定量方法
The discovery of important biomarkers is a significant step towards understanding the molecular mechanisms of carcinogenesis; enabling accurate diagnosis for, and prognosis of, a certain cancer type. Before recommending any diagnosis,…
FRET experiments can yield state-specific structural information on complex dynamic biomolecular assemblies. However, FRET experiments need to be combined with computer simulations to overcome their sparsity. We introduce (i) an automated…
Identification of drug-target interactions (DTIs) plays a key role in drug discovery. The high cost and labor-intensive nature of in vitro and in vivo experiments have highlighted the importance of in silico-based DTI prediction approaches.…
Mathematical methods of information theory constitute essential tools to describe how stimuli are encoded in activities of signaling effectors. Exploring the information-theoretic perspective, however, remains conceptually, experimentally…
Tardigrades are microscopic animals widely known for their survival capabilities under extreme conditions. They are the focus of current research in the fields of taxonomy, biogeography, genomics, proteomics, development, space biology,…
Myelination plays an important role in the neurological development of infant brain and MRI can visualize the myelination extension as T1 high and T2 low signal intensity at white matter. We tried to construct a convolutional neural network…
The predictions from an accurate prognostic model can be of great interest to patients and clinicians. When predictions are reported to individuals, they may decide to take action to improve their health or they may simply be comforted by…
Best performing nuclear segmentation methods are based on deep learning algorithms that require a large amount of annotated data. However, collecting annotations for nuclear segmentation is a very labor-intensive and time-consuming task.…
Magnetoencephalography (MEG) and Electroencephalography (EEG) source estimates have thus far mostly been derived sample by sample, i.e., independent of each other in time. However, neuronal assemblies are heavily interconnected,…
The most widely used technology to identify the proteins present in a complex biological sample is tandem mass spectrometry, which quickly produces a large collection of spectra representative of the peptides (i.e., protein subsequences)…
Tandem mass spectrometry (MS/MS) is a high-throughput technology used toidentify the proteins in a complex biological sample, such as a drop of blood. A collection of spectra is generated at the output of the process, each spectrum of which…
The ultimate goal of drug design is to find novel compounds with desirable pharmacological properties. Designing molecules retaining particular scaffolds as the core structures of the molecules is one of the efficient ways to obtain…
Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment.…
The predetermination, formation and maintenance of the primary morphogenetic gradient (bicoid gradient) of the early Drosophila embryo involves many interrelated processes. Here we focus on a system-biological analysis of the processes of…
The article presents a 3D agent-based model to simulate the dynamics of redistribution of bicoid mRNA. The model is developed on the basis of the Skeledyne software [Odell and Foe, 2008]. The model reproduces active transport by molecular…
Biochemical signal transduction, a form of molecular communication, can be modeled using graphical Markov channels with input-modulated transition rates. Such channel models are strongly non-Gaussian. In this paper we use a linear noise…
Ensuring that crops use water and nutrients efficiently is an important strategy for increasing the profitability of farming and reducing the environmental load from agriculture. Subsurface irrigation can be an alternative to surface…
Microbial metabolism of fugitive hydrocarbons produces greenhouse gas (GHG) emissions from oil sands tailings ponds (OSTP) and end pit lakes (EPL) that retain semisolid wastes from surface mining of oil sands ores. Predicting GHG…
Deep neural networks have led to state-of-the-art results in many medical imaging tasks including Alzheimer's disease (AD) detection based on structural magnetic resonance imaging (MRI) data. However, the network decisions are often…
Motivation: Human genomic datasets often contain sensitive information that limits use and sharing of the data. In particular, simple anonymisation strategies fail to provide sufficient level of protection for genomic data, because the data…