MolTrans: Molecular Interaction Transformer for drug–target interaction prediction von Huang, Kexin, Xiao, Cao, Glass, Lucas M, Sun, Jimeng

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GSEApy: a comprehensive package for performing gene set enrichment analysis in Python von Fang, Zhuoqing, Liu, Xinyuan, Peltz, Gary

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Diagnosis of Autism Spectrum Disorders Using Multi-Level High-Order Functional Networks Derived From Resting-State Functional MRI von Zhao, Feng, Zhang, Han, Rekik, Islem, An, Zhiyong, Shen, Dinggang

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iGRLDTI: an improved graph representation learning method for predicting drug–target interactions over heterogeneous biological information network von Zhao, Bo-Wei, Su, Xiao-Rui, Hu, Peng-Wei, Huang, Yu-An, You, Zhu-Hong, Hu, Lun

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Vehicle recognition algorithm based on Haar-like features and improved Adaboost classifier von Zhang, Le, Wang, Jinsong, An, Zhiyong

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GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction von Wang, Zhiqin, Li, Ruiqing, Wang, Minghui, Li, Ao

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MOMA: a multi-task attention learning algorithm for multi-omics data interpretation and classification von Moon, Sehwan, Lee, Hyunju

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BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction von Li, Min, Lu, Zhangli, Wu, Yifan, Li, YaoHang

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The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information von Morris, John H, Soman, Karthik, Akbas, Rabia E, Zhou, Xiaoyuan, Smith, Brett, Meng, Elaine C, Huang, Conrad C, Cerono, Gabriel, Schenk, Gundolf, Rizk-Jackson, Angela, Harroud, Adil, Sanders, Lauren, Costes, Sylvain V, Bharat, Krish, Chakraborty, Arjun, Pico, Alexander R, Mardirossian, Taline, Keiser, Michael, Tang, Alice, Hardi, Josef, Shi, Yongmei, Musen, Mark, Israni, Sharat, Huang, Sui, Rose, Peter W, Nelson, Charlotte A, Baranzini, Sergio E

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Graph2MDA: a multi-modal variational graph embedding model for predicting microbe–drug associations von Deng, Lei, Huang, Yibiao, Liu, Xuejun, Liu, Hui

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Supervised graph co-contrastive learning for drug–target interaction prediction von Li, Yang, Qiao, Guanyu, Gao, Xin, Wang, Guohua

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cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data von Eling, Nils, Damond, Nicolas, Hoch, Tobias, Bodenmiller, Bernd

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Cross-dependent graph neural networks for molecular property prediction von Ma, Hehuan, Bian, Yatao, Rong, Yu, Huang, Wenbing, Xu, Tingyang, Xie, Weiyang, Ye, Geyan, Huang, Junzhou

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DeepEventMine: end-to-end neural nested event extraction from biomedical texts von Trieu, Hai-Long, Tran, Thy Thy, Duong, Khoa N A, Nguyen, Anh, Miwa, Makoto, Ananiadou, Sophia

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DFBP: a comprehensive database of food-derived bioactive peptides for peptidomics research von Qin, Dongya, Bo, Weichen, Zheng, Xin, Hao, Youjin, Li, Bo, Zheng, Jie, Liang, Guizhao

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NHGNN-DTA: a node-adaptive hybrid graph neural network for interpretable drug–target binding affinity prediction von He, Haohuai, Chen, Guanxing, Chen, Calvin Yu-Chian

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CBNplot: Bayesian network plots for enrichment analysis von Sato, Noriaki, Tamada, Yoshinori, Yu, Guangchuang, Okuno, Yasushi

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LLPSDB v2.0: an updated database of proteins undergoing liquid–liquid phase separation in vitro von Wang, Xi, Zhou, Xiang, Yan, Qinglin, Liao, Shaofeng, Tang, Wenqin, Xu, Peiyu, Gao, Yangzhenyu, Li, Qian, Dou, Zhihui, Yang, Weishan, Huang, Beifang, Li, Jinhong, Zhang, Zhuqing

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Efficient gradient boosting for prognostic biomarker discovery von Li, Kaiqiao, Yao, Sijie, Zhang, Zhenyu, Cao, Biwei, Wilson, Christopher M, Kalos, Denise, Kuan, Pei Fen, Zhu, Ruoqing, Wang, Xuefeng

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DTF: Deep Tensor Factorization for predicting anticancer drug synergy von Sun, Zexuan, Huang, Shujun, Jiang, Peiran, Hu, Pingzhao

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