Job Postings

CMI - Communications Officer

UC San Diego is a world-leader in microbiome research, biomedical engineering, quantitative measurements and modeling, cellular and chemical imaging, drug discovery, “omics” sciences and much more. We draw interdisciplinary teams of these researchers together to push the boundaries of human understanding of microbiomes — the distinct constellations of bacteria, viruses and other microorganisms that live within and around humans, other species and the environment.

The objective of the Center for Microbiome Innovation (CMI), one of the many Agile Research Centers housed within the Jacobs School of Engineering, is to accelerate microbiome research and understanding through partnerships with industry sponsors. Together we will develop novel tools and methods to improve human health and benefit the environment.

Oversees a comprehensive communications program for the Center for Microbiome Innovation with complex communications requirements. The communications program usually includes written, visual, digital and electronic communications. Works with management to develop and execute organizational communication and market branding strategy. Designs and implements information campaigns.

With work direction provided by the Executive Director of the CMI, creates and implements strategic communications plans and projects primarily driven to an industry partner audience. Performs a wide range of duties in the following areas: editing, writing, scheduling external communications and features for various publications, uses email, blogs and the web, community outreach, development communications, marketing plans and implementation, social media, and special events.

Works and collaborates regularly with other senior staff to shape, create, and develop external and internal institutional relations objectives and positions. Emphasis is on maintaining excellent relations with both faculty and staff as well as existing and future industry partners to create a content-rich experience.


  • Knowledge of all aspects of communications, including strategic planning for various media venues, technical aspects and requirements of various venues, and most appropriate and effective applications.

  • Proven knowledge of the organization, its achievements, mission, vision, goals, policies, practices, infrastructure, and a strong knowledge of current affairs, and issues in higher education and/or health sciences.

  • Thorough understanding and experience in all news/media mediums including the internet, social media and other emerging technologies.

  • Experience creating clear, easy-to-navigate, informative, accurate, well-designed, and functional web sites that provide web content consistent with the organization's message and in keeping with management directives and client objectives.

  • Excellent written, verbal, interpersonal communications, active listening, and political acumen skills.

  • Thorough knowledge and skills to advise and consult with management to ensure delivery of the desired message to the target and/or broad general audiences.

  • Ability to comprehend academic research as well as industry needs and to write and translate the work in a way that is understandable to the general public.

  • Demonstrated knowledge of content management systems and/or relevant web applications used for web production and organization-specific computer application programs.

  • Knowledge and understanding of technical applications to effectively direct technical staff, or personally perform technical work, including design concepts, various media, and applications.

  • Proficiency using computer applications for web production, image handling, publishing and design, illustration, presentation preparation, animation, web interaction, and/or other state-of-the-art web communication capabilities.

  • Experience with and ability to use and learn software or platform including Adobe suite, CRM, Newsletter tools, Blog tools, Website platform management, etc.

  • Proven skills to create, develop, and implement comprehensive long and short term strategic communications plans.

  • Thorough knowledge of location protocols and channels for communication internally and externally.

  • Thorough knowledge of Microbiome research and/or industry.


  • Evening and weekend work occasionally is required.

Deadline to apply: Mon 1/27/2020

CMI - IBM - Postdoctoral Scholar - Natural Language Processing, Machine Learning, Bioinformatics & Systems Biology

The automatic knowledge base construction group in the UC San Diego-IBM Artificial Intelligence for Healthy Living (AIHL) program, led by Dr. Chun-Nan Hsu and Dr. Rob Knight, is seeking applications of a Postdoctoral Scholar in deep learning for natural language processing to extract microbiome knowledge from the scientific literature. The positions are available immediately. The project will be funded on a contract for three years.

The research group is part of the Center for Microbiome Innovation (CMI), one of the top research centers in the world in human microbiome research, developing AI, deep learning, and cutting edge data sciences to advance the understanding of the impact of microbiome to health. The knowledge base group has developed one of the most efficient and accurate algorithms in automated understanding of disease mentions in the scientific literature, winning the Best Application Award in the 2019 conference of Automated Knowledge Base Construction (AKBC). Our former master student was admitted to prestigious PhD programs with fellowships.

The group resides in the Qualcomm Institute (UC San Diego division of the California Institute for Telecommunications and Information Technology (Calit2)), the home of multidisciplinary research programs and startups at UCSD. The group has access to powerful GPU computer clouds at CMI and IBM. The group strives to deliver useful knowledge base systems and develop original, innovative, top-tier conference acceptable algorithms simultaneously. Group members work closely with CMI faculties and students and top-notch researchers from IBM in the Bay Area and around the world through frequent virtual and face-to-face meetings. 

The postdoctoral fellow will be encouraged to take initiation to explore new ideas to accomplish fully automatic knowledge base construction for human microbiome and work on grant proposals to develop into an independent leader of scientific research. 

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


  • Ph.D. in a relevant discipline, including in the areas of natural language processing, machine learning, or bioinformatics and systems biology
  • Strong record in publications in top-tier AI conferences and Bioinformatics journals
  • 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 (Neurosciences).

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.

CMI - Postdoctoral Fellow - Microbiome Technology Development at UC San Diego

The Center for Microbiome Innovation (CMI) seeks applications for a postdoctoral position in multi-omic technology and methods development.

The candidate will be responsible for designing, developing, and testing of novel tools, methods, and instruments that will enable breakthroughs in the field of microbiome research. Activities will include metagenomics-focused projects as well as metatranscriptomics, metabolomics, proteomics, and microbiology.

Scope of research:

  • Development and evaluation of novel tools, instruments, and methods for multi-omic characterization of microbiome samples
  • Analysis of human microbial communities from multiple body sites in a variety of healthy and disease states including IBD, diabetes, and cancer
  • Exposure and training with world-class bioinformatics and biostatistics teams
  • Close interaction with industry partners and opportunities for entrepreneurship 


  • Ph.D. in a relevant discipline, including in the areas of bioengineering, biomedical engineering, microbiology, biochemistry, immunology, biology, systems biology or a related field
  • Experience working with next-generation sequencing library preparation, hybridization technologies, nucleic acid extraction, qPCR/RT-PCR, flow cytometry, mammalian cell/tissue and bacterial culture, conjugation chemistry are highly desired
  • A strong research record and excellent communication and organizational skills
  • Experience with R, Python, Qiime2, or Qiita is a plus

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.

Merck KGaA, a CMI Partner - Post Doctoral Fellow Scientist

Your Role:

We are seeking a highly motivated and creative individual with a strong scientific background and hands-on experience in molecular biology or synthetic biology. The person in this role will take the lead in a high-profile, cutting-edge synthetic biology related project, which involves molecular design, engineering and evolution of enzymes and cells. In addition, this scientist will be responsible for scouting, evaluating, and developing advanced technologies which are related to the project or suitable for life science research use.  The successful candidate should have in-depth knowledge and related training in molecular biology, synthetic biology or related fields. This scientist will participate in the newly formed post-doctoral fellow program within MilliporeSigma. The post-doctoral fellow will be mentored by the senior R&D leader directly. The candidate will conduct research projects and be exposed to cutting-edge technologies. Upon successful completion of the program / project, the post-doc fellow will be placed in a regular R&D position within MilliporeSigma. 

This position is a perfect opportunity to start a career in life science industry and to gain crucial industry experience. As part of MilliporeSigma's worldwide R&D team, you will have the opportunity to advance personally and professionally and enjoy competitive compensation and benefits while helping us meet our business objectives.


Essential Job Duties:

Carry on a synthetic biology related project that involves molecular design, engineering and evolution of enzymes and cells.

Scout and identify novel technologies related to the project and the broader Life Science reagent field; conduct background scientific research based on literature, technology trends, and market competitor analysis.

Evaluate and develop new technologies to maturation and commercial readiness.

Work independently and methodically on projects and meet aggressive project timeline. Must be able to work on assigned projects independently and to complete projects of high quality in a timely manner.

Maintain accurate and timely records of experimental designs, assay development, experimental results, and data analysis.

Communicate progress against objectives effectively to scientists and managers. Ability to travel about 10% will be required in this role.


Who You Are:

Basic Qualifications:

  • PhD in the discipline of Molecular Biology, Synthetic Biology or Biological Science disciple
  • 3+years’ experience hands-on experience in NGS (next-generation sequencing) AND molecular biology OR cell engineering OR synthetic biology


Preferred Qualifications:

  • 2+ years post-doctoral research experience highly preferred
  • Strong analytical skills; ability to analyze, troubleshoot and overcome technical hurdles independently and methodically with minimal guidance preferred
  • Strong verbal and written communication skills; proven ability to summarize and present scientific findings in a professional manner preferred
  • Detail-oriented with good time management skills preferred


Job Requisition ID:  198574
Location:  Temecula
Career Level:  B - Recent University Graduate(<1 year of experience
Working time model:  full-time

CMI - Volunteer positions at all levels


The CMI is currently accepting applications for volunteers and unpaid internships at all levels (undergraduate, graduate, and post-graduate).

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

Roles in the organization that are available include:

  • Preparation and presentation of microbiome education and training material

  • 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

  • Social media and website support

  • Event planning, organization, and setup


  • Desired skills and training will be specific to the role being sought

Please send an email to with your Resume/CV and a description of the role(s) of interest.



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