1. Beyond the clause: extraction of phosphorylation information from medline abstracts, Narayanaswamy, M., Ravikumar, K. E., Vijay-Shanker, K. (2005) Bioinformatics 21 (suppl_1) : i319-i327
  2. An online literature mining tool for protein phosphorylation, Yuan, X., Hu, Z. Z., Wu, H. T., Torii, M., Narayanaswamy, M., Ravikumar, K. E., Vijay-Shanker, K., Wu, C. H. (2006) Bioinformatics 22 (13) : 1668-1669
  3. eFIP: a tool for mining functional impact of phosphorylation from literature, Arighi, C. N., Siu, A. Y., Tudor, C. O., Nchoutmboube, J. A., Wu, C. H., Shanker, V. K. (2011) Methods in Molecular Biology, 694, 63-75
  4. The eFIP system for text mining of protein interaction networks of phosphorylated proteins. Tudor CO, Arighi CN, Wang Q, Wu CH, Vijay-Shanker K. (2012) Database (Oxford) 2012:bas044
  5. Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint. Ross KE, Arighi CN, Ren J, Natale DA, Huang H, Wu CH. Front Genet. 2013 Apr 26;4:62.
  6. Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach. Torii M, Arighi CN, Wang Q, Wu CH, Vijay-Shanker K. Presented at the ACMBCB’13 (International Conference on Bioinformatics, Computational Biology and Biomedical Informatics), September 22-25, 2013.
  7. Enhancing the Interoperability of iSimp by using the BioC Format. Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K. Presented at the BioCreative IV Workshop, Bethesda, MD, October 7-9, 2013.
  8. RLIMS-P: Literature-based curation of protein phosphorylation information. Torii M, Li G, Li Z, Çelen I, Diella F, Oughtred R, Arighi C, Huang H, Vijay-Shanker K, Wu CH. Presented at the BioCreative IV Workshop, Bethesda, MD, October 7-9, 2013.
  9. Mining the Impact of Phosphorylation on PPI in Full Length Scientific Articles. Tudor CO, Arighi CN, Wu CH, Vijay-Shanker K. Presented as a poster at the BioCreative IV Workshop, Bethesda, MD, October 7-9, 2013.
  10. RLIMS-P: an online text-mining tool for literature-base extraction of protein phosphorylation information. Torii M, Li G, Li Z, Oughtred R, Diella F, Celen I, Arighi CN, Huang H, Vijay-Shanker K, Wu CH. Database (Oxford). 2014: bau081.
  11. Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. Ross KE, Arighi CN, Ren J, Huang H, Wu CH. Database (Oxford). 2013:bat038.
  12. Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system. Tudor CO, Ross KE, Li G, Vijay-Shanker K, Wu CH, Arighi CN. Database (Oxford). 2015: bav020.
  13. RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. Torii M, Arighi CN, Gang Li, Qinghua Wang, Wu CH, Vijay-Shanker K. IEEE/ACM Trans Comput Biol Bioinform. 2015 12(1):17-29.