Computational Drug Repurposing: a Big Data Approach to Mouse Brain Atlas for Alzheimer’s Disease

Sano Postdoc

Give us a chance to meet you

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.

Project title: Computational Drug Repurposing: a Big Data Approach to Mouse Brain Atlas for Alzheimer’s Disease
Closing date: 22.12.2022
Level of education: PhD
Hours: 40 hours per week
Salary indication: up to 14000 PLN gross monthly
Project period: project starts in 2023
Supervisor: Sano: Dr. Ahmed Abdeen Hamed (Clinical Data Science collab between student and postdoc Leader)

Brain atlas are powerful tools for learning about Alzheimer’s and the discovery of potential treatment. Particularly, mice brain atlases are of great interest in the space of drug repurposing.

Our efforts specifically focused on analyzing the biomedical literature that is publicly available in PubMed Central. We used means of text analysis, ontology term extraction, network models and algorithms to identify drug candidates and rank them. The results were validated from relevant data collected from clinical trials records. Our research also observed the possibility of drugs being combined to achieve a treatment. The full description of such discoveries is published in the JMIR and Pharmaceutics journals. Such analysis can enable the exploration of multiple layers of drugs, genes, proteins, cells, and compare it against various mouse strains.

This project strives to test the potency of drugs combinations on the brain of various model organisms. Therefore, this project aims at the development of a multilayer mouse brain atlas as an exploratory tool to illuminate insights that could favor the treatment of Alzheimer’s.

The main activities planned within this project involve the following:

Performing literature reviews for the state-of-the-art
Participate in planning, designing, architecting, testing the various development phases of the atlas
Perform lab test for the drug candidates that identified (in-vivo/in-vitro if needed and possible)
Perform data analysis, vetting, and plotting, and visualizing
Participate in a pair-programming activities (even without being familiar with programming)

This project is planned as a collaborative multi-institute, multidisciplinary that includes PhD students, Postdoctoral, and scientists from across the world.

You are expected to:

Contribute annotated bibliographies as basis for research on the different topics
Perform original research under the direction of one of Research Group Leaders;
Publish your work in peer-review journals and present during national and international conferences.
Participate in identifying proposal calls and funding opportunities
Participate in the efforts of outreach and collaboration with other institutes within (Poland and outside)
Demonstrate a comfortable level of ownership and independence
Co-mentor junior scientists – PhD students and MSc students (whenever applicable)

Required background and skills of the candidate:

Recent or pending PhD in relevant field, preferably computer science (no more than 5 years of postdoctoral experience).
At least one first-author research publication in a peer-reviewed scientific journal, top conference or currently in press.
Excellent written and oral English communication skills.

We offer a fixed term contract for 40 hours per week. This will be supported by an educational plan that includes attendance of courses and (international) meetings. The contract will include opportunities to participate in teaching and supervision of undergraduate and master students.

The salary, depending on relevant experience before the beginning of the employment contract, will be up to 14000 PLN gross per month, based on a full-time contract (40 hours a week) for the duration of up to 2 years with private medical care and a sports card.

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.

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;
a curriculum vitae;

Sano Postdoc