Positions available!

We are seeking outstanding Bioinformaticians and Computational Biologists to join our multidisciplinary team to study the spatial organization of the human genome

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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 collaborators in the laboratory of 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.

The Bioinformatician will also be responsible for conducting the following duties:

  • Generate customized programming solutions to improve user interaction with available bioinformatics resources
  • Implementation and adaptation of programs for high-throughput sequencing data analysis, statistical analysis of data and for data visualization
  • Develop, implement and maintain custom designed computational solutions relevant for ongoing lab-based projects
  • Develop, implement and maintain computational methods for meta-analysis of data generated in the lab as well as publicly available data
  • Interact with a high-performance computing cluster (LSF) to schedule standard data processing pipelines and data analysis workflows

Responsibilities:

MAJOR RESPONSIBILITIES:

  • Design and implement reusable bioinformatics analysis pipelines for processing next-generation sequencing, microarray, genomics, proteomics and chemogenomics data
  • Integrate computational methods/pipelines with high performance computing clusters
  • Collaborate closely with PIs and their lab members on research projects including defining the scope of the collaboration, researching on the scientific topics and implementing the appropriate bioinformatics solutions that meet timelines
  • Participates in the oral presentation of all project findings and abstracts including participation in periodic project status meetings and presentation of final project deliverables.
  • Develop rapid prototypes and custom scripts for one-off type of analysis requests
  • Develop novel algorithms and integrated data visualization applications when existing software packages are not available or adequate
  • Properly document the procedures used in computational analysis and provide summary report of results suitable for inclusion in manuscript and grant applications
  • Local establishment and customization of genomic, proteomics databases and provide batch analysis utilities that make use of these resources
  • Develop custom databases and web portals for managing raw and processed experimental data
  • Provide bioinformatics training and workshops for analysis pipelines and in-house developed software applications
  • Coordinate and collaborate with other bioinformaticians, biostatisticians, information technology professionals, and interdepartmental project teams.
  • Perform other duties as required.

Qualifications:

REQUIRED QUALIFICATIONS:

  • Master’s degree in Computer Science, a related computational discipline, or equivalent experience
  • 2 years bioinformatics-related research experience
  • Proven research record such as co-authorship on peer-reviewed publications required
  • Strong background in programming. Fluent in one programming language (Java or C/C++) and one scripting language (shell, Perl or Python)
  • Knowledge in biostatistics packages (R or Matlab) and SQL queries are strongly suggested
  • Strong communication skills, both the oral and written 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.

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