SMB Digest September 2, 2014 Volume 14 Issue 36
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,
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Access the Bulletin of Mathematical Biology, the official journal of
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Issue's Topics:
Workshop: ...Bioinformatics to Systems Bio., Oct 15-17, Turin
Conference: Bioinformatics & Comp. Bio., Mar 9-15, Hawaii
Keystone Symposia: 2015 Cardiovascular & Metabolic Disease Conf
Keystone Symposia: 2015 Plant Biology Conferences
Books: New Books Alert, Springer
StochSS: Stochastic Simulation Service, Version 1.4
Post-docs: Bioinformatics & Comp. Bio., U Connecticut Health...
Post-docs: Computational Biology, U Notre Dame
Post-docs: Computational/Statistical Modeling, U Michigan
Post-doc: Biological Data Mining, NIH, Bethesda, MD
Tenure-Track: Quantitative Biology, U Alaska Anchorage
Chair: Department of Mathematics, U Alabama
SMBnet Reminders
----------------------------------------------------
From: Paolo Romano <paolo.dm.romano@gmail.com>
Date: August 27, 2014 4:26:57 AM
Subject: Workshop: ...Bioinformatics to Systems Bio., Oct 15-17, Turin
NETTAB 2014
From high-throughput structural bioinformatics to integrative systems
biology
October 15-17, 2014, Turin, Italy
http://www.nettab.org/2014/
The deadline for the submission of abstracts for posters is set to next
September 1, 2014.
The Early registration deadline has been postponed until September 15,
2014.
The topics of the workshop are centered around methods, tools,
applications, and perspectives on structural bioinformatics, proteomics
and integrative systems biology, as well as synergies among these
disciplines.
Speakers
Ram Samudrala, University of Washington, Seattle, USA
Ada Yonath, Weizmann Institute of Science, Rehovot, Israel
Torsten Schwede, University of Basel, Switzerland
Wolfgang Marwan, Otto-von-Guericke Universität, Magdeburg, Germany
Lilia Alberghina, SYSBIO Centre of Systems Biology, University of
Milano-Bicocca, Italy
Guido Capitani, Paul Scherrer Institute, Villigen, Switzerland
Tutorial speakers
Ram Samudrala, University of Washington, Seattle, USA
Gianfranco Gilardi, University of Torino
Raffaele Calogero, University of Torino
Francesca Cordero, University of Torino
Abstracts for posters must not exceed 2 pages and must be submitted
through EasyChair at
https://www.easychair.org/conferences/?conf=nettab2014
All abstracts will be published in the proceedings. Post workshop
Supplements will be published by BMC Bioinformatics and by BMC Systems
Biology after a special Call for papers open to all presentations, both
oral and poster, given at the workshop.
See you in Torino at NETTAB 2014 Workshop.
----------------------------------------------------
From: Nurit Haspel <nurit.haspel@umb.edu>
Date: August 29, 2014 2:58:23 PM
Subject: Conference: Bioinformatics & Comp. Bio., Mar 9-15, Hawaii
BICoB-2015
7th International Conference on Bioinformatics and Computational Biology
March 9-11, 2015 - Honolulu, Hawaii, USA
Conference website: http://www.cs.umb.edu/bicob/
IMPORTANT DATES:
Paper Submission Deadline: October 24, 2014.
Notification of Acceptance: December 15, 2014.
Pre-registration and Camera-ready paper: January 16, 2015.
About BICoB
The 7th 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-2015 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 JBCB special issues).
Paper submission site:
https://www.easychair.org/conferences/?conf=bicob2015
Conference Chair: Hisham Al-Mubaid: University of Houston, Clear Lake,
USA, hisham@uhcl.edu
Program Co-Chairs:
Fahad Saeed: Western Michigan University, USA, fahad.saeed@wmich.edu
Nurit Haspel: University of Massachusetts at Boston, USA,
nurit.haspel@umb.edu
----------------------------------------------------
From: keystonesymposia <keystonesymposia@keystonesymposia.org>
Date: August 27, 2014 8:33:24 PM
Subject: Keystone Symposia: 2015 Cardiovascular & Metabolic Disease Conf
For information about the conferences, go to
http://www.keystonesymposia.org/index.cfm?e=Web.Meeting.List&tab3#Cat3
----------------------------------------------------
From: keystonesymposia <keystonesymposia@keystonesymposia.org>
Date: August 28, 2014 8:51:17 PM
Subject: Keystone Symposia: 2015 Plant Biology Conferences
For information about the conferences, go to
http://www.keystonesymposia.org/index.cfm?e=Web.Meeting.List&tab3#Cat15
----------------------------------------------------
From: Springer <SpringerAlerts@springeronline.com>
Date: August 31, 2014 5:44:59 PM
Reply-To: onlineservice@springer.com <onlineservice@springer.com>
Subject: Books: New Books Alert, Springer
NEW PRINT & EBOOKS
Mathematics
Mathematical and Computational Biology
Advances in Applied Mathematics
Book Series: Springer Proceedings in Mathematics & Statistics,
Vol. 87
Editor/s: Ansari, Ali R.
http://www.springer.com/alert/urltracking.do?id=L56b8a7dM1006f29Sa845d7bPa88e7dc
Mathematical Modeling in Renal Physiology
Book Series: Lecture Notes on Mathematical Modelling in the Life
Sciences
Layton, Anita T.; Edwards, Aurélie
http://www.springer.com/alert/urltracking.do?id=L56b8abcM1006f29Sa845d7bPa6355b3
Stochastic Processes in Cell Biology
Book Series: Interdisciplinary Applied Mathematics, Vol. 41
Bressloff, Paul C.
http://www.springer.com/alert/urltracking.do?id=L56caec2M1006f29Sa845d7bPa89eeda
----------------------------------------------------
From: Linda Petzold <petzold@cs.ucsb.edu>
Date: September 1, 2014 12:39:30 PM
Subject: StochSS: Stochastic Simulation Service, Version 1.4
We are pleased to announce the release of StochSS: Stochastic Simulation
Service, Version 1.4. StochSS is an integrated development environment
featuring state of the art algorithms for discrete stochastic
biochemical simulation. StochSS is designed to enable you to easily
scale up your simulations in complexity, deploying compute resources as
needed. The current version includes algorithms for simulation of ODEs
with sensitivity analysis, well-mixed stochastic systems, and parameter
estimation for stochastic systems.
New capabilities of Version 1.4 include spatial stochastic simulation
capabilities powered by the PyURDME spatial solver
(http://www.pyurdme.org/).
For more details and instructions on how to obtain the code, visit us at
www.StochSS.org.
Linda Petzold and Chandra Krintz
University of California Santa Barbara
Per Lotstedt and Andreas Hellander
Uppsala Universiteit
----------------------------------------------------
From: Prestine Sumagang <p.sumagang@jobtarget.com>
Date: August 28, 2014 1:05:09 PM
Subject: Post-docs: Bioinformatics & Comp. Bio., U Connecticut Health...
Job Title: POSTDOCTORAL POSITIONS IN BIOINFORMATICS AND COMPUTATIONAL
BIOLOGY
Company Name: University of Connecticut Health Center - UCONN
Location: Farmington, Connecticut, United States, 06030
UConn Health is engaged in a major expansion of its research programs in
computational biology, bioinformatics, and systems biology, as part of
several transformative state initiatives. The Bioscience Connecticut
initiative, totaling approximately $1B, includes the establishment of
the new Center for Quantitative Medicine in 2013.
The Center for Quantitative Medicine is recruiting several postdoctoral
fellows to pursue research in bioinformatics and computational systems
biology with a particular focus on algorithm development and
computational modeling of cellular processes, as well as applications of
quantitative methods to biomedicine. Positions are available in the
Laubenbacher, Mendes, and Vera-Licona research groups. The Laubenbacher
group has ongoing projects in the development and implementation of
algorithms related to modeling and simulation, with applications to
cancer and infectious diseases related to iron metabolism. A particular
focus is on immunological aspects of these and other diseases.
Vera-Licona works on algorithm and software development for the modeling
and simulation of biological systems. She is looking for a postdoc to
work on the development of computational tools for identification of
cascading failures and in silico combination therapies in complex
biological networks. Mendes studies computational methods in systems
biology, including development of simulation software, and is seeking a
postdoctoral researcher to work on creating models of iron biochemistry,
which is associated with several diseases such as cardiovascular,
cancer, neurodegenerative, and many others. There are many collaborative
activities between the three research groups. For more information about
the CQM, please visit our website at http://cqm.uchc.edu/
The successful candidates will be expected to pursue research in the
areas described above, with activities including interacting with
experimental collaborators, setting up models, data analysis workflows,
and other computational procedures, writing up and publishing results in
peer-reviewed journals, presenting results at conferences and helping
with developing new projects. The successful candidates will be
individuals with background in mathematics, computer science, or physics
with some knowledge of biology, or biologists with experience in
developing computational/mathematical models. All of these positions
will be pursuing interdisciplinary work at the boundaries of these
disciplines.
To apply, please send your CV, a brief statement of research interests,
and contact information for three references to Kathy Black at
kblack@uchc.edu
The University of Connecticut is an Affirmative Action/Equal Employment
Opportunity employer, M/F/M/PwD/PV
----------------------------------------------------
From: Kathy Phillips <Kathy.Phillips@nd.edu>
Date: August 29, 2014 8:43:53 AM
Subject: Post-docs: Computational Biology, U Notre Dame
Two Postdoctoral Research Associate Positions in Computational Biology
We invite applications for two NIH and NSF funded postdoctoral research
positions in the computational biology group in the Department of
Applied and Computational Mathematics and Statistics (ACMS), University
of Notre Dame.
The goal of the first project is to develop at Notre Dame novel,
multi-scale computational models to study blood clot formation to be
calibrated using specific experiments to be performed at the University
of Pennsylvania School of Medicine.
The second project will combine new biophysical methods, live imaging,
and advanced organ culture techniques with computer simulations to
investigate intercellular signaling in intact epithelial organs within a
controlled microenvironment. Success in this project will lead to a
better understanding of how exogenous factors impact the endogenous
regulation of organ growth and differentiation.
Priority will be given to candidates with research interests and
experience in biological modeling and parallel implementation of
computational models. Additional experience with image processing is a
plus. Successful applicants will be detail oriented, eager to learn new
techniques, and enthusiastic about biological questions that are tackled
within a multidisciplinary team environment. Positions are for 1 year
with possible extension to up to two additional years. The salary is
competitive. Applications, including curriculum vitae and research
statement, should be sent electronically to Dr. Mark Alber at:
malber@nd.edu. Applicants should also arrange for at least three letters
of recommendation to be sent to the same email address. The evaluation
of candidates will begin immediately and continue until the position is
filled.
----------------------------------------------------
From: Pej Rohani <rohani@umich.edu>
Date: August 29, 2014 12:19:54 PM
Subject: Post-docs: Computational/Statistical Modeling, U Michigan
POSTDOCTORAL RESEARCH ASSOCIATES
Departments of Ecology & Evolutionary Biology, Statistics, Mathematics
and Center for the Study of Complex Systems, University of Michigan, Ann
Arbor, USA
Applications are invited for two postdoctoral research fellowships as
part of a 5-year NIH-funded project involving an interdisciplinary team
of collaborators: Pej Rohani, Aaron King, Ed Ionides and Mercedes
Pascual. We are seeking to recruit candidates who will participate in
one of two related projects.
(1) Use computational and statistical models to understand the
immunological, spatial and climatic determinants of dengue transmission.
(2) To develop and implement computational methods for statistical
inference applied to high-dimensional, mechanistic epidemiological
systems, with a focus on polio population biology.
The ideal candidate has a PhD in statistics, applied mathematics,
applied physics, epidemiology or other highly quantitative field and
previous experience in the analysis of epidemiological or ecological
systems. The salary will be in the range of $40,000-50,000 per year
(depending on experience), plus fringe benefits. Starting date is
negotiable.
The University of Michigan is a vibrant scientific community and the
successful applicants will be afforded many opportunities for
professional development. Ann Arbor offers a rich cultural and
intellectual life in a very livable small city setting.
For further information, contact Pej Rohani (e-mail: rohani@umich.edu).
Applicants should send a cover letter, a detailed CV, a brief statement
of research interests, and the names of three referees. The cover letter
should discuss possible starting dates.
Review of applications will start on October 1st and will continue until
the posts have been filled.
----------------------------------------------------
From: Mark Knepper <knepperm@helix.nih.gov>
Date: September 1, 2014 1:32:00 PM
Subject: Post-doc: Biological Data Mining, NIH, Bethesda, MD
Postdoctoral Position in Biological Data Mining
Systems Biology Center
Division of Intramural Research (DIR)
National Heart, Lung and Blood Institute (NHLBI)
National Institutes of Health (NIH)
Health and Human Services (HHS)
POSITION DESCRIPTION: Biology is undergoing a 'big-data' revolution.
Next-generation DNA sequencing methods are routinely creating
multi-terabyte data sets that must be mined in the context of prior data
from pre-existing data sources. A postdoctoral Research Fellow position
is available for an individual with a PhD (or similar) in computer
science or a related field that has skills in machine learning, data
mining and parallel computing as well as a strong interest in biological
applications. The position is in the laboratory of Dr. Mark Knepper in
the Systems Biology Center at the National Heart, Lung, and Blood
Institute (NHLBI), the National Institutes of Health (NIH) in Bethesda,
Maryland. Dr. Knepper?s laboratory mission is to use systems
biology-based approaches to investigate intracellular mechanisms
involved in the regulation of water excretion by the kidney through
actions of the hormone vasopressin. Current studies are combining data
from next-generation DNA sequencing (NGS) methodologies with large-scale
data sets from protein mass spectrometry to model signaling networks and
transcriptional networks in kidney collecting duct cells. Projects will
involve direct day-to-day collaboration with scientists that are
generating data sets using protein mass spectrometry and NGS. The
ultimate objective is to develop treatments for common water-balance
disorders. The initial appointment can be renewed annually for up to 5
years, dependent on performance. Applicants may apply for "Pathway to
Independence" funding (K99 award) in preparation for transition to
academic positions.
REQUIREMENTS: A Ph.D. in computer science, computer engineering,
biomedical engineering, chemical engineering, bioinformatics, systems
biology, applied mathematics or a related discipline is required. Prior
experience in addressing biological questions is desirable but not
mandatory. Prior experience in modeling from biological "big" data is
beneficial, but not required. The successful applicant needs to be a
team worker with good communication skills.
SALARY/BENEFITS: The successful candidate will be offered salary and
benefits commensurate with experience and accomplishments. The
appointment would be through the Title 42 mechanism
(http://hr.od.nih.gov/benefits/pay/default.htm).
TO APPLY: E-mail a single PDF document containing 1) your Curriculum
Vitae, 2) a one-page statement of your long-term career goals and
3) contact information for at least 3 references, to Dr. Mark Knepper at
NHLBIKnepperRFRecruit@nih.gov.
Applications will begin to be examined on October 1, 2014. This
advertisement will remain open until the position is filled.
HHS and NIH are Equal Opportunity Employers.
----------------------------------------------------
From: Christine D Mattingley <cdmattingley@uaa.alaska.edu>
Date: August 29, 2014 5:27:08 PM
Subject: Tenure-Track: Quantitative Biology, U Alaska Anchorage
Assistant Professor in Quantitative Biology
The Department of Biological Sciences at the University of Alaska
Anchorage invites applications for a tenure track faculty position in
Quantitative Biology. We are broadly interested in recruiting a
candidate working at the nexus of biology and statistics/mathematics,
who uses quantitative experimental, computational, and/or mathematical
methods, and who will develop an active research program within the
department and university community.
Areas of interest include statistical analysis of large data sets,
mathematical models of complex biological phenomena, systems biology,
cell biology, population genomics and/or molecular evolution, advanced
biostatistical approaches to organismal biology, population ecology,
and/or behavior.
The successful candidate is expected to contribute to the undergraduate
and graduate teaching missions of the Department through offering
biostatistics courses, teaching advanced classes in their area of
expertise, and training graduate students. Candidates will be expected
to enhance the research mission of the department through the
development of an active, externally funded research program.
The ideal candidate will have a passion for student learning, evidenced
by a record of, or potential for, excellence in teaching, and a
commensurate record of significant contributions to quantitative
biological research. Interest in collaborative research opportunities
within and outside the Department of Biological Sciences is a plus.
Faculty in the Department of Biological Sciences participate in NSF
EPSCoR and NEON, NIH INBRE, and other cross-cutting research programs
within and outside the University of Alaska, and closely interact with
colleagues from numerous state and federal health, land, wildlife, and
fisheries management agencies. Faculty websites detailing current
research interests can be found at www.uaa.alaska.edu/biology.
The University of Alaska Anchorage (UAA) is the largest of three
universities in the University of Alaska system, serving nearly 20,000
students. Anchorage, the largest city in Alaska, with an ethnically
diverse population of 290,000, offers a lively intellectual and cultural
life, including opera, symphony, theater, art events, and a variety of
restaurants. Set between snow-capped peaks of the Chugach Mountains and
the ocean waters of Cook Inlet, the city offers ready access to state
and national forests and parks, year-round outdoor recreation, and
unsurpassed natural beauty.
The Department seeks a candidate dedicated to equity and diversity of
the campus community and to promoting an environment that increases
student knowledge about local, national, and global communities. UAA is
an AA/EO Employer and Educational Institution. Applicant must be
eligible for employment under the immigration Reform and Control Act of
1986 and subsequent amendments. Your application for employment with UAA
is subject to public disclosure under the Alaska Public Records Act.
Interested persons should apply by submit a cover letter, curriculum
vitae including recent publications, a statement of research
accomplishments and future plans, a description of teaching experience
and philosophy, and three letters of reference by applying to the
University of Alaska Anchorage online at uakjobs.com.
----------------------------------------------------
From: Zhao, Shan <szhao@ua.edu>
Date: August 29, 2014 4:20:03 PM
Subject: Chair: Department of Mathematics, U Alabama
The University of Alabama seeks an outstanding individual at the rank of
Associate or Full Professor for the position of Chair of the Department
of Mathematics. Ph.D. in Mathematics or closely related field required.
The successful candidate must be nationally/internationally recognized,
with an active research program that includes external funding, and with
the ability to help shape a progressive thriving department within a
university whose student enrollment has nearly doubled in the last ten
years and whose trajectory is upwards. The applicant should possess
proven leadership abilities, preferably with administrative experience,
and have an understanding and enthusiasm for both the teaching and
research missions. The area of expertise of the applicant is open, but
should complement those of the existing faculty and future plans for
growth in the Department.
The University of Alabama is the flagship campus of a three-campus
system. The University is located in Tuscaloosa, a city of approximately
100,000. The UA Department of Mathematics has 28 tenured/tenure track
faculty, 11 full time instructors and 40 graduate students, with
research programs in algebra, analysis, fluid dynamics, image
processing, mathematics education, optimization, scientific computing,
statistics, stochastic processes and topology. The department has an
in-house Mathematics Ph. D. program and a joint Applied Mathematics
Ph. D. program with the other two campuses. The UA Mathematics program
places emphasis on quality education at the undergraduate and graduate
levels.
Applicants should apply online at
https://facultyjobs.ua.edu/postings/35681; attach a curriculum vita
along with a letter of application and arrange for three letters of
recommendation to be sent to math@ua.edu. Statements of administrative
and leadership philosophy, research plans, and teaching philosophy and
interests should also be included. Potential candidates may contact the
chairperson of the search committee, Dr. Martyn Dixon, at mdixon@ua.edu
if additional information is desired. Beginning October 15, 2014,
applications and nominations will be reviewed on an ongoing basis and
will continue to be accepted until the position is filled. The position
is scheduled to start on August 16, 2015, or as negotiated.
The University of Alabama is an Equal Opportunity Employer/Affirmative
Action employer and actively seeks diversity among its employees. Women
and minority candidates are strongly encouraged to apply. For more
information about the Department and the University visit our website at
http://www.math.ua.edu.
----------------------------------------------------
Subject: SMBnet Reminders
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End of SMB Digest
****************************************************