NGS Research Engineer (updated)

в Center for Algorithmic Biotechnology
Город Санкт-Петербург, Russian Federation
Опубликовано 21.09.2017
Категория Биоинформатика
Тип вакансии Полная занятость
Адрес М. Василеостровская


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.

You will be working with a production bioinformatics team that supports large scale research through providing computational infrastructure, bringing and integrating new tools and algorithms, building software pipelines and web-based platforms, and helping researching do statistical analysis and interpretation.

Responsibilities of the candidate will include:

  • 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,
  • develop novel pipelines and tools when needed, and support internal users through them,
  • expose algorithms and results through visualizations and web based interfaces, either existing platforms or working with frameworks like Dash or Shiny.

A couple of examples of projects that you may deal with:

  • In a lab, as much as 10% of sequencing samples are usually mislabeled during one or another step, leading to incorrect downstream results. You will need to build a tool that will warn researchers about possible samples mix-ups. The work would include researching and testing existing methods, understanding the specifics of internal data, build a pipeline, make an interface, and teach the users through it.
  • In blood plasma cell-free DNA sequencing data, a huge amount of input ends up unmapped to a human genome. There is a hypothesis that this data may represent human microbiome harbouring important genes that may be associated with cancer development. Your task would be to make a research, identify and characterize unmapped data, present it to the researchers and get their input, and in case of the confirmed hypothesis, build a pipeline that will analyse and report unmapped data in plasma samples automatically as a part of the workflow.

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 possible directions of collaborations:

  • 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,
  • 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;
  • Python development experience,
  • passion to data visualization and presentation,  
  • understanding of HPC computing; experience with Amazon storage and computing systems is advantageous,
  • human NGS data analysis experience (DNA, RNA), understanding of common methods, tools, and databases for processing and interpretation;
  • basic knowledge of molecular biology, genomics and clinical genetics is welcomed,
  • good English (will need to participate in several weekly meetings).


Work with us:

  • full day, but working hours are flexible;
  • opportunity to participate in international conferences;
  • publications in major bioinformatics journals with our support.
  • office at the Vasilievsky Island, 5 minutes walk from the Vasileostrovskaya subway station along the pedestrian street full of cafes and restaurants,

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.