SEARCH CAREER OPPORTUNITIES

GENERAL SUMMARY OF POSITION:

In the Department of Molecular Cell & Cancer Biology of University of Massachusetts Medical School, we have developed a core team of accomplished computational biologists who work side-by-side with bench scientists to evaluate, select and develop algorithms and software pipelines to analyze, annotate, visualize and integrate various biological datasets, including those generated from high-throughput experiments such as ChIP-seq, ChIP-chip, RNA-seq, PAS-seq, iCLIP-seq, ATAC-Seq, miRNA-seq, exon sequencing, GUIDE-seq, single-cell sequencing, shRNA and gRNA screening, and CRISPR genome editing.  We are active contributors to the open-source open-development Bioconductor project. We have developed more than a dozen packages with various utilities, ranging from machine learning, peak calling, annotation, visualization, to gRNA design and evaluation.

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. 

Responsibilities include-

• Develop novel algorithms and software tools for integrated data analysis and visualization of high-throughput dataset including next-generation sequencing data and proteomics data when existing software packages are not available or adequate
• Enhance/Maintain Bioconductor packages developed in house
• Collaborate closely with PIs and their lab members on research projects including evaluating, selecting, and implementing when needed the best of breed computational solutions for the analysis of biological data
• Develop rapid prototypes and custom scripts for one-off type of analysis requests
• Properly document the procedures used in computational analysis and provide summary report of results suitable for inclusion in manuscript and grant applications

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:

• Master's degree in Bioinformatics, Computer Science, Statistics or related computational disciplines
• Minimum 1 year bioinformatics-related research experience
• Proven research record such as co-authorship on peer-reviewed