Sampo Pyysalo

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Filip GinterUniversity of TurkuVerified email at utu.fi
Junichi TsujiiArtificial Intelligence Research Center, AISTVerified email at aist.go.jp
Tomoko OHTAtextimiVerified email at textimi.com
Tapio SalakoskiProfessor of Computer Science, University of TurkuVerified email at utu.fi
Sophia AnaniadouProfessor, Computer Science, Manchester University, National Centre for Text MiningVerified email at manchester.ac.uk
Jin-Dong KimAssociate Professor of Database Center for Life ScienceVerified email at dbcls.rois.ac.jp
Jari BjörnePost-doctoral researcher, University of Turku, FinlandVerified email at utu.fi
Lars Juhl JensenUniversity of CopenhagenVerified email at cpr.ku.dk
Tapio PahikkalaProfessor, University of turku, FinlandVerified email at utu.fi
Anna KorhonenProfessor, Computer Science and Linguistics, University of CambridgeVerified email at cam.ac.uk
Katerina NastouMSCA PostDoc Fellow, Novo Nordisk Foundation Center of Protein Research, University of CopenhagenVerified email at biol.uoa.gr
Jenna KanervaDepartment of Computing, University of TurkuVerified email at utu.fi
Damian SzklarczykSIB Swiss Institute of Bioinformatics / University of ZurichVerified email at isb-sib.ch
Peer BorkDirector of EMBL HeidelbergVerified email at embl.de
Christian von MeringProfessor of Computational Biology, University of Zurich and Swiss Institute of BioinformaticsVerified email at imls.uzh.ch
Jouni JärvinenUniversity lecturer, LUT UniversityVerified email at lut.fi
Makoto MiwaAssociate Professor, Toyota Technological InstituteVerified email at toyota-ti.ac.jp
Jouni LuomaProject Researcher, TurkuNLP, University of TurkuVerified email at utu.fi
Billy ChiuPhD student at University of CambridgeVerified email at cam.ac.uk
Gamal CrichtonPathway AIVerified email at cam.ac.uk

Sampo Pyysalo

University of Turku

Verified email at utu.fi


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The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets D Szklarczyk, AL Gable, KC Nastou, D Lyon, R Kirsch, S Pyysalo, ... Nucleic acids research 49 (D1), D605-D612, 2021	4358	2021
Universal dependencies v1: A multilingual treebank collection J Nivre, MC De Marneffe, F Ginter, Y Goldberg, J Hajic, CD Manning, ... Proceedings of the Tenth International Conference on Language Resources and …, 2016	1525	2016
BRAT: a web-based tool for NLP-assisted text annotation P Stenetorp, S Pyysalo, G Topić, T Ohta, S Ananiadou, J Tsujii Proceedings of the Demonstrations at the 13th Conference of the European …, 2012	1428	2012
Overview of BioNLP’09 shared task on event extraction JD Kim, T Ohta, S Pyysalo, Y Kano, J Tsujii Proceedings of the BioNLP 2009 workshop companion volume for shared task, 1-9, 2009	799	2009
Bloom: A 176b-parameter open-access multilingual language model BS Workshop, TL Scao, A Fan, C Akiki, E Pavlick, S Ilić, D Hesslow, ... arXiv preprint arXiv:2211.05100, 2022	706	2022
Distributional semantics resources for biomedical text processing S Pyysalo, F Ginter, H Moen, T Salakoski, S Ananiadou Languages in Biology and Medicine, 2013	586*	2013
BioInfer: a corpus for information extraction in the biomedical domain S Pyysalo, F Ginter, J Heimonen, J Björne, J Boberg, J Järvinen, ... BMC bioinformatics 8, 1-24, 2007	555	2007
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest D Szklarczyk, R Kirsch, M Koutrouli, K Nastou, F Mehryary, R Hachilif, ... Nucleic acids research 51 (D1), D638-D646, 2023	464	2023
Universal Dependencies v2: An evergrowing multilingual treebank collection J Nivre, MC De Marneffe, F Ginter, J Hajič, CD Manning, S Pyysalo, ... arXiv preprint arXiv:2004.10643, 2020	429	2020
How to train good word embeddings for biomedical NLP B Chiu, G Crichton, A Korhonen, S Pyysalo Proceedings of the 15th workshop on biomedical natural language processing …, 2016	404	2016
All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning A Airola, S Pyysalo, J Björne, T Pahikkala, F Ginter, T Salakoski BMC bioinformatics 9, 1-12, 2008	367	2008
Comparative analysis of five protein-protein interaction corpora S Pyysalo, A Airola, J Heimonen, J Björne, F Ginter, T Salakoski BMC bioinformatics 9 (3), 1-11, 2008	297	2008
Multilingual is not enough: BERT for Finnish A Virtanen, J Kanerva, R Ilo, J Luoma, J Luotolahti, T Salakoski, F Ginter, ... arXiv preprint arXiv:1912.07076, 2019	281	2019
Overview of BioNLP shared task 2013 C Nédellec, R Bossy, JD Kim, JJ Kim, T Ohta, S Pyysalo, P Zweigenbaum Proceedings of the BioNLP shared task 2013 workshop, 1-7, 2013	268	2013
Event extraction for systems biology by text mining the literature S Ananiadou, S Pyysalo, J Tsujii, DB Kell Trends in biotechnology 28 (7), 381-390, 2010	265	2010
Attending to characters in neural sequence labeling models M Rei, GKO Crichton, S Pyysalo arXiv preprint arXiv:1611.04361, 2016	252	2016
Universal Dependencies 2.2 J Nivre, M Abrams, Ž Agić, L Ahrenberg, L Antonsen, MJ Aranzabe, ...	240	2018
A neural network multi-task learning approach to biomedical named entity recognition G Crichton, S Pyysalo, B Chiu, A Korhonen BMC bioinformatics 18 (1), 1-14, 2017	234	2017
Event extraction across multiple levels of biological organization S Pyysalo, T Ohta, M Miwa, HC Cho, J Tsujii, S Ananiadou Bioinformatics 28 (18), i575-i581, 2012	162	2012
Complex event extraction at PubMed scale J Björne, F Ginter, S Pyysalo, J Tsujii, T Salakoski Bioinformatics 26 (12), i382-i390, 2010	151	2010

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