Conditional similarity triplets enable covariate-informed representations of single-cell data by Chi-Jane Chen, Haidong Yi, Natalie Stanley

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Correction: HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes by Thomas M. Adams, Moray Smith, Yuhan Wang, Lynn H. Brown, Micha M. Bayer, Ingo Hein

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MDFGNN-SMMA: prediction of potential small molecule-miRNA associations based on multi-source data fusion and graph neural networks by Jianwei Li, Xukun Zhang, Bing Li, Ziyu Li, Zhenzhen Chen

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getphylo: rapid and automatic generation of multi-locus phylogenetic trees by T. J. Booth, S. Shaw, P. Cruz-Morales, T. Weber

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Omilayers: a Python package for efficient data management to support multi-omic analysis by Dimitrios Kioroglou

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TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis by Masahiro Ono

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Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data by Jinming Cheng, Xinyi Jin, Gordon K. Smyth, Yunshun Chen

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HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes by Thomas M. Adams, Moray Smith, Yuhan Wang, Lynn H. Brown, Micha M. Bayer, Ingo Hein

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Biomedical named entity recognition using improved green anaconda-assisted Bi-GRU-based hierarchical ResNet model by Ram Chandra Bhushan, Rakesh Kumar Donthi, Yojitha Chilukuri, Ulligaddala Srinivasarao, Polisetty Swetha

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AMEND 2.0: module identification and multi-omic data integration with multiplex-heterogeneous graphs by Samuel S. Boyd, Chad Slawson, Jeffrey A. Thompson

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ClearFinder: a Python GUI for annotating cells in cleared mouse brain by Stefan Pastore, Philipp Hillenbrand, Nils Molnar, Irina Kovlyagina, Monika Chanu Chongtham, Stanislav Sys, Beat Lutz, Margarita Tevosian, Susanne Gerber

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Marigold: a machine learning-based web app for zebrafish pose tracking by Gregory Teicher, R. Madison Riffe, Wayne Barnaby, Gabrielle Martin, Benjamin E. Clayton, Josef G. Trapani, Gerald B. Downes

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NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface by Andrea Conte, Nicola Gulmini, Francesco Costa, Matteo Cartura, Felix Bröhl, Francesco Patanè, Francesco Filippini

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DTI-MHAPR: optimized drug-target interaction prediction via PCA-enhanced features and heterogeneous graph attention networks by Guang Yang, Yinbo Liu, Sijian Wen, Wenxi Chen, Xiaolei Zhu, Yongmei Wang

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Predicting drug combination side effects based on a metapath-based heterogeneous graph neural network by Leixia Tian, Qi Wang, Zhiheng Zhou, Xiya Liu, Ming Zhang, Guiying Yan

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TopoQual polishes circular consensus sequencing data and accurately predicts quality scores by Minindu Weerakoon, Sangjin Lee, Emily Mitchell, Haynes Heaton

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Solu: a cloud platform for real-time genomic pathogen surveillance by Timo Saratto, Kerkko Visuri, Jonatan Lehtinen, Irene Ortega-Sanz, Jacob L. Steenwyk, Samuel Sihvonen

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