Rezarta Islamaj Dogan

ORCID

Publication Activity (10 Years)

Years Active: 2006-2022
Publications (10 Years): 18

Top Venues

Database J. Biol. Databases Curation

CoRR

AMIA

Bioinform.

University of Maryland, College Park, MD, USA (PHD)

Education History

University of Maryland, College Park, MD, USA

PHD

Publications

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 (2022)
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 (2022)
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 (2022)
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 (2021)
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 (2020)
Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu
TeamTat: a collaborative text annotation tool. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu
TeamTat: a collaborative text annotation tool. CoRR (2020)
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 (2019)
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 (2019)
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) (2019)
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 (2019)
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 (2018)
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 (2017)
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)
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)
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)
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)
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)
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)
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)
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)
Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu
NCBI disease corpus: A resource for disease name recognition and concept normalization. J. Biomed. Informatics 47 (2014)
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) (2014)
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)
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)
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)
Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu
NCBI Disease Corpus: A Valuable Resource for Disease Name Recognition and Normalization. AMIA (2013)
Donald C. Comeau, Rezarta Islamaj Dogan, W. John Wilbur
BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. AMIA (2013)
Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu
DNorm: A New Method and Online Tool for Disease Name Normalization. AMIA (2013)
Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu
DNorm: disease name normalization with pairwise learning to rank. Bioinform. 29 (22) (2013)
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) (2013)
Rezarta Islamaj Dogan, Lana Yeganova
Topics in machine learning for biomedical literature analysis and text retrieval. J. Biomed. Semant. 3 (S-3) (2012)
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) (2012)
Rezarta Islamaj Dogan, Zhiyong Lu
An Inference Method for Disease Name Normalization. AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text (2012)
Rezarta Islamaj Dogan, Zhiyong Lu
An improved corpus of disease mentions in PubMed citations. BioNLP@HLT-NAACL (2012)
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) (2011)
Rezarta Islamaj Dogan, Lana Yeganova
Topics in machine learning for biomedical literature analysis and text retrieval. BMC Bioinform. 12 (S-3) (2011)
Rezarta Islamaj Dogan, Aurélie Névéol, Zhiyong Lu
A context-blocks model for identifying clinical relationships in patient records. BMC Bioinform. 12 (S-3) (2011)
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) (2010)
Rezarta Islamaj Dogan, Aurélie Névéol, Zhiyong Lu
A Textual Representation Scheme for Identifying Clinical Relationships in Patient Records. ICMLA (2010)
Rezarta Islamaj Dogan, Zhiyong Lu
Click-words: learning to predict document keywords from a user perspective. Bioinform. 26 (21) (2010)
Rezarta Islamaj Dogan, G. Craig Murray, Aurélie Névéol, Zhiyong Lu
user search behavior through log analysis. Database J. Biol. Databases Curation 2009 (2009)
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) (2007)
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)
Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur
Characterizing RNA Secondary-Structure Features and Their Effects on Splice-Site Prediction. ICDM Workshops (2007)
Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur
A Feature Generation Algorithm for Sequences with Application to Splice-Site Prediction. PKDD (2006)

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Publication Activity (10 Years)

Top Topics

Top Venues

Rezarta Islamaj Dogan