CMI - Undergraduate Researcher – Machine Learning, Web Development
The Center for Microbiome Innovation seeks applications for a paid undergraduate student researcher position in a project on machine learning with significant web development for the Qiita (qiita.ucsd.edu) platform 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:
- Creation of a machine learning plugin for Qiita
- Enhancement of Qiita web platform to import external dataset from NCBI and EBI
- Development of UI/UX for machine learning with Qiita platform
- Experience with Github or Bitbucket in a team software development project
- Record of activities in website development
- Pursuit of undergraduate degree or coursework in Biology or a related field is a plus
Host faculty includes Rob Knight (Pediatrics and Computer Science & Engineering) and Sandrine Miller-Montgomery (Bioengineering).
Email your CV/cover letter to CMIInfo@ucsd.edu to apply.
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 (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 - 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
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
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:
- 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
- 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
Career Level: B - Recent University Graduate(<1 year of experience
Working time model: full-time