MuCoMiD: A Multitask graph Convolutional Learning Framework for miRNA-Disease Association Prediction

Growing evidence from recent studies implies that microRNAs or miRNAs could serve as biomarkers in various complex human diseases. Since wet-lab experiments for detecting miRNAs associated with a disease are expensive and time-consuming, machine learning techniques for miRNA-disease association prediction have attracted much attention in...

CBA: Cluster-Guided Batch Alignment for Single Cell RNA-seq

The power of single-cell RNA sequencing (scRNA-seq) in detecting cell heterogeneity or developmental process is becoming more and more evident every day. The granularity of this knowledge is further propelled when combining two batches of scRNA-seq into a single large dataset. This strategy is however hampered by technical differences between...

Unraveling the Complexity of the Cancer Microenvironment With Multidimensional Genomic and Cytometric Technologies

Cancers are characterized by extensive heterogeneity that occurs intratumorally, between lesions, and across patients. To study cancer as a complex biological system, multidimensional analyses of the tumor microenvironment are paramount. Single-cell technologies such as flow cytometry, mass cytometry, or single-cell RNA-sequencing have...

Geobim for digital building permit process: Learning from a case study in Rotterdam

Among the digitalization processes which are being raised in Europe and in the world, the building permit process is seen as one of the priorities by municipalities, governmental institutions and standardization organizations. However, in current practice, the building permit issuing as well as the integration of geoinformation with BIM ...

Investigating the state of play of geoBIM across Europe

In both the Geographic Information (Geo) and Building Information Modelling (BIM) domains, it is widely acknowledged that the integration of data from both domains is beneficial and a crucial step in facing the multi-disciplinary challenges of our built environment. The result of this integration – which can broadly be termed GeoBIM –could...

An integrated approach of gene expression and DNA-methylation profiles of WNT signaling genes uncovers novel prognostic markers in Acute Myeloid Leukemia

Background The wingless-Int (WNT) pathway has an essential role in cell regulation of hematopoietic stem cells (HSC). For Acute Myeloid Leukemia (AML), the malignant counterpart of HSC, currently only a selective number of genes of the WNT pathway are analyzed by using either gene expression or DNA-methylation profiles for the identification of...

Data integration strategies for bioinformatics with applications in biomarker and network discovery

Nowadays, with large amounts of data becoming available, solving biological quests is becoming more and more a data-driven activity. To support this, there is a need for tools that enable the integration of the many sources of data. This thesis presents several avenues that can be taken, showing how integration can support research in the life...

Multiplatform observations for measuring wetland landscape topography

Data Integration over Distributed and Heterogeneous Data Endpoints

Data integration is a broad area encompassing techniques to merge data between data sources. Although there are plenty of efficient and effective methods focusing on data integration over homogeneous data, where instances share the same schema and range of values, their applications over heterogeneous data are less clear. This thesis considers...

Exploiting noisy and incomplete biological data for prediction and knowledge discovery

In modern molecular biology, the vast amount of experimental data enables us to obtain more comprehensive understanding of cellular activities, from transcription to metabolism. However, due to the inherent complexity of the cell and the various limitations of the measuring techniques, these data are often noisy and incomplete. Therefore,...