Working in the Computational Medicine Team - Research Environment
The Tegnér-Björkegren laboratory for Computational Medicine is located at GV - King Gustaf V Research Institute (GV) (KS hospital Map pdf) (M1 behind the main hospital building; hitta.se link - at the blue spot).
Contact information: Johan Björkegren [here], Jesper Tegnér [here]
Our work is carried out at our Interdisciplinary Laboratory for Computational Medicine at GV belonging to Center for Molecular Medicine at Karolinska Institute. We belong to a translational research environment with the concept is to go from the patient to molecules and back with the assistance of a range of molecular, computational and whole-genome technologies.
We look for creative, bright, self-motivated and overachieving individuals. Our ambition is to develop you into a multi-lingual researcher bridging across the clinic - computational technologies - molecular medicine. We believe that this will facilitate top-notch research for the benefit of the patient.
In the laboratory we have a mix of competences ranging from mathematics, engineering, molecular biology, biomedicine to the clinic. In addition we have several ongoing international and national collaborations covering different technologies all subserving the purpose of understanding atherosclerosis. We aim for finding groups of molecular markers for diagostics as well as to understand the mechanisms governing the development of atherosclerosis. Our program cannot be excecuted without a parallell development of appropriate tools and strategies for dealing with complex multifactorial diseases.
In the laboratory we have inhouse/collaborative expertise in:
- biopsy and DNA collection from atherosclerotic patients (biopsy protocols, RNA extraction)
- whole genome technologies - gene expression (affymetrix, CAGE) and SNP profiling
- database design, integration and management
- detecting patterns in data (expression, SNP analysis, biostatistics and machine learning analysis).
- genetic mouse model for atherosclerosis
- macrophage cell system (molecular biology, siRNAi experiments)
- network analysis - data integration and inference algorithms
- computational modeling, analysis and simulation of disease relevant processes.
For several of these technologies we have ongoing international collborations (RIKEN, Estonia, South Africa, USA) which further strenghtens our systembiological pipeline.
A successful applicant is expected to be highly independent and extremely communicative thereby bridging and transforming insights originating from different intellectual cultures. We emphasize close interaction between theory, simulation techniques, data-analysis and management, experimental molecular work, animal model systems, application of genomics technologies and the clinic.
Current possibilities:
A: If you have a fellowship (Marie Curie etc) we have the possibility to provide a unique research environment. Please contact Johan (johan.bjorkegren@ki.se) and Jesper (jesper.tegner@ki.se) for an informal discussion about projects and possibilities.
B: We have an intensive ongoing collaboration with RIKEN, Japan. We have the possibility to provide projects and support for you to apply to The Royal Academy of Science (KVA, click here) for a long or short term fellowship to JAPAN. Suitable both for a computational or experimental background. Deadline 4 april, 2008. Please contact Jesper (jesper.tegner@ki.se) for further information about good projects for you.
C: We have three open positions in the laboratory.
1. Postdoctoral position (2years with possible exptension) for systems biological research using genetically modified mice susceptible to atherosclerosis (deadline march 15)
The applicant is expected to be responsible for research projects in the group based on genetically modified mice. These projects involve i) cholesterol-sensitive networks in atherosclerosis progression and regression and ii) validation of central gene-hubs in these networks.
The applicant should have a profound background (possibly post-doc experience) and strong interest in working with genetically modified mice.
The position involves responsibility in genotypic determination of the modified mice, phenotypic measurements of the mice (mainly determine the degree of atherosclerosis by en face) and also immunohistological and gene expression analyses. Experience in development of transgene and/ or knock-out mice is an advantage but not a requirement. Insights in atherosclerosis, computational analyses and systems biology approaches to disease processes are also valuable.
Within the group there is computational competence for gene network identification using algorithms which integrate transcriptional and protein profiles with phenotypic data.
The applicant will collaborate with national and international networks why excellent knowledge in spoken and written English is necessary. Profound experience in different research activities, documented by international publications, and experience with international collaborations are appreciated. The position requires good collaboration and communication skills.
The successful candidate for the post-doc position has a PhD or an equal foreign degree. The candidates who have graduated no more than 5 years before the deadline of the application are prioritized. The decision will be weighted by the following criteria: scientific skills (3), pedagogical skills (1), leader and collaboration skills (1).
Please send your application in 3 copies in English with reference SAMPOST-CGN including the following documents:
-A full CV including date of public defence, title of thesis, previous academic appointments, academic title and current position.
-A full publication list
-A brief outline of your previous and current work, including technical experience from various molecular biology methods and laboratory animal experience.
(by regular mail)
Karolinska Institutet
Institutionen för medicin, Solna
Clinical Gene Networks AB
att: Johan Björkegren
M1:01, Karolinska Universitetssjukhuset
171 76 Stockholm
SAMPOST-CGN
Contact Johan (johan.bjorkegren@ki.se) and Josefin (josefin.skogsberg@ki.se) for further information.
2. Postdoctoral position for computational modeling of atherosclerosis and algorithms for reconstructing gene networks using in-house siRNA data obtained from a macrophage cell system. (deadline march 15)
The successful candidate should have rigorous training in engineering/physics/math with a sincer and deep interest in learnig relevant parts of biology in order to make out-of-the-box contributions to (a) computational modeling of atherosclerosis (based on our mouse model) and (b) development and application of network inference algorithms for the analysis of the siRNAi data from our macrophage system. These projects are also run in collaboration with Barcelona, Spain and RIKEN, JAPAN.
The position is for one year with good possibilities for a second year.
Please send single page research description, three letters of recommendations, cv, and list of your publications to Jesper (jesper.tegner@ki.se)
3. Postdoctoral/PhD position for mangement of AtheroCode and bioinformatic analysis of gene expression and SNP data. Relevant algorithm development. (deadline march 15)
The successful postdoctoral candidate should have dual competence in engineering/physics/math and biological/medical sciences. The work targets integrationk of different datatypes, in particular but not only SNP and gene expression data. Development of relevant algorithms for that purpose. Data analysis and management of our database AtheroCode focusing on the the analysis of the human samples. These projects are also run in collboration with an FP6 project (PROCARDIS) and Estonia.
The postdoctoral position is for one year with good possibilities for a second year.
It is possible that this position could be filled as a PhD position provided that you are an outstanding candidate with exceptional grades, good recommentations and other evidence demonstrating a high degree of self-motivation. Basic degree in an engineering school or medical/biomedical program.
For the postdoc - Please send single page research description, three letters of recommendations, cv, and list of your publications to Jesper (jesper.tegner@ki.se) and Johan (johan.bjorkegren@ki.se)
For the PhD candidate- Please send single page describing the reason why you would like to do an PhD in our laboratory, three letters of recommendations, cv, and other achievments which you consider to be relevant to Jesper (jesper.tegner@ki.se)