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2025	CA-NN: a cellular automata neural network for handwritten pattern recognition Natural Computing Aamir Wali
2025	Comparative Genomics and Epigenomics of Transcriptional Regulation Annual Review of Animal Biosciences Huaijun Zhou, Emily Clark, Dailu Guan, Sandrine Lagarrigue, Lingzhao Fang, Hao Cheng, Christopher K. Tuggle, Muskan Kapoor, Ying Wang, Elisabetta Giuffra, Giorgia Egidy
2024	Identification of DNA motif pairs on paired sequences based on composite heterogeneous graph Frontiers in Genetics Qiuqin Wu, Yang Li, Qi Wang, Xiaoyu Zhao, Duanchen Sun, Bingqiang Liu
2024	Bioconvergence Revolution Nina Siragusa, Laura Matz
2024	DRANetSplicer: A Splice Site Prediction Model Based on Deep Residual Attention Networks Genes Xueyan Liu, Hongyan Zhang, Ying Zeng, Xinghui Zhu, Lei Zhu, Jiahui Fu
2024	Navigating the archaeal frontier: insights and projections from bioinformatic pipelines Frontiers in Microbiology Val Karavaeva, Filipa L. Sousa
2022	Genomics enters the deep learning era PeerJ Etienne Routhier, Julien Mozziconacci
2021	Application of Deep Learning in Plant–Microbiota Association Analysis Frontiers in Genetics Zhiyu Deng, Jinming Zhang, Junya Li, Xiujun Zhang
2021	Spliceator: multi-species splice site prediction using convolutional neural networks BMC Bioinformatics Nicolas Scalzitti, Arnaud Kress, Romain Orhand, Thomas Weber, Luc Moulinier, Anne Jeannin-Girardon, Pierre Collet, Olivier Poch, Julie D. Thompson
2021	keras_dna: a wrapper for fast implementation of deep learning models in genomics Bioinformatics Etienne Routhier, Ayman Bin Kamruddin, Julien Mozziconacci
2021	ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation PLOS Computational Biology Ramzan Umarov, Yu Li, Takahiro Arakawa, Satoshi Takizawa, Xin Gao, Erik Arner
2020	Systems biology approaches integrated with artificial intelligence for optimized metabolic engineering Metabolic Engineering Communications Mohamed Helmy, Derek Smith, Kumar Selvarajoo
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