Senior Research Associate - Dermatology

Date: July 2019

Title: Senior Research Associate

Department: Dermatology

School of Medicine

Supervisor Name and Title:  Dr. Mahmoud Ghannoum, PhD

POSITION OBJECTIVE

The Department of Dermatology is looking for a Bioinformatician who can apply information technology to biological, medical, and health research. They use computational tools to gather and analyze data in fields such as population, biology, genetics, and pharmaceutical development.  The candidate should have experience analyzing microbiome data sets, including but not limited to: amplicon sequencing data, metagenomics and machine learning output.  They will have to develop and implement novel AI approaches on data collected from various subjects (> 5,000 individuals).

The Microbiome Bioinformatics Programmer will focus on providing the analysis using post NGS microbiome data to measure and predict if lifestyle, diet and other variables contribute to the health/unhealthy composition of the gut ecology. Provide support for the function of the microbiome in the role of multi system dysbiosis ie…IBD, Crohn’s, and Cancer.  This will involve the analysis of 16S, ITS, and viral metagenomics data and finding inter-relationships of these various data sets with respect to data collected from different cohorts and including personal surveys. In addition, machine learning tools will be used to determine whether the microbiome can be used as biomarker of dysbiosis.

 

ESSENTIAL FUNCTIONS

  1. Work closely with the principal investigator.
  2. Develop systems to gather data. Examples include constructing a survey methodology, designing as clinical trial for a new medication, and programming a statistical model from population growth. 
  3. Develop databases to compile vast amounts of information from activities such as gene expression profiling and protein expression. 
  4. Create data algorithms and specialized computer software to identify and classify components of a biological system, such as DNA and protein sequences.
  5. Consult with other scientists and researchers to analyze data sets.
  6. Oversee other staff and laboratory technicians.
  7. Maintain laboratory documents and keep current with relevant scientific or medical journals.
  8. May assist with grant writing.

 

NON-ESSENTIAL FUNCTIONS

Perform other duties as assigned.

 

CONTACTS

Department: Daily contact with Primary Investigator

University: Occasional contact with other departments.

External: Frequent contact scientific collaborators to exchange information.

Students: Daily contact with student employees, staff employees, and fellows in the lab.

 

SUPERVISORY RESPONSIBILITY

  1. Will supervise students, assistants and technicians.

 

QUALIFICATIONS

Experience:  3+ years

Education/Licensing: PhD required in statistics or computer science required.

Postdoctoral experience in the bioinformatics is desired.

 

REQUIRED SKILLS

  1. Broad understanding of computational algorithms.
  2. Must be able to identify and resolve a wide range of issues, not limited to software bugs.
  3. Demonstrates good judgement in selecting methods and techniques for obtaining solutions.
  4. Must operate independently.
  5. Has knowledge of commonly-used concepts, practices, and procedures within the fields of biology, immunology, anatomy and physiology
  6. Professional and effective verbal and written communication skills.
  7. Professional and effective oral communication skills; and strong interpersonal skills with the ability to work and communicate with various individuals within and external to the University.
  8. Effective management skills; able to lead, train, work with, and elicit cooperation from team members and staff.
  9. Ability to maintain confidentiality.
  10. Must demonstrate flexibility and ability to work under pressure, fast-paced and changing environment, and conform to shifting priorities and timelines.
  11. Programming proficiency in Python, Perl, QIIME, R, either TENSOR or FastAl, any type setting program (LaTex, TeX, Metafont, etc).
  12. Exposure to PyTorch is a benefit but not essential.

 

Resumes should be sent to each of the following:

Dr. Mahmoud Ghannoum:  mag3@case.edu

Mauricio Retuerto: mar153@case.edu

Dr. Thomas McCormick: tsm4@case.edu