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Peer-Reviewed Articles

  • Yang Yang, Yang Zhang, Bing Ren, Jesse R. Dixon, Jian Ma. (2019). "Comparing 3D genome organization in multiple species using Phylo-HMRF". Cell Systems 8(6):494-505.e14. [pdf] [source code]

    • Early version appeared in Proceedings of the 23rd Annual International Conference on Research in Computational Molecular Biology (RECOMB 2019).

  • Shashank Singh, Yang Yang, Barnabas Poczos, Jian Ma. (2019). "Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Learning". Quantitative Biology, 7(2):122-137. [pdf] [source code]

  • Yang Yang, Quanquan Gu, Yang Zhang, Takayo Sasaki, Julianna Crivello, Rachel J. O'Neill, David M. Gilbert, Jian Ma. (2018). "Continuous-trait probabilistic model for comparing multi-species functional genomic data". Cell Systems 7(2):208-218.e11. [pdf] [source code]

    • Early version appeared in Proceedings of the 22nd Annual International Conference on Research in Computational Molecular Biology (RECOMB 2018).

    • Selected as one of the “RECOMB/ISCB Regulatory Systems Genomics Reading List” (2019).

  • Ruochi Zhang, Yuchuan Wang, Yang Yang, Yang Zhang, Jian Ma. (2018). "Predicting CTCF-mediated chromatin loops using CTCF-MP". In Proceedings of the 26th Conference on Intelligent Systems for Molecular Biology (ISMB 2018), Bioinformatics, 34(13):i133-i141. [pdf]

  • Yang Yang, Ruochi Zhang, Shashank Singh, Jian Ma. (2017). "Exploiting Sequence-based Features for Predicting Enhancer-Promoter Interactions". In Proceedings of the 25th Conference on Intelligent Systems for Molecular Biology (ISMB 2017), Bioinformatics, 33(14), i252-i260. [pdf] [source code]

  • Yue Deng*, Feng Bao*, Yang Yang, Xiangyang Ji, Mulong Du, Zhengdong Zhang, Meiling Wang, Qionghai Dai. (2017). "Information transduction capacity reduces the uncertainties in annotation-free isoform discovery and quantification", Nucleic acids research, 45(15), e143. (*: equal contribution)

  • Zhiquan Ren, Yang Yang, Feng Bao, Yue Deng, and Qionghai Dai. "Directed adaptive graphical Lasso for causality inference". Neurocomputing, 173:1989-1994, 2016.

  • Yang Yang, Yue Deng, Xiangyang Ji, and Qionghai Dai. "Log-sum heuristic recovery for automated isoform discovery and abundance estimation from RNA-Seq data". In Proceedings of the 5th International Conference on Information Science and Technology (ICIST), 599-603, 2015. IEEE.

Patents

  • Qionghai Dai and Yang Yang. A rendering algorithm of virtual views, CN103150729B, Granted, 12-23-2015.

  • Xiangyang Ji, Yang Yang, and Qionghai Dai. A 3D reconstruction method for outdoor scenes, CN103198524B, Granted, 08-12-2015.