Job Postings

CMI - Graduate Student Intern – Natural Language Processing, Machine Learning

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:

Unsupervised learning and few/zero shot learning for bio-concept composition, with applications in event and relation extraction and inference leading to effective construction of biomedical knowledge bases

 

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, Computer Science, & Biomedical Engineering) and Chun-Nan Hsu (Biomedical NLP).

How to Apply: Email your CV/cover letter to CMIINFO@UCSD.EDU to apply.

 

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 

 

Qualifications:

- 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 Sandrine Miller-Montgomery (Bioengineering).

 

How to Apply:

Please email a completed application form (http://cmi.ucsd.edu/PostDocApplication) and support documents to CMIInfo@ucsd.edu 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 - 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

Qualifications:

  • 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 (http://cmi.ucsd.edu/PostDocApplication) and support documents to CMIInfo@ucsd.edu 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 - 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

QUALIFICATIONS

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

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

 


 

CMI Postdoctoral Fellow - Bioinformatics

The Center for Microbiome Innovation seeks applications for a postdoctoral position in microbiome-focused bioinformatics.

Scope of research:

  • Apply and develop new methods and tools for microbiome data analyses using various -omics including 16S, metagenomic, and metabolomics data
  • Apply machine learning concepts to microbiome data
  • Benchmark tools and methods
  • Contribute to high-profile projects and prepare articles in high-impact journals

Qualifications:

  • Ph.D. in a relevant discipline, including in the areas of computer science, computational biology, biology, microbiology or a related field required
  • Familiarity with microbiome data and research required
  • Experience with programming in Python and/or R required
  • Strong research record and background in computational science, statistics and/or biology
  • Good communication skills required
  • Experience with QIIME 2, and/or Qiita is preferred
  • Proficiency with machine learning algorithms (e.g. tree-based model, dimension reduction, neural net) is preferred
  • Undergraduate or graduate coursework or degree in Biology is a plus
  • Undergraduate or graduate coursework or degree in Statistics is a plus

How to Apply:

Please email a completed application form (http://cmi.ucsd.edu/PostDocApplication) and support documents to CMIInfo@ucsd.edu 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 - 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)

Qualifications:

  • 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 (http://cmi.ucsd.edu/PostDocApplication) and support documents including any links to CMIInfo@ucsd.edu to apply.

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