Open Positions at Genestack Limited

 

We are looking for people who want to take part in the genomics revolution to join our team. Please send a covering letter and a CV to jobs@genestack.com. We welcome applicants with strong backgrounds, even if your experience does not match our requirements exactly!

Bioinformatics scientistCambridge, UK

Who are we?

Genestack is a collaborative platform for large-scale genomics data management and analysis, used by biologists and bioinformaticians from pharma, academia and biotech industries.

 

Our mission is to step up the pace of bioinformatics. We are tackling the underlying computational and scientific challenges of the field in order to provide researchers with tools that will streamline the discovery process, taking them swiftly from raw data to meaningful biological results.

 

The job

We’re looking for a brilliant bioinformatics scientist to join our Bioinformatics R&D team. The position will be full-time and based in our brand new office in central Cambridge.

 

Some of the things that you’d be doing:

  • investigating methods and tools at the forefront of bioinformatics research to solve   concrete scientific challenges encountered on a daily basis in our projects
  • analysing and exploring complex large-scale genomics datasets using the Genestack platform to answer practical biological questions
  • working closely with our highly talented software engineering team to embed bioinformatics pipelines into robust applications for the Genestack platform
  • implementing algorithms and building applications prototypes on the platform

 

We’re looking for candidates with the following skillset:

  • 3+ years of experience in bioinformatics data analysis: knowledge of data types, pipelines, databases, and typical challenges/caveats associated with bioinformatics analysis
  • Scripting proficiency with Python and/or R, including data analysis libraries (e.g. Bioconductor, pandas, numpy, etc.)
  • Proficiency with the UNIX command-line
  • Good knowledge of statistics
  • Being passionate about finding a rigorous way of investigating an ill-defined biological question
  • Ability to report scientific findings

 

What we offer:

  • competitive salary
  • flexible working hours
  • relaxed working environment
  • loads of independence

UI DeveloperCambridge, UK or St. Petersburg, Russia

Genestack is a genomics platform which is used by biologists to research, store, organize and process data. We have offices in St. Petersburg (Russia) and Cambridge (UK). We have 16 people in our team.

Our front end is in HTML, CSS (Bootstrap), JavaScript (with emphasis on jQuery). Our back end is written in Java.

We’re searching for a UI developer in St. Petersburg or Cambridge. They will:

  • conceive, code and maintain bioinformatical and administrative UIs;
  • improve our development environment.

We solve hard problems within short iterations and immovable deadlines. This is why we want a strong front end specialist.

Our candidate is a Javascript expert. The following is required:

  • fundamental JS knowledge;
  • intimate knowledge of DOM APIs;
  • expertise in jQuery;
  • understanding of OOP and FP principles, and of MVC approach;
  • ability to create UI components and build UIs with them;
  • experience with unit testing;
  • experience with modern JS tooling;
  • interest in new JS trends: React, Angular 2, Webpack, etc.
  • basic knowledge of node.js.

Our candidate is also a CSS expert. The following is required:

  • CSS fundamentals knowledge;
  • CSS3 experience (incl. flexbox);
  • proficiency with browser devtools.

Canvas and d3 experience are also very appreciated.

Some knowledge of Java is a plus.

Our UI developers design the UIs themselves. They should have some fundamental knowledge about UI design and a portfolio. We expect our candidates to have read or have knowledge of the works of Norman, Cooper, Tufte or Raskin.

We’re searching for a responsible and experienced developer, who is able to work on their own, without a manager (we don’t have any).

Contact us at cv@genestack.com with a CV and link to portfolio.

Bioinformatics Software DeveloperCambridge, UK

Responsibilities:
  • Writing new and improving existing distributed computing analysis pipelines for large scale genomic sequencing data on- and off- the cloud
  • Developing data visualisation applications to help users interact with and extract valuable biological/clinical findings from multi-terabyte datasets
  • Working closely with our clinical, pharma, agri-tech and other customers to build apps that solve real-life complex biological data challenges and advance biomedical R&D across life sciences
Necessary Skills:
  • Knowledge of Java, Python, R or other modern programming languages
  • Experience with web-development: JavaScript and HTML/CSS
  • Ability to code for both the computational backend and web-based frontend
  • An interest in working with large-scale biological data and applications
Good to haves:
  • Any previous applied bioinformatics work especially with NGS and/or microarray data
  • Experience working with big data: orchestrating large-scale computations on the cloud, building interactive visualisations of large datasets
  • Aptitude for building good looking modern UIs, awareness of current trends in web technologies

Internship projectsCambridge, UK or St.Petersburg, Russia

Here we have selected three collaborative projects that we think would be best suited for internships. However, Genestack is evolving very rapidly and is flexible to accommodate new project ideas. So, please reach out to us, if you’d like to discuss about our alternative/ upcoming projects, or should you like to propose your own project idea.

 

Project 1: Fighting Lung Microbial Infections in Cystic Fibrosis Patients

Aim: To develop a rapid sequence-to-report NGS system for microbial pathogen detection.

 

Cystic fibrosis is a genetic disorder which makes people prone to frequent lung infections by pathogens such as Aspergillus fumigatus. These infections can be quite severe and often require hospitalization. The patients must be treated with antibiotics and monitored closely.

 

In order to accurately identify and quantify the pathogens that are present in a patient’s lungs, we are building a pipeline in collaboration with a major UK NHS hospital and a global hardware manufacturer to analyse microbiome sequencing data derived from sputum samples of cystic fibrosis patients.

 

As an intern, you will take part in the development of a cloud-based Genestack application to produce interactive microbiome analysis reports for clinicians and researchers. You will also be involved in the design and validation of the bioinformatics pipeline, using published microbiome datasets as well as clinical data provided by our collaborators. You will have access to a custom-built supercomputer co-designed with Intel for this project in order to test and run the bioinformatics pipeline.

 

Project 2: NGS-based Assay to Monitor Allogeneic Bone Marrow Transplantation Success

Aim: To develop a complete NGS-based data analysis and clinical reporting system to assess donor cell engraftment after allogeneic stem-cell transplantation.

 

We are working with a department at the University of Cambridge set up recently to translate cutting edge genomics methods for advanced diagnosis and clinical management of cancer. Together we aim to improve assays for the monitoring and clinical reporting of patients after allogeneic bone marrow transplantation.

 

Chimerism analysis is the process of determining the cells’ origins of the post-transplant recipient. Discrimination of donor- or recipient-derived haematopoiesis allows evaluation of the engraftment success or rejection, which can serve as a prognostic indicator of relapse. PCR amplification of STRs and SNP-specific q-PCR have been the techniques of choice for this task, but each has its own limitations. In this project, we will develop and evaluate a promising emerging, more advanced NGS-based strategy for chimerism analysis.

 

You will help to develop new, and improve existing, cloud-based Genestack applications to produce a comprehensive, easy to understand chimerism report, aimed at researchers and clinicians. You will work alongside researchers and clinicians to improve upon the current chimerism analysis methodology, and to streamline the process from sample collection to clinical reporting via the Genestack platform.

 

Project 3: Genomics-based Crop Analysis Using Multi-omics Gene-Trait Networks

Aims: (1) To integrate multi-omics data and literature mining for constructing plant genome-scale knowledge network. (2) To develop query/visualisation features for interrogating the knowledge network and finding candidate genes and QTL associated with phenotypes.

 

Genestack is working on an Innovate UK funded collaborative project with Rothamsted Research, a major UK agri-genomics research centre and the longest running agricultural research station in the world. Over the past ten years Rothamsted Research has been developing techniques to integrate multi-omics data and literature mining for gene networks analysis. These techniques are necessary to mine the wealth of public domain data to link traits to gene function and ultimately to understand complex crop traits and improve their yields, nutritional quality, as well as tolerance against diseases or drought. However, these tools can be difficult to set up and maintain for many users, especially in the industry. Combining public and proprietary datasets for building extended knowledge bases is particularly challenging. To overcome such challenges, Genestack and Rothamsted have started to work closely on making these unique tools available on Genestack’s bioinformatics platform.

 

Rothamsted’s tools can combine public databases with custom multi-omics datasets, including homology, QTL databases, as well as pathways and hormone annotations for identifying key candidate genes in silico. Users can search for trait descriptions, refined by lists of QTLs or differently expressed genes. The results include lists of genes prioritised based on different types of evidence. All the discoveries can be explored using powerful network analytics and visualisations.

 

In this project, you will assist our effort of integrating these tools into the Genestack platform: streamlining the process of building genome-scale knowledge networks and improving upon the current network-based visual analytics. You will work with researchers at Rothamsted, and selected industry participants who will help steer the project by contributing specific requirements and needs.

 

Requirements:

For all projects listed some scripting ability is required (Python and/or R, primarily). Our internships come with a monthly stipend, and with a possibility to join the company at the end of a successful internship.

Senior Java DeveloperCambridge, UK or St.Petersburg, Russia

Genestack is a bioinformatics platform where biologists store, process and research genomic data.

We are looking for a programmer who can find elegant solutions and get things done in time.

We follow agile practices and work in small iterations. We expect our candidate to be able to split a large task into a number of smaller steps, each one having a measurable or visible result.

Tasks include, but are not limited to: development and support of the system core, API and platform applications, data storage optimization, and cluster process management (Amazon, etc).

Requirements:

  • Strong Java skills
  • Good knowledge of CS
  • Knowledge of basic principles of OOP, data structures and algorithms
  • Capability to work independently at all stages from planning to production code
  • Knowledge of code optimization, profiling, and testing
  • Ability to read other people’s code and refactoring experience
  • Experience in web application development
  • Intermediate level of English
  • Interest in working with biological applications and data

Nice to haves:

  • Experience with big data
  • Knowledge of biology and genetics
  • Python, R
  • Experience with Unix-like systems
  • Experience with JS/HTML/CSS

We offer:

  • competitive salary
  • flexible working hours
  • all the things you find in a startup: interesting problems, stimulating environment, loads of independence 

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