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University of Rochester Bioinformatics Analyst, Genomics Research Ctr - 220510 in Rochester, New York

Bioinformatics Analyst, Genomics Research Ctr

Job ID

220510

Location

School of Medicine & Dentistry

Full/Part Time

Full-Time

Favorite Job

Regular/Temporary

Regular

Opening

Full Time 40 hours Grade 054 Functional Genomics

Schedule

8:30 AM-5 PM; OCC WKENDS

Responsibilities

Position Summary:

The Genomics Research Center (GRC) at the University of Rochester is seeking a highly trained, motivated, and passionate Bioinformatics Analyst to join a collaborative Bioinformatics group providing applied bioinformatics analytical support to research scientists utilizing high-throughput sequencing and other data types for their research. The ideal candidate should have a solid foundation in molecularbiology and bioinformatics as well as be able to communicate and work with a diverse research team. The GRC Bioinformatics Group routinely performs analysis of data including, but not limited to mRNA-seq (bulk and single-cell), micro RNA-seq, total RNA-seq, ChIP-seq, ATAC-seq, whole genome and exome sequencing, methylation sequencing, and micro array using cutting edge analytical methods as well as educates the research community on best practices for informatics. The GRC provides a highly interactive environment with collaborative opportunities across basic and clinical departments, access to high performance computing clusters, highly automated analytical pipelines and integration with high-throughput sequencing infrastructure to aid in experimental design and execution for delivery of high-quality results for highly competitive projects. Candidates with a strong background in bioinformatics, computational biology, machine learning are highly encouraged to apply for this position. This position is located in Rochester, NY and located within the Wilmot Cancer Institute. This position will report directly to the Co-Director of the Genomics Research Center (GRC) and will operate with minimal supervision.

Responsibilities:

Participate in experimental design and analysis of high-throughput sequencing data generated on high-throughput sequencing instruments.

The sequence data will include:

  • genome sequence data from experimental approaches such as whole genome sequencing, exome sequencing, ChiP-Seq, and targeted resequencing panels

  • bulk and single cell RNA-seq data from tissues, cells and bacteria

  • epigenetic (ATAC, methylation) data from tissue and cells populations.

Analysis will include assessment of primary sequence data quality and evaluation of biological questions during downstream processing. Experience with alignment tools (bowtie2, STAR), read quantification tools (featureCount, MACS2), and downstream analytical tools including but not limited to R, Seurat, Monocle, DiffBind, ChIPQC, deeptools, and RMarkdown is highly desired. Routinely prepare results and figures for presentation and publication. Perform research, evaluation, and optimization of new computational tools and pipelines, as needed. Use of version control software, such as github, to ensures data reproducibility via RMarkdown documentation. This requires an extensive working knowledge of linux/unix commands, computer programming languages and application of open-source software tools.

Develop tools and pipelines to track and monitor sequence data quality and output for internal GRC quality control and grant applications. This will include the utilization of version control software (gitlab, anaconda) to ensure pipeline portability and analysis reproducibility. (20%)

Actively research publically available tools and training resources to develop formal and informal training (including development of training courses and workshops, written documents, screencasts, individual consultation, and other forms of media) Continually engage in University outreach through surveys, social media, and town hall seminars to understand community needs and assess educational impact. Tailor all educational resources to the diverse computational needs of the community. Define and modify training media as needed based on community feedback. Develop and maintain a training website to host schedules and educational materials. Collaborate with other departments at the University to provide comprehensive and multi-disciplinary opportunities.

Community Education and Support

Participate in experimental design consultation meetings with GRC customers and provide education to the URMC community in the form of individual correspondence, seminars, and GRC sponsored workshops.

Other projects and job duties as assigned.

Qualifications:

Bachelor's degree in related discipline such as Computer Science, Business, Mathematics, Statistics, Science or Engineering; and 3-4 years of related experience, preferably 1-2 years in a supervisory capacity; or an equivalent combination of education and experience.

Preferred Qualifications

  • MS degree in Bioinformatics, or related discipline, with at least 2-5 years of practical experience in analysis of high-throughput sequence data and experimental consulting for genomics applications, specifically in single-cell genomics. 3-4 years of related experience.

  • Strong background in bioinformatics, computational biology, and machine learning strongly preferred.

  • Experience with multiple computer operating systems (Windows, Mac, Linux and Unix), computer languages (C++, Java/Parallel Java, MySQL, Perl, Python and R) is essential.

  • Excellent interpersonal, presentation, and communication skills, including written communication.

How To Apply

All applicants must apply online.

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