Sano MSc Project

Project title: Misfolded protein spreading by autoregressive model

Give us a chance to meet you
  • About us:

Sano Centre for Computational Medicine is a new International Scientific Foundation located in Kraków, Poland.

Sano aspires to be a major translational scientific institute, operating at the meeting point of academic science, established MedTech industry, and emerging start-up environment, combining the best of these three perspectives.

Sano acts as a core technology and expertise provider for industry, and creator of innovation, developing state-of-the-art solutions for healthcare. Thanks to the substantial funding and excellent European partnership network, Sano will bring a critical mass to this transformational field of research, in order to translate scientific advancements onto clinical practice. Sano’s ambition is to become the Reference Centre for Computational Medicine in Central Europe and build a reputation as a leading institute on a global level.

As a cross-disciplinary institution, Sano uses machine learning/artificial intelligence (ML/AI), large scale computer simulations (HPC), data science, and other computational technologies towards overcoming global challenges in healthcare systems. The research agenda will be executed in close collaboration with Partners in Poland, EU and USA.

We value:

  • Passion – Passion in what we do, engagement in Sano operations, taking responsibility, providing initiative, being happy at work.
  • Innovation – Boldness in articulating and pursuing novel ideas, courage to think outside the box.
  • Integrity – Directness, openness, tolerance and respect. Scientific integrity (we do not cut corners).
  • Diversity – Diversity in backgrounds, cultures and opinions of Sano employees. Promotion of women in STEM.
  • About job:
  • Closing date: 15.09.2021
  • Level of education: Undergraduate (BSc, BEng)
  • Hours: approx. 16 working hours per week/40% FTE
  • Salary indication: stipend for up to 2500 PLN gross monthly
  • Degree awarding institution: TBC
  • Sano Supervisor: Dr. Alessandro Crimi (Computer Vision Data Science Research Group Leader)
  • Project start: October 2021

Most of neurodegenerative diseases are believed to be related to the spreading of misfolded proteins. Controversies still arises whether which path those proteins follows, and whether brain structures are damaged during this spreading or they were predisposing it.

Several studies have been carried out focused on Alzheimer, Parkinson, and ASL. Those studies mostly follow dynamical models:

  1. The epidemic spreading model: Iturria-Medina, Y., Sotero, R. C., Toussaint, P. J. & Evans, A. C. Epidemic spreading model to characterize misfolded proteins propagation in aging and associated neurodegenerative disorders. PLoS Comput. Biol. 10, e1003956 (2014). https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003956
  1. A diffusion model based on heat kernel: Raj, Ashish, Amy Kuceyeski, and Michael Weiner. “A network diffusion model of disease progression in dementia.” Neuron73.6 (2012): 1204-1215. https://www.sciencedirect.com/science/article/pii/S0896627312001353

A recent work related hemodynamics in the brain with structural connectivity, the approach is based on multivariate regressive model rather than diffusion model. Predicting hemodynamics on the brain connectome:

Crimi A, Dodero L, Sambataro F, Murino V, Sona D. Structurally Constrained Effective Brain Connectivity. NeuroImage. 2021 Jun 18:118288.  https://www.sciencedirect.com/science/article/pii/S1053811921005644

With this thesis we would like to investigate whether an autoregressive model produce different prediction compared to the diffusion model. Ground truth is given by Tau and beta-amyloid deposits detected by PET tracers. Pre-processed brain connectomes will be given, initial code and data will be provided.

  • Study at Sano

Postgraduate study can be a great opportunity to gain advanced training, new skills and in-depth subject knowledge. If you’re thinking about a scientific career, you’re interested in computational medicine and are looking at various options, Sano might be the perfect place for you.

Sano is a new nonprofit research institute dedicated to the advancement of computational medicine, developing sophisticated computer methods for the prevention, diagnosis and treatment of disease, to meet the overarching worldwide need for efficient, effective and streamlined healthcare.

We recognize that it is all about the skills of people involved in the project, to develop Sano into the world-class research centre for advanced computational medicine.

We’re looking for the best people around and invite all students interested in applied research within computational medicine to apply. The MSc programme at Sano is aimed at providing the next generation of healthcare technology innovators with unique skills.

By applying, you will let us know about your interest in education at Sano. We’re looking for students to work at all our Research Groups – Healthcare Informatics, Computer Vision Data Science, Modeling and Simulation, Clinical Data Science, Personal Health Data Science and Extreme-Scale Data and Computing.

We’re waiting for you!

  • What are you going to do?

You are excpected to:

  • do original research under the direction of your supervisor;
  • participate in the many seminars by internal and external speakers as well as journal clubs and group activities;
  • collaborate with students, researchers and other Sano employees. You will have the opportunity to co-learn advanced coding techniques with the help of experienced scientific programmers and data scientists.
  • What do we require ?

As our successful candidate you should have:

  • undergraduate degree – BSc, BEng or other, preferably in computer science or related field;
  • interest in pursuing applied research in a multi-disciplinary environment;
  • python programming, medical imaging experience (preferably in 3D or 4D), statistics;
  • excellent written and oral English communication skills.
  • Our Offer

We offer a stipend contract for the duration of 2021/2022 academic year, and expect the student to work on the project for approx. 16 hours per week (40% FTE). This includes attendance in courses, trainings and internal research meetings. The research will be conducted in close collaboration with supervisors at Sano and AGH.

The student will receive a stipend of up to 2500 PLN gross monthly for the duration of the contract.

Sano offers excellent opportunities for study and development, an access to many international conferences on computational medicine and a possibility to grow in a scientific society

If you feel that this job opportunity is the career that you are looking for, please apply immediately and give Sano a chance to meet you. Please, be informed that Sano will contact only with Candidates fulfilling the formal criteria.

  • Job application

Sano is an equal-opportunity employer. We prioritize diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.

Do you recognize yourself in the job profile? Then we look forward to receiving your application.

Applications in .pdf should include:

  • a cover letter with an emphasis on your research interests;
  • a curriculum vitae;
Apply for a job

Apply through Sano recruitment system. If you would like to apply for future openings feel free to send your application to our database.​