Career

Sano PhD Student 

Project title: Metagenomic studies of the human microbiome - temporal dynamics and functional analyses across different body sites 

Publication date: 19.07.2024 

Closing date: 18.08.2024 

Level of education: Master's degree 

Hours: 40 hours per week 

Salary indication: up to 5000 PLN gross gross (employer’s costs) 

Supervisors:  

Sano: dr. Tomasz Kościółek (Structural and Functional Genomics Research Group Leader)  

CMUJ: dr. Joanna Szaleniec 

Project start: October 2024 

The human microbiome occupies different ecological niches across our bodies - from the most prominent to date gut microbiome, through skin, oral, vaginal, or sinonasal microbiomes - each with their role in human health and wellbeing. The enormous technological progress is now making these dynamic and diverse ecosystems more accessible than ever and puts us on the cusp of designing personalized interventions, deriving clinically-relevant biomarkers, or creating microbiome-based biotherapeutics. 

The Structural and Functional Genomics group focuses on statistically sound, interpretable and reproducible methods and analyses. We work in a highly interdisciplinary environment bringing together biological and clinical knowledge together with large-scale computing, machine learning and statistical analyses. We are particularly interested in understanding the temporal dynamics of the microbiome and how to shape it for health; as well as describing the microbiome in terms of biochemical pathways (functions) encoded within metagenomes (or multi-omics data), rather than taxonomic information. 

In this doctoral project, you will have an opportunity to work on cutting-edge problems in metagenomics and engage in collaboration with our clinical and research partners from Poland and abroad (e.g. Switzerland, USA). There will be opportunities for you to shape the scope of your PhD, depending on your expertise and interests. 

Please note, the project is computational and any experimental (laboratory) work is possible through our partners. 

Sano PhD Student 

Project title: Evolutionary-scale interpretation of protein functions in the human gut microbiome – NCN Weave 

Publication date: 19.07.2024 

Closing date: 18.08.2024, results published 1.09.2024 

Level of education: Master's degree, enrollment at AGH doctoral school 

Hours: 40 hours per week 

Salary indication: up to 5000 PLN gross gross (employer’s costs) 

This is a competition for NCN stipend (stypendium naukowe NCN), the competition is held in accordance with relevant rules available here: 

https://www.ncn.gov.pl/sites/default/files/pliki/uchwaly-rady/2022/uchwala124_2022-zal1.pdf 

Supervisors:  

Sano: dr. Tomasz Kościółek (Structural and Functional Genomics Research Group Leader)  

AGH: dr. Maciej Malawski 

Project start: October 2024 

Recently, deep learning has caused a revolution in the field of computational biology. By learning from the wealth of protein information deposited in various protein databases, it has allowed the development of multiple computational tools for the analysis of such proteins. By applying deep learning methods to predict the three-dimensional structures of proteins at unprecedented levels of accuracy, researchers can now study the functions and interactions of proteins that have no known homologs. In the protein sequence space, by treating proteins as strings of words, deep learning models can detect evolutionary relationships that were previously out of reach, allowing for the annotation of remote homologs and orphan genes. To better understand what proteins do functionally, combining sequence and protein 3D structure information within deep learning algorithms, unlocked access to vast functional repertoire encoded in proteins. This is thus the right time to carry out a large-scale analysis of these proteins, combining deep learning based methods for protein structure prediction, the detection of very distance evolutionary relationships and function predictions, beyond the ability of standard approaches. 

In this project, we will create an atlas of human gut protein structures annotated with functions and a protein universe map to help us navigate this vast space. We will use deep learning and largescale evolutionary modeling to better understand the functionally dark proteins of the human gut metagenome. By studying the proteins and their genomic context, we will seek to identify unique proteins and their potential roles in human health and behavior. Our findings will help to prioritize future research and provide a more comprehensive view of the proteins found in the human gut. 

Please note, the project is fully computational and does not involve any experimental (laboratory) work. 

Link to apply to AGH doctoral school: 

https://rekrutacja.doktoranci.agh.edu.pl/ZagadnieniaBadawcze/?pg=Podglad&zb_id=1575 

Computer Vision Data Science group focuses its efforts on the development of AI technology for automatic analysis and interpretation of visual information in healthcare applications. Applications range from medical imaging, surgery, digital pathology, patient monitoring, etc.  

Currently, the Group’s main focus lies in neuroscience and neuroimaging. The team comprises young scientists in PhD Student and Postdoc roles and who are collaborating with the members of a separate Scientific Programmers team. 

Sano invites excellent, experienced scientists, willing to work in an academic startup environment to apply for the Group Leader position. The perfect candidate is a seasoned, independent researcher, with a history of leading a research team, keen to address new challenges and willing to work on technologies of the future in a collaborative environment. 

Group Leaders are key Sano employees, executing the organisation's research strategy to ensure scientific and commercial success. Collaboration between research Groups allows the best possible technological solutions to be incubated for clinical and industrial translation. 

Research Group Leaders are expected to work on-site, in our office at AGH University Center of Energy. 

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. 

We require from you: 

Internship in Finance Department at Sano Centre for Computational Medicine 

Postgraduate study can be a great opportunity to gain advanced training, new skills and in-depth subject knowledge. If you’re thinking about a career in accounting or finance, you’re interested in getting your first professional experience and are looking at various options, Sano might be the perfect place for you.  

Sano is a 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 students for an internship in finance department.