Toward Community Standards and Software for Whole-Cell Modeling. - Dagmar Waltemath; Jonathan R. Karr; Frank T. Bergmann; Vijayalakshmi Chelliah; Michael Hucka; Marcus Krantz; Wolfram Liebermeister; Pedro Mendes 001; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; et al. (IEEE Trans. Biomed. Eng., 2016)

3D-Stereoscopic Immersive Analytics Projects at Monash University and University of Konstanz. - Björn Sommer 001; David G. Barnes; Sarah E. Boyd; Tom Chandler; Maxime Cordeil; Tobias Czauderna; Matthias Klapperstück; Karsten Klein 001; Toàn D. Nguyên; Hieu T. Nim; Kingsley Stephens; Dany Vohl; et al. (SD&A, 2017)

iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. - Zhen Chen 009; Pei Zhao; Fuyi Li; Tatiana T. Marquez-Lago; André Leier; Jerico Nico De Leon Revote; Yan Zhu 006; David R. Powell; Tatsuya Akutsu; Geoffrey I. Webb; Kuo-Chen Chou; Alexander Ian Smith; et al. (Briefings Bioinform., 2020)

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. - Fuyi Li; Cunshuo Fan; Tatiana T. Marquez-Lago; André Leier; Jerico Nico De Leon Revote; Cangzhi Jia; Yan Zhu 006; Alexander Ian Smith; Geoffrey I. Webb; Quanzhong Liu; Leyi Wei; Jian Li 052; et al. (Briefings Bioinform., 2020)

SeqGO-CPA: Improving Compound-Protein Binding Affinity Prediction with Sequence Information and Gene Ontology Knowledge. - Chunyu Wang 002; Yan Zhu 006; Naifeng Wen; Lingling Zhao; Junjie Wang 005 (BIBM, 2021)

Visual exploration of large metabolic models. - Michael Aichem; Tobias Czauderna; Yan Zhu 006; Jinxin Zhao; Matthias Klapperstück; Karsten Klein 001; Jian Li 052; Falk Schreiber (Bioinform., 2021)

Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks. - Yan Zhu 006; Fuyi Li; Dongxu Xiang; Tatsuya Akutsu; Jiangning Song; Cangzhi Jia (Briefings Bioinform., 2021)

Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. - Meng Zhang 046; Cangzhi Jia; Fuyi Li; Chen Li 021; Yan Zhu 006; Tatsuya Akutsu; Geoffrey I. Webb; Quan Zou 001; Lachlan J. M. Coin; Jiangning Song (Briefings Bioinform., 2022)

O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine. - Yan Zhu 006; Shuwan Yin; Jia Zheng 004; Yixia Shi; Cangzhi Jia (J. Bioinform. Comput. Biol., 2022)

TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters. - Yan Zhu 006; Fuyi Li; Xudong Guo; Xiaoyu Wang 016; Lachlan J. M. Coin; Geoffrey I. Webb; Jiangning Song; Cangzhi Jia (Briefings Bioinform., 2023)

DataDTA: a multi-feature and dual-interaction aggregation framework for drug-target binding affinity prediction. - Yan Zhu 006; Lingling Zhao; Naifeng Wen; Junjie Wang 005; Chunyu Wang 002 (Bioinform., 2023)

Drug-Target Binding Affinity Prediction in a Continuous Latent Space Using Variational Autoencoders. - Lingling Zhao; Yan Zhu 006; Naifeng Wen; Chunyu Wang 002; Junjie Wang 005; Yongfeng Yuan (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)