Scientist II - Next-Gen Sequencing Analytics

The Scientist II for Next-Gen Sequencing Analytics will provide bioinformatics and analytic support to multiple projects in biopharmaceutical development at FDB sites. The job holder will require expert knowledge in the analysis of advanced molecular biology assays developed at FDBT focused on next-generation sequencing (Illumina, Oxford Nanopore) datasets and assist in expanding FDBT molecular characterization services.

External US

Essential Functions

• Provide technical knowledge and ensure efficient design, programming and implementation in Bioinformatics and data sciences to support our client and internal needs.
• Assist in developing and managing systems for analyzing, interpreting, and storing large volumes of next-generation sequence data.
• Determine and develop appropriate analytic pipelines for the analysis of a range of datasets generated including adventitious agent analysis, whole-genome viral, prokaryotic, and eukaryotic genomes, and transcriptomic profiling.
• Must have experience and working knowledge with Linux command line and have up-to-date knowledge of analysis methods for DNA sequencing and RNA sequencing datasets including but not limited to – R, perl, python, samtools, bamtools, GATK, canu, Spades, Geneious. Independent planning, execution, and interpretation of complex laboratory experiments.
• Assist or lead some direct interface with external clients to understand their needs and effectively communicate these needs to internal departments.
• Ability to work with team members and clients to help troubleshoot and solve complex problems.
• Clearly articulate in presentations to senior management and/or clients regarding problems, updates, and/or results.
• Maintain a laboratory notebook according to company guidelines.
• Summarize results and generate reports.
• Maintain analytical instrumentation as needed and interface with external vendors for instrument installation and operation qualifications.
• Trains or provides guidance to entry level scientists.
• The individual may functionally supervise the work of junior colleagues with oversight from the supervisor ensuring that the goals of the group are met.
• Ensure the lab is maintained (organized, clean, and properly supplied).

• Analysis of NGS (Next Generation Sequencing) data (DNA and RNAseq) used in entry testing of cell lines, viral stocks, bulk harvest, etc. to identify pathogens and adventitious agents. Assist in data interpretation and develop strategies to minimize confounding factors in false virus identification.
• Analysis of NGS data for viral vector characterization – perform identity testing on viral vectors to confirm vector sequence, identify/quantify variants, mutations, %GOI vs plasmid vs host cell nucleic acid.
• Analysis of NGS datasets for characterization of recombinant cell lines including confirmation of GOI of transgene expression, copy number and integrity.

• All other duties as may be assigned.

Required Skills & Abilities

• Understanding of experimental design for next-generation sequencing.
• Understanding of next-generation sequencing sample preparation including isolation, quality assessment, library preparation, and sequencing.
• Experience analyzing sequencing data sets and a general understanding of experimental design and analysis.

• Stay abreast of new technologies in the field.

• Must have experience and working knowledge with Linux command line and have up-to-date knowledge of analysis methods for DNA sequencing and RNA sequencing datasets including but not limited to – R, python, perl, samtools, bamtools, GATK, canu, Spades, Geneious
• Good understanding of data mining and information retrieval from relevant sources and databases
• Ability to work professionally as part of a team and independently.
• Ability to work on multiple projects while meeting deadlines.

• Ability to formally present problems, updates, and/or results.
• Ability to clearly communicate in writing and verbally to senior management and/or clients.
• Ability to train technical aspects of the job to analytical personnel.
• As appropriate, writes and reviews SOPs/ procedures/instructions
• As appropriate, writes and reviews analytical plans, protocols, or summary reports
• Authors SME content of technical reports (memos, development reports etc.)

Working Conditions & Physical Requirements

The physical demands described here are representative of those that must be met by an employee to successfully perform the essential functions of this job.  Reasonable accommodations may be made to enable individuals with disabilities to perform essential functions.  While performing the duties of this job, the employee is regularly required to

• Experience prolonged standing, along with some bending, stooping, and stretching.
• Use hand-eye coordination and manual dexterity sufficient to operate a keyboard, photocopier, telephone, calculator, and other office equipment.
• Potential for exposure to hazardous chemicals, gases, fumes, odors, mists, and dusts, and other hazardous materials.
• Ability to lift 50 pounds on occasion and 25 pounds regularly.
• Ability to wear PPE. 
• Attendance is mandatory.

Minimum Qualifications (in addition to required skills and abilities)

• PhD with emphasis on bioinformatics, molecular biology, biochemistry, microbiology, or related life science.
• Master's degree with emphasis on bioinformatics, molecular biology, biochemistry, microbiology, or related life science with a minimum of four (4) years of experience.
• Bachelor's degree with emphasis on bioinformatics, molecular biology, biochemistry, microbiology, or related life science with a minimum of six (6) years of experience.
• Associates degree with emphasis on bioinformatics, molecular biology, biochemistry, microbiology, or related life science with a minimum of eight (8) years of experience.

Preferred Qualifications

• Wet lab experience in next-generation sequencing sample preparation methods including sample isolation, quality assessment, library preparation, and sequencing in applications including whole-genome DNA, RNASeq for Illumina (or similar) platforms, Oxford Nanopore long read DNA and RNA Seq (or similar) as well as targeted sequencing approaches.

We are an equal opportunity and affirmative action employer.  All qualified applicants will receive consideration without regard to race, color, national origin, sex, gender identity, sexual orientation, religion, disability, protected veteran status or any other characteristic protected by applicable federal, state or local law. If an accommodation to the application process is needed, please e-mail FDBTHR@fujifilm.com or call 979-431-3500.