Lediga jobb Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology i Solna

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Research assistant

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Division
MTC is offering a research assitant position in the field of Bioinformatics to work in the group of Dr.

Vicente Pelechano. The group combines experimental and computational approaches to develop and apply novel genome-wide techniques to investigate eukaryotic transcription and gene [removed]Pelechano et al.Nature 2013, Chabbert et al. Mol. Syst. Biol. 2015, Pelechano et al. Cell 2015).

We are especially interested in understanding the regulatory mechanisms leading to the appearance of divergent gene expression programs in clonal cell population (http://pelechanolab.com/). Different cells in a population can present varying responses to the same stimulus. In some cases these differences are attributable to genetic mutations, such as the appearance of drug-resistant cells in bacterial and cancer populations. However, in other cases identical (clonal) cells can also display phenotypically heterogeneous responses. This non-genetic heterogeneity has a poorly understood origin but a significant impact on biology and human health. We combine the development of state-of-the art genome-wide approaches with the molecular dissection of fundamental biological problems.

Our lab is located in the newly established Science for Life Laboratory (SciLifeLab, http://www.scilifelab.se/) in the Karolinska Institute campus. SciLifeLab is equiped with state-of-the-art instrumentation and core facilities, and is home to the second largest sequencing cluster in Europe. SciLifeLab Stockholm is a joint effort between Karolinska Institute, the Swedish Royal Institute of Technology (KTH) and Stockholm University, and hosts research groups with diverse backgrounds and expertise, including basic biology, drug discovery, genomics, bioengineering, and translational medicine.

Duties
The available research assistant position concerns contributing to the development of computational approaches to study ribosome dynamics and RNA metabolism. The candidate will focus on the computational analysis of newly developed methods to study ribosome dynamics, mRNA degradation and tRNA processing (e.g. Pelechano et al. Cell 2015). The candidate will work together with PhD students and postdoctoral researchers in the lab and is expected to contribute his/her own ideas to the common goal of understanding how RNA biology and post-transcriptional regulation contributes to the appearance of differences across clonal populations of cells. The candidate will perform original research in genomics and computational biology, and acquire the required experimental and computational skills necessary for the completion of the project. The candidate will contribute to the implementation of analytical pipelines and integrate different kinds of genomic data to answer biologically relevant questions. The successful candidate will show scientific initiative and collaborate with other team members. The candidate is expected to communicate the scientific results by writing up scientific papers and attending scientific meetings. The ideal candidate is also expected to participate in the general duties of the team and to effectively communicate with scientists of very diverse backgrounds in a highly interdisciplinary and international environment.

Entry requirements
The successful applicant should be a positive, flexible person with good communication skills and abilities to collaborate and work in a highly dynamic international research team. The candidate needs to be able to work both in a team as well as independently. The successful applicant should have experience interpreting biological data and computationally testing their hypothesis. The successful candidate is expected to have good knowledge of molecular biology (e.g. Master level). The candidate should be proficient in NGS data analysis, Python and UNIX/Linux. Experience in other scripting languages (e.g. R, Perl) will be beneficial. Preferred experience also includes familiarity with eukaryotic translation, RNA biology, ribosome profiling analysis, CLIP or CRAC methods, RNA-Seq, and general molecular biology techniques. A strong interest in interdisciplinary technology development, and novel and creative thinking abilities are essential. Applicants wishing to integrate computational and experimental biology approaches are also encouraged to apply.

Application process
The application is to be submitted in Varbi recruitment system.

An employment application must contain the following documents in English:

- Cover letter motivating the application
- A complete curriculum vitae, previous academic or industrial positions, academic title, current position, academic distinctions, and committee work. Please include email details of potential referees.
- A complete list of publications
- A summary of current work (no more than one page)
- Verifications for crediting of illness, military service, work for labour unions or student organisations, parental leave or similar circumstances
At Karolinska Institutet a 6-month trial period is required for all permanent appointments.

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. Visa mindre

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Postdoctoral Researcher in Bioinformatics

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Division/ Department
The Center for Translational Microbiome Research (CTMR) was started in January 2016 as a collaboration between Karolinska Institutet, Science for Life Laboratory (SciLifeLab) and Ferring Pharmaceuticals.

CTMR aims to better understand the contribution of the human microbiome to physiology and pathophysiology with the goal of opening opportunities for the development of novel therapies in the area of gastroenterology, reproductive health and neonatology. The center is also part of the Horizon 2020 initiative on microbiological research, where the ONCOBIOME project gathers 17 partners from 10 countries to do research on four different types of cancer: gastrointestinal, breast, prostate, and melanoma. The focus of CTMR in the ONCOBIOME project is processing microbiome samples from a large screening program for colorectal cancer (30k individuals).

Duties
We are looking for an experienced postdoc-level researcher to join the CTMR team as a full-time bioinformatician. The applicant will take on a leading role in CTMR’s responsibilities in the large-scale ONCOBIOME project, which studies the connection between different types of cancer and the human microbiome. The position involves bioinformatics workflow development, as well as computational and biostatistical analyses of large-scale shotgun DNA sequencing data. The tasks include analysis and integration of human microbiome data with clinical metadata to identify biomarkers in clinical patient material. The bioinformatician will be heavily involved in design and implementation of the infrastructure configuration for establishing an efficient and sustainable sequencing workflow.The development work includes automating the majority of the sequence data analysis workflow. The successful applicant will also be working closely together with wet lab research engineers, to ensure high quality sample processing at all steps: DNA extraction, sequencing library preparation, sequencing, and finally data analysis.

This bioinformatics research position concerns the following main tasks:

- Taking responsibility for the bioinformatics analysis effort of the microbiome samples of the ONCOBIOME project
- Taking responsibility for implementing the bioinformatics analysis workflow of these samples, automating sequencing data processing and setting up reliable and robust downstream bioinformatic analyses.
- Producing sample profiles (e.g. taxonomic, functional) by combining data across multiple sequencing runs (including performing routine quality control of sequencing data).
- Performing biostatistical analyses of microbiome profiles in relation to cancer types and available sample metadata.
- Being involved in the design and planning of wet lab processing

Qualifications / Requirements
We are looking for an experienced postdoc-level candidate that completed his/her PhD within the last few years. You are a careful and detail-oriented person who is not afraid of responsibility. You enjoy working together in teams and are capable of close internal cooperation, as well as interacting with external collaborators that are experts in a wide variety of fields connected to our research. You have a strong desire to deliver high quality work, on time, and have experience working independently. We expect great familiarity with bioinformatics work in a Linux environment.

In addition, applicants must have:

- Experience in working with bioinformatics tools for large-scale metagenomic (DNA) analysis
- Experience producing feature count tables from raw unprocessed shotgun sequencing data using a variety of techniques
- High familiarity with at least one scripting language, e.g. Python
- Experience with statistical analysis of shotgun metagenomics data in R, Python, or similar
- Excellent oral and written communication skills
- Fluency in English

Furthermore, it is beneficial if the applicant has:

- Experience of molecular biology lab work, including troubleshooting
- A medical or biomedical background
- Experience working with case/control or population-based studies (not necessarily human)
- Experience with workflow management systems such as Snakemake and/or Nextflow, as well as working on HPC cluster systems
- Experience of microbiome and/or cancer research

We place great emphasis on personal suitability.

Entry requirements
Qualified to be employed as a postdoctor is one who has obtained a doctorate or has equivalent scientific competence.

Application process An employment application must contain the following documents in English or Swedish:

- A complete curriculum vitae, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
- A complete list of publications
- A summary of current work (no more than one page)
Interviews will be held continously during the application period. The application is to be submitted through the Varbi 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. Visa mindre

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