Rezarta Islamaj Dogan

47 papers C 1Misc 3Journal 34Unranked 8

Year	Rank	Type	Title / Venue / Authors
2022	J	`jnl`	Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework. CoRR Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj Dogan, Zhiyong Lu
2022	J	`jnl`	Comprehensive identification of Long Covid articles with human-in-the-loop machine learning. CoRR Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
2022	J	`jnl`	Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. CoRR 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
2021	J	`jnl`	NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition. J. Biomed. Informatics Rezarta Islamaj Dogan, Chih-Hsuan Wei, David Cissel, Nicholas Miliaras, Olga Printseva, Oleg Rodionov, Keiko Sekiya, Janice Ward, Zhiyong Lu
2020	J	`jnl`	Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. CoRR 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
2020	J	`jnl`	TeamTat: a collaborative text annotation tool. CoRR Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu
2020	J	`jnl`	TeamTat: a collaborative text annotation tool. Nucleic Acids Res. Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu
2019	J	`jnl`	Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 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
2019	J	`jnl`	PDC - a probabilistic distributional clustering algorithm: a case study on suicide articles in PubMed. CoRR Rezarta Islamaj Dogan, Lana Yeganova, Won Kim, Natalie Xie, W. John Wilbur
2019	J	`jnl`	PMC text mining subset in BioC: about three million full-text articles and growing. Bioinform. Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu
2019	J	`jnl`	PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database. Database J. Biol. Databases Curation Rezarta Islamaj Dogan, W. John Wilbur, Natalie Xie, Noreen R. Gonzales, Narmada Thanki, Roxanne A. Yamashita, Chanjuan Zheng, Aron Marchler-Bauer, Zhiyong Lu
2018	J	`jnl`	PMC text mining subset in BioC: 2.3 million full text articles and growing. CoRR Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu
2017	—	`conf`	BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald C. Comeau, Zhiyong Lu
2017	J	`jnl`	The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions. Database J. Biol. Databases Curation 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
2016	—	`conf`	BioCconvert: A Conversion Tool Between BioC and PubAnnotation. ICBO/BioCreative Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu
2016	J	`jnl`	BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database J. Biol. Databases Curation 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
2016	J	`jnl`	Crowdsourcing and curation: perspectives from biology and natural language processing. Database J. Biol. Databases Curation Lynette Hirschman, Karën Fort, Stéphanie Boué, Nikos Kyrpides, Rezarta Islamaj Dogan, Kevin Bretonnel Cohen
2016	—	`conf`	PubTermVariants: biomedical term variants and their use for PubMed search. BioNLP@ACL Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Dogan, Wanli Liu, Donald C. Comeau, Zhiyong Lu, W. John Wilbur
2014	J	`jnl`	Author name disambiguation for PubMed. J. Assoc. Inf. Sci. Technol. Wanli Liu, Rezarta Islamaj Dogan, Sun Kim, Donald C. Comeau, Won Kim, Lana Yeganova, Zhiyong Lu, W. John Wilbur
2014	J	`jnl`	BioC implementations in Go, Perl, Python and Ruby. Database J. Biol. Databases Curation Wanli Liu, Rezarta Islamaj Dogan, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W. John Wilbur, Donald C. Comeau
2014	J	`jnl`	BioC interoperability track overview. Database J. Biol. Databases Curation 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
2014	J	`jnl`	Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora. Database J. Biol. Databases Curation Rezarta Islamaj Dogan, Donald C. Comeau, Lana Yeganova, W. John Wilbur
2014	J	`jnl`	NCBI disease corpus: A resource for disease name recognition and concept normalization. J. Biomed. Informatics Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu
2014	J	`jnl`	Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus. Database J. Biol. Databases Curation Donald C. Comeau, Haibin Liu, Rezarta Islamaj Dogan, W. John Wilbur
2013	Misc	`conf`	BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. AMIA Donald C. Comeau, Rezarta Islamaj Dogan, W. John Wilbur
2013	J	`jnl`	BioC: a minimalist approach to interoperability for biomedical text processing. Database J. Biol. Databases Curation 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
2013	—	`conf`	BioNLP Shared Task 2013: Supporting Resources. BioNLP@ACL (Shared Task) Pontus Stenetorp, Wiktoria Golik, Thierry Hamon, Donald C. Comeau, Rezarta Islamaj Dogan, Haibin Liu, W. John Wilbur
2013	Misc	`conf`	DNorm: A New Method and Online Tool for Disease Name Normalization. AMIA Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu
2013	J	`jnl`	DNorm: disease name normalization with pairwise learning to rank. Bioinform. Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu
2013	Misc	`conf`	NCBI Disease Corpus: A Valuable Resource for Disease Name Recognition and Normalization. AMIA Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu
2013	J	`jnl`	Reports on the 2012 AAAI Fall Symposium Series. AI Mag. 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
2012	J	`jnl`	An Evolutionary Algorithm Approach for Feature Generation from Sequence Data and Its Application to DNA Splice Site Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. Uday Kamath, Jack Compton, Rezarta Islamaj Dogan, Kenneth A. De Jong, Amarda Shehu
2012	—	`conf`	An Inference Method for Disease Name Normalization. AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text Rezarta Islamaj Dogan, Zhiyong Lu
2012	—	`conf`	An improved corpus of disease mentions in PubMed citations. BioNLP@HLT-NAACL Rezarta Islamaj Dogan, Zhiyong Lu
2012	J	`jnl`	Topics in machine learning for biomedical literature analysis and text retrieval. J. Biomed. Semant. Rezarta Islamaj Dogan, Lana Yeganova
2011	J	`jnl`	A context-blocks model for identifying clinical relationships in patient records. BMC Bioinform. Rezarta Islamaj Dogan, Aurélie Névéol, Zhiyong Lu
2011	J	`jnl`	Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction. J. Biomed. Informatics Aurélie Névéol, Rezarta Islamaj Dogan, Zhiyong Lu
2011	J	`jnl`	Topics in machine learning for biomedical literature analysis and text retrieval. BMC Bioinform. Rezarta Islamaj Dogan, Lana Yeganova
2010	C	`conf`	A Textual Representation Scheme for Identifying Clinical Relationships in Patient Records. ICMLA Rezarta Islamaj Dogan, Aurélie Névéol, Zhiyong Lu
2010	J	`jnl`	Click-words: learning to predict document keywords from a user perspective. Bioinform. Rezarta Islamaj Dogan, Zhiyong Lu
2010	J	`jnl`	Extracting Rx information from clinical narrative. J. Am. Medical Informatics Assoc. 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
2009	J	`jnl`	Understanding PubMed Database J. Biol. Databases Curation Rezarta Islamaj Dogan, G. Craig Murray, Aurélie Névéol, Zhiyong Lu
2007	—	`conf`	Characterizing RNA Secondary-Structure Features and Their Effects on Splice-Site Prediction. ICDM Workshops Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur
2007	—	`—`	Feature Generation and Analysis Applied to sequence Classification for splice-Site Prediction. Rezarta Islamaj Dogan
2007	J	`jnl`	Features generated for computational splice-site prediction correspond to functional elements. BMC Bioinform. Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount
2007	J	`jnl`	SplicePort - An interactive splice-site analysis tool. Nucleic Acids Res. Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount
2006	—	`conf`	A Feature Generation Algorithm for Sequences with Application to Splice-Site Prediction. PKDD Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur