Bioinformatics engineer job description

At Sage Bionetworks, we believe that we can learn more by engaging and collaborating with people from a diversity of experiences, backgrounds and identities. We develop and apply open practices to data-driven research for the advancement of human health. We are working to establish actionable biomedical observations through the reliable analysis and responsible sharing of representative data. By improving the way scientists collaborate and by increasing the reliability of research, we will improve human health.

We are currently recruiting Bioinformatics Engineers with strong quantitative skills and experience with biomedical research projects. Key tasks will involve supporting biomedical collaborations via analysis of multimodal and clinical datasets (e.g., Electronic Health Records, multi omics, and microbiome data) through community data Challenges. This position will facilitate benchmarking efforts for biomedical method and tool assessment and will assist with the organization, analysis, and execution of DREAM Challenges.

Are you the type of person who enjoys engaging with scientists and researchers across many disciplines? Do you want to be an integral part of a team that includes computational biologists, research ethicists, software engineers, and data librarians? If so, you could be the next bioinformatics engineer to join our Challenges and Benchmarking Team.
What you'll be doing:

Perform quality assessment for biomedical datasets contributed by external collaborators Design and conduct analyses and meta-analyses across multiple datasets Summarize research findings in reports, manuscripts, and presentations to collaborators and funders Develop new methods, pipelines, and tools for analysis of data in collaboration with external partners (federal, non-profit and industry). Generate preliminary data to support grant applications. Collaborate with in-house data curation experts to select and apply data standards to datasets Set up and monitor cloud computing infrastructure and scoring routines for Challenges (e.g. DREAM) and continuous benchmarking efforts. Contribute to Sage's development of new capabilities for community Challenges and Benchmarks that advance the open science movement. Monitor Challenge discussion boards and resolve technical issues for Challenge participants.



We'd love to hear from you if you have:


A Master's (or BS +3 years experience) in Bioinformatics, Biomedical informatics, Statistics or related field, or 3+ years comparable work experience. Experience with "real-world" clinical data and clinical models such as OHDSI/OMOP preferred Data science or applied statistics experience, with fluency in one or more programming languages (e.g. R, Python, Julia) Familiarity with computing and collaboration technologies such as git, Docker, and Linux preferred. Have strong collaboration and teamwork skills. Experience in tracking project objectives and tasks is a plus. Familiarity with cloud-based technologies (OpenAPI, AWS, GCP, others) preferred, but not required Are passionate about open science, reproducible research, and collaboration.



Physical Demands


The physical demands described here are representative of those that must be met by an employee to successfully perform the essential functions of this job. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions.

Prolonged periods sitting at a desk and working on a computer. Routinely required to sit; walk; talk and hear; use hands to keyboard, finger, handle, and feel; may stoop, kneel, crouch, twist, crawl, reach, and stretch. May require travel dependent on company needs. Can work under deadlines. Must be able to lift up to 20 pounds at times.



About Sage Bionetworks


Sage Bionetworks is a nonprofit biomedical research and technology development organization that was founded in Seattle in 2009. Our focus is to develop and apply open practices to data-driven research for the advancement of human health. Data-driven research has become an important component of biomedicine, but it's not always easy to understand how to apply computational approaches appropriately or how to interpret their results. Sage believes open practices can help. Our interdisciplinary team of scientists and engineers work together to provide researchers access to tmark methods, and explore collective insights, all backed by Sage's gold-standard governance protocols and commitment to user-centered design. Sage is supported through a portfolio of competitive research grants, commercial partnerships, and philanthropic contributions.

Sage embraces diversity, equity and inclusion. We are based in Seattle, WA, and collaborate broadly throughout the world.

At Sage we have a distributed workforce and support remote and/or on-site hybrid work arrangements. (with manager approval). All interviews will be conducted virtually, unless otherwise communicated.

Sage Bionetworks is pleased to offer a comprehensive benefit package, competitive to both commercial and not-for-profit life science organizations. The plan includes: health, dental, vision, life, Accidental Death and Dismemberment and Long Term Disability benefits; paid time off; a retirement plan; flexible spending accounts; a shared incentives plan, voluntary Long Term Care insurance, and other voluntary products.

At Sage we engage equitable workplace strategies to ensure fair compensation. Actual compensation is dependent upon current market data, experience, and pay parity within our organization. This position is an associate level position, with a compensation range of $73,400 - $117,443.

Are you ready to link your passion with a purpose? At NantHealth, we build technology that simplifies healthcare. We manage the data and decisions that help the healthcare industry deliver better patient care.NantHealth's products target specific pain points that inhibit healthcare from reaching its full potential. Our payer-provider collaboration solutions increase operational efficiency, unlock savings, and enhance communications. Our treatment plan validation capabilities help payers better manage costs for oncology and autoimmune conditions. We're seeking innovative thinkers who love doing meaningful work. If you're looking to bring your skills and expertise to a growing technology company, it's time for you to join us!

To ensure we can provide the best in healthcare tech, we focus on building the best team. Through holding true to our core values - clarity, empathy, collaboration, integrity, a sense of community, and a pioneering approach - we are creating a vibrant culture where ideas can blossom, people can thrive, and success can flourish.

We value each of our employee's total wellness. From robust medical, dental, and vision insurance, to financial planning assistance, to physical and mental wellness discounts, including an optional annual subscription to the Headspace app and unlimited access to LinkedIn Learning, we understand that our company succeeds when our employees succeed as individuals.

Additional notable benefits include:

• Paid Time Off (hourly) / Flex Time Off (salaried) programs for Full Time employees
• Growth and Development opportunities
• 401(k), including a 3% company match
• Paid Holidays
• Paid Parental Leave, including a flexible return-to-work program
• Employee Assistance Program
• Discounts on popular cell phone plan providers
• Life & Disability Insurance
• Travel Assistance
• Education Assistance Program
• And much more!

NantHealth is a seeking a skilled Lead Bioinformatics Engineer to join our Team.

The required hours for this role are: Monday - Friday, 8:00 am to 5:00 pm EST

Responsibilities include:

• Process, quantify, and assess quality of biological samples and prepare the samples for sequencing.
• Retrieve and organize results following sequencing experiment completion, and perform data analysis using bioinformatics, data analysis workflows currently available in the lab, in addition to developing new data workflows.
• Prepare posters and manuscripts for scientific conferences or peer-reviewed journals, in addition to mentoring more junior members of the lab on the use of sequencing and bioinformatics technologies.
• Work closely with the other Bioinformatics Core members in maintaining the genomic data analysis resources, inducing keeping the software, databases, genome indexes and operating systems up to date.
• Help in preparing posters and presentations for scientific meetings.
• Remote employment permitted

Education & Experience Requirements:

• Position requires a Bachelor's degree in Bioinformatics, Computer Science, Computational Biology or related field of study, and two (2) years of experience in the job offered or as a Bioinformatics Engineer or Intern.
• Alternately, will accept a Master's degree in Bioinformatics, Computer Science, Computational Biology or related field.
• Requires experience with analysis of genomic data using bioinformatics.
• Working knowledge of sequencing technologies.
• Strong skills with scientific research in the field through scientific publications, conference presentations, or similar scholarly achievements.
• Programming experience with two scripting languages, either Python, Perl Ruby, or standard algorithms - data structures.
• Experience with relational database systems or writing SQL queries for data management or storage retrieval.
• Requires knowledge of next-generation sequencing technologies (primary Illumina, IonTorrent, Sanger, 454) data analysis protocols, software or data formats (read quality checks, read mapping or assembly, RNA seq, re- sequencing or SNP discovery).
• Experience parsing of next-gen datasets using programming libraries (BioPerl, BioPython).
• Experience with machine-learning tools such as scikit-learn, WEKA, or other equivalent libraries.
• Experience with cloud computing, including AWS.
• Requires experience with cloud API programming through scripting languages.
• Experience with the UNIX command line.
• Requires experience with Ubuntu and Centos Distros.
• Remote employment permitted.
• Skills and experience can be gained concurrently or as part of a graduate degree program.

NantHealth is a mandatory vaccination employer in the US and Canada for COVID-19 and its variants. At NantHealth the health and safety of our employees and their families is our top priority. In line with our corporate core value of community , doing our part to ensure our workplace is fully vaccinated is a pioneering step we can take to help stop the spread of COVID-19. The Company requires that its employees in the US and Canada be fully vaccinated, and proof of vaccination will be required prior to start. If we make you an offer and you are not yet vaccinated, we will accommodate a delay in start date. If you require a medical or religious accommodation, we will engage in the interactive process with you.

NantHealth provides equal employment opportunities to all employees and applicants for employment and prohibits discrimination and harassment of any type without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal, state or local laws.

This policy applies to all terms and conditions of employment, including recruiting, hiring, placement, promotion, termination, layoff, recall, transfer, leaves of absence, compensation and training.

Look for more than answers.


At Quest, we are on a continuous journey of discovery and development. It's this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast-moving career opportunities where you can affect change at a rate unheard of in many organizations of our size and scope. While we invest in and develop technology to drive our innovations, our ongoing success relies on our people.


Associate Bioinformatics Engineer , US Operations, hybrid - the role:


As an Associate Bioinformatics Engineer, you will work for the world leader in the industry, with a career where you will have the opportunity to collaborate and affect change while expanding your leadership skills and technical knowledge. You can make a real impact in a market that is growing and developing.

This position is in our Operations group, part of the Research and Development organization, in Advanced Diagnostics based in Lewisville, TX.The role is specific to genetic testing in a highly regulated CAP/CLIA laboratory environment using short and long-read sequencing as the basis of evidence.The right candidate will know how to balance between innovation and standards with a practical understanding of when each is appropriate.The Operations group supports, hones, and executes the processes defined by our Engineering group with emphasis in compliance and continuous improvement.Though coupled tightly to regulation through standards in validation, documentation, and data retention, the group is an integral part of the development cycle of our analysis workflows and visualization.

This candidate can work in a hybrid remote/on site capacity.Approx. 1-2 days a week onsite.

• Execute and improve sequence analysis workflows and automation

• Track, troubleshoot and mitigate issues encountered in processing production samples

• Plan and develop solutions to recurring issues to be merged back into development branch maintained by the Engineering group

• Develop and surface web-based results and dashboards for clinical geneticists, medical directors and operations lab personnel providing clarity in our process

• Generate, wrangle, merge and glean information from varied and complex data sets

• Implement RESTful APIs to various systems including LIMS, AWS job runners and other systems necessary for data processing and execution

• Perform validation, testing, and production deployment in pursuit of systems to standardize processes across all Quest Diagnostics genetic testing labs

• Support production day-to-day operations

• Maintain production documentation for compliance and supportability of all bioinformatics processes in production environment

• Produce charts and visualization in dashboards, reporting and in support of data driven hypotheses

• Perform validations, formal testing, and deployment schemes to production systems

• Perform LIS support duties (maintain database for user, tests, clients....)

• Support interface integrating and testing projects

• Be an active team player and support the group

The ideal candidate will have the following skills and experience:

• 3 yr experience using formal programming and scripting languages

• 5 yr experience working on a Linux command-line to process, parse, and merge varied data sets

• 2 yr experience working with web services and implementing API communications (REST, SOAP, etc.)

• 3 yr experience in a distributed HPC environment (cluster, cloud)

• Experience developing production grade software both supportable and extensible

• Experience with source control in a development, testing, and production environment

• Automated testing experience; CI/CD experience preferred

• Knowledge of CAP documentation requirements a plus

Current tech stack experience is a plus:

• Programming Languages: Python, PERL, Groovy

• Web Frameworks: Python Flask, React Native, Bootstrap

• Environments: R Statistical Language

• Visualization: ggplot2/tidyverse, Tableau, d3.js

• Database: MySQL, MongoDB

• Cloud Computing: AWS, DNAnexus

• Pipeline Workflow Manager: Nextflow

• Source Control: Git

• CI/CD: Gitlab, AWS CDK

• Containerizing: Docker