Farrokh Mehryary

The STRING database in 2025: protein networks with directionality of regulation (2024)

Nucleic Acids Research

Szklarczyk, Damian; Nastou, Katerina; Koutrouli, Mikaela; Kirsch, Rebecca; Mehryary, Farrokh; Hachilif, Radja; Hu, Dewei; Peluso, Matteo E.; Huang, Qingyao; Fang, Tao; Doncheva, Nadezhda T.; Pyysalo, Sampo; Bork, Peer; Jensen, Lars J.; von Mering, Christian

(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä )

RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature (2024)

Database: The Journal of Biological Databases and Curation

Nastou, Katerina; Mehryary, Farrokh; Ohta, Tomoko; Luoma, Jouni; Pyysalo, Sampo; Jensen, Lars Juhl

(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä )

STRING-ing together protein complexes: Corpus and methods for extracting physical protein interactions from the biomedical literature (2024)

Bioinformatics

Mehryary, Farrokh; Nastou, Katerina; Ohta, Tomoko; Jensen, Lars Juhl; Pyysalo, Sampo

(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä )

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest (2023)

Nucleic Acids Research

Szklarczyk Damian, Kirsch Rebecca, Koutrouli Mikaela, Nastou Katerina, Mehryary Farrokh, Hachilif Radja, Gable Annika L, Fang Tao, Doncheva Nadezha T, Pyysalo Sampo, Bork Peer, Jensen Lars J, von Mering Christian

(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))

Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations (2023)

Database: The Journal of Biological Databases and Curation

Miranda-Escalada Antonio, Mehryary Farrokh, Luoma Jouni, Estrada-Zavala Darryl, Gasco Luis, Pyysalo Sampo, Valencia Alfonso, Krallinger Martin

(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))

Optimizing text mining methods for improving biomedical natural language processing (2022)

Mehryary Farrokh

(G5 Artikkeliväitöskirja)

Overview of DrugProt BioCreative VII track: quality evaluation and large scale text mining of drug-gene/protein relations (2021)

BioCreative

Miranda Antonio, Mehryary Farrokh, Luoma Jouni, Pyysalo Sampo, Valencia Alfonso, Krallinger Martin

(Vertaisarvioimaton konferenssijulkaisu (B3))

Neural Network and Random Forest Models in Protein Function Prediction (2020)

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Hakala Kai, Kaewphan Suwisa, Björne Jari, Mehryary Farrokh, Moen Hans, Tolvanen Martti, Salakoski Tapio, Ginter Filip

(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))

Entity-pair embeddings for improving relation extraction in the biomedical domain (2020)

European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning

Mehryary F., Moen H., Salakoski T., Ginter F.

(Vertaisarvioitu artikkeli konferenssijulkaisussa (A4))

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens (2019)

Genome Biology

Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemovic, Vladimir R. Perovic, Radoslav S. Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad R.K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C. McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A. Freitas, Magdalena Antczak, Fabio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J. Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W. Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio C.E. Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, Dallas J. Larsen, Ashton R. Omdahl, Liam J. McGuffin, Danielle A. Brackenridge, Patricia C. Babbitt, Jeffrey M. Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti E.E. Tolvanen, Tapio Salakoski, Daisuke Kihara, Aashish Jain, Tomislav Šmuc, Adrian Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven E. Brenner, Christine A. Orengo, Constance J. Jeffery, Giovanni Bosco, Deborah A. Hogan, Maria J. Martin, Claire O’Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg

(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä )

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The STRING database in 2025: protein networks with directionality of regulation (2024)

RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature (2024)

STRING-ing together protein complexes: Corpus and methods for extracting physical protein interactions from the biomedical literature (2024)

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest (2023)

Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations (2023)

Optimizing text mining methods for improving biomedical natural language processing (2022)

Overview of DrugProt BioCreative VII track: quality evaluation and large scale text mining of drug-gene/protein relations (2021)

Neural Network and Random Forest Models in Protein Function Prediction (2020)

Entity-pair embeddings for improving relation extraction in the biomedical domain (2020)

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens (2019)