Informatician 3

The successful candidate will possess broad and deep scientific expertise a strong publication and track record and exceptional knowledge in genome editing long-range sequencing biomedical informatics and computational genomics. A clear understanding of the CECGT research mission is essential. The position will lead and oversee sequencing genomics and bioinformatics analyses and resources as part of CECGTs strategic growth in advanced genetic and sequencing-based research.

The incumbent will support a multidisciplinary team of embryologists stem cell biologists and senior investigators by generating managing processing and analyzing large-scale sequencing datasets. Responsibilities include the interpretation of complex high-throughput genomic data to extract biologically meaningful insights relevant to human development and disease. Key duties include independently designing developing and executing gene editing sequencing analyses and computational workflows as well as building and maintaining bioinformatics pipelines tools and software for the analysis of high-throughput sequencing data derived from research participants gametes preimplantation embryos and pluripotent stem cells.

The position will also contribute to the preparation of bioinformatics-focused presentations manuscripts and grant applications; assist in the development of long-read and advanced sequencingbased research initiatives; and perform a range of duties requiring flexibility sound judgment and specialized expertise in gamete embryo and stem cell addition the incumbent will maintain and advance their bioinformatics skill set and provide training and mentorship to personnel to meet the growing analytical demands of large-scale and complex genomic datasets.

Overall this position supports and advances the mission of the Center for Embryonic Cell and Gene Therapy through demonstrated reliability productivity professionalism accuracy timeliness problem-solving ability and a strong ethical framework appropriate to the Centers scientifically and ethically complex focus.

• Sequencing and bioinformatics analyses
  
  • Serve as the primary liaison with the CECGT research team and collaborators on research questions related to the extraction and interpretation of genomic information from high-throughput sequencing experiments and datasets.
  • Contribute to the growth of CECGT research capabilities by maintaining current knowledge of state-of-the-art long-range sequencing technologies applications and advances in bioinformatics.
  • Define project-specific requirements in collaboration with the research team and recommend optimal sequencing strategies clearly articulating the scientific value and rationale for selected approaches.
  • Provide comprehensive support to non-informatics staff in the design planning and implementation of genome editing experiments.
  • Supervise research staff in the preparation of sequencing libraries in support of NGS workflows.
• Coding and Data Analysis
  
  • Develop maintain and support computational code and applications for research projects in collaboration with the embryology and research teams.
  • Apply best practices in software development quality control versioning documentation and execution.
  • Evaluate existing commercial and open-source software and codebases and determine the most appropriate strategies for adoption customization or in-house development.
  • Independently design develop and implement computational tools pipelines workflows and software packages to discover analyze and annotate genomic information from high-throughput sequencing data including bulk and single-cell datasets derived from research participants gamete donors gametes preimplantation embryos and pluripotent stem cells.
  • Optimize and automate analytical workflows to minimize computational time while maintaining analytical accuracy and data quality.
  • Develop execute and maintain software and scripts for data visualization and large-scale data mining to effectively communicate insights derived from genomic datasets.
  • Develop and apply appropriate statistical and widely accepted bioinformatics methodologies for the analysis and interpretation of genomic data.
  • Independently conduct scientific investigations exercising professional judgment in data interpretation and guiding the embryology team through bioinformatics methods and analytical results.
• Data Management
  
  • Design oversee and manage cloud-based and/or high-performance computing (HPC) infrastructure to support next-generation sequencing research projects at CECGT.
  • Develop maintain and manage CECGT databases for next-generation sequencing data ensuring data integrity accessibility and compliance with institutional policies.
• Academic Output
  
  • Prepare bioinformatics-focused content for presentations manuscripts and grant applications with review by peers and mentors as appropriate.
  • Contribute to peer-reviewed bioinformatics manuscripts and scientific publications.
  • Participate in the preparation and delivery of oral and poster presentations at scientific meetings and conferences.
  • Contribute to bioinformatics components of grant and award proposals.
• Other duties as assigned

• PhD in Informatics or related field; OR
• Masters Degree in Informatics or related field AND 6 years of relevant experience.
  
  • 6 years of relevant research experience in a laboratory setting with concentration on and skills in both bioinformatics and molecular biology research resulting in ability to perform preparation of sequencing libraries as well as computational genomics data analysis independently.

Knowledge Skills and Abilities

• Advanced understanding of all sequencing platforms.
• Extensive knowledge of independent and unsupervised computational analysis of the next-generation sequencing datasets (bulk and single cell) from human and mouse gametes and embryos.
• Knowledge and understanding of common bioinformatics file formats (FASTQ SAM/BAM VCF BED).
• Proficient skill with existing bioinformatics tools (FastQC BWA GATK BLAST samtools bedtools bcftools freebayes etc.).
• Strong R and/or Python programming skills with emphasis on data science.
• Knowledge of setting up cluster-based and/or cloud-based computing and storage solutions for execution of NGS pipelines.
• Computing skills in a Linux environment.
• Exploratory data analysis and visualization.
• Knowledge of version control systems.
• Ability to communicate effectively in both written and oral formats.
• Ability to work independently and as part of a multidisciplinary team.
• Ability to report findings to both national and international collaborative groups.
• Ability to prioritize work demands and coordinate work with other staff.
• Motivation and ability to learn new topics to improve their craft.

• PhD degree in related field and 3 years of relevant post-doctoral work experience.
• 3 years of relevant post-doctoral experience in bioinformatics/genomics data analysis. The ideal candidate will have experience with both dry-lab bioinformatics and wet-lab method development. Additional hands-on experience in iPSC reprogramming embryo handling and ESC derivation/culture is a strong plus.
• Knowledge of and experience with long read sequencing platforms (PacBio ONT).
• Wet-lab method development experience to support NGS workflows.
• Expertise with basic molecular biology techniques. Ability to perform single-cell isolation whole-genome amplification DNA/RNA extraction PCR gel electrophoresis Sanger Sequencing NGS library prep.
• Independent proficiency in mouse and human pluripotent stem cell culture techniques (iPS reprogramming and ESC derivation; freezing thawing maintaincance and characterization of iPS/ESC cultures).

This position is located at the OHSU South Waterfront campus in Portland Oregon. As a full-time position the work schedule is expected to be 40 hours per week with schedule flexibility ensuring availability according to lab operations and needs. May be required to work evenings or weekends to cover outreach events on or off campus.