SMB Digest April 29, 2015 Volume 15 Issue 17
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,
http://www.smb.org/.
Access the Bulletin of Mathematical Biology, the official journal
of SMB, at
http://www.springer.com/11538.
Inquiries about membership or BMB fulfillment should be sent to
membership(at)smb(dot)org.
Issue's Topics:
Association of Nepalese Mathematicians in America, Nepal Relief
2015 SMB Annual Meeting early bird registration
Short course: Model fitting and inference ..., UK, June 16-19
CfP: NETTAB and Integrative Bioinformatics ..., Italy, Oct 14-16
Workshop: Multiscale Models in Mechano ..., Germany, Sep 28-30
Submission Deadline Extended: VipIMAGE 2015
CfP: Session on Computational Issues in Biology at ICNAAM 2015
PhD Position: Theoretical and Applied Mechanics ..., U of Adelaide
PhD Position: Mathematical Modelling ..., Swiss ... Institute
3 Postdoc Positions: Biomedical Informatics, Harvard Medical School
Postdoc Position: Health Policy Simulation Modeling, Stanford U
Postdoc Position: Bioinformatics and computational modeling, NIH
6 Postdoc Positions: Modeling Complex Interactions, U of Idaho
SMBnet Reminders
---------------------------------------------------------
From: Vaidya, Naveen K. <
vaidyan@umkc.edu>
Date: Mon, Apr 27, 2015 at 11:13 AM
Subject: Association of Nepalese Mathematicians in America, Nepal Relief
Dear community members,
A 7.9 magnitude earthquake slammed our country of Nepal causing devastating
loss of people and leaving the lives of many in chaos. The quake was
reported as the worst tremor in the region in more than 80 years. Dozens
of aftershocks have been felt in the same regions causing to increase the
chaos. The present situation is utterly terrifying and overwhelmingly
damaging. Victims are in the urgent need of water, food, shelter, and
medical supplies. The government of Nepal has declared the state of
emergency in the country.
On behalf of the Association of Nepalese Mathematicians in America (ANMA),
I would like to appeal to every member of the community for help. Your
generosity will be an invaluable addition to victim relief funds. At this
horrible moment with the country being immersed in tears and blood, every
dollar counts and makes a difference in victims' life. The ANMA has
created Nepal Quake Victim Relief Fund, which can be accessed by visiting
http://anmaweb.org/ and clicking on the flash entitled Donate.
We are committed to make sure that your donation will reach to the victims
in need. The ANMA executive committee members have pledged to donate the
total amount of US $1000. For questions and concerns please contact any
of the following members:
- Dr. Dhruba Adhikari, Faculty, Kennesaw State University,
dadhikar@kennesaw.edu- Dr. Naveen K. Vaidya, Faculty, University of Missouri, Kansas City,
vaidyan@umkc.edu- Mr. Deepak Basyal, Graduate Student, New Mexico State University,
dpakji@gmail.com- Dr. Keshav Pokhrel, Faculty, Mercyhurst University,
kpokhrel@mercyhurst.edu- Dr. Debendra Banjade, Faculty, Coastal Carolina University,
dpbanjade@coastal.edu- Dr. Netra Khanal, Faculty, University of Tampa,
nkhanal@ut.edu- Dr. Kailash Ghimire, Faculty, Georgia Southwestern State University,
ghimire@canes.gsw.edu- Dr. Rajendra Dhahal, Faculty, Coastal Carolina University,
rdahal@coastal.edu- Mr. Bal Kumar Khadka, Graduate Student, Florida Atlantic University,
bkhadka@fau.eduThank you for your help and support!
Sincerely yours,
Dhruba Adhikari, PhD
President
Association of Nepalese Mathematicians in America (ANMA)
---------------------------------------------------------
From: Fred Adler <
adler@math.utah.edu>
Date: Thu, Apr 23, 2015 at 8:59 AM
Subject: 2015 SMB Annual Meeting early bird registration
Early Bird registration for the SMB Annual Meeting in Atlanta
(June 30-July 3) closes on May 10! Students should register for
the Mentoring Workshop and everyone should sign up to for the
Mentoring Program (links below).
Link to Conference
http://math.gsu.edu/~smb/Link to Registration
http://math.gsu.edu/~smb/registration.htmlLink to Mentoring Workshop:
http://math.gsu.edu/~smb/workshop.htmlLink to Mentoring Program:
http://www.smb.org/meetings/mentoring.shtml---------------------------------------------------------
From: Sebastian Funk <
sebastian.funk@lshtm.ac.uk>
Date: Thu, Apr 23, 2015 at 9:30 AM
Subject: Short course: Model fitting and inference ..., UK, June 16-19
The Centre for the Mathematical Modelling of Infectious Diseases (CMMID)
at the London School of Hygiene & Tropical Medicine is are pleased to
invite applications for a 4-day course on
*Model fitting and inference for infectious disease dynamics*
The course will be held from 16-19 June. Course material will range from
the basics of model fitting to methods such as Markov-Chain Monte Carlo
(MCMC) and particle filtering, and will introduce methods used within
CMMID to analyse and forecast the recent Ebola epidemic.
The course fee varies from £400 to £800.
For more information, contact details, and to apply, please visit
http://www.lshtm.ac.uk/study/cpd/infectious_disease_modelling.html---------------------------------------------------------
From: Paolo Romano <
paolo.romano@hsanmartino.it>
Date: Thu, Apr 23, 2015 at 3:28 AM
Subject: CfP: NETTAB and Integrative Bioinformatics ..., Italy, Oct 14-16
Call for Papers and for Abstracts:
Joint NETTAB 2015 & Integrative Bioinformatics 2015 Meeting
15th Network Tools and Applications in Biology Workshop (NETTAB)
11th Integrative Bioinformatics Symposium, October 14-16, 2015, Ruvo di
Puglia (near Bari), Italy.
http://www.igst.it/nettab/2015/For information:
nettab.ib.2015@gmail.comSubmissions are welcome for oral communications, for posters and for
software demo. Talks can be submitted either as full papers or structured
abstracts. Accepted full papers on Integrative Bioinformatics topics
will appear in a special issue of the PubMed indexed Journal of
Integrative Bioinformatics (ISSN 1613-4516,
http://journal.imbio.de/).
Important Dates
* Submissions
Full papers*: May 30, 2015
Abstracts for oral communications: July 7, 2015
Abstracts for posters: September 7, 2015
Abstracts for software demo: September 7, 2015
Abstracts for late posters: October 1, 2015
* Full papers are submitted both for publication in the Journal of
Integrative Bioinformatics (JIB) and for oral communication at the meeting
* Notifications of acceptance
Full papers: July 31, 2015
Abstracts for oral communications: July 31, 2015
Abstracts for posters: September 14, 2015
Abstracts for software demo: September 14, 2015
Abstracts for late posters: October 3, 2015
* Registration deadlines
Early registration: September 17, 2015
On-line registration: October 6, 2015
Workshop
Tutorials: October 12-13, 2015
Workshop: October 14-16, 2015
---------------------------------------------------------
From: Alf Gerisch <
gerisch@mathematik.tu-darmstadt.de>
Date: Mon, Apr 27, 2015 at 8:54 AM
Subject: Workshop: Multiscale Models in Mechano ..., Germany, Sep 28-30
The research group Numerical Analysis and Scientific Computing at TU
Darmstadt is pleased to announce the international workshop
M3TB: Multiscale Models in Mechano and Tumor Biology: Modeling,
Homogenization, and Applications Darmstadt (Germany), September 28-30, 2015.
The workshop is aimed at presenting and discussing the state of the art and
future perspectives in mathematical modeling and homogenization techniques
with the focus on addressing key physiological issues in the context of
multiphase healthy and malignant biological materials. Part of the workshop
is an introductory course on asymptotic homogenization.
Invited Speaker: A. Grillo (Turin), Q. Grimal (Paris), A. Musesti
(Brescia), R. Penta (Darmstadt), K. Raum (Berlin), R. Shipley (London).
Participants are invited to present a talk/poster. Submit abstract by
May 30.
Further information:
http://num.mathematik.tu-darmstadt.de/M3TB/---------------------------------------------------------
From: João Manuel R. S. Tavares <
tavares@fe.up.pt>
Date: Fri, Apr 24, 2015 at 12:39 PM
Subject: Submission Deadline Extended: VipIMAGE 2015
Attending several requests, the organizing committee of the International
Conference VipIMAGE 2015 - V ECCOMAS THEMATIC CONFERENCE ON COMPUTATIONAL
VISION AND MEDICAL IMAGE PROCESSING (
http://www.fe.up.pt/vipimage) to be
held in October 19-21, 2015, in H10 Costa Adeje Palace, Tenerife, Spain,
has extended the submission period to May 15th.
Important dates
- Deadline for Extended Abstracts (2-4 pages): May 15, 2015
- Authors Notification: May 31, 2015
- Deadline for Papers: July 20, 2015
---------------------------------------------------------
From: Nick Cogan <
cogan@math.fsu.edu>
Date: Sun, Apr 26, 2015 at 5:48 PM
Subject: CfP: Session on Computational Issues in Biology at ICNAAM 2015
Call for Participation: Dr. Nick Cogan from Florida State University is
organizing a session at ICNAAM this year. It is a large diverse meeting
and he thought it might be a nice place to place a session on computational
issues in biology - broad enough to appeal to a variety of people. Please
feel free to send him total and abstract. There are multiple spaces, but
he believes he is limited to around 12 but am hoping for at least 6.
Please email
cogan@math.fsu.edu for details.
More information can be found at:
http://www.icnaam.org/sessions_minisymposia.htm---------------------------------------------------------
From: Edward Green <
edward.green@adelaide.edu.au>
Date: Thu, Apr 23, 2015 at 12:59 AM
Subject: PhD Position: Theoretical and Applied Mechanics ..., U of Adelaide
PhD opportunities in the Theoretical and Applied Mechanics Group, School
of Mathematical Sciences, University of Adelaide
The School of Mathematical Sciences at the University of Adelaide has a
long tradition of research excellence in Applied Mathematics, with
particular strengths in mathematical biology, fluid mechanics, and
dynamical systems. Potential PhD projects currently available in the group
include:
* Intercellular calcium signalling in the mammalian cumulus-oocyte complex
(A. Prof Yvonne Stokes)
* Modelling and quantification of filamentous yeast growth (Dr Ben Binder)
* Mechanics of the spinal disc (Dr Sarthok Sircar and Dr Edward Green)
* Modelling of the manufacturing process for Microstructured Optical
Fibres (used in biosensors and other applications) (A. Prof Yvonne Stokes)
* Models for the role of mechanics in morphogenesis and tissue development
(Dr Edward Green)
Applicants should have a Masters degree (or, in the case of Australian
applicants, a good Honours degree) in mathematics, physics, engineering or
a related subject, and must satisfy the entry requirements of the Adelaide
Graduate Centre, which include proficiency requirements in written and
spoken English. Visit
http://www.adelaide.edu.au/graduatecentre/admission/how-to-apply/ for details.
University scholarships are available for well-qualified students, which
are awarded on a competitive basis. Additional scholarship schemes are open
to citizens of certain countries. More information can be found at:
http://www.adelaide.edu.au/graduatecentre/scholarships/Potential applicants should contact prospective supervisors or the
Postgraduate Coordinator for more information (see
http://www.maths.adelaide.edu.au for contact details).
The University of Adelaide is one of Australia's leading universities and
a member of the prestigious Group of Eight. The city of Adelaide is
consistently ranked in The Economist's Top Ten Most Liveable Cities in
the World, and has an international reputation for its premium food and
wine, and cultural events, such as the annual Festival of the Arts and
Fringe Festival. For more information about Adelaide and the University,
visit
http://www.adelaide.edu.au---------------------------------------------------------
From: Nakul Chitnis <
nakul.chitnis@unibas.ch>
Date: Thu, Apr 23, 2015 at 11:09 AM
Subject: PhD Position: Mathematical Modelling ..., Swiss ... Institute
The Swiss Tropical and Public Health Institute is a public institution with
the mandate to contribute to the improvement of the health of populations
internationally and nationally through excellence in research, services,
and teaching and training.
The Department of Epidemiology and Public Health (EPH), within the Swiss
Tropical and Public Health Institute, develops and applies epidemiological,
statistical and mathematical methods to advance innovation, validation,
and application in the field of public health. In partnership with the
Department of Chemistry of the University of Basel (Prof. Anatole O.
Lilienfeld) and our partners in Chad, the Institut de Recherches en
Elevage pour le Développement (IRED) and the Centre de Support en Santé
Internationale (CSSI), we are seeking an interested candidate for the
following position:
PhD Mathematical Modelling of Dog Rabies Elimination
This PhD studentship is available in the area of meta-population and
contact network modelling approaches applied to dog rabies elimination.
Required qualifications:
(1) Master's degree in Mathematics, Statistics, Epidemiology or other
relevant field;
(2) strong quantitative, analytical and programming skills (preferably in
at least one of MATLAB, R, C++, Fortran or Python);
(3) background and/or interest in epidemiology and infectious disease
dynamics;
(4) ability to communicate effectively in spoken and written English
(ability to communicate in French is an advantage).
The successful applicant will be registered for a PhD degree at the
University of Basel, Switzerland. The studentship provides support for 3
years and covers tuition fees and a doctoral salary at Swiss National
Science Foundation scale.
Chadian candidates are especially encouraged to apply.
If you are interested, please submit your application online via the link
provided below, in English with CV, and the names of 3 references:
https://recruitingapp-2698.umantis.com/Vacancies/360/Description/2Kindly note that we can only consider applications from our online tool
(no email). The closing date for applications is 31 May 2015. The
positions are available immediately but a later starting date is
possible by negotiation.
For further information about the position please contact Prof.
Dr. Jakob Zinsstag at
jakob.zinsstag@unibas.ch or Dr. Nakul Chitnis
at
nakul.chitnis@unibas.ch.
---------------------------------------------------------
From: Doe, Aimee <
Aimee_Doe@hms.harvard.edu>
Date: Fri, Apr 24, 2015 at 11:12 AM
Subject: 3 Postdoc Positions: Biomedical Informatics, Harvard Medical School
Position 1: Areas of Interest: Epigenetic Regulation, Cancer, Genomic
Analysis, Computational Biology.
Job Description: A laboratory at the Center for Biomedical Informatics at
the Harvard Medical School (HMS) is looking for a postdoctoral Research
Associate interested in computational analysis of epigenetic mechanisms
disrupted in cancer and other disease tissues. The Research Associate will
be responsible for developing and applying statistical and computational
methods for integrative analysis of genome-wide epigenetic, transcriptional
and proteomic data, aiming to identify specific factors and molecular
mechanisms underlying misregulation of the epigenetic states. The projects
are being conducted in close cooperation with several experimental
laboratories, providing an excellent opportunity for collaborative research.
Requirements:
- Hands-on experience with DNA or RNA sequencing assays
- Good understanding of the basic statistical techniques
- A strong interest in conducting collaborative research on the topics
outlined above
- Track record of publications in peer-reviewed journals
- PhD degree in Molecular Biology, Computational Biology, or a related
discipline.
How to apply: Please send cover letter, curriculum vitae and contact
information for at least two references to Dr. Peter Kharchenko at
peter_kharchenko@hms.harvard.edu. Applications will be considered until
the position is filled.
Position 2: Postdoctoral Research Associate Position (Statistical Modeling
of the Scientific Workforce)
Summary:
The Weber Lab in the Center for Biomedical Informatics (CBMI) at Harvard
Medical School is seeking a Postdoctoral Research Associate to help model
the scientific workforce. The scientific workforce is increasingly relying
on teams to solve the most critical intellectual and social problems that
confront us today. Team collaborations, a growing trend across all
disciplines, yield publications with higher intellectual impact than
single researchers; and, the careers of young scientists are influenced by
relationships with others in the community. We are developing a systems-
based approach to studying scientific workforce dynamics that models the
mechanisms of how new collaborations form and how these influence both
the effectiveness of teams and the career trajectories of individual
scientists.
Requirements:
Candidates must have a PhD or other advance degree in statistics, computer
science, biomedical informatics, or a related field. A strong background in
statistical modeling is required. Some experience programming or working
with databases is needed due to the size of the data, though database
programmers within the Weber Lab will be available for help and training.
Candidates should be highly motivated, creative, and interested in learning
new skills. They must enjoy solving complex and challenging problems and
being part of a multidisciplinary research team. Excellent written and
verbal communication skills are essential.
Preferences:
Experience with R statistical software and/or Microsoft SQL Server is
desirable. Experience with social network analysis, natural language
processing, or data visualization would also be helpful for the project.
Terms:
The position is available immediately and can be renewed annually.
How to apply:
Email applications including curriculum vitae, summary statement of
personal objective and research interests, PDFs of the best two papers,
and the names and email addresses of three references to: Griffin M Weber,
MD, PhD,
weber@hms.harvard.eduPosition 3: Postdoctoral Research Associate Position (Probabilistic
Algorithms and Software for Biomedical Big Data)
Summary:
The Weber Lab in the Center for Biomedical Informatics (CBMI) at Harvard
Medical School is seeking a Postdoctoral Research Associate to help
develop probabilistic algorithms and software for biomedical "Big Data".
Despite all the recent attention to Big Data in both the scientific
literature and popular press, it has yet to have the same impact on
medicine as it has in other areas, such as finance, retail business,
political campaigns, and national security. We believe the key for clinical
applications of Big Data is the ability to create a holistic view of a
patient's health history by linking disparate data sources, such as
electronic health records, administrative claims, genomic data, and data
outside the healthcare system, including social media and information about
the environment. Because there are legal and ethical concerns about sharing
health data, coupled with the fact that there is no universal patient
identifier, our approach is to use probabilistic algorithms that can
protect patient privacy and scale efficiently while searching for
information about patients across datasets with billions of records.
Requirements:
Candidates must have a PhD or other advanced degree in computer science,
biomedical informatics, computational biology, artificial intelligence,
biostatics, or a related field. A strong background in collaborative
software development, and in particular probabilistic algorithms and/or
statistical modeling is required. Experience with large relational
databases and/or other Big Data tools such as Hadoop is also important.
Software components in the distributed query tool, including the patient
linkage module, will be hosted in AWS and communicate using RESTful APIs.
Candidates should be highly motivated, creative, and interested in learning
new skills. They must enjoy solving complex and challenging problems and
being part of a multidisciplinary research team. Excellent written and
verbal communication skills are essential.
Preferences:
Experience with version control software and project management tools
like JIRA are desirable. We primarily use Microsoft SQL Server and write
software in C# for .NET; though, this is not a requirement, and other
development groups that are part of this project use different
programming languages including Java, Python, Perl, and R.
Terms:
The position is available immediately and can be renewed annually.
How to apply:
Email applications including curriculum vitae, summary statement of
personal objective and research interests, PDFs of the best two papers,
and the names and email addresses of three references to: Griffin M Weber,
MD, PhD,
weber@hms.harvard.edu---------------------------------------------------------
From: Holly Chung <
chungh@stanford.edu>
Date: Fri, Apr 24, 2015 at 12:17 PM
Subject: Postdoc Position: Health Policy Simulation Modeling, Stanford U
Postdoctoral Fellowship in Health Policy Simulation Modeling, Stanford
University, Stanford, CA
Postdoctoral Fellowship in Health Policy Simulation Modeling is available
in Dr. Sylvia Plevritis' Lab located in the James H. Clark Center at
Stanford University. The fellowship will involve the development and
application of computer simulation modeling to study the impact of
alternative cancer screening and treatment strategies on cancer incidence
and mortality rates in the US population and inform health policy. The
ideal candidate should have a Ph.D. in a field related to simulation
modeling (i.e. operations research, applied mathematics) or a field that
involves training in statistical analysis of clinical data (i.e.
biostatistics, health-outcomes research, epidemiology). Experience in
stochastic simulation modeling, Monte Carlo methods, parameter
estimation, survival analysis and computer programming (C/C++, R) is
critical. Knowledge of cancer epidemiology, cancer screening and treatment
trials and analysis of cancer registry data is needed. Excellent verbal
and written communication skills are necessary. Applicants should submit
a cover letter, CV and 3 references to Ramzi Totah via email:
rtotah@stanford.edu, with subject line "Postdoctoral Fellow in Health
Policy Simulation Modeling."
---------------------------------------------------------
From: Periwal, Vipul (NIH/NIDDK) [E] <
vipulp@niddk.nih.gov>
Date: Fri, Apr 24, 2015 at 2:21 PM
Subject: Postdoc Position: Bioinformatics and computational modeling, NIH
Postdoctoral Position at the NIH
Position Title: Bioinformatics and computational modeling
Position Description:
* Theoretical systems biology with a particular emphasis on elucidating
mechanisms in disease processes, integrating physiological and genome-scale
datasets
* The Computational Medicine Section is part of the Laboratory of Biological
Modeling, a laboratory with a broad range of projects in applying
quantitative analysis to biomedical problems, ranging from genome scale
inference to diabetes and obesity.
* Strong mathematical and computational skills, some knowledge of machine
learning, and a broad knowledge of biology
* Please email a curriculum vitae, names and contact information of at
least three individuals familiar with your academic work, and a statement
of research interests and future goals to Vipul Periwal,
vipulp@niddk.nih.gov, with subject heading: Computational Medicine Search.
Employer Name: National Institute of Diabetes and Digestive and Kidney
Diseases
Position Location: Bethesda, MD
Application Deadline Date: 5/30/2015
---------------------------------------------------------
From: Philip Lagao <
philip@jobelephant.com>
Date: Fri, Apr 24, 2015 at 7:28 PM
Subject: 6 Postdoc Positions: Modeling Complex Interactions, U of Idaho
The NIH-funded Center for Modeling Complex Interactions (CMCI) at the
University of Idaho will create the intellectual, cultural, and physical
environment to foster convergence in interdisciplinary biomedical research.
The Center will address complex biomedical problems across all levels of
biological organization, from biophysical to ecological, beginning with the
study of viral co-infection. Co-infection is a common but understudied area
of infectious disease. The focal point of CMCI is the Collaboratorium, a
space and a culture for collaborative modeling. It will bring together
faculty from both the empirical and modeling realms with postdoctoral
scientists who reside in the Collaboratorium and devote full-time effort
to collaborative modeling.
We currently have openings for four postdocs in the Collaboratorium and
two in experimental laboratories:
1) epidemiological and biostatistical modeling (SP000473P)
2) transcriptomic and proteomic analysis and modeling (SP000470P)
3) deterministic and agent-based modeling (SP000472P)
4) molecular modeling of proteins (SP000471P)
5) pathogenesis of viral coinfection in mice(SP000474P)
6) molecular biology of viral coinfection in flies (SP000475P)
To apply, go to
http://apptrkr.com/608858 and search by the posting number
following each positon. Review of applications will begin May 18, 2015.
Applications will be accepted until all positions are filled.
Contact Center for Modeling Complex Interactions:
cmci@uidaho.edu or
http://www.cmciuidaho.org/---------------------------------------------------------
Subject: SMBnet Reminders
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The SMB Digest is also available on the SMB Home Page at
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The contents of this publication may be reproduced in whole or in part with
attribution.
End of SMB Digest
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