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<h4>Background</h4>With the rapid progress of molecular medicine, new target therapies for solid tumors have become available, leading to the creation of molecular tumor boards (MTBs) designated to evaluate potential individualized treatment options. Unlike other solid …
Read PDFOncogenic condensates act as biophysical sanctuaries that stabilize malignant survival programs. However, a universal regulator capable of orchestrating the integrated biophysical axes governing cellular phase behavior has remained elusive. Here, we introduce a sovereign singularity …
Read PDF<h4>Motivation</h4>The biological functions of RNAs are tightly connected to their specific RNA structures. As experimental techniques to determine high-accuracy structures are costly and time-consuming, computational prediction approaches became indispensable for biological RNA research; most notably, …
Read PDFBACKGROUND: The nectin cell adhesion molecule 4 (NECTIN4) has been implicated in tumor progression and immune evasion, yet its role and translational targeted imaging potential in lung cancer remain unclear. Therefore, this study aims to …
Read PDF<h4>Motivation</h4>Protein language models (PLMs) have revolutionized computational biology through their ability to generate powerful sequence representations for diverse prediction tasks. However, their black-box nature limits biological interpretation and translation to actionable insights. Bridging this gap …
Read PDFWhole-exome sequencing (WES) has revolutionized the diagnostics of hereditary diseases, yet its efficacy varies across populations. Data on the genetic architecture of rare hereditary disorders in many Russian regions, including the ethnically diverse Khanty-Mansi Autonomous …
Read PDF<h4>Background</h4>Metallic and metal oxide nanoparticles are increasingly explored as antimicrobial biomaterials in endodontics due to their multi-target mechanisms of action, largely mediated by metal ion release (e.g., Ag<sup>+</sup>, Cu<sup>+</sup>). However, bacterial metal resistance systems, particularly …
Read PDFIn response to the need for greater cohesion among regional conferences, the Asia Pacific Bioinformatics Network (APBioNET) set out in 2015 to realize a long-held aspiration-a single, unifying bioinformatics "super conference" for the Asia & …
Read PDFThe European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), hosted at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), remains a global, open-access platform for the submission, archiving, dissemination, and reuse of nucleotide sequence data. In 2025, …
Read PDF<h4>Motivation</h4>Methods for sharing gene regulatory information and knowledge on FAIR principles, particularly in the context of tissue-specific gene regulation, remain poorly defined and implemented, hampering discovery and clinical genetic diagnosis.<h4>Results</h4>We specified FAIR principles for tissue-specific …
Read PDF<h4>Motivation</h4>Long COVID is a multisystem condition characterized by persistent symptoms such as fatigue, cognitive impairment, and systemic inflammation following COVID-19 infection. However, its mechanisms remain poorly understood. In this study, we applied the quantum walk, …
Read PDF<h4>Background</h4>Deep mutational scanning (DMS) provides comprehensive maps of protein variant effects but remains experimentally intensive. Machine learning (ML) approaches have the potential to reduce experimental burden of DMS by predicting the functional impact of substitutions …
Read PDF<h4>Motivation</h4>Combinatorial drug therapy holds great promise for tackling complex diseases, but the vast number of possible drug combinations makes exhaustive experimental testing infeasible. Computational models have been developed to guide experimental screens by assigning synergy …
Read PDF<h4>Background and objectives</h4>Next-generation sequencing (NGS) is transforming clinical diagnostics by enabling the detection of genetic variation with unprecedented precision. However, successful implementation of NGS workflows necessitates stringent quality control. This study introduces Molecular Genetics Dashboard …
Read PDFSoftware containerization has become a cornerstone of modern computational biology, enabling researchers to package code, dependencies, and execution environments in portable and reusable units. Containers support reproducibility, facilitate collaboration, and lower barriers to deploying complex …
Read PDFWe aim to highlight problems with the biological interpretation of computationally-derived hypoxia signatures for neuro-oncology research. By reviewing important experimental work in the field, we discuss common misinterpretations of the concepts of normoxia and hypoxia. …
Read PDF<h4>Background</h4>Low-coverage whole-genome sequencing (lcWGS) has emerged as a cost-effective and robust approach for population genomic studies. Despite its advantages, publicly available resources for large-scale lcWGS datasets remain limited. To our knowledge, there is yet a …
Read PDF<h4>Summary</h4>cAMRah is a curated workflow designed to predict antimicrobial resistance (AMR) genes in microbial genomes, either in the cloud or on any personal computer running Docker containers. Numerous AMR gene-finding packages exist, each utilizing different …
Read PDF<h4>Motivation</h4>Although common data models for electronic health record (EHR) data can facilitate multi-site data organization and querying, the same medical event may still be coded differently between healthcare systems. In this paper, we present statistical …
Read PDFThe growing availability of high-dimensional, complex datasets demands analysis methods that are both interpretable and flexible. We introduce FlowSets, a novel framework for identifying and analysing flows-fuzzy, interpretable patterns-across multiple, diverse, and heterogeneous data sets. …
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