The COVID-19 pandemic highlighted the need for a rapid, convenient, and scalable diagnostic method for detecting a novel pathogen amidst a global pandemic. While command-line interface tools offer automation for SARS-CoV-2 Oxford Nanopore Technology...
Protein structure prediction servers use various computational methods to predict the three-dimensional structure of proteins from their amino acid sequence. Predicted models are used to infer protein function and guide experimental efforts. This can...
Leptin is an adipocyte-derived hormone that orchestrates different physiological processes, including energy balance, thermogenesis, immune regulation, reproduction, and tissue remodeling. These effects are mediated through interaction with the CRH2...
Deficit of human ornithine aminotransferase (hOAT), a mitochondrial tetrameric pyridoxal-5′-phosphate (PLP) enzyme, leads to gyrate atrophy of the choroid and retina (GA). Although 70 pathogenic mutations have been identified, only few enzymati...
Precision medicine is facing a critical transition driven by the growing complexity of biological data and the insufficient ability of current models to translate such data into clinically meaningful information. Linear, single-gene approaches are no...
One of the known potential effects of disease-causing amino acid substitutions in proteins is to modulate protein-protein interactions (PPIs). To interpret such variants at the molecular level and to obtain useful information for prediction purposes,...
The human operator largely relies on the perception of remote environmental conditions to make timely and correct decisions in a prescribed task when the robot is teleoperated in a remote place. However, due to the unknown and dynamic working environ...
Although not yet truly ‘comprehensive’, modern mass spectrometry-based experiments can generate quantitative data for a meaningful fraction of the human proteome. Importantly for large-scale protein expression analysis, robust data pipelines are in p...
Brewers’ spent grain (BSG) represents the major byproduct of the brewing industry and remains largely underutilized. While BSG contains a rather high amount of protein, poor functional properties limit its use as a functional ingredient for foo...
Protein–protein interactions (PPIs) are fundamental processes governing cellular functions, crucial for understanding biological systems at the molecular level. Compared to experimental methods for PPI prediction and site identification, comput...
Over the past few decades, the number of available structural bioinformatics pipelines, libraries, plugins, web resources and software has increased exponentially and become accessible to the broad realm of life scientists. This expansion has shaped...
Plasma membrane Ca2+-ATPases (PMCA) are activated by calmodulin (CaM) via a C-terminal calmodulin-binding domain, CaMBD. Although specific mutations in this domain have been linked to disease, the broader impact of alternative substitutions across th...
Background: Bioinformatics is increasingly used in various scientific works. Large amounts of heterogeneous data are being generated these days. It is difficult to interpret and analyze these data effectively. Several software tools have been develop...
Research on food-derived bioactive peptides is expanding and the need for a convenient online platform that combines a foolproof and intuitive user interface with a reliable database and tools for prediction and analysis is rising. In this regard, th...
Whole-genome sequencing (WGS) of bacterial pathogens is widely conducted in microbiological, medical, and clinical research to explore genetic insights that could impact clinical treatment and molecular epidemiology. However, analyzing WGS data of ba...
In this work, we describe the implementation of an infrastructure of conversational chatbots by using natural language processing and training within the Rasa framework. We use this infrastructure to create a chatbot assistant for the users of a bioi...
16 December 2022
Human–computer interaction tends to be intelligent and driven by technological innovation. However, there is a digital divide caused by usage barriers for older users when interacting with complex tasks. To better help elderly users efficiently...
The assembly of picornavirus capsids proceeds through the stepwise oligomerization of capsid protein subunits and depends on interactions between critical residues known as hotspots. Few studies have described the identification of hotspot residues a...
Protein–protein interactions (PPIs) play a central role in regulating cellular processes. However, the identification and characterization of senescence-associated PPIs remain challenging. In this study, we developed and evaluated an integrativ...
This paper proposes a novel three-layered software architecture for processing and analyzing sequences, medical images, and patient-reported outcomes (PROs). The aim is to provide a comprehensive end-to-end solution for patient diagnosis by integrati...
Strawberry species (Fragaria spp.) are known as the “queen of fruits” and are cultivated around the world. Over the past few years, eight strawberry genome sequences have been released. The reuse of these large amount of genomic data, and...
Precision medicine has been revolutionized by the advent of high-throughput next-generation sequencing (NGS) technology and development of various bioinformatic analysis tools for large-scale NGS big data. At the population level, biomedical studies...
The process of viral integration into the host genome is an essential step of the HIV-1 life cycle. The viral integrase (IN) enzyme catalyzes integration. IN is an ideal therapeutic enzyme targeted by several drugs; raltegravir (RAL), elvitegravir (E...
Next Generation Sequencing Technologies (NGS), particularly metabarcoding, are valuable tools for authenticating foodstuffs and detecting eventual fraudulent practices such as species substitution. This technique, mostly used for the analysis of prok...
The fungal secretome is the main interface for interactions between the pathogen and its host. It includes the most important virulence factors and effector proteins. We integrated different bioinformatic approaches and used the newly drafted genome...
Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality worldwide, characterized by marked molecular heterogeneity, late-stage diagnosis, and limited therapeutic options. Emerging evidence highlights the interplay between c...
In recent years, the use of computational pipelines for the analysis of omic data has become routine in bioinformatics, particularly with the advent of Next-Generation Sequencing (NGS) technologies. These technologies generate vast amounts of data th...
Proteins are crucial players of biological interactions within and between the organisms and thus it is important to understand the role of proteins in successful partnerships, such as insect vectors and their plant viruses. Proteomic approaches have...
Non-coding RNAs, such as miRNAs and piRNAs, play critical roles in gene regulation through base-pairing interactions with their target molecules. The recent development of the crosslinking, ligation, and sequencing of hybrids (CLASH) method has allow...
Individualized medicine enables better diagnoses and treatment decisions for patients and promotes research in understanding the molecular underpinnings of disease. Linking individual patient’s genomic and molecular information with their clinical ph...
Background/Objectives: The rapid expansion of targeted therapies has reshaped oncology by exploiting ligand-receptor interactions (LRI) to improve treatment specificity and patient outcomes. However, the data describing these ligands remain fragmente...
Background/Objectives: Mitochondrial DNA (mtDNA) is an important resource for understanding human ancestry, population diversity, and the molecular mechanisms of mitochondrial diseases. However, analyzing mtDNA thoroughly often requires advanced bioi...
The human cytomegalovirus (HCMV)-encoded cyclin-dependent kinase (CDK) ortholog pUL97 associates with human cyclin B1 and other types of cyclins. Here, the question was addressed whether cyclin interaction of pUL97 and additional viral proteins is de...
The emergence of Large Language Models (LLMs) has significantly advanced computational biology, yet their integration into autonomous, multi-agent systems (MASs) and clinical workflows remains challenging due to systemic architectural fragmentation....
NH–π interactions between polar and aromatic residues are well distributed in proteins whose stabilizing effects have been investigated in globular and fibrous proteins. In order to gain structural insights into side chain NH–π inte...
A strategy for a new type of platform for chemoinformatics software development and its first implementation are presented. The basic task of such a platform is to apply sequences of computational methods to high numbers of molecules. The implementat...
Lipases are enzymes that catalyze the hydrolysis of carboxylic esters at a lipid–water interface and are able to catalyze reactions such as alcoholysis, esterification, transesterification, and enantioselective synthesis in organic media. They...
Transposable elements (TEs) constitute a significant portion of eukaryotic genomes and play crucial roles in genome evolution, yet their diverse and complex sequences pose challenges for accurate classification. Existing tools often lack reliability...
In recent years, a bioinformatics method for interpreting genome-wide association study (GWAS) data using metabolic pathway analysis has been developed and successfully used to find significant pathways and mechanisms explaining phenotypic traits of...
Long non-coding RNAs (lncRNAs) are a rapidly expanding field of research, with many new transcripts identified each year. However, only a small subset of lncRNAs has been characterized functionally thus far. To aid investigating the mechanisms of act...
Background: N6-methyladenosine (m6A) is an abundant RNA epitranscriptomic modification in eukaryotes. The m6A machinery includes cellular writer, eraser and reader proteins that regulate m6A. Pteropus alecto (P. alecto) (the Australian black flying f...
Recent improvements in cost-effectiveness of high-throughput technologies has allowed RNA sequencing of total transcriptomes suitable for evaluating the expression and regulation of circRNAs, a relatively novel class of transcript isoforms with sugge...
IMGT®, the international ImMunoGeneTics information system® (CNRS and Montpellier University) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989, IMGT® marked the advent of immunoinformatics, which emerged at the...
13 May 2024
Background: In genomics, highly sensitive point mutation detection is particularly relevant for cancer diagnosis and early relapse detection. Next-generation sequencing combined with unique molecular identifiers (UMIs) is known to improve the mutatio...
One application of personalized medicine is the tailoring of medication to the individual, so that the medication will have the highest chance of success. In order to individualize medication, one must have a complete inventory of all current pharmac...
Qiime2 is one of the most popular software tools used for analysis of output from metabarcoding experiments (e.g., sequencing of 16S, 18S, or ITS amplicons). Qiime2 introduced a novel and innovative data exchange format: the ‘Qiime2 artifact’. Qiime2...
The healthy intestine represents a remarkable interface where sterile host tissues come in contact with gut microbiota, in a balanced state of homeostasis. The imbalance of gut homeostasis is associated with the onset of many severe pathological cond...
The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-sid...
ABCA3 is a crucial protein of pulmonary surfactant biosynthesis, associated with recessive pulmonary disorders such as neonatal respiratory distress and interstitial lung disease. Mutations are mostly private, and accurate interpretation of variants...
Electroencephalography (EEG) has existed since the early 20th century. It has proven to be a vital tool for electrophysiological studies of conditions like epilepsy. Recently, it has been revitalized as the field of machine learning has been developi...
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