Bioinformatics Analyst II - Laboratory of Dr. Susan Kaech

Job location is at 10010 N Torrey Pines Rd, La Jolla, CA 92037

The Kaech Lab studies the role T cells, and other immune cells play in viral infections and cancer, with a focus on T cell and macrophage function, metabolism and differentiation. We study the pathways involved in T cell exhaustion and tissue-residence memory as well as neuro-immune interactions in tumors and in the central nervous system.

The Bioinformatics Analyst (BA) position will work closely with the PI and other members of the lab to analyze single cell RNA & ATAC-seq datasets, single-cell spatial datasets, metabolomics and other multiomics data generated in the lab. The BA will be responsible for executing and maintaining current analysis pipelines, building new analysis pipelines, and integrating new genomics tools when appropriate. The BA will also work closely with members in collaborations for integrated analysis and interpret multiple –omics datasets as well as assist in non-pipeline bioinformatics applications. The BA will also work with scientists to visualize their data and develop high quality figures for papers when appropriate. The BA would work on multiple projects simultaneously and would result in authorship on papers. The BA will oversee the maintenance, organization and long-term storage of sequencing and omics raw and processed data

DUTIES AND RESPONSIBILITIES:

• Work independently to develop advanced computational and statistical methods for big-data analysis.
• Must be familiar with many different algorithms and software tools to generate data analysis pipelines and execute analysis in a timely manner.
• Work independently to create and implement machine learning algorithms for identifying patterns and signatures relevant to biological datasets.
• Work independently or with limited supervision on informatics research projects under direction from senior core staff or with research collaborators.
• Work with Institute researchers and contribute to scientific discovery by implementing, optimizing and executing computational approaches for DNA methylation analysis, mapping, genome sequence analysis, transcriptome analysis, and data visualization.
• Use published and available pipelines, scripts, and tools to prepare and process large datasets.
• Must be fluent in coding
• Work in a high-performance computing environment.
• Keep informed of new developments and technical advances in the bioinformatics, image processing, visualization, genomics and biological fields related to current projects.
• Research, implement, test, and present on new tools and pipelines for high-throughput data analysis.
• Independent design and coding of analysis pipelines and cutting-edge bioinformatics analysis algorithms.
• Participate in the design, coding, and presentation of novel analysis tools for cutting-edge bioinformatics analysis.
• Present advanced analysis results, tools, and pipelines at group meetings and contribute to publications in scientific journals.
• Contribute and assist with project inception, experimental design, analysis and manuscript presentation.
• Work on the preparation of data for, manuscripts, publications, grant applications, posters and other presentations.
• Present results verbally and with visual aids in one-on-one meetings, group meetings, or conferences.
• Maintain lab notebook, online code-share repositories such as GitHub, GitLab, BitBucket, etc including experimental design, time, methods, materials and results.
• Help maintain scripts, software, tools, and pipelines used in the lab.
• Help ensure that lab servers and hardware are operating properly and report all possible problems.
• Help users of lab software and servers to troubleshoot potential problems.
• Liaise with IT department and manufacturers with regard to hardware maintenance.
• Back-up data in the lab server on a regular basis.
• Performs other related duties as assigned

SUPERVISORY RESPONSIBILITIES:

This job has no supervisory responsibilities.

QUALIFICATIONS:

• MS degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics or related discipline or equivalent relevant experience
• Minimum of 3 years of relevant bioinformatics experience with a Master’s degree. If PhD, experience acquired through PhD program may be considered in lieu of professional experience.
• Hands on work experience in single cell analyses and integration, harmonization of data sets, statistics, and machine learning.
• Willingness to understand and interpret the data analysis and have a high level of scientific rigor.
• Relevant experience and proficiency in P