Author details

Full Name

K Vijay-Shanker

Affiliation

ORCID

Career Start Year

2003

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36799723	The Glycan Structure Dictionary-a dictionary describing commonly used glycan structure terms.		2023
37022994	Text mining of CHO bioprocess bibliome: Topic modeling and document classification.	PLoS One	2023
35379166	Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction.	BMC Bioinformatics	2022
34048547	emiRIT: a text-mining-based resource for microRNA information.	Database (Oxford)	2021
31361753	Using distant supervision to augment manually annotated data for relation extraction.	PLoS One	2019
29145615	iPTMnet: an integrated resource for protein post-translational modification network discovery.	Nucleic Acids Res	2018
30576489	iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature.	Database (Oxford)	2018
29860481	DEXTER: Disease-Expression Relation Extraction from Text.	Database (Oxford)	2018
30526566	Automatic gene annotation using GO terms from cellular component domain.	BMC Med Inform Decis Mak	2018
28150240	Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature.	Methods Mol Biol	2017
28472919	WebGIVI: a web-based gene enrichment analysis and visualization tool.	BMC Bioinformatics	2017
29261751	eGARD: Extracting associations between genomic anomalies and drug responses from text.	PLoS One	2017
29220476	eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality.	Database (Oxford)	2017
28150246	iPTMnet: Integrative Bioinformatics for Studying PTM Networks.	Methods Mol Biol	2017
27589962	BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.	Database (Oxford)	2016
28706471	Scalable Text Mining Assisted Curation of Post-Translationally Modified Proteoforms in the Protein Ontology.	CEUR Workshop Proc	2016
27216254	miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases.	J Biomed Semantics	2016
27170286	BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph.	Database (Oxford)	2016
27073839	DiMeX: A Text Mining System for Mutation-Disease Association Extraction.	PLoS ONE	2016
26407127	miRTex: A Text Mining System for miRNA-Gene Relation Extraction.	PLoS Comput Biol	2015
25833953	Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.	Database (Oxford)	2015
26357075	RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information.	IEEE/ACM Trans Comput Biol Bioinform	2015
26258475	pGenN, a gene normalization tool for plant genes and proteins in scientific literature.	PLoS One	2015
26238561	Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line.	Cell Stress Chaperones	2015
25122463	RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information.	Database (Oxford)	2014
24850848	iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system.	Database (Oxford)	2014
25149151	A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems.	BMC Bioinformatics	2014
24565394	A framework for biomedical figure segmentation towards image-based document retrieval.	BMC Syst Biol	2013
23955776	Predicting interacting residues using long-distance information and novel decoding in hidden Markov models.	IEEE Transactions on Nanobioscience	2013
23160411	Developing a biocuration workflow for AgBase, a non-model organism database.	Database (Oxford)	2012
23221174	The eFIP system for text mining of protein interaction networks of phosphorylated proteins.	Database (Oxford)	2012
20696046	eGIFT: mining gene information from the literature.	BMC Bioinformatics	2010
16644790	An online literature mining tool for protein phosphorylation.	Bioinformatics	2006
15961474	Beyond the clause: extraction of phosphorylation information from medline abstracts.	Bioinformatics	2005
15814565	Literature mining and database annotation of protein phosphorylation using a rule-based system.	Bioinformatics	2005
15542022	Using name-internal and contextual features to classify biological terms.	Journal of Biomedical Informatics	2004
12603047	A biological named entity recognizer.	Pac Symp Biocomput	2003