Tag-arkiv: Karolinska Institutet

Postdoctoral research fellow in Genome Architecture Imaging

Karolinska Institutet, Institutionen för Medicinsk biokemi och biofysik, Translational Medicine and Chemical Biology

A postdoctoral position is now available in the Bienko and Crosetto Laboratories for Quantitative Genome Biology (https://bienkocrosettolabs.org/) to investigate different aspects of genome organization in healthy and disease conditions using advanced single-molecule microscopy techniques.

Research environment
The Bienko and Crosetto groups are two highly integrated research groups working on genome architecture (Bienko group) and genome fragility (Crosetto group) in different contexts. We develop and apply quantitative microscopy and sequencing techniques, combined with advanced computational approaches, to investigate the link between genome architecture and fragility, and its functional consequences, in healthy and perturbed conditions, such as cancer and aging. We pioneered BLESS, the first method for direct genome-wide localization of DNA double-strand-breaks DSBs (Crosetto et al., Nature Methods 2013), and recently further advanced the technology by developing BLISS (Yan et al., Nat Commun 2017; Mirzazadeh et al., Meth Mol Biol 2018). We have also developed GPSeq, a new method based on massively parallel sequencing that enables to measure the radial nuclear position of thousands of genomic loci simultaneously (manuscript in preparation). Recently, we have established a high-throughput platform for high-resolution DNA and RNA fluorescence in situ hybridization (FISH), which enables us to probe the nuclear location and the transcriptional activity of hundreds of genomic loci in thousands of single cells.

Our labs are located at the Science for Life Laboratory (SciLifeLab) situated at the Karolinska Institute campus in Stockholm. SciLifeLab is an interdisciplinary center for molecular biosciences with focus on health and environmental research, bringing under the same roof groups from four universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University. The center features state-of-the-art technology platforms, including next-generation sequencing, high-throughput histology, super-resolution microscopy, proteomics, image analysis, and bioinformatics.

The successful candidate will join an interdisciplinary and dynamic team of international researchers, including clinicians, biologists, biotechnologists, engineers, computer scientists, and physicists. Our mission is to transform the way we understand complex biological phenomena and diseases such as cancer, by integrating next-generation sequencing technologies, single-molecule microscopy methods, and advanced computational tools.

Duties
The main goal of the project is to obtain a comprehensive atlas of chromosome shapes, locations, and the associated transcriptional activity at single-cell resolution, in different model systems. The successful candidate will primarily rely on our DNA and RNA FISH methodologies to generate large image datasets that will be analysed using state-of-the-art image analysis pipelines already implemented in our lab. The successful candidate will closely interact with researchers applying sequencing-based methods to the same model systems, as well as with expert image analysts to process the high volume of image data generated. Specific tasks include:

  1. Cell culture and preparation of samples for DNA and RNA FISH
  2. Preparation of oligonucleotide probes using liquid handling robotics
  3. Performing DNA and RNA FISH and imaging the samples
  4. Image processing and analysis in synergy with a dedicated image analyst

Entry requirements
A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc.

A clearly demonstrated prior experience in microscopy methods and previous work in the field of genome organization is mandatory. Prior experience with FISH techniques is a strong advantage. Passion for meticulous work, attention to detail, and protocol optimization and troubleshooting is necessary. A strong motivation to work in a highly interdisciplinary and collaborative environment, and willingness to interact with scientists with computational background is required. Experimentalists with a strong motivation to work alongside theoreticians and to learn analytical and programming skills are strongly encouraged to apply.

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

  • 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)
  • Verifications for crediting of illness, military service, work for labour unions or student organisations, parental leave or similar circumstances
  • Verification from the thesis defence committee or the equivalent (only if the thesis defence is scheduled within three months after the application deadline)

The application is to be submitted on the MyNetwork recruitment system.

Type of employment Temporary position longer than 6 months
Contract type Full time
Number of positions 1
Working hours 100 %
City Stockholm
County Stockholms län
Country Sweden
Reference number 2-2556/2018
Contact
  • Magda Bienko, +46 (0)72 857 29 25
Union representative
  • Anne Edgren, OFR/S, P, O, +46 (0)8-616 16 29
  • Biborka Bereczky Veress, SACO, +46 (0)70-173 85 75
  • Henry Wölling, SEKO, +46 (0)8-524 800 00
Last application date 30.Jun.2018 11:59 PM CET

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Post expires on Saturday June 30th, 2018

Postdoctoral study in exploring ubiquitination in disease pathogenesis (scholarship)

Department of Medicine, Solna, Cardiovascular Medicine division

The Department of Medicine, Solna, is one of the largest departments at Karolinska Institutet. The department consists of several units that are separated into different research groups. The core activities of the department are research, doctoral education and undergraduate education for medical and biomedical students. The research has three main profiles: allergy, cardiovascular medicine and inflammatory diseases.

Division
We are looking for a highly motivated and talented postdoctoral researcher to join the research team of Magdalena Paolino at the Department of Medicine, Solna. The Paolino team is interested in uncovering the molecular basis of diseases,  with a major focus in exploring the functions and mechanisms of ubiquitin-dependent pathways in metabolism, cancer and immunity. Our research goes from mouse genetics to therapy and strives to have important implications for disease treatment. We are recruiting an integrated team of talented experimental researchers, who will work together to help elucidate novel relevant roles of ubiquitination in health and disease. More information about the lab is available at: https://ki.se/en/meds/team-magdalena-paolino.

Our team is part of the Department of Medicine Solna (MedS) as well as of the Center for Molecular Medicine (CMM); both institutions with a long-standing tradition in supporting biomedical research, providing excellent scientific and work environment. We will soon relocate to the newly built Bioclinicum building, which will provide further state-of-the art facilities and foster collaborations with the broader scientific community at KI.

Duties
The applicant will apply state-of-the-art approaches to uncover novel physiological role(s) for ubiquitination, with a primary focus in immunity and/or cancer. He/she will work at the interface of basic and translational research with the ultimate goal of revealing the molecular basis of relevant ubiquitin-dependent human diseases, and in doing so, to discover novel strategies for therapeutic intervention. For these studies, the candidate will combine mouse genetics and in vivo disease models with a wide range of modern cell biological, immunological and molecular methods, such as flow cytometry, CRISPR/Cas9, shRNAs, microscopy, next generation sequencing, proteomics and cell culture. 

Entry requirements
The applicant is eligible to apply if he or she has obtained a PhD in the fields of Cancer biology, Immunology, Biochemistry, Molecular Biology, or related fields, no more than 2 years ago. This term can be extended under special circumstances, including: leave due to sickness, military service, positions in trade unions and student organizations, parental leave or other similar circumstances. A total of two years can be deducted due to above circumstances.

We are seeking for creative and goal-oriented candidate, with a proven scientific track record, and who thrive in an interdisciplinary and international environment. Candidates are expected to have demonstrated experience working with disease mouse models and experimental application of molecular and cellular biology techniques for cancer and/or immunology research. Previous knowledge from working with viruses, CRIPSR/Cas9 and shRNA gene editing techniques and ubiquitin-related enzymes is not mandatory but it will be consider an asset.

The applicant should be highly motivated and collaborative, and is expected to work in a diligent way to take responsibility in generating properly controlled scientific data of high quality. Ideal candidates are able to interact closely with the supervisor but at the same time are capable of working independently and taking a strong lead in managing the project. They should also demonstrate capacity to organize, plan and document experimental bench-work as well as ability to stay on top of the relevant research field. Good interpersonal and communication skills in English, spoken and written, are required.

Type of scholarship
Scholarships for carrying out postdoctoral research may be granted to persons living in other countries who come to Sweden with the intention of only staying in Sweden for all or part of their postdoctoral education at KI. Persons who are resident in Sweden and/or have carried out all or part of their academic education at KI or some other educational institution in Sweden cannot be considered for scholarships from KI. Qualified to be admitted as a postdoctor is one who has obtained a doctorate or has equivalent scientific competence. The head of the department determines whether their previous training and scholarly qualifications correspond to a Swedish PhD or higher.

A scholarship for carrying out postdoctoral research can be granted for a maximum of two years within a four year period following the receipt of a doctoral degree or equivalent. This educational scholarship is tax-exempt.The amount is set for twelve months at a time and is paid out on a monthly basis. In exceptional cases, shorter periods may be acceptable. After the two years, it might be possible to prolong the position with an employment with salary.

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

  • A complete curriculum vitae, including: date of the thesis defense, title of the thesis, previous academic positions, academic title, current position and academic distinctions.
  • A complete list of publications
  • A one page cover letter summarizing previous experience, research interests, and motivation for position
  • Names and contact details for three references that are familiar with the applicants recent research and training, including the PhD supervisor.

The application is to be submitted on the Varbi recruitment system.

First day of employment snarast
Salary månadslön
Reference number 2-2706/2018
Contact
  • Magdalena Paolino, magdalena.paolino@ki.se
Union representative
  • Lars Ährlund-Richter, SACO, 08 – 5177 34 50, lars.ahrlund@ki.se
  • Niklas Andersson, OFR, niklas.andersson@ki.se
Last application date 19.Jun.2018 11:59 PM CET

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Post expires on Tuesday June 19th, 2018

Postdoctoral studies in microfluidic modelling of type 2 diabetes (scholarship)

Karolinska Institutet, Institutionen för fysiologi och farmakologi

At the Department of Physiology and Pharmacology we teach and conduct internationally acclaimed, high-quality research in Physiology, Pharmacology, Anesthesiology and Intensive care. We have around 400 employees, 30 research groups, and 90 doctoral students. Our research fields include cellular signaling, cardiovascular and respiratory systems, neuropsychopharmacology, neuroinflammation, pharmacogenetics, regenerative medicine, Renal System, anesthesiology and intensive care, muscle physiology and pain. Our collaboration with the clinics at Karolinska University Hospital provides unique opportunities for translational research within our subjects. More information about research at http://ki.se/fyfa_english

Background
Type 2 diabetes mellitus (T2DM) constitutes a global health problem affecting 1 in 20 adults worldwide. Insulin resistance in muscles, liver and adipose tissue, loss of pancreatic islet cell function and decrease of beta cell mass are key hallmarks of T2DM. However, they are largely unaddressed by todays therapeutics that focus on disease management rather than regression or cure. T2DM manifests due to a dysfunctional interplay of multiple tissues and organs. However, because of the complexity and species-specificity of these interactions, there is a lack of experimental tools that faithfully reflect human T2DM biology, which impedes the development of new anti-diabetic medications. The main objective of the proposed project is to develop, characterize and validate a platform capable of modelling human T2DM.

Research Group
Liver function and Drug Development.
Research Profile: http://ki.se/en/fyfa/section-of-pharmacogenetics-lauschke-lab.
The research will be conducted in the group of Assistant Professor Volker Lauschke (Liver Function and Drug Development). In the group, we use 3D cell culture systems of primary human cells, microfluidics and integrative bioinformatics approaches to develop better model systems for prediction of drug toxicity and to identify novel therapeutic strategies for complex metabolic diseases, such as type 2 diabetes. In addition, we are interested in understanding the molecular basis of hepatic plasticity in liver injury and regeneration. Furthermore, we study the genetic basis of drug response and adverse drug reactions on a population-scale. The research of the group is financed by The Swedish Research Council, the Malin and Lennart Philipson Foundation, the Strategic Research Program in Diabetes, as well as the Harald Jeansson Foundation.

Duties
We are looking for a post doctoral fellow who will work towards the development of an in vitro platform for T2DM modelling. The project is subdivided in two synergistic parts:

  • The successful candidate will expand our work on microphysiological 3D models for key organs involved in T2DM biology (liver, pancreas, myocardium and adipose tissue) and benchmark their molecular phenotypes and functionality against their in vivo
  • The fellow will participate in design and calibration of a co-culture compatible microfluidic chip in which we integrate the engineered tissue models.

Following this validation, the platform will be utilized to identify novel secreted biomarkers for T2DM onset and progression and to decipher the role of genetic factors that have been reproducibly linked to T2DM risk, but whose mechanistic implications are currently unknown. Importantly, understanding the mechanisms behind these genetic risk factors holds promise to reveal new strategies for therapeutic interventions and, using a rational design approach and virtual screening, we aim to develop and test compounds targeting these factors.The announcement is for a research positions and does not include mandatory teaching obligations.

Entry requirements
Scholarships for carrying out postdoctoral research may be granted to persons living in other countries who come to Sweden with the intention of only staying in Sweden for all or part of their postdoctoral education at KI. Persons who are resident in Sweden and/or have carried out all or part of their academic education at KI or some other educational department in Sweden cannot be considered for scholarships from KI. Qualified to be admitted as a postdoctor is one who has obtained a doctorate or has equivalent scientific competence. The head of the department determines whether their previous training and scholarly qualifications correspond to a Swedish PhD or higher.

Qualifications
The candidate in question should have at least two years of laboratory experience and in-depth knowledge and interest in cell biology. A proven track record of cell culture work is required and a strong proficiency in spoken and written English is necessary. Understanding of diabetes biology and/or previous experience with microfluidic systems will be an asset. We value a person with good communications skills who is able to work quite independently. Ambition to apply for external postdoctoral fellowships is explicitly encouraged.

Type of scholarship
A scholarship for carrying out postdoctoral research can be granted for a maximum of two years within a four year period following the receipt of a doctoral degree or equivalent. This educational scholarship is tax-exempt. The amount is set for twelve months at a time and is paid out on a monthly basis. In exceptional cases, shorter periods may be acceptable.

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

  1. 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
  2. A complete list of publications
  3. A summary of current work (no more than one page)
  4. Personal letter
  5. Verifications for crediting of illness, military service, work for labour unions or student organisations, parental leave or similar circumstances
  6. Verification from the thesis defence committee or the equivalent (only if the thesis defence is scheduled within three months after the application deadline)

The application is to be submitted on the Varbi recruitment system.

First day of employment In agreement with group leader
Reference number 2-2605/2018
Contact
  • Volker Lauschke, Assistant professor, Volker.lauschke@ki.se
Union representative
  • Bo Rydqvist, SACO, 08-524 872 67, bo.rydqvist@ki.se
  • Henry Wölling, SEKO, henry.wolling@ki.se
  • Niklas Andersson, OFR, niklas.andersson@ki.se
Last application date 18.Jun.2018 11:59 PM CET

Post expires on Monday June 18th, 2018

Doctoral (PhD) student position in Biostatistics

Karolinska Institutet, MEB

The Department of Medical Epidemiology and Biostatistics (MEB) is among the largest departments of epidemiology in Europe with special focus on increasing our knowledge of the aetiology of different diseases. Our department consists of researchers, doctoral students, biostatisticians, data collectors and database administrators as well as administrative personnel, in total some 250 staff. The department is situated at campus Solna. Further information can be found at ki.se/meb

We are recruiting a student for doctoral education.

For more information regarding doctoral (PhD) education, see: http://www.ki.se/doctoral.

Research group
The biostatistics group comprises around 35 member, including 3 professors, 4 senior lecturers (universitetslektorer), applied biostatisticians, postdocs and PhD students. The group is involved in a wide variety of research projects, including population-based cohort and case-control studies, twin and family studies, survival analyses, predictive modelling, genetic epidemiology and bioinformatics.

The doctoral education project and the duties of the student
Applications are invited for a PhD research training position to work on the development of statistical methods for surrogate evaluation and clinical trial design in infectious disease. Must have a strong interest in statistical methods development, clinical trials and infectious disease research. As well as a willingness to participate in applied collaborative work.

Entry requirements for doctoral education at KI
To be eligible for doctoral education, the following requirements have to be met:

General entry requirements
A person meets the general entry requirements for doctoral/third-cycle/PhD education (according to Higher Education Ordinance Chapt 7, section 39) if he/she:

  1. has been awarded advanced/second-cycle/master qualification (i.e. master degree) or
  2. has satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the second-cycle/master level, or
  3. has acquired substantially equivalent knowledge in some other way in Sweden or abroad.

For more information regarding the general entry requirements, please see:

https://ki.se/en/phd/entry-requirements-eligibility-for-doctoral-education

Specific entry requirements Proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school. Applicants who meet the general entry requirements (1 or 2 above) from a university in one of the Nordic countries fulfill the English language requirement. For information on how other applicants can certify their English proficiency (such as through IELTS or TOEFL, previous upper secondary or university level studies), please see:

https://ki.se/en/phd/entry-requirements-eligibility-for-doctoral-education

Applicants should:

* Have a master’s degree in statistics, biostatistics or related discipline, and have a strong interest in statistical methods/theory.

* Have knowledge or training in immunology, virology, parasitology or medical training.

* Have a willingness to travel for field studies and for internships.

It is considered as a strong merit if applicant have programming skills in R.

Fluency in written and spoken English is required.

Skills and personal qualities
The applicant should be able to work well in a team, as well as having the ability to work independently.

Assessment criteria
A selection will be made among qualified applicants on the basis of the ability to benefit from doctoral education. Karolinska Institutet uses the following bases of assessment:

– Documented subject knowledge of relevance to the area of research

– Analytical skill

– Other documented knowledge or experience that may be relevant to doctoral studies in the subject

The qualifications of the applicants will be evaluated on an overall basis.

Terms and conditions
All doctoral students at KI receive financial support during their doctoral education and employment on a doctoral studentship is the most common sort of support.

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

  • A personal letter and a curriculum vitae (only in English)
  • Academic degree diplomas, transcripts of records, and if applicable, authorised translations
  • Copies of degree projects and any previous publications
  • Proof of English proficiency

All documents certifying the entry requirements must be scans of originals (scans of copies or certified copies will not be accepted). The scanned documents must be in color and both the front and the back of the documents must be scanned. Please note that there are specific documentation requirements for a number countries, please read the instructions at:

https://ki.se/en/phd/entry-requirements-eligibility-for-doctoral-education

The application and supporting documents are to be submitted through the Varbi recruitment system.

Type of employment Temporary position longer than 6 months
Contract type Full time
First day of employment According to agreement
Salary Monthly salary
Reference number 2-2461/2018
Contact
  • Lina Werner, HR-Officer, Email: lina.werner@ki.se
  • Erin Gabriel, Assistant Professor, Email: erin.gabriel@ki.se
Union representative
  • Ann Almqvist, OFR, 08-524 861 99
  • Ulrika Zagai, SACO, 08–524 871 84, ulrika.zagai@ki.se
  • Henry Wölling, SEKO, henry.wolling@ki.se
Last application date 06.Jun.2018 11:59 PM CET

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Post expires on Wednesday June 6th, 2018