SMB Digest March 11, 2015 Volume 15 Issue 10
ISSN 1086-6566
Editor: Wandi Ding ding.smb.digest(at)gmail(dot)com
Note:
Information about the Society for Mathematical Biology, including an
application for membership, may be found in the SMB Home Page,
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Access the Bulletin of Mathematical Biology, the official journal
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Issue's Topics:
Summer School: Principles-Oriented Systems..., Portugal, July 1-12
CfP: Synthetic & Systems Biology Summer School, Italy, July 5-9
CfP: Int. Workshop: Machine learning..., Italy, July 21-24
CfA: Evolutionary Quantitative..., a NIMBioS Tutorial, Aug. 10-15
MSc Position: Advanced Mathematical Biology, U of York
PhD Fellowships: Statistical Ecosystem Modelling, U of Iceland
PhD/Postdoc Positions: Theoretical and..., U of Groningen
Postdoc Position: Computational Structural Biology, UC Davis
Postdoc Position: Systems Biology of G..., U of North Carolina
Postdoc Position: Mathematical Modeling and..., U of Minnesota
Statistician Postion: Sea Level Rise Program, Climate Central
SMBnet Reminders
---------------------------------------------------------
From: Armindo Salvador <
salvador@cnc.uc.pt>
Date: Fri, Mar 6, 2015 at 7:56 AM
Subject: Summer School: Principles-Oriented Systems..., Portugal, July 1-12
International Summer School on Principles-Oriented Systems Biology
(PrOSysBio2015) Cantanhede (Portugal), July 1-12, 2015
http://www1.biocant.pt/summer_school/An intensive hands-on training program oriented towards discovering and
understanding new organization principles in organism and molecular Biology.
Focus of 2015 edition: Organizing Principles of Redox Biology
Topics covered:
- Kinetic and thermodynamic principles of thiol redox regulation
- Kinetic modeling and dynamic analysis of biomolecular networks in redox
signaling and antioxidant protection
- Design principles of biomolecular networks: methods and examples
- Evolutionary adaptation of protein composition and structure to oxidative
stress
Target audience
- Graduate students and postdocs seeking to become familiar with the
principles of redox biology and/or with computational methods for relating
design to function.
- Researchers at any level who are interested in principles of biological
organization and seek to acquire these skills.
We welcome both applicants with exact sciences or engineering backgrounds
and applicants with a biology background. However, a good quantitative
background is desirable in all cases.
Instructors:
Dean Jones (Emory University, U.S.A.)
Anita Krisko (Mediterranean Institute for Life Sciences, Croatia)
Armindo Salvador (Center for Neuroscience and Cell Biology, Portugal)
Rui Alves (University of Lleida, Spain)
Course structure
The course takes a student-oriented approach and is composed of lectures
and computational research projects. Project themes will be presented on
day 1. The first part of the course will emphasize lectures covering the
main topics. During that time students will also choose their research
projects and teams, and devise a research plan. Teams will include
students with complementary backgrounds and will be coached by tutors.
The second part of the course will be devoted to executing the research
projects. Results will be presented in the last day at a mini-symposium.
Admittance and further information:
Please visit
http://www1.biocant.pt/summer_school/page0.html Deadline for application: April 30
---------------------------------------------------------
From: Luc Morabitos <
luc.morabitos@gmail.com>
Date: Sat, Mar 7, 2015 at 4:20 AM
Subject: CfP: Synthetic & Systems Biology Summer School, Italy, July 5-9
Synthetic and Systems Biology Summer School - 2nd Edition
Taormina - Sicily, Italy, July 5-9, 2015
http://www.taosciences.it/ssbss2015/ssbss.school@gmail.comNew Speaker! Ron Weiss, MIT, USA
** Deadlines **
Student Application: March 31, 2015
Oral/Poster Submission: March 31, 2015
** List of Speakers **
* Adam Arkin, University of California Berkeley, USA
* Jef Boeke, New York University, USA
* Angela DePace, Harvard University, USA
* Forbes Dewey, MIT, USA
* Karmella Haynes, Arizona State University, USA
* Richard Kitney, Imperial College London, UK
* Timothy Lu, MIT, USA
* Philip Maini, Oxford University, UK
* Giancarlo Mauri, University of Milano - Bicocca, Italy
* Steve Oliver, Cambridge University, UK
* Velia Siciliano, MIT, USA
* Ron Weiss, MIT, USA
* Nicola Zamboni, ETH, Switzerland
** Industrial Panel **
* Jon D. Chesnut, Life Sciences Solutions Group -Thermo Fisher Scientific,
USA
* Speaker TBA, Autodesk Inc., USA
* Zach Serber, Zymergen, Inc. USA
School Directors
Jef D. Boeke, New York University, USA
Giuseppe Nicosia, University of Catania, Italy
Mario Pavone, University of Catania, Italy
Giovanni Stracquadanio, University of Oxford, UK
** Short Talk and Poster Submission **
Students may submit a research abstract for presentation. School directors
will review the abstracts and will recommend for poster or short-oral
presentation. Abstract should be submitted by March 31, 2015. The abstracts
will be published on the electronic hands-out material of the summer school.
http://www.taosciences.it/ssbss2015/index.html#applicationFormhttp://www.taosciences.it/ssbss2015/ssbss.school@gmail.com --------------------------------------------------------------
From: Luc Morabitos <
luc.morabitos@gmail.com>
Date: Sat, Mar 7, 2015 at 1:06 PM
Subject: CfP: Int. Workshop: Machine learning..., Italy, July 21-24
International Workshop on Machine learning, Optimization and big Data -
MOD 2015
An Interdisciplinary Workshop: Machine Learning, Optimization and Data
Science without Borders, Taormina - Sicily, Italy, from July 21 to 24, 2015
http://www.taosciences.it/mod-2015/modworkshop2015@gmail.comCALL FOR PAPERS
Paper submission deadline: March 31, 2015
http://www.taosciences.it/mod-2015/call-for-papers/KEYNOTE SPEAKERS
+ Vipin Kumar, University of Minnesota, USA
+ Panos Pardalos, University of Florida, USA
+ Tomaso Poggio, MIT, USA
TUTORIAL SPEAKERS
+ "Science SQL", Peter Baumann, Jacobs University Bremen, Germany
+ "Feature Selection for Supervised Classification", Mario Guarracino,
Italian National Research Council, Italy
+ "Statistical inferences in Graphical Models with applications to Market
Networks", Valeriy Kalyagin, National Research University - Higher School
of Economics, Russia
+ "Kernel Methods with Imbalanced Data", Theodore B. Trafalis, University
of Oklahoma, USA
The MOD 2015 workshop will consist of one day of tutorials, followed by
three days of main workshop sessions. We invite submissions of papers,
abstracts and demos on all topics related to Machine learning, Optimization
and Big Data including real-world applications for the workshop proceedings
(
http://www.taosciences.it/mod-2015/call-for-papers/) and proposals for
tutorials (
http://www.taosciences.it/mod-2015/call-for-tutorials/).
Paper submission guidelines:
http://www.taosciences.it/mod-2015/submissions/Any questions regarding the submission process can be sent to workshop
organizers:
modworkshop2015@gmail.com --------------------------------------------------------------
From: Catherine Crawley <
ccrawley@nimbios.org>
Date: Fri, Mar 6, 2015 at 10:30 AM
Subject: CfA: Evolutionary Quantitative..., a NIMBioS Tutorial, Aug. 10-15
The National Institute for Mathematical and Biological Synthesis (NIMBioS)
is now accepting applications for its Tutorial, "Evolutionary Quantitative
Genetics," to be held August 10-15, 2015, at NIMBioS.
The content of this tutorial will be similar to the workshop held at
NIMBioS in 2014. For information about the Evolutionary Quantitative
Genetics 2014 tutorial held at NIMBioS, visit
http://www.nimbios.org/tutorials/TT_eqg.
Location: NIMBioS at the University of Tennessee, Knoxville
Co-Organizers: Stevan J. Arnold, Integrative Biology, Oregon State Univ.
and Joe Felsenstein, Genome Sciences, Univ. of Washington, Seattle
Instructors: Patrick Carter, Evolutionary Physiology, Washington State
Univ., Pullman; Tyler Hether, Biological Sciences, Univ. of Idaho, Moscow;
Adam Jones, Biology, Texas A&M Univ.; Emilia Martins, Biology, Indiana
Univ., Bloomington; Brian O'Meara, Ecology & Evolutionary Biology, Univ. of
Tennessee; Liam Revell, Biology, Univ. of Massachusetts, Boston; and
Michael Whitlock, Zoology, Univ. of British Columbia
Co-Sponsor: The American Society of Naturalists
For more information about the tutorial and a link to the online application
form, go to
http://www.nimbios.org/tutorials/TT_eqg2015There are no fees associated with this tutorial. Tutorial participation in
the tutorial is by application only. Individuals with a strong interest in
the topic, including post-docs and graduate students, are encouraged to
apply, and successful applicants will be notified within two weeks of the
application deadline.
Food and Lodging: Breakfast and lunch will be provided at NIMBioS each day
of the tutorial, as well as coffee and mid-morning and mid-afternoon snacks.
NIMBioS is not covering other expenses for participants, but a block of
rooms will be reserved at a nearby hotel. More information will be
available on our website soon about lodging, room rates, and how
participants can make reservations.
Application deadline: May 1, 2015
--------------------------------------------------------------
From: Martin Bees <
martin.bees@york.ac.uk>
Date: Mon, Mar 9, 2015 at 7:56 AM
Subject: MSc Position: Advanced Mathematical Biology, U of York
Applications are open for the MSc in Advanced Mathematical Biology at the
University of York, based in the beautiful Roman/Viking city of York in the
UK, due to start October 2015.
The MSc in Advanced Mathematical Biology is an intensive one-year taught
programme that will prepare students either for a career in industry in the
quantitative life sciences or for further academic research in Mathematical
Biology. It will provide insight into processes over a wide range of scales;
from highly symmetric capsids (the cases that surround viruses), through
soft matter and suspensions of biased swimming cells to the dynamics of
food-webs and diseases. Advanced statistical methods, systems biology and
biological fluid dynamics will be covered, and there will be emphasis on
applications to policy and industry throughout. This programme aspires to
fill the language gap between technical mathematical concepts and real
world applications in the biological and life sciences. Students will
gain a comprehensive grounding in cutting edge theory coupled to training
in the subtleties of application.
An important part of the programme is a summer work-based placement. At the
end of the spring term, students will select a placement from a list of
academic and industrial institutions across the sector. Students will
spend a period of three months working closely with their chosen
institution with a placement supervisor, assessed via a dissertation.
This year, taught modules are likely to include:
Applications of Group Theory in Virology; Bayesian Statistics;
Bioinformatics; Biological and Soft Matter; Biological Fluid Dynamics;
Conservation Ecology & Biodiversity; Ecological Modelling; Essential
Mathematical Biology; Field & Laboratory Experimental Skills; Issues in
Modern Biology (research based seminars); Modelling with MATLAB; Numerical
Techniques for Modelling Biological Systems; PDEs; Stochastic Processes;
Survival Analysis; and a Group Research Project.
Scholarships: funding for the relatively low fees can be obtained from a
variety of sources, including the York Masters Opportunity Scholarships.
Please see the webpage for the programme.
http://maths.york.ac.uk/www/MScBiology --------------------------------------------------------------
From: Gunnar Stefansson <
gstefans@gmail.com>
Date: Wed, Mar 4, 2015 at 9:16 AM
Subject: PhD Fellowships: Statistical Ecosystem Modelling, U of Iceland
PhD Fellowships in the Division of Applied Mathematics at the University of
Iceland
The University of Iceland is pleased to offer two PhD fellowships within
the Applied Mathematics Division for students interested in Quantitative
Ecology, Ecosystem Modelling, and Statistics:
Modellers at the Science Institute of the University of Iceland are
presently implementing an Atlantis and an Ecopath with Ecosim (EwE) model
for the Icelandic waters. Atlantis is a deterministic, whole of ecosystem
biogeochemical model that includes oceanographic, ecological, economic,
and social components. EwE is a whole of ecosystem model consisting of
three principal components: Ecopath - a mass-balanced, static snapshot
of a marine system; Ecosim - a time dynamic simulation module; and
Ecospace - a spatial and temporal dynamic module.
The recipients will work closely with researchers developing these ecosystem
models to expand the scope and broaden the impact of these models. They
will work to evaluate alternative economic, ecological, and environmental
objectives and social responses on the Icelandic marine ecosystem within a
management strategy evaluation framework.
Both fellowships are fully-funded for 3 years. The ideal candidate for
these fellowships will have a strong background in mathematics and
statistics or ecology with a strong interest in quantitative ecology and
ecosystem modeling; interest in policy and management; strong programming
skills in R; and some experience with C languages.
Applicants should possess an MSc degree and good verbal and written skills
in English are required.
These fellowships will be under the direction of Prof. Gunnar Stefansson
(e-mail:
gunnar@hi.is;
http://www.hi.is/~gunnar/).
Studies will commence immediately. An initial relocation and an annual
travel allowance are included. Please note there is no closing date and
the positions will be filled once suitable candidates are found.
The Applied Mathematics Division is a research unit under the Science
Institute of the University of Iceland. The unit covers the following
research areas; operation research, probability theory, theoretical and
applied statistics, ecosystem modeling, biostatistics, numerical analysis
and computational intelligence.
The application should contain a cover letter, a full curriculum vitae
including documentation of academic degrees and a minimum of two
references. Applications should be sent as e-mail attachments in PDF
format to Prof. Gunnar Stefansson,
gunnar@hi.is (Applied Mathematics
Division, Science Institute. University of Iceland, Dunhagi 5,
107 Reykjavik, Iceland).
For additional information about the positions, please contact
Dr. Christopher David Desjardins at
christop@hi.is.
---------------------------------------------------------------------
From: Rampal S. Etienne <
r.s.etienne@rug.nl>
Date: Thu, Mar 5, 2015 at 2:21 AM
Subject: PhD/Postdoc Positions: Theoretical and..., U of Groningen
Three PhD student or postdoc position are available at the Groningen
Institute for Evolutionary Life Sciences (formerly the Centre for
Ecological and Evolutionary Studies), at the University of Groningen,
The Netherlands. The positions are part of the VICI project 'On the origin
of species assemblages' awarded to prof. Rampal S. Etienne
(
r.s.etienne@rug.nl). The aim of this program is twofold:
1. developing a fully stochastic, dynamical, eco-evolutionary and
data-friendly theory of community assembly, and
2. testing and informing this theory with model-oriented experiments and
field studies of both macro-organisms and micro-organisms. The details of
the positions can be found here:
PhD position Theoretical eco-evolutionary assembly of ecological communities
http://www.rug.nl/about-us/work-with-us/job-opportunities/overview?details=00347-02S0004E9P&cat=phdPostdoc position Theoretical eco-evolutionary assembly of ecological
communities
http://www.rug.nl/about-us/work-with-us/job-opportunities/overview?details=00347-02S0004EAP&cat=wpPhD or Postdoc position Simultaneous Estimation and Selection of Species
Diversification Models
http://www.tangram-tis.nl/10378/Vacatures/00347-02S0004EMP/Vacature-PhD-or-Postdoc-Simultaneous-Estimation-and-Selection-of-Species-Diversification?category=Groepspecifiek_RUG_Categorie%2CGroepspecifiek_RUG_Categorie2!!Categorie!!RUC.PROM---------------------------------------------------------
From: Javier Arsuaga <
jarsuaga@ucdavis.edu>
Date: Wed, Mar 4, 2015 at 2:21 PM
Subject: Postdoc Position: Computational Structural Biology, UC Davis
POSTDOCTORAL POSITION ANNOUNCEMENT
A postdoctoral position in Computational Structural Biology is available
at the Department of Molecular and Cellular Biology at the University of
California Davis (UC Davis) starting on September 1st, 2015.
The aim of this NIH funded project is to develop mathematical, statistical
and computational methods to analyze chromatin conformation capture (CCC)
data, with a focus on 3D genome architecture and topology. The postdoctoral
fellow will join an interdisciplinary team of researchers in Mathematical
and Computational Biology, Biostatistics and Bioinformatics at UC Davis and
at the University of California, San Francisco (UCSF).
We are seeking applicants with a PhD in Mathematics, Statistics,
Computational Biology or related field. The ideal candidate will have a
strong background in Computational Biology and/or Computational
Topology/Geometry, and/or Statistics. Excellent writing and oral
communication skills are expected.
The initial appointment is for one year, with possible renewal to a second
year. Interested applicants should send CV and three references to Prof.
Javier Arsuaga (
jarsuaga@ucdavis.edu). Applications will be considered
until the position is filled.
The University of California is an affirmative action/equal opportunity
employer.
---------------------------------------------------------------
From: Elston, Timothy C <
timothy_elston@med.unc.edu>
Date: Thu, Mar 5, 2015 at 3:46 PM
Subject: Postdoc Position: Systems Biology of G..., U of North Carolina
Postdoctoral Position: Systems Biology of G Protein Signaling
The University of North Carolina, Schools of Medicine and Arts and Sciences
Heterotrimeric G proteins serve as a signaling nexus in a myriad of normal
and diseased cell states. Many extracellular signals (e.g. hormones,
peptides, cytokines, lights) are perceived by 7-transmembrane receptors,
often referred to as G protein coupled receptors (GPCRs), that stimulate
the activation state of the cytoplasmic G protein complex. Interestingly,
the majority of non-animal cells (protists, fungi, plants, amoeba and many
others) bind GTP without the need for a GPCR. This recent discovery opens
up new opportunities to find novel mechanisms that regulate G protein
signaling. This project tightly integrates experimental investigations
with mathematical modeling to discover and characterize novel signaling
motifs that regulate pathway activity in the glucose sensing system of
Arabidopsis. The project is a continuation of a well established
collaboration between the labs of Drs. Alan Jones and Tim Elston
(Fu, et al 2014 Cell 156:1084-1095). The ideal applicant will have
experience with deterministic and stochastic modeling methods, and a
willingness to learn the experimental techniques needed to test their
mathematical models. Interested individuals should contact Tim Elston
(
timothy_elston@med.unc.edu) and Alan Jones (
alan_jones@unc.edu).
--------------------------------------------------------------
From: Harrydeo Singh <
mathdept@umn.edu>
Date: Tue, Mar 10, 2015 at 1:27 PM
Subject: Postdoc Position: Mathematical Modeling and..., U of Minnesota
Funding is available for a Postdoctoral Associate/Research Associate
position in the School of Mathematics at the University of Minnesota-
Minneapolis, beginning as early as May 1, 2015.
The position involves mathematical modeling and analysis of pattern
formation in developmental biology, particularly in early development of
Drosophila. Applicants should have a Ph.D. in Mathematics, Science or
Engineering and have experience in mathematical modeling and computational
analysis in biology, biophysics or medicine. The degree is required by the
beginning date of appointment. Knowledge of Fortran or C/C++ is also
required.
The immediate group consists of eight researchers who are analyzing models
of cell movement in single and multicellular systems, stochastic effects
in pattern formation, and signal transduction and pattern formation in
developmental biology. In addition, the School of Mathematics and the
Institute for Mathematics and Its Applications at Minnesota provide a very
rich research environment for a post-doctoral fellow.
The salary will be commensurate with qualifications and experience. The
initial appointment will be for one year, with continuation contingent
upon performance and availability of funding. Please submit your CV,
research statement and arrange for three letters of recommendation. Also,
any offer will be contingent upon a successful background check. Letters
could be loaded on the mathjobs website or be sent to: Professor Hans
Othmer, School of Mathematics, 127 Vincent Hall, University of Minnesota,
206 Church St SE Minneapolis, MN 55455.
The University of Minnesota is committed to the policy that all persons
shall have equal access to its programs, facilities, and employment
without regard to race, color, creed, national origin, sex, age, marital
status, disability, public assistance status, veteran status, or sexual
orientation.
--------------------------------------------------------------
From: Timothy Grandia <
tgrandia@climatecentral.org>
Date: Wed, Mar 4, 2015 at 1:22 PM
Subject: Statistician Postion: Sea Level Rise Program, Climate Central
Statistician - Sea Level Rise Program
Job Description
Climate Central is seeking an energetic, talented statistical scientist
who wants to make a tangible, global impact with targeted research. Strong
candidates will be fluent in extreme value statistics, spatial statistics
and Bayesian approaches. The statistician will sit within Climate Central's
nationally recognized sea level rise program, and provide critical research
and analysis for our U.S. and soon-to-launch global programs.
Climate Central is a growing nonprofit and non-advocacy organization
dedicated to researching and publicizing key findings on our changing
climate and its impacts. Our scientists and communicators work together to
reach the most people possible using all the tools at our disposal.
Climate Central's sea level rise program is a recognized leader in both
climate science and communication. Our peer-reviewed research has been
downloaded more than 20,000 times; major news outlets including the New
York Times, USA Today, AP, NBC, CBS and NPR have frequently featured our
findings; we have testified in the U.S. Senate; and our web tools are
winning practical use from NGOs to local governments.
Responsibilities
- Develop and improve local flood risk projections, nationally and
globally, integrating sea level rise forecasts and storm surge statistics
and projections
- Develop and improve methods for interpolating projections in space
- Play key role in research on error in digital elevation models
- Write and contribute to peer-reviewed papers, plus reports for wider
audiences
- Provide general statistical research support
Qualifications
- PhD in statistics or equivalent education/experience
- Expertise in extreme value statistics, spatial statistics and Bayesian
approaches
- Facility with big data, data acquisition and data wrangling
- Proficiency with R, geospatial packages/GIS, Matlab ideal; C++ or
python a plus
- Strong communication skills, and the ability to work well both
independently and in close collaboration within a small team, are essential
Location
The location for this position is Climate Central's Princeton, N.J.
headquarters.
Compensation
Compensation is competitive, with very generous benefits.
Diversity
Climate Central strongly encourages diverse candidates to apply. We are an
Equal Employment Opportunity employer and as such do not discriminate
against any applicant for employment or employee on the basis of race,
color, religious creed, gender, age, marital status, sexual orientation,
national origin, disability, veteran status or any other classification
protected by applicable discrimination laws.
Apply
Please send your cover letter, resume and salary expectations to
iweinberg@climatecentral.org, with the exact subject line, "Statistician"
(no quotes). Due to the volume of employment applications and queries
received, Climate Central is unable to respond to each application
individually. Applicants will be contacted directly if selected as a
candidate.
Search will close when successful candidate is recruited to fill this
position.
---------------------------------------------------------------
Subject: SMBnet Reminders
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