ECBG

The European Center for Bioinformatics and Genomics (ECBG) was established in 2007 as an interdisciplinary research consortium founded by the Institute of Bioorganic Chemistry of the Polish Academy of Sciences (IBCH PAS) and Poznan University of Technology (PUT). From the very beginning, its activities have been initiated and coordinated by Prof. Marek Figlerowicz (IBCH PAS) and Prof. Jacek Błażewicz (PUT).

The central idea behind ECBG was to create a multifunctional technological platform enabling large-scale, multi-level studies of complex biological systems in vitro, in vivo, and in silico. From its inception, the Center has focused on the development, implementation, and commercialization of innovative bioinformatics and multiomics technologies, particularly those supporting medical diagnostics and therapy.

The initial phase (2007-2013) aimed to build a strong foundation for advanced structural and functional genomics research. The ECBG consortium established modern laboratory facilities, implemented the first genomic data analysis tools, and launched national and international collaborations in the field of genomics. With approx. PLN 50M in funding, a unique national research center was created, bringing together complementary laboratories dedicated to structural genomics (Protein Bioengineering, Subcellular Structure Analysis, NMR), functional genomics (Microarrays and Deep Sequencing, Mass Spectrometry, Cell and Tissue Culture), and bioinformatics (Structural and Systems Bioinformatics, Nano- and Biosystems, RNA Structural Analysis, Functional Genomics, RNA Bioinformatics, Protein Bioinformatics).

In the second stage (2014-2020), focus shifted to high-throughput and large-scale genomic studies, with special emphasis on developing unique database resources and analytical tools. With funding from the Operational Programme Smart Growth (POIR 4.2) amounting to ~ PLN 112M, at ECBG, the world’s largest genomic databases for the Polish population were created: the Polish Genomic Map (~6,000 genomes) and the Polish Microbiome Map. Novel bioinformatics tools for large-scale genomic analysis and ancient DNA studies were also developed. Notably, the first interdisciplinary project in Poland on the origins of the Piast dynasty was carried out (PLN 6M), resulting in the establishment of the Polish Center for Archeogenomics.

Parallel investments included modernization of instrumentation and expansion of structural genomics facilities with advanced tools for biomolecular interaction studies (~PLN 3.5M). Since 2015, ECBG has been included in the Polish Research Infrastructure Roadmap as one of 70 centers strategic for science and the economy.

The third stage (2020-2023) focused on cutting-edge technologies in systems biology, particularly single-cell analyses and the application of artificial intelligence (AI) for integrating and analyzing multidimensional biomedical and clinical data. With funding of ~PLN 200M (POIR 4.2), ECBG established the MOSAIC platform, comprising: (i) state-of-the-art multiomics laboratory equipment, (ii) unique biomedical and clinical databases for over 5,000 oncology and cardiology patients, (iii) AI-based tools for data standardization, integration, and clinical decision support.

Additionally, in the framework of ECBG-MOSAIC project, new laboratories were opened at the IBCH PAS Center for Innovation and Social Education (over 1,000 m² of new space) and in Building B on Wieniawskiego Street (400 m² of modernized user labs).

At the same time, a high-throughput screening (HTS) platform was established with ~PLN 12.8M funding from the Ministry of Science and Higher Education, now integrated into the European infrastructure EU-OPENSCREEN ERIC.

Between 2020-2023, ECBG infrastructure supported over 100 projects annually, conducted by IBCH PAS teams and collaborators from more than 30 national and international institutions and companies. This resulted in nearly 600 scientific articles, seven patents, as well as numerous PhD, MSc, and BSc theses.

Looking ahead, ECBG plans to focus on the practical applications of AI in synthetic biology and medicine, aligning with global trends and European/national strategic priorities. In 2025, with PLN 40M funding from the FENG 2.4 program, ECBG launched the MOSAIC 3D project, aimed at creating infrastructure for disease modeling both in vitro and in silico. This includes establishing a biobank of induced pluripotent stem cell (iPSC) lines, addressing the urgent need for new research models to enable the development of personalized therapies.

ECBG is the only center in Poland offering the infrastructure for systemic, multi-omics research that integrates different levels of biological analysis. The uniqueness of ECBG is built on three pillars:

• state-of-the-art research equipment,
• database resources and bioinformatics tools,
• expertise and experience of the staff.

ECBG comprises the following laboratories:

From IBCH PAS:

• Laboratory of Genomics
• Laboratory of Single-Cell Analysis
• Laboratory of Mass Spectrometry
• Cell and Tissue Culture Laboratory
• Laboratory of Invertebrate Model Organisms
• Laboratory of Mammalian Model Organisms
• Laboratory of Bioinformatics

From PUT:

• Laboratory of Structural and Systems Bioinformatics
• Laboratory of Nano- and Biosystems
• Laboratory of RNA Structural Analysis
• Laboratory of Functional Genomics
• Laboratory of RNA Bioinformatics
• Laboratory of Protein Bioinformatics

ECBG infrastructure is placed across three locations in Poznan: (i) IBCH PAS campus on Noskowskiego Street; (ii) Polish Optical Internet Research Center (CBPIO), headquarters of PSNC, on Jana Pawła II Street; (iii) Poznan University of Technology Teaching Center on Piotrowo Street.

Research equipment

ECBG offers the most advanced research infrastructure in Poland, enabling comprehensive genomic analyses, including (epi)genomics, (epi)transcriptomics, and metagenomics, using nearly all currently available technologies. The Center includes, among others:

• two Biomek i5 automated pipetting stations (Beckman) for nucleic acid isolation and library preparation for 96 samples simultaneously,
• four next-generation sequencing platforms (Illumina: MiSeq, NextSeq 550, NovaSeq 6000, NovaSeq X Plus – the highest-throughput sequencer on the market, one of two in Poland), capable of sequencing 176 human genomes simultaneously (~17,000 genomes per year),
• the only third-generation Sequel IIe PacBio sequencer in Poland, generating HiFi long reads, ideal for detecting large genomic variants, gene isoforms, and transcripts,
• a semi-confocal Nikon Eclipse Ti2-E spinning disk microscope with a STED module for super-resolution imaging, allowing detailed ultrastructural analysis of cells and molecular interactions,
• Amnis ImageStream imaging flow cytometer (Cytek Biosciences) for advanced morphological and molecular analysis of cells in motion, combining flow cytometry with imaging,
• single-cell encapsulation systems Chromium Controller (10x Genomics) and Drop-Seq (Fluigent), enabling high-throughput isolation and analysis of individual cells, opening avenues to study cellular heterogeneity and discover new cell subpopulations.

As part Through the MOSAIC platform, ECBG also offers comprehensive proteomic and metabolomic analyses using advanced mass spectrometry (e.g., LC-ESI-timsTOF Pro, Orbitrap Exploris 480).

Computational resources and databases

ECBG operates one of the most powerful biomedical computing infrastructures in Europe. It consists of a 40-server cluster, each with two processors (2×32 CPU cores) and 2 TB RAM. Five servers are equipped with GPUs, each featuring four NVIDIA A100 cards for advanced AI calculations and training of complex neural network models. The infrastructure is supported by two ultra-fast NVMe arrays (100 TB each), a 100 Gbps network, and dedicated 25 Gbps storage interfaces, ensuring minimal data access latency.

Data storage and archiving are enabled by an integrated 5.8 PB repository (Dell PowerScale) supplemented with Dell PowerProtect. An additional 2.5 PB storage space is built on NetApp StorageGrid technology and integrated with NetApp FAS/AFF servers, supporting automated data replication (FabricPools) and 2D/3D visualization in augmented reality environments.

ECBG also houses unique genomic and multiomic datasets collected within the ECBG-GMP and ECBG-MOSAIC projects, including: (i) genomic data of 6,000 Polish residents (including national and ethnic minorities), creating the Polish Genome Map, the only globally representative database of the entire Polish population, and (ii) multiomic and clinical data from over 5,000 oncology and cardiology patients, available within the MOSAIC platform.

Biological models

Research at ECBG encompasses a diverse range of models: from viruses and bacteria, cell cultures, organoids, to invertebrates and mammals. The Center offers access to unique experimental models, including transgenic mouse lines for studies on cardiovascular and neurodegenerative diseases, as well as the aging process. Since 2025, the ECBG-MOSAIC 3D project has been establishing the first Polish biobank of patient-derived induced pluripotent stem cells (iPSCs) from cardiology and oncology patients.

Staff and expertise

ECBG’s greatest asset is its people – over 70 specialists in genomics, transcriptomics, flow cytometry, proteomics, metabolomics, structural biology, cell culture, model organisms, bioinformatics, and artificial intelligence.

ECBG experts provide comprehensive support – from grant applications and experimental design to research execution and data analysis. The Center’s interdisciplinary approach fosters scientific development and supports other institutions in initiating strategic and innovative projects.

Projects

Strategic projects that led to the establishment and expansion of ECBG:

ECBG – European Centre for Bioinformatics and Genomics – MOSAIC 3D (FENG.02.04-IP.04-0012/24). Co‑funded under the European Funds for the Modern Economy 2021-2027, Action 2.4 Research Infrastructure for the Modern Economy. Implemented by IBCH PAS together with the affiliated Poznan Supercomputing and Networking Center. Project Leader: Prof. Marek Figlerowicz; Deputy Project Leaders: Dr. Natalia Koralewska, Dr. Ireneusz Stolarek. Project duration: 2025-2028.

ECBG – European Centre for Bioinformatics and Genomics – MOSAIC (POIR.04.02.00-00-D017/20). Co‑funded by the European Regional Development Fund under the Operational Programme Smart Growth 2014-2020. Implemented by a consortium: IBCH PAS (leader) together with the affiliated Poznan Supercomputing and Networking Center, Poznan University of Technology, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, and Stefan Kardynał Wyszynski National Institute of Cardiology. Project Leader: Prof. Marek Figlerowicz; Deputy Project Leaders: Dr. Natalia Koralewska, Dr. Eng. Cezary Mazurek, Dr. Ireneusz Stolarek. Project duration: 2021-2023.

ECBG – European Centre for Bioinformatics and Genomics (POIR.04.02.00-30-A004/16). Co‑funded by the European Regional Development Fund under the Operational Programme Smart Growth 2014-2020. Implemented by IBCH PAS and Poznan University of Technology. Project Leader: Prof. Marek Figlerowicz; Deputy Project Leader: Prof. Luiza Handschuh. Project duration: 2016-2023.