BERT-GT: cross-sentence n-ary relation extraction with BERT and Graph Transformer

PT Lai, Z Lu - Bioinformatics, 2020 - academic.oup.com
Motivation A biomedical relation statement is commonly expressed in multiple sentences
and consists of many concepts, including gene, disease, chemical and mutation. To …

pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature

PH Li, TF Chen, JY Yu, SH Shih, CH Su… - Nucleic Acids …, 2022 - academic.oup.com
With the proliferation of genomic sequence data for biomedical research, the exploration of
human genetic information by domain experts requires a comprehensive interrogation of …

[HTML][HTML] RDKG-115: assisting drug repurposing and discovery for rare diseases by trimodal knowledge graph embedding

C Zhu, X Xia, N Li, F Zhong, Z Yang, L Liu - Computers in Biology and …, 2023 - Elsevier
Rare diseases (RDs) may affect individuals in small numbers, but they have a significant
impact on a global scale. Accurate diagnosis of RDs is challenging, and there is a severe …

tmVar 3.0: an improved variant concept recognition and normalization tool

CH Wei, A Allot, K Riehle, A Milosavljevic, Z Lu - Bioinformatics, 2022 - academic.oup.com
Motivation Previous studies have shown that automated text-mining tools are becoming
increasingly important for successfully unlocking variant information in scientific literature at …

Automatic extraction of ranked SNP-phenotype associations from text using a BERT-LSTM-based method

B Bokharaeian, M Dehghani, A Diaz - BMC bioinformatics, 2023 - Springer
Extraction of associations of singular nucleotide polymorphism (SNP) and phenotypes from
biomedical literature is a vital task in BioNLP. Recently, some methods have been …

ViMRT: a text-mining tool and search engine for automated virus mutation recognition

Y Tong, F Tan, H Huang, Z Zhang, H Zong, Y Xie… - …, 2023 - academic.oup.com
Motivation Virus mutation is one of the most important research issues which plays a critical
role in disease progression and has prompted substantial scientific publications. Mutation …

VarChat: the generative AI assistant for the interpretation of human genomic variations

F De Paoli, S Berardelli, I Limongelli, E Rizzo… - …, 2024 - academic.oup.com
Motivation In the modern era of genomic research, the scientific community is witnessing an
explosive growth in the volume of published findings. While this abundance of data offers …

The global prevalence and ethnic heterogeneity of iron-refractory iron deficiency anaemia

S Fan, T Zhao, L Sun - Orphanet Journal of Rare Diseases, 2023 - Springer
Background Iron-refractory iron deficiency anaemia (IRIDA) is an autosomal recessive iron
deficiency anaemia caused by mutations in the TMPRSS6 gene. Iron deficiency anaemia is …

Variomes: a high recall search engine to support the curation of genomic variants

E Pasche, A Mottaz, D Caucheteur, J Gobeill… - …, 2022 - academic.oup.com
Motivation Identification and interpretation of clinically actionable variants is a critical
bottleneck. Searching for evidence in the literature is mandatory according to …

Computational strategies in nutrigenetics: constructing a reference dataset of nutrition-associated genetic polymorphisms

GM De Filippis, M Monticelli, A Pollice, T Angrisano… - medRxiv, 2023 - medrxiv.org
Objective: This study aimed to build a comprehensive dataset of human genetic
polymorphisms associated with nutrition by integrating data from multiple sources, including …