Staff Scientist, Bioinformatics Java Developer
Thermo Fisher Scientific

South San Francisco, California
$129,400.00 - $194,050.00 per year

This job has expired.


Job Description

Do you have a passion for innovative ideas and groundbreaking discoveries? With over $1 billion invested annually in R&D, at Thermo Fisher Scientific you'll help solve some of the world's toughest challenges, from giving cancer patients hope, ensuring safe drinking water and helping law enforcement tackle cases through forensics. We empower our teams to put science into meaningful action and give our R&D colleagues the autonomy, resources and tools they need to take science a step beyond.

Discover Impactful Work:

We're seeking a highly skilled individual with experience developing algorithms and annotation sources for next-generation DNA sequencing. The successful candidate will be part of a multi-disciplinary team responsible for developing and launching cutting edge applications for Ion Torrent Sequencing instruments to advance genomic research, especially in Oncology and personalized medicine. They will prototype, adopt, improve, develop, optimize, perform training and documentation, and validate algorithms for assay design and functional annotation of DNA sequencing data for oncology, inherited disease, and other applications. Be responsible for variant annotation using public and proprietary annotation databases. The environment is collaborative, working with bioinformatics teams, project teams and software teams. ork in a fast paced, complex setting to hard deliverables . Critical thinking, determination to succeed, focus on quality, and the drive to deliver are key attributes.

A Day in the Life:

This position will contribute to solutions driving easy, automated analysis of human genetic variation obtained by high-throughput sequencing; will develop algorithms and applications for inferring biological knowledge from millions of short reads, and will optimize and validate application software.

  • Keep up to date with the latest developments in algorithms for analysis of next-generation sequencing and applications of sequencing, especially for personalized medicine and human health. Will be responsible for two core algorithms. The first algorithm is for predicting the functional protein changes resulting from nucleotide changes. The second algorithm performs selection and pooling of optimal primers for DNA amplification.
  • Maintain, extend, improve, benchmark, support, test, train and document these algorithms, coordinating with software teams for integrating these into software releases, and with bioinformatics, support, and program teams who use these algorithms. These are production level software.
  • Identify, update and work with V&V teams to validate annotation sources which help scientists interpret variants. These include public annotation sources (dbSNP, Cosmic, etc) and proprietary annotations.
  • Develop prototypes quickly, will integrate these methods into production software, and will collaborate with key internal and external groups.
  • Other responsibilities include giving internal and external presentations, and keeping abreast of the latest developments in genomics.
Keys to Success:

Education/ Experience
  • PhD in computer science, computational biology, biostatistics, bioinformatics, or similar with 1-3 years of related work or post doc experience
  • May consider MS degree with 4-5 years of related work or post doc experience OR BS degree with 6-7 yrs of related work or post doc experience
  • Background in DNA sequencing technologies, bioinformatics, genetics, biology.
  • Experience building models in complex disciplines, including recent relevant experience.
  • Demonstration of rapid prototyping experience, leading to development of production code that is robust, fast, and highly accurate is strongly preferred.
Knowledge, Skills, Abilities
  • Experience with Algorithms development / Scientific computing. Hands-on experience in developing bioinformatics analysis methods/algorithms for sequencing data is strongly preferred.
  • Strong programming experience in Java.
  • Ability to engage in clear written and oral communication.
  • Excellent problem solver, analytic thinker and quick learner
  • Strong statistical background, previous industry experience, familiarity with common bioinformatics tools and databases, experience with high performance computing, understanding of assay design, experience working in cancer biology or human genetics, data science, experience with clinical testing, are all highly advantageous. In-depth knowledge of bioinformatics databases in genomics, oncology, genetics, inherited disease, and similar disciplines. Development of efficient and scalable algorithms. Experience with cloud computing. Experience with development of production software. Experience with unit testing, functional testing. Experience with agile software development. Experience working with global teams.
Thermo Fisher Scientific is an EEO/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.

Accessibility/Disability Access

Job Seekers with a Disability: Thermo Fisher Scientific offers accessibility service for job seekers requiring accommodations in the job application process. For example, this may include individuals requiring assistance because of hearing, vision, mobility, or cognitive impairments. If you are a job seeker with a disability, or assisting a person with a disability, and require accessibility assistance or an accommodation to apply for one of our jobs, please submit a request by telephone at 1-855-471-2255*. Please include your contact information and specific details about your required accommodation to support you during the job application process.

*This telephone line is reserved solely for job seekers with disabilities requiring accessibility assistance or an accommodation in the job application process. Messages left for other purposes, such as not being able to get into the career website, following up on an application, or other non-disability related technical issues will not receive a response.

Compensation and Benefits
The salary range estimated for this position based in California is $129,400.00-$194,050.00.

This position may also be eligible to receive a variable annual bonus based on company, team, and/or individual performance results in accordance with company policy. We offer a comprehensive Total Rewards package that our U.S. colleagues and their families can count on, which includes:
  • A choice of national medical and dental plans, and a national vision plan, including health incentive programs
  • Employee assistance and family support programs, including commuter benefits and tuition reimbursement
  • At least 120 hours paid time off (PTO), 10 paid holidays annually, paid parental leave (3 weeks for bonding and 8 weeks for caregiver leave), accident and life insurance, and short- and long-term disability in accordance with company policy
  • Retirement and savings programs, such as our competitive 401(k) U.S. retirement savings plan
  • Employees' Stock Purchase Plan (ESPP) offers eligible colleagues the opportunity to purchase company stock at a discount
For more information on our benefits, please visit: https://jobs.thermofisher.com/global/en/total-rewards


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