Job Location: San Francisco, CA
The Chan Zuckerberg Biohub ( https://www.czbiohub.org ) is a one-of-a-kind independent nonprofit research institute that brings together three powerhouse universities – Stanford, UC Berkeley, and UC San Francisco – into a single collaborative technology and discovery engine. CZ Biohub itself supports some of the brightest, boldest engineers, data scientists, and biomedical researchers to make breakthroughs in medicine and develop new technologies, frequently in collaboration with our partner universities. We are guided by our values of scholarly excellence; disruptive innovation; hands-on engineering/hacking/building; partnership and collaboration; open communication and respect; inclusiveness; and opportunity for all.
Our Vision
- We pursue large scientific challenges that cannot be pursued in conventional environments
- We enable individual investigators to pursue their riskiest and most innovative ideas
- The technologies developed at CZ Biohub facilitate research by scientists and clinicians at our home institutions and beyond
Diversity of thought, ideas, and perspectives are at the heart of CZ Biohub and enable disruptive innovation and scholarly excellence. We are committed to cultivating an inclusive organization where all colleagues feel inspired and know their work makes an important contribution.
The Biohub’s Summer Internship Program offers currently enrolled undergraduate students the opportunity to work on research projects in a one-of-a-kind environment onsite in San Francisco, CA. This 10-week program provides interns with hands-on experience, mentorship and training, and personal and professional development designed to meet interns where they are at while also propelling them forward in their career.
The internship program goals are to:
- Help interns build a strong foundation in scientific research and laboratory skills
- Provide scientific education and enrichment to underserved and underrepresented groups in STEM (Students from historically marginalized or underrepresented groups are strongly encouraged to apply.)
- Establish valuable and sustainable mentoring relationships
- Equip interns with the skills and network needed to be competitive in STEM
- Build a pipeline of STEM professionals
The Opportunity
The Data Science (Qualitative Cell Science) platform is seeking a talented undergraduate student to join the team for the 10-week program in San Francisco, CA. This team is working at the intersection of computational biology and quantitative cell biology. They work with Biohub’s research groups with the aim of understanding cellular biology at multiple scales ranging from transcriptome, epigenome, proteome of single cells to multicellular organism’s development. The team leads the Tabula projects – making transcriptomic atlases of model organisms such as mouse, zebrafish, and human tissues. They are also eager to implement and test new computational tools and algorithms which can expand the capabilities of Biohub investigators. During the internship, the intern will learn how cutting-edge computational tools are applied to fundamental biological questions and participate in innovative research at Biohub. The successful candidate may work on one or more of the following projects:
- Spatial transcriptomics technology allows us to measure the physical location of transcripts such that we can map the observed transcriptome to its position within the tissue. Next-Generation Sequencing (NGS)-based spatial transcriptomics methods can capture the whole transcriptome, 20K-30K genes, yet not at the single-cell resolution, but scales from 1-10 cells. Since the observed transcripts are potentially from multiple cell-types, there needs to be a decomposition of the measured transcriptome into known cell-types, which is called deconvolution. Although there are many deconvolution algorithms published over the past years, it is unclear how a user should choose an algorithm, and how one could interpret the deconvolution results. The intern will work to test and benchmark computational deconvolution algorithms for spatial transcriptomics datasets, then streamline the deconvolution workflows to be used at CZ Biohub and beyond. The intern will have the opportunity to learn the basics of spatial transcriptomics technology and basic statistical methods used for benchmarking different algorithms.
Skills Required –
- Enrolled in a science/engineering degree/major (e.g. biology, physics, mathematics, engineering, computer science, etc.)
Preferred Qualifications –
- Familiarity with scientific programming (ideally in Python)
- A key factor of any single cell RNA sequencing (scRNA-seq) dataset is the depth at which the sample is sequenced. Depending on the sequencing depth, all, most, or only some of the RNA molecules inside a cell may be accurately detected. While semi-quantitative rules of thumb exist for determining what sequencing depth is sufficient for any given experiment, we would like to establish a statistical framework to determine if a dataset is of sufficient sequencing depth for downstream analysis. The intern will computationally downsample our sequencing datasets with different levels of sequencing depth, then compute the information saved in these downsampled datasets. By increasing the simulated sequencing depth, we would like to see at which point the information saturates, which will give a quantitative metric of sequencing saturation. In addition, a systematic study of sequencing depth at the per-gene or per-cell type level is needed. The intern will learn the basics of single-cell RNA-sequencing technology, statistics, as well as computational tools to interface with sequencing data while developing computational workflow to assess the sequencing depth.
Skills Required –
- Enrolled in a quantitative degree/major (e.g. physics, mathematics, engineering, computer science, etc.)
- Taken classes for undergraduate level of statistics and linear algebra
- Enthusiasm and curiosity about conducting research and discussing work in a collaborative and open fashion
Preferred Qualifications –
- Programming experience (Python)
- Datahub aims at structuring data and information generated by teams across the Biohub. This starts at a high level, developing systems to handle tracking projects, experiments, data, and associated metadata, and goes down to collating the output of multiple experiments into singular resources. These frameworks help scientists at the Biohub contextualize information being generated, to accomplish a multitude of tasks. This can be anything from identifying ambiguous signals in old proteomics experiments using current data, to collating data from multiple teams with shared sample biologies and pathologies. This framework leans heavily on dynamic programming, generalizability, and utilizing graph data structures effectively. The intern will have an opportunity to learn different domains of software engineering with the aim of contributing software components to the Datahub with three potential directions. 1) The intern could learn NextJS to develop user interfaces to visualize, explore, and alter data. 2) The intern could improve or build new logic in the backend to pipe data or micro-services for developers to access. 3) The intern could learn how to graph-based theory to curate graph databases and develop useful analytical methods with the databases for meta and omics data. An ideal outcome would be the intern not only contributing code, but also integrating their own ideas and insight into the project.
Skills Required –
- Experience in programming (JavaScript, Python)
Preferred Qualifications –
- Familiarity with the frameworks: NodeJS, NextJS, Pandas/NumPy
- Experience with API development, website development, Git
- Experience with ETL Pipelines, Rust, and Java
- Experience with GraphDBs (or experience with any SQL/NoSQL databases)
- Skilled at dynamic programming
- Familiarity with experimental/biomedical data
You Will
- Receive support through a 10-week research experience
- Receive mentorship to support your personal and professional development
- Gain and enhance your technical and transferable skills through trainings and seminars
- Learn how to design, plan, and carry out laboratory and/or computational scientific experiments
- Present at the end-of-program symposium
- Build relationships with peers and colleagues
You Have
Program Eligibility –
- Must be a current undergraduate student (enrolled full time at a college or university both Spring 2023 and Fall 2023 terms)
- Must be able to commit to the 10-week Summer Internship Program (May 30, 2023-August 4, 2023)
- Must be able to be onsite at the Biohub for the duration of the program
Intern Benefits
- Hands-on, one-of-a-kind experience
- Hourly compensation
- Opportunity to live in CZ Biohub-sponsored housing
- Invaluable relationships
- Trainings and seminars
- Social events/activities
Chan Zuckerberg Biohub requires all employees, contractors, and interns, regardless of work location or type of role, to provide proof of full COVID-19 vaccination, including a booster vaccine dose, if eligible, by their start date. Those who are unable to get vaccinated or obtain a booster dose because of a disability, or who choose not to be vaccinated due to a sincerely held religious belief, practice, or observance must have an approved exception prior to their start date.
What We Provide
- Resources to disrupt and innovate at the frontiers of our knowledge of biology and disease
- A collegial and collaborative environment consisting of diverse expertise
- Existing collaborations within CZ Biohub: Technology Platforms (Bioengineering, Computational Microscopy, Data Science, Genomic Sequencing, Mass Spectrometry/Proteomics), Infectious Disease , and Quantitative Cell Science
- Access to collaborators, resources and facilities at our three partner universities (Stanford, UC Berkeley, and UC San Francisco) and at partner organizations in the Bay Area and beyond
- Competitive compensation and benefits commensurate with the experience
Benefits
We offer a robust benefits program that enables the important work Biohubbers do everyday. Our benefits include healthcare coverage, life and disability insurance, commuter subsidies, family planning services with fertility care, childcare stipend, 401(k) match, flexible time off and a generous parental leave policy. In addition, we honor our commitment to career development and our value of scholarly excellence through regular onsite opportunities to learn from the world’s leading scientists.
CZ Biohub is an equal opportunity employer committed to diversity of thought, ideas and perspectives. We are committed to cultivating an inclusive organization where all Biohubbers feel inspired and know their work makes an important contribution. Therefore, we provide employment opportunities without regard to age, race, color, ancestry, national origin, religion, disability, sex, gender identity or expression, sexual orientation, or any other protected status in accordance with applicable law.
Pursuant to the San Francisco Fair Chance Ordinance, we will consider for employment qualified applicants with arrest and conviction records.
Headhunters and recruitment agencies may not submit resumes/CVs through this Web site or directly to managers. CZ Biohub does not accept unsolicited headhunter and agency resumes. CZ Biohub will not pay fees to any third-party agency or company that does not have a signed agreement with CZ Biohub.
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