Bioinformatics Engineer I/II - San Francisco, United States - Gordian Biotechnology
Description
Do you want to be part of a brilliant team, using single-cell genomics to forge new paths in drug discovery? At Gordian, we combine unique large-scale in vivo perturbation screens with novel analysis approaches to identify therapeutic targets for complex diseases with unmet medical need.
The Destination:
Gordian Biotechnology is a therapeutics company whose mission is to cure age-related diseases and ultimately allow people to lead longer, healthier lives.
Traditional ex vivo screening methods have failed to produce effective treatments, as age-related diseases have complex causes that include interactions with the aged environment.
To address this problem, Gordian's platform is the first and only to enable pooled in vivo tests at scale in our proprietary "patient avatars". We are able to deliver and test hundreds of therapeutics in individual animals, and scale efficacy testing to cover every therapeutic target at the beginning of the drug discovery process (more info on our website). We can choose targets that really impact disease biology, to develop and commercialize therapies for the world's deadliest diseases, and eventually for the processes of aging itself.
The Journey:
Our mission is audacious, and the path will be full of both challenges and excitement. Two things characterize the Gordian experience: 1) We work as a team, with ownership in our own roles and trust in each other. 2) We strive for extraordinary outcomes, and in doing so grow our skills and capability.
Team – Relying on each other begins with transparency. We set clear goals, visibly connecting individuals and teams to our company objectives. This empowers each of us to make autonomous decisions about our work, knowing how they will affect the bigger picture. Our communication happens out in the open. We give and receive feedback from a perspective of helping each other grow, share mistakes, and ask for help.
Extraordinary – Every day, we ask ourselves 'How could this process/outcome be even better?'. Knowing our overall mission, we do what we think helps us make the most progress, without asking for permission. We don't shy away from big challenges or unknown territory, but find a way to excel. Our colleagues are amazing, both at what they do and as people. They inspire us to keep up, to not let them down, and be inspiring in return.
Like any cutting-edge research environment, Gordian doesn't believe in a standard 9 to 5 day. We set ambitious project goals and support each other to meet them, while maintaining the balance individuals need to thrive and achieve excellence. Our team is geared towards helping each other out and maintaining a culture of intellectual and social fun. We like getting things done and keep standing meetings to a minimum. This year, in accordance with our unlimited vacation policy, each member took an average of 4.5 weeks of (offline) vacation, not including major holidays. We unwind with weekly team lunches, and support each others' projects both experimentally and by 'pre-mortem' meetings to discuss possible failure modes and experimental design.
If this environment sounds appealing, help us bring it to life. We are at the beginning of a long journey, and want both your ability and your personality along for the ride. Our culture is a source of great pride; it represents both who we are, and who we wish to be.
You can dive deeper here.
About the Role:
Your mission as Bioinformatics Engineer is to take the software backbone of Gordian's in vivo screening platform to the next level, by designing , modifying and managing our bioinformatics tools and codebases ensuring that they can handle the ever growing amount of data we collect and align with Gordian's ongoing and future needs and objectives.
Gordian has multidimensional data across many cell types, with thousands of biological perturbations, in many species. Our data is unique, and making sense of it will require your methodological analysis not only within each dataset, but across DNA sequencing, gene expression, transcriptome analysis and microscopy/imaging data. In this role you'll use and extend state of the art tools for processing single cell transcriptomic data, in order to make these data accessible to all scientists at Gordian. You'll stay current with advancements in bioinformatics and use this knowledge to integrate cutting-edge technologies/methodologies into our workstream.
Your work will happen in constant dialogue with both bioinformaticians and biologists and you'll develop clear and informative reports, dashboards and notebooks to translate complex biological data into insights, while maintaining the integrity and organization of our data through automated workflows.
Additionally, you'll work to enhance and transition bioinformatics workflows into our cloud platform (AWS, GCP, etc.). These workflows will be used by the whole company, and you'll ensure a seamless integration with the rest of our software through code coverage, testing and documentation.
In this role you'll combine a mindset of process optimization and reliability with intrepid build-from-scratch creativity.
In your first month, you'll have completed onboarding and have ramped up on Gordian's cloud platforms, workflow frameworks and current bioinformatics pipelines, scripts and tools. Additionally you'll access existing code bases and workflows to better understand process/dataflow and identify areas for improvement and optimization.
By three months you'll successfully adapt and integrate at least one major workflow used to process data onto the cloud and will optimize our existing data processing pipeline for reliability/reproducibility/efficiency while deploying supporting features based on feedback from relevant stakeholders.
In six months you'll have designed and implemented multiple bioinformatics tools and introduced cutting edge technologies that align with future project and company goals. You'll also create a framework for continuous improvement and integration for deployment of informatics pipelines and implement automated systems for meaning and organizing the company's data.
About You :
You have a history of successful execution, both in- and outside of your job description.
You want a chance to do your best work, immerse yourself and excel, alongside people who will inspire you and whom you'll be excited to spend your days with.
You truly want to play a key role in an early-stage startup screening new targets for intractable diseases of aging: A fast-paced environment full of both uncertainty and new challenges, demanding relentless resourcefulness.
You have a strong data engineering background with knowledge of genomic and bioinformatic data types and processes and are thoroughly comfortable with Python, NoSQL/SQL, Git and with using workflow languages such as Nextflow, WDL/Cromwell or Snakemake in a cloud computing environment(s) (AWS/GCP).
You have developed and shared code in a professional software environment within a lifesciences organization and you have knowledge of distributed version control systems and an understanding of good code practices and standards.
You have a knowledge of sequencing data, cellranger and common workflows for DNA/RNA sequencing. You're a crisp communicator, and are able to seamlessly manage collaboration with cross functional partners and teams. You can distill analysis output into visualizations, tabulations, etc that effectively document and communicate results to those with and without a computational background.
Strong candidates will have contributed to work that should be evident from Git repositories and/or publications and accessible interactive data (i.e. ).
The Details:
Gordian aims to provide everything you need to thrive. Beyond our community and science, you'll have enough equity to be a true stakeholder in the company, competitive salary, full health/dental/vision/life insurance, 401k with match, onsite lunch paid for 3 days a week, an onsite gym, whatever vacation you need to be at your peak, remote work flexibility, and access to world-class mentors and advisors to support your professional growth. Our building is in the heart of the biotech capital of South San Francisco.