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2017

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:


http://www.biocenter.helsinki.fi/salazar/index.html


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
JOBPOSTF00023P

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

Summary:
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: 
Analysis 
  • 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) 

Qualifications: 
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) 
Expectations
  • 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

RESEARCH PROJECT

"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.

CANDIDATE PROFILE
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.

POSITION AND APPLICATION DETAILS
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

TENURE-TRACK ASSISTANT PROFESSOR - SYSTEMS BIOLOGY open

Department of nvironmental Health Sciences 
UNIVERSITY OF SOUTH CAROLINA 

TENURE-TRACK ASSISTANT PROFESSOR -SYSTEMS BIOLOGY 

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