BioNLP and Text Mining Lab

2017

Mahmood A, Rao S, McGarvey P, Wu C, Madhavan S, Vijay-Shanker K. eGARD: Extracting associations between genomic anomalies and drug responses from text. PLoS ONE 12(12): e0189663. https://doi.org/10.1371/journal.pone.0189663
Hongzhan Huang, Cecilia N. Arighi, Karen E. Ross, Jia Ren, Gang Li, Sheng-Chih Chen, Qinghua Wang, Julie Cowart, K. Vijay-Shanker, Cathy H. Wu iPTMnet: an integrated resource for protein post-translational modification network discovery. Nucleic Acids Research, 2017, gkx1104
Ruoyao Ding, Emmanuel Boutet, Damien Lieberherr, Michel Schneider, Michael Tognolli, Cathy H Wu, K Vijay-Shanker, Cecilia N Arighi eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. Database, 2017, bax081
Gupta, S., Mahmood, A., Ross, K., Wu, C., Vijay-Shanker, K. Identifying Comparative Structures in Biomedical Text.. Proceedings of the BioNLP 2017 workshop. 2017. pp. 206-215.
Li G, Wu CH, Vijay-Shanker K. Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction. Proceedings of the BioNLP 2017 workshop. 2017. pp. 184-193.
Liang Sun, Yongnan Zhu, A S M Ashique Mahmood, Catalina O. Tudor, Jia Ren, K. Vijay-Shanker, Jian Chen, and Carl J. Schmidt. WebGIVI: a web-based gene enrichment analysis and visualization tool. BMC Bioinformatics 18, no. 1 (2017). doi:10.1186/s12859-017-1664-2.

2016

Mahmood ASMA, Wu T-J, Mazumder R, Vijay-Shanker K (2016) DiMeX: A Text Mining System for Mutation-Disease Association Extraction. PLoS ONE 11(4): e0152725. doi:10.1371/journal.pone.0152725
Peng, Y., Arighi, C., Wu, C.H. and Vijay-Shanker, K. BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. Database, 2016, p.baw072.
Gupta, S., Ross, K. E., Tudor, C. O., Wu, C. H., Schmidt, C. J., & Vijay-Shanker, K. miRiaD: A text mining tool for detecting associations of micrornas with diseases.. Journal of biomedical semantics, 7(1), 9.

2015

Peng Y, Gupta S, Wu CH, Vijay-Shanker K. An extended dependency graph for relation extraction in biomedical texts. In Proceedings of BioNLP workshop. pp. 21-30. 2015.
Peng Y, Arighi C, Wu CH, Vijay-Shanker K. Extended dependency graph for BioC-compatible protein-protein interaction (PPI) passage detection in full-text articles.. In Proceedings of the BioCreative V Workshop. pp. 30-35. 2015.
Li G, Ross K, Arighi C, Peng Y, Wu CH, Vijay-Shanker K. miRTex: A text mining system for miRNA-Gene relation extraction. PLOS Computational Biology, 11(9), 1-24. 2015.
Catalina O Tudor, Karen E Ross, Gang Li, K Vijay-Shanker, Cathy H Wu, Cecilia N Arighi. Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system. Database, 2015: bav020.

2014

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. 2014, 15:285.
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. 2014.
Comeau DC, Batista-Navarro R, Dai HJ, Doğan RI, Jimeno Yepes A, Khare R, Lu Z, Marques H, Mattingly C, Neves M, Peng Y, Rak R, Rinaldi F, Tsai TH, Verspoor, K, Wiegers T, Wu CH, Wilbur WJ. BioC Interoperability Track Overview. Database. 2014.
Torii M*, Li G*, Li Z, Oughtred R, Diella F, Çelen I, Arighi CN, Huang H, K. Vijay-Shanker K, Wu CH (2014) RLIMS-P: An online text mining tool for literature- based extraction of protein phosphorylation information. Database (2014). [*First authorship shared]
Torii M, Arighi CN, Li G, Wang Q, Wu CH, Vijay-Shanker K. (accepted). 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.
Ross KE, Tudor CO, Li G, Ding R, Celen I, Arighi CN, Wu CH, Natale DA. (2014). Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology for Multi-Faceted Disease Analysis. International Conference on Biomedical Ontology.
Samir Gupta, Catalina O Tudor, Cathy H Wu, Carl J Schmidt, and K Vijay-Shanker. Automatically Identifying Biological Functions of microRNAs from the Literature. In Proceedings of Sixth International Symposium on Semantic Mining in Biomedicine SMBM 2014, Aveiro, Portugal, October 2014.
Karen E Ross, Catalina O Tudor, Gang Li, Ruoyao Ding, Irem Celen, Cecilia N Arighi, Cathy H Wu, and Darren A Natale. Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology for Multi-Faceted Diseases Analysis. In Proceedings of the Fifth International Conference on Biomedical Ontologies ICBO 2014, Houston, TX, October 2014.

2013

Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K. Enhancing the interoperability of iSimp by using the BioC format. BioCreative IV workshop. pp.5-9. Oct 2013.
Torii M, Li G, Li Z, Çelen I, Diella F, Oughtred R, Arighi C, Huang H, Vijay-Shanker K., Wu CH. RLIMS-P: Literature-based curation of protein phosphorylation information. BioCreative IV workshop. pp.247-253. Oct 2013.
Comeau DC, Doğan RI, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia V, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC: A minimalist approach to interoperability for biomedical text processing. Database. 2013.
Torii M, Arighi C, Wang Q, Wu CH, Vijay-Shanker K. Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach. ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB). 2013. (in print)
Comeau DC, Doğan RI, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia V, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. Database. 2013.
Arighi CN, Tudor CO, Torii M, Li G, Huang H, Wu CH, Vijay-Shanker K. Text Mining Tools for Studying KinaseSubstrate Networks and Protein Interaction Networks of Phosphorylated Proteins. International Plant and Animal Genome XXI Conference. San Diego, CA. 2013.
Wu CH, Arighi CN, Lee JY, Torii M, Tudor CO, Li G, Wang Q, Huang H, Vijay-Shanker K. iPTMnet: Integrative Bioinformatics for Knowledge Discovery of PTM Networks. International Plant and Animal Genome XXI Conference. San Diego, CA. 2013.
Gupta S, Malik S, Pollock L, Vijay-Shanker K. Part-of-Speech Tagging of Program Identifiers for Improved Text-Based Software Engineering Tool. 21st Annual International Conference on Program Comprehension, IEEE, May 2013. (AWARDED Conference Best Research Paper Award)
Howard M, Gupta S, Pollock L, Vijay-Shanker K. Automatically Mining Software-Based, Semantically-Similar Words from Comment-Code Mappings. The 10th Working Conference on Mining Software Repositories, IEEE, May 2013. (AWARDED the conference Best Research Paper Award)

2012

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. 2012 bas044.
Tudor CO, Vijay-Shanker K.. RankPref: Ranking sentences describing relations between biomedical entities with an application. Proceedings of the 2012 Workshop on Biomedical Natural Language Processing. pp. 163-172. 2012.
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 (BIBM2012). pp. 211-216. 2012.
Wu CH, Arighi CN, Lee JY, Torii M, Tudor CO, Li G, Wang Q, Huang H, Vijay-Shanker K. iPTMnet: Integrative Bioinformatics for Knowledge Discovery of PTM Networks. HUPO 11th Annual World Congress. Boston, MA.