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The Wellcome Trust Sanger Institute
  • Cambridge, UK




Salary range: £36,000-£44,000 per annum depending on experience plus excellent benefits. Fixed Term Contract for 3 Years.

Open Targets has recently launched Open Targets Genetics (https://genetics.opentargets.org), a portal that aggregates large scale GWAS data with functional genomics data to identify potential drug targets at disease-associated loci.

A Statistical Geneticist role funded by Open Targets, is available at the Wellcome Sanger Institute in a new team under the leadership of Dr. Maya Ghoussaini. This is an exciting opportunity for you to participate in the enhancement of the existing Open Targets Genetics Portal through de development of new functionality and features.

You will actively engage in the integration of new eQTL datasets and tissue-specific chromatin interaction datasets.

You will have the opportunity to work across a range of analysis such as:
  • Aggregate large scase GWAS data from multiple consortia and across a wide range of disease and traits.
  • Perform association analysis on UK Biobank data with a particular focus on therapeutic areas important for Open Targets
  • Work together with other members of the Open Targets team on statistical genetics analysis for large scale sequence analysis
  • Work with existing members of the team to integrate genetic and cell-specific genomic data to identify and validate causal links between targets and diseases and improve the Genetics Portal.


We welcome candidates with a background in statistical genetics or relevant discipline with advanced level of programming skills suitable for statistical genetic analyses of complex diseases. Experience in functional genomics data analysis is highly desirable. You will have the opportunity to interact with active computational and experimental research teams using cutting edge genomic techniques.

Essential Skills

  • PhD in Statistical Genetics, Computational Biology or a closely related discipline.
  • Advanced level programming skills suitable for statistical genetic analyses, such as R, Python, MATLAB.
  • Firm grounding in statistical methods of complex disease genetics such as genome wide association studies, fine-mapping, high-throughput expression data, whole exome/genome sequencing, PheWAS, Mendelian Randomisation.
  • Previous experience in working with large-scale genetic datasets.
  • Ability to work to tight timelines.
  • Demonstrable good project management and organisational skills.
  • Fluent in written and spoken English.
  • Ability to communicate ideas and results effectively.
  • Ability to work independently and organise own workload.


Ideal Skills

  • Experience in functional genomics data analysis (RNAseq, ChIPseq, etc);
  • Experience with generating reproducible bioinformatics pipelines;
  • A strong track record in preparing publications and other written materials;
  • Interest in target validation and translational research.


Other information



Open Targets is a pioneering public-private initiative between GlaxoSmithKline (GSK), Biogen, Takeda, Celgene, Sanofi, EMBL-EBI (European Bioinformatics Institute) and the WSI (Wellcome Sanger Institute), located on the Wellcome Genome Campus in Hinxton, near Cambridge, UK.

Open Targets aims to generate evidence on the biological validity of therapeutic targets and provide an initial assessment of the likely effectiveness of pharmacological intervention on these targets, using genome-scale experiments and analysis. Open Targets aims to provide an R&D framework that applies to all aspects of human disease, to improve the success rate for discovering new medicines and share its data openly in the interests of accelerating drug discovery.

Genome Research Limited is an Equal Opportunity employer. As part of our dedication to gender equality and promoting women's careers in science, we hold an Athena SWAN Bronze Award. We will consider all qualified applicants without discrimination on grounds of disability, sexual orientation, pregnancy or maternity leave status, race or national or ethnic origin, age, religion or belief, gender identity or re-assignment, marital or civil partnership status, protected veteran status (if applicable) or any other characteristic protected by law.

Please include a covering letter and CV with your application

Closing date: 28th February, however applications will be reviewed on an ongoing basis and therefore the post may be filled before the deadline.
Planet Pharma
  • San Diego, CA

SUMMARY

The Bioinformatics Scientist will be based at our client's R&D laboratory. This resource will work collaboratively with bench scientists to build tools, analyze sequence results, and integrate data. We are seeking a Bioinformatics Scientist who is passionate about making real differences in the field of molecular diagnostics and is enthusiastic about working in an exciting startup environment. This position requires a person with a strong commitment to science and technology and with demonstrated knowledge in genomics, bioinformatics, statistics, and programming. The candidate should be energetic, open-minded, detail-oriented and results driven.


Primary Job Responsibilities:

  • Implement analysis workflows for the identification and interpretation of actionable cancer somatic mutations from different types of tumor and normal tissue samples of cancer patients.
  • Data analysis projects involving the results from large cohorts of patients involved in clinical trials.
  • Select, test, and implement bioinformatics pipelines for the analysis, annotation, and interpretation of cancer genomic data
  • Perform analysis of aggregated results from patient cohorts, applying the appropriate multivariate statistical analysis, machine learning, and visualization methods
  • Mine sequencing data and provide feedback to R&D team.
  • Present results of analyses to internal stakeholders and customers/collaborators
  • Implement quality control metrics and procedures to prevent and detect errors
  • Insure that all work is properly documented, code is under change control, and provenance of data is maintained
  • Work closely with IT specialists to build and maintain robust infrastructure


REQUIREMENTS

  • PhD/MSc in bioinformatics, computer science, applied mathematics/physics, genetics, and/or quantitative biological sciences.
  • 3-5 year expertise in computational biology and bioinformatics focused on NGS applications including genome variation, cancer genomics, transcriptomics, etc.
  • In-depth knowledge of NGS genomic data analysis and bioinformatics tools (BWA, SamTools, GATK, FreeBayes, MuTect, VarScan etc.) and current data formats (e.g. VCF, BAM/SAM).
  • Scripting or programming expertise for bioinformatics (Perl/Python, Java, C/C++) is a must.
  • Versed in the inner workings and limitations of modern high-throughput sequencing platforms (Illumina, Ion Torrent).
  • Proven ability to develop data analysis methods & algorithms, use of common machine learning tools (e.g. SciKit, Weka), and proficiency in the use of common statistical analysis tools (e.g. R, MatLab) is highly desirable.
  • Ability to quantify accuracy and performance of algorithms/tools/pipelines with respect to metrics, datasets, and the literature.
  • UNIX environment expertise including clustering and parallelization of analysis jobs is necessary.
  • Experience with cloud computing environments (e.g. AWS, Google), distributed computing tools (StartCluster, Hadoop, Spark), and containerization (e.g. Docker) is highly desirable.
  • Exposure to public data sources, such as TCGA, CCLE, Ensembl, GTEx, Achilles, etc.
  • Prior industry experience as well as record of developing clinical pipelines is desirable.
  • Track record of successful interactions with bench biologists, a scientific publication record, and excellent communication skills are pluses.
  • Ability to prioritize and deliver research in a fast-paced, milestone-driven environment.
  • Strong work ethic, emphasizing both efficiency and quality of work.
  • Publication of original scientific work in relevant journals.
European Bioinformatics Institute (EMBL-EBI)
  • Hinxton, UK
Metagenomics is a rapidly expanding field in which the depth and breadth of data are constantly increasing. Consequently, the number of published research articles associated with the field is growing, but much of the information found in these articles is not associated with the sequence data and/or key biological traits are missed due to the complex nature of the data.

The overall goal of the EMERALD project is to use machine learning to make metagenomics datasets more reusable, and then perform analyses on these data to discover and identify novel secondary metabolite biosynthetic gene clusters (SMGCs). The project will develop methods to identify potentially missing information about sample metadata by comparing to other datasets and/or information gained from text mining (provided by the project partner).

These enriched metadata fields will be used to help enrich our biome classifications and to identify potentially mislabelled datasets. The results will be integrated into the MGnify database, making them more accessible to the wider user community. In the second element of this project, we will work collaboratively with the Literature Service team (whom will search for evidence in research papers for information on novel SMGCs), and use machine learning approaches to aid the identification of both known and novel SMGC in metagenomics datasets.

Your role


We are seeking to recruit a machine learning data scientist who will develop and apply cutting edge machine learning algorithms for the EMERALD (Enriching MEtagenomics Results using Artificial intelligence and Literature Data) project. This position will be located within the Sequence Families Team that is responsible for the MGnify metagenomics resource at the European Bioinformatics Institute (EMBL-EBI). This post holder will work in close collaboration with the Literature Services Team, also based at the EMBL-EBI, whom are also project partners.

Key Roles/Duties:

  • Scientific requirements gathering

  • Evaluating different machine learning frameworks/technologies for different analysis problems

  • Developing and benchmarking prototype mining algorithms for the classification of samples and discovery of SMGCs

  • Work with project partners across EMBL-EBI, other EMBL-EBI teams, and other grant collaborators

  • Identify potentially mislabelled datasets, which may involve verification from literature and/or data producers

  • Integrate data from project partners to enhance machine learning classifiers

  • Develop tools and run periodic updates to MGnify production databases

  • Interface with potential users of the developed tool

  • Writing reports and publications, giving presentations, as required



You have


Higher degree, preferably PhD, in a the area of life sciences and/or text mining and machine learning.

The ideal candidate will have experience working within a bioinformatics environment for at least 3 years as a post-doctoral fellow (or equivalent experience).



  • Strong scripting skills in Python, although other languages would be considered for the right candidate

  • Experience using different machine learning frameworks, the data that they are most appropriately applied to and their limitations

  • Approaches and development of benchmark datasets

  • Knowledge of metagenomics approaches, both taxonomic and functional analyses

  • Ability to work with different data types produced within MGnify (e.g. FASTA, Biome, XML, JSON)

  • Agile development methodologies and version control with Git/GitHub

  • Unix/Linux proficiency



The candidate will need to be able to work independently, as well as interact with the rest of the development team. Flexible approach and ability to take on new skills. Good communication skills and attention to detail are essential, as is the ability to work to deadlines.

Excellent English, written and oral.

You might also have




  • Relational database querying and basic schema design (e.g. MySQL, Postgresql)

  • Knowledge of secondary metabolite gene clusters

  • Experience of knowledge of other software for gene cluster identification (e.g. AntiSMASH, ClusterFinder)

  • Experience writing scientific papers



Why join us


At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 22 member states and two associate member states. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation. For more information about pay and benefits click here

We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.

If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.

What else do I need to know


For a complete Job Description click here

To apply please submit a covering letter and CV through our online system.

Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. Visa information will be discussed in more depth with applicants selected for interview.

EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.

This position is limited to the grant duration specified.

Applications will close at 23:00 GMT on the date listed above.
The Wellcome Trust Sanger Institute
  • Cambridge, UK




Salary range: £36,000-£44,000 per annum depending on experience plus excellent benefits. Fixed Term Contract for 3 Years.

Open Targets has recently launched Open Targets Genetics (https://genetics.opentargets.org), a portal that aggregates large scale GWAS data with functional genomics data to identify potential drug targets at disease-associated loci.

A Statistical Geneticist role funded by Open Targets, is available at the Wellcome Sanger Institute in a new team under the leadership of Dr. Maya Ghoussaini. This is an exciting opportunity for you to participate in the enhancement of the existing Open Targets Genetics Portal through de development of new functionality and features.

You will actively engage in the integration of new eQTL datasets and tissue-specific chromatin interaction datasets.

You will have the opportunity to work across a range of analysis such as:
  • Aggregate large scase GWAS data from multiple consortia and across a wide range of disease and traits.
  • Perform association analysis on UK Biobank data with a particular focus on therapeutic areas important for Open Targets
  • Work together with other members of the Open Targets team on statistical genetics analysis for large scale sequence analysis
  • Work with existing members of the team to integrate genetic and cell-specific genomic data to identify and validate causal links between targets and diseases and improve the Genetics Portal.


We welcome candidates with a background in statistical genetics or relevant discipline with advanced level of programming skills suitable for statistical genetic analyses of complex diseases. Experience in functional genomics data analysis is highly desirable. You will have the opportunity to interact with active computational and experimental research teams using cutting edge genomic techniques.

Essential Skills

  • PhD in Statistical Genetics, Computational Biology or a closely related discipline.
  • Advanced level programming skills suitable for statistical genetic analyses, such as R, Python, MATLAB.
  • Firm grounding in statistical methods of complex disease genetics such as genome wide association studies, fine-mapping, high-throughput expression data, whole exome/genome sequencing, PheWAS, Mendelian Randomisation.
  • Previous experience in working with large-scale genetic datasets.
  • Ability to work to tight timelines.
  • Demonstrable good project management and organisational skills.
  • Fluent in written and spoken English.
  • Ability to communicate ideas and results effectively.
  • Ability to work independently and organise own workload.


Ideal Skills

  • Experience in functional genomics data analysis (RNAseq, ChIPseq, etc);
  • Experience with generating reproducible bioinformatics pipelines;
  • A strong track record in preparing publications and other written materials;
  • Interest in target validation and translational research.


Other information



Open Targets is a pioneering public-private initiative between GlaxoSmithKline (GSK), Biogen, Takeda, Celgene, Sanofi, EMBL-EBI (European Bioinformatics Institute) and the WSI (Wellcome Sanger Institute), located on the Wellcome Genome Campus in Hinxton, near Cambridge, UK.

Open Targets aims to generate evidence on the biological validity of therapeutic targets and provide an initial assessment of the likely effectiveness of pharmacological intervention on these targets, using genome-scale experiments and analysis. Open Targets aims to provide an R&D framework that applies to all aspects of human disease, to improve the success rate for discovering new medicines and share its data openly in the interests of accelerating drug discovery.

Genome Research Limited is an Equal Opportunity employer. As part of our dedication to gender equality and promoting women's careers in science, we hold an Athena SWAN Bronze Award. We will consider all qualified applicants without discrimination on grounds of disability, sexual orientation, pregnancy or maternity leave status, race or national or ethnic origin, age, religion or belief, gender identity or re-assignment, marital or civil partnership status, protected veteran status (if applicable) or any other characteristic protected by law.

Please include a covering letter and CV with your application

Closing date: 28th February, however applications will be reviewed on an ongoing basis and therefore the post may be filled before the deadline.
European Bioinformatics Institute (EMBL-EBI)
  • Hinxton, UK
Are you an experienced software developer with good working knowledge of fundamental algorithms and data structures? The Iqbal research group at the European Bioinformatics Institute (EMBL-EBI) is looking for a programmer to join their growing team, and play a vital role in developing software used to analyse the DNA of pathogens underlying global health threats such as TB and malaria.

Many problems in the analysis of DNA can be cast as algorithms on strings or graphs. Localised differences in DNA can cause bacterial and parasite strains to differ in medically and biologically important ways - for example being resistant to an antibiotic or being able to infect humans. Detecting and classifying these differences (either between genomes or between noisy experimental subsamples of genomes) can be translated into string and graph problems. The Iqbal group develops such methods. Their work ranges from development of novel algorithms and data structures, to concrete implementations translating research ideas into clinical practise. For example their Mykrobe predictor software has been integrated into Public Health England’s tuberculosis pipeline, and we are now collaborating with people using it in India, Vietnam and Madagascar. Dr Iqbal spent 8 years in the software industry after his PhD, working in development and software management in embedded operating systems for mobile device and network drivers, before returning to academia. The rest of the group have degrees in maths, physics and biology.


Your role


As a Scientific Software Developer, you would lead the development and maintenance of key scientific software developed by the Iqbal group. One important area of work is the further development of gramtools, a software suite for analysing genome sequence data based on a modified Burrows Wheeler transform. Another is co-development of pandora, which does similar things for new nanopore data applied to bacteria. Currently there are two PhD students doing active development, and that is about to increase to three.

Your specific goals and tasks would include:

  • Develop, implement and maintain advanced algorithms and data structures, in particular in gramtools and pandora , but also in other applications related to genome graphs and succinct data structures.

  • Collaborate closely with other team members who are developing modifications of and tools based on gramtools, pandora and/or other graph genome software.

  • Apply these software to empirical datasets, profile, evaluate performance and update design, implementation and/or algorithms as appropriate.

  • Provide training and support for other team members as they improve their software skills



Key people to work with are PhD students who are innovating, prototyping and developing algorithms based on existing libraries, which then often need to be re implemented or refactored into a library that can be widely used

Key challenges:

  • Understanding novel algorithms and data structures

  • Learning about alternative approaches from the literature and comparing them with our approaches

  • Learning (on the job) enough of the science to understand the software requirements

  • Adjusting to changing requirements as properties of novel structures or algorithms are only learned about during development.



You have


We are looking for a person who has the right skill set and is happy collaborating on a range of projects. Our new Scientific Software Developer should have:

  • Experience in developing software

  • Proficiency in C and/or C++ (preference for C++ given existing code base)

  • Experience with studying advanced data structures and algorithms, both on paper/pseudocode, and in implementation

  • Experience with code profiling tools, code correctness tools, version control.

  • Competence with Linux

  • At least some experience with Python

  • Excellent communication skills - essential to effective collaboration within the team and users of our software

  • A degree in some quantitative subject



You might also have




  • Proficiency with Python

  • Experience with numerical or statistical algorithms

  • Experience of working in a scientific setting



Why join us


This is a really exciting opportunity to work on novel data structures and algorithms in a context which can have both scientific and medical impact. We develop these methods for the use of the bioinformatics community, and for our own projects (for example studying 100,000 TB genomes, or malaria parasites from around the world). We are also closely involved in analysing data from the new Oxford Nanopore sequencing machines. So there is a huge array of exciting problems. We are a friendly group, with a range of backgrounds, and a real ethos of helping each other. At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 22 member states and two associate member states. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation. For more information about pay and benefits click here

We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.

If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.

What else do I need to know


Useful links:

The initial contract is for a period of three years with the possibility of a fixed-term extension. To apply please submit a covering letter and CV through our online system.

Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. Visa information will be discussed in more depth with applicants selected for interview.

EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.

Applications will close at 23:00 BST on the date listed above.
The Wellcome Trust Sanger Institute
  • Cambridge, UK




Salary range: £36,000-£44,000 per annum depending on experience plus excellent benefits. Fixed Term Contract for 3 Years.

Open Targets has recently launched Open Targets Genetics (https://genetics.opentargets.org), a portal that aggregates large scale GWAS data with functional genomics data to identify potential drug targets at disease-associated loci.

A Statistical Geneticist role funded by Open Targets, is available at the Wellcome Sanger Institute in a new team under the leadership of Dr. Maya Ghoussaini. This is an exciting opportunity for you to participate in the enhancement of the existing Open Targets Genetics Portal through de development of new functionality and features.

You will actively engage in the integration of new eQTL datasets and tissue-specific chromatin interaction datasets.

You will have the opportunity to work across a range of analysis such as:
  • Aggregate large scase GWAS data from multiple consortia and across a wide range of disease and traits.
  • Perform association analysis on UK Biobank data with a particular focus on therapeutic areas important for Open Targets
  • Work together with other members of the Open Targets team on statistical genetics analysis for large scale sequence analysis
  • Work with existing members of the team to integrate genetic and cell-specific genomic data to identify and validate causal links between targets and diseases and improve the Genetics Portal.


We welcome candidates with a background in statistical genetics or relevant discipline with advanced level of programming skills suitable for statistical genetic analyses of complex diseases. Experience in functional genomics data analysis is highly desirable. You will have the opportunity to interact with active computational and experimental research teams using cutting edge genomic techniques.

Essential Skills

  • PhD in Statistical Genetics, Computational Biology or a closely related discipline.
  • Advanced level programming skills suitable for statistical genetic analyses, such as R, Python, MATLAB.
  • Firm grounding in statistical methods of complex disease genetics such as genome wide association studies, fine-mapping, high-throughput expression data, whole exome/genome sequencing, PheWAS, Mendelian Randomisation.
  • Previous experience in working with large-scale genetic datasets.
  • Ability to work to tight timelines.
  • Demonstrable good project management and organisational skills.
  • Fluent in written and spoken English.
  • Ability to communicate ideas and results effectively.
  • Ability to work independently and organise own workload.


Ideal Skills

  • Experience in functional genomics data analysis (RNAseq, ChIPseq, etc);
  • Experience with generating reproducible bioinformatics pipelines;
  • A strong track record in preparing publications and other written materials;
  • Interest in target validation and translational research.


Other information



Open Targets is a pioneering public-private initiative between GlaxoSmithKline (GSK), Biogen, Takeda, Celgene, Sanofi, EMBL-EBI (European Bioinformatics Institute) and the WSI (Wellcome Sanger Institute), located on the Wellcome Genome Campus in Hinxton, near Cambridge, UK.

Open Targets aims to generate evidence on the biological validity of therapeutic targets and provide an initial assessment of the likely effectiveness of pharmacological intervention on these targets, using genome-scale experiments and analysis. Open Targets aims to provide an R&D framework that applies to all aspects of human disease, to improve the success rate for discovering new medicines and share its data openly in the interests of accelerating drug discovery.

Genome Research Limited is an Equal Opportunity employer. As part of our dedication to gender equality and promoting women's careers in science, we hold an Athena SWAN Bronze Award. We will consider all qualified applicants without discrimination on grounds of disability, sexual orientation, pregnancy or maternity leave status, race or national or ethnic origin, age, religion or belief, gender identity or re-assignment, marital or civil partnership status, protected veteran status (if applicable) or any other characteristic protected by law.

Please include a covering letter and CV with your application

Closing date: 28th February, however applications will be reviewed on an ongoing basis and therefore the post may be filled before the deadline.
European Bioinformatics Institute (EMBL-EBI)
  • Hinxton, UK
We are looking to appoint a highly motivated Senior Bioinformatician to develop processing pipelines and drive the development of visualisation tools for spatially-resolved single-cell genomics data.

Recent advances in the area of single cell genomics have facilitated the possibility of generating a
Human Cell Atlas(HCA), where cutting-edge molecular biology techniques can be used to refine our understanding of cell types within the human body, thereby building a platform for future transformative research in understanding tissue homeostasis and, ultimately, disease1-3.

The Marioni group is a world leader in computational biology, with a particular focus on developing methods for data generated using single cell genomics technologies4-8. Irene Papatheodorou’s team analyses expression data sets at tissue or single cell level and develops Expression Atlas, a resource that provides information about the expression of genes and proteins in different cells, tissues, developmental stages and conditions.

1. Young et al., Science, 2018.
2. Hagai et al., Nature (in press)
3. Gomes et al., BiorXiv, www.biorxiv.org/content/early/2017/11/22/217489
4. Haghverdi et al., Nature Biotechnology, 2018
5. Lun et al., Nature Methods, 2017
6. Vallejos et al., Nature Methods, 2017
7. Achim et al., Nature Biotechnology, 2015
8. Buettner et al., Nature Biotechnology, 2015

Your role


You will generate production-quality processing pipelines for single cell, spatial transcriptomics data and meta-data. Additionally, you will work together with software engineers to develop a user interface that will visualise the data where a cell’s location within a tissue as well as its molecular profile will be available. The interface will open the possibility of overlaying a cell’s molecular signature with its location in a tissue and will be made available through the single cell component of Expression Atlas the
Single Cell Expression Atlas in the first instance. The Single Cell Expression Atlas is EMBL-EBI’s portal for the Human Cell Atlas It will provide a robust infrastructure for visualising and analysing cells within a 3D environment and will be critical to the success of the Human Cell Atlas.

You will be based with the groups of John Marioni and Irene Papatheodorou at the EMBL-EBI and collaborate closely with the group of Sarah Teichmann at the Wellcome Sanger Institute.

You have


The successful candidate will:

  • Design and implement processing pipelines for spatial transcriptomics data and meta-data

  • Gather requirements from researchers working in the field of spatial transcriptomics to inform processing pipelines and visualisation tool development

  • Collaborating with other members of the team, web developers, bioinformaticians and curators to develop a complete data flow from raw data and meta-data to visualisation.

  • Collaborating with other EMBL-EBI resources, especially the HCA’s Data Ingest team

  • Collaborating with external partners, especially within the HCA

  • Contributing to publications describing data sets and processes.



Qualifications and Experience:

You should hold a PhD or higher degree in bioinformatics or computer science. Research experience in genomics would be highly desirable and experience working on spatial transcriptomics analysis is highly advantageous. You should have experience working in a Unix-based environment, good programming skills, excellent Unix shell scripting skills.

You might also have


Previous experience in working in a continuous deployment environment with source control and management of releases and in gene expression data analysis is highly desirable. Experience working in large scientific projects would be an advantage

Why join us


At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 22 member states and two associate member states and proud to be an equal-opportunity employer. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation.

We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.

If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library. For more information about pay and benefits click here.

What else do I need to know


This position is grant limited up to the project duration 31/06/2021. The Wellcome Strategic Support Science (WSSS) award aims to demonstrate the utility of a human cell atlas as a healthy reference and will focus on selected tissues, primarily of barrier and immune function. These will be profiled in adults as well as during human development, and in inflammatory disorders. A large team of scientists will be generating single cell as well as spatially resolved gene expression data. A key aspect of this grant is the integration of these two lines of work. The work proposed will create an unprecedented amount of high-quality, openly accessible data for deposition into the HCA Data Coordination Platform

Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. Visa information will be discussed in more depth with applicants selected for interview. To apply please submit a covering letter and CV, through our online system.

EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.

Applications will close at 23:00 BST on the date listed above.
European Bioinformatics Institute (EMBL-EBI)
  • Hinxton, UK
Are you an experienced software developer with good working knowledge of fundamental algorithms and data structures? The Iqbal research group at the European Bioinformatics Institute (EMBL-EBI) is looking for a programmer to join their growing team, and play a vital role in developing software used to analyse the DNA of pathogens underlying global health threats such as TB and malaria.

Many problems in the analysis of DNA can be cast as algorithms on strings or graphs. Localised differences in DNA can cause bacterial and parasite strains to differ in medically and biologically important ways - for example being resistant to an antibiotic or being able to infect humans. Detecting and classifying these differences (either between genomes or between noisy experimental subsamples of genomes) can be translated into string and graph problems. The Iqbal group develops such methods. Their work ranges from development of novel algorithms and data structures, to concrete implementations translating research ideas into clinical practise. For example their Mykrobe predictor software has been integrated into Public Health England’s tuberculosis pipeline, and we are now collaborating with people using it in India, Vietnam and Madagascar. Dr Iqbal spent 8 years in the software industry after his PhD, working in development and software management in embedded operating systems for mobile device and network drivers, before returning to academia. The rest of the group have degrees in maths, physics and biology.


Your role


As a Scientific Software Developer, you would lead the development and maintenance of key scientific software developed by the Iqbal group. One important area of work is the further development of gramtools, a software suite for analysing genome sequence data based on a modified Burrows Wheeler transform. Another is co-development of pandora, which does similar things for new nanopore data applied to bacteria. Currently there are two PhD students doing active development, and that is about to increase to three.

Your specific goals and tasks would include:

  • Develop, implement and maintain advanced algorithms and data structures, in particular in gramtools and pandora , but also in other applications related to genome graphs and succinct data structures.

  • Collaborate closely with other team members who are developing modifications of and tools based on gramtools, pandora and/or other graph genome software.

  • Apply these software to empirical datasets, profile, evaluate performance and update design, implementation and/or algorithms as appropriate.

  • Provide training and support for other team members as they improve their software skills


Key people to work with are PhD students who are innovating, prototyping and developing algorithms based on existing libraries, which then often need to be re implemented or refactored into a library that can be widely used

Key challenges:

  • Understanding novel algorithms and data structures

  • Learning about alternative approaches from the literature and comparing them with our approaches

  • Learning (on the job) enough of the science to understand the software requirements

  • Adjusting to changing requirements as properties of novel structures or algorithms are only learned about during development


You have


We are looking for a person who has the right skill set and is happy collaborating on a range of projects. Our new Scientific Software Developer should have:

  • Experience in developing software

  • Proficiency in C and/or C++ (preference for C++ given existing code base)

  • Experience with studying advanced data structures and algorithms, both on paper/pseudocode, and in implementation

  • Experience with code profiling tools, code correctness tools, version control.

  • Competence with Linux

  • At least some experience with Python

  • Excellent communication skills - essential to effective collaboration within the team and users of our software

  • A degree in some quantitative subject



You might also have




  • Proficiency with Python

  • Experience with numerical or statistical algorithms

  • Experience of working in a scientific setting


Why join us


This is a really exciting opportunity to work on novel data structures and algorithms in a context which can have both scientific and medical impact. We develop these methods for the use of the bioinformatics community, and for our own projects (for example studying 100,000 TB genomes, or malaria parasites from around the world). We are also closely involved in analysing data from the new Oxford Nanopore sequencing machines. So there is a huge array of exciting problems. We are a friendly group, with a range of backgrounds, and a real ethos of helping each other. At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 22 member states and two associate member states. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation. For more information about pay and benefits click here

We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.

If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.

What else do I need to know


Useful links:

To apply please submit a covering letter and CV through our online system.
Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. Visa information will be discussed in more depth with applicants selected for interview.

EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.

Applications will close at 23:00 BST on the date listed above.
The Wellcome Trust Sanger Institute
  • Cambridge, UK

Salary in the region of  £47,812 - £57,853 dependent on experience) plus excellent benefits


3 Years Contract


The Translational Cancer Genomics Group investigates how abnormalities in the DNA of cells contribute to cancer and impact on patient responses to therapy. This provides fundamental insights into disease mechanisms with implications for the development of improved therapies (https://www.sanger.ac.uk/science/groups/garnett-group). The lab is a mixture of wet-lab experimental and data scientists.


We are seeking to recruit a Principal Software Developer to facilitate the work of the group by supporting the computational analysis of next-generation sequencing datasets.  


The primary role will be to conduct the genetic analysis of hundreds of new cancer models being generated as part of the Human Cancer Model Initiative (https://www.sanger.ac.uk/science/collaboration/human-cancer-model-initiative-hcmi /https://ocg.cancer.gov/programs/HCMI). The candidate will ideally have experience in the analysis of next generations sequencing data (WGS, RNAseq), including calling of single nucleotide variants, detecting copy number alterations, analysis of mutational signatures and clonal dynamics, and analysis of gene expression data. The candidate should have experience in statistics as well as working with state-of-the-art algorithms. The candidate will also have the opportunity to integrate genomic datasets with results from systematic drug testing and genetic screens, and will support the work of students and postdocs in the laboratory.


The post-holder must be a team player and good communicator, and be able to understand the scientific background and technical detail of the team's projects. The candidate will be proficient at devising and implementing software solutions and statistical analyses. This role would suit somebody with significant previous bioinformatics experience and experience with next-generation sequencing data analysis. The successful candidate will work in conjunction with other computational biologists in the group and the wider Cancer Programme at the Sanger Institute.



Essential Skills

  •  Analysis of next-generation sequencing data 

  • Demonstrable record in biostatistics / bioinformatics 

  • Strong skills in the R programming language or equivalent 

  • Advanced degree (e.g. PhD) or equivalent research experience 

  • Demonstrable record of computational data analysis and/or software development 

  • Excellent communication skills (written and verbal) 

  • Proficiency in one or more scripting languages 

  • Ability to work independently and organise own workload 


Ideal Skills



  •  Familiar with working on the unix command line 

  • Knowledge of cancer genomics 

  • Experience of working with biological analysis pipelines on multi-node compute clusters 


Other information


The Wellcome Sanger Institute is a charitably funded research centre and committed to training the next generation of genome scientists. Focused on understanding the role of genetics in health and disease and a world leader in the genomic revolution, our mission is to use genome sequences to advance understanding of human and pathogen biology in order to improve human health. We aim to provide results that can be translated into diagnostics, treatments or therapies that reduce global health burdens. Our science is large-scale and organised into Programmes, led by our Faculty who conceive and deliver our science, and supported by our Scientific Operations teams responsible for all data production pipelines at the Institute.


Our Campus: Set over 125 acres, the stunning and dynamic Wellcome Genome Campus is the biggest aggregate concentration of people in the world working on the common theme of Genomes and BioData. It brings together a diverse and exceptional scientific community, committed to delivering life-changing science with the reach, scale and imagination to pursue some of humanity’s greatest challenges.


Our Benefits: Our employees have access to a comprehensive range of benefits and facilities including:



  • Group Defined Contribution Pension Scheme and Life Assurance

  • Group Income Protection

  • Private Health Insurance

  • 25 days annual leave, increasing by one day a year to a maximum of 30

  • Family friendly environment including options for flexible and part-time working, a childcare voucher scheme, Campus Nursery and Summer holiday club

  • Two days paid Employee Volunteering Leave a year

  • Employee Discount Scheme

  • Campus Gym, tennis courts, cricket pitch and sports hall plus a range of dining facilities

  • Active Campus Sports and Social Club

  • Free Campus Bus Service


Genome Research Limited is an Equal Opportunity employer. As part of our commitment to equality, diversity and inclusion and promoting equality in careers in science, we hold an Athena SWAN Bronze Award and have an active Equality, Diversity and Inclusion programme of activity. We will consider all applicants without discrimination on grounds of disability, sexual orientation, pregnancy or maternity leave status, race or national or ethnic origin, age, religion or belief, gender identity or re-assignment, marital or civil partnership status, protected veteran status (if applicable) or any other characteristic protected by law. We are open to a range of UK-based flexible working options including part-time or full-time employment as well as flexible hours due to caring or other commitments.


Please include a covering letter and CV with your application. Closing date: 30th November 2018 


Applications will be considered and reviewed on an on-going basis and therefore the post may be filled before the deadline.

Wellcome Trust Sanger Institute
  • Hinxton, UK
  • Salary: £38k - 58k

We are seeking to appoint a visionary computer architecture researcher to join our IT team in the role of Technical Innovator. This unique, exciting and forward-thinking role will be at the cutting-edge of technology, defining the future of our hardware and software pathways to shape our organisation and Campus.


The Sanger Institute is a world leader in bioinformatics research for the benefit of human health. Specifically, our scientific niche is in large-scale, high-throughput biology, often incorporating systematic genome-wide screens. These are enabled by major data generation platforms in DNA sequencing, cellular genetics and mouse genetics with an accompanying large IT platform supporting computational data analysis.


To support such a vibrant, wide-ranging and creative research community, the Sanger Institute has one of the world’s largest life science IT facilities. Our facilities currently provide research groups with HPC clusters that deliver more than 20,000 compute cores, 15 PB of high performance Lustre file systems and data repositories exceeding 16PB.


The recent addition of a Flexible Compute Environment, based on OpenStack and 100GB/s software defined networking, exceeds 6000 further CPU’s and provides 1PB of high performance object storage to our customers. This new environment provides exciting opportunities to our research community both for collaboration and to embrace otherwise disruptive technologies as they come to market.


Such flexibility is key to our being able to adapt to the rapidly developing requirements of our scientific environment. Remaining at the leading edge of technology will be key to our IT strategy over the forthcoming years.


We are therefore delighted to announce that we are looking for an enthusiastic individual to compliment our existing IT staff. This exciting role is to look 5+ years ahead to what may be possible, rather than technology that is available today. You will evaluate how it aligns with our developing scientific challenges and how we can further engage with our strategic commercial and scientific IT partners to develop the solutions that we will need in the future.


For such a blue-sky research position, you should possess a mixture of talents and qualifications, and will be able to demonstrate:



  • A strong and creative problem-solving mentality.

  • An open and enquiring approach to IT, its challenges and how to overcome them.

  • Highly self-motivated and with a will to share and disseminate information

  • An ability to present new ideas and opportunities to a wider audience of both highly technical and non-technical audiences

  • Provide contributions to wider audiences through peer review papers and conference presentations and posters.

  • The proven ability to rapidly learn and evaluate new methods and tools

  • Excellent written, verbal and numerical skills.

  • Forward and independent thinking!


We believe that this post would be ideally suited to someone with a high degree in a computation or mathematic or scientific background. Specific knowledge of cloud or HPC technologies is desirable but a deep understanding and the implementation of today’s IT technologies, such as machine learning and computation approaches is more important.


This is a fantastic opportunity to not just join a world leading genetics research institute but also to help shape its IT future!


Closing date: 12th November, 2018