----------------------------------------------------
Subject: SMB Digest v12i29
SMB Digest July 17, 2012 Volume 12 Issue 29
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(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:
NSF Webinar, Jul 19, AGEP Program
Support Available for Activities at NIMBioS, UT, Knoxville
Conference: Bioinformatics & Comp. Biology, Mar 4-6, Honolulu
ToC: BMB, Vol 74, Issue 8
PhDs/Post-docs: Modelling Human-Environment Systems, U Guelph
Post-doc: Computational Neuroscience, UT San Antonio
Funding Opportunity: NIH Director's Early Independence Awards
SMBnet Reminders
----------------------------------------------------
From: Henry Warchall <hwarchal@NSF.GOV>
Date: July 16, 2012 11:18:28 AM
Subject: NSF Webinar, Jul 19, AGEP Program
The NSF Mathematical and Physical Sciences (MPS) Directorate and the
Division of Human Resource Development (HRD) will host a webinar at 3 PM
Eastern Time on Thursday, July 19. The Webinar will discuss the
Alliances for Graduate Education and the Professoriate (AGEP) program
(NSF 12-554) and the MPS AGEP Graduate Research Student supplement
opportunity.
The AGEP program is committed to the national goal of increasing the
numbers of under-represented minorities (URMs), including African
Americans, Hispanic Americans, American Indians, Alaska Natives, Native
Hawaiians and other Pacific Islanders, as well as URMs with
disabilities, in the science and engineering workforce.
The webinar will consist of three parts:
-Introduction by Dean Evasius, Head of the MPS Office of
Multidisciplinary Activities
-Overview of the AGEP program by Jessie DeAro, AGEP Program Director,
HRD
-Audience question and answer session
The webinar, to be hosted using WebEx online meeting software, will be
recorded and made available for subsequent listening. Registration is
required.
Webinar registration deadline: Wednesday, 7/18/2012 by 3:00 pm
Eastern Time
Webinar announcement and link to registration page:
[www.nsf.gov/events/event_summ.jsp?cntn_id=124693&org=DMS]
AGEP program page: [www.nsf.gov/funding/pgm_summ.jsp?pims_id=5474]
AGEP program FAQ:
[www.nsf.gov/publications/pub_summ.jsp?ods_key=nsf12071]
MPS AGEP ? GRS supplement opportunity: [www.nsf.gov/pubs/2012/nsf12021/nsf12021.jsp]
----------------------------------------------------
From: Catherine Crawley <ccrawley@nimbios.org>
Date: July 13, 2012 8:53:00 AM
Subject: Support Available for Activities at NIMBioS, UT, Knoxville
Support Available for Activities at the National Institute for
Mathematical and Biological Synthesis
September 1, 2012 is the deadline for requests for support for Working
Groups, Investigative Workshops, Postdoctoral Fellows, Sabbaticals, and
Short-term Visitors for activities beginning spring 2013 at the National
Institute for Mathematical and Biological Synthesis (NIMBioS). All areas
of research at the interface of biology and mathematics will be
considered. NIMBioS, located at the University of Tennessee-Knoxville,
is an NSF-sponsored initiative to foster interdisciplinary research at
the interface between mathematical and biological sciences. The
institute's mission is to cultivate cross-disciplinary approaches in
mathematical biology and to develop a cadre of researchers who address
fundamental and applied biological problems in creative ways. Other
NIMBioS sponsors include DHS and USDA, with additional support from the
University of Tennessee-Knoxville. More details are posted at
http://www.nimbios.org .
Related Links:
NIMBioS Working Groups http://www.nimbios.org/workinggroups/
NIMBioS Investigative Workshops http://www.nimbios.org/workshops/
Postdoctoral Fellowships http://www.nimbios.org/postdocs/
Sabbaticals http://www.nimbios.org/visitors/sabbatical
Short-term Visits http://www.nimbios.org/visitors/
----------------------------------------------------
From: Al-Mubaid, Hisham <HISHAM@uhcl.edu>
Date: July 11, 2012 12:08:36 PM
Subject: Conference: Bioinformatics & Comp. Biology, Mar 4-6, Honolulu
5th International Conference on Bioinformatics and Computational Biology
- BICoB2013
March 4-6, 2013 - Honolulu, Hawaii, USA
http://bicob.ece.iastate.edu/
Paper Submission Deadline: October 28, 2012
Notification of Acceptance: December 15, 2012
The 5th international conference on Bioinformatics and Computational
Biology (BICoB) provides an excellent venue for researchers and
practitioners in the fields of bioinformatics and computational biology
to present and publish their research results and techniques. The BICoB
conference seeks original and high quality papers in the fields of
bioinformatics, computational biology, systems biology, medical
informatics and the related disciplines. The conference also includes a
Best Paper Award given during the conference banquet. We also encourage
work in progress and research results in the emerging and evolutionary
computational areas. Computational techniques have already enabled
unprecedented advances in modern biology and medicine. This continues to
be a vibrant research area with broadening of computational techniques
and new emerging challenges. Work in the computational methods related
to, or with application in, bioinformatics is also encouraged including:
data mining, text mining, machine learning, modeling and simulation,
pattern recognition, data visualization, biostatistics, etc. The topics
of interest include (and are not limited to):
Genome analysis: Genome assembly, genome and chromosome annotation,
gene finding, alternative splicing, EST analysis, comparative genomics
and metagenomics.
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.
Submission Procedures
Papers will be accepted only by electronic submission (PDF only). A full
paper should be submitted by October 28, 2012 at the following website:
https://cmt.research.microsoft.com/BICOB2013/ .
Journal Publication: Authors of selected high quality papers in
BICoB-2013 will be invited to submit extended version of their papers
for possible publication in bioinformatics journals (e.g., JBCB, IJCA,
etc.).
Important Dates:
Paper Submission Deadline Oct. 28, 2012
Notification of Acceptance Dec. 15, 2012
Camera-Ready Manuscript Jan. 20, 2013
----------------------------------------------------
From: Springer <springeralerts@springer.delivery.net>
Date: July 13, 2012 2:10:05 PM
Subject: ToC: BMB, Vol 74, Issue 8
Volume 74 Number 8 is now available on SpringerLink
http://www.springerlink.com/content/0092-8240/74/8/
Connect with the Society for Mathematical Biology on Facebook
"Like" the Society for Mathematical Biology's Facebook page to stay
informed about the latest society news, conferences and discussions.
IN THIS ISSUE:
Modeling Non-inherited Antibiotic Resistance
M. C. J. Bootsma, M. A. Horst, T. Guryeva, B. H. Kuile & O. Diekmann
Effect of Model Selection on Prediction of Periodic Behavior in Gene
Regulatory Network
TomᨠGedeon, Graham Cummins & Jeffrey J. Heys
Modeling of Hysteresis in Gene Regulatory Networks
J. Hu, K. R. Qin, C. Xiang & T. H. Lee
Linking Dispersal and Immigration in Multidimensional Environments
Ryan A. Chisholm & Simon A. Levin
Original Article
An Evolution Model for Sequence Length Based on Residue
Insertion-Deletion Independent of Substitution: An Application to the GC
Content in Bacterial Genomes
Sophie Lèbre & Christian J. Michel
Modeling Quasispecies and Drug Resistance in Hepatitis C Patients
Treated with a Protease Inhibitor
Libin Rong, Ruy M. Ribeiro & Alan S. Perelson
The Coalescence of Intrahost HIV Lineages Under Symmetric CTL Attack
Sivan Leviyang
Insights into Cell Membrane Microdomain Organization from Live Cell
Single Particle Tracking of the IgE High Affinity Receptor FceRI of Mast
Cells
Flor A. Espinoza, Michael J. Wester, Janet M. Oliver, Bridget S. Wilson,
Nicholas L. Andrews, Diane S. Lidke & Stanly L. Steinberg
Linearized Forms of Individual-Level Models for Large-Scale Spatial
Infectious Disease Systems
Grace P. S. Kwong & Rob Deardon
Least Squares Estimation in Stochastic Biochemical Networks
Grzegorz A. Rempala
----------------------------------------------------
From: Chris Bauch <cbauch@uoguelph.ca>
Date: July 11, 2012 9:59:47 AM
Subject: PhDs/Post-docs: Modelling Human-Environment Systems, U Guelph
Fully funded postdoctoral and PhD positions available
Modeling coupled human-environment forest-grassland ecosystems
School of Environmental Sciences, University of Guelph
We are seeking 1 or 2 postdoctoral fellows (2 year terms) and 1 or 2 PhD
students (3 year terms) to join in a recently funded project on modeling
naturally occurring forest-grassland mosaic landscapes and their
interactions with human interventions. Work will be based in the Global
Ecological Change laboratory, School of Environmental Sciences,
University of Guelph led by Professor Madhur Anand. The trainees will
have the opportunity (and indeed may be required) to travel to Brazil
and/or India to conduct fieldwork and meet with collaborators, but the
work will mainly involve mathematical and/or computational modeling in
Guelph. As such, applicants should have a strong quantitative skill set
and ability to program in C, C++, Matlab, R or similar languages.
Applications should also have a publication record in ecological
modeling, excellent communication skills, leadership potential and the
ability to work well in groups. Trainees may be co-supervised with
collaborators (e.g., Professor Chris Bauch, Mathematics and Statistics,
Guelph). Guelph is about one hour?s drive from Toronto and its many
attractions and opportunities. Guelph has consistently been ranked as
one of the top 10 places to live in Canada. Please send a letter of
interest indicating why your background is fitting, representative
publications, a CV, and the names and contact information of three
references to manand@uoguelph.ca. Applications will be sought until
suitable candidates are found. Start date is flexible (can be as early
as Fall 2012) but preferably will be in Spring 2013. This project is
being funded by the James S. McDonnell Foundation.
----------------------------------------------------
From: Kay Robbins <krobbins@cs.utsa.edu>
Date: July 12, 2012 2:54:31 PM
Subject: Post-doc: Computational Neuroscience, UT San Antonio
Job Description: We are seeking a highly motivated postdoctoral fellow
in computational neuroscience and signal processing to be part of an
interdisciplinary research alliance working to develop computational
models and data analysis methods in support of a research program in
neuroergonomics ('the study of the brain and body at work'). An overall
goal of the research is to discover underlying principles describing the
relationship of non-invasively recorded EEG brain dynamics and motivated
behavior (recorded by body motion capture, eye tracking, etc) in
interactive, information-rich human-system operating environments and to
apply these principles to support overall performance of complex system
operations.
The ideal candidate will have strong background in statistical learning,
data analysis, and/or visualization preferably with research experience
in neuroscience or cognitive science. The candidate will be based at
University of Texas at San Antonio (UTSA) and will work closely with
researchers and students at participating universities and will present
the research at conferences and in the open research literature. The
candidate will also collaborate with Army Research Laboratory (ARL),
Aberdeen, MD, to assist data analysis from successively more complex and
realistic experiments and with academic research groups at UC San Diego
University of Michigan, National Chiao Tung University, and University
of Osnabruck.
Minimum Requirements: Ph.D. in Electrical Engineering, Computer Science,
Statistics, or related area. Both beginning and more senior postdoctoral
candidates are encouraged to apply. US citizenship is not required but
will be given priority.
Preferred Qualifications: Strong statistical learning skills with
experience in design, analysis, and statistical signal
processing/machine learning applied to data from complex experimental
designs.
Instructions to Applicants: Applicants should submit a cover letter and
CV, including the names and contact information of three references.
Include in the cover letter accompanying the application a summary of
your research experience and goals. Please send application materials by
e-mail to:
Yufei Huang, Associate Professor, Department of Electrical and
Computer Engineering, University of Texas at San Antonio;
yufei.huang@utsa.edu; http://engineering.utsa.edu/~yfhuang/;
(210) 458-6270; E-mail subject: CTA Postdoc.
The University of Texas at San Antonio is an Equal
Opportunity/Affirmative Action Employer. As part of the application
process, applicants will be invited to complete an online confidential
and voluntary self-disclosure card.
----------------------------------------------------
From: Murcia, Ellie (NIH/OD) <murciae@OD.NIH.GOV>
Date: July 13, 2012 2:40:29 PM
Resent-From: Raymond Mejia <mejiar@helix.nih.gov>
Subject: Funding Opportunity: NIH Director's Early Independence Awards
Funding Opportunity Announcement:
2013 NIH Director's Early Independence Awards
The National Institutes of Health Common Fund announces the 2013 funding
opportunity for the NIH Director's Early Independence Awards (EIA).
The EIA initiative allows exceptional junior scientists to accelerate
their transition to an independent research career by "skipping" the
traditional postdoctoral training. To be eligible, candidates must be
within one year (before or after) of completion of their terminal degree
or clinical residency at the time of application. Each institution (as
defined by a unique DUNS identifier) may submit up to only two
applications in response to this FOA.
To facilitate the "matching" of prospective candidates with potential
host institutions, the NIH Common Fund has created a Matching Web
Resources
<http://commonfund.nih.gov/earlyindependence/matchingportal/index.aspx>
site in which institutions may indicate to prospective candidates their
interest in hosting EIA awardees and provide pertinent information.
Interested institutions are encouraged to provide information on the
website by September 1, 2012.
Letters of intent are due December 30, 2012. Applications are due
January 30, 2013. See the instructions in the RFA-RM-12-018
<http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-12-018.html>.
Additional information, including Frequently Asked Questions about the
Early Independence Awards initiative is available at:
http://commonfund.nih.gov/earlyindependence/faq.aspx. Send questions to
earlyindependence@mail.nih.gov.
The NIH Common Fund supports goal-driven, research networks in which
investigators generate data to solve technological problems, and/or
otherwise pilot resources and tools that will be stimulatory to the
broader research community. The research products of Common Fund
programs are expected to catalyze disease-specific research supported by
the NIH Institutes and Centers. Additional information about the NIH
Common Fund can be found at http://commonfund.nih.gov.
About the National Institutes of Health (NIH):
NIH, the nation's medical research agency, includes 27 Institutes and
Centers and is a component of the U.S. Department of Health and Human
Services. NIH is the primary federal agency conducting and supporting
basic, clinical, and translational medical research, and is
investigating the causes, treatments, and cures for both common and rare
diseases. For more information about NIH and its programs, visit
www.nih.gov.
----------------------------------------------------
Subject: SMBnet Reminders
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End of SMB Digest
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