Senior Bioinformatics Scientist

92121, San Diego
Jan 12, 2022
Required Education
Position Type
Full time

This position offers a unique opportunity for a talented Senior Scientist to lead bioinformatics development across multiple functional groups working at the cutting edge of Protein Production Engineering, enabling the development of life saving medicines. The successful candidate will collaborate with the Strain Engineering, Fermentation and Analytical Development R&D teams to mine internal and public genomic, transcriptomic, and proteomic datasets. The candidate will be responsible for processing large next-generation sequencing (NGS) datasets and applying machine-learning (ML) approaches to combine multi-factorial Target Protein Expression data to identify targets for strain and/or target protein engineering. This position may require visits to the Pelican facility but can be remote. 

Pelican Expression TechnologyTM (a wholly owned subsidiary of Ligand Pharmaceuticals) utilizes a proprietary protein production platform to help our partners develop protein therapeutics which meaningfully improve existing treatment paradigms and create novel therapies for biological targets linked to critical diseases still waiting to successfully be addressed.

Essentials for Working at Ligand * Ligand is a dynamic, fast-paced organization committed to creating shareholder value and addressing unmet medical needs through developing and acquiring cutting-edge, royalty-bearing technologies and establishing research collaborations that make major life-saving global drugs possible. To be successful at Ligand, employees must be innovative, efficient, versatile, self-starters who take great pride in their work and want to contribute to something significant.

Essential Role Responsibilities

Technical Scope

  • Develop databases to compile information from activities such as gene expression profiling and protein expression
  • Develop computational methods for integrative analysis of multi-omic datasets
  • Apply machine learning and statistical analysis to produce predictive models supporting therapeutic protein development
  • Develop pipelines and test algorithms to optimize analysis of NGS data including RNA-seq
  • Apply best practice computational methods to analyze large-scale biological data for next-generation sequencing, etc. in a fast-paced product development environment
  • Design and develop pipelines to address novel analytical challenges and to automate established analysis both locally and in the cloud computing environment
  • Collaborate with interdisciplinary teams to drive data analysis, integration, and application across various omics platforms
  • Work across the Pelican Business Unit to offer bioinformatics and/or biostatistics support
  • Expand and manage R&D informatics capabilities including genomic and plasmid DNA databases, sequence and statistical analysis tools, data workflows and platforms.
  • Collaborate with IT to manage and maintain Cloud Data Computing and Storage infrastructure

Experience and Skills

  • M.S./ Ph.D. in computational biology, bioinformatics, genomics, systems biology, statistical genetics, data science, or a closely related field.
  • 3+ years of industry experience preferred
  • Thorough knowledge of bioinformatics methods, applications programming, web development and data structures
  • Experience with Python (preferred), Perl, HTML, relational databases and SQL and programming in a UNIX/LINUX environment
  • Demonstrated expertise with NGS analysis, standard bioinformatics tools, statistical tools, and public datasets
  • Experience with one or more of the following:
    • Genome-wide NGS experiments such as RNA-seq/WG-seq or their targeted AmpliSeq counterparts
    • Illumina's BaseSpace Sequence Hub
    • Bioinformatics software development
    • Algorithms or machine-learning models that combine multiple data types
    • Working closely with wet-lab scientists to optimize NGS library construction methods
    • LIMS and informatics software development and integration
  • Demonstrated ability and experience as follows:
    • Ability to perform effectively in a cross-functional, matrixed environment where collaboration and influencing skills are paramount
    • Ability to work flexible work schedules, including weekends, as required
    • Detail oriented and highly organized with a strong business/technical acumen
    • Effectively multi-tasks to meet deadlines and commitments
    • Excellent project- and time-management abilities and strong follow-through skills required
    • Proactively takes initiative to identify, research and solve complex technical problems and issues; communicates status in a timely manner
    • Works independently, sets priorities and makes decisions with general guidance and supervision
  • Must be able to travel up to 10% (US and internationally)
  • Other skills and abilities as required


  • The company offers competitive benefits including medical, dental, vision, Short/Long term disability and life insurance, as well as 401(k) match, Stock Options, Bonus, and paid time leave.

Additional Information

  • All new hires are required to go through a background and reference check
  • Ligand is an EEO/AA/Disability/Vets employer
  • Must be legally authorized to work in the US without sponsorship
  • Ligand celebrates the diversity of life and welcomes all individuals to apply