Our research interests cover the methodological advances in data science and their application to topical biomedical challenges, with the focus on advancing transcriptomics and metagenomics on the road to precision medicine.
In this manner we have played a lead role in the SEQC consortium co-ordinated by the U.S. Food and Drug Administration (FDA) for the benchmarking of large-scale gene expression profiling technologies, including RNA-Seq. Currently, in the second phase of SEQC we are investigating the complementarity of targeted RNA-Seq and genome sequencing for refined cancer diagnosis.
We are also active in the MetaSUB International Consortium where we do focus on establishing environmental metagenomics assays in healthcare as well as on enabling the use of environmental microbiome analysis for forensic purposes.
Our interdisciplinary team comprises of the following people:
Paweł Łabaj is the Bioinformatics Group Leader at the Malopolska Centre of Biotechnology, Jagiellonian University in Krakow. He is also the European Continental Director for the MetaSUB Consortium, and part of the organising committee of the CAMDA challenge.
Agata is a biotechnology graduate with a specialisation in bioinformatics from Silesian University of Technology. She is currently a research assistant at Malopolska Centre of Biotechnology and also a PhD student at Silesian University of Technology. Her work revolves around microarray and next-generation sequencing technologies. She is involved in the SEQC2 project as well as other projects aimed at finding methods for improved genes and alternative transcripts expression profiling
Dagmara Błaszczyk is a PhD student at the Malopolska Centre of Biotechnology, Jagiellonian University. She studied Biotechnology at Faculty of Automatic Control, Electronics and Computer Science at Silesian University of Technology. Her background is in bioinformatics, machine learning and image analysis.
Dedan is a PhD student at the Malopolska Centre of Biotechnology, Jagiellonian University under the Biomedical program. His background is in Biochemistry & Molecular Biology, and Bioinformatics, and was part of various research projects. Currently his focus is on metagenomics, and unearthing microbial patterns and interactions that explain their relationship with their ecological niche.
Kasia is a graduate of Bioinformatics at the Faculty of Biochemistry, Biophysics and Biotechnology at the Jagiellonian University. As a Lab Manager for bioinformatics groups she ensures that laboratories operate smoothly, which requires cooperation with partners and administration from and outside the MCB. On the other hand, as an independent biologist, she is involved in various research projects, such as the gut microbiome research project to support uniform hospitals in the fight
Michał Kowalski is a biologist(B.Sc) and biotechnologist (M.Sc) by training, with both degrees obtained at Jagiellonian University. He is in love with programming and data science, and constantly developing skills (especially machine learning) to make improvements in the world of bioinformatics. He is mainly interested in microbiomes and metagenomics by the example of participation in "Using the potential of the environmental microbiome in forensics" grant.
Witek is an AGH graduate (B. Eng. in ICT), currently doing his masters in IT at Jagiellonian University. He has a background in commercial programming, but his main point of focus is machine learning and its practical applications in different bioinformatical contexts. He is involved in various research projects such as weakly supervised information extraction from biomedical texts, a grant regarding analysis of gut microbiome of COVID-19 patients, or analysis of pulmonological risk.
The aim of the project is to explore forensic potentail of environmental microbiome. In the course of the project we will collect about 1000 samples (4 seasons, 80 locations, triplicates) which will be profiled with deep WMS. Thise will be further analysed with both classical and reference agnostic approaches in order to identify unique location marker which can be used to design targeted sequencing panel and well as predictive model.
The project is funded by The Nationale Center for Research and Development (DOB-BIO10/03/01/2019) and is run in cooperation with: Central Forensic Laboratory of the Police, Pomeranian Medical University, Warsaw Medical University, and Ardigen
Extended microbiome characterization by the exploitation of the microbial intra-community synergies -- towards better understanding of the Exposome
Scientific research improves our understanding of the influence of the 'environment' on human health and well-being. As 'environment' we should understand not only climate, different types of pollution, or how friendly the city design is but also all organisms (microbiome) that are living in our surrounding (city, work, home), 'on us' (skin) or 'in us' (gut). All these together are known as 'exposome'.
Thanks to technological advancement in past years we are now able to study those microbiomes more effectively and learn the ways of how they are affecting us. There are projects focusing on gut microbiome and its connection with diseases (e.g. inflammatory bowel syndrome or ulcerative colitis) while others are studying skin microbiome or what lives in our urban surroundings e.g. public transport systems such as subways.
All these studies, however, are mostly focused on the exploration and uncovering which bacteria/viruses/fungi we do see, what could be their function and what it really means to us and to our well-being. The missing component of those studies is knowledge and understanding of why some species are living together in specific places. The gain of such knowledge is crucial for understanding the complex functions of those microbes and what is their influence on our lives. Microbiomes should be seen as one 'meta-organism' where different organisms are delivering unique functions that provide a self sustainable living environment for them.
In our project, we will aim to discover those unknowns with novel Data Science and Big Data approaches for better understanding of such 'meta-organism', how certain species are contributing to the society, what are the dependencies among them in terms of their or our survival and reveal any visible and discreet connections between them. We will look at selected problems from three complementary views: i) who is there among known organisms, ii) what 'actions' are seen, iii) what is the composition of genetic material found. We will then combine this knowledge and explore it with context-specific information. This novel approach will allow us to discover new functionalities and/or new species that are relevant for the interesting phenomena.
Project is funded by National Science Centre SONATA BIS 10 programme (2020/38/E/NZ2/00598)
The City of Krakow, in cooperation with Prof. Wojciech Branicki (Human Genome Variation Research Group), Dr. Paweł Łabaj (Bioinformatics Research Group), and Prof. Krzysztof Pyrć (Virology Research Group) carried out an analysis of the contamination of urban space with the SARS-CoV-2 virus. Various locations in Krakow selected based on the analysis of human migration processes were monitored.
The work is done in collaboration with International MetaSUB consortium and its MetaCoV, MetaMED and MetaSEW projects. The work will continue and will allow quick identification of the threat or indicate the growing virus hazard before human cases appear.
The primary objective is to develop standard analysis protocols and quality control metrics for fit-for-purpose use of Next Generation Sequencing (NGS) data to enhance regulatory science research and precision medicine. The project consists of three specific aims: (1) to develop quality metrics for reproducible NGS results from both whole genome sequencing (WGS) and targeted gene sequencing (TGS), (2) to benchmark bioinformatics methods for WGS and TGS towards the development of standard data analysis protocols, and (3) to assess the joint effects of key parameters affecting NGS results and interpretation for clinical application.
We aim to build a molecular profile of cities around the globe to improve their design, functionality, and impact on health. Public transportation systems represent the densest interaction space for millions of people each day, and yet, there is little known about the dynamics of the microbiome and metagenomics profile on these surfaces, and most importantly, how these dynamics and our interactions with these surfaces can impact an individual’s health, as well as the health of a city.
The increasing relevance of Big Data forms one of the grand challenges in modern life sciences. Analysing large data sets is consequently emerging to be one of the scientific key techniques in the post-genomic era. Recently, the growing need for the analysis of massive data has further accelerated by the advent and fast development of high-throughput next-generation sequencing technologies and the necessarily increasing cohort size of biomedical studies. Still, the data analysis bottleneck limits the rate with which technological advances in genome-scale experimental platforms can actually provide new medical and biological insights.
CAMDA focuses on the analysis of massive data in the life sciences. It introduces and evaluates new approaches and solutions to the Big Data challenge. The conference presents new techniques in the field of bioinformatics, data analysis, and statistics for the handling and processing of large data sets, the combination of multiple data sources, and effective computational inference.
An essential part of CAMDA is its open-ended data analysis challenge of complex data sets, often featuring novel technological platforms, exceptionally large cohorts, and heterogeneous data sources and types. Academic and industrial researchers worldwide alike are invited to take the CAMDA challenge. Accepted contributions are presented in short talks, and the results of analyses are discussed and compared at the CAMDA conference. Both contestants and other interested researchers are welcome at the meeting. Posters can provide an additional opportunity for presenting and discussing work.
ATAC-seq (Assay For Transposase-Accessible Chromatin Sequencing) is a fast and sensitive high-throughput sequencing method for epigenomic profiling of open chromatin, DNA-binding proteins, and nucleosome position. ATAC-seq uses hyperactive Tn5 transposase to simultaneously cut and ligate adapters for high-throughput sequencing at regions of increased accessibility. This technique will allow multidimensional assays of the regulatory landscape of chromatin with a relatively simple and fast protocol.
The work was performed within EPIQC project.
CollaboratorsDaniela Bezdan, University of Tuebingen, Germany; Joaquin Dopazo, Fundación Progreso y Salud, Seville, Spain; Marius Dybwad, Norwegian Defence Research Establishment, Norway; Andre Kahles, ETH Zurich, Switzerland; David Kreil, Boku University Vienna, Austria; Christopher Mason, Weill Cornell, NY, U.S.A.; Joanna Polańska, Silesian University of Technology, Gliwice, Poland; Ryszard Przewłocki, Maj Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland; Witold Rudnicki, University of Białystok, Poland; Ugur Sezerman, Acibadem University, Turkey; Chen Suo, Fudan University, Shanghai, China; Klas Udekwu, Swedish University of Agricultural Sciences, Uppsala, Sweden; Wenzhong Xiao, Stanford University, U.S.A.;
Browse through a few of our select publications below to read the abstract