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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. open


"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