Position Description

The University of Washington, Department of Laboratory Medicine and Pathology is a broad and dynamic department that strives for a consistent level of high achievement in all of its activities. The Department offers full diagnostic services in all areas of Laboratory Medicine and Pathology, is a top ranked research organization as measured by research awards from the National Institutes of Health and offers an array of specialized educational training programs.

The UW Medicine Department of Laboratory Medicine and Pathology brings together state-of-the-art technology and highly trained, world renowned personnel to provide comprehensive diagnostic and personalized service to physicians, community hospitals, independent laboratories, and other health care organizations. Our operations are based at the University of Washington Medical Center, Harborview Medical Center, South Lake Union, Northwest Hospital and the Seattle Cancer Care Alliance. Faculty members also serve at Seattle Children's Hospital, the Veteran's Administration Puget Sound Healthcare System, and the Fred Hutchinson Cancer Research Center. These collaborative efforts have generated innovative, translational studies in the basic mechanisms of disease as they apply to diagnostic laboratory medicine and pathology.

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.

• Term of appointment: This full-time, 12-month position has immediate availability for an initial one-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 per month ($68,460 annually)

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;

* 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.

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.

Qualifications

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.

Instructions

Applicants should send (via Interfolio) their CV, cover letter, 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 - agrening@uw.edu

Equal Employment Opportunity Statement

University of Washington is an affirmative action and equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, creed, religion, national origin, sex, sexual orientation, marital status, pregnancy, genetic information, gender identity or expression, age, disability, or protected veteran status.

Benefits Information

A summary of benefits associated with this title/rank can be found at https://hr.uw.edu/benefits/benefits-orientation/benefit-summary-pdfs/. Appointees solely employed and paid directly by a non-UW entity are not UW employees and are not eligible for UW or Washington State employee benefits.

Commitment to Diversity

The University of Washington is committed to building diversity among its faculty, librarian, staff, and student communities, and articulates that commitment in the UW Diversity Blueprint (http://www.washington.edu/diversity/diversity-blueprint/). Additionally, the University's Faculty Code recognizes faculty efforts in research, teaching and/or service that address diversity and equal opportunity as important contributions to a faculty member's academic profile and responsibilities (https://www.washington.edu/admin/rules/policies/FCG/FCCH24.html#2432).

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Disability Services

To request disability accommodation in the application process, contact the Disability Services Office at 206-543-6450 or dso@uw.edu.