Bioinformatics Analyst I - Plant Biology Laboratory, Dr. Todd Michael

  • Salk Institute for Biological Studies
  • La Jolla, CA, USA
  • Apr 19, 2021
Full time Biology/Biotechnology/Life Sciences

Job Description

Application Instructions:

Employment History Include your last ten (10) years of employment history, or length of your employment history if less, including all positions (even those that are not relevant to this position) and periods of unemployment. Incomplete information could disqualify you from further consideration.


The Michael Group in the Plant Biology Laboratory at the Salk Institute focuses on sequencing and analyzing plant genomes. The Bioinformatics Analyst I (BAI) position will work closely with the PI and other members of the lab to analyze plant genome data generated in the lab. The BAI will be responsible for executing and maintaining current analysis pipelines, building new analysis pipelines, and integrating new genomics tools when appropriate. The BAI will also work closely with members of the lab and larger Plant Biology group to interpret genomics data as well as assist in non-pipeline bioinformatics applications.

There will be a specific focus on assembling plant genomes from Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT) long read sequencing technologies. The BAI will stay current on best practices and update the genome assembly pipelines according to advances in the sequencing technologies. The BAI will develop gene prediction strategies and ensure that the gene prediction pipeline integrates appropriate data types to ensure high quality gene models. In addition to genome assembly and analysis, the BAI will be responsible for analyzing and integrating multi-omic data sets such as resequencing, single cell, ATAC-seq, and DNA methylation.

Other efforts will include the collection, integration and analyses of plant multi-omic data to enable discovery by lab-based biologists. The BAI will also work with scientists to visualize their data and develop high quality figures for papers when appropriate. The position will include presentation of scientific results to the larger Plant Biology Laboratory and scientific writing.


(25%) Research Design and Presentation

  • Contribute and assist with project inception, experimental design, analysis and result 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 digital and analog lab notebook, including experimental design, time, methods, materials and results.

(45%) Data Analysis

  • Assist host lab researchers and collaborators contribute to scientific discovery by assembling plant genomes, predicting genes, annotating gene sets, and integrating multi-omic datasets.
  • Work closely with researchers from multiple laboratories and scientific backgrounds simultaneously.
  • 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 cloud computing environment.
  • Keep informed of new developments and technical advances in the data science and machine learning fields by reading primary literature and vendor websites.
  • Assist in the analyses of genomics/next-gen sequencing data, including, but not limited to: RNA-Seq, ChIP-Seq, GRO-Seq, Hi-C, Bisulfite-Seq, single-cell RNA-Seq and other emerging methods.

(15%) Advanced Data Analysis

  • Keep abreast of new scientific advances in bioinformatics, data science, artificial intelligence, machine learning 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 data analysis algorithms.
  • Participate in the design, coding, and presentation of novel analysis tools for cutting-edge data analysis.
  • Present advanced analysis results, tools, and pipelines at group meetings, scientific conferences, and scientific journals under the supervision of senior core personnel.

(10%) Data Science Training and Support

  • Provide assistance and training to researchers on how to analyze and interpret plant genome data.
  • Help educate and advise researchers on the pros and cons of available analysis tools, and approaches, in one-on-one training sessions, or larger group workshops.
  • Ensure users are aware of the limitations of analyses and approaches to help ensure high standard of scientific research.

(5%) Data Maintenance and Management

  • Help maintain scripts, software, website, tools, wiki, and pipelines.
  • Help ensure that servers, hardware and cloud instances relevant to data analyses are operating properly and report all possible problems.
  • Liaise with IT department and manufacturers with regard to hardware or software maintenance.
  • Upload genomic data to SRA/NCBI for long term retention.



  • A minimum of 6 months analysis experience with genome analysis OR 1 year experience in multi-omics analyses.
  • Programming experience (Perl, Bash, Python, C/C++, Java, or R)
  • Strong presentation and communication skills.
  • Experience working in a Linux/UNIX operating system in a high-performance computing environment
  • Familiarity with cloud computing and containerization.
  • Familiarity with next-generation sequencing technologies and assays.


  • Experience with analyzing plant genomes and/or plant biology.
  • Background and/or experience with machine-learning algorithms and/or computational modeling.



  • BA/BS degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics, related discipline or equivalent.


  • 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 students.
  • Ability to interact diplomatically and professionally with all levels of Institute staff and external contacts.
  • Ability to identify, download, install, troubleshoot and assess new analysis tools.
  • 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 data integration and data mining.
  • High proficiency in a scientific programming language (Perl, Python, C/C++, Java, R or Web applications)                                 
  • Demonstrated knowledge and experience with MAC or Linux/UNIX operating systems.
  • Theoretical and practical knowledge of biological sciences (particularly clinical and molecular biology).


  • Must be willing to work a flexible schedule to support research needs.
  • Successful completion of the Institute's background investigation.
  • Must be willing to sign a confidentiality agreement.


This position requires constant adjusting focus, seeing, sitting, touching/feeling, and working inside. 

Application Details

Apply Here:


 Equal Opportunity Employer/Protected Veterans/Individuals with Disabilities


When inquiring or applying for positions at the Salk Institute for Biological Studies, please also reference

Applicants with dual-career considerations can find university jobs such as professor jobs, dean jobs, chair / department head jobs, and other faculty jobs and employment opportunities at the Salk Institute for Biological Studies and at other institutions of higher education in the region on