Sampo Pyysalo
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Explore the profile of Sampo Pyysalo including associated specialties, affiliations and a list of published articles.
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45
Citations
5742
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Recent Articles
1.
Nourani E, Makri E, Mao X, Pyysalo S, Brunak S, Nastou K, et al.
Database (Oxford)
. 2025 Jan;
2025.
PMID: 39824652
Lifestyle factors (LSFs) are increasingly recognized as instrumental in both the development and control of diseases. Despite their importance, there is a lack of methods to extract relations between LSFs...
2.
Szklarczyk D, Nastou K, Koutrouli M, Kirsch R, Mehryary F, Hachilif R, et al.
Nucleic Acids Res
. 2024 Nov;
53(D1):D730-D737.
PMID: 39558183
Proteins cooperate, regulate and bind each other to achieve their functions. Understanding the complex network of their interactions is essential for a systems-level description of cellular processes. The STRING database...
3.
Nourani E, Koutrouli M, Xie Y, Vagiaki D, Pyysalo S, Nastou K, et al.
Bioinformatics
. 2024 Oct;
40(11).
PMID: 39412443
Motivation: Despite lifestyle factors (LSFs) being increasingly acknowledged in shaping individual health trajectories, particularly in chronic diseases, they have still not been systematically described in the biomedical literature. This is...
4.
Nastou K, Koutrouli M, Pyysalo S, Jensen L
Bioinform Adv
. 2024 Oct;
4(1):vbae116.
PMID: 39411448
Motivation: Despite significant progress in biomedical information extraction, there is a lack of resources for Named Entity Recognition (NER) and Named Entity Normalization (NEN) of protein-containing complexes. Current resources inadequately...
5.
Mehryary F, Nastou K, Ohta T, Jensen L, Pyysalo S
Bioinformatics
. 2024 Sep;
40(9).
PMID: 39276156
Motivation: Understanding biological processes relies heavily on curated knowledge of physical interactions between proteins. Yet, a notable gap remains between the information stored in databases of curated knowledge and the...
6.
Nastou K, Mehryary F, Ohta T, Luoma J, Pyysalo S, Jensen L
Database (Oxford)
. 2024 Sep;
2024.
PMID: 39265993
In the field of biomedical text mining, the ability to extract relations from the literature is crucial for advancing both theoretical research and practical applications. There is a notable shortage...
7.
Nastou K, Koutrouli M, Pyysalo S, Jensen L
Bioinformatics
. 2024 Sep;
40(Suppl 2):ii45-ii52.
PMID: 39230709
Motivation: Dictionary-based named entity recognition (NER) allows terms to be detected in a corpus and normalized to biomedical databases and ontologies. However, adaptation to different entity types requires new high-quality...
8.
Miranda-Escalada A, Mehryary F, Luoma J, Estrada-Zavala D, Gasco L, Pyysalo S, et al.
Database (Oxford)
. 2023 Nov;
2023.
PMID: 38015956
It is getting increasingly challenging to efficiently exploit drug-related information described in the growing amount of scientific literature. Indeed, for drug-gene/protein interactions, the challenge is even bigger, considering the scattered...
9.
Luoma J, Nastou K, Ohta T, Toivonen H, Pafilis E, Jensen L, et al.
Bioinformatics
. 2023 Jun;
39(6).
PMID: 37289518
Motivation: The recognition of mentions of species names in text is a critically important task for biomedical text mining. While deep learning-based methods have made great advances in many named...
10.
Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, et al.
Nucleic Acids Res
. 2022 Nov;
51(D1):D638-D646.
PMID: 36370105
Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known, but novel interactions continue to be discovered, and...