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longle 12-27-2011 07:53 AM

Bioinformatics Specialist - Massachusetts General Hospital Pathology Department
Position: Bioinformatics Specialist I
Institution: Massachusetts General Hospital, Boston, MA
Department: Pathology
Reports To: Diagnostic Molecular Pathology Laboratory Director and Clinical Next-Generation Sequencing Project Leader
Salary: Commensurate with level of experience
Hours: 40 Hrs/week
Status: Full-time

The MGH Pathology Department and Cancer Center have led the field of clinical genetic profiling for personalized cancer diagnosis and treatment through recent efforts which include routine clinical use of the MGH SNaPshot assay ( and ALK rearrangement testing (

We are seeking additional highly motivated and experienced bioinformatics specialists to expand our group. The bioinformatics team will lead efforts in the development and implementation of an informatics pipeline for clinical tumor genotyping analysis based on targeted next generation sequencing.

The responsibilities will include:

. Working with staff molecular pathologists to build a robust informatics platform for analyzing sequencing data from clinical samples during assay development;
. Developing tools or applying existing software to support sequence alignment, variant calling, inter-sample comparison, algorithm evaluation, data management, data retrieval, and remote/web access;
. Developing a scalable database for variant curation and analysis;
. Helping to establish the physical and computational infrastructure to implement the informatics pipeline for routine patient testing;
. Managing the informatics pipeline during operation;
. Developing and documenting standard operating procedures based on best practices and standards, quality control measures, and quality improvement programs;
. Teaching and training of staff, residents, fellows, and technologists.

Minimum qualifications

. Preferably a MS/Ph.D. in bioinformatics, computation biology, computer science, or another equivalent field; a master's degree in the aforementioned fields combined with extensive practical experience (1+ years) in a sequencing center may substitute
. Strong analytical, computing, and statistical skills
. Successful candidates should be fluent with UNIX/Linux (command line and Bash shell environment) and Windows operating systems, have a strong programming/scripting background, and be proficient in working with large datasets.

Preferred qualifications
. Strong teamwork/collaboration and interpersonal skills
. Knowledge and practical experience with programming languages (e.g., Java, C or C++), a scripting language (e.g., Perl, Python), and a statistical environment (e.g., Matlab, R)
. Proficiency with database platforms (MySQL, Postgres, SQL, HDF5)
. Experience with cluster computing and large scale data storage (either traditional grid, Hadoop MapReduce, Hadoop+Cassandra, Brisk)
. Knowledge of system administration and networking
. Experience with code development, optimization, and testing
. Proficiency in both written and spoken English with excellent communication skills (presentations, reports, documentation)
. Must be detail-oriented, focused, creative, and independent
. Background in biology, molecular biology, or biochemistry
. Other preferred knowledge/skills: experience in a clinical diagnostics lab; experience with laboratory information management systems; experience with knowledge management systems like semantic mediawiki/SMW+

The position is open for immediate filling.

If interested, please provide:

1. A brief statement why you are an ideal candidate for this position.
2. Curriculum vitae listing education, qualifications, and experiences, including a list of scientific publications.
3. The names and contact information of at least two references willing to write a letter of recommendation or to speak on the phone.

Please contact:
Long Phi Le, MD, PhD

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