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Motivation. Cancer heterogeneity is observed at multiple biological levels. To improve our understanding of these differences and their relevance in medicine, approaches to link organ- and tissue-level information from diagnostic images and…
Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…
Detecting the interactions of genetic compounds like genes, SNPs, proteins, metabolites, etc. can potentially unravel the mechanisms behind complex traits and common genetic disorders. Several methods have been taken into consideration for…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…
Characterizing the transcriptome architecture of the human brain is fundamental in gaining an understanding of brain function and disease. A number of recent studies have investigated patterns of brain gene expression obtained from an…
Disease heterogeneity has been a critical challenge for precision diagnosis and treatment, especially in neurologic and neuropsychiatric diseases. Many diseases can display multiple distinct brain phenotypes across individuals, potentially…
A substantial focus of research in molecular biology are gene regulatory networks: the set of transcription factors and target genes which control the involvement of different biological processes in living cells. Previous statistical…
Whereas the relationship between criticality of gene regulatory networks (GRNs) and dynamics of GRNs at a single cell level has been vigorously studied, the relationship between the criticality of GRNs and system properties at a higher…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
Network medicine is an emerging area of research dealing with molecular and genetic interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale biomedical data generation offers a unique opportunity to assess…
Accurate diagnosis of psychiatric disorders plays a critical role in improving the quality of life for patients and potentially supports the development of new treatments. Many studies have been conducted on machine learning techniques that…
Dementia is a progressive neurodegenerative disorder with multiple etiologies, including Alzheimer's disease, Parkinson's disease, frontotemporal dementia, and vascular dementia. Its clinical and biological heterogeneity makes diagnosis and…
The cerebral cortex is composed of multiple cortical areas that exert a wide variety of brain functions. Although human brain neurons are genetically and areally mosaic, the three-dimensional structural differences between neurons in…
The brain's structural and functional systems, protein-protein interaction, and gene networks are examples of biological systems that share some features of complex networks, such as highly connected nodes, modularity, and small-world…
Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…
Functional connectivity plays an essential role in modern neuroscience. The modality sheds light on the brain's functional and structural aspects, including mechanisms behind multiple pathologies. One such pathology is schizophrenia which…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…