Researcher in bioinformatics
Sort on published: 2017-11-01
Uppsala University is a comprehensive research-intensive university with a strong international standing. Our mission is to pursue top-quality research and education and to interact constructively with society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has 42,000 students, 7,000 employees and a turnover of SEK 6.7 billion.
The Department of Immunology, Genetics and Pathology at Uppsala University (http://www.igp.uu.se) has a broad research profile with several strong research groups focused on Genomics, Cancer and Molecular Diagnostics. Research is presently conducted in the following areas: Medical and Clinical Genetics, Immunology, Pathology, Tumor Biology and Vascular Biology. Parts of the organization are also integrated with the departments for Clinical Genetics, Immunology and Pathology-Cythology at Akademiska sjukhuset, Uppsala. The department provides a well-developed infrastructure for advanced molecular sciences, including access to front-line technology as well as core facilities for cell analyses, DNA sequencing and genotyping. The Department has a yearly turnover of around 340 million SEK with a staff of around 340 people, 120 of which are PhD-students.
As a bioinformatician in the group, you will be responsible for the informatics part of several projects. This means that you, together with other team members, will plan the project work, perform the data analysis using various tools. Opportunities will exist to develop your own methods of analysis or test new methods generated by others on various datasets. One of the responsibilities will be the analysis of data generated from Illumina/Affymetrix/Agilent array platforms, in conjunction with analyzes of genetic variation in translational cancer-oriented research projects. Second responsibility will include analyses of large-scale highly parallel DNA sequencing datasets (exomes and genomes) in the context of the same projects. The third main responsibility will include analyses of gene expression (from array and sequence data) as well as analyses of CpG methylome. The successful candidate should also have the ability to introduce other employees/students to bioinformatics and communicate well with the other members of the group; therefore good interpersonal skills will be highly valued.
The successful candidate should have a Ph.D. degree in bioinformatics. The successful candidate should also have a solid well documented background as a biologist/bioinformatician and a well demonstrated experience and publication track record in the field of bioinformatics. The candidate should be familiar with programmatic access to the most important online biological databases (biotools and webservices such as BioMart API and NCBI E-Utilities API) and have experience in primer design and primers/SNP searches. Previous experience with remote shell scripting (Uppmax) and usage of Circos-plots for visualizing genetic variation are additional merits. The candidate should also show the ability to introduce other employees/students to bioinformatics and communicate well with the other members of the group; therefore good interpersonal skills will be highly valued.
Documented experience in array-based platforms (Illumina SNP and CpG-methylome arrays), in particular oriented to the study of structural variation in human genome, is highly valued.
Previous experience with the Nexus copy number software is ideal.
Expertise in next-generation sequencing (NGS) genome analysis, quality controls and SNP mutations and copy number changes detection using NGS pipelines, free open-source software and/or self-implemented scripts is also extremely important.
- Analyzing DNA methylation data from Illumina’s beadchips or WGBS
- Feature selection and classification algorithms and methods for classifying samples according to a selected phenotype based on genetic and epigenetic markers
- Developing and applying machine learning methods and applications to analyze DNA methylation data in order to discover biomarkers of ageing, cancer and other disease.
- Developing visual-based analytical software for investigating DNA methylation and gene expression data in selected gene pathways.
- Unsupervised learning methods for finding cancer subtypes based on DNA methylation and/or genetic markers.
Application: The application should contain an application letter with the motivation to join the group, curriculum vitae and list of scientific publications of the candidate. The name and contact details of the PhD supervisor should also be included.
Pay: According to individual qualifications
Type of employment: general temporary employment until 2019-08-13
Working hours: 100%
For more information about the position, please contact
Jan Dumanski,018-471 5035,firstname.lastname@example.org
You are welcome to apply no later than November 15, 2017. UFV-PA 2017/3547.
We decline offers of recruitment and advertising help. We only accept the application the way described in the advertisement.
Placement: Department of Immunology, Genetics and Pathology
Type of employment: Full time , Temporary position longer than 6 months
Pay: fixed pay
Number of positions: 1
Working hours: 100%
County: Uppsala län
Ellena Papaioannou, Seko
Per Sundman, Saco-rådet 018-471 1485
Suzanne Borén Andersson, TCO/ST 018-471 6251
Number of reference: UFV-PA 2017/3547
Last application date: 2017-11-15