SMB Digest August 16, 2016 Volume 16 Issue 33
ISSN 1086-6566

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

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Issue's Topics:
Workshop: Transient Dynamics & Epilepsy, Sep 6, U Exeter, UK
Workshop: BioDynamics, Sep 7-9, U Exeter, UK
Newsletter: NIMBioS, U Tennessee, US
ToC: Systems Biology and Medicine, Volume 8, Issue 5
Post-doc: Computational Epigenetics, NIH, US
Research Fellow: Uncertainty Quan. for Healthcare, U Exeter, UK
NIH: New Funding Opportunities for H3Africa
SMBnet Reminders


From: Warren, Sarah <>
Date: Fri, Aug 12, 2016 at 5:11 AM
Subject: Workshop: Transient Dynamics & Epilepsy, Sep 6, U Exeter, UK

Workshop on Transient Dynamics and Epilepsy
Tuesday 6 September 2016, 10.00 - 17.00
University of Exeter

You are invited to a one-day workshop focused around identifying
mathematical challenges involving transient network dynamics and their
application to epilepsy.

The aims of this EPSRC-funded workshop are to:
-Present the latest advances in epilepsy research and the theory of
transient dynamics on networks.
-Make connections from mathematical theory to health related
applications, in particular epilepsy.
-Provide an opportunity to develop a network of collaborative links
between computational neuroscientists and clinical researchers studying

For more information and to register please visit:


From: Warren, Sarah <>
Date: Thu, Aug 11, 2016 at 3:20 AM
Subject: Workshop: BioDynamics, Sep 7-9, U Exeter, UK

BioDynamics Workshop 2016
7-9 September 2016
University of Exeter, UK

We would like to invite you to the next BioDynamics Workshop, which will
take place in Exeter on 7-9 September 2016. This will be the third in a
series of international workshops designed to bring together biologists,
mathematicians, clinicians, physicists, and computer scientists who are
interested in dynamics and networks in the biological and medical
sciences. BioDynamics 2016 promises to provide an exciting opportunity
for scientists to present both methods and data in a multidisciplinary
forum and hear how interdisciplinary collaborations can provide major
conceptual advances in our understanding of complex biomedical systems.

Confirmed keynote speakers include:

Professor Nick Talbot FRS, University of Exeter, United Kingdom
An integrated model of plant infection by the rice blast fungus
Magnaporthe oryzae

Professor Peter Hunter FRS, The University of Auckland, New Zealand
Linking the Physiome Project with healthcare

Professor Gareth Leng FRSE, The University of Edinburgh, United Kingdom
The neuroendocrine brain: modeling model systems

Dr Greg Worrell, Mayo Clinic, Rochester, Minnesota, United States
Spatial and temporal prediction of epileptic seizures

Professor Angela McLean FRS, University of Oxford, United Kingdom
Using viral sequences to learn viral dynamics

Professor Philip Ingham FRS, Nanyang Technological University, Singapore
Spatio-temporal dynamics of cell fate specification and differentiation
in a vertebrate embryo

For more information visit:


From: NIMBioS <>
Date: Thu, Aug 11, 2016 at 10:36 AM
Subject: Newsletter: NIMBioS, U Tennessee, US

For the bi-monthly newsletter from the National Institute for
Mathematical and Biological Synthesis, go to


From: Systems Biology and Medicine <>
Date: Fri, Aug 12, 2016 at 5:29 PM
Subject: ToC: Systems Biology and Medicine, Volume 8, Issue 5



From: Sung, Mia (NIH/NIA/IRP) [E] <>
Date: Tue, Aug 9, 2016 at 6:45 PM
Subject: NIH: Post-doc: Computational Epigenetics, NIH, US

Department of Health and Human Services
National Institutes of Health, National Institute on Aging

Postdoctoral opportunity in Computational Epigenomics at the National
Institutes of Health, USA

A competitive postdoctoral fellowship is available, pending approval, at
the National Institute on Aging, NIH, for developing computational
methods to analyze high-throughput sequencing- based chromatin assays.
The successful applicant will work in the laboratory of Dr. Myong-Hee
Sung, Transcription Systems Dynamics and Biology Unit located on the
Johns Hopkins Bayview campus, Baltimore, Maryland.

We are seeking highly motivated recent Ph.D. scientists who are
interested in investigating outstanding questions in epigenomics using
statistical and computational tools. An ideal candidate will have a
Ph.D. degree in mathematics, physics, engineering, or a related
quantitative discipline, and has some knowledge in molecular biology or
genomics methods. Proficiency in one or more programming languages such
as C++, Python, R, MATLAB, Perl is required, in addition to familiarity
of commonly used computational genomics tools. To apply, please send a
cover letter, curriculum vitae, and contact information for 3 references

Relevant publications:
-Sung MH et al. Genome-wide footprinting: ready for prime time? Nature
Methods 2016 (PMID: 26914206)
-Sung MH et al. DNase footprint signatures are dictated by factor
dynamics and DNA sequence. Molecular Cell 2014 (PMID: 25242143)
-Kieffer-Kwon KR et al. Interactome maps of mouse gene regulatory
domains reveal basic principles of transcriptional regulation. Cell 2013
(PMID: 24360274)

About training at NIH: Postdoctoral training in the NIH Intramural
Research Program (IRP) provides the opportunity for recent doctoral
degree recipients to enhance their research skills in the resource-rich
National Institutes of Health (NIH) environment, which consists of more
than 1200 laboratories/research projects located on the main campus in
Bethesda, MD and the surrounding area as well as in Baltimore and
Frederick, MD; Research Triangle Park, NC; Hamilton, MT; Framingham, MA;
and Detroit, MI. Trainees pursue basic, translational, and clinical
research free from the demands of obtaining grants and teaching,
although opportunities to do both are available. At the NIH, postdocs
work in a highly collaborative research environment with leading
scientists and clinicians. The postdoctoral community at the NIH is
large (approximately 4,000 strong) and vibrant. Trainees come from
across the U.S. and around the world. Support for international postdocs
is provided by the NIH Division of International Services.

Eligibility: To be eligible for postdoctoral training in the NIH IRP,
individuals must hold a doctoral degree (PhD, MD, DDS, or the
equivalent) and have no more than five years of relevant research
experience since receipt of their most recent doctoral degree. U.S.
citizens and permanent residents are appointed to Postdoctoral
Intramural Research Training Awards (IRTAs); citizens of other nations
are appointed as Visiting Fellows.

Stipend and Benefits: The stipends for postdoctoral trainees at the NIH
are adjusted yearly; with supplements for prior experience, multiple
degrees, and expertise in areas of current interest to the NIH such as
mathematics, engineering, chemistry, and bioinformatics. Note that
stipends for Postdoc IRTAs and Visiting Fellows are identical. Benefits
include health insurance for the trainee and his/her family, and support
for coursework related to the trainee's research and travel to meetings
is often available. In addition, the NIH Fellows Committee (FelCom) and
the NIH Office of Intramural Training & Education (OITE) sponsor a wide
range of career development and social activities. The OITE includes an
Office of Postdoctoral Services, a Career Services Center and Career

DHHS and NIH are Equal Opportunity Employers. The NIH is dedicated to
building a diverse community in its training and employment programs.


From: Warren, Sarah <>
Date: Thu, Aug 11, 2016 at 3:20 AM
Subject: Research Fellow: Uncertainty Quan. for Healthcare, U Exeter, UK

Research Fellow in Uncertainty Quantification for Healthcare

We are seeking a Research Fellow to join the recently funded EPSRC
Centre for Predictive Modelling in Healthcare, a 2M award which brings
together outstanding scientists from our Systems Biomedicine, Dynamics
Systems and Statistical Sciences research groups. With an additional 3M
in research funding, the interface between mathematics, computer science
and healthcare is one of the most rapidly expanding areas within the
University, and the successful candidate will join a research team
currently consisting of 14 PDRAs and 10 PhD students, where they will be
collocated with researchers from the Wellcome Trust ISSF funded Centre
for Biomedical Modelling and Analysis, housed in our state of the art
Research Innovation Learning and Development (RILD) building.

The successful candidate will work on a project entitled "Data-Model
Fusion and Uncertainty Quantification". They will be mentored by the
Centre Director Professor John Terry and will work on a day-to-day basis
with Professor Peter Challenor and Dr Marc Goodfellow. The role is
available from 01 November 2016, or a mutually agreeable date very soon
thereafter, for a period of 36 months. Individuals who successfully
secure fellowship funding during their appointment will be considered
for an open ended academic appointment. The primary focus of the project
will be on techniques to develop Bayesian emulators for uncertainty
quantification, including efficient experimental design and techniques
to estimate model structure and parameters from observations. These
methods will be developed, in collaboration with the candidate, within
the Centre with a view to novel healthcare applications, for example in
cardiac arrhythmias, neurological disorders or endocrine malfunction.
The successful candidate will have a strong background in all or most
of: Gaussian processes, uncertainty quantification, machine learning,
methods for model parameter inference from observations and constructing
mathematical models of biological or clinical data, and have a
demonstrable interest in interdisciplinary collaboration. Applicants
should hold, or be about to obtain, a PhD in mathematics, physics or a
related discipline.

For full details visit:

The closing date for applications is 26 August 2016. It is anticipated
that interviews will take place in the week commencing 19 September


From: Murcia, Ellie (NIH/OD) [E] <murciae@OD.NIH.GOV>
Date: Sat, Aug 13, 2016 at 8:36 AM
Resent-from: Raymond Meja <>
Subject: NIH: New Funding Opportunities for H3Africa

New NIH Funding Opportunities for H3Africa

Human Heredity and Health in Africa(H3Africa
<>) aims to enhance the
capacity for genomics and environmental health research, in Africa by
African scientists, and to understand the genetic and environmental
factors that determine disease susceptibility.

H3Africa was recently approved for a second 5 years of funding and is
soliciting applications<>
for seven different RFAs:

-Human Heredity and Health in Africa (H3Africa):
Ethical, Legal, and Societal Issues (ELSI) Research Program

-Human Heredity and Health in Africa (H3Africa): Ethical,
Legal, and Societal Issues (ELSI) Collaborative Centers

-Human Heredity and Health in Africa (H3Africa): Research Projects

-Human Heredity and Health in Africa (H3Africa): Collaborative Centers

-Human Heredity and Health in Africa (H3Africa): Coordinating Center

-Human Heredity and Health in Africa (H3Africa): Informatics Network

-Human Heredity and Health in Africa (H3Africa):
Global Health Bioinformatics Research Training Program

Only Investigators at African Institutions are eligible to apply, and
awards will be made directly to the African institution. However,
investigators at non-African Institutions may participate as
collaborators. Applications are due November 15, 2016.

The NIH Common Fund<> (formerly the NIH
Roadmap) encourages collaboration and supports a series of exceptionally
high impact, trans-NIH programs. These programs are supported by the
Common Fund, and managed by the NIH Office of the Director in
partnership with the various NIH Institutes, Centers, and Offices.

The National Institutes of Health (NIH) - "The Nation's Medical Research
Agency" - includes 27 Institutes and Centers and is a component of the
U. S. Department of Health and Human Services. It is the primary federal
agency for conducting and supporting basic, clinical and translational
medical research, and it investigates the causes, treatments and cures
for both common and rare diseases. For more information about the NIH
and its programs, visit the NIH website<>.


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