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3 POST-DOC POSITIONS ARE CURRENTLY AVAILABLE
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Post-doctoral Researcher in Lipidomics Position: We have an opening for an individual wishing to join a multidisciplinary project in the systems biology of severe asthma. The successful candidate will be expected to develop LC-MS/MS-based methods for oxylipin quantification in a range of biological matrices. Applicants should have a Ph.D. in mass spectrometry and/or bioanalytical chemistry, with experience in small molecule mass spectrometry as well as biological sample preparation techniques. We are especially interested in candidates with prior experience working with eicosanoids or other bioactive lipids in inflammatory systems. Experience or interest in working with bioinformatics tools for pathway reconstruction and network analysis as well as multivariate statistics is a significant merit. Research: This project is part of the consortium U-BIOPRED (Unbiased BIOmarkers used for PREDicting disease progression and medication efficacy), which is funded by the Innovative Medicines Initiative (IMI; http://www.imi.europa.eu). The overall project aims are to use biomarker profiles comprised of various types of high-dimensional data, integrated with an innovative systems biology approach into distinct phenotype handprints that will enable improved prediction of therapeutic efficacy relative to single or clustered biomarkers of one data type towards the goal of identifying novel targets. Accordingly, this position involves the development of mass spectrometry methods for oxylipin profiling of sputum, saliva, plasma and bronchoalveolar lavage fluid (BALF) from patients with severe asthma. These fingerprint data on oxylipin levels in asthmatics will be an integral part of the global handprint. As such, studies will be performed in close collaboration with the U-BIOPRED partners enabling the successful candidate to gain direct experience in the applications of multiple omics methodologies towards a common research hypothesis. In addition, to U-BIOPRED activities the candidate will work closely with researchers in the Center for Allergy Research at the Karolinska Institutet to examine the role of oxylipins in a range of allergy- and inflammatory-related pathologies. These efforts will involve quantifying oxylipin mediators and then integrating these results with data acquired from other platforms in combination with patient clinical metadata to create pathways of disease etiology and pathology. Results will be incorporated into relational database structures and analyzed with omics-integrating bioinformatics tools and pathway maps in collaboration with the Kyoto University Bioinformatics Center (http://genome.jp/kegg/). The specific long-term aims of the project are to investigate the mechanisms of chronic inflammatory diseases from a systems biology perspective, towards the goal of understanding the mechanism of disease and its subsequent resolution. Environment: The Department of Medical Biochemistry and Biophysics (MBB) and Institute of Environmental Medicine (IMM) have a strong research tradition in bioactive lipids including awarding of the Nobel Prize. Current research efforts are focused on leukotrienes and oxylipins in general, which are important chemical mediators of inflammatory and allergic reactions. The Karolinska Institutet is one of Europe's largest medical universities and contains commensurate resources and infrastructure. A total of 600 research groups span the full spectrum of medical disciplines and includes 2,000 researchers, 1,000 technicians, and 2,300 postgraduate students from all parts of the world who take part in both basic and clinical research. Start date: Funding is available immediately, but the start date is negotiable. This position is initially available for 12 months, with potential renewal for an additional 24 months. Salary: Salary includes health insurance and is negotiable depending upon applicant experience. Applications: Send applications, including research experience, CV and at least two references to Craig Wheelock (craig.wheelock@ki.se) or Sven-Erik Dahlén (Sven‑Erik.Dahlen@ki.se). The position is open until filled, but applications should be received by January 31st for full consideration. Further Information: For additional details of the departments and research interests: Click here for a pdf version of this announcement |
Post-doctoral Researcher in Metabolomics Position: We have an opening for an individual wishing to join a multidisciplinary project in the systems biology of inflammation. The successful candidate will be expected to develop GCxGC-TOF/MS- and APGC-MS/MS-based methods for quantification of small molecules in a range of biological matrices. Applicants should have a Ph.D. in mass spectrometry and/or bioanalytical chemistry, with extensive experience in GC/MS-based analyses of small molecules as well as biological sample preparation techniques. We are especially interested in candidates with prior experience in programming and statistical analysis, including the use of R and SIMCA-P+, as well as database construction. Research: The overall project aims are to elucidate the mechanisms of chronic inflammatory diseases through integrated metabolomics, lipidomics and proteomics studies. The position involves development of mass spectrometry methods for metabolite profiling of bronchoalveolar lavage fluid (BALF), plasma, atherosclerotic plaques and other matrices. Developed methods will be employed in translational research to analyze patient samples from a range of inflammatory diseases, including asthma, chronic obstructive pulmonary disease (COPD), and atherosclerosis. Studies will be performed in close collaboration with clinicians at the Karolinska Hospital. As part of the envisioned systems biology approach, metabolomics data will be augmented with proteomics and transcriptomics data collected at the Karolinska Biomics Center. Data will be incorporated into relational database structures and analyzed with omics-integrating bioinformatics tools and pathway maps in collaboration with the Kyoto University Bioinformatics Center (http://genome.jp/kegg/). Accordingly, the successful candidate will work closely with both clinical as well as bioinformatics collaborators. The specific long-term aims of the project are to investigate the mechanisms of chronic inflammatory diseases from a systems perspective, towards the goal of understanding the etiology of disease pathology as well as its subsequent resolution. Environment: The Department of Medical Biochemistry and Biophysics (MBB) has a strong research tradition that includes Pehr Edman who developed protein sequencing as well as three investigators who have received the Nobel Prize. The Department has recently initiated a new analytical facility that includes acquisition of a GCxGC-TOF/MS system dedicated to this project. Additional equipment in the facility includes new LC-MS/MS and Orbitrap systems. Presently, MBB consists of 10 research divisions which are involved in teaching and research within the fields of protein chemistry, redox biochemistry, metabolism, lipid research, inflammation research, structural biochemistry, molecular biochemistry, tissue biology, and developmental biology. The Karolinska Institutet is one of Europe's largest medical universities and contains commensurate resources and infrastructure. A total of 600 research groups span the full spectrum of medical disciplines and includes 2,000 researchers, 1,000 technicians, and 2,300 postgraduate students from all parts of the world who take part in both basic and clinical research. Start date: Funding is available from March 2010, but the start date is negotiable. This position is initially available for 12 months, with potential renewal for an additional 12 months based upon mutual agreement. Salary: Salary is stipend-based and includes health insurance. Applications: Send applications, including research experience, CV and at least two references to Craig Wheelock (craig.wheelock@ki.se). The position is open until filled, but applications should be received by January 31st for full consideration. Further Information: For additional details of the department and research interests: Click here for a pdf version of this announcement |
Post-doctoral Researcher in Bioinformatics Position: We have an opening for an individual wishing to join a multidisciplinary project in systems biology of inflammation. The successful candidate will be expected to develop bioinformatics approaches for the analysis of high throughput data from omics-based studies. Applicants should have a Ph.D. in a relevant discipline preferably bioinformatics, statistics, computer science or other quantitative field, with demonstrated experience in developing computational approaches to analyzing large datasets. We are especially interested in candidates with prior experience in network construction and statistical analysis, including the use of R and Bioconductor. Experience with multivariate statistics including the use of SIMCA-P+ or SAS as well as database construction would be an advantage. Research: This project is a collaborative effort between the Karolinska Institutet and the Bioinformatics Center at Kyoto University. The overall project aims are to elucidate the mechanisms of chronic inflammatory diseases through integrated metabolomics, lipidomics, proteomics, and transcriptomics studies. Developed bioinformatics approaches will be employed in translational research to analyze patient samples from a range of inflammatory diseases, including asthma, chronic obstructive pulmonary disease (COPD), and atherosclerosis. Studies will be performed in close collaboration with clinicians at the Karolinska Hospital enabling the successful candidate to be directly involved in translational systems biology efforts. Collected data will be incorporated into relational database structures and analyzed with omics-integrating bioinformatics tools. We are specifically interested in the application of network analysis methods for linking disparate gene, protein and metabolite data from multiple biological compartments to construct a model of disease. The specific long-term aims of the project are to investigate the mechanisms of chronic inflammatory diseases from a systems perspective, towards the goal of understanding the etiology of disease pathology as well as its subsequent resolution. Environment: The Department of Medical Biochemistry and Biophysics (MBB) has a strong research tradition that includes Pehr Edman who developed protein sequencing as well as three investigators who have received the Nobel Prize. The Karolinska Institutet is one of Europe's largest medical universities and contains commensurate resources and infrastructure. A total of 600 research groups span the full spectrum of medical disciplines and includes 2,000 researchers, 1,000 technicians, and 2,300 postgraduate students from all parts of the world who take part in both basic and clinical research. The Kyoto University Bioinformatics Center (KUBiC) was established in 2001 to promote basic and applied research in bioinformatics, with focus on uncovering and utilizing the cellular functions of all organisms through the reconstruction of protein-protein interaction networks from genomic information. This approach is exemplified by their development of the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. KUBiC is also responsible for operation of the GenomeNet database service with the support of massive parallel computing capability provided by a SGI Origin 3800. Start date: It is expected that the successful candidate will apply in collaboration with the Karolinska Institutet and Kyoto University for a postdoctoral fellowship from the Japanese Society for the Promotion of Science (JSPS, http://www.jsps.go.jp/english/). The application deadline for fellowships to initiate in fall 2010 is May 1st, 2010. The successful candidate can begin project work earlier at the Karolinska Institutet if desired, with the understanding that they will move to Kyoto University in the fall of 2010. Funding to begin at the Karolinska Institutet if desired is available from March 2010. The overall start date is negotiable, but it is expected that the candidate will begin at Kyoto University during the fall of 2010. Salary: Salary at the Karolinska Institutet is stipend-based and includes health insurance. Salary at Kyoto University is according to JSPS regulations Applications: Send applications, including research experience, CV and at least two references to Craig Wheelock (craig.wheelock@ki.se). The position is open until filled, but applications should be received by January 31st for full consideration. Further Information: For additional details of the departments and research interests: Interested candidates are referred to the following papers: L Folkersen, D Diez, CE Wheelock, JZ Haeggström, S Goto, P Eriksson, A Gabrielsen, 2009. GeneRegionScan: A Bioconductor package for probe level analysis of specific, small regions of the genome. Bioinformatics 25(15):1978-1979. CE Wheelock, ÅM Wheelock, S Kawashima, D Diez, M Kanehisa, M van Erk, R Kleemann, JZ Haeggstrom, S Goto, 2009. Systems biology approaches and pathway tools for investigating cardiovascular disease. Molecular BioSystems 5(6):588-602. CE Wheelock, S Goto, L Yetukuri, FL D’Alexandri, C Klukas, F Schreiber, and M Orešič, 2009. Bioinformatics strategies for the analysis of lipids. In “Lipidomics: Methods in Molecular Biology”. Editor: Donald Armstrong, Humana Press Inc, Totowa, New Jersey, USA 580:339-368. CN Hayes, D Diez, N Joannin, W Honda, M Kanehisa, M Wahlgren, CE Wheelock, and S Goto, 2008. varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. Bioinformatics 24(21):2564-2565. Click here for a pdf version of this announcement |
Ph.D. positions
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Undergraduate Positions
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We are always willing to assit in the preparation of joint grant applicaitons for students or post-doctoral scholars interested in working in our laboratory. See our Funding page for a list of current support. In addition, a number of Swedish organizations offer post-doctoral support including the Swedish Research Council (VR) and the Karolinska Institutet (KI). Contact Craig Wheelock for further information. |
