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Position: Bioinformatician
Institution: Karolinska Institutet
Department: Oncology-Pathology
Location: Solna, Stockholm, Sweden
Duties: Within our research group and associated/collaborating teams most aspects of breast cancer research are covered including basic tumor biology, pathology, bioinformatics and clinical trials.Your main tasks will be to develop and setup analytical pipelines for NGS-data with focus on genomics (WGS, WES and targeted sequencing) but also on transcriptomic (RNA-seq) data and their integration. You will be working with several highly unique clinical cohorts such as longitudinal primary tumor-metastatic samples and therapy-resistant versus therapy-naive tumors. The position will involve applying advanced bioinformatics and statistical methods for analysis and interpretation of large datasets and high-dimensional genomic and transcriptomic data
Requirements: PhD (or MSc with 3+ years of related experience) in computer science, bioinformatics or similar with emphasize on genomic data analysis. Strong background in large-scale NGS data analysis using tools such as GATK, VarScan, MuTect, Cufflinks, Kallisto etc. Programming skills in statistical software environments, preferably in R and/or Python. Should be well-versed in visualizing high-dimensional data, for instance, using packages such as ggplot2, matplotlib etc. Working experience in UNIX/Linux environment and bash scripting, for instance, for automating large-scale analyses. Experience in public bioinformatics databases (UCSC, Ensembl etc) and associated analytical pipelines. Experience in biostatistics
   
Text: Login and apply English Swedish Norwegian Danish Finnish German Norwegian (nynorsk) Dutch Chinese (BETA) Polish Bioinformatician Login and apply Karolinska Institutet, Dept of Oncology-Pathology, Research group Bergh 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. The research group Professor Jonas Bergh´s research group is performing leading breast cancer research of highest scientific level. Within the research group and associated/collaborating teams most aspects of breast cancer research are covered including basic tumor biology, pathology, bioinformatics and clinical trials. The research group has access to a well-characterized comprehensive tumor biobank as well as several clinical study cohorts. Many projects are run as multidisciplinary, global collaborations. Duties Your main tasks will be to develop and setup analytical pipelines for NGS-data with focus on genomics (WGS, WES and targeted sequencing) but also on transcriptomic (RNA-seq) data and their integration. You will be working with several highly unique clinical cohorts such as longitudinal primary tumor-metastatic samples and therapy-resistant versus therapy-naive tumors. The position will involve applying advanced bioinformatics and statistical methods for analysis and interpretation of large datasets and high-dimensional genomic and transcriptomic data. You will be reporting directly to the PI and/or the associated project leader. Qualifications Absolute Requirements PhD (or MSc with 3 years of related experience) in computer science, bioinformatics or similar with emphasize on genomic data analysis. Strong background in large-scale NGS data analysis using tools such as GATK, VarScan, MuTect, Cufflinks, Kallisto etc. Programming skills in statistical software environments, preferably in R and/or Python. Should be well-versed in visualizing high-dimensional data, for instance, using packages such as ggplot2, matplotlib etc. Working experience in UNIX/Linux environment and bash scripting, for instance, for automating large-scale analyses. Experience in public bioinformatics databases (UCSC, Ensembl etc) and associated analytical pipelines. A successful candidate should possess excellent interpersonal communication skills (written and verbal English), have the motivation to work in multidisciplinary teams and should be willing to work on multiple projects in parallel. Experience in biostatistics. Excellent documentation skills. Preferred Requirements Experience in NGS data pipelines and related packages in Bioconductor Experience in integration of genomic and transcriptomic data Experience in cancer-related databases such as TCGA, COSMIC, dbSNP etc. Experience in precision cancer medicine and drug response profiling will be big plus Experience in cancer genomics, especially related to breast cancer, will be very valuable Experience in high-performance computing (cluster computing, parallelization, etc). General knowledge in molecular biology and breast cancer research Form of employment This is a fixed term employment for 6 month, with possibility of extension for 18 month. Application process The application is to be submitted on the MyNetwork recruitment system. Karolinska Institutet is one of the world’s leading medical universities. Its vision is to significantly contribute to the improvement of human health. Karolinska Institutet accounts for the single largest share of all academic medical research conducted in Sweden and offers the country’s broadest range of education in medicine and health sciences. The Nobel Assembly at Karolinska Institutet selects the Nobel laureates in Physiology or Medicine. Pursuant to the regulations of the Swedish National Archives, applications are kept on file for two years after the appointment has gained legal force. The regulations do not apply to attachments that have been printed or otherwise published. Karolinska Institutet strives to provide a workplace that has approximately the same number of women and men, is free of discrimination and offers equal opportunity to everyone. For temp agencies and recruiters, and to salespersons: We politely, yet firmly, decline direct contact with temp agencies and recruiters, as well as those selling additional job announcements. Type of employment Temporary position 3-6 months Contract type Full time First day of employment According to agreement Salary Månadslön City Solna County Stockholms län Country Sweden Reference number 2-770/2018 Contact Johan Hartman, 073 976 02 42, johan.hartman@ki.se Union representative Mimmi Shoshan, SACO, 46 8 517 754 60 Andreas Lundqvist, SACO, 46 8 517 768 84, andreas.lundqvist@ki.se Helen Eriksson, OFR, 46 8 517 762 79 Published 06.Feb.2018 Last application date 13.Mar.2018 11:59 PM CET Share links Login and apply Return to job vacancies Karolinska Institutet is using Varbi recruitment system in the recruitment process. COOKIES × Modal title
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