Asst Professor-Research

Location
Aurora, CO
Posted
Feb 21, 2017
Institution Type
Four-Year Institution



University of Colorado - School of Medicine

Asst Professor-Research

The CU School of Medicine (CU SOM) Dean's Office recently established the Human Immunology and Immunotherapy Initiative (HI3) to make the CU SOM a leader in human immunology research and clinical applications thereof. The HI3 is focused on building the necessary infrastructure to become a premier facility, including Human Immune Monitoring Shared Resources (HIMSR), Translational Research Networking, Pre-Clinical Models Service, GMP Immunotherapeutic Production, faculty recruitment, and research training efforts. The HI3 HIMSR provides standardized, state-of-the-art peripheral blood and tissue sample processing, biobanking, and immune monitoring assays at the genomic, proteomic, and cellular level. The HIMSR also supports the integration of data from these immune monitoring assays with clinical data, including archiving, data mining, bioinformatics and statistical analysis. The HI3 HIMSR Core seeks a full-time data scientist/bioinformatician to integrate systems immunology data with clinical data, identify novel disease-specific biomarkers with diagnostic and therapeutic applications, and provide associated statistical analyses.

The position will have a primary appointment in the Department of Immunology and Microbiology with the option of a secondary appointment within the Colorado School of Public Health.

This position is a technical and scientific role that involves analysis of large-scale next-generation immune repertoire sequencing (Rep-Seq of TCRs and BCRs) data, flow cytometry and mass cytometry (CyTOF) data. The ideal candidate will be expected to use modern toolkits including, but not limited to, Python, R, MATLAB, and Github. Understanding of Big Data technologies will be immensely beneficial. The successful candidate will have in-depth knowledge of high-throughput sequencing technologies, flow and mass cytometry, experience with large genomic and single-cell proteomic (flow) data sets, and their computational analysis to successfully utilize and understand these data. Projects may additionally include understanding MHC-dependent peptide presentation, TCR recognition of peptide/MHC complexes, understanding mass spec peptide ligandomes, immune cell signaling pathways, and biomarkers for patient responses to new drugs.

The work place is professional and dynamic with immense learning and growth potential. An essential characteristic of an ideal candidate is an innate desire to learn new methods and technologies and adapt to the demands of a fast paced and ever-evolving research environment. The successful candidate must be able to work independently, yet collaborate effectively with co-workers. Excellent written and verbal communication skills are critical.

The individual must be able to quickly grasp the objectives of research projects, and assemble solutions from a range of technologies, standards and approaches. The ability to interact within a confidential clinical data environment to integrate the clinical data with the scientific assay data is a necessity. Previous experience working in an academic environment is a plus.

BIOINFORMATICS DUTIES:
  • Collaborate with investigators on ongoing projects and facilitate the completion of computational tasks related to these projects
  • Make recommendations to investigators about the correct computational tools for testing scientific hypotheses and reaching valid conclusions
  • Participate in research design with investigators for determining best practices pertaining to the bioinformatic analysis in new and ongoing projects
  • Work with investigators to improve the computational analysis methods on current projects
  • Analysis and troubleshooting of poor quality data arising from biological issues or analysis artifacts
  • Perform independent bioinformatics research based on the emergence of new genomic/genetic/epigenetic/proteomic datasets, tools, and other resources that contributes to the understanding the mission of the department
  • Interpret, analyze, report, and publish the results of independent and collaborative research
  • Contribute to the production of peer-reviewed research papers, oral presentations, posters, and the generation of well-designed figures and tables for collaborative and independent research
  • Prepare datasets for publication and deposit in controlled-access databases
  • Streamline large scale data analysis, e.g. using new technologies for distributed computing
  • Run best practice annotation, machine learning approaches to derive insights

SOFTWARE DEVELOPMENT DUTIES:
  • Compare, evaluate, and implement new features and technologies, and integrate them into the computing environment
  • Conceptualize design, implement, and develop solutions for complex system/programs independently
  • Rapid prototyping of new methods and protocols
  • Maintain and update documentation as needed
  • Provide technical analysis, design, development, conversion, and implementation work
  • Deploy tools for self-service use
  • Work as a project leader, as needed, for projects of moderate complexity

Knowledge, Skills, and Abilities:
  • Expertise in designing, developing, testing, and deploying bioinformatics applications
  • Proficiency with application design and data modeling
  • Ability to define and solve logical problems for highly technical applications
  • Strong communication skills with both technical and non-technical clients
  • Ability to lead activities on structured team development projects
  • Ability to select, adapt, and effectively use a variety of programming methods



Qualifications

Minimum Requirements:
  • PhD, MD, or equivalent terminal degree in biostatistics, computational physics/biology, bioinformatics, computer science or related field, biological sciences, immunology, biochemistry, or related discipline
  • Expert programming skills in Python, R, and MATLAB
  • Experience working with large genomic and genetic datasets, including NGS and array, and appropriate analytical tools
  • Excellent data visualization and communication skills
  • The ability to speak and write the English language in a clear and concise voice


Preferred Qualifications:
  • Postdoctoral experience in biological systems, cancer biology, autoimmunity, infectious diseases, or immunology with a bioinformatics or computational biology mentor
  • Expert understanding of next-generation sequencing data, flow and mass cytometry data, and bioinformatics algorithms is preferred
  • Development and production environment that are Cloud based
  • Strong background in one or more of: population analytics, machine learning, statistical methods, algorithm development, variant annotation and interpretation
  • Ability to rapidly learn new mathematical and statistical approaches and programming techniques
  • Exceptional interpersonal skills, demonstrates the ability to work well with University of Colorado colleagues and external organizations

Salary and Benefits:

Salary is commensurate with skills and experience. The University of Colorado offers a full benefits package. Information on University benefits programs, including eligibility, is located at Employee Services.

The University of Colorado Denver is dedicated to ensuring a safe and secure environment for our faculty, staff, students and visitors. To assist in achieving that goal, we conduct background investigations for all prospective employees.

The University of Colorado strongly supports the principle of diversity. We encourage applications from women, ethnic minorities, persons with disabilities and all veterans. The University of Colorado is committed to diversity and equality in education and employment.

The Immigration Reform and Control Act requires that verification of employment eligibility be documented for all new employees by the end of the third day of work. Alternative formats of this ad are available upon request for persons with disabilities.


Application Materials Required:Cover Letter, Resume/CV, List of References

Application Materials Instructions:

Applications are accepted electronically at CU Careers, refer to requisition ID: 07473

When applying, applicants must include:
  1. A letter of application which specifically addresses the job requirements and outlines qualifications
  2. A current Resume/CV
  3. The names, addresses, daytime telephone numbers and e-mail addresses for three professional references, either attached to your resume/CV or uploaded as a separate document
Please be advised that the University does check references as part of the employment process.

Please do not submit any of your application material (via email) to the job posting contact.



Job Category: Faculty

Primary Location: Aurora

Department: H0001 -- Anschutz Medical Campus - 21577 - SOM-Immunology Microbiology

Schedule: Full-time

Posting Date: Nov 15, 2016

Closing Date: Ongoing

Posting Contact Name: Kim Jordan, PhD

Posting Contact Email: kimberly.jordan@ucdenver.edu

Position Number: 00729884

PI96904001