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Post-doc in mathematical modeling on phenotypic evolution and embryonic development: open

1.Job/ project description:

The postdoc could choose between three main research projects:

a. Mathematical modeling of phenotypic evolution in populations with embryonic development.

b. Mathematical modeling of gene network and embryonic development evolution.

c. Mathematical modeling of organ development and their evolution in mammalian teeth or Drosophila wing.

The actual project will be chosen together with the candidate depending on his/her interests and skills.

The research will take place in the Isaac Salazar-Ciudad's group in the Center of Excellence in Experimental and computational developmental biology of the Biotechnology Institute of the University of Helsinki, Finland.

The job is for 1 year and renewable for 1 extra year.

2. Background:

Why organisms are the way they are?

Can we understand the processes by which complex organisms are build in each generation and how these evolved?

The process of embryonic development is now widely acknowledged to be crucial to understand evolution since any change in the phenotype in evolution (e.g. morphology) is first a change in the developmental process by which this phenotype is produced. Over the years we have come to learn that there is a set of developmental rules that determine which phenotypic variation can possibly arise in populations due to genetic mutation (the so called genotype-phenotype map). Since natural selection can act only on existing phenotypic variation, these rules of development have an effect on the direction of evolutionary change.

Salazar-Ciudad's group is devoted to understand these developmental rules and how these can help to better understand the direction of evolutionary change. The ultimate goal is to modify evolutionary theory by considering not only natural selection in populations but also developmental biology in populations. For that aim we combine mathematical models of embryonic development that relate genetic variation to morphological variation with population models. The former models are based on what is currently known in developmental biology.

Salazar-Ciudad's group is in close collaboration with Jukka Jernvall's group and other groups within the center of excellence in experimental and computational developmental biology. The center includes groups working in tooth, wing, hair and mammary glands development. In addition to evolutionary and developmental biologists the center of excellence includes bioinformaticians, populational and quantitative geneticists, systems biologists and paleontologists.

"The Academy of Finland's Centres of Excellence are the flagships of Finnish research. They are close to or at the very cutting edge of science in their fields, carving out new avenues for research, developing creative research environments and training new talented researchers for the Finnish research system."

3. Requirements:

The applicant must hold a PhD in either evolutionary biology, developmental biology or, preferably, in evolutionary developmental biology (evo-devo). Applicants with a PhD in theoretical, mathematical or systems biology are also welcome.

Programming skills or a willingness to acquire them is required.

The most important requirement is a strong interest and motivation on science and evolution. A capacity for creative and critical thinking is also required.

4. Description of the position:

The fellowship will be for a period of up to 1+1 years (100% research work: no teaching involved).

Salary according to Finnish postdoc salaries.

5. The application must include:

-Motivation letter including a statement of interests

-CV (summarizing degrees obtained, subjects included in degree and grades, average grade).

-Summary of PhD project, its main conclusions and its underlying motivation.

-Application should be sent to Isaac Salazar-Ciudad by email:


No official documents are required for the application first stage but these may be required latter on.

6. Deadline:

There is no specific deadline, the position will be filled as soon as a suitable candidate is found.

7. Examples of recent publications by Isaac Salazar-Ciudad group.

Brun-Usan M, Marín-Riera M, Grande C, Truchado-Garcia M, Salazar-Ciudad I. A set of simple cell processes is sufficient to model spiral cleavage. Development. 2017 Jan 1;144(1):54-62.

-Salazar-Ciudad I, Marín-Riera M. Adaptive dynamics under development-based genotype-phenotype maps. Nature. 2013 May 16;497(7449):361-4.

-Salazar-Ciudad I, Jernvall J. A computational model of teeth and the developmental origins of morphological variation. Nature. 2010 Mar 25;464(7288):583-6.

8. Interested candidates should check our group webpage:


The center of Excellence webpage:


posted 2017.07.05

Postdoc: Systems Biology of converging signal transduction pathways, Penn State open

We seek a postdoc to join a collaborative project between Prof. Réka Albert (Physics) and Prof. Sally Assmann (Biology) at the Pennsylvania State University. The project will integrate computational analysis (by graph theoretical and dynamic modeling methods) and experimental investigation to develop dynamic models of convergent signal transduction pathways in plant biology. The specific setting will be plant guard cells, epidermal cells that enclose microscopic pores, stomata, through which plants take up CO2 and, inevitably, lose water. In response to the plant hormone abscisic acid (ABA; an indicator of drought and other stresses), and to elevated concentrations of CO2 (the substrate for photosynthesis), complex signaling networks are activated in guard cells that drive stomatal closure. The Albert and Assmann groups have a strong track record of collaboration in this field (e.g. PLOS Biol. 2006, PLOS Comp. Biol. 2014). The postdoctoral associate will build on this foundation to construct a network model of guard cell ABA and CO2 signaling. (S)he will also develop graph theoretical and combinatorial logic methods to describe convergent and overlapping directed networks, with implications for the general phenomenon of cross-talk in biological systems.

The ideal candidate should have experience with network analysis and dynamic modeling. Requirements include a Ph.D. in Physics, Mathematics, or other quantitative science and experience with modeling biological systems. Due to the collaborative nature of the project, the successful candidate will be an excellent interdisciplinary communicator and team player. 

Interested applicants should write to rza1 @ psu.edu and include a CV. 

posted 2017.06.26

Theoretical biophysics postdoc opening open

Department of Health and Human Services 
National Institutes of Health 
National Heart, Lung and Blood Institute 

One postdoctoral position is immediately available in Jian Liu lab - Theoretical Cellular Physics Section of Biochemistry and Biophysics Center at the National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD. 

Appointment and salary are dependent on experience. The initial appointment period of this position is one-year.  Appointment beyond one-year is contingent upon mutual agreements between the PI and the postdoc, and could be extended up to 5 years. The project is part of 2017 DDIR innovation awards - the collaborative NIH intramural project that involves close synergy between a theorist (Jian Liu lab, NHLBI), a developmental biologist (Ajay Chitnis Lab, NICHD), and an experimental biophysicist (Kandice Tanner Lab, NCI) at NIH Bethesda main campus. The theoretical problem we are aiming to address is in the general paradigm of cell motility and the feedback between mechanics and signaling pathways.  

Applicants should have PhD in theoretical chemistry, physics, applied math or engineering. Highly motivated candidates with strong background in theoretical physics and numerical simulations, and good communication skills are desirable. For more information, see: https://www.nhlbi.nih.gov/research/intramural/researchers/pi/liu-jian Applicants should submit, in a PDF file, a letter of interest, curriculum vitae, and arrange three letters of reference to: Dr. Jian Liu at liuj7  @ nih.gov. 

HHS and NIH are Equal Opportunity Employers. Applications from women, minorities and persons with disabilities are strongly encouraged.

posted 2017.06.19

Postdoctoral Fellow open

Systems Biology as a Tool for Rational Drug Design

Duration: 12 months, starting immediately
Closing date: July 1st, 2017

About 40% of all marketed drugs target G protein-coupled receptors (GPCRs). However, linking in vitro with in vivo data is still an unsolved challenge. InterAx Biotech AG has initiated a collaborative project on Rational Drug Design with the Paul Scherrer Institute in Villigen, Switzerland. Together, we are looking for an excellent and highly motivated systems biologist who wants to be part of a very challenging project with high academic and industry impact.


InterAx Biotech AG is a rapidly growing Swiss Biotech company based in Villigen, Switzerland. We are a friendly and dynamic interdisciplinary team fully committed to the discovery of functional selective therapeutics for G protein-coupled receptors (GPCRs). The company builds on its unique Biosensor engineering platform and on its computational approaches to discover the next life-changing therapeutics.


The Paul Scherrer Institute (PSI) is the largest research centre for natural and engineering sciences within Switzerland. PSI performs cutting-edge research in the fields of matter and materials, energy and environment and human health. By performing fundamental and applied research, PSI works on sustainable solutions for major challenges facing society, science and economy. PSI is committed to the training of future generations. Therefore about one quarter of PSI staff are post-docs, post-graduates or apprentices. Altogether PSI employs 2000 people.


We are looking for a


Postdoctoral Fellow


Your tasks


  • Develop a mathematical model of G protein-coupled receptor (GPCR) signaling focusing on the temporal aspects of ligand-receptor interactions and its implications on biased signaling
  • Determine optimal conditions for acquisition of experimental data
  • Integrate and optimize the model with experimental data
  • Predict from the model the most informative wet-lab assays to characterize drug candidates
  • Regularly report and discuss the progress of the project with the industry partner

Your profile

  •  PhD in biology, biochemistry, computer science or in a related area
  •  Experience in modelling of biochemical networks
  •  Knowledge of GPCR biology
  •  Good knowledge of English

Contact us


If you are interested to join an inspirational and successful team, in which your contribution is essential and highly valued, please send your application including CV, motivation letter and references to Dr. Aurélien Rizk and apply online at https://www.psi.ch/pa/job-opportunities/1546

posted 2017.05.12

Scientific developer position at Institut Curie in Systems Biology Group open

Development of systems biology methodology and software with applications to cancer research in the  context of European projects

Duration: 18-36 months with possibility of extension, starting immediately

Institut Curie is one of the biggest European institutions for cancer research with strong and old interdisciplinary traditions. It also comprises a hospital specialized in cancer treatment, and therefore dispose of a continuum of expertise from fundamental research to patient care. It is located in the centre of Paris in a both cultural and scientific rich environment (http://curie.fr).

The "Bioinformatics and Computational Systems Biology of Cancer" Unit (U900 INSERM, Mines ParisTech, Institut Curie) involves about 90 researchers and students. It is a very active and growing interdisciplinary team of biologists, physicians, mathematicians, statisticians, physicists and computer scientists (http://u900.curie.fr). Our research group focuses on deciphering determinants of tumorigenesis and tumor progression and proposing new strategies to combat cancer. The domains of expertise are big data analysis; signaling network construction and mathematical modeling; study of synthetic interactions in cancer mechanisms, drug response prediction, patient stratification and many others (http://sysbio.curie.fr).

The group has long term experience in implementing scientific methodology of data and biological network analysis into user-friendly software packages, currently used by other researchers world-wide (the list of developed software can be found at http://sysbio.curie.fr/software).

Job description and skills
The candidate must be proficient in developing systems biology tools and methods and implementing them into software usable by others. Experience with at least one of the high-level programming languages such as JAVA, Matlab or Python will be needed for the candidate's mission. Fluent English both spoken and written is required. Familiarity in scripting languages such as R is a plus. Experience in systems biology projects, knowledge of the methods for statistical analysis of omics data and/or biological networks and basic knowledge of molecular biology are an advantage.

Master degree with experience of several years or PhD level in computer science, bioinformatics or systems biology

Send CV, motivation letter, and contacts details of 2-3 references to bcsb81  @  curie.fr

posted 2017.05.12

Fully funded PhD positions in Germany open

Carry out your own PhD project! Fully funded PhD positions in Germany


Closing Date:   30-04-17


Institution:   Hector Fellow Academy


Main text:

Carry out your own PhD project!

- in Systems Biology -

supervised by

Prof. Jens Timmer (University of Freiburg) 

At the Hector Fellow Academy you get the opportunity to realize a self-developed research project under supervision of Hector Fellow Prof. Jens Timmer. The Hector Fellows are a community of outstanding professors from different research institutions across Germany. They have been honored by the Hector Foundation for their merit in research and teaching within natural sciencesinformaticsmathematicsmedicine psychology and engineering. At the Academy they pass on their expertise to prospective young scientists.

Your profile

You are enthusiastic about developing and investigating an innovative research idea within the discipline of Prof. Timmer? You have a master's degree in a scientific or engineering subject with excellent grades? You stand out from your peers due to your strong commitment and independent work? You are team oriented and communicative? You are willing to change your place of residence to Freiburg?

Our offer

Our PhD students are employed as full-time research assistants at the University of Freiburg for a period of three years. The salary is determined by the institute's guidelines (according to the general pay scale of German universities approx. 47,000 EUR gross income per year). In addition, Hector Fellow PhD students receive grants for research expenses (15,000 EUR per year) and are given the opportunity to gain interdisciplinary expertise and relevant soft skills by participating in selected training activities.

Your application

Apply with your innovative, high-quality research idea via our Application Portal.

Current application period: January 1st  ̶  April 30th, 2017

Further information regarding the application process and the Hector Fellow Academy is available on www.hector-fellow-academy.de.



posted 2017.04.18

Graduate position for a PhD in systems biology in evolution and development open

1.Job/ project description:

The main objectives of the PhD project is to:

Develop computational models of organ development (morphogenesis and pattern formation) and their evolution in mammalian teeth, hair or Drosophila wing.

The research will take place in the Center of Excellence in Experimental and computational developmental biology of the Biotechnology Institute of the Helsinki University under the supervision of Isaac Salazar-Ciudad.

Embryonic development is one of the most amazing phenomena in life. During development a single cell transforms into a complex functional organism made of many cells, different cell types and a specific spatial distribution of those in space. How embryos organize themselves so that each cell ends up located in a specific position in the body is the central question of pattern formation and morphogenesis. This process involves the interaction of many genes in complex networks and the interaction of those with cells' and tissue's mechanical properties. In addition, this process is now widely acknowledged to be crucial to understand evolution since any change in the phenotype in evolution (e.g. morphology) would be first a change in the developmental process by which this phenotype is produced. Understanding development, thus, would allows us to understand which phenotypic variation can arise in populations due to genetic mutation (the so called genotype-phenotype map) and that, together with natural selection, would determine the direction of evolution. Understanding this link between development and evolution is a central aspect of the research in Salazar-Ciudad group.

Computational models are important tools to understand how gene networks interact with cell and tissue mechanical properties in development. There is currently a huge amount of data on how genes interact during development but data alone do not directly lead to understanding. The large number of genes involved, the complexity of the gene networks and cell and tissue mechanics in development require the building of precise quantitative hypotheses, the building of mathematical models to explore the consequences of these hypotheses and the comparison between models' predictions and well designed quantitative experiments. The center of experimental and computational developmental biology is a pioneering center combining models and experiments with this approach. In that sense the PhD will include collaborating with experimental developmental biologists, bioinformaticians, populational and quantitative geneticists, systems biologists, mathematicians, paleontologists and other evolutionary biologists.

The modeling will focus on integrating gene network regulation, cell-cell communication, cell mechanical interactions and developmental mechanisms in general and, optionally, artifical in silico evolution.

2. Requirements:

The applicant must be a biologists preferably with a strong background in either evolutionary biology, developmental biology or theoretical biology. Some knowledge of ecology, zoology, cell and molecular biology are also desirable.

Bioinformaticians, systems biologists or computer biologists that do not have a degree in biology or a strong background in biology will not be considered (e.g. no engineers or computer scientists).

Programming skills or a willingness to acquire them is required.

The most important requirement is a strong interest and motivation on science, embryonic development and evolution. A capacity for creative and critical thinking is also required.

3. Description of the position:

The fellowship will be for a period of up to 3-4 years (100% research work: no teaching involved).

The purpose of the fellowship is research training leading to the successful completion of a PhD degree.

Salary according to Finnish PhD student salaries.

4. The application must include:

-Application letter including a statement of interests

-CV (summarizing degrees obtained, subjects included in degree and

grades, average grade)

-Application should be sent to Isaac Salazar-Ciudad by email:

isaac.salazar @ helsinki.fi

Foreign applicants are advised to attach an explanation of their university's grading system. No official documents are required for the application first stage but these may be required latter on.

5. Examples of recent publications by Isaac Salazar-Ciudad group.

-Salazar-Ciudad I1, Marín-Riera M. Adaptive dynamics under

development-based genotype-phenotype maps.

Nature. 2013 May 16;497(7449):361-4.

-Salazar-Ciudad I, Jernvall J. A computational model of teeth and

the developmental origins of morphological variation. Nature. 2010

Mar 25;464(7288):583-6.

6. Interested candidates should check our group webpage:


The selected candidates will start as soon as an agreement is reached.

Isaac Salazar-Ciudad: isaac.salazar@helsinki.fi

posted 2017.03.27

Postdoctoral position in bioinformatics/computational biology at Stanford Center for Cancer Systems Biology open

The Stanford CCSB aims to identify mechanisms by which tumor cells "teach" the immune system to tolerate them, with a focus on little-studied interactions in lymph nodes, which are a frequent precursor to wider metastasis. We are analyzing tumor-immune interactions with a variety of high-thoughput assays including RNA-seq and single-cell imaging.

This is an opportunity for a postdoctoral fellow to develop and apply methods for identifying biomarkers and processes involved in lymph node and distant metastasis, initially focusing on public datasets. The candidate should have, or be close to completing, a Ph.D. in bioinformatics or computational biology, though those with a background in other quantitative computational fields will be considered. Strong computational skills as well as knowledge of machine learning and prediction methods are essential, as is a genuine interest in the scientific questions being investigated in the Center. Experience with a programming language suitable for biostatistical analysis (such as R or Python) is required, and UNIX/Linux cluster computing experience is strongly recommended. Experience with genomic analyses (microarray analyses, RNAseq analyses) is preferred; integration of large data sets, and analyses of multiple types of omics data would all be valuable assets.

The candidate should have strong written and verbal English skills, communication and interpersonal skills. You will be working closely with experimental and clinical collaborators, so should be willing to communicate across disciplinary boundaries and take the initiative in projects. Attention to detail and ability to work on multiple projects are important.

Further information about the Center and scientific aims can be found at http://ccsb.stanford.edu. Please submit a CV and the names of at least two references by email to Andrew Gentles: andrew DOT gentles AT stanford.edu

posted 2017.03.09

Nooyi Endowed Chair The Bioengineering Department at the University of Texas at Arlington open

Nooyi Endowed Chair
The Bioengineering Department at the University of Texas at Arlington

Apply Now

The Bioengineering Department at The University of Texas at Arlington invites applications for the Nooyi Endowed Chair position, focusing on systems biology, with a tentative date of starting employment in Fall 2017. This position is expected to be at the full professor level and is part of the College of Engineering's search for 12 tenure-oriented faculty members in thematic areas which are research thrusts of UTA's Strategic Plan 2020: Bold Solutions | Global Impact: Health and the Human Condition, Sustainable Urban Communities, Global Environmental Impact, and Data-Driven Discovery. The key objective is to hire faculty members with outstanding qualifications who share the University's core values of high standards of excellence in teaching, innovative and collaborative research, and service, combined with fostering an open and inclusive environment. Major emphasis will be on potential collaboration for research with faculty members from other departments across UTA and outside the University, as well as local premier medical universities such as The University of Texas Southwestern Medical Center and others.

Duties and Responsibilities

The successful candidate must have demonstrated internationally recognized research programs in the areas including, but not limited to, big data analytics, molecular and computational modeling, and systems biology. He/she is expected to lead the university's effort to establish a research cluster at the intersection of human health and data-driven discovery with a focus on the development of joint degree-granting programs in bioinformatics, medical informatics, and big data analytics. These anticipated new programs will combine teaching and research expertise and interest from bioengineering, computer science, biology and biochemistry. Candidate will be expected to teach and develop graduate courses in these areas, supervise graduate students, and serve on departmental, college and university committees.

Minimum Qualifications

Applicants must have earned a Ph.D. or M.D./Ph.D. degree in bioengineering or a related field and have a significant level of teaching, research and scholarship accomplishments commensurate with the rank of full professor with tenure.

The University, College and Department

The University of Texas at Arlington is a Carnegie Research-1 "highest research activity" institution. With a projected global enrollment of close to 57,000 in AY 2016-17, UTA is the largest institution in The University of Texas System. Guided by its Strategic Plan Bold Solutions | Global Impact, UTA fosters interdisciplinary research within four broad themes: health and the human condition, sustainable urban communities, global environmental impact, and data-driven discovery. UTA was recently cited by U.S. News & World Report as having the second lowest average student debt among U.S. universities. U.S. News & World Report also ranks UTA fifth in the nation for undergraduate diversity. The University is a Hispanic-Serving Institution and is ranked as the top four-year college in Texas for veterans on Military Times' 2017 Best for Vets list. The College of Engineering is home to seven departments: Bioengineering; Civil Engineering; Computer Science and Engineering; Electrical Engineering; Industrial, Manufacturing, and Systems Engineering; Materials Science and Engineering; and Mechanical and Aerospace Engineering. With more than 7,000 students, the College is the third-largest in Texas and offers the most comprehensive engineering degree programs in the region. It offers 10 baccalaureate, 14 master's, and 9 doctoral degree programs and has ties to numerous Fortune 500 companies in the region. The College is enjoying extraordinary growth in graduate and undergraduate student enrollment and in student graduation. This growth has been concomitant with growth in research expenditures, collaboration, innovation and entrepreneurship by faculty and students. The college currently has eight active NSF CAREER grants, four of which were awarded in 2015-16. The Bioengineering Department has a joint graduate program with The University of Texas Southwestern Medical Center in Dallas, and the University of Texas at Dallas, providing excellent opportunities for collaboration with clinicians and scientists from these institutions. Historically a graduate program, the department added an undergraduate program in 2012 and awarded its first baccalaureate degrees in 2016. Faculty are active in the areas of biomaterials and tissue engineering; biomechanics and orthopedics; medical imaging; nanomedicine and nanotechnology, with per-faculty research expenditures totaling more than $300,000.

Application Instructions

To apply, applicants should go to http://www.uta.edu/hr/careers/faculty-search and submit their application, including a cover letter, curriculum vitae, statements of research and teaching objectives, and contact information for at least five references. Questions about the position should be addressed to michael.cho@uta.edu. Review of applications will continue until the positions are filled.

EEO/AA Policy

UTA is an Equal Opportunity/Affirmative Action institution. Minorities, women, veterans and persons with disabilities are encouraged to apply. Additionally, the University prohibits discrimination in employment on the basis of sexual orientation. A criminal background check will be conducted on finalists. UTA is a tobacco free campus.

posted 2017.03.09

3-year PhD Studentship for computational biology in Imperial College London open

3-year PhD Studentship for computational biology in Imperial College London
Computational biology: In silico design and optimisation of novel host-directed therapies

We invite applications for an NC3R-funded PhD studentship to develop a mathematical/computational method to design and optimise a new and promising IFNγ immunotherapy for invasive fungal infection.

Invasive fungal infection usually occurs in patients under immunosuppressive treatments, such as chemotherapy for cancer, leukaemia and lymphoma and potent corticosteroid therapy. This project focuses on most common fungal infection of lung, aspergillosis, resulting in a mortality of nearly 100% if not diagnosed or treated and 30-85% even if treated. To develop a mathematical/computational method to design the immunotherapy, we will develop a mathematical model that can describe the regulatory mechanisms leading to progression of chronic fungal lung infection, and use the mathematical model to quantify and assess the fungicidal impact of IFNγ, determine and validate the optimal timing for administration of IFNγ, both alone and in combination with antifungal drugs, and predict optimal prophylaxis regimens for IFNγ therapy. Our in silico approach will identify most ethical and scientifically valid experiments to be conducted, replacing the initial infection experiments with computer simulation.

Applicants should have a Masters degree (or equivalent qualification) in a relevant area (computational biology, applied mathematics, control theory, or closely aligned disciplines), experiences in modelling and analysis of biological systems using differential equations and numerical methods, and strong interests in fungal biology. We look for highly motivated applicants with excellent interpersonal, written and oral communication skills and enthusiasm for exposure to a diversity of scientific projects.The PhD student will be co-supervised by Dr Reiko Tanaka and Dr Elaine BIgnell (Manchester), and the project involves close interactions with clinicians in the National Aspergillosis Centre (NAC).

The student will be based in the Department of Bioengineering, Imperial College London.

A stipend and home UK/EU fees for 3 years will be awarded. The studentship is available only to UK or EU nationals. Interested applicants should first send a current CV (with the names of 2 referees) and personal statement to Dr Reiko Tanaka (r.tanaka@imperial.ac.uk) by e-mail. Suitable candidates will be then asked to complete an electronic application form at Imperial College London in order for their qualifications to be addressed by College Registry.

More information on research activities in Dr Tanaka's group is found in http://www.bg.ic.ac.uk/research/r.tanaka. For the funding information, please see https://www.nc3rs.org.uk/studentship-vacancies.

Closing date: 10 April 2017

Start date: before 1 October 2017

posted 2017.03.08

Bioinformatician/Computational Biologist open

Job Title: Bioinformatics Specialist I 
Job Posting ID: 3032741
Salary Plan: Full-Time, Exempt
Lab: Walker
Direct Supervisor: Bruce D. Walker, M.D.
Email Contact: David Collins (drcollins [at] mgh.harvard.edu)
Employing Hospital and Department:
Ragon Institute of MGH, MIT, and Harvard
Minimum degree and field of knowledge: Bachelor's
Years experience required: 2

A position is open for a full-time bioinformatician at the Ragon Institute of MGH, Harvard and MIT. The candidate will perform computational analysis of data generated from HIV patient specimens. Knowledge gained from these studies will inform the design of more effective vaccines and treatments against HIV.

Job Duties: 
Under the direction of the principal investigator and collaborating bench scientists, and with guidance from other computational biologists at the Ragon Institute, the candidate will develop and implement analytical pipelines for the analysis of high-throughput assay data including single-cell and population RNA-seq, atomic-resolution protein structure data, and high-dimensional flow and mass cytometry. In addition to communicating methods and results to lab members and collaborators, the candidate will be expected to contribute to manuscript preparation. The candidate will contribute to multiple projects with the goal of improving our understanding of human immunology and enabling the development of novel HIV therapies. Specific responsibilities include the following: 
  • Advise bench scientists as they design experiments to produce robust data sets that are amenable to analysis and statistical testing. 
  • Communicate with collaborators to understand and develop requirements and specifications for analysis. 
  • Develop reproducible pipeline for data analysis of specific assay data (e.g., single-cell RNA-Seq) 
  • Integrate multiple data types using system approaches for generating novel biological insights 
  • Write detailed reports to be used to disseminate results to collaborators and prepare manuscripts 
Data management and high performance computing
  • Implement creative solutions for large volume data management challenges (e.g. databases) 
  • Create reusable high performance computing solutions for processing large data sets (e.g. write specific parallel code or scripts to send multiple jobs to a queue) 

Minimum Qualifications
  • Bachelor's or Master's degree with 2 or more years of demonstrated bioinformatics or computational biology experience 
  • Proficiency in R and a scripting language (Python especially preferred)
  • Familiarity with high performance computing and computing clusters
 Preferred Qualifications 
  • Prior experience with single-cell RNA-seq analysis strongly preferred
  • Familiarity with network analysis 
  • Familiarity with bioinformatic databases, such as GEO, UCSC Genome Browser, and MSigDB; and workflows such as those within Galaxy and GenePattern 
  • Experience with version control tools (preferably Git) 
  • Demonstrate integrity, excellence, accountability, and teamwork in all interactions
  • Good oral and written communication skills
  • Ability to maintain organized, detailed, and up-to-date documentation 
  • Strong interest in human immunology and infectious disease research
Application Information: 
The position is open immediately, although the start date is flexible. Please submit a cover letter, CV, and references to David Collins
(drcollins [at ] mgh.harvard.edu). Unfortunately, due to the number of applications we receive, we may not be able to reply individually to all inquiries. All applicants must be able to come to Cambridge, MA USA for an interview.

The above job description details the major duties and qualifications of the listed position. The employee hired to this position confirms that he/she is able to perform all duties outlined. Although the specific duties and responsibilities of this position may vary slightly, the supervisor of this position will ensure that the employee hired to this position is trained and qualified to complete each task assigned. If the duties or responsibilities of this position need to change significantly, then the supervisor must submit an updated job description to the Office Manager for review.

posted 2017.01.25

Postdoctoral Position in "Dynamical Systems Biology" at the University of Lille, France. closed


"Topic: Nonlinear dynamics study of stress-induced cell death decisions."

A challenge in biology is to understand the design principles of complex biochemical networks that are required to execute sophisticated regulatory functions in the cell. A theoretical framework to study this issue consists in comprehensively investigating the dynamical properties of small biochemical circuits combining a few elemental feedforward and feedback loop! motifs.

Our team is investigating, computationally and experimentally, the stress-induced cellular response - adaptation or death - depending on the type, intensity and duration of the stress. The adaptation process relies on negative feedback or incoherent feedforward loops while the death decision relies on positive feedback loops. In addition, cellular response shows significant cell-to-cell variability. These features motivate us to investigate the nonlinear and stochastic dynamics of minimal biochemical circuits that combine these motifs.

This theoretical project requires to perform extensive dynamical system analysis of a broad class of low-dimensional differential equation biochemical models, by using and combining various approaches (linear stability, bifurcation, phase-space, control theory and stochastic approaches). This project is closely related with other experimental and systems-bi! ology projects in our team.

The candidate should have (i) a strong background in applied mathematics or physics, especially in the field of nonlinear dynamical systems; (ii) some interest for biology.

The position is for one year renewable, and would start anytime in the first semester of 2017. Net annual salary is about 28000€ and includes a benefits package (health insurance, retirement and unemployment benefits). The laboratory (http://www.phlam.univ-lille1.fr/) is located on the Villeneuve d'Ascq campus of the University of Lille. Lille is a lively city connected by highspeed train to Brussel (30mn), Paris (1h) and London (1h30). Applicants should send a letter of motivation, a CV including a complete list of publication and at least 2 letters of recommendation to: quentin.thommen@univ-lille1.fr and Benjamin.pfeuty@univ-lille1.fr

For more informations: http://www.phlam.univ-lille1.fr/spip.php?article1066

posted 2017.01.08


Department of nvironmental Health Sciences 


The Department of Environmental Health Sciences (ENHS) in the Arnold School of Public Health at the University of South Carolina (UofSC) seeks scholars committed to research excellence in environmental health and invites applications for a tenure-track position at the assistant professor level in the area of Systems Biology. The candidate should have expertise in computational and/or modeling approaches to examine (sub-)cellular, organismal or ecosystem-level biological responses to environmental pollutants, pathogens, or perturbations. Preferred candidates will have completed one year of post-doctoral experience or equivalent, have the ability to establish an innovative, extemally-funded research program, and to develop specialty graduate/undergraduate courses in the area of expertise. Collaborations with faculty in ENHS and UofSC, as well as extemally, are expected. 
Refer Questions to: RSNORMAN [ at ] mailbox.sc.edu 

For a complete job description or to apply online, please visit: http://uscjobs.sc.edu (requisition #011248) AA/EEO employer.

posted 2017.01.05