An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. - Cecilia N. Arighi; Ben Carterette; K. Bretonnel Cohen; Martin Krallinger; W. John Wilbur; Petra Fey; Robert J. Dodson; Laurel Cooper; Ceri E. Van Slyke; Wasila M. Dahdul; Paula M. Mabee; Donghui Li; et al. (Database J. Biol. Databases Curation, 2013)

PPInterFinder - a mining tool for extracting causal relations on human proteins from literature. - Kalpana Raja; Suresh Subramani; Jeyakumar Natarajan (Database J. Biol. Databases Curation, 2013)

A hybrid named entity tagger for tagging human proteins/genes. - Kalpana Raja; Suresh Subramani; Jeyakumar Natarajan (Int. J. Data Min. Bioinform., 2014)

ProNormz - An integrated approach for human proteins and protein kinases normalization. - Suresh Subramani; Kalpana Raja; Jeyakumar Natarajan (J. Biomed. Informatics, 2014)

Natural Language Processing and Data Mining for Clinical Text. - Kalpana Raja; Siddhartha Jonnalagadda (Healthcare Data Analytics, 2015)

Classification of Clinically Useful Sentences in MEDLINE. - Mohammad Amin Morid; Siddhartha R. Jonnalagadda; Marcelo Fiszman; Kalpana Raja; Guilherme Del Fiol (AMIA, 2015)

Automated Citation Retrieval System for Clinical Knowledge Management. - Kalpana Raja; Andrew J. Sauer; Melanie R. Klerer; Siddhartha R. Jonnalagadda (AMIA, 2015)

Concept based Information Retrieval for Clinical Case Summaries. - Jakob Stöber; Bret S. E. Heale; Kelley Fulghum; Guilherme Del Fiol; Heejun Kim; Kalpana Raja; Siddhartha Jonnalagadda (TREC, 2015)

Agile text mining for the 2014 i2b2/UTHealth Cardiac risk factors challenge. - James Cormack; Chinmoy Nath; David Milward; Kalpana Raja; Siddhartha R. Jonnalagadda (J. Biomed. Informatics, 2015)

HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways. - Suresh Subramani; Raja Kalpana; Pankaj Moses Monickaraj; Jeyakumar Natarajan (J. Biomed. Informatics, 2015)

Towards Evidence-Based Precision Medicine: Extracting Population Information from Biomedical Text using Binary Classifiers and Syntactic Patterns. - Kalpana Raja; Naman Dasot; Pawan Goyal 002; Siddhartha R. Jonnalagadda (CRI, 2016)

CRTS: A type system for representing clinical recommendations. - Ravi Prakash Garg; Kalpana Raja; Siddhartha R. Jonnalagadda (CoRR, 2016)

A Hybrid Citation Retrieval Algorithm for Evidence-based Clinical Knowledge Summarization: Combining Concept Extraction, Vector Similarity and Query Expansion for High Precision. - Kalpana Raja; Andrew J. Sauer; Ravi Prakash Garg; Melanie R. Klerer; Siddhartha R. Jonnalagadda (CoRR, 2016)

Classification of clinically useful sentences in clinical evidence resources. - Mohammad Amin Morid; Marcelo Fiszman; Kalpana Raja; Siddhartha Jonnalagadda; Guilherme Del Fiol (J. Biomed. Informatics, 2016)

Mining protein phosphorylation information from biomedical literature using NLP parsing and Support Vector Machines. - Kalpana Raja; Jeyakumar Natarajan (Comput. Methods Programs Biomed., 2018)

Discovery of novel inhibitors targeting movement protein for controlling the transmission of banana bunchy top virus infection in plantain by structure-based virtual screening. - Archana Prabahar; Subashini Swaminathan; Kalpana Raja; Srividhya Vellingiri; Ramalingam Jegadeesan; Bharathi Nathan (Int. J. Bioinform. Res. Appl., 2018)

Automated Extraction and Visualization of Protein-Protein Interaction Networks and Beyond: A Text-Mining Protocol. - Kalpana Raja; Jeyakumar Natarajan; Finn Kuusisto; John W. Steill; Ian Ross; James A. Thomson; Ron M. Stewart (Protein-Protein Interaction Networks, 2020)

Advancement in predicting interactions between drugs used to treat psoriasis and its comorbidities by integrating molecular and clinical resources. - Matthew T. Patrick; Redina Bardhi; Kalpana Raja; Kevin He; Lam C. Tsoi (J. Am. Medical Informatics Assoc., 2021)

Large language models in biomedical natural language processing: benchmarks, baselines, and recommendations. - Qingyu Chen 001; Jingcheng Du; Yan Hu; Vipina Kuttichi Keloth; Xueqing Peng; Kalpana Raja; Rui Zhang 028; Zhiyong Lu; Hua Xu 001 (CoRR, 2023)

Representing and utilizing clinical textual data for real world studies: An OHDSI approach. - Vipina Kuttichi Keloth; Juan M. Banda; Michael J. Gurley; Paul M. Heider; Georgina Kennedy; Hongfang Liu; Feifan Liu; Timothy Miller 002; Karthik Natarajan; Olga V. Patterson; Yifan Peng 002; Kalpana Raja; et al. (J. Biomed. Informatics, 2023)

Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach. - Yan Hu; Vipina Kuttichi Keloth; Kalpana Raja; Yong Chen 016; Hua Xu 001 (Bioinform., 2023)

Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models. - Robert J. Millikin; Kalpana Raja; John W. Steill; Cannon Lock; Xuancheng Tu; Ian Ross; Lam C. Tsoi; Finn Kuusisto; Zijian Ni; Miron Livny; Brian Bockelman; James A. Thomson; et al. (BMC Bioinform., 2023)

Predicting Protein-Protein Interactions Using Self-Attention-Based Deep Neural Networks and FastText Embeddings. - I. R. Oviya; N. Shanmukha Sravya; Kalpana Raja (ICCCNT, 2024)