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ORCIDBibTeX records: Kalpana Raja
@article{DBLP:journals/bioinformatics/HuKRCX23,
author = {Yan Hu and
Vipina Kuttichi Keloth and
Kalpana Raja and
Yong Chen and
Hua Xu},
title = {Towards precise {PICO} extraction from abstracts of randomized controlled
trials using a section-specific learning approach},
journal = {Bioinform.},
volume = {39},
number = {9},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad542},
doi = {10.1093/BIOINFORMATICS/BTAD542},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuKRCX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MillikinRSLTRTKNLBTS23,
author = {Robert J. Millikin and
Kalpana Raja and
John W. Steill and
Cannon Lock and
Xuancheng Tu and
Ian Ross and
Lam C. Tsoi and
Finn Kuusisto and
Zijian Ni and
Miron Livny and
Brian Bockelman and
James A. Thomson and
Ron M. Stewart},
title = {Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge
using co-occurrence and transformer models},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {412},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05539-y},
doi = {10.1186/S12859-023-05539-Y},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MillikinRSLTRTKNLBTS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/KelothBGHKLLMNPPRRRSWWWWZBRBRHEX23,
author = {Vipina Kuttichi Keloth and
Juan M. Banda and
Michael J. Gurley and
Paul M. Heider and
Georgina Kennedy and
Hongfang Liu and
Feifan Liu and
Timothy A. Miller and
Karthik Natarajan and
Olga V. Patterson and
Yifan Peng and
Kalpana Raja and
Ruth M. Reeves and
Masoud Rouhizadeh and
Jianlin Shi and
Xiaoyan Wang and
Yanshan Wang and
Wei{-}Qi Wei and
Andrew E. Williams and
Rui Zhang and
Rimma Belenkaya and
Christian G. Reich and
Clair Blacketer and
Patrick B. Ryan and
George Hripcsak and
No{\'{e}}mie Elhadad and
Hua Xu},
title = {Representing and utilizing clinical textual data for real world studies:
An {OHDSI} approach},
journal = {J. Biomed. Informatics},
volume = {142},
pages = {104343},
year = {2023},
url = {https://doi.org/10.1016/j.jbi.2023.104343},
doi = {10.1016/J.JBI.2023.104343},
timestamp = {Thu, 29 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/KelothBGHKLLMNPPRRRSWWWWZBRBRHEX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2305-16326,
author = {Qingyu Chen and
Jingcheng Du and
Yan Hu and
Vipina Kuttichi Keloth and
Xueqing Peng and
Kalpana Raja and
Rui Zhang and
Zhiyong Lu and
Hua Xu},
title = {Large language models in biomedical natural language processing: benchmarks,
baselines, and recommendations},
journal = {CoRR},
volume = {abs/2305.16326},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.16326},
doi = {10.48550/ARXIV.2305.16326},
eprinttype = {arXiv},
eprint = {2305.16326},
timestamp = {Wed, 07 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-16326.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/PatrickBRHT21,
author = {Matthew T. Patrick and
Redina Bardhi and
Kalpana Raja and
Kevin He and
Lam C. Tsoi},
title = {Advancement in predicting interactions between drugs used to treat
psoriasis and its comorbidities by integrating molecular and clinical
resources},
journal = {J. Am. Medical Informatics Assoc.},
volume = {28},
number = {6},
pages = {1159--1167},
year = {2021},
url = {https://doi.org/10.1093/jamia/ocaa335},
doi = {10.1093/JAMIA/OCAA335},
timestamp = {Sun, 22 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/PatrickBRHT21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:series/mimb/RajaNKSRTS20,
author = {Kalpana Raja and
Jeyakumar Natarajan and
Finn Kuusisto and
John W. Steill and
Ian Ross and
James A. Thomson and
Ron M. Stewart},
editor = {Stefan Canzar and
Francisca Rojas Ringeling},
title = {Automated Extraction and Visualization of Protein-Protein Interaction
Networks and Beyond: {A} Text-Mining Protocol},
booktitle = {Protein-Protein Interaction Networks, Methods and Protocols},
series = {Methods in Molecular Biology},
volume = {2074},
pages = {13--34},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-1-4939-9873-9\_2},
doi = {10.1007/978-1-4939-9873-9\_2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/series/mimb/RajaNKSRTS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cmpb/RajaN18,
author = {Kalpana Raja and
Jeyakumar Natarajan},
title = {Mining protein phosphorylation information from biomedical literature
using {NLP} parsing and Support Vector Machines},
journal = {Comput. Methods Programs Biomed.},
volume = {160},
pages = {57--64},
year = {2018},
url = {https://doi.org/10.1016/j.cmpb.2018.03.022},
doi = {10.1016/J.CMPB.2018.03.022},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cmpb/RajaN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/PrabaharSRVJN18,
author = {Archana Prabahar and
Subashini Swaminathan and
Kalpana Raja and
Srividhya Vellingiri and
Ramalingam Jegadeesan and
Bharathi Nathan},
title = {Discovery of novel inhibitors targeting movement protein for controlling
the transmission of banana bunchy top virus infection in plantain
by structure-based virtual screening},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {14},
number = {4},
pages = {305--320},
year = {2018},
url = {https://doi.org/10.1504/IJBRA.2018.10009939},
doi = {10.1504/IJBRA.2018.10009939},
timestamp = {Fri, 11 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijbra/PrabaharSRVJN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/MoridFRJF16,
author = {Mohammad Amin Morid and
Marcelo Fiszman and
Kalpana Raja and
Siddhartha Jonnalagadda and
Guilherme Del Fiol},
title = {Classification of clinically useful sentences in clinical evidence
resources},
journal = {J. Biomed. Informatics},
volume = {60},
pages = {14--22},
year = {2016},
url = {https://doi.org/10.1016/j.jbi.2016.01.003},
doi = {10.1016/J.JBI.2016.01.003},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/MoridFRJF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cri/RajaDGJ16,
author = {Kalpana Raja and
Naman Dasot and
Pawan Goyal and
Siddhartha R. Jonnalagadda},
title = {Towards Evidence-Based Precision Medicine: Extracting Population Information
from Biomedical Text using Binary Classifiers and Syntactic Patterns},
booktitle = {Summit on Clinical Research Informatics, {CRI} 2016, San Francisco,
CA, USA, March 21-24, 2016},
publisher = {{AMIA}},
year = {2016},
url = {http://knowledge.amia.org/amia-59309-cri2016-1.3011827/t003-1.3012832/f003-1.3012833/a040-1.3012875/a042-1.3012870},
timestamp = {Fri, 25 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cri/RajaDGJ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/GargRJ16,
author = {Ravi Prakash Garg and
Kalpana Raja and
Siddhartha R. Jonnalagadda},
title = {{CRTS:} {A} type system for representing clinical recommendations},
journal = {CoRR},
volume = {abs/1609.01592},
year = {2016},
url = {http://arxiv.org/abs/1609.01592},
eprinttype = {arXiv},
eprint = {1609.01592},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/GargRJ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/RajaSGKJ16,
author = {Kalpana Raja and
Andrew J. Sauer and
Ravi Prakash Garg and
Melanie R. Klerer and
Siddhartha R. Jonnalagadda},
title = {A Hybrid Citation Retrieval Algorithm for Evidence-based Clinical
Knowledge Summarization: Combining Concept Extraction, Vector Similarity
and Query Expansion for High Precision},
journal = {CoRR},
volume = {abs/1609.01597},
year = {2016},
url = {http://arxiv.org/abs/1609.01597},
eprinttype = {arXiv},
eprint = {1609.01597},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/RajaSGKJ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/SubramaniKMN15,
author = {Suresh Subramani and
Raja Kalpana and
Pankaj Moses Monickaraj and
Jeyakumar Natarajan},
title = {HPIminer: {A} text mining system for building and visualizing human
protein interaction networks and pathways},
journal = {J. Biomed. Informatics},
volume = {54},
pages = {121--131},
year = {2015},
url = {https://doi.org/10.1016/j.jbi.2015.01.006},
doi = {10.1016/J.JBI.2015.01.006},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/SubramaniKMN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/CormackNMRJ15,
author = {James Cormack and
Chinmoy Nath and
David Milward and
Kalpana Raja and
Siddhartha R. Jonnalagadda},
title = {Agile text mining for the 2014 i2b2/UTHealth Cardiac risk factors
challenge},
journal = {J. Biomed. Informatics},
volume = {58},
pages = {S120--S127},
year = {2015},
url = {https://doi.org/10.1016/j.jbi.2015.06.030},
doi = {10.1016/J.JBI.2015.06.030},
timestamp = {Fri, 21 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/CormackNMRJ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/MoridJFRF15,
author = {Mohammad Amin Morid and
Siddhartha R. Jonnalagadda and
Marcelo Fiszman and
Kalpana Raja and
Guilherme Del Fiol},
title = {Classification of Clinically Useful Sentences in {MEDLINE}},
booktitle = {{AMIA} 2015, American Medical Informatics Association Annual Symposium,
San Francisco, CA, USA, November 14-18, 2015},
publisher = {{AMIA}},
year = {2015},
url = {https://knowledge.amia.org/59310-amia-1.2741865/t007-1.2744224/f007-1.2744225/2248288-1.2744262/2246142-1.2744259},
timestamp = {Wed, 17 Apr 2024 11:47:40 +0200},
biburl = {https://dblp.org/rec/conf/amia/MoridJFRF15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/RajaSKJ15,
author = {Kalpana Raja and
Andrew J. Sauer and
Melanie R. Klerer and
Siddhartha R. Jonnalagadda},
title = {Automated Citation Retrieval System for Clinical Knowledge Management},
booktitle = {{AMIA} 2015, American Medical Informatics Association Annual Symposium,
San Francisco, CA, USA, November 14-18, 2015},
publisher = {{AMIA}},
year = {2015},
url = {https://knowledge.amia.org/59310-amia-1.2741865/t005-1.2744350/f005-1.2744351/2249331-1.2744703/2242055-1.2744700},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/RajaSKJ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/trec/StoberHFFKRJ15,
author = {Jakob St{\"{o}}ber and
Bret S. E. Heale and
Kelley Fulghum and
Guilherme Del Fiol and
Heejun Kim and
Kalpana Raja and
Siddhartha Jonnalagadda},
editor = {Ellen M. Voorhees and
Angela Ellis},
title = {Concept based Information Retrieval for Clinical Case Summaries},
booktitle = {Proceedings of The Twenty-Fourth Text REtrieval Conference, {TREC}
2015, Gaithersburg, Maryland, USA, November 17-20, 2015},
series = {{NIST} Special Publication},
volume = {500-319},
publisher = {National Institute of Standards and Technology {(NIST)}},
year = {2015},
url = {http://trec.nist.gov/pubs/trec24/papers/NU\_UU\_UNC-CL.pdf},
timestamp = {Wed, 03 Feb 2021 08:31:23 +0100},
biburl = {https://dblp.org/rec/conf/trec/StoberHFFKRJ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/crc/p/RajaJ15,
author = {Kalpana Raja and
Siddhartha Jonnalagadda},
editor = {Chandan K. Reddy and
Charu C. Aggarwal},
title = {Natural Language Processing and Data Mining for Clinical Text},
booktitle = {Healthcare Data Analytics},
pages = {219--249},
publisher = {Chapman and Hall/CRC},
year = {2015},
url = {http://www.crcnetbase.com/doi/abs/10.1201/b18588-9},
doi = {10.1201/B18588-9},
timestamp = {Tue, 18 Aug 2015 15:30:18 +0200},
biburl = {https://dblp.org/rec/books/crc/p/RajaJ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijdmb/RajaSN14,
author = {Kalpana Raja and
Suresh Subramani and
Jeyakumar Natarajan},
title = {A hybrid named entity tagger for tagging human proteins/genes},
journal = {Int. J. Data Min. Bioinform.},
volume = {10},
number = {3},
pages = {315--328},
year = {2014},
url = {https://doi.org/10.1504/IJDMB.2014.064545},
doi = {10.1504/IJDMB.2014.064545},
timestamp = {Mon, 11 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijdmb/RajaSN14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/SubramaniRN14,
author = {Suresh Subramani and
Kalpana Raja and
Jeyakumar Natarajan},
title = {ProNormz - An integrated approach for human proteins and protein kinases
normalization},
journal = {J. Biomed. Informatics},
volume = {47},
pages = {131--138},
year = {2014},
url = {https://doi.org/10.1016/j.jbi.2013.10.003},
doi = {10.1016/J.JBI.2013.10.003},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/SubramaniRN14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/ArighiCCKWFDCSDMLHGJRMBDBLCSPHALCMCBWLWTRSNCDW13,
author = {Cecilia N. Arighi and
Ben Carterette and
K. Bretonnel Cohen and
Martin Krallinger and
W. John Wilbur and
Petra Fey and
Robert J. Dodson and
Laurel Cooper and
Ceri E. Van Slyke and
Wasila M. Dahdul and
Paula M. Mabee and
Donghui Li and
Bethany R. Harris and
Marc Gillespie and
Silvia Jimenez and
Phoebe M. Roberts and
Lisa Matthews and
Kevin G. Becker and
Harold J. Drabkin and
Susan M. Bello and
Luana Licata and
Andrew Chatr{-}aryamontri and
Mary L. Schaeffer and
Julie Park and
Melissa A. Haendel and
Kimberly Van Auken and
Yuling Li and
Juancarlos Chan and
Hans{-}Michael M{\"{u}}ller and
Hong Cui and
James P. Balhoff and
Chi{-}Yang Wu and
Zhiyong Lu and
Chih{-}Hsuan Wei and
Catalina O. Tudor and
Kalpana Raja and
Suresh Subramani and
Jeyakumar Natarajan and
Juan Miguel Cejuela and
Pratibha Dubey and
Cathy H. Wu},
title = {An overview of the BioCreative 2012 Workshop Track {III:} interactive
text mining task},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bas056},
doi = {10.1093/DATABASE/BAS056},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/ArighiCCKWFDCSDMLHGJRMBDBLCSPHALCMCBWLWTRSNCDW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/RajaSN13,
author = {Kalpana Raja and
Suresh Subramani and
Jeyakumar Natarajan},
title = {PPInterFinder - a mining tool for extracting causal relations on human
proteins from literature},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bas052},
doi = {10.1093/DATABASE/BAS052},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/RajaSN13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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