NGS Research Engineer

The Center for Algorithmic Biotechnology of the Institute of Translational Biomedicine SPbU, in collaboration with AstraZeneca Oncology, seeks for a research engineer to work on NGS analysis projects, who will:

• communicate with AstraZeneca oncology researchers and production bioinformaticians to understand their goals and needs,
• search, evaluate, and integrate new algorithms and technologies for specific needs and types of data,
• develop, test and apply accredited bioinformatics workflows to patient data and large scale research projects,
• when needed, develop novel pipelines and tools, and support internal users through them.

As part of the team you will work with internal resources as well with international partners to avoid re-inventing the wheel. Here are some of directions:

• help Brad Chapman (HSPH Bioinformatics Core) to develop and support bcbio-nextgen, internally used HTS workflow system,
• partner with academic and commercial groups such as DNANexus, SolveBio, Genologics, on platform development,
• support and develop the NGS Reporting Suite - an internal pipeline for variation prioritization, quality control, and visualization of sequencing data,
• explore cutting-edge technologies, like:
  • the use of linked reads such as 10X / Chromium to improve structural variation detection,
  • single-cell technologies to study tumour evolution,
  • long-read technologies to investigate tumour samples without a clear driver event,
  • technologies like BioGraph and PetaGene to improve data storage efficiency,
  • investigate new methods to work on liquid biopsy sequencing data;
  • take part in oncology genomics research, and help to manage experiments and prepare publications.

Candidate requirements:

• strong knowledge of Unix/Linux ecosystem and command line tools,
• human NGS data analysis experience (DNA, RNA), understanding of common methods, tools, and databases for processing and interpretation,
• understanding of a cluster computing, and of Amazon storage and computing systems,
• strong Python experience,
• basic knowledge of molecular biology, genomics and clinical genetics,
• good English (will need to participate in several weekly meetings).

Work with us:

• full day, but working hours are flexible;
• office at the Vasilievsky Island, 5 minutes from a subway station;
• opportunity to participate in international conferences;
• publications major bioinformatics journals with our support.

If you are passionate about open source software development and establishing genomics platforms to change cancer patient care, you should apply. Your responsibilities are flexible and depend on both your interests and expertise. In case you are worried about specific job requirements, do talk to us - your interest and motivation are way more important than ticking all the boxes of a given job description.

Contacts

a.lapidus@spbu.ru