Job Postings

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. 

CMI Research Applications Programmer

Job Description

Under the direction of the CMI Director in conjunction with sponsoring PIs, the incumbent will serve as a principal programmer for the Center, applying skills as a seasoned, experienced software professional with a full understanding of industry practices, community standards and relevant policies and procedures to medium-sized projects or portions of large projects with moderate scope and complexity. Resolves a wide range of issues. Demonstrates competency in selecting tools, methods and techniques to obtain results.

Interacting with CMI researchers, the incumbent will plan, organize and direct the gathering of requirements and subsequent design, development and support of multiple CMI web applications. Design, develop and present prototypes that meet the requirements; turn these prototypes into production quality code; and perform extensive end-to-end testing to verify that system meets performance and reliability. Monitor and support deployed applications during field studies, detecting and correcting operational problems and resolving problems as required.

CMI labs develop a broad range of web-based and mobile applications that are critical to its research mission. For example:

• LabMan, a web-based platform to help and accelerate sample processing in the web lab by generating the processing sample plates and keeping track of all components and machines available in the laboratory. LabMan’s requirements were initially defined by the wet lab members of the Knight Lab and will be expanded by other members of the CMI.

• Qiita is an open-source web-based platform that enables non-bioinformaticians to perform their own metagenomic analyses and meta-analyses easily using standardized pipelines such as such as Qiime2 and GNPS. Qiita’s requirements and improvements are guided on the expectation of its users and delivered by monthly releases. Qiita’s users ranges from experienced bioinformaticians doing complex meta-analysis to biologist, ecologist or clinicians processing their first study.

• Metadata Wizard, an open-source web-based platform to enable researchers to create rules and descriptions of their metadata to create Qiita-compliant sample information to streamline downstream analyses and metaanalyses for microbiome-related research projects. 

• Global Natural Products Social Molecular Networking (GNPS, https://gnps.ucsd.edu/), a web-platform provides public data set deposition and/or retrieval through the Mass Spectrometry Interactive Virtual Environment (MassIVE) data repository. The GNPS analysis infrastructure further enables online dereplication, automated molecular networking analysis, and crowdsourced MS/MS spectrum curation. Each data set added to the GNPS repository is automatically reanalyzed in the next monthly cycle of continuous identification.

The web applications programmer will also have the opportunity to work with graduate students, postdoctoral fellows and staff scientists to create new tools to advance microbiome research and to promote a deeper integration of tools to address multi-omic analyses.

Qualifications

  • A Bachelor's Degree in related; area and/or equivalent experience/training.

  • Proven experience with programming in a linux environment using SQL databases as well as experience programming web pages for web-based applications using Apache/Tomcat.

  • Demonstrated experience in Java and Python. 

  • Demonstrated experience with relational databases: PostgreSQL and MySQL. 

  • Experience with variety of software applications such as Microsoft Office, Project ,Visio, Visua Studio and Eclipse.

  • Advanced skills associated with software design, modification, implementation and deployment, including object-oriented programming concepts. 

  • Demonstrated experience designing web-based user interfaces. 

  • Ability to understand functional needs and how systems can support those needs. Ability to develop conversion and system implementation plans.

  • Demonstrated broad problem solving skills.

  • Intermediate knowledge of secure software development.

  • Demonstrated ability to interface with management on a regular basis.

  • Proven ability to contribute technical narrative to grant proposals.

  • Solid experience with identification and use of code libraries and open-source forums.

  • Experience with planning for deployment and creation of feedback mechanisms.

  • Demonstrated software repository skills. Testing and test planning skills.

  • Strong experience with common programming tools. Ability to follow software specifications.

  • Ability to communicate technical information to technical and non-technical personnel at various levels in the organization.

  • Demonstrated effective communication and interpersonal skills.

  • Self-motivated and works independently and as part of a team. Able to learn effectively and meet deadlines.

Positions available in the Chu Lab at UC San Diego

Hiu Chu is new to UC San Diego and CMI, previously with Sarkis Mazmanian at Caltech. Her focus is on the microbiome using gnotobiotic mice in her new lab at ACTRI - and she's hiring! See below for an excerpt from her lab website:

 

  • Lab Manager & Research Technicians: We are currently accepting applications for a Lab Manager or Staff Research Associate. This position will have the opportunity to lead and participate in research projects while managing a dynamic new lab. If interested, please email Hiu with your CV and three references, and a brief summary of your leadership & management style. Excellent organizational and communication skills are required.

 

  • Postdocs: We are actively recruiting post-doctoral fellows who have a strong interest and/or prior training in immunology or microbiology. To apply for a postdoctoral fellowship in the laboratory, please send your CV with a statement of interests and three references to Hiu.

 

  • Graduate students: If you are a UCSD graduate student looking for a lab, email Hiu and we can set up a time to meet. We are always seeking inspired, enthusiastic, and curious graduate students to join our group! For prospective graduate students interested in the lab, please see the Biomedical Sciences website to apply for the graduate program.

 

  • Undergraduate students: Outstanding and inquisitive undergraduate students are welcome in the lab. Ideally, students interested in research should join the lab no later than their sophomore year, but all candidates will be considered. Please contact Hiu with your prior experience, relevant coursework, and an estimate of how much time you plan to spend in lab (hours/week).

 

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