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Items: 33

1.

Using distant supervision to augment manually annotated data for relation extraction.

Su P, Li G, Wu C, Vijay-Shanker K.

PLoS One. 2019 Jul 30;14(7):e0216913. doi: 10.1371/journal.pone.0216913. eCollection 2019.

2.

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature.

Ren J, Li G, Ross K, Arighi C, McGarvey P, Rao S, Cowart J, Madhavan S, Vijay-Shanker K, Wu CH.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay128.

3.

Automatic gene annotation using GO terms from cellular component domain.

Ding R, Qu Y, Wu CH, Vijay-Shanker K.

BMC Med Inform Decis Mak. 2018 Dec 7;18(Suppl 5):119. doi: 10.1186/s12911-018-0694-7.

4.

DEXTER: Disease-Expression Relation Extraction from Text.

Gupta S, Dingerdissen H, Ross KE, Hu Y, Wu CH, Mazumder R, Vijay-Shanker K.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay045.

5.

eGARD: Extracting associations between genomic anomalies and drug responses from text.

Mahmood ASMA, Rao S, McGarvey P, Wu C, Madhavan S, Vijay-Shanker K.

PLoS One. 2017 Dec 20;12(12):e0189663. doi: 10.1371/journal.pone.0189663. eCollection 2017.

6.

eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality.

Ding R, Boutet E, Lieberherr D, Schneider M, Tognolli M, Wu CH, Vijay-Shanker K, Arighi CN.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax081.

7.

iPTMnet: an integrated resource for protein post-translational modification network discovery.

Huang H, Arighi CN, Ross KE, Ren J, Li G, Chen SC, Wang Q, Cowart J, Vijay-Shanker K, Wu CH.

Nucleic Acids Res. 2018 Jan 4;46(D1):D542-D550. doi: 10.1093/nar/gkx1104.

8.

Scalable Text Mining Assisted Curation of Post-Translationally Modified Proteoforms in the Protein Ontology.

Ross KE, Natale DA, Arighi C, Chen SC, Huang H, Li G, Ren J, Wang M, Vijay-Shanker K, Wu CH.

CEUR Workshop Proc. 2016 Aug;1747. pii: http://ceur-ws.org/Vol-1747/BIT103_ICBO2016.pdf. Epub 2016 Nov 29.

9.

WebGIVI: a web-based gene enrichment analysis and visualization tool.

Sun L, Zhu Y, Mahmood ASMA, Tudor CO, Ren J, Vijay-Shanker K, Chen J, Schmidt CJ.

BMC Bioinformatics. 2017 May 4;18(1):237. doi: 10.1186/s12859-017-1664-2.

10.

iPTMnet: Integrative Bioinformatics for Studying PTM Networks.

Ross KE, Huang H, Ren J, Arighi CN, Li G, Tudor CO, Lv M, Lee JY, Chen SC, Vijay-Shanker K, Wu CH.

Methods Mol Biol. 2017;1558:333-353. doi: 10.1007/978-1-4939-6783-4_16.

11.

Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature.

Wang Q, Ross KE, Huang H, Ren J, Li G, Vijay-Shanker K, Wu CH, Arighi CN.

Methods Mol Biol. 2017;1558:213-232. doi: 10.1007/978-1-4939-6783-4_10.

12.

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.

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.

Database (Oxford). 2016 Sep 1;2016. pii: baw121. doi: 10.1093/database/baw121. Print 2016.

13.

miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases.

Gupta S, Ross KE, Tudor CO, Wu CH, Schmidt CJ, Vijay-Shanker K.

J Biomed Semantics. 2016 Apr 29;7(1):9. doi: 10.1186/s13326-015-0044-y.

14.

BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph.

Peng Y, Arighi C, Wu CH, Vijay-Shanker K.

Database (Oxford). 2016 May 11;2016. pii: baw072. doi: 10.1093/database/baw072. Print 2016.

15.

DiMeX: A Text Mining System for Mutation-Disease Association Extraction.

Mahmood AS, Wu TJ, Mazumder R, Vijay-Shanker K.

PLoS One. 2016 Apr 13;11(4):e0152725. doi: 10.1371/journal.pone.0152725. eCollection 2016.

16.

miRTex: A Text Mining System for miRNA-Gene Relation Extraction.

Li G, Ross KE, Arighi CN, Peng Y, Wu CH, Vijay-Shanker K.

PLoS Comput Biol. 2015 Sep 25;11(9):e1004391. doi: 10.1371/journal.pcbi.1004391. eCollection 2015.

17.

RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information.

Torii M, Arighi CN, Li G, Wang Q, Wu CH, Vijay-Shanker K.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb;12(1):17-29. doi: 10.1109/TCBB.2014.2372765.

18.

pGenN, a gene normalization tool for plant genes and proteins in scientific literature.

Ding R, Arighi CN, Lee JY, Wu CH, Vijay-Shanker K.

PLoS One. 2015 Aug 10;10(8):e0135305. doi: 10.1371/journal.pone.0135305. eCollection 2015.

19.

Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line.

Sun L, Lamont SJ, Cooksey AM, McCarthy F, Tudor CO, Vijay-Shanker K, DeRita RM, Rothschild M, Ashwell C, Persia ME, Schmidt CJ.

Cell Stress Chaperones. 2015 Nov;20(6):939-50. doi: 10.1007/s12192-015-0621-0. Epub 2015 Aug 5.

20.

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 Mar 31;2015. pii: bav020. doi: 10.1093/database/bav020. Print 2015.

21.

A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems.

Peng Y, Torii M, Wu CH, Vijay-Shanker K.

BMC Bioinformatics. 2014 Aug 23;15:285. doi: 10.1186/1471-2105-15-285.

22.

RLIMS-P: an online text-mining tool for literature-based 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 Aug 13;2014. pii: bau081. doi: 10.1093/database/bau081. Print 2014.

23.

iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system.

Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K.

Database (Oxford). 2014 May 21;2014. pii: bau038. doi: 10.1093/database/bau038. Print 2014.

24.

A framework for biomedical figure segmentation towards image-based document retrieval.

Lopez LD, Yu J, Arighi C, Tudor CO, Torii M, Huang H, Vijay-Shanker K, Wu C.

BMC Syst Biol. 2013;7 Suppl 4:S8. doi: 10.1186/1752-0509-7-S4-S8. Epub 2013 Oct 23.

25.

Predicting interacting residues using long-distance information and novel decoding in hidden Markov models.

Kern C, González AJ, Liao L, Vijay-Shanker K.

IEEE Trans Nanobioscience. 2013 Sep;12(3):158-64. doi: 10.1109/TNB.2013.2263810. Epub 2013 Aug 15.

PMID:
23955776
26.

The eFIP system for text mining of protein interaction networks of phosphorylated proteins.

Tudor CO, Arighi CN, Wang Q, Wu CH, Vijay-Shanker K.

Database (Oxford). 2012 Dec 5;2012:bas044. doi: 10.1093/database/bas044. Print 2012.

27.

Developing a biocuration workflow for AgBase, a non-model organism database.

Pillai L, Chouvarine P, Tudor CO, Schmidt CJ, Vijay-Shanker K, McCarthy FM.

Database (Oxford). 2012 Nov 17;2012:bas038. doi: 10.1093/database/bas038. Print 2012.

28.

eGIFT: mining gene information from the literature.

Tudor CO, Schmidt CJ, Vijay-Shanker K.

BMC Bioinformatics. 2010 Aug 9;11:418. doi: 10.1186/1471-2105-11-418.

29.

An online literature mining tool for protein phosphorylation.

Yuan X, Hu ZZ, Wu HT, Torii M, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, Wu CH.

Bioinformatics. 2006 Jul 1;22(13):1668-9. Epub 2006 Apr 27.

PMID:
16644790
30.

Beyond the clause: extraction of phosphorylation information from medline abstracts.

Narayanaswamy M, Ravikumar KE, Vijay-Shanker K.

Bioinformatics. 2005 Jun;21 Suppl 1:i319-27.

PMID:
15961474
31.

Literature mining and database annotation of protein phosphorylation using a rule-based system.

Hu ZZ, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, Wu CH.

Bioinformatics. 2005 Jun 1;21(11):2759-65. Epub 2005 Apr 6.

PMID:
15814565
32.

Using name-internal and contextual features to classify biological terms.

Torii M, Kamboj S, Vijay-Shanker K.

J Biomed Inform. 2004 Dec;37(6):498-511.

33.

A biological named entity recognizer.

Narayanaswamy M, Ravikumar KE, Vijay-Shanker K.

Pac Symp Biocomput. 2003:427-38.

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