Karolinska Institutet, Institutionen för onkologi-patologi, Forskargrupp Lehtiö
At the Department of Oncology-Pathology basic, translational and clinical research and educational activities related to cancer is carried out. Approximately 300 people from over 40 nations are currently working at the department. 37 research groups with various cancer research profiles are involved and we have around 120 PhD students. The Department of Oncology-Pathology is responsible for undergraduate courses in Pathology, Oncology and Forensic Medicine for medical students, as well as for Tumor biology courses for biomedicine students and Pathology courses for opticians.
Description of work place
The position will be placed in the Cancer proteomics Mass spectrometry research group at Science for Life Laboratory (SciLifeLab). The group is headed by Professor Janne Lehtiö, who is heading the group and a proteomics facility at KI and SciLifeLab. SciLifeLab is a collaboration effort between four universities in Stockholm and Uppsala: Stockholm University, Karolinska Institutet, Royal Institute of Technology (KTH) and Uppsala University. The center combines state-of-the-art equipment with a broad knowledge in translational medicine and molecular biosciences. From 2013 SciLifeLab have an assignment from the government to work as a national infrastructure and the vision is to make SciLifeLab a competitive center for high-throughput biosciences meant for research within health and environment. The Stockholm node of SciLifeLab is composed of a large number of groups, which formally belongs to a department at one of the three universities in Stockholm or are taking part through an industrial collaboration.
Description of research group/core facility
Lehtiö group is a translational group of scientists with a drive to improve human proteome analysis by developing new methods that can be applied to improve personalized cancer treatment. Our group includes researchers and staff from various disciplines working as a team to gain new knowledge. Our main focus is on cancer proteome analysis. Proteomics is a research field aiming to study proteins on a systems level by simultaneous analysis of thousands of proteins. We aim to gain new knowledge on proteins in the context of biological networks, to discover biomarkers and understand how genome changes impact the proteome level. In addition to the MS-data, we also generate genomic and transcriptomic data at SciLifeLab, which are used together with proteomics data to gain new knowledge on cancer. The research group is closely associated with the regional and national MS core facilities (SciLifeLab and BioMS), that provides fee-for-service sample analysis as well as support to plan and perform larger in-depth proteomics projects.
We now need to strengthen our group with a postdoc bioinformatician within the field of multi-omics data analysis and cancer research.
Area of responsibilities/duties
We are looking for an outstanding postdoc with focus on bioinformatics with experience from analysis of omics data. The position requires solid expertise in genomics, transcriptomics and/or proteomics data analysis and communication skills as well as willingness to team work. The current position offers a great possibility for cutting edge research combining proteomics and genomics data, together with an engaged group of scientists. You can contribute to science and medicine.
The postdoc will work on integrative and translational analysis of multiple levels of omics data derived from tumor specimens. The focus will be on applying 'omics' methods on biologically/clinically oriented research questions and to analyze the acquired data. The postdoc will take part in cancer omics based research, with a focus on the analysis and interpretation of complex in house generated and public domain data. This includes both to apply established data analysis steps as well as to investigate new strategies and solutions for the analysis of quantitative biological data. The postdoc will also take part in developing our proteogenomics analysis pipeline.
Experimental design, genomics/transcriptomics/proteomics pipeline development and statistical analysis of the quantitative data are important components of the work, and it is expected that the applicant is acquainted with software and programming languages related to omics data analysis.
Enabling omics datasets to a wide scientific audience is important. Building and maintaining databases and webpages that allows easy interrogation of data will be an important part of the work. Further, the postdoc is expected to engage in helping junior bioinformaticians and interact with researcher and staff in the group, contributing with her/his expertise in bioinformatics.
The employment is a 2 year position with possibility to further employment. We offer a very stimulating and diverse work in a team of very motivated co-workers.
Qualifications
- PhD in biology, medicine, bioinformatics, computer science or mathematical statistics.
- Documented experience in bioinformatics, including experience with for instance NGS, MS proteomics, drug sensitivity/resistance screens or analysis of data from other high-throughput / high-dimensionality generating methods.
- Working experience in systems biology/systems medicine, large-scale data analysis, integration and visualization.
- Programming experience in: Python and R
- Knowledge in statistical methods
- A understanding of cell- and molecular experimental methods.
- Excellent communications skills
- Fluent in English language
Other merits:
- Knowledge of cancer biology and current translational cancer research
- Experience in interdisciplinary interactions with scientists and clinicians
- Experience on building and handling interactive user friendly web-based visualization tools
- Experience in working in HPC environments
- Experience in applied Artificial Intelligence methods (GBM, DNN, SVM, etc, etc)
- Experience in network (i.e. Modularity/K-Core/Topology Analysis, Gephi Visualization), enrichment (i.e. GSEA, RankSum),
- The ability to interpret omics data in a biological context
- Basic skills in JavaScript, Shiny, HTML5, SQL, Perl, WebGL
- Basic Linux server sys admin
- Basic Joomla Site sys admin
Since the position involves close interaction with several researchers, emphasis is placed on personal skills such as:
- Very good collaborative and pedagogic skills
- Excellent communication skills and analytical skills
- Curious and eager to solve biological questions
Application procedure
The application should include:
- Application letter
- Curriculum vitae, qualifications and description of previous research/work
- Publication list (with three most relevant publications marked)
For more info and to apply please go to link
