Computational biology and bioinformatics  
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Peer Reviewed Publications

My Google Scholar Page

2022

  • Weissenbacher, Davy, ..., Qing Han, Jinfeng Zhang, ... Automatic Extraction of Medication Mentions from Tweets - Overview of the BioCreative VII Shared Task 3 Competition Database, accepted, 2022.
  • Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Kai Wang, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak, 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, Saipradeep VG, Zhiyong Lu.
    Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. Database, accepted, 2022.
  • Chenran Wang, Yang Chen, Yuan Zhang, Keqiao Li, Menghan Lin, Feng Pan, Wei Wu, Jinfeng Zhang. A Reinforcement Learning Approach for Protein-Ligand Binding Pose Prediction. BMC Bioinformatics, In press, 2022.
  • Arslan Erdengasileng, Qing Han, Tingting Zhao, Shubo Tian, Xin Sui, Keqiao Li, Wanjing Wang, Jian Wang, Ting Hu, Feng Pan, Yuan Zhang, Jinfeng Zhang. Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification. Database, Volume 2022, 2022, baac066, https://doi.org/10.1093/database/baac066

2021

  • Xin Sui, Wanjing Wang, Jinfeng Zhang. Text Mining Drug-Protein Interactions using an Ensemble of BERT, Sentence BERT and T5 models. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 54, 2021.
  • Arslan Erdengasileng, Keqiao Li, Qing Han, Shubo Tian, Jian Wang, Ting Hu, Jinfeng Zhang. A BERT-Based Hybrid System for Chemical Identification and Indexing in Full-Text Articles. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 130, 2021.
  • Qing Han, Shubo Tian, Jinfeng Zhang. A PubMedBERT-based Classfier with Data Augmentation Strategy for Detecting Medication Mentions in Tweets. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 198, 2021.
  • Meng-Han Chung, Jun Zhou, Xiaodong Pang, Yuchuan Tao, Jinfeng Zhang. BioKDE: a Deep Learning Powered Search Engine and Biomedical Knowledge Discovery Platform. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 254, 2021.
  • Shubo Tian, Jinfeng Zhang.Multi-label topic classification for COVID-19 literature annotation using an ensemble model based on PubMedBERT. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 302, 2021.
  • Kaixian Yu, Zihan Cui, Xin Sui, Xing, Qiu Jinfeng Zhang. Biological network inference with GRASP: a Bayesian network structure learning method using adaptive sequential Monte Carlo. Frontiers in Genetics, accepted.
  • Zihan Cui, Yuhang Liu, Jinfeng Zhang, Xing Qiu, Super-delta2: An Enhanced Differential Expression Analysis Procedure for Multi-Group Comparisons of RNA-seq Data, Bioinformatics, 2021, btab155.
  • Savannah D. Savadel, Thomas Hartwig, Zachary M. Turpin, Daniel L. Vera, Pei-Yau Lung, Xin Sui, Max Blank, Wolf B. Frommer, Jonathan H. Dennis, Jinfeng Zhang, Hank W. Bass. The native cistrome and sequence motif families of the maize ear. PLoS Genetics, 2021, 17(8):e1009689.
  • Shubo Tian, Arslan Erdengasileng, Xi Yang, Yi Guo, Yonghui Wu, Jinfeng Zhang, Jiang Bian, Zhe He. Transformer-based named entity recognition for parsing clinical trial eligibility criteria. Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August, 2021, 49:1–6.
  • Zahraa Khamis, Xiaodong Pang, Zihan Cui, Qingxiang Amy Sang, Jinfeng Zhang. Cytochrome P450-2D6: a novel biomarker in liver cancer health disparity PLoS One, accepted.

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