定量方法
Navigating the complex landscape of single-cell transcriptomic data presents significant challenges. Central to this challenge is the identification of a meaningful representation of high-dimensional gene expression patterns that sheds…
Protocol standardization and sharing are crucial for reproducibility in life sciences. In spite of numerous efforts for standardized protocol description, adherence to these standards in literature remains largely inconsistent. Curation of…
Differential expression (DE) plays a fundamental role toward illuminating the molecular mechanisms driving a difference between groups (e.g., due to treatment or disease). While any analysis is run on particular cells/samples, the intent is…
Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…
The success of therapeutic antibodies relies on their ability to selectively bind antigens. AI-based antibody design protocols have shown promise in generating epitope-specific designs. Many of these protocols use an inverse folding step to…
Interactions between SARS-CoV-2 and the immune system during infection are complex. However, understanding the within-host SARS-CoV-2 dynamics is of enormous importance, especially when it comes to assessing treatment options. Mathematical…
Deep learning has proven to successfully learn variations in tissue and cell morphology. Training of such models typically relies on expensive manual annotations. Here we conjecture that spatially resolved gene expression, e.i., the…
Imbalance in the 3D structure of plants can be an important indicator of insufficient light or nutrient supply, as well as excessive wind, (formerly present) physical barriers, neighbor or storm damage. It can also be a simple means to…
Background and objective. Circular statistics and Rayleigh tests are important tools for analyzing the occurrence of cyclic events. However, current methods fail in the presence of measurement bias, such as incomplete or otherwise…
The discovery of therapeutics to treat genetically-driven pathologies relies on identifying genes involved in the underlying disease mechanisms. Existing approaches search over the billions of potential interventions to maximize the…
Bioprocesses are often characterized by nonlinear and uncertain dynamics. This poses particular challenges in the context of model predictive control (MPC). Several approaches have been proposed to solve this problem, such as robust or…
Mechanistic growth models play a major role in bioprocess engineering, design, and control. Their reasonable predictive power and their high level of interpretability make them an essential tool for computer aided engineering methods.…
Prediction of ligand binding sites of proteins is a fundamental and important task for understanding the function of proteins and screening potential drugs. Most existing methods require experimentally determined protein holo-structures as…
Alzheimer's disease has an increasing prevalence in the population world-wide, yet current diagnostic methods based on recommended biomarkers are only available in specialized clinics. Due to these circumstances, Alzheimer's disease is…
Systems biology relies on mathematical models that often involve complex and intractable likelihood functions, posing challenges for efficient inference and model selection. Generative models, such as normalizing flows, have shown…
Assessment of risk prediction models has primarily utilized measures of discrimination, the ROC curve AUC and C-statistic. These derive from the risk distributions of patients and nonpatients, which in turn are derived from a population…
Computational predictions of mass spectra from molecules have enabled the discovery of clinically relevant metabolites. However, such predictive tools are still limited as they occupy one of two extremes, either operating (a) by fragmenting…
Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be…
Micro RNAs (miRNA) are a type of non-coding RNA, which are involved in gene regulation and can be associated with diseases such as cancer, cardiovascular and neurological diseases. As such, identifying the entire genome of miRNA can be of…
It has been repeatedly reported that the collective dynamics of social insects exhibit universal emergent properties similar to other complex systems. In this note, we study a previously published data set in which the positions of…