Job Postings

CMI - IBM Graduate Student Researcher – Data-Driven Microbiome Analyst

Job Description

The Center for Microbiome Innovation seeks applications for a paid graduate student researcher position in a project on machine learning applied to microbiome research. The work is part of an ongoing collaboration between the CMI and IBM Research through IBM’s Horizons Network.


Scope of Research:

  • Develop and apply novel methods for computational analysis of microbiome datasets.
  • Benchmark and evaluate methods for anomaly detection on multivariate data.
  • Work with high-performance data structures to operate on biological data.
  • Utilize communication skills for oral presentations and writing skills for written reports of scientific results and progress.
  • Assist in the preparation of text, and figures to support scientific publications in top-tier journals.
  • Assist in preparing and presenting results to local and external collaborators.



  • Experience with Python and the scientific python stack (scipy, numpy, scikit-learn, matplotlib, etc).
  • Interest in bridging the gap between biology and computer science.
  • Coursework on precision medicine, biology or microbiology is a plus but not required.
  • Must be a student at UC San Diego


How to Apply:

Email your CV/cover letter to and if available a link to your GitHub profile.


Arizona State University | Postdoctoral Research Scholar

In partnership with Arizona State University’s Biodesign Center for Health, the Postdoctoral Research Scholar will take a leadership role in a Gut Microbiome project (probiotics, microbiome-autism) funded by Sun Genomics. You will work closely with leading experts in research on Microbiome and Autism, Dr. Krajmalnik-Brown and Dr. Jim Adams, in a uniquely collaborative and productive lab. You will be exposed to many research topics associated with Microbiome and Autism, and will have the opportunity to start and lead this new exciting project. 


  • Project management, meeting coordination and leadership 
  • Experimental design and implementation, data analyses, and report/manuscript preparation 
  • Identifying, coordinating, and leading the writing of manuscripts 
  • Coordinating among team members and leading the team's efforts in delivering milestones to Sun Genomics 
  • Processing samples in a wet lab environment 

Required Qualifications: 

  • Recent Ph.D. (within the past four years) in Microbiology, Bioinformatics, Biostatistics, Environmental Engineering, Chemical engineering, Computer Science or Allied discipline 
  • Hands on experience with large datasets and data analysis and integration oR, tableau, or other big data stat modeling software experience 
  • Experience in project management, team leadership, and effective communications. 
  • Excellent oral and written communication skills. 

Preferred Qualifications: 

  • Interest in host-microbiome interactions, microbe-microbe interactions, microbe-environment interactions, Microbiome and Autism 
  • Hands on experience with metagenomics analysis 
  • Hands-on experience with lab-scale bioreactor operations, and ideally some metabolites analysis (like short chain fatty acids). 
  • Experience mentoring graduate and undergraduate students.

Rutgers University | Tenure-Track Assistant Professor in Microbiome Bioinformatics

The Center for Advanced Biotechnology and Medicine (CABM) at Rutgers University seeks an outstanding candidate for a tenure-track Assistant Professor faculty position with expertise in Microbiome Bioinformatics. CABM, founded in 1985, has an outstanding track record in fundamental biomedical research and includes faculty within Rutgers Biomedical and Health Sciences (RBHS) and Rutgers–New Brunswick. This position can have a tenure home in one of many departments in the Schools comprising Rutgers Biomedical and Health Sciences (RBHS). The successful candidate will be provided with a competitive startup package, access to high-performance computing clusters and other core resources, and modern laboratory space at CABM, and will be expected to develop and maintain a strong, externally funded research program, and participate in collaborative projects with other Departments and Institutes on the Rutgers campus. Major duties and responsibilities include developing a robust research program to conduct a broad range of microbiome studies, including studies related to human health, development, and disease. Applicants with translational research interests relevant to metabolic disorders, cancer, or neurological disease are encouraged to apply. Research involving microbiome-derived drug discovery, related computational research for systems biology and/or network modeling, and extensions into plant, animal and environmental systems also is of interest. Although the major focus is bioinformatics development, having a wet-laboratory based program for data generation and analysis also could be desirable within the bioinformatic context. The successful candidate will also be expected to support the educational goals and activities of Rutgers University through teaching and service, including participation in the teaching of professional, graduate, and undergraduate students, and mentorship of trainees. The successful candidate will gradually assume teaching responsibility commensurate with the teaching load of other tenure-track faculty in the department. Salary will be commensurate with experience. Women and minorities are encouraged to apply.

Requires a Ph.D. or equivalent graduate degree in Computational Biology, Mathematics, Evolutionary Biology, Molecular Biology, or a related discipline with at least 3 years postdoctoral research experience related to the microbiome or related field, a demonstrated record of significant research, the potential to make substantial contributions as an independent investigator, and a commitment to teaching professional, undergraduate, and graduate students. Junior candidates with current grant funding or grants under review are preferred. Prior experience in obtaining external support for large-scale computation, and the development and maintenance of shared data analytics services is also desirable. In addition, this position requires excellent presentation skills, strong technical writing skills, and proficiency in using informatic platforms for data analysis. The demonstrated ability to develop bioinformatic tools, and lead tool development projects, including computational pipelines, and build reference databases is critical. An outstanding publication record, consistent with the candidate’s training and experience is required. Must possess expertise and technical skills necessary to successfully conduct studies involving: 16S rRNA, sequencing, metagenomics, metabolomics, and studies of expression of individual genes and pathways, and whole genome-wide analytical tools.

CMI Postdoctoral Fellow - Machine Learning, Bioinformatics & Systems Biology


The Center for Microbiome Innovation seeks applications for a postdoctoral position in microbiome-focused machine learning and bioinformatics for projects in collaboration with industry partners.


Scope of research:

- Lead a team of undergraduate and graduate researcher in the development of novel algorithms and approaches for predicting phenotypes of interest

- Develop tools, software, and data analysis pipelines for machine learning with microbiome data

- Apply the latest innovations in mathematical concepts, statistics, and feature selection in machine learning 



- Ph.D. in a relevant discipline, including in the areas of machine learning, bioinformatics, systems biology or a related field

- Familiarity with microbiome data and research

- Strong research record and background in statistics, math, and/or computational science

- Proficiency with machine learning algorithms (e.g. tree-based model, dimension reduction, neural net)- 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 Andrew Bartko (Bioengineering).


How to Apply:

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.


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 Postdoctoral Fellow - Bioinformatics Lead: Microbiome, Food & Nutrition

The Center for Microbiome Innovation seeks applications for a bioinformatician to work on collaborative research projects with industry partners in the fields of food and nutrition. 

Scope of research:

  • Work as the lead bioinformatician with scientists from other disciplines on projects focused on the microbiome, nutrition, and food
  • Develop microbiome analysis tools to assess the significant relationships between self-reported data (e.g. lifestyle, diet) and multi-omic microbiome data (e.g. 16S, metagenomics, metabolomics)


  • Ph.D. in a relevant discipline, including in the areas of computer science, data science, computational biology, bioinformatics, bioengineering, microbiology or a related field required
  • Experience with programming in Python and/or R required
  • Strong research record and background in computational science, statistics and/or biology required
  • Experience with QIIME 2, and Qiita preferred 
  • Evidence of good communication skills with partners outside academia and scientists from different disciplines (e.g. microbiologists, nutritionists, statisticians) preferred
  • Undergraduate or graduate coursework or degree in Biology or a related field a plus
  • Undergraduate or graduate coursework or degree in Statistics a plus

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

Other positions at the CMI

The CMI is currently accepting applications for independently-funded postdoctoral scholars, graduate students, and visiting scholars. We also accept volunteers and unpaid internships at all levels (undergraduate, graduate, and post-graduate).

On-the-job training will be provided, enabling practical real-world experience working experience in a fast-paced research environment focused on industry collaborations. Course-credit and the opportunity to contribute to peer-reviewed publications may be available for some positions.

Roles in the organization that are available include:

  • Laboratory experience with multi-omic data generation (metagenomic, metabolomic, metatranscriptomic, etc.)

  • Microbiome analysis using QIIME2, Qiita, and GNPS as well as study metadata normalization and transformation in Python

  • Open-source development of bioinformatics tools, websites, and visualizations

  • Preparation and presentation of microbiome education and training material

  • Social media and website support

  • Event planning, organization, and setup


  • Desired skills and training will be specific to the role being sought and level of funding, so please fill out our Interest Form

You may also send an email directly to with your Resume/CV and a description of the role(s) of interest after completing the form.



General CMI Position Interest Form


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