Senior bioinformatics scientist job description

Who We Are
Ovation.io is a clinical informatics company providing operations software and data tools for the advancement of precision medicine. Compelled by the philosophy that data drives action, Ovation is creating products that make it easier for labs to bring innovative tests to the patients that need them.

Since its founding in March of 2017, Ovation has grown to develop and support world-class SaaS products used by clinical and translational labs around the globe. Along the way, Ovation's team has developed an unparalleled level of competency in this space with particular expertise in the fields of molecular diagnostics and clinical data utilization.
Who You AreA collaborator within a fast-paced team who can adapt to new challenges in real time.Someone who strives to see connections and pursue opportunities where others cannot.Passionate for mission-driven work with a desire to be an important contributor.Enthusiastic about science, technical details, and reproducible evidence driven research and disciplined in data quality and performance.A person capable of having a deep appreciation of the challenges faced by patients and Ovation's potential role in helping drug developers accelerate delivery of life-changing precision medicines to the patients that need them.
What You Will DoWork with engineering teams to develop strategies for end-to-end management of large clinical genomic data sets to bridge wet lab NGS protocols, harmonizing interpretation of data from different sequencing platforms and cutting-edge analyses of variants.Analyze whole genomes and transcriptomes from small RNA viromes to human genomes to benchmark their technical validity and genomic relevance.Perform exploratory genetic analysis on genomes to increase the power of biomedical discovery in human disease areas.Design and guide wetlab NGS workflows in customer clinical labs to generate consistently high quality sequence data from challenging specimens.Document, analyze and interpret project specific data to create and present genomics summaries and reports for delivery.
What You BringExperience in bioinformatic pipelines and analyses of different genomes and transcriptomes including variant calling in human genomics.Deep understanding of concepts behind common and rare variant analysis, fine mapping, and phased sequencing.Good working knowledge of NGS methods, literature and milestone genomic projects like those associated with 1000 Genomes and UK biobank.Strong familiarity with bioinformatics algorithms and software tools for genomic analysis at DNA, methylation, and RNA levels, including open source platforms like GitHub.Experience with executing tools in Linux, Python notebook and AWS.Solid understanding of statistical concepts routinely used in bioinformatic analyses.Experience in a diagnostic CLIA/CAP environment with research data of unknown clinical significance.PhD in clinical human genomic and bioinformatics or related preferred.#LI-RC1
Join us! Ovation is excited to be building the next-generation of cloud-based operations software and data tools for diagnostics and discovery. We're a small but rapidly growing team that values transparency, integrity, aptitude, and grit. We work in an open and supportive environment that encourages experiments, strives for perfection, and expects failures as part of the learning process in a fast-paced, innovation-driven company.

A satisfactory background check is required by Ovation and will be subject to state or local regulations, including but not limited to your driving records, credit records, criminal records, education records, personal references, previous and current employers.

Ovation is an equal opportunity employer and we value diversity as a core of company culture. We do not discriminate on the basis of race, religion, color, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status.

At Nautilus, we have a big and important mission: improve the health of millions by unleashing the potential of the proteome to accelerate drug development and enable a new world of precision and personalized medicine. We are developing a single-molecule protein analysis platform of unprecedented sensitivity, scale, and ease of use that we believe will democratize access to the proteome - one of the most dynamic and valuable sources of biological insight. To accomplish this, we are pursuing hard scientific problems with an entrepreneurial mindset and creating a world-class team of builders, innovators, and dreamers across a wide range of disciplines.

We are looking for a Senior Bioinformatics Scientist to join our Bioinformatics team. Your work will focus on development of new data acquisition and analytics approaches to be incorporated in future iterations of Nautilus instrumentation. To that end, you will work together with the Platform Integration experimental team to support all phases of research from ideation through proof-of-concept. The role is highly collaborative; success is measured by the degree to which you elevate the capabilities of your peers in pursuit of scientific insight. Frequent activities in this role include consulting with experimentalists on experimental design, implementing data visualizations and statistical approaches to answer key experimental questions, building pipelines to automate common analysis tasks, and designing databases to organize experimental data and enable longitudinal analysis.

This role reports to the Associate Director of Bioinformatics and is based in San Carlos, CA. A minimum of three days in office, preferred.

ResponsibilitiesYou will contribute to analysis of Nautilus data at various phases of processing including image analysis, object registration, image alignment, stochastic binding data analysis, single-molecule identification, and quantification.You will prototype novel data analysis and visualization approaches to support research in a fast-paced environment with input from experimentalists. You will create, maintain, and extend experimentalist-facing data processing pipelines accessible through a web-based user-interface.You will devise strategies for capturing experimental data and metadata in Nautilus databases amenable for future longitudinal analyses.You will leverage an understanding of capabilities and limitations of existing bioinformatics solutions at Nautilus to inform plans for data analysis of incoming experimental data.You will coordinate effectively with multiple cross-functional teams including bioinformatics, software engineering, instrument firmware, and computer vision to meet current data analysis needs and anticipate future ones. You will mentor bioinformaticists and scientists across a range of experience levels.You will effectively communicate complex bioinformatic approaches and concepts to scientists who may not have a background in bioinformatics.You will develop and apply statistical learning approaches to generate clear visuals and statistics from biologically relevant datasets.You will participate in code and design reviews alongside your bioinformatics colleagues.

RequirementsA minimum of PhD in Bioinformatics, Data Science, or related field and 5+ years of experience developing novel computational approaches in genomics, transcriptomics, or proteomics You must have familiarity with core concepts of molecular biology and/or proteomics You must have the proven ability to guide experimental design You must have expertise in data quality assessment and visualization You must have expertise in computational modeling and statistics You must have experience with programming in Python or RYou must have the ability to follow direction as well as work independently You must have excellent written and oral communication skills You must have a willingness to learn and grow within a transformative company You also have proven problem-solving skills and collaborative, teamwork-oriented nature You also have a willingness to wear multiple hats and help out colleagues whenever necessary Optional experience in programming in C++ or any other strongly-typed language a plus Optional experience with use of various integration, functional, and/or unit test frameworks to prove correctness of automated data analysis algorithms & pipelines

Preferred SkillsExperience in image and/or signal processing Experience building or managing relational data sets and databases to collect experimental data over time Experience with Snakemake, Luigi, Airflow, Toil, or similar batch workflow management systems Experience with Amazon Web Services, with a focus on Athena, Batch, EC2, ECR, Glue, Lambda, and S3Experience with deploying software using containerization technologies, such as Docker and Kubernetes

Nautilus Team CultureWe are curious go-getters: this is a team of life-long learners who aren't afraid to tackle the big challenges and we embrace the journey We are detail oriented: we do great science by working smart & with diligence where we learn from our trials and mistakes We are easy to work with: we want our workplace to be one where everyone can share their perspective and be treated with respect and kindness
#LI-Onsite

GRAIL is a healthcare company whose mission is to detect cancer early, when it can be cured. GRAIL is focused on alleviating the global burden of cancer by developing pioneering technology to detect and identify multiple deadly cancer types early. The company is using the power of next-generation sequencing, population-scale clinical studies, and state-of-the-art computer science and data science to enhance the scientific understanding of cancer biology, and to develop its multi-cancer early detection blood test. GRAIL is headquartered in Menlo Park, CA with locations in Washington, D.C., North Carolina, and the United Kingdom. GRAIL, LLC is a wholly-owned subsidiary of Illumina, Inc. (NASDAQ:ILMN). For more information, please visit www.grail.com.

This role is part of the computational biology and machine learning group within the Bioinformatics & Data Science team at GRAIL whose work is at the heart of the company's products: from classifier algorithms for cancer screening to scientific software pipelines for rapid model development. You will work with diverse teams including computational biologists, machine learning engineers, clinical scientists, assay scientists, and product managers. In this role, you will lead analyzing some of the largest, richest biological datasets in the world to derive biological insights and guide product innovation. Your work will result in exciting discoveries in cancer biology, impactful publications, and potential future products.
Responsibilities

Lead the design and execution of rigorous studies to extract cancer biology insights to promote scientific and technical innovation models and analyze large, complex NGS datasets using rigorous statistical methods to generate insights. Perform end-to-end analyses that include data gathering, processing, analysis, iteration with stakeholders, and presentation/publication of study results Interact cross-functionally with other teams including assay, software, clinical, operations, product development, and external collaborators build, present, and report analyses that reinforce scientific rigor and quality and which maintain GRAIL's statistical culture.

Requirements

* Ph.D. in cancer biology, cancer genomics, cancer immunology, computational biology, bioinformatics, genetics, statistics, or related field with 3+ years of industry experience
* Deep knowledge of cancer genetics, mechanisms of cancer evolution, or tumor-immune system interactions
* Proven track record of frequently cited publications, impactful computational tools, and methods, products, or data sets released to market or used by the scientific community or presentations at international conferences
* Deep understanding of modern statistical methods for the analysis of genomic datasets
* Demonstrated ability to apply these skills to uncover new biological insights from large genomics datasets
* Demonstrated expertise in at least one programming language (R and Python), and proficiency in a Linux environment
* Results-oriented: superb follow-through, drive, and creative problem-solving
* Clear, positive, and proactive communicator in verbal and written communications

Bonus

Experience at the interface of machine learning and cancer biology

Proficiency in version control tools, and reproducible research practices

GRAIL is an Equal Employment Office and Affirmative Action Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability or any other legally protected status. We will reasonably accommodate all individuals with disabilities so that they can participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment. Please contact us to request accommodation.

Following extensive monitoring, consideration of business implications, and advice from internal and external experts, GRAIL US has made the decision to require that all U.S. employees be "Fully Vaccinated" with the COVID-19 vaccine. "Fully Vaccinated" is defined as two weeks after both doses of a two-dose vaccine (e.g. Pfizer or Moderna) or two weeks since a single-dose vaccine (e.g. Johnson & Johnson) has been administered. Absent a qualifying exemption, all GRAIL US employees are to comply with this requirement, including providing documentation of such vaccination status, as a condition of employment. Anyone unable to be vaccinated, either because of a sincerely held religious belief or a medical condition or disability that prevents them from being vaccinated, can request a reasonable accommodation for consideration by GRAIL.