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2025	PmiProPred: A novel method towards plant miRNA promoter prediction based on CNN-Transformer network and convolutional block attention mechanism International Journal of Biological Macromolecules Haibin Li, Jun Meng, Zhaowei Wang, Yushi Luan
2025	Advances in Fungal Promoter Engineering for Enhancing Secondary Metabolite Biosynthesis Biotechnology Journal Nan Pu, Huawei Zhang
2024	RNAirport: a deep neural network-based database characterizing representative gene models in plants Journal of Genetics and Genomics Sitao Zhu, Shu Yuan, Ruixia Niu, Yulu Zhou, Zhao Wang, Guoyong Xu
2024	Bioinformatics in Russia: history and present-day landscape Briefings in Bioinformatics Muhammad A Nawaz, Igor E Pamirsky, Kirill S Golokhvast
2024	2024 3rd International Conference on Sentiment Analysis and Deep Learning (ICSADL) Mohammad Moin Uddin, Jasrin Shiddike, Afsana Ahmed, Tanveer Ahsan
2023	Deep learning and support vector machines for transcription start site identification PeerJ Computer Science José A. Barbero-Aparicio, Alicia Olivares-Gil, José F. Díez-Pastor, César García-Osorio
2022	Nonlinear physics opens a new paradigm for accurate transcription start site prediction BMC Bioinformatics José Antonio Barbero-Aparicio, Santiago Cuesta-Lopez, César Ignacio García-Osorio, Javier Pérez-Rodríguez, Nicolás García-Pedrajas
2022	Genome-Wide Prediction of Transcription Start Sites in Conifers International Journal of Molecular Sciences Eugeniya I. Bondar, Maxim E. Troukhan, Konstantin V. Krutovsky, Tatiana V. Tatarinova
2022	Genomics enters the deep learning era PeerJ Etienne Routhier, Julien Mozziconacci
2022	Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-Seq Data via DeeReCT-TSS Genomics, Proteomics & Bioinformatics Juexiao Zhou, Bin Zhang, Haoyang Li, Longxi Zhou, Zhongxiao Li, Yongkang Long, Wenkai Han, Mengran Wang, Huanhuan Cui, Jingjing Li, Wei Chen, Xin Gao
2020	Genome annotation across species using deep convolutional neural networks PeerJ Computer Science Ghazaleh Khodabandelou, Etienne Routhier, Julien Mozziconacci
2020	Identification of Regulatory SNPs Associated with Vicine and Convicine Content of Vicia faba Based on Genotyping by Sequencing Data Using Deep Learning Genes Felix Heinrich, Martin Wutke, Pronaya Prosun Das, Miriam Kamp, Mehmet Gültas, Wolfgang Link, Armin Otto Schmitt
2020	An intelligent computational model for prediction of promoters and their strength via natural language processing Chemometrics and Intelligent Laboratory Systems Muhammad Tahir, Maqsood Hayat, Sarah Gul, Kil To Chong
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