Employment Type : Full-Time
The Senior Genomics Bioinformatics Programmer is responsible for the implementation and overall supervision of bioinformatics analyses pipelines necessary for interpretation of assays that are based on massively parallel sequencing technologies. In this capacity, the incumbent will interact with teams of experimental and computational scientists and trainees who work together to design, execute and analyze complex experiments investigating transcriptional mechanisms that control immune cell development and function. Current assays include RNA-seq, single cell RNA-seq, ChIP-Seq, ATAC-Seq, and three-dimensional chromatin conformation capture assays. The incumbent will maintain and update ‘best practice’ computational methods and provide training and oversight to members of the laboratory in the application of assay-specific bioinformatics tools. Will interface with technical support at the San Diego Super Computer Center to maintain laboratory-specific computational infrastructure necessary for data storage and analysis. As necessary, will generate new software tools and/or provide direction to trainees to develop such tools for problems lacking appropriate analytical methods. Additionally, they will be involved in writing primary research publications and grant applications and will be encouraged to attend and contribute to scientific meetings on related topics. Bachelor's Degree in biological science, computational/programming, or related area and/or; equivalent experience/training. A minimum of five (5+) or more years of senior-level bioinformatics experience in a research setting. In-depth knowledge of bioinformatics methods, applications programming, web development and data structures. Experience with programming languages (Python and R are required, strong candidates will also have experience with Perl, C#, C++, or Java). Demonstrated experience using UNIX/Linux. In-depth knowledge of bioinformatics programming design, modification and implementation. Experience in development of complex bioinformatic, knowledge-based application software. Ability to analyze scientific technical information. Advanced understanding of relational databases, web interfaces and operating systems. Proven ability to download high-throughput data sets, trouble shoot sequencing data, conduct standard statistical analysis and data visualization. Advanced project management skills. Proven ability to organize, prioritize and manage multiple project activities effectively and deal with changing priorities. Thorough knowledge of modern biology and applicable field of research. Working knowledge of biological systems including transcription, genetics, and epigenetics. Proven interpersonal skills in order to work with both technical and non-technical personnel at all levels in the organization, including senior project leadership. Proven ability to receive input and integrate ideas from colleagues to develop computational solutions that meet the needs of the laboratory. Advanced ability to interface with management on a regular basis. Ability to communicate and deal effectively and productively with people at all levels of responsibility in various functional areas. In-depth knowledge of web, application and data security concepts and methods. Ability to communicate technical information in a clear and concise manner. Ability to communicate and teach complex concepts to scientists from various fields. Excellent communication skills for oral presentations, written reports, and one-on-one training. Ability to lead a team, meet deadlines and demonstrate problem solving skills. Ability to work independently, as well as part of a team, establishing and maintaining good working relationships with P.I., supervisor, postdoctoral scholars, and other members of the research group. Ph.D Degree or equivalent experience/ training in bioinformatics, computer science or related field with programming and server experience or related combination of education and experience. Experience with bioinformatics and metagenomics software and resources for analyzing high-throughput sequencing datasets. Employment is subject to a criminal background check. Occasional evenings and weekends may be required.
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