Projects

Academic projects

• Role of transposable elements and PIWI-interacting RNAs in myelodysplastic syndrome and their potential clinical applications
  • project ID: NU20-03-00412
  • partners: Institute of Hematology and Blood Transfusion
  • annotation: Myelodysplastic syndrome (MDS) is a malignant hematopoietic disorder characterized by aberrant differentiation of hematopoietic stem cells (HSCs). Genome instability is one of the key features of MDS HSCs and mobilization of transposable elements (TEs) is a known destabilizing factor of the genome integrity. PIWI-interacting RNAs (piRNAs) inhibit TE mobilization, functioning as central players in stem cell mechanisms to preserve genome integrity. Despite recent advances in the understanding of MDS pathogenesis, the role of TEs and piRNAs in development and progression of the disease has not been studied yet. We will analyze transcription of TEs and piRNAs by next generation sequencing and examine their activity in MDS. Besides the implication in the MDS pathogenesis, utilization of TEs and piRNAs as potential molecular markers of the disease progression will be tested. Moreover, possible effect of azacitidine treatment on TE and piRNA transcriptions will be addressed to prove their applicability as novel predictive markers for the drug responsiveness and relapse prevention.
• Circular RNAs and their relation to RNA splicing in the pathogenesis of myelodysplastic syndromes
  • project ID: GA20-19162S
  • partners: Institute of Hematology and Blood Transfusion
  • annotation: Mutations in RNA splicing factors represent the most common molecular alterations in myelodysplastic syndromes (MDS). Despite some advances in the understanding of their roles in MDS pathogenesis, the impact of mutated splicing factors on circular RNAs (circRNAs) has not been studied. CircRNAs constitute a class of RNAs with a covalently closed continuous loop that has recently been discovered to be widespread and abundant. Because most circRNAs are produced by backsplicing, we hypothesize that the aberrant splicing seen in MDS also affects circRNA formation. With respect to the various regulatory functions of circRNAs, their deregulation likely contributes to MDS pathogenesis. Moreover, altered levels of particular circRNAs might serve as new molecular biomarkers for the prognosis and therapeutic response in MDS management. Moreover, circRNAs might form a new class of molecular targets for MDS treatment. In this project, we will use next generation sequencing and perform integrative data analyses and functional studies to identify and characterize circRNA roles in MDS pathogenesis.
• Operational tolerance in kidney transplantation
  • project ID: NV19-06-00031
  • partners: Institute for Clinical and Experimental Medicine
  • annotation: Operational tolerance (OT) has been observed in patients who stopped their immunosuppression for more than a year and no destructive alloimmune response was noticed. B cell-related immunophenotypic and transcriptomic signatures were identified so far among OT kidney transplant recipients. The aim of this project is to evaluate peripheral blood transcriptomic profile using RNA-sequencing in newly identified european cohort of OT patients and compared it with well-defined controls. Moreover, we plan to validate protective role of several transcripts associated with OT in a large patient population. Next, we plan to evaluate B cell immunophenotypes in patients with long-term graft function and with chronic rejection. The identification and validation of biomarkers of operational tolerance / immune quiescence may thus allow construct bedside clinical tests enable to guide immunosuppression.
• Long non-coding RNAs in myelodysplastic syndromes: clinical relevance and implication in the pathogenesis
  • project ID: NV17-31398A
  • partners: Institute of Hematology and Blood Transfusion
  • annotation: Long non-coding RNAs (lncRNAs) regulate hematopoietic lineage differentiation at almost every stage and their abnormal expression may contribute to various hematopoietic disorders. They may become useful diagnostic and prognostic markers contributing to detection of the MDS progression and increase of the patients’ survival, and even potential therapeutic targets in future. In the proposed project, genome-wide screening of lncRNA levels in MDS patients will be employed to compare expression profiles between various risk groups of patients with the aim to find lncRNAs with significantly different levels and relevance to MDS diagnostics. Because the knowledge about individual lncRNAs is often limited to the simple transcript annotation, the causes, roles and consequences of deregulated lncRNAs in the pathogenesis of MDS will be studied by experimental and computational approaches.
• XGENE.ORG – a public tool for integrated analysis of microarray, microRNA and methylation data
  • project ID: NT14539
  • partners: Institute of Hematology and Blood Transfusion
  • annotation: This project significantly extends the current public XGENE.ORG web tool in order to facilitate integrated knowledge discovery from raw mRNA, miRNA and methylation data with concurrent utilization of the structured genomic background knowledge. There are two main project outputs: the tool (and the methodology behind it) itself and the particular results reached in cooperation with clinical and biological departments working in the fields of myelodysplastic syndrome and germ cell tumors. The solution is based on relational learning algorithms, stochastic optimization, statistics and development of web applications. The tool outputs namely 1) biologically understandable patterns having a form of sets or annotated networks of specific related elements such as genes, proteins, miRNA sequences or methylation islands interconnected with particular subsets of biological samples under study and 2) predictive models classifying samples characterized by measurable molecular markers with unknown phenotypes.
• SUPREME: Sustainable Predictive Maintenance for Manufacturing Equipment
  • project ID: EU FP7 314311
  • partners: CENTRE TECHNIQUE DES INDUSTRIES MECANIQUES (CETIM) – project coordinator
  • annotation: The project impact was the proof of predictive maintenance efficiency, reduction of down-time and energy consumption in manufacturing industry, demonstrated in a coated paper mill. The project resulted in the development of the SUPREME reference model, which defined requirements for the SUPREME modules and their interactions. It delivered a state-of-the-art overview, specified a test platform with strong involvement from paper industry partners, and initiated instrumentation to collect machine data for tool development. Furthermore, it enhanced methodologies and tools for the Reliability and Maintainability module to support future applications.

Industrial projects

• Open prediction system
  • partners: Certicon, TDE
  • annotation: This project developed a universal prediction system that combined AI techniques with classical statistical analysis. The system was originally designed for the prediction of gas consumption, where it helped local distribution companies manage daily contractual limits. Its application demonstrated that the method reduced penalties by improving the accuracy of short-term consumption forecasts.
• Intelligent Diagnosis And Learning In Centrifugal Pumps
  • partners: Rockwell Automation, Certicon
  • annotation: This project addressed the problem of on-line diagnosis of cavitation in centrifugal pumps. The solution was in development and application of the Open Prediction System (OPS) to cavitation diagnosis. The application of OPS resulted in an algorithmic framework for diagnosis of cavitation in centrifugal pumps. The diagnosis was based on repeated evaluation of a data scan providing full record of input signals which are observed for a fixed short period of time. Experimental verification of the algorithmic framework and the proposed methodology proved that a condition monitoring system built upon them was capable of diagnosing a wide range of cavitation conditions that can occur in a centrifugal pump, including the very early incipient cavitation.
• Intelligent Pump Diagnostics and Control
  • partners: Certicon, Grundfos
  • annotation: This project developed a methodology for intelligent pump control in household heating systems. The control strategy was designed to continuously balance flow demands, user comfort, and electrical power consumption by adjusting pump speed. Comfort was defined as minimizing both deviations from the set temperature and noise within the system.
• Capitalizing on Aggregate Data for Gaining Process Understanding
  • partners: Rockwell Automation, Abbott
  • annotation: Continuous improvement of pharmaceutical manufacturing operations has not evolved at the same rate as it has in other industries. Though time-series data are routinely collected as part of equipment control systems, the data are usually not thoroughly evaluated. This project investigated batch data, in-process and release test data, and time-series data from various operations in an effort to determine which parameters are most critical to the target pharmaceutical variable (dissolution, yield, etc.). We provided an evidence of the value of process analytical technology (PAT) initiatives focused on the analysis of historical process data through the quantification of the impact of individual process and raw material parameters on key product quality attributes.