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AntigenApp: a laboratory data management system for nanobody generation and sequence analysis
<h4>Motivation</h4>Nanobodies are single domain antibodies derived from the unique heavy chain-only immunoglobulins of the camelid family, and have broad applications in biosciences, including as imaging and diagnostic agents. The generation of nanobodies is a multi-stage …
Read PDFDysregulated serum levels of human tissue kallikreins, hK7 and hK10, as potential biomarkers of asthma
<h4>Background</h4>Asthma is a highly prevalent inflammatory disease worldwide with limited diagnostic and therapeutic approaches.<h4>Objective</h4>This study was conducted to explore the possible role of hK7 and hK10 in asthma progression and evaluate them as potential biomarkers …
Read PDFA case-based explainable graph neural network framework for mechanistic drug repositioning
Drug repositioning offers a cost-effective alternative to traditional drug development by identifying new uses for existing drugs. Recent advances leverage Graph Neural Networks (GNNs) to model complex biological data, showing promise in predicting novel drug-disease …
Read PDF13CFLUX - third-generation high-performance engine for isotopically (non)stationary 13C metabolic flux analysis
<h4>Summary</h4>13C-based metabolic flux analysis is a cornerstone of quantitative systems biology, yet its increasing data complexity and methodological diversity place high demands on simulation software. We introduce 13CFLUX(v3), a third-generation simulation platform that combines a …
Read PDFTAGINE: fast taxonomy-based feature engineering for microbiome analysis
<h4>Summary</h4>TAGINE is a feature engineering algorithm that leverages the microbial taxonomic tree to optimize feature sets in microbiome data for predictive modeling. The algorithm starts with features at high taxonomic levels and iteratively splits them …
Read PDFOmniBio: an easy-to-use web app for kinetic growth parameter calculation from microplate reader data
OmniBio is a user-friendly web application designed to streamline the analysis of microbial growth curves from microplate reader data, eliminating the need for coding skills or cumbersome file preprocessing. Built in R, using the gcplyr …
Read PDFpolars-bio-fast, scalable, and out-of-core operations on large genomic interval datasets
<h4>Motivation</h4>Genomic studies very often rely on computationally intensive analyses of relationships between features, which are typically represented as intervals along a 1D coordinate system (such as positions on a chromosome). In this context, the Python …
Read PDFPredicting VNN resistance in European sea bass using machine learning on high dimensional low sample size data
Aquaculture is a rapidly growing sector in the global food production chain as a recognized fundamental source of high-quality proteins. One of the crucial tasks in aquaculture is phenotype prediction. While machine learning research has …
Read PDFExpressional and prognostic value of cytokine receptor-like factor 3 in liver hepatocellular carcinoma patients via integrated bioinformatics analyses and experiments
<h4>Background</h4>Liver hepatocellular carcinoma is a highly prevalent and lethal malignancy. The orphan cytokine receptor-like factor 3, although evolutionarily conserved and implicated in hematopoiesis and neuroprotection, remains poorly characterized in liver hepatocellular carcinoma.<h4>Objective</h4>To investigate the expression …
Read PDFA Neuro-Symbolic Bioinformatics Framework for Unlocking Chordate Physiological Dark Data and Validating Allometric Scaling
Animal functional trait data are essential for macroecology, but massive datasets remain locked in unstructured scientific literature. Traditional manual extraction is inefficient, and general-purpose artificial intelligence (AI) systems struggle with complex biological tables and numerical …
Read PDFCompeting subclones and fitness diversity shape tumor evolution across cancer types
<h4>Motivation</h4>Intratumor heterogeneity arises from ongoing somatic evolution and complicates cancer diagnosis, prognosis, and treatment. Reconstructing evolutionary dynamics typically requires spatiotemporal samples, which are often unavailable in clinical settings. Computational approaches that can infer tumor evolutionary …
Read PDFSPRM: spatial process and relationship modeling for multiplexed images
<h4>Motivation</h4>There has been tremendous recent growth both in technologies for measurement of many different markers in the same tissue and in resulting datasets (especially from projects such as HuBMAP and the Human Cell Atlas). Analysis …
Read PDFImprovement of a phylogenetic footprinting method for transcription factor binding sites recognition based on the use of bootstrap trials for the analysis of large bacterial genomic data
The rapid development of high-throughput sequencing technologies has led to an explosive accumulation of high-quality bacterial genome sequence data - their number is approaching three million, and this growth continues. This, in turn, provides additional …
Read PDFPDBe: enhanced structural data exploration to facilitate discovery
Protein Data Bank in Europe (PDBe) is a founding member of the worldwide Protein Data Bank (wwPDB), delivering open access to experimentally determined macromolecular structures. PDBe also delivers enriched annotations contributed by the PDBe-Knowledge Base …
Read PDFA Bayesian-Based Integrative Bioinformatics Analysis Nominates Oncogenic Drivers in Neuroblastoma
Identifying targetable oncogenic drivers remains a challenge in neuroblastoma, the most common extracranial solid malignancy in children. We applied a Bayesian algorithm for integrative analysis of expression and copy-number, iExCN, to nominate oncogenic drivers in …
Read PDFLipidLocator: an open source Shiny web application for spatial lipidomics
<h4>Motivation</h4>Spatial lipidomics enables the study of how lipids are distributed within tissues, providing insights into tissue structure and function. However, analyzing complex mass spectrometry (MS) imaging (MSI) data remains challenging due to limited tools for …
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