定量方法
Growing evidence from recent studies implies that microRNA or miRNA could serve as biomarkers in various complex human diseases. Since wet-lab experiments are expensive and time-consuming, computational techniques for miRNA-disease…
Automation is becoming ubiquitous in all laboratory activities, leading towards precisely defined and codified laboratory protocols. However, the integration between laboratory protocols and mathematical models is still lacking. Models…
Light-sheet fluorescence microscopy (LSFM) enables real-time whole-brain functional imaging in zebrafish larvae. Conventional one photon LSFM can however induce undesirable visual stimulation due to the use of visible excitation light. The…
Biological signaling pathways based upon proteins binding to one another to relay a signal for genetic expression, such as the Bone Morphogenetic Protein (BMP) signaling pathway, can be modeled by mass action kinetics and conservation laws…
Sickle cell anemia is a genetic disorder that is widespread in many regions of the world. Early diagnosis through screening and preventive treatments are known to reduce mortality in the case of sickle cell disease (SCD). In addition, the…
In the context of the EU GRACIOUS project, we propose a novel procedure for similarity assessment and grouping of nanomaterials. This methodology is based on the (1) Arsinh transformation function for scalar properties, (2) full curve shape…
Due to its implication in cancer treatment, the Warburg Effect has received extensive in silico investigation. Flux Balance Analysis (FBA), based on constrained optimization, was successfully applied in the Warburg Effect modelling. Yet,…
In the context of the EU Horizon 2020 GRACIOUS project, we proposed a quantitative Weight of Evidence (WoE) approach for hazard classification of nanomaterials (NMs). This approach is based on the requirements of the European Regulation on…
Recent advances in machine learning have enabled generative models for both optimization and de novo generation of drug candidates with desired properties. Previous generative models have focused on producing SMILES strings or 2D molecular…
Microbiology culture reports contain critical information for important clinical and public health applications. However, microbiology reports often have complex, semi-structured, free-text data that present a barrier for secondary use.…
Research into deep learning models for molecular property prediction has primarily focused on the development of better Graph Neural Network (GNN) architectures. Though new GNN variants continue to improve performance, their modifications…
Hypertension is the leading global cause of cardiovascular disease and premature death. Distinct hypertension subtypes may vary in their prognoses and require different treatments. An individual's risk for hypertension is determined by…
Urinalysis is a standard diagnostic test to detect urinary system related problems. The automation of urinalysis will reduce the overall diagnostic time. Recent studies used urine microscopic datasets for designing deep learning based…
We introduce the RIKEN Microstructural Imaging Metadatabase, a semantic web-based imaging database in which image metadata are described using the Resource Description Framework (RDF) and detailed biological properties observed in the…
Effective biosecurity practices in swine production are key in preventing the introduction and dissemination of infectious pathogens. Ideally, biosecurity practices should be chosen by their impact on bio-containment and bio-exclusion,…
Mathematical modeling and simulation is a promising approach to personalized cancer medicine. Yet, the complexity, heterogeneity and multi-scale nature of cancer pose significant computational challenges. Coupling discrete cell-based models…
In most models of collective motion in animal groups each individual updates its heading based on the current positions and headings of its neighbors. Several authors have investigated the effects of including anticipation into models of…
Animal groups frequently move in a highly organized manner, as represented by flocks of birds and schools of fish. Despite being an everyday occurrence, we do not yet fully understand how this works. What type of social interactions between…
Motivation: The importance of clinical data in understanding the pathophysiology of complex disorders has prompted the launch of multiple initiatives designed to generate patient-level data from various modalities. While these studies can…
Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic…