SMB Digest Volume 19 Issue 21

June 25, 2019
This issue’s editor:


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Issue’s Topics:
Conference: Nordic Biomathematics Days, 22-23 Oct, Helsinki
Special Session: Comp. Proteomics, NETTAB, Nov 11-13, Italy
Conference: Parallel & Distributed Comp…., Dec 5-7, Australia
AIBS: Meet Lawmakers, Help Inform Science Policy, US
AIBS: Communication Boot Camp for Scientists
PhD Position: Evolution of Gene Networks & the Origins…, Barcelona
PhD Position: Human Cooperation Modeling & Climate, Paris
Post-doc: Cancer Ecology, U Utah
Post-doc: Mathematics/Data Science Applied…, U Birmingham, UK
Post-doc: Infectious Disease Modeling, UC San Diego
NIH: Extramural Nexus Update
SMBnet Reminders


from: Kisdi, Eva <>
date: Jun 20, 2019, 8:15 AM
subject: Conference: Nordic Biomathematics Days, 22-23 Oct, Helsinki

We are glad to announce the first Nordic Biomathematics Days, a new
initiative to pull people of this field together predominantly from the
Nordic countries. The first meeting will be in Helsinki, 22-23 October
2019 (Tue-Wed). We hope that in the future, there will be similar
workshops annually, rotating in the Nordic countries.

Confirmed speakers: Odo Diekmann (Utrecht University), Susanne Ditlevsen
(University of Copenhagen) and Peter Jagers (Chalmers University). More
information and a link to registration (deadline 6 September) is on the
conference website


from: Romano Paolo <>
date: Jun 19, 2019, 4:11 AM
subject: Special Session: Comp. Proteomics, NETTAB, Nov 11-13, Italy


November 11-13, 2019
Fisciano Campus, University of Salerno, Italy

NB! Deadline: Sunday June 30, 2019 (four-page abstracts for oral

A Special session of the meeting will be devoted to Computational
Proteomics, but contributions on usual NETTAB and BBCC topics are also
Computational Proteomics topics include bioinformatics methods, tools
and platforms for:
-Standardization of data and methods
-Annotation, visualization, integrated discovery
-Protein identification and validation
-Biomarker discovery
-Quantitative proteomics
-Single cell proteomics
-Targeted proteomics
-Molecular imaging by mass spectrometry
-Microbial proteomics

Abstracts must be submitted through EasyChair at .

Submission deadline: Sunday JUNE 30, 2019.
Notification to authors: Monday September 2, 2019

Abstracts length: MAX FOUR A4 PAGES.
Templates are available for MS Word and LaTeX.

See detailed instructions at .


Tutorial 1, Monday November 11, 2019 (09:00 – 11:00)
Analysis of scRNA-seq using R
Annamaria Carissimo, Monika Krzak, Dario Righelli and Claudia Angelini
Institute for Applied Mathematics “Mauro Picone” (IAC),
National Research Council, Naples, Italy.

Tutorial 2, Thursday November 14, 09:00 – 17:00
Label-free quantification with OpenMS
Oliver Kohlbacher, Julianus Pfeuffer and Timo Sachsenberg
University of Tuebingen, Germany

For further information, please email to or .


from: <>
date: Jun 23, 2019, 9:34 PM
subject: Conference: Parallel & Distributed Comp…., Dec 5-7, Australia

The 20th International Conference on Parallel and Distributed Computing,
Applications and Technologies (PDCAT 2019)

Gold Coast, Australia
Dec 5-7, 2019
Sponsored by Griffith University and IEEE Computer Society
Web Site:

Paper Submission Page:

Important Dates
Full paper submission due: 1 July 2019
Notification acceptance: 30 Aug. 2019
Camera-ready paper due: 15 Sep. 2019


from: American Institute of Biological Sciences <>
date: Jun 14, 2019, 10:01 AM
subject: AIBS: Meet Lawmakers, Help Inform Science Policy, US



from: American Institute of Biological Sciences <>
date: Jun 19, 2019, 12:07 PM
subject: AIBS: Communication Boot Camp for Scientists



from: Salazar, Isaac <>
date: Jun 17, 2019, 10:12 AM
subject: PhD Position: Evolution of Gene Networks & the Origins…, Barcelona

Graduate position: Barcelona Evolution of gene networks and the origins
of organismal complexity.

The position is the Autonomous University of Barcelona (UAB) and in the
Centre de Recerca Matemàtica (CRM). The CRM is in the UAB campus.

The main project questions are:
-How should gene networks and cell interactions be organized to lead to
biological complexity?
-How is such organization achieved in evolution?
-How does gene network organization affect variational properties of the
phenotype (e.g. evolvability)?
-Any other question of the applicants interest that is related to the
previous questions.

We will use computational models of the genotype-phenotype map and
computational models of evolution by natural selection to study such
questions for the case of organismic complexity (e.g. anatomy). The
genotype-phenotype maps models we develop are based on realistic gene
network models of pattern formation and morphogenesis that lead to
realistic 3D multicellular phenotypes.

The position is in Salazar-Ciudad’s group and it entails obtaining a PhD
from the UAB. Salazar-Ciudad group is between the Genetics department in
the UAB ( and the mathematics research center, CRM and ItemId=CO009211

The main tasks of the student include using and modifying existing
models of embryonic development (e.g. EmbryoMaker) in order to simulate
the development of complex morphologies. These models will be combined
with models of evolution, in a population context with mutation, genetic
drift and natural selection on morphology (see for example
Salazar-Ciudad and Marin-Riera, 2013). he gene networks found to lead to
the development of complex and robust phenotypes in evolution would be
analyzed to extract general regularities, if any, these gene networks
need to fulfill. The main tasks, thus, consist in simulation,
theorizing, data analysis, coding, literature searching, writing and
presenting results in conferences. We seek candidates highly motivated
for theoretical work and data analysis with a broad understanding of the
evolutionary theory and/or developmental biology and/or modeling.

-Candidates should have a University Degree and a Master’s Degree in
biology, physics or mathematics within the European Higher Education
System (minimum 300 ECTS) or equivalent by September 2019.
-Scientific programming skills or a willingness to acquire them is
-The most important requirement is a strong interest and motivation on
science and evolution. A capacity for creative and critical thinking is
also required.

Salary and conditions
-The salary would be the standard one graduate students in Spain.
Barcelona is a vibrant, multicultural hub with a high quality of life
and a thriving cultural scene.
-Working time is of 37,5 hours per week.

The application must include:
-Application letter including a statement of interests and motivation.
-CV (including publications, the contribution of the applicant in each
publication, degrees obtained, subjects included in degree and grades,
average grade)
-Foreign applicants, especially non-EU applicants, should attach an
explanation of their University’s grading system. All documents should
be in English, no official translation is required in the initial
application but may be requested afterwards.
-Applications should be sent to Isaac Salazar-Ciudad by email:

The start date is negotiable between autumn 2019 and early 2020.


from: Regis Ferriere <>
date: Jun 21, 2019, 9:06 AM
subject: PhD Position: Human Cooperation Modeling & Climate, Paris

Three-year PhD position on modeling the evolution of human cooperation
in the context of climate change and climate extremes.

Full-time, fully funded position based in Paris, France.
Starting October 1, 2019.

Project summary: Promoting human cooperation towards public goods is
particularly challenging, and quantitative theory is scarce. We propose
to develop general models for the joint evolutionary dynamics of
cooperation and social norms, and apply these models to the problem of
cooperation in response to anthropogenic climate change. Of particular
interest is the effect of environmental fluctuations, including extreme
climatic events, with the goal of predicting their effects across scales
of time, space, and social structure. This interdisciplinary project
will advance the mathematical framework of cultural evolution and human
cooperation, and yield novel insights into the emergence and dynamics of
‘cultures of cooperation’ in the face of global environmental

Advising: The doctoral student will be co-advised by Regis Ferriere
(IBENS Paris and CNRS-ENS/PSL UMI iGLOBES at the University of Arizona),
Sylvie Méléard (Centre de Mathématiques Appliquées, Ecole Polytechnique,
Palaiseau), Jean-Baptiste André (Institut Jean Nicod du Département
d’Etudes Cognitives de l’ENS Paris) and Sylvain Billiard (Laboratoire
Evo-Eco-Paléo de l’Université de Lille). The graduate program and
primary advisor will be determined according to the student’s main areas
of training and long-term objectives. The student will be based in
Paris, France, with an official affiliation with CNRS-ENS/PSL UMI
iGLOBES at the University of Arizona where s/he will be given the
opportunity to work for extended time.

Required qualification: We are looking for highly motivated applicants
with a strong interest in mathematical and numerical modeling of
population dynamics. Applicants’ background may be in behavior,
cognition, ecology, and/or evolution with strong experience in theory
and modeling; or in applied mathematics (stochastic processes, game
theory, dynamical systems…), theoretical physics or computational
science with strong experience or motivation for applications to
behavior, ecology, and evolution.

Applying: Applicants should have completed a Master degree or equivalent
by the position start date. Applications should include a detailed CV
(including name and contact information of two references) and a cover
letter (statement of interest). Applications should be sent to Regis
Ferriere at Review of applications will begin
immediately and continue until the position has been filled.


from: Fred Adler <>
date: Jun 21, 2019, 8:55 AM
subject: Post-doc: Cancer Ecology, U Utah

The University of Utah is part of an multi-disciplinary team led by
Andrea Bild’s lab at the City of Hope that unites mathematical,
computational and lab biologists with data scientists and physicians to
address the joint genetic and phenotypic evolution of cancers. This
project is part of the Cancer Systems Biology Consortium

We are seeking a postdoctoral researcher to join our highly
collaborative team to develop mathematical and statistical approaches to
model and analyze sequential clinical, single cell genetic sequence and
transcriptome data from patients with late stage breast and ovarian

Candidate qualifications include:
PhD in a quantitative science (mathematics, computational biology, or
statistics) or life science with strong focus on mathematical modeling,
computation or data analysis.

Application Process:
Please send the following to
1. Cover letter, highlighting experience with quantitative methods for
understanding biological data
2. CV
3. Names and contact information for three references


from: <>
date: Jun 21, 2019, 4:05 PM
subject: Post-doc: Mathematics/Data Science Applied…, U Birmingham, UK

As part of establishing the Centre for Systems Modelling and
Quantitative Biomedicine at the University of Birmingham later this
year, I am looking to hire a post-doctoral researcher with a strong
background in mathematics or data science (especially dynamical systems,
bifurcation theory, complex networks or parameter estimation from data).

Housed within the medical school, this new Centre will create
opportunities for researchers from quantitative disciplines (such as
mathematics, physics and computer science) to interface directly with
biomedical and clinical researchers to undertake impactful research for
societal benefit.

Closes on the 15th July – Post-Doctoral Research Fellow 81383:
UoB jobs:


from: Martin, Natasha <>
date: Jun 24, 2019, 4:53 PM
subject: Post-doc: Infectious Disease Modeling, UC San Diego

Applications are invited for a postdoctoral fellowship in modeling of
HIV and hepatitis C virus transmission and prevention among substance
using populations in the Department of Infectious Diseases and Global
Public Health at University of California San Diego
In particular, the goals are to inform public health policymaking
through evaluating the population level impact of combination prevention
interventions on incidence of infections and disease-related mortality
among substance using populations in a range of global settings.
Additionally, what are the optimal/most cost-effective portfolios of
interventions to achieve specific public health targets?

This highly interdisciplinary research will involve collaboration with
epidemiologists, clinicians, statisticians, policymakers, and public
health researchers. The postdoctoral scholar will work under the primary
supervision of Dr. Natasha Martin
(, and use dynamic epidemic
models, calibration to surveillance data, and cost-effectiveness
evaluation techniques. Scholars will benefit from biweekly seminars and
trainee sessions on substance use, HIV and related infections, journal
clubs, and grant writing circles.

The initial appointment will be for one year, with option for renewal
for up to two additional years based on performance. Applicants should
have a PhD in a relevant discipline (applied mathematics, epidemiology,
engineering, statistics and related fields). Salary will be
commensurate with qualification and experience and include travel to
conferences/collaborators. Applicants from under-represented minority
populations are encouraged to apply.

Review of applications will begin immediately and continue until the
position is filled. Applicants should submit a cover letter, their CV,
and at least two names of potential referees. For further information,
please contact Natasha Martin (


from: NIH Extramural Nexus (NIH/OD) <>
date: Jun 17, 2019, 8:13 PM
subject: NIH: Extramural Nexus Update

NIH Update: Notifying NIH of Sexual Harassment, Notices of Special
Interest, and Loan Repayment Program Outcomes

Please see


Subject: SMBnet Reminders

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