14 papers · ranked by Valyu relevance
Danila Valko, Jorge Marx Gómez
The Lightning Network (LN) is the most widely adopted second-layer solution for Bitcoin, enabling fast, low-cost transactions through a decentralized payment channel network. Despite its growing importance and the increasing interest from researchers across disciplines, progress in LN research is often impeded by…
Andrews Frimpong Adu, Elliot Sarpong Menkah, Peter Amoako-Yirenkyi, Samson Pandam Salifu
De novo genome assembly using de Bruijn graphs (DBGs) typically relies on fixed-length $k$-mers as the nodes of the graph. While this approach is effective, it presents a fundamental trade-off: smaller $k$ values tend to collapse repeats, whereas larger $k$ values can result in fragmentation, particularly in…
Taha Mohseni Ahooyi, Benjamin Stear, J. Alan Simmons, Vincent T. Metzger + 40 more
The Data Distillery Knowledge Graph (DDKG) is a framework for semantic integration and querying of biomedical data across domains. Built for the NIH Common Fund Data Ecosystem, it supports translational research by linking clinical and experimental datasets in a unified graph model. Clinical standards such as ICD-10…
F. Kirchner, D.C.F. Wieland, S. Irvine, S. Schimek + 11 more
Scientific communities have recognized the importance of well-documented metadata generated during research. However, ensuring that metadata is findable, accessible, interoperable, and reusable (FAIR) remains a significant challenge. To address this, scientific communities are working towards making metadata available…
Adrián Rošinec, Terézia Slanináková, Tomáš Pavlík, Róbert Randiak + 8 more
The volume of molecular dynamics (MD) simulation data shared via public repositories is rapidly increasing; however, fragmentation across multiple independent repositories, each employing distinct dataset identifiers and metadata schemas, hinders the efficient exploration and reuse of these data. In this study, we…
Karoline Mauer, Anandhi Iyappan, Simon Parker, Bilge Sürün + 7 more
Legal and technical developments drive data sharing via federated infrastructures, especially in the field of human omics. This requires interoperability across technical, syntactic, organizational, and semantic layers. The German Human Genome-Phenome Archive (GHGA) has been building a national, federated…
Michail Lazaratos, Neele Haacke, Jasmin Gaugel, Miriam Ulz + 4 more
metaKEGG is a comprehensive software package designed to streamline the visualization and integration of pathway enrichment results from multi-omics data, providing accessible and detailed insights into the molecular mechanisms driving health and disease. Unlike standard pipeline approaches, metaKEGG incorporates novel…
Harald Witte, Deepak Raveendran Unni, Philip Krauss, Vasundra Touré + 3 more
Background The Swiss Personalized Health Network (SPHN) facilitates the interoperability and secure sharing of health-related data for research in Switzerland, in line with the findable, accessible, interoperable, and reusable (FAIR) principles. Since medical datasets can be highly sensitive, access is often governed…
Lea Gütebier, Stefan Groß, Benjamin Winter, Max Blumenstock + 5 more
Background Efficiently finding and exploring relevant health studies is critical for informed, evidence-based health care. However, study information remains distributed across multiple resources, hindering interoperability, search, and reuse. Enhancing the findability of study data is a key challenge in promoting the…
Qi Wang, Shuting Chen, Xintian Miao, Yuntao Liu + 2 more
After constructing the MMD heterogeneous graph, we designed a novel random walk model to effectively capture the relational information among microbes, metabolites, and drugs within the graph. The model generates explainable and biologically meaningful walk sequences that integrate diverse microbe, drug, and metabolite…
Yeji Lee, Soyeong Kim, Yuna Park, Eunah Jeong + 6 more
Understanding the complex nature of multifunctional interactions among genes is crucial for interpreting omics data. We developed NetCrafter, an ontology-driven platform for constructing de novo gene networks that are specific to each input gene list and quantitatively defined by ontology-weighted similarity. By…
Chunyu Ma, Shaopeng Liu, Stephanie Won, David Koslicki + 1 more
Our MetagenomicKG integrates data from seven sources: GTDB taxonomy (), NCBI taxonomy (), KEGG (), RTX-KG2 (), BV-BRC (), MicroPhenoDB (), and NCBI AMRFinderPlus Prediction () (see [btag421-F1]). MetagenomicKG is a directed multigraph comprising 1.25 million nodes and 56 million edges. Nodes are categorized into 14…
Muhtasim Noor Alif, Khandakar Tanvir Ahmed, Sudipto Baul, Wei Zhang
Modern sequencing technologies can now capture multiple omic layers from the same biological system, but integrating these views into a coherent model is far from trivial. Graph-based deep learning has become an attractive strategy because it can represent complex molecular interactions and sample relationships in a…
Heinrich Lukas Weil, Kevin Schneider, Dominik Brilhaus, Timo Mühlhaus + 1 more
Scientific communication depends on the production of FAIR (findable, accessible, interoperable, reusable) data. Yet when datasets are shared, they remain hard to interpret across domains because annotations are tied to heterogeneous file formats and implicit semantics. We present a format-agnostic method for…