The Greninger Lab has an outstanding opportunity for a 1.0 FTE Postdoctoral Scholar in the area of syphilis immunology and genomics for a newly funded project. The Greninger Lab has made major contributions to the genomics of Treponema pallidum, developing new wet-lab and dry-lab pipelines for whole genome sequencing, genome finishing, and deep profiling of the immunoevasive TprK gene, as well as phage display profiling of the serological response to this mercurial pathogen. The goal of the present work is to contribute greater functional interpretation of the sequences available for Treponema pallidum as well as proteome-wide profiling of the rabbit and human immune response to Treponema pallidum, with the goal of contributing to the development of an effective vaccine. The Greninger Lab works closely with the laboratory of Dr. Lorenzo Giacani in support of these goals. The work requires a highly invested PhD-level individual with prior experience in molecular biology, biochemistry, microbiology/virology/immunology, and informatics skills. Responsibilities include constructing and teaching others on the generation of next-generation sequencing libraries, performing and overseeing immunoprecipitations, analyzing sequencing data, visualizing data and programming figures, drafting of manuscripts and grants for submission, combined with follow-on wet-lab experiments to confirm hypotheses generated in the above screens.

This full-time, 12-month position has immediate availability for an initial two-year appointment. The position will be renewable annually contingent on performance and available funding.

The base salary range for this position will be $5,705 - $7,283 per month ($68,460 - $87,396 annually), commensurate with experience and qualifications, or as mandated by a U.S. Department of Labor prevailing wage determination. 

General Duties:

·        Bioinformatic analysis of display libraries (generally phage display) for the rabbit and human immune response to Treponema pallidum and to associated vaccine candidates

·        Design, optimization, and automation of phage display and antigen profiling immune experiments, including immunoprecipitation and sequencing library generation

·        Bioinformatic and phylogenetic analysis of Treponema pallidum genomes and full-length TprK haplotypes

·        Development of next-generation sequencing analysis pipelines for taxonomical analysis and pathogen genome visualization.

·        Creation and optimization of next-generation sequencing libraries for pathogen genomics. Genome finishing of pathogens, including optimization of high-throughput methods.

·        Supervise and analyze quantitative pathogen load determination using RT-qPCR, qPCR, ddPCR, including optimization of new assays

·        Supervise performance of molecular procedures including but not limited to real-time PCR, Sanger sequencing, PCR product detection DNA sequencing and next generation sequencing;

·        Drafting of manuscripts for open-access publication

·        Perform work accurately, precisely and meet test completion deadlines;

·        Maintain complete, accurate, legible, secure records.  Thoroughly document any modifications using appropriate document and version control.

·        Analyze experimental data and report to the Director; determine what modifications and follow-up experiments are necessary to generate relevant data;

·        Identify long and short-term goals; initiate research program/projects;

·        Contribute technical knowledge when initiating new projects to determining feasibility of goals and objectives of the study;

·        Contribute data and analyses for grant submissions;

·        Perform preliminary experiments for assay development;

·        Work with R, python, Geneious, Excel, and bash command line;

·        Accommodate schedule changes to cooperatively accomplish required daily work, coordinate with Laboratory supervisor/manager;

·        Collaborate with research team to create opportunities and ancillary research projects to enhance technical assay methodology or content through the expansion of existing or development of new projects;

·        Review the scientific process of each research project, analyze issues, understand scientific procedures and statistical analysis; report data using graphs and charts;

·        Provide ongoing feedback; identify development opportunities and actively solicit input on work methods;

·        Perform other duties as required.

Conditions of Employment:

·        Will be considered essential staff and as such will be required to report to work when scheduled despite inclement weather.

·        Must be able to meet with all shifts on a regular basis.

·        May work weekends and holidays.

·        May be asked to work hours beyond normal open hours of the laboratory depending on staffing needs and current testing requirements. 

·        Sit at a desk or bench 30” to 37” high.

·        Use a computer keyboard and mouse.

·        Communicate by telephone and email.

·        Work with bio hazardous specimens, including tissues and fluids, which may be infected with microorganisms. May be exposed to bloodborne pathogens through needle stick or biohazard spill.

·        Work with and transport hazardous materials, such as solvents, acids and bases.

·        Lift containers (weighing 40 pounds or less) of supplies, reports, and specimens.

·        Wear protective equipment, such as gloves, gowns, masks and goggles, when appropriate.

·        Operate equipment such as a centrifuge, computer keyboard & printer, fume hood, biosafety cabinet, pipetting device, and syringe with needle.

Safety/Response to Emergencies:

·        Maintain awareness of safety procedures; implement safety rules and regulations in compliance with institution standards.

·        Train staff in safety, and maintain safety as a priority within the department.

·        Have and exercise knowledge of laboratory safety and proper precautions when dealing with bio-hazardous, radioactive, corrosive, explosive and/or flammable materials.

·        Recognize potential safety hazards and take corrective action to resolve hazards or notify appropriate personnel.

·        Participate in interdepartmental efforts to facilitate a safe environment for all staff and patients.

·        Ensure staff knows location of safety information and supplies and are able to access information in response to queries or emergency situations.

·        Ensure staff keeps abreast of safety procedures including fire plan, disaster drills, evacuation routes, etc.

·        Participate in laboratory disaster preparedness drills.

Policies and Procedures:

·        Follows established policies, procedures and techniques at all times.

·        Integrates new or revised procedures into the workplace.

·        Perform other duties as required.

Postdoctoral scholars are represented by UAW 4121 and are subject to the collective bargaining agreement, unless agreed exclusion criteria apply. For more information, please visit the University of Washington Labor Relations website.

Education requirement, minimum: PhD in pathogen genomics, molecular biology, microbiology/virology/immunology, bioinformatics or foreign equivalent

Additional Requirements:

·        At least three years of combined experience in genomics and microbiology/virology/immunology

·        Prior first-author publications

·        Prior coding experience with R, python, and/or UNIX.

·        Able to program/code data visualization and figure generation.

·        Previous experience with next-generation sequencing analysis and genomics

·        Strong written and communication skills;

·        Ability to problem-solve and troubleshoot.

Desired:

·        Proficient at R, python, and/or bash.

·        Contribute to and maintain github repositories

·        Data analysis skills beyond basic statistical knowledge.

Applicants should upload in interfolio their CV, cover letter, diversity statement, and contact information for at least three references addressed to Alex Greninger, MD, PhD, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA