Correcting scale distortion in RNA sequencing data by Christopher Thron, Farhad Jafari

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scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder by Xiaoxu Cui, Renkai Wu, Yinghao Liu, Peizhan Chen, Qing Chang, Pengchen Liang, Changyu He

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Direct coupling analysis and the attention mechanism by Francesco Caredda, Andrea Pagnani

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Zim4rv: an R package to modeling zero-inflated count phenotype on regional-based rare variants by Xiaomin Liu, Yi-Ju Li, Qiao Fan

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MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction by Dhekra Saeed, Huanlai Xing, Barakat AlBadani, Li Feng, Raeed Al-Sabri, Monir Abdullah, Amir Rehman

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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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Causal models and prediction in cell line perturbation experiments by James P. Long, Yumeng Yang, Shohei Shimizu, Thong Pham, Kim-Anh Do

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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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GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes by Tongjun Xiang, Huibao Feng, Xin-hui Xing, Chong Zhang

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BiomiX, a user-friendly bioinformatic tool for democratized analysis and integration of multiomics data by Cristian Iperi, Álvaro Fernández-Ochoa, Guillermo Barturen, Jacques-Olivier Pers, Nathan Foulquier, Eleonore Bettacchioli, Marta Alarcón-Riquelme, PRECISESADS Flow Cytometry Study Group, PRECISESADS Clinical Consortium, Divi Cornec, Anne Bordron, Christophe Jamin

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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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DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes by Mohamed Elmanzalawi, Takatomo Fujisawa, Hiroshi Mori, Yasukazu Nakamura, Yasuhiro Tanizawa

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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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A metric and its derived protein network for evaluation of ortholog database inconsistency by Weijie Yang, Jingsi Ji, Gang Fang

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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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