Publications

Comeau DC, Doğan RIslamaj, Ciccarese P, Cohen KBretonnel, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M et al..  2013.  BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013:bat064.

Comeau DC, Doğan RIslamaj, Ciccarese P, Cohen KBretonnel, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M et al..  2013.  BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013:bat064.

Comeau DC, Doğan RIslamaj, Ciccarese P, Cohen KBretonnel, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M et al..  2013.  BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013:bat064.

Comeau DC, Batista-Navarro RTheresa, Dai H-J, Doğan RIslamaj, Yepes AJimeno, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M et al..  2014.  BioC interoperability track overview. Database (Oxford). 2014

Kim S, Doğan RIslamaj, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S et al..  2016.  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016

Kim S, Doğan RIslamaj, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S et al..  2016.  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016

Kim S, Doğan RIslamaj, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S et al..  2016.  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016

Kim S, Doğan RIslamaj, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S et al..  2016.  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016

Kim S, Doğan RIslamaj, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S et al..  2016.  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016

Kim S, Doğan RIslamaj, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S et al..  2016.  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016

Kim S, Doğan RIslamaj, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S et al..  2016.  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016

Kim S, Doğan RIslamaj, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S et al..  2016.  BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016

Doğan RIslamaj, Chatr-aryamontri A, Kim S, Wei C-H, Peng Y, Comeau D, Lu Z.  2017.  BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP 2017. :171–175.

Doğan RIslamaj, Chatr-aryamontri A, Kim S, Wei C-H, Peng Y, Comeau D, Lu Z.  2017.  BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP 2017. :171–175.

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM et al..  2018.  Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 15(141)

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM et al..  2018.  Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 15(141)

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM et al..  2018.  Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 15(141)

Chen Q, Peng Y, Lu Z.  2019.  BioSentVec: creating sentence embeddings for biomedical texts. IEEE International Conference on Healthcare Informatics (ICHI).

Du J, Chen Q, Peng Y, Xiang Y, Tao C, Lu Z.  2019.  ML-Net: multi-label classification of biomedical texts with deep neural networks. J Am Med Inform Assoc. 26(11):1279-1285.

Chen Q, Peng Y, Keenan T, Dharssi S, N EAgro, Wong WT, Chew EY, Lu Z.  2019.  A multi-task deep learning model for the classification of Age-related Macular Degeneration. AMIA Jt Summits Transl Sci Proc. 2019:505-514.

Chen Q, Peng Y, Keenan T, Dharssi S, N EAgro, Wong WT, Chew EY, Lu Z.  2019.  A multi-task deep learning model for the classification of Age-related Macular Degeneration. AMIA Jt Summits Transl Sci Proc. 2019:505-514.

Peng Y, Lee S, Elton DC, Shen T, Tang Y-xing, Chen Q, Wang S, Zhu Y, Summers R, Lu Z.  2020.  Automatic recognition of abdominal lymph nodes from clinical text. Proceedings of the 3rd Clinical Natural Language Processing Workshop.

Keenan TDL, Chen Q, Peng Y, Domalpally A, Agrón E, Hwang CK, Thavikulwat ATherese, Lee DHana, Li D, Wong WT et al..  2020.  Deep learning automated detection of reticular pseudodrusen from fundus autofluorescence images and color fundus photographs in the Age-Related Eye Disease Study 2 (AREDS2) . Investigative Ophthalmology & Visual Science. 61:1644.

Keenan TDL, Chen Q, Peng Y, Domalpally A, Agrón E, Hwang CK, Thavikulwat ATherese, Lee DHana, Li D, Wong WT et al..  2020.  Deep learning automated detection of reticular pseudodrusen from fundus autofluorescence images and color fundus photographs in the Age-Related Eye Disease Study 2 (AREDS2) . Investigative Ophthalmology & Visual Science. 61:1644.

Keenan TDL, Chen Q, Peng Y, Domalpally A, Agrón E, Hwang CK, Thavikulwat AT, Lee DH, Li D, Wong WT et al..  2020.  Deep Learning Automated Detection of Reticular Pseudodrusen from Fundus Autofluorescence Images or Color Fundus Photographs in AREDS2. Ophthalmology.