karolinska institutet phd

Doctoral (PhD) student position in 3D Genome Biology

Karolinska Institutet

Application deadline

August 1, 2021, the research group.

A PhD position is now available in the Bienko Lab ( https://bienkocrosettolabs.org/ ) at the Karolinska Institutet and Science for Life Laboratory in Stockholm.

As a PhD student, you will gain extensive knowledge on how the genome is spatially organized in the cell nucleus and learn to design, perform, and critically interpret the results of experiments aimed at addressing fundamental open questions in the field.

You will be part of an international, dynamic research environment ( https://www.scilifelab.se/ ) where you will work alongside scientists from many different fields and backgrounds, which will foster your creativity and help you shape your project in unconventional ways.

Our ultimate mission is to understand how the complex higher-order structure of chromatin in mammalian cells is established during the cell cycle, how it is dynamically reshaped during cell differentiation, and how it is rewired during carcinogenesis.

The doctoral student project and the duties of the doctoral student

Preliminary observations made in our laboratory suggest that the blueprint of the 3D genome of interphase nuclei might be hidden in the complex three-dimensional (3D) structure of mitotic chromosomes.

Your main task will be studying how the 3D genome configuration characteristic of interphase nuclei is re-established at the onset of every G1 cell cycle phase in human cells. Furthermore, you will investigate the dynamics and mechanisms of chromatin condensation during mitosis.

Specifically, throughout the four years of your PhD studies, you will be challenged and guided to pursue three major aims, using a combination of cutting-edge sequencing, microscopy, and advanced computational methods:

Aim 1: Map the radial structure of metaphase chromosomes. Initially, you will get familiar with our recently developed GPSeq method for mapping the radial arrangement of chromatin in interphase nuclei ( Nature Biotechnology 2020) and work to adapt GPSeq to study the spatial arrangement of chromatin in mitotic chromosomes (mGPSeq).

Aim 2: Visualize the structure and placement of metaphase chromosomes. Instructed by results obtained using the mGPSeq method, you will apply super-resolution microscopy techniques to visualize the spatial organization of relevant histone marks, individual genomic regions, and structural proteins on metaphase chromosomes, and trace them as cells enter/exit mitosis.

Aim 3: Model the dynamics of chromatin compaction/decompaction. In the last part of your PhD studies, you will be challenged to learn and apply advanced mathematical and computational approaches for 3D genome modeling (under the supervision of an expert senior scientist). Thanks to the extensive knowledge that you will have accumulated in Aims 1 and 2, you will be in a unique position to build a long-awaited model of how the interphase 3D genome is remodeled into the mitotic one, and vice versa.

What do we offer?

A creative and inspiring environment full of expertise and curiosity. Karolinska Institutet is one of the world’s leading medical universities. Our vision is to pursue the development of knowledge about life and to promote a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. As a doctoral student you are offered an individual research project, a well-educated supervisor, a vast range of elective courses and the opportunity to work in a leading research group. Karolinska Institutet collaborates with prominent universities from all around the world, which ensures opportunities for international exchanges. You will be employed on a doctoral studentship which means that you receive a contractual salary. Employees also have access to our modern gym for free and receive reimbursements for medical care.

Eligibility requirements for doctoral education

In order to participate in the selection for a doctoral position, you must meet the following general (A) and specific (B) eligibility requirements at latest by the application deadline.

It is your responsibility to certify eligibility by following the instructions on the web page Entry requirements (eligibility) for doctoral education.

A) General eligibility requirement You meet the general eligibility requirement for doctoral/third-cycle/PhD education if you:

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

Follow the instructions on the web page Entry requirements (eligibility) for doctoral education.

*If you claim equivalent knowledge, follow the instructions on the web page Assessing equivalent knowledge for general eligibility for doctoral education.

B) Specific eligibility requirement

You meet the specific eligibility requirement for doctoral/third-cycle/PhD education if you:

– Show proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school.

Follow the instructions on the web page English language requirements for doctoral education.

Verification of your documents Karolinska Institutet checks the authenticity of your documents. Karolinska Institutet reserves the right to revoke admission if supporting documents are discovered to be fraudulent. Submission of false documents is a violation of Swedish law and is considered grounds for legal action.

(A) and (B) can only be certified by the documentation requirement for doctoral education .

Skills and personal qualities

• You hold a master’s degree in Biology or Biotechnology or equivalent with a strong focus on molecular biology
• You have basic skills in bioinformatics
• You are interested in fundamental/basic research, as well as in methods development
• You are curiosity-driven and have a problem-solving mindset
• You are driven by challenges and seemingly unsolvable problems
• You can focus on a problem until you have solved it
• You like working in the lab and are meticulous
• You have a collegial spirit and work well with others

You don’t need to have expertise in bioinformatics, but you are expected to learn to process and (at least partially) analyze the data that you will be generating, under the supervision of senior bioinformaticians in the group.

Application process

Submit your application and supporting documents through the Varbi recruitment system. Use the button in the top right corner and follow the instructions. We prefer that your application is written in English, but you can also apply in Swedish.

A selection will be made among eligible applicants on the basis of the ability to benefit from doctoral education. The qualifications of the applicants will be evaluated on an overall basis.

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.

All applicants will be informed when the recruitment is completed.

Want to make a difference? Join us and contribute to better health for all

Last updated: 2021-07-01

Content Responsible: David Gotthold( [email protected] )

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Doctoral programme in Epidemiology

Epidemiology can be defined as the science of disease occurrence in the population and its determinants. Disease is caused by complex interactions between genetic, environmental, lifestyle, social and behavioral factors.

Programme overview

Epidemiology draws on central concepts, principles and methods, and can be considered the methodological backbone in a number of medical research disciplines. A common feature of epidemiological applications is their theoretical and methodological basis, including tools for defining problems, designing studies and interpreting study results.

In the context of a strong research and educational environment, the Doctoral Programme in Epidemiology supply doctoral courses and other activities. The target group is doctoral students at Karolinska Institutet, who pursue doctoral studies in the field of epidemiology and related areas. Students with diverse professional and educational backgrounds take part in programme activities.

The overall aims of the programme are:

• to contribute to doctoral training at Karolinska Institutet by supplying doctoral courses and other activities of high quality, on tools for defining problems, central concepts, principles and methods essential for designing, conducting, analysing, interpreting, reporting, communicating and critiquing epidemiological studies,
• to consider progression, i.e. gradual deepening and complexity of knowledge and skills, in terms of subject matter, scientific and ethical approach as well as generic skills, as an issue of specific importance, and,
• to be excellent in education, meaning that the education should be scientifically based and be grounded in educational research.

Epidemiology courses

Courses include introductory and more advanced courses in theory and methods, as well as courses focused on specific areas of epidemiological applications. A set of core courses in theory and methods (Epidemiology, I, II and III, and Biostatistics I, II and III) are arranged every academic year. A variety of elective courses are arranged regularly in order to enable tailoring of individualised study plans. Even more advanced courses are given more sporadically.

The courses are to be followed in a logical order and imply a gradual deepening and complexity of knowledge and skills, with regard to subject matter as well as scientific and ethical approach, and the ability to make judgements.

The courses are announced in the KI course catalogue for every semester.

Courses Spring semester 2024

Courses Fall semester 2023

Courses Spring semester 2023

Courses Fall semester 2022

Courses Spring semester 2022

Courses Fall semester 2021

Courses Spring semester 2021

Courses Fall semester 2020

Courses Spring semester 2020

Other educational activities

Doctoral student activities

Doctoral student activities arrange one to two activities per semester. These activities are planned and supported by the head of the programme.

Steering group

The steering group for the Doctoral Programme in Epidemiology has the overall responsibility for the curriculum design and the quality of the programme by monitoring and evaluating teaching and learning activities.

Members of the Steering group:

Anita Berglund, head of programme

Matteo Bottai, teacher representative IMM

Mark Clements, teacher representative MEB

Maria Feychting, teacher representative IMM

Thomas Frisell, teacher representative KEP

Amaia Calderon Larrañaga, teacher representative NVS

Nicola Orsini, teacher representative GPH

Jette Möller, teacher representative GPH

Sara Öberg, teacher representative MEB

Giorgi Beridze, student representative NVS

Anna Humphreys, student representative IMM

Application and admission

Do you want to sign up for the doctoral programme in Epidemiology?

As a doctoral student at Karolinska Institutet (KI) you can sign up for one or more doctoral programmes and thus obtain information on the courses and activities that are arranged. An expression of interest is submitted when you apply for admission to doctoral education. In addition, you can submit your expression of interest to any programme at any time during the doctoral education. If you are interested in the courses and activities etc. in the Epidemiology programme, please send an email to Johanna Bergman (e-mail address [email protected] . This means that you will receive information directly from this programme. You may choose from what is offered, but you do not commit to participate in any activity. To attend a course organized within the framework of the programme, you need to apply as described below.

Application and admission to courses on doctoral level

Application to courses is made directly in the Course catalogue at KI. The available courses on the doctoral level are announced once per semester. The catalogue for courses is published on ki.se around April 15 or October 15 and is open for application during one month.

After the application period is closed the applicant can only be admitted according to availability. A late application is made directly to the course organizer. KI's courses are open for registered doctoral students at all universities and colleges. If space allows, other applicants may also be accepted.

Formal note about admission (or not) is emailed to the applicants within a month after the application time is closed. If you are not admitted, you will be asked for interest to be on the waiting list. The applicant needs to confirm participation by a form signed by the applicant and his/her supervisor.

Course catalogue

All syllabi for courses at doctoral level at KI are collected in the KIWAS database.

Do you want to become a doctoral student at KI?

Doctoral education at KI (aiming for a Ph.D. degree) is to a large extent based on the individual research project of each doctoral student. The starting date is different for each doctoral student. The thematic doctoral programmes at KI are not organized “programmes” (e.g. as Master’s degree programmes) in the sense that a whole class studies together. Once admitted to doctoral education at KI, the doctoral student can sign up to one or several of KI’s doctoral programmes to obtain information about the courses and activities that are arranged within the specific research fields.

Information about how to become a doctoral student at KI and the procedure from recruitment to admission.

News and announcements

25 January, 2024, Workshop: All you wanted to know about publishing but never dared to ask Historical:

25 April, 2023 - Peer Review with Confidence: a Workshop for PhD Students Plenary talk by  Miguel Hernán: What does “learning from data” mean? A taxonomy of tasks for health data science Workshop - Transporting treatment effects from randomized trials to real world target populations Workshop - Causal inference with competing events Workshop - Advanced Quantitative Genetics Using Twin and Family Data, 7-9 June, 2022 Flyer Workshop "Outcome-wide Epidemiology and Causal Inference" with Tyler J. VanderWeele, 15 March 2022 Flyer Webinar on ”Open science within register-based research: Opportunities and challenges” Learning statistical inference: a novel approach for the case of interaction effects Workshop - Transporting treatment effects from randomized trials to real-world target populations Workshop “Introduction to Python for Health Researchers”, arranged by the Doctoral Programme in Epidemiology at Karolinska Institutet Webinar - Impact of the Covid-19 pandemic on the conduct of scientific research and communication of its results

Anita Berglund

Johanna bergman.

Transforming the understanding and treatment of mental illnesses.

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• Research Funded by NIMH
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PhD Training at Karolinska Institutet

The NIH-KI Collaborative Doctoral Program in Neuroscience bridges U.S. and Swedish PhD requirements in a flexible manner and is open for students to apply from both the NIH and KI side. For additional inquiries on intake through the KI side please contact the KI Partnership co- Director Dr. Sarah Bergen to understand the requirements.

NIH intake Process

For the NIH-intake pathway, applicants (US Citizen or Permanent Resident) must identify mentors at NIH and KI who will accept them as a PhD student. Prospective applicants must apply to the NIH graduate application database and prepare a brief (1-2 pg) description of the proposed thesis research and identify a mentor pair (at NIH and a supervisor at KI) with whom they envision doing their research. In doing so, this initiates communications between both potential supervisors and gives a better sense to the student of whether the intended mentor pair will support them upon admission into the graduate program. Once accepted into the NIH-KI program, and with the active involvement and concurrence of the two supervisors, the student should work with their mentors to establish a plan with an estimated timeline for research and required KI coursework. For additional inquiries on this pathway please contact the NIH Partnership co- Director Dr. Janet Clark .

Language of Training and Thesis

English is widely and often excellently spoken by Swedes; hence, there is no real language barrier in the program. Almost all classes at KI are taught in English. The thesis must be in English.

The joint PhD program at NIH and KI offers unparalleled opportunities for training and productive dissertation research in neuroscience. The program is designed so that students and supervisors can create an individual study plan for each student that supports personal scientific growth and an international scientific experience.

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