SMB Digest June 17, 2015 Volume 15 Issue 24
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
Note:
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Issue's Topics:
Workshop: Porous Media Modelling..., Aug 27-28, U Dundee
Conference: Computational Modeling of..., Oct 6-7, Cambridge U
Workshop: Bringing Maths to Life, Oct 19-21, Naples, Italy
International Congress: Glaucoma, Oct 29-31, Milan, Italy
Conference: Synthetic Biology, Dec 14-18, Paris
PhD Position: Projecting Effects of Vaccination..., Dutch...
PhD Positions: Mathbio/Epid&Ecol/Network..., RMIT U, Melbourne
Post-doc: Math/Biostats/Epidemiology, Norwegian U Life Sciences
Tenure-Track: Life Sciences, Centrum Wiskunde &..., Netherlands
NIGMS: MIRA Pilot..., PRAT Symposium, Funding Opportunities,...
SMBnet Reminders
----------------------------------------------------
From: Raluca Eftimie <reftimie@maths.dundee.ac.uk>
Date: June 16, 2015 at 5:45:58 AM
Subject: Workshop: Porous Media Modelling..., Aug 27-28, U Dundee
We are pleased to announce the International Workshop on Porous Media
Modelling in Biological Processes: Perspectives on Analytical and
Computational Methods Enabling Data Inversion, 27-28 August 2015,
University of Dundee, Dundee.
The workshop aims to bring together leading experts and young
researchers in the areas of both porous media and theoretical and
computational modeling to identify appropriate methods enabling data
inversion and model calibration for complex biological processes. It is
hoped that the intra-disciplinary ideas presented in this workshop will
give rise to a synergetic effect in these research areas related to
porous media, ultimately leading to a deeper understanding of the
current limitations and future perspectives on mathematical modelling
approaches suitable for data inversion.
For further information on this event, you may visit the workshop
website: http://www.maths.dundee.ac.uk/pmmbp/
or contact directly the organisers: Dr. Dumitru Trucu
(trucu@maths.dundee.ac.uk) and Dr. Raluca Eftimie
(reftimie@maths.dundee.ac.uk).
----------------------------------------------------
From: Filippo Castiglione <filippo.castiglione@gmail.com>
Date: June 10, 2015 at 8:14:25 AM
Subject: Conference: Computational Modeling of..., Oct 6-7, Cambridge U
1st International Conference on Computational Modeling of Metabolic
Health, Inflammation and type 2 Diabetes (MMH 2015)
October 6-7, 2015
Cambridge, United Kingdom
website: www.mission-t2d.eu/Workshop
IMPORTANT DATES:
Abstract Submission: 20 July, 2015
Authors Notification: 31 July, 2015
Registration: 15 September, 2015
CALL FOR PAPERS
MMH 2015 aims at bringing together researchers from the biological,
physical, computational and mathematical sciences who have a common
interest in the investigation of diabetes and inflammatory diseases
through modeling. We welcome those who are interested in mathematical
(discrete and continuous), computer science and logic-based modeling,
software and hardware tools developers.
This year's conference will take place in the Computer Laboratory at
Cambridge University in the UK.
Topics that will be addressed by MMH 2015 include but are not limited
to:
-Mathematical and computational models of metabolism
-Models of Inflammation and Immune system
-Modeling of metabolic pathways and responses
-Systems biology of metabolic disorders, obesity and type 2 diabetes
-Biomedical engineering and clinical informatics of diabetes
Prospective authors are invited to submit a one-page abstract in
electronic format via email. Submitted abstracts will be selected for
oral presentation and for a poster session which includes five-minutes
talk.
Authors of selected abstracts will be invited to submit full research
papers to be published in a special issue of a peer reviewed
international journal (to be announced).
INVITED SPEAKERS
-Franco Celada, New York University School of Medicine, New York, NY,
USA
-Caroline Colijn, Imperial College, London, UK
-Claudio Franceschi, University of Bologna, Bologna, Italy
-Reinhard Laubenbacher, University of Connecticut Health Center,
Farmington, CT, USA
-Philip Maini, University of Oxford, UK (to be confirmed)
-Ben van Ommen, Netherlands Organisation for Applied Scientific Research
(TNO), Zeist, the Netherlands
-Marco Viceconti, University Sheffield & Insigneo Institute for
In Silico Medicine, Sheffield, UK
ORGANIZATION
-Pietro Liò, University of Cambridge, Cambridge, UK
-Filippo Castiglione, National Research Council of Italy, Rome, Italy
-Paolo Tieri, National Research Council of Italy, Rome, Italy
-Gianluca Ascolani, University of Cambridge, UK
Contacts: pl219@cam.ac.uk, f.castiglione@iac.cnr.it
For submission of abstracts for presentation, registration and fees see
the conference website.
Sponsored by the EU project MISSION-T2D
----------------------------------------------------
From: Bringing Maths to Life (Organizing Secretariat) <info@bmtl.it>
Date: June 15, 2015 at 4:52:20 AM
Subject: Workshop: Bringing Maths to Life, Oct 19-21, Naples, Italy
It is a pleasure to invite you for the 2nd edition of the Workshop
Bringing Maths to Life (BMTL), which will be held October 19-21, 2015,
in Naples at the Centro Congressi Federico II. This workshop lets
biologists and mathematicians join forces to address key areas in
biology that face demanding mathematical challenges. Discussing existing
cases to identify gaps or to share existing solutions should help these
disciplines in successfully linking up.
Important deadlines:
June 30th, 2015 - Early registration and booking accommodation
June 30th, 2015 - Submission of abstracts
Topics include:
(i) Dynamics of genomes - Technological advances that facilitate
whole-genome and whole-population sequencing, coupled with experiments
that 'watch' evolution in action, have brought insights into studies of
mutation rates and genome evolution. In this session, we discuss the
molecular mechanisms and evolutionary processes that shape the structure
and function of genomes and that govern genome dynamics.
(ii) Dynamics of pattern recognition - Motif searching in DNA, RNA and
proteins is a key process to discover emergent properties of cells,
tissues and organisms. It requires always more complex and
comprehensive algorithms that can incorporate the growing up to date
information from experimental sets. This session will provide an
overview on current methods for motif searching and experimental
validation.
(iii) Dynamics of biological networks - Networks representing complex
biological functions and activities are useful to interpret
physiological processes in the cell, pathological states, and to
investigate the potential effects of drug therapies, to name a few.
Several mathematical models and algorithms are available for the
different tasks involved in their integration, analysis and
characterization, although difficulties arise in case of big data and
dynamic systems, both at local and global scale.
(iv) Dynamics of genetic variation - Routine production of large data
set resulted in a comprehensive catalogs of genetic variability and the
knowledge of functional units of genomes improved thanks to the
combination of effective prediction tools and large validation sets. In
this session we want to provide examples of in silico prediction of
functional consequences of mutations and experimental validation of
genomic features.
Invited speakers include:
Chris Bowler, France
Marco Cosentino Lagomarsino, France
Giuseppe Jurman, Italy
Sebaastian Meijsing , Germany
Morgane Thomas-Chollier, France
Panos Pardalos, United States
Peter Van Loo, United Kingdom
For details and regular updates: www.bmtl.it
Register at: https://secure.webol.info/bmtl/en/register-here.php
Abstract info: http://www.bmtl.it/en/abstract-info.php?Preview=ok
Abstract submission: http://www.bmtl.it/en/abstract-submission.php
----------------------------------------------------
From: Riccardo Sacco <riccardo.sacco@polimi.it>
Date: June 15, 2015 at 2:25:00 AM
Subject: International Congress: Glaucoma, Oct 29-31, Milan, Italy
This fall, we are starting an exciting new congress: The International
Congress of Advanced Technologies and Treatments for Glaucoma (ICATTG).
The first edition, of hopefully many, will be held from October 29th
until the 31st, 2015 at the Politechnico di Milano, Milan, Italy.
It is our great pleasure to invite you to be a part of it! Registration
is now open!
The congress is the first worldwide event in the area comprising
Medicine, Biology, Clinics, Therapeutics, Engineering and Mathematics.
It is the extension of the Workshop Integrated Multidisciplinary
MIP-Politecnico-Milano-300x108Approaches in the Study and Care of the
Human Eye: Clinical Experience - Mathematical Modeling - New
Technologies that was held in Milano, 26-27 June 2013, under the joint
organization of the proposers of the present initiative, and falls
within the Official Agreement for Academic Collaboration between IUPUI,
Indianapolis, USA, and the Politecnico di Milano.
For more information, see http://www.glaucomacongress.com/
----------------------------------------------------
From: François KEPES <francois.kepes@issb.genopole.fr>
Date: June 17, 2015 at 4:51:52 AM
Subject: Conference: Synthetic Biology, Dec 14-18, Paris
Do not hesitate to disseminate this first announcement to your contacts,
and to display the poster available at
https://indico.math.cnrs.fr/event/742/.
Due to the limited number of seats in the conference room, registration
(https://indico.math.cnrs.fr/event/742/registration/) to participate in
the conference is compulsory.
If you have any queries, please send them to:
François Képès : francois.kepes@issb.genopole.fr (scientific programme)
Elisabeth Jasserand : jasserand@ihes.fr (practical organisation).
CELLULAR and MOLECULAR BIOTECHNOLOGY
Entretiens interdisciplinaires de Bures
14-18 December 2015
Institut des Hautes Études Scientifiques
Synthetic Biology is heralded as a novel approach to the engineering of
biosystems that will set the scene for a flourishing knowledge-based
bio-economy. Benefits for the fundamental understanding of biological
phenomena are also claimed, as rational construction of a system based
on hypothesized design principles can be used to test assumptions. The
keywords of synthetic biology are rational design, decoupling of
conception and fabrication, standardization and component re-use,
modularity and hierarchy, orthogonality and context-insensitivity.
However, each keyword raises questions of desirability and feasibility.
These questions remain ongoing areas of inquiry for the field and
require multi-faceted approaches. Beyond the current hype surrounding
it, what is the value of synthetic biology for the progress in
understanding of biological systems and for the establishment of new
biotechnological production platforms?
----------------------------------------------------
From: Hans Bogaards <hans.bogaards@rivm.nl>
Date: June 11, 2015 at 12:57:45 PM
Subject: PhD Position: Projecting Effects of Vaccination..., Dutch...
Project description
In order to prevent serious illness and disease outbreaks, the Dutch
government offers free vaccination against specific infectious diseases
to all children through the National Immunization Programme. The most
recent additions to this Programme are the vaccines against
pneumococcus, associated amongst others with meningitis, and against
papillomavirus, associated with various forms of cancer. Both
pneumococcus and papillomavirus are characterized by the existence of
various strains. The vaccines protect against a selected set of all
strains that can cause disease, being so-called polyvalent vaccines. An
anticipated effect of polyvalent vaccination is the elimination of
vaccine-specific strains from the population. A possible unwanted effect
is the take-over by other strains against which the vaccine is not
protective, such that the health benefit partly disappears. This
phenomenon is known as type-replacement and is caused by competition
between pathogenic strains. This project aims to deliver a better
assessment of type-replacement and its long-term consequences for the
effectiveness of polyvalent vaccination. Partners in this project are
the University Medical Centres of Utrecht (Paediatrics) and of Leiden
(Medical Statistics).
Your challenge
Quantification of interactions between pathogenic strains requires
diverse statistical techniques (graphical models, multi-state modelling,
survival analysis) for a diversity of data structures. The question is
which techniques and which data are informative for inferring
competitive interactions, and which are sensitive for the occurrence of
type-replacement. To this end, you will develop dynamic transmission
models for multi-strain pathogens that can incorporate a variety of
interactions between strains. You will use these models to simulate data
for the joint occurrence of multiple strains in epidemiological studies.
You will develop statistical techniques based on simulated data and
apply these to available data on pneumococcus and papillomavirus. You
will investigate indications for type-replacement and answer the
question how type-replacement may alter the expected health benefit of
vaccination. In the end, your research provides a consistent methodology
for multi-strain modelling that can be used to describe the
effectiveness of pneumococcal vaccination in an adequate way.
You will publish your findings in scientific journals and present your
findings on international conferences. After four years, your research
is intended to result in an academic dissertation. An abroad stay as
part of your PhD research belongs to the possibilities.
Your profile
We seek a highly motivated, enthusiastic researcher with an MSc or
comparable degree in (applied) mathematics, physics, biostatistics,
theoretical biology or bioinformatics. Excellent verbal and written
command of English is required, programming experience in C/C++ and R
are welcome. We expect affinity with the promotion of public health
through prevention of infectious diseases.
Terms of employment
You will be stationed at the Dutch National Institute of Public Health
and the Environment (RIVM). Appointment takes place based on 36 working
hours a week for the initial term of one year. Your contract will be
prolonged in case of good performance. Salary is in conformity with that
of a PhD student (OIO) at a Dutch university. The closing date for
applications is June 30th 2015.
More information
Dr. J.A. Bogaards, Project leader (hans.bogaards@rivm.nl,
tel +3130-2744765)
Dr. J. Wallinga, Head Dept. Infectious Disease Modelling
(jacco.wallinga@rivm.nl, tel. +3130-2742553)
Proclaimer RIVM http://www.rivm.nl/Proclaimer
----------------------------------------------------
From: Lewi Stone <lewistone2@gmail.com>
Date: June 15, 2015 at 7:42:50 AM
Subject: PhD Positions: Mathbio/Epid&Ecol/Network..., RMIT U, Melbourne
We invite applications for two PhD studentships in the School of
Mathematical and Geospatial Sciences, RMIT University, Melbourne,
Australia, The applicants will have the opportunity to work on subjects
that cross the interface of mathematical biology, theoretical
epidemiology and ecology, and network theory. The Department has a
vibrant group of active researchers in these areas, and intends to build
this group further. Please contact Prof. Lewi Stone, in the first
instance by emailing: lewistone2@gmail.com
----------------------------------------------------
From: Olav Reksen <olav.reksen@nmbu.no>
Date: June 15, 2015 at 2:52:01 AM
Subject: Post-doc: Math/Biostats/Epidemiology, Norwegian U Life Sciences
For information about the post-doctoral position, see
http://www.jobbnorge.no/ledige-stillinger/stilling/114975/post-doctoral-research-fellow-in-mathematics-biostatistics-epidemiology-refnr-15-02198
----------------------------------------------------
From: Roeland Merks <Roeland.Merks@cwi.nl>
Date: June 12, 2015 at 2:55:04 AM
Subject: Tenure-Track: Life Sciences, Centrum Wiskunde &..., Netherlands
Centrum Wiskunde & Informatica (CWI) invites excellent postdoctoral
researchers to apply for a tenure-track position in Life Sciences.
The young and lively Life Sciences group at CWI performs fundamental
research on algorithms, theory, models and simulations on topics from
the Life Sciences. The core themes of the group are biomodeling and
biosystems analysis, combinatorial algorithms for computational biology,
computational genomics, medical informatics, neuroinformatics and
scientific computing for systems biology.
As a researcher at CWI Amsterdam you are expected to perform fundamental
and application-oriented research, to supervise Ph.D. students, to
participate in or lead research projects together with other academic
institutes or industry, and to acquire external funding. You are able to
work as an independent researcher who can set his/her own research
agenda, as demonstrated by previous post-doctoral work experience. You
can connect to current research at CWI while at the same time bringing
in substantial new expertise.
Requirements:
We are looking for a candidate who is demonstrably an expert in the
field of mathematics/computer science/computational science for the
Life Sciences. The candidate is willing to cooperate within the Life
Sciences group and CWI and to build up interdisciplinary collaborations
with researchers in the Life Sciences, e.g., with experimental
biologists. A preference will be given to candidates who convincingly
show how they strengthen existing core themes of the group or build
bridges between them.
The candidate has the ambition and potential to acquire personal
research grants such as VENI/VIDI/VICI (NWO) or ERC grants (EU), as well
as to acquire external funding for applied research (e.g. from NWO, STW,
EU or industry). Moreover, she/he should have post-doctoral experience,
and excellent communication skills.
For more information, see
http://www.cwi.nl/jobs/tenure-track-position-in-life-sciences.
----------------------------------------------------
From: Dieffenbach, Ann (NIH/NIGMS) [E] <DIEFFENA@NIGMS.NIH.GOV>
Date: June 15, 2015 at 8:51:21 AM
Subject: NIGMS: MIRA Pilot..., PRAT Symposium, Funding Opportunities,...
For contents of NIGMS Network information, see
https://list.nih.gov/cgi-bin/wa.exe?A2=ind1506&L=nigms_network&F=&S=&P=62
----------------------------------------------------
Subject: SMBnet Reminders
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