SMB Digest September 16, 2015 Volume 15 Issue 37
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
Note:
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Issue's Topics:
Conference: Undergraduate, Funding Deadline is Sep 18, NIMBioS
Conference: Stochastic Dyn. Syst. in Bio., Jan 18-22, Cambridge
Conference: Bioinformatics & Comput. Biol., Apr 4-6, Las Vegas
Conference: Information Syst., Jun 13-17, Ljublijana, Slovenia
Conferences: Keystone, Cancer Biology, Other Conferences, 2016
New PhD Program: Quantitative Biosciences, Georgia Tech
PhD Positions: Quantitative Biol. & Medical Genetics, McGill U
PhD Positions: Optimization in Comput. Systems Biology, Spain
Post-doc: Modeling of Autoimmune Type-1 Diabetes, Kansas St U
Post-docs: Interface of Math & Biology, NIMBioS, U Tennessee
Lecturer: Applied Mathematics/Mathematical Biology, U Melbourne
Research Fellow: Infectious Disease Modelling, London
Fellows Program: Keystone, Sep 30 Deadline Extended
SMBnet Reminders
----------------------------------------------------
From: Catherine Crawley <ccrawley@nimbios.org>
Date: September 15, 2015 at 9:30:56 AM
Subject: Conference: Undergraduate, Funding Deadline is Sep 18, NIMBioS
Deadline approaching to request funding to attend the Undergraduate
Research Conference at the Interface of Mathematics and Biology,
Nov. 21-22, 2015.
A limited amount of support is available to cover the cost of
registration and lodging for the conference, hosted by the National
Institute for Mathematical and Biological Synthesis (NIMBioS).
Funding Request Deadline: September 18
The conference, to be held at Univ. of Tennessee Conference Center in
Knoxville, TN., provides opportunities for undergraduates to present
their research at the interface of biology and mathematics. Student
talks and posters will be featured as well as a plenary speaker, a panel
on career opportunities, a graduate school showcase, and other
networking opportunities. Conference registration deadline is
November 13. If you have or plan to request our funding, do not register
for the conference until you have been contacted by NIMBioS about the
status of your funding request. For more information, go to
http://www.nimbios.org/education/undergrad_conf2015
----------------------------------------------------
From: Konstantinos Zygalakis <k.zygalakis@soton.ac.uk>
Date: September 12, 2015 at 3:37:15 AM
Subject: Conference: Stochastic Dyn. Syst. in Bio., Jan 18-22, Cambridge
Isaac Newton Institute Programme on Stochastic Dynamical Systems in
Biology: Numerical Methods and Applications
Opening Workshop (SDBW01), Cambridge UK, 18-22 Jan 2016
In the past decades, quantitative biology has been driven by new
modelling-based stochastic dynamical systems and partial differential
equations. Examples from gene regulation, molecular signalling, cell
division and molecular transport, as recently revealed by live cell
images, have shown that many processes in cells and in molecular biology
are inherently driven by stochastic events. One of the biggest
challenges we propose to address in this programme is to develop methods
and analysis, as well as efficient algorithms for simulations, to bridge
the range of different biological scales.
In support of this goal, the programme will focus on
-Analysis of stochastic dynamical systems and applications in molecular
and cellular biology.
-Development of efficient computational methods for simulating
stochastic equations over various scales.
-Identifying new research areas.
The aim of this opening workshop is to introduce participants to the
different subject areas of the programme. In particular, this workshop
will include a number of mini-courses aimed at senior graduate and
postgraduate students, together with high level overview talks, given by
world experts, which will highlight some of the major open problems in
the field.
Limited funding is available to partially cover the costs of junior
participants from the U.S. and the U.K. Please see the workshop website
for details.
The following introductory mini-courses are planned as part of the
workshop:
-Stochastic Simulation of Models Arising in the Life Sciences I
(non-spatial models). David Anderson (University of Wisconsin)
-Stochastic Simulation of Models Arising in the Life Sciences II
(spatial models). Samuel Isaacson (Boston University)
-Narrow escape theory, first passage time to a small hole and
applications to modelling cell biology processes. David Holcman (Ecole
Normale Superieure)
List of workshop speakers:
Ruth Baker (University of Oxford)
Neil Dalchau (Microsoft Research)
Jasmine Foo (University of Minnesota)
Mike Giles (University of Oxford)
Ray Goldstein (University of Cambridge)
Des Higham (University of Strathclyde)
Stefan Klumpp (Max-Planck-Institut)
Rachel Kuske (University of British Columbia)
Yihan Lin (California Institute of Technology)
Scott McKinley (Tulane University)
Johan Paulsson (Harvard University)
Linda Petzold (University of California, Santa Barbara)
Christof Schüette (Freie Universität Berlin)
Blerta Shtylla (Pomona College)
Ben Simons (University of Cambridge)
Peter Swain (University of Edinburgh)
Eric Vanden-Eijnden (New York University, Courant Institute)
Darren Wilkinson (University of Newcastle)
Further workshop details: http://www.newton.ac.uk/event/sdbw01
Deadline for applications: 11th October 2016
----------------------------------------------------
From: Nurit Haspel <nurit.haspel@umb.edu>
Date: September 11, 2015 at 2:53:07 PM
Subject: Conference: Bioinformatics & Comput. Biol., Apr 4-6, Las Vegas
BICoB-2016
8th International Conference on Bioinformatics and Computational Biology
April 4-6 - Las Vegas, NV, USA
Conference website: http://www.cs.umb.edu/bicob/
IMPORTANT DATES:
Paper Submission Deadline: October 30, 2015.
Notification of Acceptance: December 18, 2015.
Pre-registration and Camera-ready paper: January 20, 2016.
About BICoB
The 8th International Conference on Bioinformatics and Computational
Biology (BICoB) provides an excellent venue for researchers and
practitioners in the fields of 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. In recent years,
bioinformatics and computational biology have experience significant
advances driven by computational techniques in bioinformatics. The BICoB
conference seeks original and high quality papers in the fields of
bioinformatics, computational biology, systems biology, medical
informatics and the related areas. Work in the computational methods
related to, or with application in, bioinformatics is also encouraged
including: bio-data mining, text mining, machine learning,
biomathematics, modeling and simulation, pattern recognition, data
visualization, biostatistics, .etc. The topics of interest include (and
are not limited to):
Genome analysis: Genome assembly, genome annotation, gene finding,
alternative splicing, EST analysis and comparative genomics.
Sequence analysis: Multiple sequence alignment, sequence search and
clustering, function prediction, motif discovery, functional site
recognition in protein, RNA and DNA sequences.
Phylogenetics: Phylogeny estimation, models of evolution, comparative
biological methods, population genetics.
Structural Bioinformatics: Structure matching, prediction, analysis and
comparison; methods and tools for docking; protein design
Analysis of high-throughput biological data: Microarrays (nucleic acid,
protein, array CGH, genome tiling, and other arrays), EST, SAGE, MPSS,
proteomics, mass spectrometry.
Genetics and population analysis: Linkage analysis, association
analysis, population simulation, haplotyping, marker discovery, genotype
calling.
Systems biology: Systems approaches to molecular biology, multiscale
modeling, pathways, gene networks.
Computational Proteomics: Filtering and indexing sequence databases,
Peptide quantification and identification, Genome annotations via mass
spectrometry, Identification of post-translational modifications,
Structural genomics via mass spectrometry, Protein-protein interactions,
Computational approaches to analysis of large scale Mass spectrometry
data, Exploration and visualization of proteomic data, Data models and
integration for proteomics and genomics, Querying and retrieval of
proteomics and genomics data etc.
Journal Publication: Authors of selected high quality papers in
BICoB-2016 will be invited to submit extended version of their papers
for possible publication in bioinformatics journals (selected high
quality papers in previous years were published in the Journal of
Bioinformatics and Computational Biology (JBCB) special issues).
Paper submission site: https://www.easychair.org/conferences/?conf=bicob2016
Conference chair:
Hisham Al-Mubaid, University of Houston at Clear Lake, hisham@uhcl.edu
Program Co-Chairs:
Nurit Haspel: University of Massachusetts at Boston, USA,
nurit.haspel@umb.edu
Thomas Loerger: Texas A&M University, USA, ioerger@cs.tamu.edu
----------------------------------------------------
From: Djurica Salamon <djurica.salamon@dmi.uns.ac.rs>
Date: September 16, 2015 at 3:20:04 AM
Subject: Conference: Information Syst., Jun 13-17, Ljublijana, Slovenia
Please find attached CALL FOR PAPERS for The 28th International
Conference on Advanced Information Systems Engineering (CAiSE 2016).
Conference will be organized on 13-17 June 2016, in Ljubljana
(Slovenia).
Details can be found at: http://caise2016.si/
Important dates
-Paper submission deadline: 30th November 2015
-Notification of acceptance: 16th February 2016
-Camera-ready of all papers: 25th March 2016
----------------------------------------------------
From: keystonesymposia <keystonesymposia@keystonesymposia.org>
Date: September 9, 2015 at 5:12:09 PM
Subject: Conferences: Keystone, Cancer Biology, Other Conferences, 2016
For information on Keystone Symposia 2016 Cancer Conferences, see
http://www.keystonesymposia.org/index.cfm?e=Web.Meeting.List&tab3#Cat2
Additionally, the links on the left of the page provide information on
2016 Conferences about Cardiovascular, Cellular & Molecular Biology,
Development, Drug Discovery, Genetics/Genomics, Immunology, Infectious
Diseases, Metabolic Diseases, Neurobiology, Plant Biology, and
Technologies.
----------------------------------------------------
From: Joshua S. Weitz <jsweitz@gatech.edu>
Date: September 9, 2015 at 9:14:28 AM
Subject: New PhD Program: Quantitative Biosciences, Georgia Tech
We are actively recruiting strong undergraduates from the physical
sciences, biological sciences, mathematics, engineering and computing to
join an interdisciplinary Ph.D. program in Quantitative Biosciences
(QBioS) at Georgia Tech. Applications are welcome by December 15, 2015
for entrance in August 2016: http://qbios.gatech.edu
The QBioS Ph.D. at Georgia Tech was established in 2015 by an
interdisciplinary group of over 40 participating program faculty from
seven schools in the College of Sciences, including Applied Physiology,
Biology, Chemistry and Biochemistry, Earth and Atmospheric Sciences,
Mathematics, Physics and Psychology:
http://qbios.gatech.edu/people/faculty
The mission of QBioS at Georgia Tech is to educate students and advance
research in quantitative biosciences, enabling the discovery of
scientific principles underlying the dynamics, structure, and function
of living systems. The Ph.D. training program is designed to prepare
students from a diversity of backgrounds for fulfilling careers in
academia, industry and government. The training program features:
-Foundational courses in Quantitative Biosciences
-Rotations in modeling and/or experimental groups
-Selection of thesis advisor from all program faculty
-Rigorous and personalized quantitative training
-Five-year program of study from entrance to defense
Interested students should apply via the links here:
http://qbios.gatech.edu/prospective-student/overview
Students are encouraged to email us at admissions@qbios.gatech.edu for
more information, as well as consult the FAQs for information on
courses, research, and applications materials:
http://qbios.gatech.edu/prospective-student/faqs
----------------------------------------------------
From: Simon Gravel <simon.gravel@gmail.com>
Date: September 15, 2015 at 1:10:46 PM
Subject: PhD Positions: Quantitative Biol. & Medical Genetics, McGill U
Quantitative Biology and Medical Genetics for the World
Program Announcement
The "Quantitative Biology and Medical Genetics for the World" program at
McGill is offering a number of prestigious Queen Elizabeth II
scholarships for Commonwealth citizens to pursue a PhD at McGill
University.
The Program The Canadian Queen Elizabeth II Diamond Jubilee Scholarships
(QEII) program is a new program established by the Association of
Universities and Colleges of Canada to create a community of leading
Canadian and Commonwealth scholars. For background see:
http://www.univcan.ca/programs-services/international-programs/canadian-queen-elizabeth-ii-diamond-jubilee-scholarships/
"Quantitative Biology and Medical Genetics for the World" at McGill is
supported by the QEII program and coordinated by the McGill University
and Génome Québec Innovation Centre (MUGQIC), one of Canada's leading
institutions for genome research. The goal is to provide
interdisciplinary training at a PhD level interfacing between
high-throughput biology and quantitative sciences. While applicants can
be from any Commonwealth country, we will favour students with
nationality from countries where similar training opportunities are not
readily available. PhD students are admitted for studies at McGill
commencing in January and September of each year.
The first QEII scholarships will be available to start in January 2016.
The deadline for applications for this start date in the Department of
Human Genetics is September 20, 2015.
More information can be found at:
http://simongravel.lab.mcgill.ca/Documents/QEII_IncomingStudents.pdf
----------------------------------------------------
From: jr banga <jrbanga@gmail.com>
Date: September 16, 2015 at 8:34:12 AM
Subject: PhD Positions: Optimization in Comput. Systems Biology, Spain
TWO MARIE-CURIE PhD POSITIONS AT IIM-CSIC
(Spanish Council for Scientific Research), Vigo (Spain)
Topic: OPTIMIZATION in COMPUTATIONAL SYSTEMS BIOLOGY.
https://goo.gl/85Op8t
JOB DESCRIPTION
Applications are invited for two Early Stage Researcher Positions in
computational systems biology under the supervision of Prof. Julio R.
Banga, IIM-CSIC (Spain), starting in early 2016.
Position ESR6: novel optimization methods for systematic development
of dynamic models of biological systems.
Position ESR7: optimal control methods to explain and predict
operating principles in biochemical pathways.
Duration: 36 months. These Early Stage Researchers (ESRs) will be hired
for 36 months each and will be expected to pursue a PhD. Candidates
must be in possession of a relevant Masters degree (or very close to
obtaining it) at the time of appointment.
Salary will be excellent, in the range of 33-36 kiloeuros gross/year,
according to EU regulations (Marie Curie ITN Early Stage Researcher
conditions).
Other benefits: the ESRs will be involved in a Marie-Curie network with
excellent opportunities for scientific and personal development,
including funding for short stays at top-class research groups in
Germany and the UK, plus regular training events and meetings across
Europe.
FURTHER INFORMATION (including HOW TO APPLY): https://goo.gl/85Op8t
----------------------------------------------------
From: Majid Jaberi <jaberi@vet.ksu.edu>
Date: September 14, 2015 at 9:03:48 AM
Subject: Post-doc: Modeling of Autoimmune Type-1 Diabetes, Kansas St U
Start date: November 2015
Job Summary: Applications are invited for a postdoctoral position with
the Institute of Computation Comparative Medicine (ICCM)
http://iccm.k-state.edu/. The interdisciplinary research-based center
ICCM is envisioned as an incubator where quantitative oriented
researchers will collaborate with bench scientists and clinicians to
apply novel methods to practical problems in comparative pharmacology
and toxicology. The ICCM enthusiastically encompasses the concept of One
Health and strives to optimally utilize animal data to advance the
health and wellbeing of both animals and humans. The position is also
part of the Mathematics Department for Mathematical Biology Lab at
Kansas State University (KSU), Manhattan.
The new post-doctoral fellow position is immediately available to
conduct research in autoimmune type 1 diabetes (T1D). A PhD in
biomathematics/biostatistics or related field in Computational Biology
(with a background in computational systems modeling, programming MATLAB
or C++ and parallel computing) along with documented experience
conducting either physiological based or population-based mixed effect
of T-cell inter- and intra-clonal competition modeling is required. The
project aims at understanding the leading role in regulating
immunological tolerance and resistant homeostasis observed in
autoreactive and regulatory T-cell responses.
How to Apply: The position is for one year with possible extension for
up to two more years subject to satisfactory progress and mutual
agreement. Please send a cover letter, resume and contact information
for three professional references to cvmjobs@vet.k-state.edu. Please
reference Requisition Number 5582 in the subject line of your email.
Screening of applicants begins September 30, 2015 and will continue
until the position is filled. KSU is an equal opportunity employer and
actively seeks diversity among its employees. Background check is
required.
Contact Information: For further information about this position, please
contact Dr. Majid Jaberi-Douraki through jaberi@vet.k-state.edu or
jaberi@math.k-state.edu or at 785-532-4733.
Total Rewards:
Heath Insurance and Wellness
Life Insurance
Leave and Holidays
Tuition Assistance
Retirement Plans
Worker's Compensation
For additional information refer to the benefits summary
(http://www.k-state.edu/hr/current-employees/benefits/summary.html).
Kansas State University is an Equal Opportunity Employer of individuals
with disabilities and protected veterans and actively seeks diversity
among its employees. Background check required.
----------------------------------------------------
From: Catherine Crawley <ccrawley@nimbios.org>
Date: September 9, 2015 at 2:40:54 PM
Subject: Post-docs: Interface of Math & Biology, NIMBioS, U Tennessee
Call for Postdoctoral Fellowship Applications at NIMBioS -- Next
Deadline: December 11, 2015
The National Institute for Mathematical and Biological Synthesis
(NIMBioS), located at the Univ. of Tennessee, Knoxville, is currently
accepting applications for postdoctoral scholarship at the interface
between mathematics and biology. Highest priority will be given to those
with explicit plans to develop their ability to effectively carry on
research across these fields. We are particularly interested in
requests to support research that integrates diverse fields, requires
synthesis at multiple scales, and/or makes use of or requires
development of new mathematical/computational approaches. NIMBioS
Postdoctoral Fellows are chosen based upon indications that the
applicant's research plans are consistent with the mission of NIMBioS,
the applicant has the demonstrated ability to carry out the proposed
research, and the opportunities provided through NIMBioS will enhance
the capacity for the research to be completed in an efficient and timely
manner. Support: annual stipend of $51,000, full University of Tennessee
employee fringe benefits, and an annual travel allowance of $3,000.
How to apply: Complete the online application and submit a brief project
description, references, and CV following the guidelines available at
http://www.nimbios.org/postdocs/
Helpful tips for submitting a successful application are available at
http://www.nimbios.org/postdocs/#tips
Deadline: NIMBioS postdoctoral requests for support are reviewed two
times per year, and the selected researchers are offered positions at
NIMBioS where they conduct research that is mostly self-directed. The
deadline for activities beginning in summer/fall 2016 is December 11,
2015 but applications for positions starting later in 2016 are also
accepted at this time. All letters of recommendation must be submitted
before the request deadline.
The National Institute for Mathematical and Biological Synthesis
(NIMBioS) (http://www.nimbios.org) brings together researchers from
around the world to collaborate across disciplinary boundaries to
investigate solutions to basic and applied problems in the life
sciences. NIMBioS is sponsored by the National Science Foundation, with
additional support from The University of Tennessee, Knoxville.
----------------------------------------------------
From: Lynne Pryor <lpryor@unimelb.edu.au>
Date: September 14, 2015 at 1:02:17 AM
Subject: Lecturer: Applied Mathematics/Mathematical Biology, U Melbourne
For information about a Lecturer Position in Applied Mathematics, in the
area of modelling in mathematical biology, see
http://jobs.unimelb.edu.au/caw/en/job/886426/lecturer-in-applied-mathematics-mathematical-biology
----------------------------------------------------
From: Emilia Vynnycky <Emilia.Vynnycky@phe.gov.uk>
Date: September 11, 2015 at 11:22:22 AM
Subject: Research Fellow: Infectious Disease Modelling, London
Research Fellow in Infectious Disease Modelling
Faculty of Epidemiology & Population Health, London School of Hygiene &
Tropical Medicine
Salary: £37,106 to £42,139 Per annum, inclusive
Closing Date: Wednesday 07 October 2015
Interview Date: To be confirmed
Reference: GAV1
We are seeking to recruit a highly motivated and organised Research
Fellow to work on modelling the impact of measles-rubella vaccination in
over 70 countries on the burden of Congenital Rubella Syndrome (CRS), a
preventable cause of mortality and significant lifelong disability. The
work is funded by the GAVI Alliance, which, as part of a major
initiative to reduce the burden of CRS, has supported eligible countries
to introduce measles-rubella vaccine since 2013.
The work involves calculating the numbers of cases and deaths associated
with CRS in GAVI-eligible and other low and middle-income countries and
the uncertainty associated with these estimates. The estimates play a
key role in GAVI Alliance's Strategic Demand Forecasting. The post
requires a high degree of personal initiative, involving a broad range
of complex, original, and computationally-demanding scientific work, and
is collaborative with the Centers for Disease Control, Atlanta, USA. The
post-holder will be based at the London School of Hygiene & Tropical
Medicine and will be supervised by Emilia Vynnycky.
The post-holder is expected to have a PhD or equivalent experience in
mathematics, statistics, epidemiology, or other subject with a major
modelling component, experience of mathematical modelling of dynamic
systems or of the transmission of infections and of using programming
languages, ideally C/C++ (the programming language used for existing
models in this project).
The appointment is available immediately and is currently funded until
31 July 2016 with a possibility of extension. Starting salary will be in
the range £37,106-£42,139 per annum on LSHTM's Academic Pathway scale at
Research Fellow Grade 6.
Applications should be made on-line via
https://jobs.lshtm.ac.uk/Vacancy.aspx?ref=GAV1. The reference for this
post is GAV1. Applications should include the names and email contacts
of 2 referees who can be contacted immediately if shortlisted. Any
queries regarding the application process may be addressed to
jobs@lshtm.ac.uk. The London School of Hygiene & Tropical Medicine is
committed to being an equal opportunities employer.
----------------------------------------------------
From: keystonesymposia <keystonesymposia@keystonesymposia.org>
Date: September 13, 2015 at 5:06:35 PM
Subject: Fellows Program: Keystone, Sep 30 Deadline Extended
For information about the Keystone Symposia Fellows Program, see
http://www.keystonesymposia.org/fellows#utm_source=2015FellowsEmail2&utm_medium=banner&utm_campaign=2015FellowsEmail2
----------------------------------------------------
Subject: SMBnet Reminders
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End of SMB Digest
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