iProLINK

Publications

• Wang Q, Ross KE, Huang H, Ren J, Li G, Vijay-Shanker K, Wu CH, Arighi CN.
  Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature.
  Methods Mol Biol. 2017;1558:213-232. doi: 10.1007/978-1-4939-6783-4_10. PubMed PMID: 28150240.
  
• Gupta S, Ross KE, Tudor CO, Wu CH, Schmidt CJ, Vijay-Shanker K.
  miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases.
  J Biomed Semantics. 2016 Apr 29;7(1):9. doi: 10.1186/s13326-015-0044-y. PubMed PMID: 27216254; PubMed Central PMCID: PMC4877743.
  
• Ding R, Arighi CN, Lee JY, Wu CH, Vijay-Shanker K.
  pGenN, a gene normalization tool for plant genes and proteins in scientific literature.
  PLoS One. 2015 Aug 10;10(8):e0135305. doi: 10.1371/journal.pone.0135305. eCollection 2015. PubMed PMID: 26258475; PubMed Central PMCID: PMC4530884.
  
• Kim S, Islamaj Doğan R, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S, Santos A, Campos D, Oliveira JL, Singh O, Jonnagaddala J, Dai HJ, Su EC, Chang YC, Su YC, Chu CH, Chen CC, Hsu WL, Peng Y, Arighi C, Wu CH, Vijay-Shanker K, Aydın F, Hüsünbeyi ZM, Özgür A, Shin SY, Kwon D, Dolinski K, Tyers M, Wilbur WJ, Comeau DC.
  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.
  Database (Oxford). 2016 Sep 1;2016. pii: baw121. doi: 10.1093/database/baw121. Print 2016. PubMed PMID: 27589962; PubMed Central PMCID: PMC5009341.
• Peng Y, Arighi C, Wu CH, Vijay-Shanker K.
  BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph.
  Database (Oxford). 2016 May 11;2016. pii: baw072. doi: 10.1093/database/baw072. Print 2016. PubMed PMID: 27170286; PubMed Central PMCID: PMC4915133
• Li G, Ross KE, Arighi CN, Peng Y, Wu CH, Vijay-Shanker K.
  miRTex: A Text Mining System for miRNA-Gene Relation Extraction.
  PLoS Comput Biol. 2015 Sep 25;11(9):e1004391. doi: 10.1371/journal.pcbi.1004391. eCollection 2015. PubMed PMID: 26407127; PubMed Central PMCID: PMC4583433
• Tudor CO, Ross 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 (Oxford) 2015: bav020. doi: 10.1093/database/bav020. PMID: 25833953. PMCID: PMC4381107.
  
• Torii M, Li G, Li Z, Oughtred R, Diella F, Celen I, Arighi CN, Huag H, Vijay-Shanker K, Wu CH.
  RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information.
  Database (Oxford) 2014: bau081. doi: 10.1093/database/bau081. PMID: 25122463. PMCID: PMC4131691
• Torii M, Arighi CN, Li G, 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.
  In Proceedings of Computational Biology and Bioinformatics, IEEE/ACM Transactions, 2014, 12(1): 17-29
• Peng Y, Torii M, Wu CH, Vijay-Shanker K.
  A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems.
  BMC Bioinformatics. 15:285. pp. 1-18. doi: 10.1186/1471-2105-15-285. PMID:25149151. PMCID:PMC4262219.
• 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: bau038. doi: 10.1093/database/bau038. PMID: 24850848. 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: bat038. doi: 10.1093/database/bat038. PMID: 23749465. PMCID: PMC3675891.
  
• Lopez LD, Yu J, Arighi C, Tudor CO, Torii M, Huang H, Vijay-Shanker K, Wu CH
  A Framework for Biomedical Figure Segmentation Towards Image-based Document Retrieval.
  BMC Systems Biology 2013, 7 (Suppl 4): S8. doi: 10.1186/1752-0509-7-S4-S8. PMID: 24565394. 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:bas044. doi: 10.1093/database/bas044. PMID: 23221174. PMCID: PMC3514748.
  
• Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K
  iSimp: A Sentence Simplification System for Biomedical Text.
  IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2012, Philadelphia, USA, October 2012, 211-216.
• Lopez LD, Yu J, Tudor CO, Arighi CN, Huang H, Vijay-Shanker K, Wu CH
  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, Vijay-Shanker K.
  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. PMID: 21082428.
  
• Tudor CO, Schmidt CJ, Vijay-Shanker K.
  eGIFT: mining gene information from the literature.
  BMC Bioinformatics 2010; 11:418. doi: 10.1186/1471-2105-11-418. PMID: 20696046; 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; 22(13):1668-9. PMID: 16644790.
  
• Liu H, Hu ZZ, Zhang J, Wu C.
  BioThesaurus: a web-based thesaurus of protein and gene names.
  Bioinformatics 2006; 22(1):103-5. 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; 21(11):2759-65. PMID: 15814565.
  
• Hu ZZ, Mani I, Hermoso V, Liu H, Wu CH.
  iProLINK: an integrated protein resource for literature mining.
  Comput Biol Chem 2004; 28(5-6):409-16. PMID: 15556482.
  

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