SEARCH CAREER OPPORTUNITIES

The laboratory of Job Dekker PhD HHMI is seeking outstanding candidates to join a multidisciplinary team of molecular biologists, statisticians and bioinformaticians.

We are a highly interdisciplinary lab, combining experimental and computational efforts to study how genomes function.  We are funded by the Howard Hughes Medical Institute, and NIH. Recently we established the Center for 3D Structure and Physics of the Genome, as part of the NIH 4D Nucleome Consortium, to study the spatial organization of the human genome.

The Dekker Lab is one of the leading labs in the world that studies how the genome is organized in three dimensions in the cell nucleus.  To explore and study genome folding we first developed several genomics technologies such as 3C, 5C and Hi-C (Dekker, Science 2002, Dostie Genome Res. 2006, Lieberman Aiden, van Berkum, Science 2009).  These technologies employ deep sequencing to produce massive genome-wide chromatin interaction maps that we then analyze using a whole suite of computational and bioinformatic methods that we developed ourselves, and in collaboration with our close collaborator Leonid Mirny (MIT).  (See Lajoie, Nature Methods 2009, Imakaev, Nature Methods 2012).

Our research has revealed new insights into the mechanisms of long-range gene regulation by distal enhancers (Sanyal, Nature 2012), the compartmentalization of chromatin in distinct functional domains (Nora, Nature 2012), the internal organization of the chromatin fiber (Dekker, JBC 2008), the structure of mitotic chromosomes (Naumova, Science 2013), and the overall organization of entire genomes inside the nucleus (Gibcus, Mol. Cell 2013).

Recently NIH started the 4D Nucleome initiative (https://commonfund.nih.gov/4dnucleome/index).  Our lab heads one of the largest centers in this network.  In our center we employ state-of-the-art genomics, imaging, genome engineering, computational modeling and bioinformatic approaches to study the structure and biophysics of the human genome.  We are looking for enthusiastic bioinformaticians and computational biologists to participate in and lead the analysis component of our center.  In these positions, you would be playing a key role in the Center, as well as in the international 4D Nucleome consortium to explore this exciting new area of genome sciences.

GENERAL SUMMARY OF POSITION:

Under the direction of a member of the faculty, the Bioinformatician is responsible for the design, development, evaluation and iterative modification of a technical infrastructure to expedite the quantitative evaluation of data resulting from studies that are laboratory based.  The position will entail the establishment and maintenance of applicable in-house bioinformatics resources and interaction with individual lab members on customized research projects, as well independent projects that are solely computational. 

MAJOR RESPONSIBILITIES:

• Establish general bioinformatics resources for day-to-day use by members of the laboratory.
• In collaboration with a member of the faculty, generate customized programming solutions to improve user interaction with available bioinformatics resources
• Implement and adapt programs for microarray analysis, high-throughput sequencing data analysis, cis regulatory motif identification, and multi-genome protein motif searches.
• Independently develop, implement and maintain custom designed computational solutions relevant for ongoing lab-based projects.
• Independently develop, implement and maintain computational methods for meta-analysis of data generated in the lab as well as publicly available data.
• Independently execute a scientific computational project (e.g. a project that can result in a first author publication)
• Supervise entry level bioinformaticians.
• Local establishment and customization of model organism genomic databases and tools for batch sequence analysis utilizing these resources.
• Interpret and present study results in support of laboratory members.
• Provide tabular and written summaries of approaches and analyses in a form suitable for inclusion in manuscripts or grant applications, as well as media for presentation at scientific meetings
• Develop and implement custom bioinformatics programming solutions in collaboration with lab as necessary
• Coordinate and collaborate with other research computing expertise at the Medical School as necessary
• Participate in conference calls and data management meetings as needed
• Perform other duties as required

REQUIRED QUALIFICATIONS:

• BS in computer science, or equivalent experience
• 2 years of experience in relevant setting
• Co-authorships on peer-reviewed publications are strongly suggested but not required
• Strong background in statistical methodology, software languages and computer systems (Perl, C++, R, MySQL, etc.)
• Experience in writing basic search algorithms and the ability to generate new algorithms and programs for custom data manipulation and analysis
• Excellent communication skills, both oral and written, and interpersonal skills necessary to interact with a wide range of individuals.

PREFERRED QUALIFICATIONS:

• Familiarity with programming techniques for analyzing data sets that do not fit in memory.
• Numpy/Scipy/HDF5 experience is a plus.
• Experience using BIG DATA (NGS data a plus, multi-TB)
• Experience using relation databases, SQL and or structured data formats (e.g. HDF5).
• Web experience (PHP, JavaScript, JSON, REST) is a plus.
• Experience using a compute cluster (LSF, SGE).
• Co-authorships on peer-reviewed publications are preferred.
• Normal visual acuity, hearing and manual dexterity.