Related papers: How shall we use the proteomics toolbox for biomar…
An endeavor central to precision medicine is predictive biomarker discovery; they define patient subpopulations which stand to benefit most, or least, from a given treatment. The identification of these biomarkers is often the byproduct of…
Precision medicine has become a central focus in breast cancer management, advancing beyond conventional methods to deliver more precise and individualized therapies. Traditionally, histopathology images have been used primarily for…
Proteins are complex biomolecules that play a central role in various biological processes, making them critical targets for breakthroughs in molecular biology, medical research, and drug discovery. Deciphering their intricate, hierarchical…
The histological assessment of human tissue has emerged as the key challenge for detection and treatment of cancer. A plethora of different data sources ranging from tissue microarray data to gene expression, proteomics or metabolomics data…
Motivation: Gene selection has become a common task in most gene expression studies. The objective of such research is often to identify the smallest possible set of genes that can still achieve good predictive performance. The problem of…
Discovering new medicines is the hallmark of human endeavor to live a better and longer life. Yet the pace of discovery has slowed down as we need to venture into more wildly unexplored biomedical space to find one that matches today's high…
Owing to the complexity of higher eukaryotic cells, a complete proteome is likely to be very difficult to achieve. However, advantage can be taken of the cell compartmentalization to build organelle proteomes, which can moreover be viewed…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and…
Large variability between cell lines brings a difficult optimization problem of drug selection for cancer therapy. Standard approaches use prediction of value for this purpose, corresponding e.g. to expected value of their distribution.…
The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long…
Imaging biomarkers in neuro-oncology are used for diagnosis, prognosis and treatment response monitoring. Magnetic resonance imaging is typically used throughout the patient pathway because routine structural imaging provides detailed…
Biological systems are influenced by fluid mechanics at nearly all spatiotemporal scales. This broad relevance of fluid mechanics to biology has been increasingly appreciated by engineers and biologists alike, leading to continued expansion…
Diffusion probabilistic models have made their way into a number of high-profile applications since their inception. In particular, there has been a wave of research into using diffusion models in the prediction and design of biomolecular…
Medical imaging is an important research field with many opportunities for improving patients' health. However, there are a number of challenges that are slowing down the progress of the field as a whole, such optimizing for publication. In…
The concept of personalised medicine in cancer therapy is becoming increasingly important. There already exist drugs administered specifically for patients with tumours presenting well-defined mutations. However, the field is still in its…
Motivation: Radiomics refers to the high-throughput mining of quantitative features from radiographic images. It is a promising field in that it may provide a non-invasive solution for screening and classification. Standard machine learning…
Prostate cancer is the second most common form of cancer, though most patients have a positive prognosis with many experiencing long-term survival with current treatment options. Yet, each treatment carries varying levels of intensity and…
Conventional histopathology has long been essential for disease diagnosis, relying on visual inspection of tissue sections. Immunohistochemistry aids in detecting specific biomarkers but is limited by its single-marker approach, restricting…
Accurate and interpretable diagnostic models are crucial in the safety-critical field of medicine. We investigate the interpretability of our proposed biomarker-based lung ultrasound diagnostic pipeline to enhance clinicians' diagnostic…