publications | Halil Kilicoglu

2024

Journal Article

Text classification models for assessing the completeness of randomized controlled trial publications based on CONSORT reporting guidelines

Lan Jiang, Mengfei Lan, Joe D Menke, Colby J Vorland, and Halil Kilicoglu

Scientific Reports, Sep 2024

Bib HTML

@article{jiang2024text,
  title = {Text classification models for assessing the completeness of randomized controlled trial publications based on CONSORT reporting guidelines},
  author = {Jiang, Lan and Lan, Mengfei and Menke, Joe D and Vorland, Colby J and Kilicoglu, Halil},
  journal = {Scientific Reports},
  volume = {14},
  number = {1},
  pages = {21721},
  year = {2024},
  month = sep,
  publisher = {Nature Publishing Group UK London},
  doi = {10.1038/s41598-024-72130-7},
  url = {https://doi.org/10.1038/s41598-024-72130-7},
}

Journal Article

Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach

M Janina Sarol, Gibong Hong, Evan Guerra, and Halil Kilicoglu

Database, Aug 2024

Bib HTML

@article{sarol2024integrating,
  title = {{Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach}},
  author = {Sarol, M Janina and Hong, Gibong and Guerra, Evan and Kilicoglu, Halil},
  journal = {Database},
  volume = {2024},
  pages = {baae079},
  year = {2024},
  month = aug,
  publisher = {Oxford University Press UK},
  doi = {10.1093/database/baae079},
  url = {https://doi.org/10.1093/database/baae079},
}

Journal Article

Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics

Sarah Mullin, Robert McDougal, Kei-Hoi Cheung, Halil Kilicoglu, Amanda Beck, and Caroline J Zeiss

Journal of Biomedical Semantics, Jul 2024

Bib HTML

@article{mullin2024chemical,
  title = {Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics},
  author = {Mullin, Sarah and McDougal, Robert and Cheung, Kei-Hoi and Kilicoglu, Halil and Beck, Amanda and Zeiss, Caroline J},
  journal = {Journal of Biomedical Semantics},
  volume = {15},
  number = {1},
  pages = {13},
  year = {2024},
  month = jul,
  publisher = {Springer},
  doi = {10.1186/s13326-024-00314-1},
  url = {https://doi.org/10.1186/s13326-024-00314-1},
}

Journal Article

Assessing citation integrity in biomedical publications: corpus annotation and NLP models

Maria Janina Sarol, Shufan Ming, Shruthan Radhakrishna, Jodi Schneider, and Halil Kilicoglu

Bioinformatics, Jun 2024

Bib HTML

@article{10.1093/bioinformatics/btae420,
  author = {Sarol, Maria Janina and Ming, Shufan and Radhakrishna, Shruthan and Schneider, Jodi and Kilicoglu, Halil},
  title = {{Assessing citation integrity in biomedical publications: corpus annotation and NLP models}},
  journal = {Bioinformatics},
  volume = {40},
  number = {7},
  pages = {btae420},
  year = {2024},
  month = jun,
  doi = {10.1093/bioinformatics/btae420},
  url = {https://doi.org/10.1093/bioinformatics/btae420},
}

Book Chapter

NLP Applications—Biomedical Literature

Rui Zhang, Andrej Kastrin, Dimitar Hristovski, Marcelo Fiszman, and Halil Kilicoglu

Jun 2024

Bib HTML

@inbook{Zhang2024,
  author = {Zhang, Rui and Kastrin, Andrej and Hristovski, Dimitar and Fiszman, Marcelo and Kilicoglu, Halil},
  editor = {Xu, Hua and Demner Fushman, Dina},
  title = {NLP Applications---Biomedical Literature},
  booktitle = {Natural Language Processing in Biomedicine: A Practical Guide},
  year = {2024},
  month = jun,
  publisher = {Springer International Publishing},
  address = {Cham},
  pages = {351--395},
  isbn = {978-3-031-55865-8},
  doi = {10.1007/978-3-031-55865-8_13},
  url = {https://doi.org/10.1007/978-3-031-55865-8_13},
}

Journal Article

Enhancing the coverage of SemRep using a relation classification approach

Shufan Ming, Rui Zhang, and Halil Kilicoglu

Journal of Biomedical Informatics, May 2024

Bib HTML

@article{ming2024enhancing,
  title = {{Enhancing the coverage of SemRep using a relation classification approach}},
  author = {Ming, Shufan and Zhang, Rui and Kilicoglu, Halil},
  journal = {Journal of Biomedical Informatics},
  volume = {155},
  pages = {104658},
  year = {2024},
  month = may,
  issn = {1532-0464},
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2024.104658},
  url = {https://doi.org/10.1016/j.jbi.2024.104658},
}

Journal Article

Repurposing non-pharmacological interventions for Alzheimer’s disease through link prediction on biomedical literature

Yongkang Xiao, Yu Hou, Huixue Zhou, Gayo Diallo, Marcelo Fiszman, Julian Wolfson, Li Zhou, Halil Kilicoglu, You Chen, Chang Su, Hua Xu, William G Mantyh, and Rui Zhang

Scientific Reports, Apr 2024

Bib HTML

@article{xiao2024repurposing,
  title = {{Repurposing non-pharmacological interventions for Alzheimer's disease through link prediction on biomedical literature}},
  author = {Xiao, Yongkang and Hou, Yu and Zhou, Huixue and Diallo, Gayo and Fiszman, Marcelo and Wolfson, Julian and Zhou, Li and Kilicoglu, Halil and Chen, You and Su, Chang and Xu, Hua and Mantyh, William G and Zhang, Rui},
  journal = {Scientific Reports},
  volume = {14},
  number = {1},
  pages = {8693},
  year = {2024},
  month = apr,
  publisher = {Nature Publishing Group UK London},
  doi = {10.1038/s41598-024-58604-8},
  url = {https://doi.org/10.1038/s41598-024-58604-8},
}

Journal Article

Automatic categorization of self-acknowledged limitations in randomized controlled trial publications

Mengfei Lan, Mandy Cheng, Linh Hoang, Gerben Ter Riet, and Halil Kilicoglu

Journal of Biomedical Informatics, Apr 2024

Bib HTML

@article{lan2024automatic,
  title = {Automatic categorization of self-acknowledged limitations in randomized controlled trial publications},
  author = {Lan, Mengfei and Cheng, Mandy and Hoang, Linh and Ter Riet, Gerben and Kilicoglu, Halil},
  journal = {Journal of Biomedical Informatics},
  volume = {152},
  pages = {104628},
  year = {2024},
  month = apr,
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2024.104628},
  url = {https://doi.org/10.1016/j.jbi.2024.104628},
}

Journal Article

Complementary and Integrative Health Information in the literature: its lexicon and named entity recognition

Huixue Zhou, Robin Austin, Sheng-Chieh Lu, Greg Marc Silverman, Yuqi Zhou, Halil Kilicoglu, Hua Xu, and Rui Zhang

Journal of the American Medical Informatics Association, Feb 2024

Bib HTML

@article{zhou2024complementary,
  title = {Complementary and Integrative Health Information in the literature: its lexicon and named entity recognition},
  author = {Zhou, Huixue and Austin, Robin and Lu, Sheng-Chieh and Silverman, Greg Marc and Zhou, Yuqi and Kilicoglu, Halil and Xu, Hua and Zhang, Rui},
  journal = {Journal of the American Medical Informatics Association},
  volume = {31},
  number = {2},
  pages = {426--434},
  year = {2024},
  month = feb,
  publisher = {Oxford University Press},
  doi = {10.1093/jamia/ocad216},
  url = {https://doi.org/10.1093/jamia/ocad216},
}

Editorial

Semantics-enabled biomedical literature analytics

Halil Kilicoglu, Faezeh Ensan, Bridget McInnes, and Lucy Lu Wang

Journal of Biomedical Informatics, Feb 2024

Bib HTML

@article{kilicoglu2024semantics,
  title = {Semantics-enabled biomedical literature analytics},
  author = {Kilicoglu, Halil and Ensan, Faezeh and McInnes, Bridget and Wang, Lucy Lu},
  journal = {Journal of Biomedical Informatics},
  pages = {104588},
  year = {2024},
  month = feb,
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2024.104588},
  url = {https://doi.org/10.1016/j.jbi.2024.104588},
}

Journal Article

Publication of Results of Registered Trials With Published Study Protocols, 2011-2022

Colby J Vorland, Andrew W Brown, Halil Kilicoglu, Xiangji Ying, and Evan Mayo-Wilson

JAMA Network Open, Jan 2024

Bib HTML

@article{vorland2024publication,
  title = {Publication of Results of Registered Trials With Published Study Protocols, 2011-2022},
  author = {Vorland, Colby J and Brown, Andrew W and Kilicoglu, Halil and Ying, Xiangji and Mayo-Wilson, Evan},
  journal = {JAMA Network Open},
  volume = {7},
  number = {1},
  pages = {e2350688--e2350688},
  year = {2024},
  month = jan,
  publisher = {American Medical Association},
  doi = {10.1001/jamanetworkopen.2023.50688},
  url = {https://doi.org/10.1001/jamanetworkopen.2023.50688},
}

2023

Journal Article

Methodology reporting improved over time in 176,469 randomized controlled trials

Halil Kilicoglu, Lan Jiang, Linh Hoang, Evan Mayo-Wilson, Christiaan H Vinkers, and Willem M Otte

Journal of Clinical Epidemiology, Oct 2023

Bib HTML

@article{kilicoglu2023methodology,
  title = {Methodology reporting improved over time in 176,469 randomized controlled trials},
  author = {Kilicoglu, Halil and Jiang, Lan and Hoang, Linh and Mayo-Wilson, Evan and Vinkers, Christiaan H and Otte, Willem M},
  journal = {Journal of Clinical Epidemiology},
  volume = {162},
  pages = {19--28},
  year = {2023},
  month = oct,
  publisher = {Elsevier},
  doi = {10.1016/j.jclinepi.2023.08.004},
  url = {https://doi.org/10.1016/j.jclinepi.2023.08.004},
}

Workshop Paper

Examining the Causal Impact of First Names on Language Models: The Case of Social Commonsense Reasoning

Sullam Jeoung, Jana Diesner, and Halil Kilicoglu

In Proceedings of the 3rd Workshop on Trustworthy Natural Language Processing (TrustNLP 2023), Jul 2023

Bib HTML

@inproceedings{jeoung-etal-2023-examining,
  title = {{Examining the Causal Impact of First Names on Language Models: The Case of Social Commonsense Reasoning}},
  author = {Jeoung, Sullam and Diesner, Jana and Kilicoglu, Halil},
  booktitle = {Proceedings of the 3rd Workshop on Trustworthy Natural Language Processing (TrustNLP 2023)},
  month = jul,
  year = {2023},
  address = {Toronto, Canada},
  publisher = {Association for Computational Linguistics},
  url = {https://aclanthology.org/2023.trustnlp-1.7},
  doi = {10.18653/v1/2023.trustnlp-1.7},
  pages = {61--72},
}

Conference Poster

Repurposing Drugs for Alzheimer’s Diseases through Link Prediction on Biomedical Literature

Yongkang Xiao, Yu Hou, Huixue Zhou, Gayo Diallo, Marcelo Fiszman, Julian Wolfson, Halil Kilicoglu, You Chen, Hua Xu, William G Mantyh, and Rui Zhang

In 2023 IEEE 11th International Conference on Healthcare Informatics (ICHI), Jun 2023

Bib HTML

@inproceedings{xiao2023repurposing,
  title = {Repurposing Drugs for Alzheimer's Diseases through Link Prediction on Biomedical Literature},
  author = {Xiao, Yongkang and Hou, Yu and Zhou, Huixue and Diallo, Gayo and Fiszman, Marcelo and Wolfson, Julian and Kilicoglu, Halil and Chen, You and Xu, Hua and Mantyh, William G and Zhang, Rui},
  booktitle = {2023 IEEE 11th International Conference on Healthcare Informatics (ICHI)},
  pages = {750--752},
  year = {2023},
  month = jun,
  organization = {IEEE},
  address = {Houston,TX},
  doi = {10.1109/ICHI57859.2023.00137},
  url = {https://doi.org/10.1109/ICHI57859.2023.00137},
}

Journal Article

Developing a knowledge graph for pharmacokinetic natural product-drug interactions

Sanya B Taneja, Tiffany J Callahan, Mary F Paine, Sandra L Kane-Gill, Halil Kilicoglu, Marcin P Joachimiak, and Richard D Boyce

Journal of Biomedical Informatics, Apr 2023

Bib HTML

@article{taneja2023developing,
  title = {Developing a knowledge graph for pharmacokinetic natural product-drug interactions},
  author = {Taneja, Sanya B and Callahan, Tiffany J and Paine, Mary F and Kane-Gill, Sandra L and Kilicoglu, Halil and Joachimiak, Marcin P and Boyce, Richard D},
  journal = {Journal of Biomedical Informatics},
  volume = {140},
  pages = {104341},
  year = {2023},
  month = apr,
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2023.104341},
  url = {https://doi.org/10.1016/j.jbi.2023.104341},
}

Journal Article

A comment-driven evidence appraisal approach to promoting research findings into practice when only uncertain evidence is available

Shuang Wang, Halil Kilicoglu, and Jian Du

Health Research Policy and Systems, Mar 2023

Bib HTML

@article{wang2023comment,
  title = {A comment-driven evidence appraisal approach to promoting research findings into practice when only uncertain evidence is available},
  author = {Wang, Shuang and Kilicoglu, Halil and Du, Jian},
  journal = {Health Research Policy and Systems},
  volume = {21},
  number = {1},
  pages = {25},
  year = {2023},
  month = mar,
  publisher = {Springer},
  doi = {10.1186/s12961-023-00969-9},
  url = {https://doi.org/10.1186/s12961-023-00969-9},
}

Workshop Paper

Commonsense-Aware Prompting for Controllable Empathetic Dialogue Generation

Yiren Liu, and Halil Kilicoglu

In AAAI’23 Workshop on Knowledge Augmented Methods for NLP, Feb 2023

Bib HTML

@inproceedings{liu2023commonsense,
  title = {Commonsense-Aware Prompting for Controllable Empathetic Dialogue Generation},
  author = {Liu, Yiren and Kilicoglu, Halil},
  booktitle = {AAAI’23 Workshop on Knowledge Augmented Methods for NLP},
  year = {2023},
  month = feb,
  url = {https://knowledge-nlp.github.io/aaai2023/papers/012-ComPrompt-poster.pdf},
}

2022

Conference Paper

Methodological information extraction from randomized controlled trial publications: a pilot study

Linh Hoang, Yingjun Guan, and Halil Kilicoglu

In AMIA Annual Symposium Proceedings, Nov 2022

Bib HTML

@inproceedings{hoang2022methodological,
  title = {Methodological information extraction from randomized controlled trial publications: a pilot study},
  author = {Hoang, Linh and Guan, Yingjun and Kilicoglu, Halil},
  booktitle = {AMIA Annual Symposium Proceedings},
  volume = {2022},
  pages = {542},
  year = {2022},
  month = nov,
  organization = {American Medical Informatics Association},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148349/},
}

Journal Article

Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature

Dalton Schutte, Jake Vasilakes, Anu Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R Bishop, Terrence Adam, and Rui Zhang

Journal of Biomedical Informatics, Jul 2022

Bib HTML

@article{schutte2022discovering,
  title = {{Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature}},
  author = {Schutte, Dalton and Vasilakes, Jake and Bompelli, Anu and Zhou, Yuqi and Fiszman, Marcelo and Xu, Hua and Kilicoglu, Halil and Bishop, Jeffrey R and Adam, Terrence and Zhang, Rui},
  journal = {Journal of Biomedical Informatics},
  volume = {131},
  pages = {104120},
  year = {2022},
  month = jul,
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2022.104120},
  url = {https://doi.org/10.1016/j.jbi.2022.104120},
}

Commentary

Is the future of peer review automated?

Robert Schulz, Adrian Barnett, René Bernard, Nicholas JL Brown, Jennifer A Byrne, Peter Eckmann, Małgorzata A Gazda, Halil Kilicoglu, Eric M Prager, Maia Salholz-Hillel, Gerben Riet, Timothy Vines, Colby J Vorland, Han Zhuang, Anita Bandrowski, and Tracey L Weissgerber

BMC Research Notes, Jun 2022

Bib HTML

@article{schulz2022future,
  title = {Is the future of peer review automated?},
  author = {Schulz, Robert and Barnett, Adrian and Bernard, Ren{\'e} and Brown, Nicholas JL and Byrne, Jennifer A and Eckmann, Peter and Gazda, Ma{\l}gorzata A and Kilicoglu, Halil and Prager, Eric M and Salholz-Hillel, Maia and ter Riet, Gerben and Vines, Timothy and Vorland, Colby J and Zhuang, Han and Bandrowski, Anita and Weissgerber, Tracey L},
  journal = {BMC Research Notes},
  volume = {15},
  number = {1},
  pages = {203},
  year = {2022},
  month = jun,
  publisher = {Springer},
  doi = {10.1186/s13104-022-06080-6},
  url = {https://doi.org/10.1186/s13104-022-06080-6},
}

Conference Paper

Investigating the impact of weakly supervised data on text mining models of publication transparency: a case study on randomized controlled trials

Linh Hoang, Lan Jiang, and Halil Kilicoglu

In AMIA Summits on Translational Science Proceedings, Mar 2022

Bib HTML

@inproceedings{hoang2022investigating,
  title = {Investigating the impact of weakly supervised data on text mining models of publication transparency: a case study on randomized controlled trials},
  author = {Hoang, Linh and Jiang, Lan and Kilicoglu, Halil},
  booktitle = {AMIA Summits on Translational Science Proceedings},
  volume = {2022},
  pages = {254},
  year = {2022},
  month = mar,
  publisher = {American Medical Informatics Association},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9285178/},
}

2021

Workshop Paper

UIUC_BioNLP at SemEval-2021 Task 11: A Cascade of Neural Models for Structuring Scholarly NLP Contributions

Haoyang Liu, M. Janina Sarol, and Halil Kilicoglu

In Proceedings of the 15th International Workshop on Semantic Evaluation (SemEval-2021), Aug 2021

Bib HTML

@inproceedings{liu-etal-2021-uiuc,
  title = {{UIUC}{\_}{B}io{NLP} at {S}em{E}val-2021 Task 11: A Cascade of Neural Models for Structuring Scholarly {NLP} Contributions},
  author = {Liu, Haoyang and Sarol, M. Janina and Kilicoglu, Halil},
  booktitle = {Proceedings of the 15th International Workshop on Semantic Evaluation (SemEval-2021)},
  month = aug,
  year = {2021},
  address = {Online},
  publisher = {Association for Computational Linguistics},
  url = {https://aclanthology.org/2021.semeval-1.45},
  doi = {10.18653/v1/2021.semeval-1.45},
  pages = {377--386},
}

Journal Article

Toward assessing clinical trial publications for reporting transparency

Halil Kilicoglu, Graciela Rosemblat, Linh Hoang, Sahil Wadhwa, Zeshan Peng, Mario Malički, Jodi Schneider, and Gerben Riet

Journal of Biomedical Informatics, Apr 2021

Bib HTML

@article{kilicoglu2021toward,
  title = {Toward assessing clinical trial publications for reporting transparency},
  author = {Kilicoglu, Halil and Rosemblat, Graciela and Hoang, Linh and Wadhwa, Sahil and Peng, Zeshan and Mali{\v{c}}ki, Mario and Schneider, Jodi and ter Riet, Gerben},
  journal = {Journal of Biomedical Informatics},
  volume = {116},
  pages = {103717},
  year = {2021},
  month = apr,
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2021.103717},
  url = {https://doi.org/10.1016/j.jbi.2021.103717},
}

Journal Article

Drug repurposing for COVID-19 via knowledge graph completion

Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, and Halil Kilicoglu

Journal of Biomedical Informatics, Mar 2021

Bib HTML

@article{zhang2021drug,
  title = {{Drug repurposing for COVID-19 via knowledge graph completion}},
  author = {Zhang, Rui and Hristovski, Dimitar and Schutte, Dalton and Kastrin, Andrej and Fiszman, Marcelo and Kilicoglu, Halil},
  journal = {Journal of Biomedical Informatics},
  volume = {115},
  pages = {103696},
  year = {2021},
  month = mar,
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2021.103696},
  url = {https://doi.org/10.1016/j.jbi.2021.103696},
}

Journal Article

Attention-gated graph convolutions for extracting drug interaction information from drug labels

Tung Tran, Ramakanth Kavuluru, and Halil Kilicoglu

ACM Transactions on Computing for Healthcare, Jan 2021

Bib HTML

@article{tran2021attention,
  title = {Attention-gated graph convolutions for extracting drug interaction information from drug labels},
  author = {Tran, Tung and Kavuluru, Ramakanth and Kilicoglu, Halil},
  journal = {ACM Transactions on Computing for Healthcare},
  volume = {2},
  number = {2},
  pages = {1--19},
  year = {2021},
  month = jan,
  publisher = {ACM New York, NY, USA},
  doi = {10.1145/3423209},
  url = {https://doi.org/10.1145/3423209},
}

Correspondence

Automated screening of COVID-19 preprints: can we help authors to improve transparency and reproducibility?

Tracey Weissgerber, Nico Riedel, Halil Kilicoglu, Cyril Labbé, Peter Eckmann, Gerben Ter Riet, Jennifer Byrne, Guillaume Cabanac, Amanda Capes-Davis, Bertrand Favier, Shyam Saladi, Peer Grabitz, Alexandra Bannach-Brown, Robert Schulz, Sarah McCann, Rene Bernard, and Anita Bandrowski

Nature Medicine, Jan 2021

Bib HTML

@article{weissgerber2021automated,
  title = {Automated screening of COVID-19 preprints: can we help authors to improve transparency and reproducibility?},
  author = {Weissgerber, Tracey and Riedel, Nico and Kilicoglu, Halil and Labb{\'e}, Cyril and Eckmann, Peter and Ter Riet, Gerben and Byrne, Jennifer and Cabanac, Guillaume and Capes-Davis, Amanda and Favier, Bertrand and Saladi, Shyam and Grabitz, Peer and Bannach-Brown, Alexandra and Schulz, Robert and McCann, Sarah and Bernard, Rene and Bandrowski, Anita},
  journal = {Nature Medicine},
  volume = {27},
  number = {1},
  pages = {6--7},
  year = {2021},
  month = jan,
  publisher = {Nature Publishing Group US New York},
  doi = {10.1038/s41591-020-01203-7},
  url = {https://doi.org/10.1038/s41591-020-01203-7},
}

2020

Journal Article

Broad-coverage biomedical relation extraction with SemRep

Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, and Dongwook Shin

BMC Bioinformatics, May 2020

Bib HTML

@article{kilicoglu2020broad,
  title = {{Broad-coverage biomedical relation extraction with SemRep}},
  author = {Kilicoglu, Halil and Rosemblat, Graciela and Fiszman, Marcelo and Shin, Dongwook},
  journal = {BMC Bioinformatics},
  volume = {21},
  pages = {1--28},
  year = {2020},
  month = may,
  publisher = {Springer},
  doi = {10.1186/s12859-020-3517-7},
  url = {https://doi.org/10.1186/s12859-020-3517-7},
}

2019

Journal Article

Menagerie: A text-mining tool to support animal-human translation in neurodegeneration research

Caroline J Zeiss, Dongwook Shin, Brent Vander Wyk, Amanda P Beck, Natalie Zatz, Charles A Sneiderman, and Halil Kilicoglu

PLoS ONE, Dec 2019

Bib HTML

@article{zeiss2019menagerie,
  title = {{Menagerie: A text-mining tool to support animal-human translation in neurodegeneration research}},
  author = {Zeiss, Caroline J and Shin, Dongwook and Vander Wyk, Brent and Beck, Amanda P and Zatz, Natalie and Sneiderman, Charles A and Kilicoglu, Halil},
  journal = {PLoS ONE},
  volume = {14},
  number = {12},
  pages = {e0226176},
  year = {2019},
  month = dec,
  publisher = {Public Library of Science San Francisco, CA USA},
  doi = {10.1371/journal.pone.0226176},
  url = {https://doi.org/10.1371/journal.pone.0226176},
}

Journal Article

Towards a characterization of apparent contradictions in the biomedical literature using context analysis

Graciela Rosemblat, Marcelo Fiszman, Dongwook Shin, and Halil Kilicoglu

Journal of Biomedical Informatics, Oct 2019

Bib HTML

@article{rosemblat2019towards,
  title = {Towards a characterization of apparent contradictions in the biomedical literature using context analysis},
  author = {Rosemblat, Graciela and Fiszman, Marcelo and Shin, Dongwook and Kilicoglu, Halil},
  journal = {Journal of Biomedical Informatics},
  volume = {98},
  pages = {103275},
  year = {2019},
  month = oct,
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2019.103275},
  url = {https://doi.org/10.1016/j.jbi.2019.103275},
}

Journal Article

Impact of peer review on discussion of study limitations and strength of claims in randomized trial reports: a before and after study

Kerem Keserlioglu, Halil Kilicoglu, and Gerben Ter Riet

Research Integrity and Peer Review, Sep 2019

Bib HTML

@article{keserlioglu2019impact,
  title = {Impact of peer review on discussion of study limitations and strength of claims in randomized trial reports: a before and after study},
  author = {Keserlioglu, Kerem and Kilicoglu, Halil and Ter Riet, Gerben},
  journal = {Research Integrity and Peer Review},
  volume = {4},
  pages = {1--8},
  year = {2019},
  month = sep,
  publisher = {Springer},
  doi = {10.1186/s41073-019-0078-2},
  url = {https://doi.org/10.1186/s41073-019-0078-2},
}

Journal Article

Confirm or refute?: A comparative study on citation sentiment classification in clinical research publications

Halil Kilicoglu, Zeshan Peng, Shabnam Tafreshi, Tung Tran, Graciela Rosemblat, and Jodi Schneider

Journal of Biomedical Informatics, Mar 2019

Bib HTML

@article{kilicoglu2019confirm,
  title = {Confirm or refute?: A comparative study on citation sentiment classification in clinical research publications},
  author = {Kilicoglu, Halil and Peng, Zeshan and Tafreshi, Shabnam and Tran, Tung and Rosemblat, Graciela and Schneider, Jodi},
  journal = {Journal of Biomedical Informatics},
  volume = {91},
  pages = {103123},
  year = {2019},
  month = mar,
  publisher = {Elsevier},
  doi = {10.1016/j.jbi.2019.103123},
  url = {https://doi.org/10.1016/j.jbi.2019.103123},
}

Journal Article

Expanding vocabularies for complementary and alternative medicine therapies

Lou Ann Scarton, Liqin Wang, Halil Kilicoglu, Margaret Jahries, and Guilherme Del Fiol

International Journal of Medical Informatics, Jan 2019

Bib HTML

@article{scarton2019expanding,
  title = {Expanding vocabularies for complementary and alternative medicine therapies},
  author = {Scarton, Lou Ann and Wang, Liqin and Kilicoglu, Halil and Jahries, Margaret and Del Fiol, Guilherme},
  journal = {International Journal of Medical Informatics},
  volume = {121},
  pages = {64--74},
  year = {2019},
  month = jan,
  publisher = {Elsevier},
  doi = {10.1016/j.ijmedinf.2018.11.009},
  url = {https://doi.org/10.1016/j.ijmedinf.2018.11.009},
}

2018

Journal Article

Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing

Thomas C Rindflesch, Catherine L Blake, Michael J Cairelli, Marcelo Fiszman, Caroline J Zeiss, and Halil Kilicoglu

Journal of Biomedical Semantics, Dec 2018

Bib HTML

@article{rindflesch2018investigating,
  title = {Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing},
  author = {Rindflesch, Thomas C and Blake, Catherine L and Cairelli, Michael J and Fiszman, Marcelo and Zeiss, Caroline J and Kilicoglu, Halil},
  journal = {Journal of Biomedical Semantics},
  volume = {9},
  pages = {1--14},
  year = {2018},
  month = dec,
  publisher = {Springer},
  doi = {10.1186/s13326-018-0192-y},
  url = {https://doi.org/10.1186/s13326-018-0192-y},
}

Shared Task Paper

A multi-task learning framework for extracting drugs and their interactions from drug labels

Tung Tran, Ramakanth Kavuluru, and Halil Kilicoglu

In Text Analysis Conference (TAC 2018) Proceedings, Nov 2018

Bib HTML

@inproceedings{tran2018multi,
  title = {A multi-task learning framework for extracting drugs and their interactions from drug labels},
  author = {Tran, Tung and Kavuluru, Ramakanth and Kilicoglu, Halil},
  booktitle = {Text Analysis Conference (TAC 2018) Proceedings},
  year = {2018},
  month = nov,
  address = {Gaithersburg, MD},
  publisher = {NIST},
  url = {https://tac.nist.gov/publications/2018/participant.papers/TAC2018.ttran.proceedings.pdf},
}

Journal Article

Semantic annotation of consumer health questions

Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E Shooshan, Laritza Rodriguez, Kate Masterton, and Dina Demner-Fushman

BMC Bioinformatics, Feb 2018

Bib HTML

@article{kilicoglu2018semantic,
  title = {Semantic annotation of consumer health questions},
  author = {Kilicoglu, Halil and Ben Abacha, Asma and Mrabet, Yassine and Shooshan, Sonya E and Rodriguez, Laritza and Masterton, Kate and Demner-Fushman, Dina},
  journal = {BMC Bioinformatics},
  volume = {19},
  pages = {1--28},
  year = {2018},
  month = feb,
  publisher = {Springer},
  doi = {10.1186/s12859-018-2045-1},
  url = {https://doi.org/10.1186/s12859-018-2045-1},
}