Sep 2026· Zenodo (CERN European Organization for Nuclear Research)
Bioinformatics and Genomic Networks
Abstract
The integration of artificial intelligence (AI) and deep learning with the biomedical research marks a critical inflection point, shifting the paradigm from addressing symptoms to predicting and acting at the molecular level. In many diagnostic models, the chain reaction triggered by a chronic infection is often overlooked. In this review, we examine the capability of AI models to unravel these complex dynamics within viral-host systems. By analyzing 39 key studies, we evaluate the application of novel computational methods in two major domains: advanced clinical diagnostics and de novo drug design. Silently existing chronic conditions, such as chronic Hepatitis, can lead to immune exhaustion, leaving individuals more susceptible to secondary infections including SARS-CoV-2 (COVID-19) and Human Papillomavirus (HPV). For diagnostics, we focus on genomic surveillance, radiomics, and Explainable AI (XAI) for identifying multi-organ pathologies. For pharmacology, we examine the transformative role of generative models, including AlphaFold 3, HelixFold 3, and large foundational models (Evo 2, Geneformer, ESM-2). We discuss Graph Neural Networks (GraphDTA) and diffusion models in successfully identifying novel antimicrobial agents like Halicin and Abaucin. Finally, we explore clinical and regulatory barriers to the full integration of AI in mapping patient pathologies.
Agile methods continue to gain popularity. In particular, the Scrum method appears to be on the verge of becoming a de-facto standard in the industry, leading the so called Agile movement. While there are success stories and recommendations, there is little scientifically valid evidence of the challenges in the adoptio...
A. Marchenko, P. Abrahamsson· Agile Conference· 59 citations· ⚡11
A comprehensive taxonomy of the challenges faced when a medium-scale organization decided to adopt software platforms is provided, namely: business challenges, organizational challenges, technical challenges, and people challenges.
Yaser Ghanam, F. Maurer, P. Abrahamsson· Information and Software Tec...· 41 citations· ⚡3
It is shown that high article processing charges are not sufficiently justified by the publishers, which often lack transparency and may prevent authors from adopting OA.
D. Graziotin, Xiaofeng Wang, P. Abrahamsson· Scientometrics· 21 citations· ⚡1
MCGLPPI, a novel geometric representation learning framework that combines graph neural networks (GNNs) with the MARTINI molecular coarse-grained (CG) model to predict overall PPI properties accurately and efficiently, offers an effective and efficient solution for PPI overall property predictions.
Yang Yue, Shu Li, Yihua Cheng et al.· bioRxiv· 15 citations
Abstract Predicting properties from coordinate–category data—sets of vectors paired with categorical information—is fundamental to computational science, manifesting in materials science as predicting formation energies or elastic moduli from crystal structures. While large language models (LLMs) have increasingly been...
Nawaf Alampara, Santiago Miret, Kevin Maik Jablonka· Nature Computational Science· 13 citations
PepPCBench enables a robust evaluation of PFNN-based methods and supports their continued development for peptide-protein structure prediction, and highlights the influence of peptide length, conformational flexibility, and training set similarity on prediction accuracy.
Si-Long Zhai, Huifeng Zhao, Ji-Ke Wang et al.· Journal of Chemical Informat...· 13 citations· ⚡1
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