SMB Digest June 24, 2015 Volume 15 Issue 25
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:
ToC: BMB, Volume 77, Issue 6
PhD Position: Biological Physics, Leiden U
PhD Position: Deciphering Regulatory Interactions..., Utrecht U
Student/Post-doc Positions: Computation. Immunology, Bar-Ilan U
Post-doc: Cell Cycle Modeling, Virginia Tech
Post-doc: Computational Epigenomics, NIH, Baltimore
Post-doc: Pharmacometrics, U Cape Town
Post-doc: Mechanics of Plant Root Growth & Bending, Utrecht U
SMBnet Reminders
----------------------------------------------------
From: Springer <springer@alerts.springer.com>
Date: June 21, 2015 at 9:33:08 AM
Reply-To: Springer <onlineservice@springer.com>
Subject: ToC: BMB, Volume 77, Issue 6
Volume 77 Number 6 is now available at
http://link.springer.com/journal/11538/77/6?wt_mc=alerts.TOCjournals
In this issue
Metabolic Free Energy and Biological Codes: A 'Data Rate Theorem' Aging
Model
Rodrick Wallace
A Computational Model of the Dendron of the GnRH Neuron
Xingjiang Chen & James Sneyd
Modelling Dominance Hierarchies Under Winner and Loser Effects
Klodeta Kura, Mark Broom & Anne Kandler
A Modelling Framework for Gene Regulatory Networks Including
Transcription and Translation
R. Edwards, A. Machina, G. McGregor & P. van den Driessche
Effects of CCN1 and Macrophage Content on Glioma Virotherapy: A
Mathematical Model
Karly Jacobsen, Luke Russell, Balveen Kaur & Avner Friedman
Laplacian Dynamics with Synthesis and Degradation
Inom Mirzaev & David M. Bortz
A Mathematical Framework for Understanding Four-Dimensional
Heterogeneous Differentiation of CD4+ T Cells
Tian Hong, Cihan Oguz & John J. Tyson
A Computational Approach to Steady State Correspondence of Regular and
Generalized Mass Action Systems
Matthew D. Johnston
A Model for Interstitial Drainage Through a Sliding Lymphatic Valve
Charles Heppell, Tiina Roose & Giles Richardson
A Nonlocal Model for Contact Attraction and Repulsion in Heterogeneous
Cell Populations
K. J. Painter, J. M. Bloomfield, J. A. Sherratt & A. Gerisch
Wavelength Selection in Gyrotactic Bioconvection
S. Ghorai, R. Singh & N. A. Hill
A Simple Protein Synthesis Model for the PURE System Operation
Fabio Mavelli, Roberto Marangoni & Pasquale Stano
----------------------------------------------------
From: Roeland Merks <Roeland.Merks@cwi.nl>
Date: June 24, 2015 at 4:55:16 AM
Subject: PhD Position: Biological Physics, Leiden U
Leiden University is currently looking for a student for a joint PhD
project between the groups of Daniela Kraft and Luca Giomi at the
Casimir Research School at Leiden University. The project will
investigate the interplay between curvature and the organisation of
lipid domains in membranes supported by colloidal and micro-fabricated
scaffolds. The student will use a combined experimental and
computational approach to develop a fundamental framework and unravel
the biologically relevant correlation between local geometry and
membrane composition.
The four year position is available immediately, with latest starting
date in June 2016. Candidates should hold an MSc degree in physics,
physical chemistry or material science, and should have affinity for
experimental and computational work in soft matter.
Applications consisting of a resume, a motivation letter, and two
references should be sent to:
giomi@lorentz.leidenuniv.nl and kraft@physics.leidenuniv.nl.
----------------------------------------------------
From: Kirsten ten Tusscher <khwjtuss@hotmail.com>
Date: June 23, 2015 at 9:16:23 AM
Subject: PhD Position: Deciphering Regulatory Interactions..., Utrecht U
PhD: Deciphering regulatory interactions underlying repetitive lateral
root formation (1,0 fte)
Job description
The root system of a plant is crucial for its survival and yield, as it
ensures anchorage to the substrate as well as access to water and
nutrients. Lateral root patterning, the positioning of lateral roots
along the main root of a plant, is a major determinant of overall root
system architecture. Due to the complexity of this developmental
process, involving factors such as root growth mechanics, gene
regulation and hormonal signalling that act at different spatial and
temporal scales and interact in complex manners, lateral root patterning
has thus far remained poorly understood.
In the current project we aim to develop state-of-the art multi-scale
models of plant root development to increase our understanding of
lateral root patterning. For this we will intensively collaborate with
experimental groups. The project is funded by a Vidi-grant awarded to
Dr. K. ten Tusscher.
The candidate will develop sophisticated multi-scale models
incorporating root growth dynamics, genetic regulation and hormonal
signalling. Goal is to unravel how these processes together give rise to
the oscillation-type dynamics that underly the regular formation of
lateral roots along the main root. In addition, the candidate will
investigate the role of spatial, long range interactions between lateral
roots at different positions along the main root in this patterning
process.
Qualifications
For the above described project we are looking for a PhD candidate with
a proven experience in multi-scale modeling and either a biological
background or a keen interest in biology.
Offer
The candidate is offered a full-time PhD position for four years.
The salary is supplemented with a holiday bonus of 8% and an end-of-year
bonus of 8,3% per year. In addition we offer: a pension scheme, a
partially paid parental leave, flexible employment conditions.
Conditions are based on the Collective Labour Agreement Dutch
Universities. The research group will provide the candidate with
necessary support on all aspects of the project.
The gross salary is in the range between 2.125 euros,- and maximum
2.717 euros,- per month.
About the organisation
Utrecht University has great ambitions for its teaching quality and
study success rates. This also applies to its clear research profiles
which are centred around four themes: Dynamics of Youth, Institutions,
Life Sciences and Sustainability. Utrecht University plays a prominent
role in our society and contributes to finding the answers to topical
and future societal issues.
The Faculty of Science consists of six departments: Biology,
Pharmaceutical Sciences, Information and Computing Sciences, Physics and
Astronomy, Chemistry and Mathematics. The Faculty is home to 3500
students and nearly 2000 staff and is internationally renowned for the
quality of its research. The Faculty's academic programmes reflect
developments in today's society.
The candidate will be working in the Theoretical Biology Group at the
Biology Department of Utrecht University, The Netherlands. The work will
take place in the Computational Developmental and Evolutionary Biology
subgroup of Dr. Kirsten ten Tusscher.
About the Group
The researchers of the Theoretical Biology Group use mathematical
modeling and computer simulations to perform fundamental biological
research in a variety of biological disciplines ranging from
developmental biology and immunology to evolution.
The Theoretical Biology group is part of the Institute of Biodynamics
and Biocomplexity (IBB), which focuses on the interaction between
experiments, theory and modeling to obtain a systems level understanding
of complex dynamic biological processes and their evolution. The IBB is
embedded in one of the largest Biology departments in the Netherlands
(>200 new students per year), and collaborates with other departments of
the Faculty of Science, the Faculty of Medicine, and the Hubrecht
Institute in Utrecht.
The Theoretical Biology Group teaches Systemsbiology to biology students
at the bachelor and master level. PhD students in the group have diverse
backgrounds ranging from biology, mathematics, physics to computer
science, and typically half of them are from abroad.
Additional information
Additional information about the vacancy can be obtained from:
Dr. Kirsten ten Tusscher, email: k.h.w.j.tentusscher@uu.nl.
As part of the selection procedure, candidates are expected to give an
oral presentation of their prior research.
Apply
To apply please attach a letter of motivation, curriculum vitae and
(email) addresses of two referees. The application deadline is
31/08/2015.
----------------------------------------------------
From: Ramit Mehr <prof.ramit.mehr@gmail.com>
Date: June 18, 2015 at 4:33:10 AM
Subject: Student/Post-doc Positions: Computation. Immunology, Bar-Ilan U
Student and postdoc positions in Computational Immunology
The Computational Immunology Lab of Prof. Ramit Mehr in Bar-Ilan
University, Israel (http://immsilico2.lnx.biu.ac.il) is recruiting
research Students at all levels (undergrad projects, MSc or PhD) and
Post-Doctoral Trainees.
Prof. Ramit Mehr is a leader in computational immunology. The work
performed in her group has led to several discoveries, which have
significantly advanced the field beyond the state of the art. The group
applies modeling and simulation, bioinformatics and statistical analysis
to immunological questions. Our main focus is the development,
population dynamics and function of B, T and NK cell repertoires, in
health, aging, autoimmune diseases and cancer.
Prof. Mehr devotes much time to career training and has a good track
record in terms of the careers of lab alumni. Over 50% of PhD alumni
published several papers before submitting their theses, and most MSc
students have published at least one. All of them presented their work
in national (PhDs also in international) scientific meetings. As a
result, over 50% of PhD alumni have gone on to post-doctoral training,
and all PhD and most MSC alumni work in bioinformatics and related
fields.
We have several fascinating projects, including:
-Lineage tree - based studies of mutations in antibody genes
-Analysis of lymphocyte repertoires
-Simulations of antibody gene rearrangement
-Math modeling of lymphocyte population dynamics
-Math modeling of immune cell recovery from stem cell transplantation
-Analysis of stem cell transplantation patient data
-Analysis of cell marker data from HIV patients
More info: http://immsilico2.lnx.biu.ac.il/Open-Positions.html
Candidates - please send email to ramit.mehr@biu.ac.il , stating the
position you're interested in. Please attach your CV, grades and
publications so far, and the names and contact information of two people
who can recommend you.
----------------------------------------------------
From: John Tyson <tyson@vt.edu>
Date: June 23, 2015 at 3:05:24 PM
Subject: Post-doc: Cell Cycle Modeling, Virginia Tech
Postdoc: Cell Cycle Modeling, Virginia Tech
Seeking a postdoctoral associate with experience in mathematical
modeling to join a team exploring the molecular basis of cell cycle
checkpoints in budding yeast. The research will be supervised
Drs. John Tyson, Jean Peccoud and Neil Adames on the campus of
Virginia Tech in Blacksburg, VA.
Responsibilities and Expertise: construct, analyze, simulate and
optimize stochastic models of the spindle assembly checkpoint and the
DNA damage checkpoint in Saccharomyces cerevisiae. cell cycle
checkpoints. Will require close attention to experimental data from our
lab and the literature, expertise in building realistic models using
chemical rate equations, familiarity with nonlinear dynamical systems
theory and stochastic simulations (Gillespie's stochastic simulation
algorithm), and facility using software tools for bifurcation analysis
and parameter estimation.
Expectations: participate in lab meetings, interact productively with
graduate and undergraduate students, make presentations at professional
meetings, publish results in peer-reviewed scientific journals, and
participate in grant proposal preparation.
Qualifications: a Ph.D. degree in applied mathematics, biophysical
chemistry, biomedical engineering or other relevant discipline; a strong
background in mathematical modeling; good team-working and communication
skills. A genuine interest in computational cell biology is necessary.
To Apply: submit a curriculum vitae and statement of interest online at:
www.jobs.vt.edu (Posting #SR0150080). Three letters of recommendation
should be sent via email to Dr. John Tyson, Department of Biological
Sciences, MC 0406, Virginia Tech, Blacksburg VA 24061 USA or as a pdf
attachment to: tyson@vt.edu. Review of applications will begin July 15,
2015.
Virginia Tech is an Equal Opportunity/Affirmative Action Institution.
----------------------------------------------------
From: Sung, Myong-Hee (NIH/NCI) [E] <sungm@mail.nih.gov>
Date: June 20, 2015 at 9:36:35 AM
Subject: Post-doc: Computational Epigenomics, NIH, Baltimore
Postdoctoral fellowship opportunity in Computational Epigenomics at
National Institutes of Health, USA
A postdoctoral fellowship is available, pending administrative approval,
at the National Institute on Aging, NIH, for developing computational
methods to analyze high-throughput sequencing-based chromatin assays.
The successful applicant will work in the laboratory of Dr. Myong-Hee
Sung at the Bayview campus, Baltimore, Maryland, beginning in September,
2015. We are seeking highly motivated recent Ph.D. scientists who are
interested in investigating outstanding questions in epigenomics using
statistical and computational tools. Relevant publications for future
projects include Sung et al. Mol Cell 2014 (PMID: 25242143); Kwon et al.
Cell 2013 (PMID: 24360274); Hakim et al. Genome Res 2013 (PMID:
23212947); Sung and Hager, Nat Gen 2011 (PMID: 22030604). An ideal
candidate will have a Ph.D. degree in mathematics, physics, engineering,
or a related quantitative discipline, and has some knowledge in
molecular biology or genomics methods. Interested individuals must send
a cover letter, CV, and contact information for 3 references to:
sungm@mail.nih.gov
About training at NIH: Postdoctoral training in the NIH Intramural
Research Program (IRP) provides the opportunity for recent doctoral
degree recipients to enhance their research skills in the resource-rich
National Institutes of Health (NIH) environment, which consists of more
than 1200 laboratories/research projects located on the main campus in
Bethesda, MD and the surrounding area as well as in Baltimore and
Frederick, MD; Research Triangle Park, NC; Hamilton, MT; Framingham, MA;
and Detroit, MI. Trainees pursue basic, translational, and clinical
research free from the demands of obtaining grants and teaching,
although opportunities to do both are available. At the NIH, postdocs
work in a highly collaborative research environment with leading
scientists and clinicians. The postdoctoral community at the NIH is
large (approximately 4,000 strong) and vibrant. Trainees come from
across the U.S. and around the world. Support for international postdocs
is provided by the NIH Division of International Services.
Eligibility: To be eligible for postdoctoral training in the NIH IRP,
individuals must hold a doctoral degree (PhD, MD, DDS, or the
equivalent) and have no more than five years of relevant research
experience since receipt of their most recent doctoral degree. U.S.
citizens and permanent residents are appointed to Postdoctoral
Intramural Research Training Awards (IRTAs); citizens of other nations
are appointed as Visiting Fellows.
Stipend and Benefits: The stipends for postdoctoral trainees at the NIH
are adjusted yearly; with supplements for prior experience, multiple
degrees, and expertise in areas of current interest to the NIH such as
mathematics, engineering, chemistry, and bioinformatics. Note that
stipends for Postdoc IRTAs and Visiting Fellows are identical. Benefits
include health insurance for the trainee and his/her family, and support
for coursework related to the trainee's research and travel to meetings
is often available. In addition, the NIH Fellows Committee (FelCom) and
the NIH Office of Intramural Training & Education (OITE) sponsor a wide
range of career development and social activities. The OITE includes an
Office of Postdoctoral Services, a Career Services Center and Career
Library.
The NIH is dedicated to building a diverse community in its training and
employment programs.
----------------------------------------------------
From: Paolo Denti <paolo.denti@uct.ac.za>
Date: June 22, 2015 at 5:21:55 AM
Subject: Post-doc: Pharmacometrics, U Cape Town
The Division of Clinical Pharmacology at the University of Cape Town
(South Africa) is looking for highly a motivated science/engineering PhD
graduate to join the pharmacometrics group as a post-doctoral fellow.
Pharmacometrics is an emerging discipline that applies mathematical
modelling and simulation to pharmacology, aiding the interpretation of
data from clinical trials, helping decision making, and improving study
design. This fellowship is a great opportunity for a scientist in
quantitative sciences to apply their expertise within the framework of
biomedical research, and pharmacometrics is a highly-sought set of
professional skills both in academia and in the pharmaceutical industry.
Our division has established clinical and pharmacokinetic/
pharmacodynamic expertise in the area of tuberculosis, HIV, and malaria.
The pharmacometrics group within the division is active internationally
and supported by on-going collaborations with some of the most renowned
modelling groups worldwide.
What you need:
A PhD in engineering, physics, mathematics or (bio-)statistics obtained
within the past 5 years.
OR a PhD in biological sciences AND evidence of keen interest and
proficiency towards the quantitative side of the subject.
Experience with computer programming (e.g. R, Matlab, C++) and data
analysis. Previous experience in pharmacometrics (e.g. NONMEM, Monolix)
would be advantageous, but not essential.
A good command of English, passion about scientific research, and the
ability to work within a team.
What we offer:
Mentorship and guidance to learn pharmacometrics (although the candidate
is expected to be able to learn independently).
A range of research projects, mainly in the area of PK/PD of TB/HIV, and
malaria.
A generous scholarship renewable for up to 3 years.
For more details (please take notice of all the conditions of the
award):
http://www.clinpharm.uct.ac.za/wp-content/uploads/2015/06/Postdoc-Announcement-2015-UCT-pharmacometrics-website.pdf
To apply, please email paolo.denti@uct.ac.za with your CV and a letter
of motivation.
----------------------------------------------------
From: Kirsten ten Tusscher <khwjtuss@hotmail.com>
Date: June 23, 2015 at 9:16:23 AM
Subject: Post-doc: Mechanics of Plant Root Growth & Bending, Utrecht U
Postdoc: mechanics of plant root growth and bending (1,0 fte)
Job description
The root system of a plant is crucial for its survival and yield, as it
ensures anchorage to the substrate as well as access to water and
nutrients. Lateral root patterning, the positioning of lateral roots
along the main root of a plant, is a major determinant of overall root
system architecture. Due to the complexity of this developmental
process, involving factors such as root growth mechanics, gene
regulation and hormonal signalling that act at different spatial and
temporal scales and interact in complex manners, lateral root patterning
has thus far remained poorly understood.
In the current project we aim to develop state-of-the art multi-scale
models of plant root development to increase our understanding of
lateral root patterning. For this we will intensively collaborate with
experimental groups. The project is funded by a Vidi-grant awarded to
Dr. K. ten Tusscher.
The candidate will be developing a model for the mechanics of root
growth, incorporating processes such as cell growth, division and
expansion, asymmetric growth leading to root bending and root waving, as
well as emergence of lateral roots from the main plant root. His/her
challenge will be to develop a model that is biologically realistic, yet
computationally efficient.
Qualifications
For the above described project we are looking for a postdoctoral
researcher with a firm knowledge and established experience in the
computational modelling of mechanical processes and a genuine interest
in (plant) biology.
Offer
The candidate is offered a full-time position for two years.
The salary is supplemented with a holiday bonus of 8% and an end-of-year
bonus of 8,3% per year. In addition we offer: a pension scheme, a
partially paid parental leave, flexible employment conditions.
Conditions are based on the Collective Labour Agreement Dutch
Universities. The research group will provide the candidate with
necessary support on all aspects of the project.
The gross salary is in the range between 2.977 euros,- and maximum
3.908 euros,- per month.
About the organisation
Utrecht University has great ambitions for its teaching quality and
study success rates. This also applies to its clear research profiles
which are centred around four themes: Dynamics of Youth, Institutions,
Life Sciences and Sustainability. Utrecht University plays a prominent
role in our society and contributes to finding the answers to topical
and future societal issues.
The Faculty of Science consists of six departments: Biology,
Pharmaceutical Sciences, Information and Computing Sciences, Physics and
Astronomy, Chemistry and Mathematics. The Faculty is home to 3500
students and nearly 2000 staff and is internationally renowned for the
quality of its research. The Faculty's academic programmes reflect
developments in today's society.
The candidate will be working in the Theoretical Biology Group at the
Biology Department of Utrecht University, The Netherlands. The work will
take place in the Computational Developmental and Evolutionary Biology
subgroup of Dr. Kirsten ten Tusscher.
About the Group
The researchers of the Theoretical Biology Group use mathematical
modeling and computer simulations to perform fundamental biological
research in a variety of biological disciplines ranging from
developmental biology and immunology to evolution.
The Theoretical Biology group is part of the Institute of Biodynamics
and Biocomplexity (IBB), which focuses on the interaction between
experiments, theory and modeling to obtain a systems level understanding
of complex dynamic biological processes and their evolution. The IBB is
embedded in one of the largest Biology departments in the Netherlands
(>200 new students per year), and collaborates with other departments of
the Faculty of Science, the Faculty of Medicine, and the Hubrecht
Institute in Utrecht.
The Theoretical Biology Group teaches Systemsbiology to biology students
at the bachelor and master level. PhD students in the group have diverse
backgrounds ranging from biology, mathematics, physics to computer
science, and typically half of them are from abroad.
Additional information
Additional information about the vacancy can be obtained from:
Dr. Kirsten ten Tusscher, email: k.h.w.j.tentusscher@uu.nl. As part of
the selection procedure, candidates are expected to give an oral
presentation of their prior research.
Apply
To apply please attach a letter of motivation, curriculum vitae and
(email) addresses of two referees. The application deadline is
31/08/2015.
----------------------------------------------------
Subject: SMBnet Reminders
To subscribe to the SMB Digest please point your browser at
https://list.auckland.ac.nz/sympa/info/math-smbnet
and complete the subscription information. Alternatively, if you prefer
to simply receive notice when the next issue is available, send mail to
LISTSERV@listserv.biu.ac.il with "subscribe SMBnet Your Name"
in the body of the mail (omit the quotes and include your name).
After you subscribe, you will receive a greeting with additional
information.
Submissions to appear in the SMB Digest may be sent to
SMBnet(at)smb(dot)org .
Items of interest to the mathematical biology community may be submitted
for inclusion in the SMBnet archive. See instructions at:
http://smb.org/publications/SMBnet/pubs/fyi .
The SMB Digest is also available on the SMB Home Page at
http://smb.org/publications/SMBnet/digest/ .
The contents of this publication may be reproduced in whole or in part
with attribution.
End of SMB Digest
****************************************************