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Bioinformatics Analyst II, Plant Molecular & Cellular Biology Laboratory Dr. Wolfgang Busch

Salk Institute for Biological Studies
La Jolla, CA
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Job Details

The CRoPS project aims to develop crop plants that sequester more carbon via extensive root systems containing recalcitrant carbon polymers to fight climate change. A major component of this research is to conduct genetic and genomic analysis for understanding traits relevant for this. Many of the genetic analysis depend on image acquisition and image processing.The Bioinformatics Analyst II will work closely with other members of the CRoPS project and the Busch laboratory to advance image acquisition image processing, statistical genetics and genomics research projects. The analyst will contribute directly to research projects in the CRoPS project in the context of several computational analysis areas by implementing, optimizing and executing computational approaches for image segmentation and analysis, genome wide association mapping, genome sequence analysis, transcriptome analysis, and data visualization. Finally, the analyst will play part in administrating shared computer resources, such as compute and storage servers.ESSENTIAL FUNCTIONS Research Design and Presentation (5%)
  • Contribute and assist with project inception, experimental design, analysis and manuscript presentation
  • Assist with 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, including experimental design, time, methods, materials and results
Bioinformatics Analysis (85%)
  • Assist Institute researchers and contribute to scientific discovery by implementing, optimizing and executing computational approaches for image segmentation and analysis, genome wide association mapping, genome sequence analysis, transcriptome analysis, and data visualization
  • Work independently or with limited supervision on informatics research projects under direction from senior core staff or with research collaborators
  • Use published pipelines, scripts, and tools to prepare and process large datasets
  • 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, and test, and present on new tools and pipelines for high­ throughput data analysis
  • Participate in the 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
ICG Bioinformatics Core Facility Maintenance and Management (10%)
  •  Help maintain core scripts, software, website, tools, wiki, and pipelines
  • 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
  •  4 years related experience or equivalent combination of education and experience.
  • A minimum of 1 year analysis experience with image analysis
  • Programming experience
  • Fluency in at least 2 common programming languages (Perl, Bash, Python, CIC++, Java, or R)
  • Experience in high performance computing
  • Good presentation and communication skills
  •  Experience with machine-learning algorithms and/or computational modeling
  • Experience with GPU computing
  • Experience with deep learning based image segmentation
  • Experience in statistics and machine
  • Experience in biology
  • Background in next-generation sequencing technologies and
  •  Bachelor’s degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics or related discipline or equivalent experience.
  •  MS or PhD degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics, or related discipline.
  •  Proven organizational and time management skills to successfully set priorities, meet established deadlines and recognize new problems with constantly changing priorities and frequent interruptions
  • Strong communication skills (both verbal and written) needed to interact professionally and effectively in the work environment. Ability to read, comprehend, and discuss research materials. Proven ability to write, edit and proofread research results. Skill at explaining difficult concepts and training users and discuss
  • Ability to interact diplomatically and professionally with all levels of Institute staff and external contacts tools
  • Ability to identify, download, install, troubleshoot and assess new analysis tools
  • Experience analyzing images
  • Experience with Standard business office equipment and commonly used software and tools, such as Microsoft Office , electronic mail, and the internet
  •  Experience applying machine learning approaches for image processing, data integration and data mining
  • High proficiency in scientific programming languages (Perl, Python, C/C++, Java, R or Web applications)
  • Demonstrated knowledge and experience with MAC or Linux/UNIX operating systems
  • Experience in performing image analysis unsupervised and in recommending modifications to algorithms and workflows to meet the needs of research projects. Demonstrated ability to contribute to experimental design and assist with the analysis and interpretation of results
  • Theoretical and practical knowledge of biological sciences (particularly genetic and molecular biology).
  •  Satisfactory completion of the lnstitute's background
  • Must be willing to sign confidentiality agreement
  • Must be willing to work in an animal-related research environment
PHYSICAL REQUIREMENTS/MENTAL ACTIVITIES/ENVIRONMENTAL CONDITIONSThis position will be constantly adjusting focus, grasping, handling, hearing, keying, seeing, sitting, talking, touching/feeling, analyzing, calculating, communicating, reading, reasoning, writing and working inside. 


Working at Salk Institute for Biological Studies

The Salk Institute for Biological Studies is one of the world's preeminent basic research institutions, where internationally renowned faculty probe fundamental life science questions in a unique, collaborative, and creative environment. Focused on both discovery and mentoring future generations of researchers, Salk scientists make groundbreaking contributions to our understanding of cancer, aging, Alzheimer's, diabetes, and cardiovascular disorders by studying neuroscience, genetics, cell and plant biology, and related disciplines.

Faculty achievements have been recognized with numerous honors, including Nobel Prizes and memberships in the National Academy of Sciences. Founded in 1960 by polio vaccine pioneer Jonas Salk, M.D., the Institute is an independent nonprofit organization and architectural landmark.

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