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2020 – today
- 2023
[j39]Qingyu Chen
, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu:
LitCovid in 2022: an information resource for the COVID-19 literature. Nucleic Acids Res. 51(D1): 1512-1518 (2023)- [i13]Li Fang, Qingyu Chen, Chih-Hsuan Wei, Zhiyong Lu, Kai Wang:
Bioformer: an efficient transformer language model for biomedical text mining. CoRR abs/2302.01588 (2023) - [i12]Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu:
BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasets. CoRR abs/2306.11189 (2023) - 2022
- [j38]Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu:
BioRED: a rich biomedical relation extraction dataset. Briefings Bioinform. 23(5) (2022) - [j37]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) - [j36]Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Zhiyong Lu:
A sequence labeling framework for extracting drug-protein relations from biomedical literature. Database J. Biol. Databases Curation 2022(2022) (2022) - [j35]Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu:
tmVar 3.0: an improved variant concept recognition and normalization tool. Bioinform. 38(18): 4449-4451 (2022) - [c14]Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu:
BioRED: A Comprehensive Biomedical Relation Extraction Dataset. AMIA 2022 - [c13]Shankai Yan, Ling Luo, Li Fang, Daniel Veltri, Andrew J. Oler, Rajarshi Ghosh, Chih-Hsuan Wei, Morgan Similuk, Kai Wang, Zhiyong Lu:
PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles. AMIA 2022 - [i11]Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu:
tmVar 3.0: an improved variant concept recognition and normalization tool. CoRR abs/2204.03637 (2022) - [i10]Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu:
BioRED: A Comprehensive Biomedical Relation Extraction Dataset. CoRR abs/2204.04263 (2022) - [i9]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) - [i8]Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu:
LitCovid in 2022: an information resource for the COVID-19 literature. CoRR abs/2209.13428 (2022) - [i7]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu:
AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning. CoRR abs/2211.16944 (2022) - 2021
- [j34]Kyubum Lee, Chih-Hsuan Wei, Zhiyong Lu:
Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature. Briefings Bioinform. 22(3) (2021) - [j33]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) - 2020
- [j32]Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu:
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PLoS Comput. Biol. 16(4) (2020) - [i6]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) - [i5]Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu:
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP). CoRR abs/2010.16413 (2020) - [i4]Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy NguyenXuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi:
BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research 9: 136 (2020)
2010 – 2019
- 2019
- [j31]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) - [j30]Yi-Yu Hsu, Mindy Clyne, Chih-Hsuan Wei, Muin J. Khoury, Zhiyong Lu:
Using deep learning to identify translational research in genomic medicine beyond bench to bedside. Database J. Biol. Databases Curation 2019: baz010 (2019) - [j29]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) - [j28]Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu:
PubTator central: automated concept annotation for biomedical full text articles. Nucleic Acids Res. 47(Webserver-Issue): W587-W593 (2019) - [c12]Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu:
Biomedical Mention Disambiguation using a Deep Learning Approach. BCB 2019: 307-313 - [c11]Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu:
A Text-Mining System for Concept Annotation in Biomedical Full Text Articles. BCB 2019: 540 - [i3]Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu:
Biomedical Mention Disambiguation using a Deep Learning Approach. CoRR abs/1909.10416 (2019) - [i2]Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu:
BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale. CoRR abs/1912.10846 (2019) - 2018
- [j27]Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu:
Assisting document triage for human kinome curation via machine learning. Database J. Biol. Databases Curation 2018: bay091 (2018) - [j26]Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch:
Overview of the BioCreative VI text-mining services for Kinome Curation Track. Database J. Biol. Databases Curation 2018: bay104 (2018) - [j25]Chih-Hsuan Wei, Lon Phan, Juliana Feltz, Rama Maiti, Tim Hefferon, Zhiyong Lu:
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine. Bioinform. 34(1): 80-87 (2018) - [j24]Dongseop Kwon, Sun Kim, Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
ezTag: tagging biomedical concepts via interactive learning. Nucleic Acids Res. 46(Webserver-Issue): W523-W529 (2018) - [j23]Alexis Allot, Yifan Peng, Chih-Hsuan Wei, Kyubum Lee, Lon Phan, Zhiyong Lu:
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC. Nucleic Acids Res. 46(Webserver-Issue): W530-W536 (2018) - [j22]Kyubum Lee, Maria Livia Famiglietti, Aoife McMahon, Chih-Hsuan Wei, Jacqueline A. L. MacArthur, Sylvain Poux, Lionel Breuza, Alan Bridge, Fiona Cunningham, Ioannis Xenarios, Zhiyong Lu:
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. PLoS Comput. Biol. 14(8) (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
- [j21]Sylvain Poux, Cecilia N. Arighi, Michele Magrane, Alex Bateman, Chih-Hsuan Wei, Zhiyong Lu, Emmanuel Boutet, Hema Bye-A-Jee, Maria Livia Famiglietti, Bernd Roechert, The UniProt Consortium:
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. Bioinform. 33(21): 3454-3460 (2017) - [c10]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
- [j20]Robert Leaman, Chih-Hsuan Wei, Cherry Zou, Zhiyong Lu:
Mining chemical patents with an ensemble of open systems. Database J. Biol. Databases Curation 2016 (2016) - [j19]Jiao Li, Yueping Sun, Robin J. Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Thomas C. Wiegers, Zhiyong Lu:
BioCreative V CDR task corpus: a resource for chemical disease relation extraction. Database J. Biol. Databases Curation 2016 (2016) - [j18]Chih-Hsuan Wei, Yifan Peng, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Jiao Li, Thomas C. Wiegers, Zhiyong Lu:
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. Database J. Biol. Databases Curation 2016 (2016) - [j17]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
Beyond accuracy: creating interoperable and scalable text-mining web services. Bioinform. 32(12): 1907-1910 (2016) - [j16]Yifan Peng, Chih-Hsuan Wei, Zhiyong Lu:
Improving chemical disease relation extraction with rich features and weakly labeled data. J. Cheminformatics 8(1): 53:1-53:12 (2016) - [c9]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 - [c8]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
Large-scale Semantic Indexing with Biomedical Ontologies. ICBO/BioCreative 2016 - 2015
- [j15]Robert Leaman, Chih-Hsuan Wei, Zhiyong Lu:
tmChem: a high performance approach for chemical named entity recognition and normalization. J. Cheminformatics 7(S-1): S3 (2015) - [j14]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedical Text. IEEE J. Biomed. Health Informatics 19(4): 1385-1391 (2015) - 2014
- [j13]Kimberly Van Auken, Mary L. Schaeffer, Peter McQuilton, Stanley J. F. Laulederkind, Donghui Li, Shur-Jen Wang, G. Thomas Hayman, Susan Tweedie, Cecilia N. Arighi, James Done, Hans-Michael Müller, Paul W. Sternberg, Yuqing Mao, Chih-Hsuan Wei, Zhiyong Lu:
BC4GO: a full-text corpus for the BioCreative IV GO task. Database J. Biol. Databases Curation 2014 (2014) - [j12]John D. Burger, Emily Doughty, Ritu Khare, Chih-Hsuan Wei, Rajashree Mishra, John S. Aberdeen, David Tresner-Kirsch, Ben Wellner, Maricel G. Kann, Zhiyong Lu, Lynette Hirschman:
Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing. Database J. Biol. Databases Curation 2014 (2014) - [j11]Ritu Khare, Chih-Hsuan Wei, Yuqing Mao, Robert Leaman, Zhiyong Lu:
tmBioC: improving interoperability of text-mining tools with BioC. Database J. Biol. Databases Curation 2014 (2014) - [j10]Jui-Chen Hsiao, Chih-Hsuan Wei, Hung-Yu Kao:
Gene Name Disambiguation UsingMulti-Scope Species Detection. IEEE ACM Trans. Comput. Biol. Bioinform. 11(1): 55-62 (2014) - [c7]Ritu Khare, Chih-Hsuan Wei, Zhiyong Lu:
Automatic Extraction of Drug Indications from FDA Drug Labels. AMIA 2014 - [c6]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
SimConcept: a hybrid approach for simplifying composite named entities in biomedicine. BCB 2014: 138-146 - [c5]Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu:
Text mining tools for assisting literature curation. BCB 2014: 590-591 - [c4]Yuqing Mao, Chih-Hsuan Wei, Zhiyong Lu:
NCBI at the 2014 BioASQ Challenge Task: Large-scale Biomedical Semantic Indexing and Question Answering. CLEF (Working Notes) 2014: 1319-1327 - 2013
- [j9]Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert J. Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila M. Dahdul, Paula M. Mabee, Donghui Li, Bethany R. Harris, Marc Gillespie, Silvia Jimenez, Phoebe M. Roberts, Lisa Matthews, Kevin G. Becker, Harold J. Drabkin, Susan M. Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa A. Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Müller, Hong Cui, James P. Balhoff, Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy H. Wu:
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database J. Biol. Databases Curation 2013 (2013) - [j8]Chih-Hsuan Wei, Bethany R. Harris, Hung-Yu Kao, Zhiyong Lu:
tmVar: a text mining approach for extracting sequence variants in biomedical literature. Bioinform. 29(11): 1433-1439 (2013) - [j7]Chih-Hsuan Wei, Hung-Yu Kao:
Unsupervised corpus distillation for represented indicator measurement on focus species detection. Int. J. Data Min. Bioinform. 8(4): 413-426 (2013) - [j6]Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu:
PubTator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res. 41(Webserver-Issue): 518-522 (2013) - [c3]Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu:
DNorm: A New Method and Online Tool for Disease Name Normalization. AMIA 2013 - 2012
- [j5]Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, W. John Wilbur:
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information. Database J. Biol. Databases Curation 2012 (2012) - [j4]Chih-Hsuan Wei, Bethany R. Harris, Donghui Li, Tanya Z. Berardini, Eva Huala, Hung-Yu Kao, Zhiyong Lu:
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database J. Biol. Databases Curation 2012 (2012) - 2011
- [j3]Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illés Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sérgio Matos, David Campos, Karin Verspoor, Kevin M. Livingston, W. John Wilbur:
The gene normalization task in BioCreative III. BMC Bioinform. 12(S-8): S2 (2011) - [j2]Chih-Hsuan Wei, Hung-Yu Kao:
Cross-species gene normalization by species inference. BMC Bioinform. 12(S-8): S5 (2011) - 2010
- [j1]Koun-Tem Sun, Chih-Hsuan Wei, Yi-Yu Hsu, Wen-Chun Liu, Ting-Tsung Chang:
On Deriving an Equation of the Mutation Rate of the Hepatitis B Virus. J. Convergence Inf. Technol. 5(5): 131-137 (2010) - [c2]Chih-Hsuan Wei, Hung-Yu Kao:
Represented indicator measurement and corpus distillation on focus species detection. BIBM 2010: 657-662
2000 – 2009
- 2009
- [c1]Chih-Hsuan Wei, I-Chin Huang, Yi-Yu Hsu, Hung-Yu Kao:
Normalizing Biomedical Name Entities by Similarity-Based Inference Network and De-ambiguity Mining. BIBE 2009: 461-466
Coauthor Index
[j39] [i13] [i12] [j38] [j37] [j36] [j35] [c14] [c13] [i11] [i10] [i9] [i8] [i7] [j34] [j33] [j32] [i6] [i5] [j31] [j30] [j29] [j28] [c12] [c11] [i3] [i2] [j27] [j26] [j25] [j24] [j23] [j22] [i1] [j21] [c10] [j20] [j19] [j18] [j17] [j16] [c9] [c8] [j15] [j14] [j13] [j12] [j11] [c7] [c6] [c5] [c4] [j9] [j8] [j6] [c3] [j5] [j4] [j3]
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