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Tudor CO, Rose KE, Li G, Vijay-Shanker K, Wu CH, Arighi CN.
Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.
Database pii: bav020. doi: 10.1093/database/bav020. 2015. PubMed PMID: 25833953. PubMed Central PMCID: PMC4381107


Torii M, Arighi CN, Wang Q, Wu CH, Vijay-Shanker K.
RLIMS-P 2.0: A generalizable rule-based information extraction system for literature mining of protein phosphorylation information.
IEEE Transactions on Computational Biology and Bioinformatics (TCBB) 12 (1): 17-29. doi: 10.1109/TCBB.2014.2372765. 2015.


Torii M, Li G, Li Z, Oughtred R, Diella F, Celen I, Arighi CN, Huang H, Vijay-Shanker K, Wu CH.
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information.
Database (Oxford). 2014 Aug 13;2014. pii: bau081. doi: 10.1093/database/bau081. Print 2014. PubMed PMID: 25122463; PubMed Central PMCID: PMC4131691.


Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K.
iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system.
Database (Oxford). 2014 May 21;2014. pii: bau038. doi: 10.1093/database/bau038. Print 2014. PubMed PMID: 24850848; PubMed Central PMCID: PMC4028706.


Ross KE, Arighi CN, Ren J, Huang H, Wu CH.
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint.
Database (Oxford). 2013 Jun 7;2013:bat038. doi: 10.1093/database/bat038. Print 2013. PubMed PMID: 23749465; PubMed Central PMCID: PMC3675891.


Luis D. Lopez, Jingyi Yu, Cecilia Arighi, Catalina O Tudor, Manabu Torii, Hongzhan Huang, K. Vijay-Shanker, and Cathy Wu.
A Framework for Biomedical Figure Segmentation Towards Image-based Document Retrieval.
iBMC Systems Biology 2013, 7 (Suppl 4): S8. PubMed PMID: 24565394; PubMed Central PMCID: PMC3856606.


Tudor CO, Arighi CN, Wang Q, Wu CH, Vijay-Shanker K.
The eFIP system for text mining of protein interaction networks of phosphorylated proteins.
Database (Oxford). 2012 Dec 5;2012:bas044. doi: 10.1093/database/bas044. Print 2012. PubMed PMID: 23221174; PubMed Central PMCID: PMC3514748.


Yifan Peng, Catalina O Tudor, Manabu Torii, Cathy H Wu, K Vijay-Shanker.
iSimp: A Sentence Simplification System for Biomedical Text.
IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2012, Philadelphia, USA, October 2012, 211-216. PubMed PMID: 24850848; PubMed Central PMCID: PMC4028706.


Luis D Lopez, Jingyi Yu, Catalina O Tudor, Cecilia N Arighi, Hongzhan Huang, K Vijay-Shanker, Cathy H Wu.
Robust Segmentation of Biomedical Figures Toward an Image-based Document Retrieval.
IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2012, Philadelphia, USA, October 2012.


Arighi CN, Siu AY, Tudor CO, Nchoutmboube JA, Wu CH, Shanker VK.
eFIP: a tool for mining functional impact of phosphorylation from literature.
Methods Mol Biol. 2011;694:63-75. doi: 10.1007/978-1-60761-977-2_5. PubMed PMID: 21082428.


Tudor CO, Schmidt CJ, Vijay-Shanker K.
eGIFT: mining gene information from the literature.
BMC Bioinformatics. 2010 Aug 9;11:418. doi: 10.1186/1471-2105-11-418. PubMed PMID: 20696046; PubMed Central PMCID: PMC2929241.


Yuan X, Hu ZZ, Wu HT, Torii M, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, Wu CH.
An online literature mining tool for protein phosphorylation.
Bioinformatics. 2006 Jul 1;22(13):1668-9. Epub 2006 Apr 27. PubMed PMID: 16644790.


Liu H, Hu ZZ, Zhang J, Wu C.
BioThesaurus: a web-based thesaurus of protein and gene names.
Bioinformatics. 2006 Jan 1;22(1):103-5. Epub 2005 Nov 2. PubMed PMID: 16267085.


Hu ZZ, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, Wu CH.
Literature mining and database annotation of protein phosphorylation using a rule-based system.
Bioinformatics. 2005 Jun 1;21(11):2759-65. Epub 2005 Apr 6. PubMed PMID: 15814565.


Hu ZZ, Mani I, Hermoso V, Liu H, Wu CH.
iProLINK: an integrated protein resource for literature mining.
Comput Biol Chem. 2004 Dec;28(5-6):409-16. PubMed PMID: 15556482.



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