Katerina C. Nastou

This study identifies five proteins whose sequential changes in plasma precede spontaneous labour onset, implicating the IL-33/ST2 axis in labour timing and identifying LMOD1 as a novel marker.

The paper presents a longitudinal transcriptomic atlas of maternal peripheral blood during healthy pregnancy, identifying 720 pregnancy-specific genes and nine transcriptional modules associated with immune and metabolic changes.

The paper develops a Lifestyle Factor Ontology and annotated corpus for detecting lifestyle factors in biomedical texts, achieving 76% F-score with a transformer-based NER system.

The paper introduces a manually annotated corpus and a relation extraction model to identify physical protein interactions from biomedical literature, integrating results into the STRING database.

The paper improves dictionary-based named entity recognition by using a Transformer model to automatically generate block lists, increasing precision in text mining.

FAVA infers high-quality functional protein interaction networks from scRNA-seq and proteomics data, outperforming existing methods and identifying interactions for understudied proteins.

The paper introduces CoNECo, a corpus for NER and NEN of protein complexes, achieving F1-scores of 73.7% and 61.2% with transformer-based and dictionary-based taggers, respectively.

RegulaTome provides a comprehensive corpus of biomedical relations, enabling improved relation extraction with a Transformer model achieving 66.6% F1-score.

The paper introduces S1000, a new corpus for species name recognition in biomedical text, achieving high accuracy with both deep learning and dictionary-based methods.

LiGIoNs is a pHMM-based method for detecting and classifying ligand-gated ion channels, outperforming existing methods and enabling subfamily classification.

This paper reviews linear B-cell epitope prediction methods available via command-line interface and introduces a consensus classifier to improve performance for vaccine design.

This study identifies candidate proteins and connectors in the BLAD interactome using network analysis and clustering.

PerMemDB is a database of eukaryotic peripheral membrane proteins, containing 241,173 entries from 1,216 organisms, annotated with interaction data and domain predictions using MBPpred.

AmyCo is a database classifying 74 amyloid-related diseases into amyloidosis and clinical conditions associated with amyloidosis, providing detailed annotations and references to external databases.

The paper analyzes SNPs in VGICs to identify disease-associated mutations and their functional impact on ion channel structure and function.