Kimberly M. Van Auken

Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity

The paper develops sentence classification models to identify biocuration-relevant sentences for gene expression and protein kinase activity from scientific literature, achieving high F1 scores with GPT and BioBERT.

Updates to the Alliance of Genome Resources Central Infrastructure

The paper updates the Alliance of Genome Resources' central infrastructure, adding tools and enhancing data management and curation capabilities.

Semantic Representation of Neural Circuit Knowledge in Caenorhabditis elegans

The paper develops CeN-CAM, a semantic model based on GO-CAM, to represent causal relationships in C. elegans neural circuits and behaviors using literature data.

Biochemical Pathways Represented by Gene Ontology Causal Activity Models Identify Distinct Phenotypes Resulting from Mutations in Pathways

The paper converts human GO-CAMs to mouse GO-CAMs to link gene pathway perturbations with phenotypes, showing distinct outcomes from glycolysis and gluconeogenesis gene mutations.

Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

The paper introduces a Gene Ontology annotation quality control system that identifies and corrects errors in gene product co-annotation by analyzing mutual exclusivity patterns across biological processes.