Job Postings

CMI - IBM - Postdoctoral Fellow - 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 Fellow 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 - IBM Graduate Student Researcher – Natural Language Processing, Machine Learning

The Center for Microbiome Innovation seeks applications for a paid graduate student researcher 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
  • Weekly supervised and self-supervised machine learning and active learning for NLP Biomedical concept understanding
  • Event and relation extraction and inference

Additional Qualifications:

  • Pursuing graduate degree 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
  • Must be a student at UC San Diego

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

Email your CV/cover letter to CMIInfo@ucsd.edu and a link to your code portfolio 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 - IBM 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

Qualifications:

  • 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
  • Must be a student at UC San Diego

Email your CV/cover letter to CMIInfo@ucsd.edu and a link to your code portfolio 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 - IBM Undergraduate Researcher - Biomedical Knowledge Base Development

The Center for Microbiome Innovation seeks applications for a paid undergraduate researcher position in a project on biomedical knowledgebase 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

Qualifications:

  • 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
  • Must be a student at UC San Diego

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

 

How to Apply:

Email your CV/cover letter to CMIInfo@ucsd.edu and a link to your code portfolio 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.

UC San Diego - TROEMEL Lab - Postdoc

A postdoctoral position is available in Emily Troemel’s lab at the University of California-San Diego to study host/pathogen interactions in the simple nematode host C. elegans. The Troemel lab studies infection of C. elegans by natural intracellular pathogens, including microsporidia (fungal pathogens) and the Orsay virus. We seek candidates who have obtained a PhD in the last 2 years. The ideal candidate will be a highly motivated individual with critical thinking skills, a productive work ethic, and the ability to work cooperatively. Experience in molecular biology, genetics, and microscopy is preferred.

The initial appointment will be for 1 year and will be renewable for up to a total of 3 years. Salary will be commensurate with NIH standards.

For more information on our lab, please see:
http://www.biology.ucsd.edu/labs/troemel/Lab_website/Home_page.html

Applicants should send curriculum vitae, statement of research interests and experience, and the names of three references to: etroemel@ucsd.edu

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