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Han M, Yin Y, Zhang H, Wang H. (2023) Hierarchical Semantic Augmentation Graph Neural Network for Drug-Disease Association Prediction. IEEE BIBM 2023. DOI: 10.1109/BIBM58861.2023.10385961

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Han M, Li W, Zhang H, Yin Y. (2023) Semantic-guided Graph Neural Network for Heterogeneous Graph Embedding. Expert Systems with Applications 232:120810. doi

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Huang W, Zhang H, Li Z, and Yin Y. (2022) Mutual Information Estimation-Based Disentangled Representation Network for Medical Image Fusion. IEEE BIBM 2022, Las Vegas, pp. 991–998. doi: 10.1109/BIBM55620.2022.9995221 Best Student Paper Award

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Wang X, Wang J, Huang S, Zhang H, Yin Y. (2021) HDMC: a novel deep learning based framework for removing batch effects in single-cell RNA-seq data. Bioinformatics. doi:10.1093/bioinformatics/btab821

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Jin C, Shi Z, Zhang H, and Yin Y. (2021) Predicting lncRNA–protein interactions based on graph autoencoders and collaborative training. IEEE BIBM 2021.

Li W, Zhang H, Zhao Q, Liu J, and Yin Y. (2021) Adversarial Dual-Channel Variational Graph Autoencoder for Synthetic Lethality Prediction in Human Cancers. IEEE BIBM 2021.

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Li W, Zhao Q, Zhang H, Quan X, Xu J, and Yin Y. (2021) Bayesian Multi-scale Convolutional Neural Network for Motif Occupancy Identification. IEEE BIBM 2020, pp. 293–298. doi: 10.1109/BIBM49941.2020.9313556

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Wang X, Yi H, Wang J, Zhan D, Yin Y, Zhang H. (2020) GDASC: A GPU parallel based web server for detecting hidden batch factors. Bioinformatics. doi:10.1093/bioinformatics/btaa427

Yi H^, Huang L^, Yang B^, Zhang H, Yin Y#. (2020) AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses. Nucleic Acids Res. doi:10.1093/nar/gkaa351

Orton L^, Fitzek E^, Feng X^, Grayburn SW, Mower JP, Liu K, Zhang C, Duvall MR, Yin Y#. (2020) Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution. Journal of Experimental Botany. doi:10.1093/jxb/eraa149

Becker B, Feng X^, Yin Y, Holzinger A. (2020) Desiccation tolerance in streptophyte algae and the algae to land plant transition: Evolution of LEA and MIP protein families within the Viridiplantae. Journal of Experimental Botany. doi:10.1093/jxb/eraa105

Su X, Xu J, Yin Y, Quan X, Zhang H. (2019) Antimicrobial Peptide Identification Using Multi-scale Convolutional Network. BMC Bioinformatics 20:730. doi

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Li W, Yin Y, Quan X, Zhang H. (2019) Gene Expression Value Prediction Based on XGBoost Algorithm. Frontiers in Genetics. doi

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Driscoll CB, Meyer KA, Šulčius S, Brown NM, Dick GJ, Cao H^, Gasiūnas G, Timinskas A, Yin Y, Landry ZC, Otten TG, Davis TW, Watson SB, Dreher TW. (2018) A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales. Harmful Algae 77:93–107.

Han W, Ibarra G, Gupta M, Yin Y, Elsawa S. (2018) Elevated Expression of GLI3 in Germinal Center Diffuse Large B Cell Lymphoma. Leukemia and Lymphoma. doi

Huang L, Zhang H, Wu P, Entwistle S+, Li X^, Yohe T+, Yi H, Yang Z, Yin Y#. (2017) dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. Nucleic Acids Res. (database issue 2018) 46(D1):D516–D521. doi:10.1093/nar/gkx894

Yang X, …, Fitzek E^, …, Yin Y, …, Tuskan GA. (2017) The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nature Communications 8:1899. doi

Jiang X, Zhang H, Quan X, Yin Y. (2017) A Heterogeneous Networks Fusion Algorithm Based on Local Topological Information for Neurodegenerative Disease. Current Bioinformatics 12(5):387–397.

Jiang X, Quan X, Zhang H, Zhan D, Yin Y. (2017) Disease-related Gene Module Detection Based on A Multi-label Propagation Clustering Algorithm. PLoS One 12(5):e0178006. doi

Huo L, Zhang H, Huo X, Yang Y^, Li X^, Yin Y#. (2017) pHMM-tree: Phylogeny of Profile Hidden Markov Models. Bioinformatics 33(7):1093–1095. doi:10.1093/bioinformatics/btw779

Wysocki W, Riuz-Sanches E, Yin Y, Duvall M. (2016) The floral transcriptomes of four bamboo species (Bambusoideae; Poaceae): support for common ancestry among woody bamboos. BMC Genomics 17:384. doi

Yu J, Wu G, Jurick WM Jr, Gaskins VL, Yin Y, Yin G, Bennett JW, Shelton DR. (2016) Genome sequence of Penicillium solitum RS1, which causes postharvest apple decay. Genome Announc. 4(3):e00363-16. doi

Ekstrom A+, Yin Y#. (2016) ORFanFinder: automated identification of taxonomically restricted orphan genes. Bioinformatics 32(13):2053–2055. doi

Hu L, Taujale R^, Song J, Guo J, Yin Y#. (2016) Draft genome sequence of Talaromyces verruculosus ("Penicillium verruculosum") strain TS63-9. Journal of Biotechnology 219:5–6. doi

Yang X, Leeben-Mack J, Chen F, Yin Y. (2015) Plant Comparative and Functional Genomics. International Journal of Genomics 2015:924369. doi

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Cary JW*, Han Z*, Yin Y*, Lohmar JM, Shantappa S, Harris-Coward PY, Mack B, Ehrlich KC, Wei Q, Arroyo-Manzanares N, Uka V, Vanhaecke L, Bhatnagar D, Yu J, Nierman WC, Johns MA, Sorensen D+, Shen H^, De Saeger S, Diana Di Mavungu J, Calvo AM. (2015) Transcriptome analysis of Aspergillus flavus reveals veA-dependent regulation of secondary metabolite gene clusters, including the novel aflavarin cluster. Eukaryot Cell 14:983–997. doi Articles of Significant Interest — Editors' Selection

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