Biology subjects

Vlamos, P.

Publications and source records attributed to Vlamos, P..

3 recordsLinked to original sources

bioRxiv2026

Enrich.AI: An Agentic AI Platform for Interactive GeneSet Enrichment Analysis and Biological Interpretation

Motivation: Enrichment analysis is widely used to extract biological meanings from gene lists. However, the large number of available tools and reference libraries often make the interpretation of results challenging. Inexperienced users lack clear guidance on which datasets and terms are most relevant to their data, whereas experienced researchers must navigate large result sets and consult multiple resources to identify biologically relevant findings. Integrating AI into this process can help to bridge these gaps. Results: We present Enrich.AI, a conversational biology assistant that integrates statistical enrichment analysis with automated biological interpretation. The agent operates on an LLM-based ReAct architecture and dynamically selects among the tools for enrichment (220+ gene set libraries), literature search (40+ million publications via Europe PMC), gene annotation, and database retrieval. Given a gene list and a short description of the biological context, Enrich.AI produces a written interpretation grounded in the retrieved literature and six interactive, configurable visualizations. A conversational interface enables human-in-the-loop refinement, letting researchers without programming experience explore results iteratively. The reliability of these interpretations was validated through a systematic evaluation on 50 gene sets, demonstrating high faithfulness to retrieved evidence and a low hallucination rate.

bioinformatics↗

bioRxiv2022

DRDs and Brain Derived Neurotrophic Factor share a common therapeutic ground: A novel bioinformatic approach sheds new light towards pharmacological treatment of Cognitive and Behavioral Disorders.

Cognitive and behavioral disorders are subgroups of mental health disorders. Both cognitive and behavioral disorders can occur in people of different ages, genders, and social backgrounds and they can cause serious physical, mental or social problems. The risk factors for these diseases are numerous, with a range from genetic and epigenetic factors to physical factors. In most cases, the appearance of such a disorder in an individual is a combination of his genetic profile and environmental stimuli. To date, researchers have not been able to identify the specific causes of these disorders and as such, there is urgent need for innovative study approaches. The aim of the present study was to identify the genetic factors which seem to be more directly responsible for the occurrence of a cognitive and/or behavioral disorder. More specifically, through bioinformatics tools and software as well as analytical methods such as systemic data and text mining, semantic analysis, and scoring functions, we extracted the most relevant single nucleotide polymorphisms (SNPs) and genes connected to these disorders. All the extracted SNPs were filtered, annotated, classified, and evaluated in order to create the "genomic grammar" of these diseases. The identified SNPs guided the search for top suspected genetic factors, dopamine receptors D and Neurotrophic Factor BDNF, for which regulatory networks were built. The identification of the "genomic grammar" and underlying factors connected to cognitive and behavioral disorders can aid the successful disease profiling, the establishment of novel pharmacological targets and provide the basis for personalized medicine, which takes into account the patients genetic background as well as epigenetic factors.

bioinformatics↗

bioRxiv2022

An updated evolutionary and structural study of TBK1 reveals highly conserved motifs as potential pharmacological targets in neurodegenerative diseases.

TANK binding kinase 1 protein (TBK1) is a kinase that belongs to the I{kappa}B (IKK) family. TBK1, also known as T2K, FTDALS4, NAK, IIAE8 and NF-{kappa}B, is responsible for the phosphorylation of the amino acid residues Serine and Threonine. This enzyme is involved in various key biological processes, including interferon activation and production, homeostasis, cell growth, autophagy, insulin production and the regulation of TNF-, IFN-{beta} and IL-6. Mutations in the TBK1 gene alter the proteins normal function and may lead to an array of pathological conditions, including disorders of the Central Nervous System. The present study sought to elucidate the role of the TBK1 protein in Amyotrophic Lateral Sclerosis (ALS), a human neurodegenerative disorder. A broad evolutionary and phylogenetic analysis of TBK1 was performed across numerous organisms to distinguish conserved regions important for the proteins function. Subsequently, mutations and SNPs were explored and their potential effect on the enzymes function was investigated. These analytical steps, in combination with the study of the secondary, tertiary, and quaternary structure of TBK1, enabled the identification of conserved motifs, which can function as novel pharmacological targets and inform therapeutic strategies for Amyotrophic Lateral Sclerosis.

bioinformatics↗