integrative profiling lab. Further wet-lab
resources are available if required. The appointee will be expected to
develop and deliver genomics and/or computational biology subjects for
life sciences students, and possibly (depending on experience and
qualifications) also to students in other disciplines.

Close date: 10 Aug 2016

For position information and to apply online go to, click on the relevant option
(Current Staff or Prospective Staff), and search under the job title or
job number 0039325.


From: Rebecca Segal <>
Date: Tue, Jul 5, 2016 at 2:55 PM
Subject: Tenured/Tenure-track: Math Biology, Virginia Commonwealth U

Position: One senior faculty position (9-month) as Professor or
Associate Professor of Mathematics in the Department of Mathematics and
Applied Mathematics beginning August 16, 2017. The Department and
University Web pages may be found at and  The Ph.D. program Web page may be found at

Responsibilities of Position: Maintain a vigorous research program and a
record of excellent teaching at both the undergraduate and graduate
levels.  Assume a leadership role in the Ph.D. program in Systems
Modeling and Analysis.

Qualifications: A Ph.D. in Mathematics or Applied Mathematics, or
related field, is required at the time of the appointment.  The
applicant should be internationally recognized in areas related to
Mathematical Biology, and must already be tenured at their current
institution.  Preference will be given to candidates with a proven track
record of external funding and Ph.D. student advisement. Applicants must
have a record of successful teaching, as well as experience with working
in and fostering a diverse faculty, staff, and student environment, or
the commitment to do so.

The Department: The mission of the Department of Mathematics and Applied
Mathematics is to offer a strong undergraduate and graduate education,
with an increasing focus on the development of cross-disciplinary
efforts that will prepare our students for real-world applications and
stimulating employment and career opportunities. Key current objectives
of the department include the continued development of our Ph.D.
program, which emphasizes applications of mathematics to the medical and
biological sciences and research in both applied and theoretical
discrete mathematics, the improvement of student outcomes in our lower
level courses, and the continued strengthening of our department's track
in secondary education preparation. We are looking for ambitious faculty
members to help grow and strengthen the department by expanding
teaching, research, and grant activity.  We are excited about the
opportunities to grow in these areas and are particularly interested in
mathematicians with similar interests.

How to Apply for the Position: To apply, candidates must submit
electronically through the
following: a cover letter that clearly delineates how they meet the
qualifications outlined above, a current curriculum vitae, and contact
information for four references. In addition, candidates must submit
electronically through the following: a cover
letter, an AMS Standard Cover Sheet, a current curriculum vitae, and
detailed teaching and research statements. Applicants must also have
four letters of recommendation, of which one must address the
applicant's effectiveness as a teacher, submitted electronically through

Applicants must be eligible to work in the U.S.A. Applications will be
considered until the position is filled; however, applications received
by September 15, 2016, will be given priority.

"Virginia Commonwealth University is an equal opportunity, Affirmative
Action University providing access to education and employment without
regard to age, race, color, national origin, gender, religion, sexual
orientation, veteran's status, political affiliation or disability."


From: Henry Warchall <>
Date: Thu, Jul 7, 2016 at 1:19 PM
dmsnews <>
Subject: NSF: Funding Opportunity, Quantum Information Science

Information about a new cross-cutting NSF activity is now available:
Connections in Quantum Information Science (CQIS)

Please see
for details.

From the Program Synopsis:
Demands for novel computers, secure communication, and higher resolution
sensors have pushed technology beyond the scaling limits of classical
technologies, into the area of Quantum Information Science (QIS).
Research in QIS spans many disciplines, relying on advances in physical
sciences, materials science, computer science, mathematics, and
engineering. Support is needed to advance this fundamental research and
catalyze development of innovative technologies in QIS that will
strongly benefit the nation's continued scientific and economic health
as well as its future workforce. The Connections in Quantum Information
Science (CQIS) program will examine concepts and paradigms harnessing
fundamental quantum properties for exploration of new scientific
frontiers and development of new technologies that lie at the interface
of traditional scientific disciplines. This will provide the fundamental
knowledge and tools necessary to predict and control the quantum
behavior of molecules, atoms, and electrons, creating entirely new
material assemblies, devices, and engineering systems.


From: Henry Warchall <>
Date: Fri, Jul 8, 2016 at 1:45 PM
dmsnews <>
Subject: NSF: Funding Opportunity, Security and Trustworthy Cyberspace

An updated NSF program solicitation is now available: Secure and
Trustworthy Cyberspace (SaTC)

Please see for

Proposal Submission Windows:
LARGE and MEDIUM Projects:  October 12, 2016 - October 19, 2016
SMALL Projects:  November 2, 2016 - November 16, 2016
CYBERSECURITY EDUCATION Projects:  December 1, 2016 - December 15, 2016

From the Program Synopsis:
The SaTC program welcomes proposals that address cybersecurity and
privacy, and draw on expertise in one or more of these areas: computing,
communication, and information sciences; engineering; economics;
education; mathematics; statistics; and social and behavioral sciences.
Proposals that advance the field of cybersecurity and privacy within a
single discipline or interdisciplinary efforts that span multiple
disciplines are both encouraged.


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