SMB Digest Volume 19 Issue 26

August 28, 2019
This issue’s editor:


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Issue’s Topics:
Conference: Quant. Approaches in Biol., Oct 4-5, Northwestern U
Boot Camp: Communications, Oct 7-8, AIBS, Washington, DC
Conference: Undergrad. Research…, Nov 16-17, NIMBioS, U Tenn.
Scholarship Deadlines: Keystone Symposia
Newsletter: NIMBioS, Jul/Aug 2019
Post-doc: Deep Learning to Study Pattern Formation, Rice U
Post-doc: …Development of Anti-drub Antibodies, US FDA
Post-docs: Basque Center for Applied Mathematics, Spain
Post-docs: Mathematical Biology, Simons, U Pennsylvania
Post-docs: Multiscale Soft-Tissue Modelling, U Glasgow
NIH: Selected Intramural Research & Other Job Openings
SMBnet Reminders


from: Alexandria Volkening <>
date: Aug 26, 2019, 1:01 PM
subject: Conference: Quant. Approaches in Biol., Oct 4-5, Northwestern U

The 2nd Annual Conference on Quantitative Approaches in Biology will be
held from October 4-5, 2019 at Northwestern University in Evanston, IL.

This two-day conference, held by the NSF-Simons Center for Quantitative
Biology, will include guest speakers, lightning talks, poster sessions,
an undergraduate research competition, and a reception. Registration and
abstract submission for lightning talks and/or posters is open at
Questions can be directed to Tosin Akeredolu or Tiffany Leighton Ozmina
at and

For more details, see the conference website:


from: American Institute of Biological Sciences <>
date: Aug 26, 2019, 2:02 PM
subject: Boot Camp: Communications, Oct 7-8, AIBS, Washington, DC



from: Catherine Crawley <>
date: Aug 13, 2019, 11:05 AM
subject: Conference: Undergrad. Research…, Nov 16-17, NIMBioS, U Tenn.

The National Institute for Mathematical and Biological Synthesis
(NIMBioS) will host the 11th annual Undergraduate Research Conference at
the Interface of Mathematics and Biology on Nov. 16-17, 2019, at the
Univ. of Tennessee Conference Center in Knoxville, TN.

The conference provides opportunities for undergraduates to present
their research at the interface of biology and mathematics. Student
talks and posters will be featured as well as a plenary speaker, a panel
on career opportunities, a graduate school showcase, and other
networking opportunities. Faculty and students are invited to attend, as
well as high school teachers.

A limited amount of support is available to cover the cost of
registration, lodging and travel – deadline is September 25 to request
funding. Conference registration deadline is October 16.

If you have or plan to request funding, do not register for the
conference until you have been contacted by NIMBioS about the status of
your funding request. For more information, go to


from: keystonesymposia <>
date: Aug 17, 2019, 11:27 PM
subject: Scholarship Deadlines: Keystone Symposia



from: NIMBioS <>
date: Aug 14, 2019, 9:26 AM
subject: Newsletter: NIMBioS, Jul/Aug 2019



from: Oleg Igoshin <>
date: Aug 13, 2019, 11:27 AM
subject: Post-doc: Deep Learning to Study Pattern Formation, Rice U

A postdoctoral position in systems/mathematical biology is available in
the Prof. Oleg Igoshin group ( at the
Department of Bioengineering at Rice University, for a collaborative
project between the labs of Ankit Patel (Baylor college of Medicine, and Roy Welch (Syracuse University). We are
looking for a motivated postdoctoral fellow to work with Drs. Igoshin
and Patel to use datasets from Welch lab for understanding mechanisms of
bacterial multicellularity. The position is supported by newly awarded
NSF grant (RoL: Deep-learning framework to quantify emergent phenotypes
for functional gene annotation).

BRIEF PROJECT DESCRIPTION: The goal of this work is to leverage recent
advantages in machine learning to connect the collective behavior of
cells in a bacterial biofilm to their underlying genetic networks. How
cells self-organize into complex tissues is one of the greatest puzzles
in modern developmental biology and a hallmark example of emergent
behavior – complex patterns arising from simpler interacting components.
Despite tremendous progress, even the best-studied model systems lack an
understanding of the emergent properties that bridge developmental
phenomena from molecules to cells, tissues, and eventually complete
organisms. Biofilms formed by the soil bacterium Myxococcus xanthus are
a great model system to study emergent behavior. Under starvation, an
M. xanthus biofilm initiates a developmental program during which cells
aggregate into mounds and then differentiate into distinct cell types.
Many of the genes that influence M. xanthus development have been
identified, but researchers lack metrics to systematically understand
their role in coordinating self-organization dynamics. This project aims
to link genes and emergent behavior through machine-learning-based
quantification of the developmental impact of gene disruptions.

required for this position. We strongly prefer candidates with
(1) training both in computational approaches and in biological
sciences; (2) experience or strong interest in machine learning, image
analysis and/or data science and (3) publications in the field of
theoretical biophysics or systems biology. Passion for interdisciplinary
collaboration and English proficiency are also expected. The successful
applicant will be responsible for developing deep-learning-based image
quantification methods that allow us to robustly quantify and group
collective behavior phenotypes.

APPLICATION PROCEDURE: Applicants should submit their CV, contact
information for 3 professional references, and a short (less than
2 page) statement justifying their interest in the position to . Shortlisted applicants will be invited to apply.


from: Yogurtcu, Osman <>
date: Aug 15, 2019, 7:22 AM
subject: Post-doc: …Development of Anti-drub Antibodies, US FDA

Position Title: Modeling and Simulation of Development of Anti-drug

Position Description: An ORISE research fellowship is available
immediately at the Office of Biostatistics and Epidemiology (OBE) at the
Center for Biologics Evaluation and Research (CBER), Food and Drug
Administration (FDA) in Silver Spring, Maryland. The successful
candidate will participate in the development of an immune response
model to predict immunogenicity and simulate anti-drug antibody
development among hemophilia patients treated with recombinant factor
products. The goal of this project is the development of a computational
tool to enhance efficacy and safety evaluation of current and
next-generation engineered therapeutic products, leading to
personalized, optimal treatment regimens for hemophilia patients. Under
the guidance of a mentor, the participant will develop and apply novel
techniques to model and simulate interactive components of the human
immune system, as well as perform literature reviews, data collection,
model development, presentation of research results, and preparation of
scientific manuscripts. This position is a post-doctoral fellowship
through the Oak Ridge Institute for Science and Education (ORISE).

The qualified candidate should have received a doctoral degree in one of
the relevant fields. Degree must have been received within five years of
the appointment start date. This position is only open for US citizens,
permanent residents (Green Card holders) or individuals residing in US
for 3 years during the last 5 years on a valid US visa. Preferred
skills/experience are
-knowledge of immunology, modeling and programming skills,
-experience with differential equations,
-excellent written and oral communication skills,
-solid background and skills in both biology and computing science

Candidates will be offered competitive salary and health benefits.
Highly motivated candidates should apply through
(Reference Code: FDA-CBER-2019-0023). Candidates may contact Dr. Osman
Yogurtcu ( regarding the project and the
application process.

Employer Name: FDA/CBER, Office of Biostatistics and Epidemiology
Position Location: Silver Spring, MD, United States


from: BCAM recruitment <>
date: Aug 13, 2019, 5:19 AM
subject: Post-docs: Basque Center for Applied Mathematics, Spain

Postdoctoral Fellowship in Metabolic Modelling: Predictive metabolic
modelling of microbiomes and human metabolism through Monte Carlo

Postdoctoral Fellowship in Machine Learning Driven Atomistic Simulations
for Energy & Health


from: Mori, Yoichiro <>
date: Aug 14, 2019, 2:25 PM
subject: Post-docs: Mathematical Biology, Simons, U Pennsylvania

Simons Postdoctoral Fellows in Mathematical Biology at the University of

The Program for Mathematical Biology of the University of Pennsylvania
solicits applications for the Simons Postdoctoral Fellows in
Mathematical Biology, as part of the Math + X activities supported by
the Simons Foundation. Fellows will be intellectually independent, but
supervised by two faculty mentors, one in the biological sciences and
another in the mathematical sciences. Research areas of interest to
prospective faculty mentors include mathematical modeling in
evolutionary biology and ecology, genetics, biophysics and physiology as
well as the mathematical analysis associated with problems that arise in
these areas. The prospective applicant should have completed his/her
Ph.D. in some area of mathematical biology, but any strong candidate
whose work and experience has significant overlap with the areas
mentioned above is welcome to apply. Such areas may include dynamical
systems, the analysis of PDE, numerical analysis and scientific
computing, probability theory, soft condensed matter physics or fluid

We anticipate sustained intellectual activity in the Program with
subsequent cohorts of fellows in future years, a regular seminar series,
short- and long-term visitors, as well as workshops in specific areas of
mathematical biology, as supported by the Simons Foundation. The Simons
Postdoctoral Fellows are invited to be active participants in these

The term of the Simons Postdoctoral Fellowship is two years, with a
possibility of renewal for a third year. The starting annual salary is
$63,000 plus benefits, with annual discretionary funds of $5,000 that
the Simons Fellow may use for travel or supplies (computers etc.). The
position comes with no teaching responsibilities, but teaching
opportunities may be available if the Fellow desires.

Applications should be submitted through MathJobs:

Applications will be accepted until the positions are filled.
Prospective Fellows are encouraged to contact possible mentors in
advance of submitting an application. The anticipated start date is Fall
2019, but will be determined on a case-by-case basis.

Any questions about the fellowships should be directed to Yoichiro Mori
( or to Joshua Plotkin (,
Co-Directors of the Simons Program in Mathematical Biology at the
University of Pennsylvania.

The University of Pennsylvania is strongly committed to Penn’s Action
Plan for Faculty Diversity and Excellence and to creating a more diverse
faculty (for more information see:
The University of Pennsylvania is an EOE. Minorities/Women/Individuals
with disabilities/Protected Veterans are encouraged to apply.


from: Peter Stewart <>
date: Aug 22, 2019, 1:48 PM
subject: Post-docs: Multiscale Soft-Tissue Modelling, U Glasgow

The EPSRC SofTMech Centre ( at the University of
Glasgow is recruiting two post-doctoral research assistants to work on
multiscale soft-tissue modelling in collaboration with leading research
groups at MIT and Politecnico di Milano. The posts are funded for three
years starting in January 2020. We encourage candidates with suitable
backgrounds to apply via the following links:

Please note if you wish to be considered for both jobs, you need to fill
in the application for each position.

The closing date for applications is 19th September 2019.

For informal enquiries, please contact the SofTMech Executive Director,
Professor Nick Hill at


from: Owens, Roland (NIH/OD) [E] <>
date: Aug 21, 2019, 4:10 PM
resent-from: Mejia, Raymond (NIH/NHLBI) [E] <>
subject: NIH: Selected Intramural Research & Other Job Openings

Senior Scientist Epidemiology and Biostatistics Program, NCI-DCEG
(deadline: September 5)

The Division of Cancer Epidemiology and Genetics (DCEG), National Cancer
Institute (NCI), National Institutes of Health (NIH) is recruiting an
accomplished Senior Scientist in the Epidemiology and Biostatistics
Program (EBP). DCEG’s epidemiologists, geneticists, and
biostatisticians conduct population and multidisciplinary research to
discover the genetic and environmental determinants of cancer and new
approaches to cancer prevention. The Division’s research has an impact
on public health policy in the United States and around the world.

The Senior Scientist will provide overall direction to a new prospective
cohort study of 200,000 adults in the US to understand the etiology and
natural history of cancer, which can inform new approaches in precision
prevention and early detection of cancer. The Senior Scientist will
oversee the DCEG cohort coordinating center of approximately five staff
members and all cohort activities and be responsible for the overall
success of the cohort. The Senior Scientist will also play a key role in
consulting with DCEG Principal Investigators and provide technical and
scientific advice. Additionally, the Senior Scientist will serve as
liaison to NCI and NIH standing committees and represent the Division to
other agencies and outside organizations to coordinate activities,
enhance communication, and develop new initiatives and infrastructure.

The successful candidate will hold a doctoral degree in epidemiology or
a related field, have substantial relevant experience and responsibility
for managing and directing large prospective epidemiological cohort
studies, and be a successful supervisor. He or she must also be
recognized as an international expert in cancer epidemiology;
demonstrate expertise in managing a complex, outstanding program of
epidemiological research; have exemplary skills and innovative
approaches to epidemiological research and relevant new technologies;
and have extensively published in peer-reviewed scientific or medical
journals and presented at scientific meetings.

Salary and benefits are commensurate based on the incumbent’s
qualifications and experience. The Senior Scientist is a Full-Time
Equivalent Employment position. More information on this position is
available at
Full Federal benefits including leave, health and life insurance,
long-term care insurance, retirement, and savings plan (401k equivalent)
will be provided. Interested individuals should send a cover letter
briefly summarizing research interests, accomplishments and scientific
management experiences; curriculum vitae and bibliography; copies of up
to five publications or reprints; and the names and address of three
references to: Dr. Hannah Yang, Division of Cancer Epidemiology and
Genetics, National Cancer Institute, 9609 Medical Center Drive, Room
7E440, email: Opening August 7, 2019, and closing
September 5, 2019.

This position is subject to a background investigation. The NIH is
dedicated to building a diverse community in its training and employment
programs. DHHS, NIH, and NCI are equal opportunity employers.

Senior Investigator / Branch Chief
Epidemiology Sciences Branch, NHLBI
(review begins: September 15)

The Division of Intramural Research (DIR) of the National Heart, Lung,
and Blood Institute (NHLBI) is seeking to recruit an exceptional and
visionary leader for the position of Senior Investigator (Branch Chief)
to establish and direct a new innovative population sciences research
program at the NIH Bethesda, MD, campus focused on key issues relevant
to the mission of NHLBI.

The Epidemiology Sciences Branch, located in Bethesda, MD, will focus on
population health with an emphasis on epidemiology, population genetics,
chronic disease management, health services, health disparities,
behavioral sciences, or implementation and dissemination research while
taking advantage of the robust basic science and clinical center
environment at NIH. The ultimate goal of the intramural research program
is to perform robust scientific and clinical research that leads to a
better understanding of biology and clinical pathology. To attain this
goal, we have built a strong basic science foundation and coupled it
closely with innovative technology development and an outstanding
clinical research program, both at the NIH Clinical Center and in
partnership with local hospitals. There are strong interactions with a
wide range of independent research groups, and the position offers
exceptional opportunities for interdisciplinary collaboration within and
outside of the NIH including the Framingham and Jackson Heart Studies.

The existing faculty in the NHLBI DIR is an outstanding group of
internationally recognized biomedical researchers covering a wide range
of basic and clinical research topics (please see
complemented by the other research institutes within the Intramural
Research Program (please see

The successful candidate should have a strong track record of
achievement, expertise and experience in the area of population health.
Applicants must have an M.D., PhD., M.D./Ph.D. or equivalent doctoral
degree. Salary is commensurate with research experience and
accomplishments. Appointees may be US citizens, resident aliens, or
non-resident aliens with or eligible to obtain a valid employment
authorized visa.

Applications from women, minorities and persons with disabilities are
strongly encouraged. Applicants should send a 1-2 page descriptive
letter of interest and research proposal, curriculum vitae (please
include in your C.V. a description of your mentoring and outreach
activities, especially those involving women and persons from racial,
ethnic or other groups that are underrepresented in biomedical
research) and complete bibliography, and arrange for three letters of
reference to be sent to:
Robert S. Balaban, Ph.D., Scientific Director, NHLBI
C/O Dan Fogarty
Review of applications will begin on or about September 15, 2019, but
applications will be accepted until the position is filled. DHHS and NIH
are equal opportunity employers.

Staff Scientist
Occupational and Environmental Epidemiology Branch, NCI-DCEG
(review begins: September 30)

The Division of Cancer Epidemiology and Genetics (DCEG), National Cancer
Institute (NCI), National Institutes of Health (NIH), is recruiting a
Staff Scientist in the Occupational and Environmental Epidemiology
Branch (OEEB).

OEEB combines genetic, molecular and epidemiologic data to understand
cancer etiology, chemical carcinogenesis and mechanisms of action of
known or suspected occupational and environmental carcinogens. Branch
investigators are leading state-of-the-art high-throughput studies that
evaluate germline genomics, metabolomics, transcriptomics, epigenetics,
microbiomics and other high-dimensional biomarkers of normal blood and
other biological samples.

The successful candidate will provide bioinformatic support for multiple
projects as a Staff Scientist to OEEB investigators, including the
following activities: accessing, extracting and preparing data for
analysis, developing and maintaining bioinformatics pipelines,
conducting analysis of molecular epidemiology data within and across
omic platforms including use of integrative analytic methods, organizing
results into clear presentations and concise summaries of work, and
maintaining experience with state-of-the-art bioinformatics tools and
data repositories.

The successful candidate must hold a doctoral degree in bioinformatics,
biostatistics, computer science, computational biology or other related
disciplines. The ability to communicate effectively in speech and in
writing is important, as demonstrated by a track record of publications
in peer-reviewed literature as part of a research team. The successful
applicant will possess many (although not necessarily all) of the
following skills: the ability to program efficiently in at least one
programming language (e.g., Python, Perl, C/C++, and/or JAVA);
experience with processing and analyzing large datasets for at least one
of the following: GWAS, transcriptomics, methylomics, metabolomics,
microbiomics, next generation sequencing; experience with publicly
available software in the genetics field for applicants who specialize
in genetic analyses (e.g., GCTA, Bolt-LMM, Rvtests, Predixcan, LDSC,
RareMetal UCSC Genome Browser etc.); proficiency in R/Bioconductor;
experience with public bioinformatics databases (e.g., dbGAP, TCGA,
ENCODE, 1000 Genomes, TARGET, GTEX, HMP); experience with bash scripting
and working in a Linux environment (especially a computer cluster
environment); experience with core statistical methods (e.g. linear
regression, logistic regression, etc.); and a demonstrated ability to
self-educate in current and evolving bioinformatics techniques and

Applications will be accepted through September 30, 2019. Selection for
this position will be based solely on merit, with no discrimination for
non-merit reasons such as race, color, religion, gender, sexual
orientation, national origin, political affiliation, marital status,
disability, age, or membership or non-membership in an employee
organization. NIH encourages the application and nomination of qualified
women, minorities and individuals with disabilities. NIH provides
reasonable accommodations to applicants with disabilities. If you
require reasonable accommodation during any part of the application and
hiring process, please notify us. The decision on granting reasonable
accommodation will be made on a case-by-case basis. This position is
subject to a background investigation. Salary is commensurate with
research experience.


Subject: SMBnet Reminders

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