Related papers: Large-scale generation of computational models fro…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…
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…
Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise…
Our ability to produce human-scale bio-manufactured organs is critically limited by the need for vascularization and perfusion. For tissues of variable size and shape, including arbitrarily complex geometries, designing and printing…
Synthetic data generation using large language models (LLMs) demonstrates substantial promise in addressing biomedical data challenges and shows increasing adoption in biomedical research. This study systematically reviews recent advances…
Interrogation of biological pathways is an integral part of omics data analysis. Large language models (LLMs) enable the generation of custom pathways and gene sets tailored to specific scientific questions. These targeted sets are…
Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional…
This paper presents a comprehensive survey of various established mathematical models pertaining to Somitogenesis, a biological process. The study begins by revisiting and replicating the findings from prominent research papers in this…
Understanding individual-level human mobility is critical for a wide range of applications. As such, real-world trajectory datasets provide valuable insights into actual movement behaviors and patterns of life but are often constrained by…
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Mathematical models and algorithms are an essential part of mathematical research data, as they are epistemically grounding numerical data. In order to represent models and algorithms as well as their relationship semantically to make this…
In this paper, a multi-objective approach for the design of composite data-driven mathematical models is proposed. It allows automating the identification of graph-based heterogeneous pipelines that consist of different blocks: machine…
While Multimodal Large Language Models have achieved human-like performance on many visual and textual reasoning tasks, their proficiency in fine-grained spatial understanding, such as route tracing on maps remains limited. Unlike humans,…
Multi-omics data offer unprecedented insights into complex biological systems, yet their high dimensionality, sparsity, and intricate interactions pose significant analytical challenges. Network-based approaches have advanced multi-omics…
Biomedical knowledge is fragmented across siloed databases -- Reactome for pathways, STRING for protein interactions, ClinicalTrials.gov for study registries, DrugBank for drug vocabularies, DGIdb for drug-gene interactions, SIDER for side…
With the rapid development of autonomous vehicles, there is an increasing demand for scenario-based testing to simulate diverse driving scenarios. However, as the base of any driving scenarios, road scenarios (e.g., road topology and…
The BioModels database is one of the premier databases for computational models in systems biology. The database contains over 1000 curated models and an even larger number of non-curated models. All the models are stored in the…