
Rezarta Islamaj Dogan
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2020 – today
- 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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