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2020 – today
- 2024
[j35]Rezarta Islamaj
, Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Tiago Melo Almeida, Richard A. A. Jonker, Sofia I R. Conceição, Diana F. Sousa, Cong-Phuoc Phan, Jung-Hsien Chiang, Jiru Li, Dinghao Pan, Wilailack Meesawad, Richard Tzong-Han Tsai, M. Janina Sarol, Gibong Hong, Airat Valiev, Elena Tutubalina, Shao-Man Lee, Yi-Yu Hsu, Mingjie Li, Karin Verspoor, Zhiyong Lu:
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII. Database J. Biol. Databases Curation 2024 (2024)- [j34]Rezarta Islamaj, Chih-Hsuan Wei, Po-Ting Lai, Ling Luo, Cathleen Coss, Preeti Gokal Kochar, Nicholas Miliaras, Oleg Rodionov, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Zhiyong Lu:
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop. Database J. Biol. Databases Curation 2024 (2024) - 2023
- [j33]Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed Alliheedi, João Rafael Almeida, Rui Antunes, Robert Bevan, Yung-Chun Chang, Arslan Erdengasileng, Matthew Hodgskiss, Ryuki Ida, Hyunjae Kim, Keqiao Li, Robert E. Mercer, Lukrécia Mertová, Ghadeer Mobasher, Hoo-Chang Shin, Mujeen Sung, Tomoki Tsujimura, Wen-Chao Yeh, Zhiyong Lu:
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII. Database J. Biol. Databases Curation 2023 (2023) - [j32]Chih-Hsuan Wei, Ling Luo, Rezarta Islamaj, Po-Ting Lai, Zhiyong Lu:
GNorm2: an improved gene name recognition and normalization system. Bioinform. 39(10) (2023) - [j31]Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu:
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning. Patterns 4(1): 100659 (2023) - [i8]Shubo Tian, Qiao Jin, Lana Yeganova, Po-Ting Lai, Qingqing Zhu, Xiuying Chen, Yifan Yang, Qingyu Chen, Won Kim, Donald C. Comeau, Rezarta Islamaj, Aadit Kapoor, Xin Gao, Zhiyong Lu:
Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health. CoRR abs/2306.10070 (2023) - 2022
- [j30]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu:
Assigning species information to corresponding genes by a sequence labeling framework. Database J. Biol. Databases Curation 2022(2022) (2022) - [j29]Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Wang Kai, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Saipradeep Vg, Zhiyong Lu:
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. Database J. Biol. Databases Curation 2022(2022) (2022) - [j28]Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Joseph Denicola, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Nicholas Miliaras, Zoe Punske, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Susan Schmidt, Zhiyong Lu:
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles. Database J. Biol. Databases Curation 2022(2022) (2022) - [i7]Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj Dogan, Jingcheng Du, Li Fang, Wang Kai, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Zhiyong Lu:
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. CoRR abs/2204.09781 (2022) - [i6]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj Dogan, Zhiyong Lu:
Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework. CoRR abs/2205.03853 (2022) - [i5]Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu:
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning. CoRR abs/2209.08124 (2022) - 2021
- [j27]Rezarta Islamaj Dogan, Chih-Hsuan Wei, David Cissel, Nicholas Miliaras, Olga Printseva, Oleg Rodionov, Keiko Sekiya, Janice Ward, Zhiyong Lu:
NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition. J. Biomed. Informatics 118: 103779 (2021) - [c14]Rezarta Islamaj, Dongseop Kwon, Sun Kim, Zhiyong Lu:
TeamTat: A Collaborative Text Annotation Tool for Creating Gold-Standard Corpora. AMIA 2021 - [c13]Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Dorothy Trinh, Deborah Whitman, Keiko Sekiya, Zhiyong Lu:
NLM-Chem, a Gold-Standard Corpus for Chemical Entity Recognition in PubMed Full Text Literature. AMIA 2021 - 2020
- [j26]Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu:
TeamTat: a collaborative text annotation tool. Nucleic Acids Res. 48(Webserver-Issue): W5-W11 (2020) - [i4]Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu:
TeamTat: a collaborative text annotation tool. CoRR abs/2004.11894 (2020) - [i3]Lana Yeganova, Rezarta Islamaj Dogan, Qingyu Chen, Robert Leaman, Alexis Allot, Chih-Hsuan Wei, Donald C. Comeau, Won Kim, Yifan Peng, W. John Wilbur, Zhiyong Lu:
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. CoRR abs/2008.03397 (2020)
2010 – 2019
- 2019
- [j25]Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu:
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 2019: bay147 (2019) - [j24]Rezarta Islamaj Dogan, W. John Wilbur, Natalie Xie, Noreen R. Gonzales, Narmada Thanki, Roxanne A. Yamashita, Chanjuan Zheng, Aron Marchler-Bauer, Zhiyong Lu:
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database. Database J. Biol. Databases Curation 2019: baz064 (2019) - [j23]Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu:
PMC text mining subset in BioC: about three million full-text articles and growing. Bioinform. 35(18): 3533-3535 (2019) - [i2]Rezarta Islamaj Dogan, Lana Yeganova, Won Kim, Natalie Xie, W. John Wilbur:
PDC - a probabilistic distributional clustering algorithm: a case study on suicide articles in PubMed. CoRR abs/1912.02077 (2019) - 2018
- [i1]Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu:
PMC text mining subset in BioC: 2.3 million full text articles and growing. CoRR abs/1804.05957 (2018) - 2017
- [j22]Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer M. Rust, W. John Wilbur, Donald C. Comeau, Kara Dolinski, Mike Tyers:
The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions. Database J. Biol. Databases Curation 2017: baw147 (2017) - [c12]Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald C. Comeau, Zhiyong Lu:
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP 2017: 171-175 - 2016
- [j21]Lynette Hirschman, Karën Fort, Stéphanie Boué, Nikos Kyrpides, Rezarta Islamaj Dogan, Kevin Bretonnel Cohen:
Crowdsourcing and curation: perspectives from biology and natural language processing. Database J. Biol. Databases Curation 2016 (2016) - [j20]Sun Kim, Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer M. Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia N. Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydin, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur, Donald C. Comeau:
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database J. Biol. Databases Curation 2016 (2016) - [c11]Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Dogan, Wanli Liu, Donald C. Comeau, Zhiyong Lu, W. John Wilbur:
PubTermVariants: biomedical term variants and their use for PubMed search. BioNLP@ACL 2016: 141-145 - [c10]Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu:
BioCconvert: A Conversion Tool Between BioC and PubAnnotation. ICBO/BioCreative 2016 - 2014
- [j19]Donald C. Comeau, Riza Theresa Batista-Navarro, Hong-Jie Dai, Rezarta Islamaj Dogan, Antonio Jimeno-Yepes, Ritu Khare, Zhiyong Lu, Hernani Marques, Carolyn J. Mattingly, Mariana L. Neves, Yifan Peng, Rafal Rak, Fabio Rinaldi, Richard Tzong-Han Tsai, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur:
BioC interoperability track overview. Database J. Biol. Databases Curation 2014 (2014) - [j18]Donald C. Comeau, Haibin Liu, Rezarta Islamaj Dogan, W. John Wilbur:
Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus. Database J. Biol. Databases Curation 2014 (2014) - [j17]Rezarta Islamaj Dogan, Donald C. Comeau, Lana Yeganova, W. John Wilbur:
Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora. Database J. Biol. Databases Curation 2014 (2014) - [j16]Wanli Liu, Rezarta Islamaj Dogan, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W. John Wilbur, Donald C. Comeau:
BioC implementations in Go, Perl, Python and Ruby. Database J. Biol. Databases Curation 2014 (2014) - [j15]Wanli Liu, Rezarta Islamaj Dogan, Sun Kim, Donald C. Comeau, Won Kim, Lana Yeganova, Zhiyong Lu, W. John Wilbur:
Author name disambiguation for PubMed. J. Assoc. Inf. Sci. Technol. 65(4): 765-781 (2014) - [j14]Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu:
NCBI disease corpus: A resource for disease name recognition and concept normalization. J. Biomed. Informatics 47: 1-10 (2014) - 2013
- [j13]Rezarta Islamaj Dogan, Yolanda Gil, Haym Hirsh, Narayanan Chatapuram Krishnan, Michael Lewis, Çetin Meriçli, Parisa Rashidi, Victor Raskin, Samarth Swarup, Wei Sun, Julia M. Taylor, Lana Yeganova:
Reports on the 2012 AAAI Fall Symposium Series. AI Mag. 34(1): 93-100 (2013) - [j12]Donald C. Comeau, Rezarta Islamaj Dogan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur:
BioC: a minimalist approach to interoperability for biomedical text processing. Database J. Biol. Databases Curation 2013 (2013) - [j11]Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu:
DNorm: disease name normalization with pairwise learning to rank. Bioinform. 29(22): 2909-2917 (2013) - [c9]Donald C. Comeau, Rezarta Islamaj Dogan, W. John Wilbur:
BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. AMIA 2013 - [c8]Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu:
NCBI Disease Corpus: A Valuable Resource for Disease Name Recognition and Normalization. AMIA 2013 - [c7]Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu:
DNorm: A New Method and Online Tool for Disease Name Normalization. AMIA 2013 - [c6]Pontus Stenetorp, Wiktoria Golik, Thierry Hamon, Donald C. Comeau, Rezarta Islamaj Dogan, Haibin Liu, W. John Wilbur:
BioNLP Shared Task 2013: Supporting Resources. BioNLP@ACL (Shared Task) 2013: 99-103 - 2012
- [j10]Rezarta Islamaj Dogan, Lana Yeganova:
Topics in machine learning for biomedical literature analysis and text retrieval. J. Biomed. Semant. 3(S-3): S1 (2012) - [j9]Uday Kamath, Jack Compton, Rezarta Islamaj Dogan, Kenneth A. De Jong, Amarda Shehu:
An Evolutionary Algorithm Approach for Feature Generation from Sequence Data and Its Application to DNA Splice Site Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1387-1398 (2012) - [c5]Rezarta Islamaj Dogan, Zhiyong Lu:
An Inference Method for Disease Name Normalization. AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text 2012 - [c4]Rezarta Islamaj Dogan, Zhiyong Lu:
An improved corpus of disease mentions in PubMed citations. BioNLP@HLT-NAACL 2012: 91-99 - 2011
- [j8]Rezarta Islamaj Dogan, Lana Yeganova:
Topics in machine learning for biomedical literature analysis and text retrieval. BMC Bioinform. 12(S-3): I1 (2011) - [j7]Rezarta Islamaj Dogan, Aurélie Névéol, Zhiyong Lu:
A context-blocks model for identifying clinical relationships in patient records. BMC Bioinform. 12(S-3): S3 (2011) - [j6]Aurélie Névéol, Rezarta Islamaj Dogan, Zhiyong Lu:
Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction. J. Biomed. Informatics 44(2): 310-318 (2011) - 2010
- [j5]Rezarta Islamaj Dogan, Zhiyong Lu:
Click-words: learning to predict document keywords from a user perspective. Bioinform. 26(21): 2767-2775 (2010) - [j4]James G. Mork, Olivier Bodenreider, Dina Demner-Fushman, Rezarta Islamaj Dogan, François-Michel Lang, Zhiyong Lu, Aurélie Névéol, Lee B. Peters, Sonya E. Shooshan, Alan R. Aronson:
Extracting Rx information from clinical narrative. J. Am. Medical Informatics Assoc. 17(5): 536-539 (2010) - [c3]Rezarta Islamaj Dogan, Aurélie Névéol, Zhiyong Lu:
A Textual Representation Scheme for Identifying Clinical Relationships in Patient Records. ICMLA 2010: 995-998
2000 – 2009
- 2009
- [j3]Rezarta Islamaj Dogan, G. Craig Murray, Aurélie Névéol, Zhiyong Lu:
Understanding PubMed® user search behavior through log analysis. Database J. Biol. Databases Curation 2009 (2009) - 2007
- [b1]Rezarta Islamaj Dogan:
Feature Generation and Analysis Applied to sequence Classification for splice-Site Prediction. University of Maryland, College Park, MD, USA, 2007 - [j2]Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount:
Features generated for computational splice-site prediction correspond to functional elements. BMC Bioinform. 8 (2007) - [j1]Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount:
SplicePort - An interactive splice-site analysis tool. Nucleic Acids Res. 35(Web-Server-Issue): 285-291 (2007) - [c2]Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur:
Characterizing RNA Secondary-Structure Features and Their Effects on Splice-Site Prediction. ICDM Workshops 2007: 89-94 - 2006
- [c1]Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur:
A Feature Generation Algorithm for Sequences with Application to Splice-Site Prediction. PKDD 2006: 553-560
Coauthor Index
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last updated on 2024-10-30 21:32 CET by the dblp team
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