Subject: Society for Mathematical Biology Digest

SMB Digest  November 22, Volume 16  Issue 47
ISSN 1086-6566

Editor: Wandi Ding: ding.smb.digest(at)gmail(dot)com

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:  
   CfP: Conf: Bioinformatics & Comp Biology, Hawaii, March 20-22
   MBI Workshop: Women Advancing Mathematical Biology, April 24-28
   CfP: Special Session on AIS @ CEC 2017, June 5-8
   Keystone Symposia 2017: Infectious Diseases Conferences
   AIBS November 2016 Newsletter
   PhD Position: Modelling Spine Calcium Dynamics, U of Exeter
   PhD Positions: Controlling Noise Effects in Models..., U of Exeter 
   PhD Positions: Developing Gaze Training for..., U of Exeter
   PhD Positions: Human Population/Quantitative..., U of Adelaide
   Postdoc Position: Computational Biology, Frankfurt Institute...
   Postdoc Position: Spatial Modeling, NIMBioS
   Postdoc and Faculty Positions: Mathematical Institute, Oxford
   Postdoc Position: Math Modelling/Systems Biology, RCSI
   Faculty Position: Synthetic & Systems Biology, Arizona State U
   Faculty Positions: Bioengineering, Indiana U
   SMBnet Reminders


From: Ding, Qin <DINGQ@ecu.edu>
Date: Fri, Nov 18, 2016 at 10:23 AM
Subject: CfP: Conf: Bioinformatics & Comp Biology, Hawaii, March 20-22

BICOB-2017 - Call for Papers
9th International Conference on Bioinformatics and Computational Biology 
(BICOB), March 20 - 22, 2017 - Honolulu, Hawaii, USA
Important Dates
- Paper Submission Deadline: November 30, 2016 (extended)
- Notification of Acceptance: December 30, 2016 
- Pre-registration and Camera-ready Manuscripts: January 20, 2017
- Paper submission site: https://easychair.org/conferences/?conf=bicob2017
- Conference website:  http://sce.uhcl.edu/bicob17/


From: Rebecca Segal <rasegal@vcu.edu>
Date: Thu, Nov 17, 2016 at 2:43 PM
Subject: MBI Workshop: Women Advancing Mathematical Biology, April 24-28

Applications are still being accepted for the workshop "Women Advancing 
Mathematical Biology: Understanding Complex Systems with Mathematics"
which will be held at the Mathematical Biosciences Institute on April 
24-28, 2017. Applications received by December 10, 2016 will receive 
priority. This workshop will tackle a variety of biological and medical 
questions using mathematical models to understand complex system dynamics. 
Working in collaborative teams of 4-5, each with a senior research mentor, 
participants will spend a week making significant progress with a research 
project and foster innovation in the application of mathematical, 
statistical, and computational methods in the resolution of significant 
problems in the biosciences.

For more information about the workshop and application instructions go 
to: https://mbi.osu.edu/event?id=1067#description


From: Mario Pavone <mpavone@dmi.unict.it>
Date: Mon, Nov 21, 2016 at 3:13 PM
Subject: CfP: Special Session on AIS @ CEC 2017, June 5-8


Artificial Immune Systems: Algorithms, Simulation, Modelling & Theory
IEEE CEC 2017 Special Session, June 5-8, 2017, Donostia - 
San Sebastián, Spain


* SUBMISSION deadline: January 16, 2017

Manuscripts should be prepared according to the standard format and page 
limit of regular papers specified in CEC 2017 webpage: http://www.cec2017.org
and submitted via the official submission system.


From: Jane Peterson <janelp@keystonesymposia.org>
Date: Thu, Nov 17, 2016 at 5:40 PM
Subject: Keystone Symposia 2017: Infectious Diseases Conferences

The 2017 conferences in our Infectious Diseases series are:

Hemorrhagic Fever Viruses (S3)

Cellular Stress Responses and Infectious Agents (S4)

New Developments in Our Basic Understanding of Tuberculosis (A5)

Viral Immunity: Mechanisms and Consequences (B4)

Malaria: From Innovation to Eradication (B5)

HIV Vaccines (C9)

Modeling Viral Infections and Immunity (E1)


From: AIBS <membership@aibs.org>
Date: Fri, Nov 18, 2016 at 9:22 AM
Subject: AIBS November 2016 Newsletter

American Institute of Biological Sciences (AIBS) November 2016 Newsletter.



From: Tsaneva-Atanasova, Krasimira <K.Tsaneva-Atanasova@exeter.ac.uk>
Date: Sat, Nov 19, 2016 at 1:20 PM
Subject: PhD Position: Modelling Spine Calcium Dynamics, U of Exeter


Project Description:
Nerve cells (neurones) in the brain communicate with one another at 
connect ions called synapses. A chemical (neurotransmitter) is released 
from a neuron and travels across the synapse to activate receptors in the 
adjacent neuron. Synapses can change their strength (known as "synaptic 
plasticity") by altering the number of receptors found on the surface of 
the neuron in the synapse. This process is thought to underlie learning 
and memory, because the memory is likely to be stored in a circuit of 
interconnected neurons. The critical trigger for synaptic plasticity is 
the influx of calcium ions into very small compartments of neurones called 
spines, tiny structures approximately 1 millionth of a metre in diameter. 
However, this influx of calcium ions can also trigger cell death after 
ischaemic injury that occurs during stroke so it must be tightly regulated.

Plasticity of excitatory synapses is a key mechanism by which we alter the 
flow of information in the brain and encode memories. Individual synapses 
occur at thousands of postsynaptic dendritic spines separated from the 
dendrite by a thin neck making each spine a semi-autonomous entity. It is 
thought that this is what underpins synapse specific plasticity enabling 
high capacity memory. However, recently it has become clear that cross talk 
between coactive spines is the basis for many forms of synaptic plasticity, 
but the mechanism, requirements and biological function for this spine-spine 
communication remain unknown. Similarly, the precise calcium signals that 
differentiate plasticity from cell death processes are also unknown. This 
project aims to address these questions using a combination of mathematical 
modelling and high-resolution imaging data collected with high-powered laser 
microscope. In order to capture the complex geometry of the system we will 
employ advanced mathematical techniques for spatio-temporal modelling and 
analysis such as finite element methods. 

This work is important because it will lead to a wealth of new information 
about synaptic plasticity and cell death processes, and hence the 
mechanisms underlying learning and memory and ischaemic brain damage. 
Furthermore, dysfunction in the ability to undergo synaptic plasticity is 
thought to underlie the altered neuronal activity in several brain 
diseases, such as Alzheimer?s disease, schizophrenia and autism. Therefore, 
the mechanisms that we will study in this research will add to our 
knowledge about these debilitating diseases, and may contribute to 
developing therapies.

Academic Supervisors:
Main Supervisor: Professor Krasimira Tsaneva-Atanasova (University of 
Co-supervisor: Dr Jack Mellor (University of Bristol)

Application deadline:
5th December 2016
GBP 14,296 per annum for 2016-17


From: Tsaneva-Atanasova, Krasimira <K.Tsaneva-Atanasova@exeter.ac.uk>
Date: Sat, Nov 19, 2016 at 1:25 PM
Subject: PhD Positions: Controlling Noise Effects in Models..., U of Exeter 


Project Description:
This is a project that combines biological modelling and general 
mathematical analysis of the influence of noise on multiple-timescale 
systems. It will give the student the opportunity to work on open 
mathematical questions and see their results applied in experiments on 
living cells. 

Many types of cells such as neurons, heart and hormone-
releasing cells generate impulses of electrical activity, organized as 
single spikes or bursts of impulses. In cells of the pituitary gland ? the 
master hormonal gland of the body ? the features of electrical activity 
patterns determine how much hormone is released into the circulation. 
Hence, understanding how the characteristic features of electrical activity 
arise is crucial to understanding how these cells function, and how they 
may malfunction in disease. Mathematical modelling and analysis techniques 
have proven very successful in helping unravel fundamental mechanisms 
controlling the behaviour of excitable cells. 

Electrical activity is driven by the interactions between ion channels of 
the cell membrane, which produce noisy electrical currents. The 
mathematical models of electrical activity thus contain random and 
deterministic parts, which typically appear as separate terms (e.g., the 
deterministic drift and the Brownian-motion induced diffusion in stochastic 
differential equations). In experimental practice this distinction is not 
as clear. For example, ion channels in cells with electrical activity 
generate noisy signals, driving systematically the electrical and chemical 
activity in the cell, which operate also on several time scales. It is 
still unclear how this randomness influences electrical activity in real 

This PhD project will investigate how one can use control to identify the 
systematic (deterministic) component of trajectories in dynamical systems 
with random inputs (such as ion channel noise) that operate on two or 
three different time scales (such as spiking or bursting cells). A first 
goal to separate a systematic, approximately periodic, signal without 
knowledge of the period using control and geometric methods in a 
reconstructed phase space. Preliminary investigations with noise on a 
single time scale interacting with a two-timescale oscillation (spiking) 
have shown that this is in principle possible. It is an open question how 
this can be generalized to periodic behaviours with a more complicated 
geometry (such as bursting), interacting with noise effects that occur on 
two time scales. Another open question is how the geometric control and 
noise identification is related to extended time-delayed feedback, which 
creates a reference signal from a geometric time series of past outputs. 

Main supervisor: Prof Krasimira Tsaneva-Atanasova (University of Exeter)
Co-supervisor: Dr Jan Sieber (University of Exeter)
Co-supervisor: Dr Joël Tabak (University of Exeter)

Location: University of Exeter, Streatham Campus, Exeter, Devon


From: Tsaneva-Atanasova, Krasimira <K.Tsaneva-Atanasova@exeter.ac.uk>
Date: Sat, Nov 19, 2016 at 1:26 PM
Subject: PhD Positions: Developing Gaze Training for..., U of Exeter


Project Description:

Learning to use a prosthetic limb is inherently difficult and requires a 
huge amount of concentration. Like learning how to wield a new tool for 
the first time, amputees need to acquire the confidence and dexterity 
required for skilled action. In order to produce accurate goal-directed 
movements the motor system requires accurate and timely visual information 
making the timing and location of the person's gaze, with relation to the 
movement of their limbs, critical for skilled behaviour. There is, however, 
no structured training protocol for use with prosthetic hands. We aim to 
develop a novel gaze training regime to facilitate the use of a prosthetic 
hand to skilfully interact with objects.

In the first part of the project, the student will undertake an 
observational study to determine what factors lead some individuals to 
become skilled with a prosthesis faster than others. We will test large 
numbers of intact (i.e., without amputation) participants learning to use 
a state-of-the-art myoelectric prosthetic arm simulator, which is 
controlled by muscle feedback but ergonomically designed to fit over the 
wrist of an intact hand. Participants will move objects of different of 
sizes and weights from one location to another with a range of precision 
requirements and in the presence of a range of obstacles. Over multiple 
sessions we will measure hand and object kinematics, fingertip forces, 
and eye path with a head-mounted eye tracker. We will then develop a data-
driven mathematical model of the eye tracking and biomechanical performance 
data. Statistical analysis of the patterns of eye movement will provide 
new insights into the 'signature' of good performance using the prosthetic 

The second phase will use the data from Project 1 to develop a training 
protocol that will adopt the 'expert signatures' from project work 1 as a 
prototype for a trainee to follow. We will focus predominantly on the 
signature of expertise derived from the gaze behaviour measures and 
implement a gaze training protocol. We will then test the efficacy of this 
novel training with new set of intact participants using the prosthetic 
simulator, tracking their performance in comparison to individuals who 
will receive a sham training protocol.

In the final stage of the project work, the gaze training protocol will be 
used in a sample of upper-limb-amputees as they learn how to use their new 
prosthesis. As this state of the project will not be limited to 
myoelectric prosthetic users, this will also allow us to test the 
generalizability of our training protocol. The students will be involved 
in these experiments by running model simulations and data analysis to 
provide quantitative information for the training protocol as well as 
focussing on completing the write-up of their PhD thesis.


From: Yassine Souilmi <yassine.souilmi@adelaide.edu.au>
Date: Mon, Nov 21, 2016 at 6:16 PM
Subject: PhD Positions: Human Population/Quantitative..., U of Adelaide

PhDs Position in Human Population/Quantitative/Statistical Genetics using 
ancient DNA, Australian Centre for Ancient DNA (ACAD), University of 
Adelaide, South Australia

We have three (3) PhD positions for highly motivated students to join our 
dynamic research team in one of the world's leading ancient DNA centres. 
Candidates must have a 1st Class Honours or Masters degree, an excellent 
undergraduate academic record and meet the English Language Proficiency 
(ELP) requirement. The call is open to international and domestic students 
with a background in bioinformatics, programming or population/quantitative
/statistical genetics. In addition, a passion for human history and 
archaeology is desirable along with demonstrable analytical skills. The 
projects will suit hard-working and self-motivated candidates equipped with 
good skills in critical and independent thinking. Training will focus on 
the analysis of Next-Generation Sequencing data with a special emphasis on 
the utilisation and expansion of population and quantitative genetic 
methods for paleogenomic data. Successful candidates will also have the 
opportunity to assist in the development and application of cutting-edge 
reference genome approaches for humans and other organisms. Training 
opportunities to advance wet-laboratory techniques can be offered in 

Great computational skills are required and a successful candidate would 
be competent in:

- Querying a SQL (PostgresQL) database
- Data analysis and management skills
- Fluency in using Linux systems, with a good hands-on experience with 
Bash scripting
- Advanced programming in a scripting language such as Python and/or R

This is a great opportunity to study abroad (for international candidates) 
as Adelaide is a vibrant cosmopolitan city with a Mediterranean climate 
guaranteeing a great lifestyle. Interested applicants are encouraged to 
send a resume and a cover letter to either Dr Yassine Souilmi 
(yassine.souilmi@adelaide.edu.au) or Dr Ray Tobler 
( raymond.tobler@adelaide.edu.au ).



From: Esteban Vargas <eva11@helmholtz-hzi.de>
Date: Wed, Nov 16, 2016 at 1:27 PM
Subject: Postdoc Position: Computational Biology, Frankfurt Institute... 

Postdoc Position in Computational Biology

The new group of Systems Medicine at the Frankfurt Institute for Advanced 
Studies invites applications for a 2 years PostDoc position in 
Computational biology. 

Major duties:
- Develop mathematical models describing diseases using deterministic 
models, stochastic models, and compartmental models.
- Analyze clinical and experimental data from collaborators using machine 
learning and bioinformatics approaches.
- Develop novel algorithms to treat diseases.
- Publish research findings in scientific journals and present them at 
major scientific meetings.
- A PhD degree in a quantitatively-oriented field, such as engineering, 
computer science or applied mathematics.
- Excellent command of English.
- Knowledge in analytical and quantitative methods.
- Experience in MATLAB or R, Linux and LaTex.
- Knowledge of immunology is a plus.
Please send questions or your application with a motivation letter, 
outlining your interest in the position, along with your curriculum vitae 
which should include the names and contact details of three referees, to

Positions are open until filled. The planned start date is April 2017. 


From: Catherine Crawley <ccrawley@nimbios.org>
Date: Thu, Nov 17, 2016 at 10:45 AM
Subject: Postdoc Position: Spatial Modeling, NIMBioS

New! Postdoctoral Fellowship in Spatial Modeling at NIMBioS

The National Institute for Mathematical and Biological Synthesis (NIMBioS), 
located at the Univ. of Tennessee, Knoxville, is currently accepting 
applications for a two-year postdoctoral fellowship in spatial modeling 
with an interest in GIS, remote sensing, large spatial datasets and spatial 

An applicant may propose to make advances on conceptual or methodological 
problems related to spatial modeling or to the application of spatial 
analyses to advance management of the environment and natural resources 
or of human or environmental health and diseases. Possible topics include, 
but are not limited to:

- Developing new tools for handling and analyzing Big Data (e.g., NEON)
- Spatial, landscape explicit transmission of diseases
- Linking fine scale and large scale ecological processes
- Physiology trait mapping and links with climatic changes or extreme 
weather events
- Spatial modeling of biodiversity and ecosystem services

Reflecting the interdisciplinary nature of this position, candidates with 
a PhD or equivalent in biology, mathematics, statistics, computer science, 
geography, environmental science, epidemiology, civil or environmental 
engineering, or any other relevant field will be considered.

Support: annual stipend of $51,000, full University of Tennessee employee 
fringe benefits, and an annual travel allowance of $3,000.

Deadline: The deadline is December 18, 2016, for fellowship research 
beginning late spring 2017. All letters of recommendation must be submitted 
before the request deadline.

How to apply: Follow the guidelines at http://www.nimbios.org/postdocs/.


From: Radek Erban <erban@maths.ox.ac.uk>
Date: Thu, Nov 17, 2016 at 1:24 PM
Subject: Postdoc and Faculty Positions: Mathematical Institute, Oxford

We invite applications for several independent postdoctoral research
fellowships in the Mathematical Institute, University of Oxford.
We also have a faculty vacancy in networks and nonlinear systems.
The deadline for our fellowship applications is 1st December.
The adverts can be find here:

Hooke Research Fellowship (3 years):

Titchmarsh Research Fellowship (3 years):

Sylvester Research Fellowship (5 years):

Associate Professorship or Professorship (permanent):


From: Marc Sturrock <marcsturrock@rcsi.ie>
Date: Tue, Nov 22, 2016 at 4:57 AM
Subject: Postdoc Position: Math Modelling/Systems Biology, RCSI

Here is a link to a new postdoc position at the Royal College of Surgeons 
in Ireland.
Further enquiries can be sent to patsyconnolly@rcsi.ie


From: Xiao Wang <xiaowang@asu.edu>
Date: Wed, Nov 16, 2016 at 12:24 PM
Subject: Faculty Position: Synthetic & Systems Biology, Arizona State U

The School of Biological and Health Systems Engineering at Arizona State 
University is looking to hire faculty members in Synthetic and Systems 
Biology, broadly defined. 

Please follow this link 

for detailed description of the position and instructions for submitting 
an application. Review of applications will start on November 30, 2016, 
and continue on a rolling base until positions are filled.


From: Dompke, Michele Renee <mdompke@indiana.edu>
Date: Mon, Nov 21, 2016 at 2:44 PM
Subject: Faculty Positions: Bioengineering, Indiana U

Indiana University, School of Informatics and Computing, Bioengineering 
Faculty Positions in Intelligent Systems Engineering.

As part of its rapidly expanding program in Intelligent Systems 
Engineering (ISE), the School of Informatics and Computing (SoIC) at 
Indiana University (IU) Bloomington invites applications for multiple
computational, theoretical and experimental faculty positions at 
assistant, associate and full professor levels in the broad area of 
computational, experimental and theoretical Biological and Biomedical
Engineering. Duties include teaching, research, and service.

Apply online at: http://indiana.peopleadmin.com/postings/2730


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