Job Postings

CMI - Undergraduate Researcher - Biomedical Knowledge Base Development


The Center for Microbiome Innovation seeks applications for a paid undergraduate researcher position in a project on biomedical knowledge base development for the UC San Diego-IBM Artificial Intelligence for Healthy Living (AIHL) program. 


Scope of research:

- Manual annotation of biomedical literature

- Curation and evaluation of machine learning results

- Aggregation and transformation of microbiome-related literature



- Strong skills in programming in Python, SQL, and Javascript.

- Experience of Github or Bitbucket in a team software development project 

- Good grades in college level Biology or Biology AP at high school is a plus


Host faculty include Rob Knight (Pediatrics and Computer Science & Engineering) and Chun-Nan Hsu (Biomedical Informatics).


How to Apply:

Email your CV/cover letter to to apply.

Note: If you have relatives employed at UC San Diego, you must include the name, relationship and department where employed in your resume or cover letter. This information is used only for the purpose of complying with the University’s nepotism policy.

CMI & Danone Nutricia Research- Postdoctoral Fellow - Nutrition

The Center for Microbiome Innovation seeks applications for a motivated Postdoctoral research fellow with a strong background in nutrition and dietary assessment to work into a collaborative program between UC San Diego-American Gut and Danone Nutricia Research.

The appointee will provide dietary assessment and analysis expertise for a multidisciplinary team working to understand the food factors influencing the gut microbiota.

Scope of research:

  • Investigate the links between dietary patterns, foods and gut microbiome in collaboration with bio-computationists, microbiologists, data scientists and nutritionists involved in the program. Evaluate and scope potential adaptation of existing or in development food questionnaire tools adapted to different countries.

Qualifications & requirements:

  • Ph.D. in nutrition
  • Strong skills in quantitative assessment techniques and interpretation of dietary intake data. Experience collecting and processing food records, 24-hour dietary recalls and/or food frequency questionnaires including data cleaning, data management and data analysis.
  • Statistical analysis good basic knowledge in order to be able to work in collaboration with data managers & biostatisticians.
  • Previous programming experience would be a plus.
  • Basic knowledge on gut microbiome
  • Ability to work independently in a very strong collaborative environment Excellent communication skills:
    • good spoken and written English
    • ability to communicate at different levels and in different environments including meetings and conferences: exchanges with the CMI, the private partner and with scientists from different fields: microbiologists, nutritionists, statisticians
    • scientific writing skills.

Host faculty include Rob Knight (Pediatrics and Computer Science & Engineering), and Sandrine Miller-Montgomery (Bioengineering).

Please email a completed application form ( and support documents to to apply.

Note: If you have relatives employed at UC San Diego, you must include the name, relationship, and department where employed in your resume or cover letter. This information is used only for the purpose of complying with the University’s nepotism policy.

CMI - Graduate Student Intern – Natural Language Processing, Machine Learning (July-August only)

The Center for Microbiome Innovation seeks applications for a paid graduate student researcher summer internship in biomedical text mining and understanding for the UC San Diego-IBM Artificial Intelligence for Healthy Living (AIHL) program.

Scope of Research:

  • Learning from structured ontologies
  • Unsupervised weakly supervised machine learning and active learning for NLP Biomedical concept understanding
  • Event and relation extraction and inference

Additional Qualifications:

  • Pursuing M.S. in a relevant discipline, including in the areas of natural language processing, machine learning, or bioinformatics and systems biology
  • Portfolio of projects using Python, SQL, and Javascript
  • Undergraduate or graduate coursework or degree in Biology or a related field is a plus

Host faculty include Rob Knight (Pediatrics and Computer Science & Engineering) and Chun-Nan Hsu (Biomedical Informatics).

Email your CV/cover letter to to apply.

CMI - Undergraduate Researcher – Microbiome Metadata Normalization

The Center for Microbiome Innovation seeks applications for a paid undergraduate researcher position in a project on microbiome metadata normalization to increase the number of samples available for machine learning in the UC San Diego-IBM Artificial Intelligence for Healthy Living (AIHL) program.

Scope of Research:

  • Metadata reannotation, correction, and standardization
  • Creation and curation of data dictionaries
  • Aggregation and transformation of microbiome-related literature into metadata


  • Experience with Python and Excel
  • Good grades in college-level Biology or Biology AP at high school
  • Coursework or experience data science or epidemiology is a plus

Email your CV/cover letter to to apply.

UC San Diego - Chu Lab - Postdoctoral Fellow in Mucosal Immunology

An NIH-funded postdoctoral fellow position is available in the Chu lab at UC San Diego. We are focused on the fundamental role of commensal microbiota in the education, induction, and maintenance of the host immune system during health and disease. Our research is centered at the interface of microbiome and immunology, with the goal of mechanistically understanding the role of the microbiome in preventing and treating immune-mediated diseases such as inflammatory bowel disease (IBD).

We are seeking highly motivated, independent, and creative individuals with proven experimental expertise, and a strong interest in mucosal immunology and the gut microbiome. Current projects in the laboratory include:

  1. immune signaling pathways involved in sensing immunomodulatory signals from the gut microbiome, and
  2. the development of commensal antigen-specific regulatory T cells in the maintenance of intestinal tolerance.

We are looking for postdoctoral fellows with interest in mucosal immunology and IBD, with:

  • PhD and/or MD in immunology, cell biology, and/or related disciplines, with a track record of peer-reviewed publications.
  • Experience in using immunological techniques including multiparameter flow cytometry and sorting, imaging, ex vivo and mouse models.
  • Experience in cell culture of human and mouse primary cells and cell lines.
  • Preferred experience with mucosal and systemic tissue collection, cell isolation, and cellular assays to assess immune responses.

Desired, but not required qualifications, include

  • Experience in design and analysis of single cell RNAseq experiments.
  • Experience in studies involving germ-free & gnotobiotic mice.
  • Experience in studies using mouse models of IBD & infectious diseases.
  • Knowledge in bioinformatic analysis of microbial genetics, metagenomes, and/or metabolomes.

Our laboratory is highly committed to the career development of its trainees. Please visit our website for more details: Please send a cover letter with a short description of research interests, a CV, and contact information of three references to Hiutung Chu at

UC San Diego - Assistant Professor - Systems Engineering

The University of California, San Diego, Jacobs School of Engineering (, invites applications for a tenure-track faculty position (Assistant Professor) in our dynamic and rapidly growing engineering school. The Jacobs School of Engineering is committed to building an excellent, diverse and inclusive faculty, staff and student body. Partnership with industry and our community is at the core of the University's mission; the successful applicant will be expected to establish a vigorous program of high quality research that complements existing collaborative research programs and reflects UC San Diego's leadership as a research university. Faculty in the Jacobs School of Engineering benefit from the presence of numerous major research centers at UC San Diego and the Jacobs School's leadership in fostering interdisciplinary basic research and collaborations with industry.

The appointment will be in the Jacobs School of Engineering, within one or more of our six departments:

  • Bioengineering (BENG),
  • Computer Science and Engineering (CSE),
  • Electrical and Computer Engineering (ECE),
  • Mechanical or Electrical Engineering (MAE),
  • Nanoengineering (NANO), and/or
  • Structural Engineering (SE).

The open position is in the fields of

  • Designing systems at scale
  • Analysis, control and design optimization of complex systems
  • AI for complex systems designs
  • Model based engineering
  • Uncertainty in complex systems design
  • Computational methods for multiphysics, multiscale and multifidelity analysis and optimization of interconnected systems

This position requires teaching of university students and applicants are required to have a PhD or advancement to candidacy at the time of application. The degree should be in bioengineering, computer science, electrical engineering, engineering physics, computer engineering, mechanical engineering, aerospace engineering, nanoengineering, structural engineering, or a related area. Candidates with experience with or willingness to engage in activities that contribute to diversity and inclusion are especially encouraged to apply.

NC State University - Assistant Professor and Extension Specialist - Microbiome Extension

The Department of Plant and Microbial Biology in the College of Agriculture and Life Sciences at North Carolina State University invites outstanding applicants for a tenure-track Extension Specialist and Assistant Professor in agricultural microbiomes. Understanding and harnessing microbiomes to improve crop production and enhance stress resilience is an urgent priority for advancing sustainable management of agricultural systems. The current explosion in microbiome technologies is only expected to grow given expectations of a future with increased population demand and more extreme climate conditions.

Possible focal areas for this position include but are not limited to plant foliar or root symbionts, root-microbe-soil interactions, nutrient acquisition and cycling, pre- and post-harvest microbial systems, and commercial treatment of seed with beneficial microbes to improve field performance. A well-qualified individual would be able to contribute to multiple areas of relevance to North Carolina. The applicant’s research and extension program is expected to enhance sustainable agriculture in NC, particularly for high-value crops in the North Carolina agricultural industry.

The microbiome extension specialist would serve as a bridge between existing faculty research in basic microbiome science and the applied research needs of growers, processors, and the agricultural biotech industry in the region. The candidate will be expected to work closely with plant and microbial research programs in the department, as well as with research and extension faculty in the Departments of Crop and Soil Science, Entomology and Plant Pathology, Horticultural Science, and Biological and Agricultural Engineering.

Applicants should have a Ph.D. in plant biology, microbiology, crop science, soil science, or related discipline, and a commitment to excellence in extension and engagement with constituencies outside the university. Applicants will be expected to demonstrate the potential to build a strong, integrated research and extension program. Inclusiveness and diversity are critical to the success of the university. Therefore, the selected candidate will be expected to foster an environment that is welcoming of all groups.

To apply for this position, visit and provide: (1) cover letter; (2) curriculum vitae; (3) research statement; (4) extension statement incorporating a vision for how you plan to engage with constituents throughout the state of North Carolina; (5) contact information for three references. Confidential inquiries and nominations should be directed to Dr. Christine Hawkes, Search Chair,

Review of applications will begin July 1, 2019 and continue until the position is filled.

Gloucester Marine Genomics Institute - Research Scientist - Marine Microbial Biotechnology

Gloucester Marine Genomics Institute (GMGI) is an exciting new independent marine biotechnology research institute that is applying innovative genomic technologies to marine science for discoveries that impact fisheries and human health. GMGI is exploring the incredible genetic diversity of marine microorganisms for new applications in biotechnology and medicine including development of probiotics for aquaculture. GMGI is looking for a Scientist with a background in marine microbiology and microbial engineering, and experience studying and modulating host-microbe interactions to lead this program. The ideal candidate will have strong leadership skills, excellent communication skills and the ability to work with a multi-disciplinary team of collaborators from academia and the biotech industry. This position is an extraordinary opportunity for an innovative and entrepreneurial scientist who is excited to be part of the team building a world-class research institute.


  • Oversee the collection of samples from the marine environment and preparation of samples for DNA sequencing and culturing
  • Bioinformatic analysis of genomic and metagenomic data for species identification and discovery of genes and/or biosynthetic gene clusters encoding biological or chemical entities of commercial interest
  • Develop and optimize cultivation conditions for bacteria and fungi from a variety of marine sources and oversee the expansion of a repository of novel bacteria and fungi
  • Develop assays for screening for selected target activities or products
  • Molecular cloning for heterologous expression of specific proteins or products
  • Microbial engineering for improved production of novel chemical and biological entities
  • Method development for identification of probiotic cultures for dietary supplementation in aquaculture
  • Establish collaborations with academic and biotech industry partners for projects of mutual interest
  • Establish new research projects consistent with GMGI’s mission
  • Assist in grant writing and fund-raising efforts for the institution
  • Lead publication of results in scientific journals and reports • Give presentations to stakeholders, general public and scientific audiences
  • Contribute to GMGI’s commitment to create a scientific community on Cape Ann
  • Supervise technical staff and interns


  • PhD, or equivalent post-graduate experience in microbiology, microbial engineering, marine natural products, or related field
  • Experience generating and analyzing next generation sequencing data for genomic, metagenomic, transcriptomic analysis
  • Strong mathematical and computational skills and experience with standard bioinformatic and statistic software packages
  • Knowledge of commonly used languages for biological data analysis (e.g. Python, R)
  • Familiarity with the Linux environment and basic knowledge in command line software and shell scripting
  • Experience cloning into heterologous expression systems
  • Experience in engineering secondary metabolism or natural products biosynthesis
  • Experience with benchtop fermentation reactors and small-scale purification technologies
  • Understanding of probiotic mode-of action and strain safety
  • History of success as a driving force in research projects with a track record of successfully awarded grants
  • Strong publication record and a capacity to conduct innovative, high-quality research
  • Excellent communication and teamwork skills • Demonstrated record of leadership, integrity and flexibility
  • Enthusiasm and commitment to GMGI’s mission for science and education


How to Apply: Please send a cover letter and curriculum vitae to Andrea Bodnar,

University of Alberta - Postdoctoral Position in Childhood Obesity and Gut Microbiome

Division of Endocrinology, Department of Pediatrics

The Division of Endocrinology, Faculty of Medicine and Dentistry, Department of Pediatrics at the University of Alberta, is offering a postdoctoral position in childhood obesity and gut microbiome. The post-doc fellow will be responsible for the provision of higher-level managerial oversight of research clinical trials, involvement in the integration of multiple components of data (diet, physical activity, targeted metabolomics, microbiome data) and providing expert biostatistical expertise in analysis of such a complex dataset. The post-doc will take the lead on writing manuscripts related to the clinical trial design and health outcomes of the research clinical trials; he/she will also present interim and final data at relevant international conferences (i.e. Keystone obesity, Obesity Society, Microbiome). 

The post-doc fellow will also work in partnership with different stakeholder groups to implement and evaluate knowledge translation activities for numerous grants and assist in the supervision of graduate students at the PhD and MSc levels. Other responsibilities include: coordinate with other project staff; communicate with the project co-investigators; screen, recruit and enroll study participants; and prepare ethics applications and reports as needed. 

The post-doc fellow will be required to have completed their PhD within the past 5 years in an area related to Food Science, Biological Sciences, Microbiology and Immunology, or equivalent, preferably with research experience in metabolic and immunological interactions between the microbiome and its host in relation to health, and in the neuroendocrinology of energy balance in childhood obesity. The post-doc fellow should have strong written and verbal communication skills, including experience working with and presenting to a variety of audiences. The applicant should enjoy working as part of a multidisciplinary team. 

To Apply: Interested applicants should submit an application consisting of a cover letter, a curriculum vitae, a sample of your writing, and contact information for three references to: 

Dr. Andrea Haqq 

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