Doctoral Student in Cell Biology and Computational Microscopy Imaging
Title: Doctoral Student in Cell Biology and Computational Microscopy Imaging
Application Closed (Deadline: 20.Feb.2023)
KTH Royal Institute of Technology in Stockholm has grown to become one of Europe’s leading technical and engineering universities, as well as a key centre of intellectual talent and innovation. We are Sweden’s largest technical research and learning institution and home to students, researchers and faculty from around the world. Our research and education covers a wide area including natural sciences and all branches of engineering, as well as architecture, industrial management, urban planning, history and philosophy.
Project description
Third-cycle subject: Biological Physics
The Science for Life Laboratory (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research. The combination of the highly interdisciplinary expertise and research projects at the department is unique in Sweden and also at an international level. This expertise ranges across cell biology, biochemistry, biophysics and theory. Recently, the SciLifeLab and Wallenberg National Program started the Data-Driven Life Science (DDLS) program in order to accelerate life science research through innovations in AI and data science.
The AICell Lab (https://aicell.io) in the department of Applied Physics at KTH and SciLifeLab is a new research group funded by the DDLS Fellows program. The group, led by Wei Ouyang, focuses on building AI systems for data-driven cell and molecular biology. To expand the team, we are now opening a position for a doctoral student in biological physics with a focus on cell biology, automation and AI-augmented microscopy imaging.
Whole-cell modeling enables a holistic and quantitative view of cell biology and allows performing in-silico experimentation which has a great potential in revolutionizing system biology, synthetic biology, medicine and other applications in life science. However, modeling the entire cell is an extremely complex task and is heavily limited by our understanding of the biological systems. As a newly formed research group, we would like to take the grand challenge of modeling the human cell through recent advances in artificial intelligence and multi-omics data generation. To enable large-scale AI and data-driven whole cell modeling, we are currently building a smart microscopy imaging farm to ramp up the production rate of image data. The imaging farm consists of multiple microscopes and fluidic systems, robotic arms, liquid handling robots and automatic incubators. The farm will be used for performing automated brightfield/fluorescence imaging, long-term live cell imaging, tracking, spatial-omics and multiplexing imaging. For the whole-cell modeling project, we aim to build an AI-powered automated imaging system to actively detect, monitor and track the live human cells under drug and genetic perturbations. We would like to develop AI models which read changes in cell morphology and fluorescence markers, to generate control signals for driving the microscope, capture rare events and create balanced dataset for modeling.
You will be responsible for actively and effectively designing and implementing wet lab experiments in the imaging farm, including cell culture, sample preparation and microscopy imaging. Importantly, you will also actively work with other researchers in the group to develop and adapt protocols for the automated imaging farm and AI models. Besides wet lab skills, you will elaborate on your computational skills, e.g., by writing Python scripts to control the imaging farm, train AI models and develop automated data analysis workflows. In later stages of the project you will also design and conduct additional, custom validation experiments, which may involve different molecular biology techniques.
Supervision: Professor Hjalmar Brismar and Assistant Professor Wei Ouyang are proposed to supervise the doctoral student. Decisions are made on admission.
What we offer
The possibility to study in a dynamic and international research environment in collaboration with industries and prominent universities from all over the world. Read more
A workplace with many employee benefits and monthly salary according to KTH’s Doctoral student salary agreement.
A postgraduate education at an institution that is active and supportive in matters pertaining to working conditions, gender equality and diversity as well as study environment.
Work and study in Stockholm, close to nature and the water.
Learning and thriving in a young and ambitious research group
Admission requirements
To be admitted to postgraduate education (Chapter 7, 39 § Swedish Higher Education Ordinance), the applicant must have basic eligibility in accordance with either of the following:
passed a second cycle degree (for example a master’s degree), or
completed course requirements of at least 240 higher education credits, of which at least 60 second-cycle higher education credits, or
acquired, in some other way within or outside the country, substantially equivalent knowledge
Type in the special eligibility the applicant also shall meet.
In addition to the above, there is also a mandatory requirement for English equivalent to English B/6, read more here
Selection
In order to succeed as a doctoral student at KTH you need to be goal oriented and persevering in your work. During the selection process, candidates will be assessed upon their ability to:
independently pursue his or her work,
collaborate with others,
work comfortable in an interdisciplinary team,
have a professional approach,
analyse and work with complex issues,
demonstrate a solid understanding in cell and molecular biology,
demonstrate prior experience with cell culture, molecular biology, microscopy imaging and other wet lab skills,
demonstrate prior experience with developing, establishing, optimizing, and trouble-shootingwet lab protocols,
cross disciplines, and demonstrate a passion for lab automation, AI and other computational skills,
acquired basic skills in programming languages such as Python and R.
Prior experience in data analysis workflow development and machine learning is beneficial.
After the qualification requirements, great emphasis will be placed on personal competency.
Target degree: Doctoral degree
Information regarding admission and employment
Only those admitted to postgraduate education may be employed as a doctoral student. The total length of employment may not be longer than what corresponds to full-time doctoral education in four years ’ time. An employed doctoral student can, to a limited extent (maximum 20%), perform certain tasks within their role, e.g. training and administration. A new position as a doctoral student is for a maximum of one year, and then the employment may be renewed for a maximum of two years at a time.
Union representatives
You will find contact information for union representatives on KTH’s website.
Doctoral section (Students’ union on KTH Royal Institute of Technology)
You will find contact information for doctoral section on the section’s website.
Application
Apply for the position and admission through KTH’s recruitment system. It is the applicant’s responsibility to ensure that the application is complete in accordance with the instructions in the advertisement.
Applications must be received at the last closing date at midnight, CET/CEST (Central European Time/Central European Summer Time).
Applications must include the following elements:
CV including your relevant professional experience and knowledge.
Application letter with a brief description of why you want to pursue research studies, about what your academic interests are and how they relate to your previous studies and future goals. (Maximum 2 pages long).
Copies of diplomas and grades from previous university studies and certificates of fulfilled language requirements (see above). Translations into English or Swedish if the original document is not issued in one of these languages. Copies of originals must be certified.
Representative publications or technical reports: For longer documents, please provide a summary (abstract) and a web link to the full text.
Other
Striving towards gender equality, diversity and equal conditions is both a question of quality for KTH and a given part of our values.
For information about processing of personal data in the recruitment process please read here.