SMB Digest July 1, 2015 Volume 15 Issue 26
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
Note:
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Issue's Topics:
Workshop: ...in Microbiome Research, Jul 27-28, NIMBioS
Workshop: Connecting Models to Data..., Nov 8-9, Mérida, Mexico
Books: New Books Alert, Springer
PhD Position: Gastrointestinal Electrophysiology..., U Auckland
PhD Position: Pharmacometrics & Comp. Disease Modelling, Berlin
Post-doc: Neuroimaging Data/Brain Networks, CMU/U Pittsburgh
SMBnet Reminders
----------------------------------------------------
From: Catherine Crawley <ccrawley@nimbios.org>
Date: June 26, 2015 at 8:52:22 AM
Subject: Workshop: ...in Microbiome Research, Jul 27-28, NIMBioS
The National Institute for Mathematical and Biological Synthesis
(NIMBioS) invites you to join the live stream of our Investigative
Workshop, "Computational Advances in Microbiome Research," to be held
July 27-28, 2015, at NIMBioS.
Objectives: Recent years have seen a tremendous upswing in microbial
community research, ranging from studies of the human microbiome to
investigations of biogeochemical cycling in global soil and oceans and
coral mucus ecosystems. This has been triggered in large part by the
decreasing cost, increasing ubiquity, and democratization of analysis
methods for high-throughput sequencing, which has made both
amplification-based and shotgun metagenomic profiling of microbial
communities accessible to diverse research fields. Microbial community
studies have a long history derived from a variety of research areas,
however, including ecology, soil and ocean biochemistry, human and
environmental toxicology, air quality and environmental monitoring,
agriculture, and biodefense. As the methods necessary for modern data
analysis have become more complex, new computational approaches have
developed independently in many of these subfields, but there have been
few opportunities to integrate knowledge and bioinformatic techniques
across microbial community research areas.
The overarching goal of this workshop is to bring together and integrate
novel bioinformatic techniques from diverse areas of microbial community
research. This will allow us more specifically to:
-Share the state of the art in microbial community analysis from diverse
fields.
-Identify techniques from one field that are useful in others.
-Identify gaps in computational and statistical techniques not currently
addressed in any subfields.
-Identify gaps in biological knowledge that could be addressed by new
quantitative methods.
The workshop is designed as a small, focused workshop bringing together
the top thought leaders in computational microbial community analysis
techniques from a variety of biological application areas. We anticipate
this will foster new ideas, accelerate the pace of biological discovery
by disseminating current techniques across fields, provide a starting
point for new collaborations, and identify gaps that might be targeted
by future funding opportunities. Participation in the workshop is by
invitation only.
Co-Organizers: Jill Banfield, Earth and Planetary Science and
Environmental Science, Policy and Management, Univ. of California,
Berkeley and Curtis Huttenhower, Biostatistics (Computational Biology
and Bioinformatics), School of Public Health, Harvard Univ.
Live Stream. The Workshop will be streamed live. Note that NIMBioS
Investigative Workshops involve open discussion and not necessarily a
succession of talks. In addition, the schedule as posted may change
during the Workshop. To view the live stream, visit
http://www.nimbios.org/videos/livestream. Join the discussion on Twitter
using #CAMRws.
For more information, visit
http://www.nimbios.org/workshops/WS_microbiome
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: Ivanek-Miojevic, Renata <RIvanek@cvm.tamu.edu>
Date: June 26, 2015 at 4:24:38 PM
Subject: Workshop: Connecting Models to Data..., Nov 8-9, Mérida, Mexico
Connecting Models to Data: analysis of infection carriage and
transmission data
This 2-day post-conference workshop will be held in conjunction with
ISVEE 14 in Mérida, Yucatán, Mexico. Registration is open at
http://www.eventure-online.com/eventure/welcome.form?type=participant&congress=40_15111&c=a6fec280-d210-4953-971f-3bcf6f469d41
and there are still spots available.
Learning Outcomes: The workshop aims to teach attendees the statistical
approaches for analysis of field and experimental infection carriage and
transmission data to estimate the parameters relevant to control of
infectious diseases either directly or through the development of
mathematical models of infectious diseases (e.g., rates of infection
transmission and the pattern and duration of infection stages in a
host). This will be achieved through a combination of lectures and
hands-on practicals using freely available R software. Attendees' basic
understanding of mathematical modeling of infectious diseases and
statistics would be beneficial but is not required. A few pre-recorded
lectures on the basic modeling/statistical concepts will be provided
free of charge to interested participants.
Instructors: Rebecca Smith, Renata Ivanek, Gustavo Monti, Gavin J.
Gibson
When: 8-9 November 2015 (two days).
Cost per participant: 400 USD.
Contact: rlsdvm@illinois.edu
For more information, please download pdf at
isvee2015.org/wp-content/uploads/2015/02/22_SMITH_ConnectingModelsToData.pdf
----------------------------------------------------
From: Springer <SpringerAlerts@springeronline.com>
Date: July 1, 2015 at 9:01:03 AM
Reply-To: Springer <onlineservice@springer.com>
Subject: Books: New Books Alert, Springer
NEW PRINT & EBOOKS
Mathematics
Mathematical and Computational Biology
An Introduction to Continuous-Time Stochastic Processes
Book Series: Modeling and Simulation in Science, Engineering and
Technology
Capasso, Vincenzo; Bakstein, David
http://www.springer.com/-/2/AU5J675MxIV6JZQW5pWT
Branching Process Models of Cancer
Book Series: Stochastics in Biological Systems, Vol. 1.1
Durrett, Richard
http://www.springer.com/-/4/AU5J675MxIV6JZQW5pWT
----------------------------------------------------
From: Leo Cheng <l.cheng@auckland.ac.nz>
Date: June 25, 2015 at 3:37:40 AM
Subject: PhD Position: Gastrointestinal Electrophysiology..., U Auckland
PhD Positions: Gastrointestinal Electrophysiology/Motility, U Auckland,
New Zealand
The Gastrointestinal Motility group based at the Auckland Bioengineering
Institute, University of Auckland, New Zealand is recruiting PhD
students.
The research group seeks to apply mathematical and engineering
techniques to improve the understanding of both normal and abnormal gut
function. In particular, we target a number of functional motility
disorders and seek to translate our techniques to improving human
health. The group is well established with a strong track record with
high-impact publications and international awards. The group maintain
close links with surgeons/clinicians in Auckland and also have close
collaborations and joint grants with universities in USA, Australia,
Germany and Belgium.
Ideal candidates are excellent, motivated students who are interested in
translational research projects with an undergraduate degree in
engineering, applied maths, physics, medicine or equivalent. Background
knowledge of gastrointestinal physiology is not a pre-requisite, but
some experiences with signal/image processing, mathematical modelling or
instrumentation would be preferred.
The Auckland Bioengineering Institute (ABI) is a cross-faculty research
institute funded primarily from national and international research
grants. It hosts approximately 100 PhD and ME students. ABI staff are
devoted to research and supervision of post-graduate projects.
We have a variety of interesting projects including:
-Image-based analysis and modelling of the pacemaker cells in the
stomach and small intestine
-Analysis of the repolarisation phase of gastric slow wave activity via
novel signal processing techniques
-Development of novel high-resolution electrode platforms for measuring
electrical activity from the stomach/small intestine.
More information is available at:
http://www.abi.auckland.ac.nz/en/about/our-research/gi-system.html
Please send expressions of interest via email to <gi.bioeng@gmail.com>,
stating the project/research area you are interested in. Please attach
your CV, grades, and list of skills and research interests as a single
pdf file.
----------------------------------------------------
From: Cornelia Boehnstedt <cornelia.boehnstedt@fu-berlin.de>
Date: June 30, 2015 at 1:59:49 PM
Subject: PhD Position: Pharmacometrics & Comp. Disease Modelling, Berlin
The Graduate Research Training Program PharMetrX: Pharmacometrics &
Computational Disease Modelling is an interdisciplinary PhD program
bridging pharmacy and mathematics. PharMetrX provides its graduate
students a unique opportunity to experience research in drug development
and optimising drug therapy.
PharMetrX offers:
-a transdisciplinary research environment
-a competitive three-year research fellowship
-a structured research training curriculum of basic and advanced
academic and industry modules
-a joint supervision of the scientific progress by both program chairs
-an individual research and development plan
-an individual mentorship from one of the industry partners
We are currently inviting applications to start the PharMetrX PhD
program in March 2016.
PharMetrX is open to candidates with a university degree in natural/life
sciences or medicine.
Deadline for applications: September 15th, 2015.
For details see https://www.PharMetrX.de.
PharMetrX is a joint program of the Freie Universität Berlin and the
Universität Potsdam, supported by several global research-driven
pharmaceutical companies.
----------------------------------------------------
From: Ghuman, Avniel <ghumana@upmc.edu>
Date: June 26, 2015 at 11:22:08 AM
Subject: Post-doc: Neuroimaging Data/Brain Networks, CMU/U Pittsburgh
Applications are invited for a postdoctoral position to support a
collaboration between researchers at Carnegie Mellon University and the
University of Pittsburgh, USA to develop new methods to combine
multimodal neuroimaging data to understand brain networks.
The research will focus on the development of new tools to combine high
dimensional MEG (magnetoencephalography), fMRI, and structural MRI data
to discover brain network structure. This will include developing
algorithms to understand similarities between data types (neurovascular
relationships, structure-function relationships, etc.) as well as
discovering what unique information each modality provides. These tools
will be developed with the purpose of uncovering how brain networks are
disturbed in existing multimodal data from individuals with autism
spectrum disorder and schizophrenia. Furthermore, these tools will be
developed with aim of applying it to large pubic neuroimaging datasets,
such as those being released as part of the Human Connectome Project.
Applicants should hold a Ph.D. in Neuroscience, Computer Science,
Mathematics, Statistics, Engineering or a related field. Advanced skills
in multivariate statistics, missing data problems, graph theory,
dimensionality reduction, network analysis, machine learning and/or
computational neuroscience are required. Experience with analysis of
human neuroimaging data is desirable. Applicants should have a strong
track record of publication.
The position is fully funded. The initial period is 1 year with
additional years depending on fit and progress. Interested applicants
should send a letter of interest, a CV, and the names and contact
information for 3 researchers who can provide a recommendation. For
further information or to submit an application, please contact Avniel
Ghuman, Ph.D. at ghumana@upmc.edu or Aarti Singh at aarti@cs.cmu.edu .
The position is available immediately and applications will be
considered until the position is filled.
----------------------------------------------------
Subject: SMBnet Reminders
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