Documents

This workflow is part of the EJP RD case study on CAKUT published here: Bayjanov, J.R., Doornbos, C., Ozisik, O. et al. Integrative analysis of multi-omics data reveals importance of collagen and the PI3K AKT signalling pathway in CAKUT. Sci Rep 14, 20731 (2024). https://doi.org/10.1038/s41598-024-71721-8

Beyond Topology: Deterministic and Order-Preserving Graph Visualization with the Keçeci Layout

Mehmet Keçeci1 1ORCID : https://orcid.org/0000-0001-9937-9839, İstanbul, Türkiye

Received: 03.07.2025

Özet/Abstract:

The visualization of scientific data is a fundamental step in uncovering hidden patterns and relationships within complex systems. While conventional force-directed graph layout algorithms (e.g., spring layout) are effective at displaying the general topology and clustering tendencies of ...

Protein domains can be viewed as building blocks, essential for understanding structure-function relationships in proteins. However, each domain database classifies protein domains using its own methodology. Thus, in many cases, boundaries between different domains or families differ from one domain database to the other, raising the question of domain definition and enumeration. The answer to this question cannot be found in a single database. Rather, expert integration and curation of various ...

Keçeci Deterministic Zigzag Layout (Keçeci Zigzag Layout Algorithm, Keçeci Layout) is a deterministic node layout algorithm designed for graph visualization in Python. Its primary purpose is to position the nodes of a graph in a predefined, sequential, and repeatable manner. The algorithm processes nodes sequentially, placing them along a user-defined primary axis (e.g., top-down or left-to-right) while applying an offset on the secondary axis in a zigzag pattern. This zigzag pattern helps prevent ...

Many systems encountered in nature and engineering exhibit complex and hierarchical geometric structures. Fractal geometry provides a powerful tool for understanding and modeling these structures. However, existing deterministic circle packing fractals, such as the Apollonian gasket, often adhere to fixed geometric rules and may fall short in accurately reflecting the diversity of observed structures. Addressing the need for greater flexibility in modeling physical and mathematical systems, this ...

This study comprehensively examines the profound technological and methodological synergies existing between observations made via interferometric detectors such as LIGO and Virgo, which have revolutionized the field of gravitational wave (GW) astrophysics, and the rapidly advancing quantum computing (QC) technologies. As both disciplines aim to perform measurements pushing the limits of precision, the effective control and mitigation of environmental and quantum-originated noise pose a critical ...