Job Postings

CMI Communications Officer

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.

Qualifications

  • Proven experience and 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.

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

  • 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.

  • Experience 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.

  • Thorough 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.

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

  • 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.

  • 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.

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

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

  • Demonstrated knowledge of Microbiome research and/or industry.

University of Geneva - Post-doctoral researcher in Bioinformatics / Environmental Genomics

 

A postdoc position (50 % to 100%) is available in the Department of Genetics and Evolution, University of Geneva, as part of a Swiss National Science Foundation project. The hosting laboratory is specialized in molecular ecology and evolution of microbial eukaryotes and is currently involved in several projects aiming at development of new environmental genomics tools for environmental biomonitoring.

Objectives: The position will focus on adapting and developing algorithms and statistical methods for the processing and data mining of high-throughput DNA sequencing data applied to the detection and quantitative assessment of environmental biodiversity responses to pollution in aquatic ecosystems. A part of the position will be dedicated to the maintenance of bioinformatics tools already developed and routinely used in our lab.

Rationale: Aquatic ecosystems are threatened by the rapid expansion of industrial activities. Solutions could  emerge from the development of innovative tools based on the monitoring of biological communities in order  to detect and measure the specificity and the magnitude of environmental impacts. Although multiple dimensions of the information delivered by high-throughput DNA sequencing technologies show great promise, many others remain unexplored. Hence, the development of powerful algorithms and robust statistical analyses are required to comprehend and fully exploit patterns of biodiversity changes and ensure fast and reliable assessments.

Required and preferred qualifications. We are looking for a highly motivated and autonomous researcher interested in bioinformatics and environmental genomics.

Applicants are expected to have:

• Experience in high-throughput sequencing data analysis (metabarcoding and/or metatranscriptomics and/or metagenomics).

• Experience in statistic tools applied to microbial ecology

• A background in programming (C, C++, Python, JavaScript, node.js), preferentially applied to bioinformatics and pipeline design and development.

• Proficiency in descriptive/inferential biostatistics and/or machine learning (R, Python or MATLAB).

Mode of application

To apply, please send an email to Jan Pawlowski (jan.pawlowski@unige.ch) and Tristan Cordier (tristan.cordier@unige.ch) containing a short letter of motivation, a detailed CV (including a brief description of research interests, previous employments and publication list), and contact details of at least two references (letters of recommendation are optional).

Job starts September 2018. The initial appointment is for a year, possibility of extension for a second year.

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 the UC San Diego-IBM Artificial Intelligence for Healthy Living (AIHL) program.

 

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), Siavash Mirarab (Electrical and Computer Engineering), and Sandrine Miller-Montgomery (Bioengineering).

 

How to Apply:

 

Email your CV/cover letter 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 - Natural Language Processing, Machine Learning, Bioinformatics & Systems Biology

 

The Center for Microbiome Innovation seeks applications for a postdoctoral position 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

- 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 research record

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

 

How to Apply:

Email your CV/cover letter 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 - Undergraduate Student Researcher – Machine Learning

 

The Center for Microbiome Innovation seeks applications for a paid undergraduate student researcher position in a project on machine learning in the UC San Diego-IBM Artificial Intelligence for Healthy Living (AIHL) program. 

 

Scope of work:

- Assist with the evaluation and benchmarking of machine learning algorithms on microbiome data

- Assist with the evaluation and benchmarking of feature selection in microbiome data

- Assist with the analysis and visualization of microbiome data

 

Additional Qualifications:

- Strong skills in Python are required; Javascript is a plus

- Experience or coursework in data science and machine learning

- Undergraduate degree or coursework in Biology or a related field is a plus

- Experience with Github or Bitbucket in a team software development project

 

How to Apply:

Email your CV/cover letter 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 - Undergraduate Researcher - Biomedical Knowledge Base Development

 

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

 

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

 

How to Apply:

Email your CV/cover letter 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, Bioinformatics & Immunology in Neuropsychiatric Disorders

The Center for Microbiome Innovation (CMI) seeks applications for a postdoctoral position in immunology and bioinformatics to engage in a microbiome-focused analysis of the microbiome and inflammation regulation in children and adults affected by mental health conditions including obsessive compulsive disorder (OCD) and autism spectrum disorders (ASD).

 

Scope of research:

- Immunophenotyping via flow cytometry, cellular techniques for inflammation regulation, immunoassays, and molecular techniques

- Analysis of microbial communities in the gut and oral microbiome

- Curation and transformation of multi-parameter clinical phenotype and behavior information

- Integration of multi-omic data to examine microbiome-brain connection

- Wet and dry lab activities

 

Qualifications:

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

- Strong research record

- Experience with Python and/or R is a plus

Host faculty include Suzi Hong (Psychiatry, Family Medicine and Public Health) and David Rosenberg (Psychiatry), and Rob Knight (Pediatrics and Computer Science & Engineering).

 

How to Apply:

Email your CV/cover letter to CMIInfo@ucsd.edu by September 9, 2018 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.

Biota - Data Scientist

 

Candidate: You are passionate about the company’s vision to deliver actionable insights using microbial g enomics. You are a self-starter with an inextinguishable fire to compete and succeed. You thrive in an environment that requires crisp judgment, pragmatic decision-making, rapid course-corrections, and comfort with market ambiguity. You discharge your duties within a culture of mutual team respect, high performance, humility, and humor.

Company Goals for the next 18 months:

● Design, refine, and execute on Biota’s Subsurface DNA Diagnostics platform to provide actionable insights customers in the oil and gas industry. Analysis will primarily focus on amplicon-based sequencing.

● Participate in execution of external collaborations with geologists and petroleum engineers to provide commercial value for oil and gas customers by integrating genomics derived insights from Biota’s services. (O&G specific).

● Participate in design and implementation of state-of-the-art bioinformatics pipeline to process all forms of DNA sequence data (target genes, shotgun metagenomics, microarray) to enhances Biota’s mission (Bioinformatics specific).

● Implement Python-based computational pipelines for DNA sequence analysis, incorporating open-sourced tools (e.g. QIIME, SourceTracker, Emperor, Scikit-learn, Scikit-bio, PICRUSt, etc.) to deliver customer projects.

● Execute procedures for data storage, organization, and computation that optimize analysis turnaround time and increasingly leverage the strength of Biota’s proprietary Subsurface DNA Database, working towards a ‘turn-key’ computational pipeline implementation.

● Provide guidance in the development of current and future intellectual property and participate in top-tier research activities at the intersection of genomics and subsurface science.

● Serve as an example for the company’s values and behaviors as articulated in the Team Operating Agreement.

Location: This position is based in our company’s R&D center in San Diego.

Compensation : Competitive base salary, bonus, stock options, and a benefits package including paid vacation, medical coverage, and telecommuting options.

Skills breakdown:

● Data analysis: 70%

● Software development: 20%

● Project management: 10%

Required experience:

● 2 years experience analyzing microbial ecology datasets using industry standard tools such as QIIME, MG-RAST, skbio, with co-authored publications (preferred).

● Scripting and data science experience in Python using sklearn and jupyter notebooks.

Email your CV and cover letter to tishoey@biota.com to apply.

Biota - Data Engineer

 

Candidate: You are passionate about the company’s vision to pioneer genomic diagnostics in the energy industry. You are a self-starter with an inextinguishable fire to compete and succeed. You thrive in an environment that requires crisp judgment, pragmatic decision-making, rapid course-corrections, and comfort with market ambiguity. You discharge your duties within a culture of mutual team respect, high performance, humility, and humor.

Company Goals for the next 18 months:

● Lead implementation of procedures for data storage, organization, and computation that optimize analysis turnaround time and increasingly leverage the strength of Biota’s proprietary Subsurface DNA Database, working towards a scalable ‘turn-key’ computational pipeline implementation.

● Work with Technology team to design database structures to handle integration of multiple data sources to deliver scalable Subsurface DNA Diagnostics products, including metadata capture, entry, and validation.

● Participate in development and maintenance of Biota’s Python codebase to ensure efficient and on-time delivery of customer projects by building great datasets from challenging and varied sources for analytics and machine learning.

● Participate in maintenance of infrastructure supporting the business and technology development, including AWS, firewalls, VPNs between environments and related tools.

● Serve as an example for the company’s values and behaviors as articulated in the TeamOperating Agreement.

Location: This position is based in our company’s R&D center in San Diego.

Education: B.S with +3 years experience or M.S degree in Computer Science or related discipline

Requirements:

● A strong desire to learn and contribute across a variety of technologies and disciplines.

● Ability to quickly diagnose and solve problems collaboratively.

● 4+ years experience programming in Python using matplotlib, jupyter, seaborn, scikit-learn required.

● Experience using source control/repositories (Git, GitHub) required.

● Experience designing, building and managing relational and NoSQL required.

● Experience designing, managing, building, configuring, administering, operating and maintaining components of an AWS cloud platform required.

● Familiarity with web development tools, Django, Flask, D3 preferred.

● Documentation of development, analytical or data visualization abilities and interests, potentially from an online source (personal website, github, or other sources) preferred.

Compensation : Competitive base salary, bonus, stock options, and a benefits package including paid vacation, medical coverage, and telecommuting options.

Email your CV and cover letter to tishoey@biota.com to apply.

Genentech - Associate Scientist / Scientist - Research Mass Spectrometrist (San Francisco)

The Structure Elucidation Group in Genentech's Small Molecule Pharmaceutical Sciences Department has an outstanding opportunity available for a talented and innovative Associate Scientist/Scientist with strong mass spectrometry skills. The role explores and implements new technologies to support the development of novel small molecule therapeutics for the treatment of significant unmet medical needs. The position works collaboratively with scientists from the Analytical, Process Chemistry, and Pharmaceutics groups to investigate side-products, impurities, and degradants in drug substance and drug product development. This scientist in this position independently designs, plans, and executes protocols to resolve issues related to unknown compound identification. The right candidate is excited by research at the cutting edge of mass spectrometry, and is able to identify new applications of mass spectrometry that can be applied to small molecule structure elucidation problems to ultimately drive innovation to solve those problems. Highly motivated candidates with a passion for innovation are encouraged to apply.

Qualifications

  • PhD in Chemistry, Natural Products, Biochemistry, or a closely related field.

  • Minimum of 2 years post-doctoral experience; industrial experience is beneficial.

  • Experience using molecular orbital and density functional theory calculations to aid in assignment of ion structures.

  • Strong background in organic chemistry and/or natural products identification.

  • Strong desire to work in a collaborative, multi-disciplinary environment.

  • Broad experience with mass spectrometry techniques and the application of those techniques for elucidation of unknown small molecule chemical structures.

  • Evidence of sustained productivity and independent contributions in science, as demonstrated by a strong publication and presentation record.

  • Highly organized, motivated, able to work independently in a collaborative team-oriented setting, and possess strong analytical, organizational, and communication skills. 

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