Preliminary exploration of mRNA, lncRNA, and miRNA expressions in the bovine jejunum unveils novel aspects of Mycobacterium avium subspecies paratuberculosis infections by Yahui Gao, Jie Cao, Bo Han, Dongxiao Sun

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Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex by Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Sophia Cinquemani, Nicholas J. Eagles, Daianna Gonzalez-Padilla, Sean K. Maden, Joel E. Kleinman, Thomas M. Hyde, Stephanie C. Hicks, Kristen R. Maynard, Leonardo Collado-Torres

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Combined analyses of mRNA and miRNA transcriptome reveal the molecular mechanisms of theca cells physiological differences in geese follicular selection stage by Xinyue Hu, Hengli Xie, Xi Zhang, Yueyue Lin, Shenqiang Hu, Jiwei Hu, Hua He, Liang Li, Hehe Liu, Jiwen Wang

Subjects: “…miRNA-seq…”
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Renal Single-Cell RNA Sequencing and Digital Cytometry in Dogs with X-Linked Hereditary Nephropathy by Candice P. Chu, Daniel Osorio, Mary B. Nabity

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Immune-related hub genes and their role in psoriasis pathogenesis by Tingting Yin, Tingting Zhang, Lei Ma

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Transcriptome sequencing reveals significant RNA variation in human sperm samples by Weiming Chen, Lei Yu, Zhenyu Jia, Jianguo Zhu

Subjects: “…RNA-seq…”
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Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications by Farhana Manzoor, Cyruss A. Tsurgeon, Vibhuti Gupta

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Protocol for unlocking alternative polyadenylation insights from bulk RNA-seq data with PolyAMiner-Bulk by Venkata Jonnakuti, Sriya Jonnakuti, Hari Krishna Yalamanchili

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Protocol for mapping 2′-O-methylation using nanopore direct RNA-seq data with NanoNm by Yanqiang Li, Jiayi Chen, Yunxia Wang, Dean Li, Jiahan Li, Yang Yi, Lili Zhang, Qi Cao, Kaifu Chen

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Comprehensive bioinformatics analysis identified HMGB3 as a promising immunotherapy target for glioblastoma multiforme by Libin Wang, Peizhi Xu, Xinglong Li, Qinghua Zhang

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Construction of a novel inflammatory-related prognostic signature of acute myelocytic leukemia based on conjoint analysis of single-cell and bulk RNA sequencing by Yongfen Huang, Ping Yi, Ping Yi, Yixuan Wang, Lingling Wang, Yongqin Cao, Jingbo Lu, Kun Fang, Kun Fang, Yuexin Cheng, Yuqing Miao, Yuqing Miao

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Single-Cell and Single-Nuclei transcriptomics profiling reveals dynamic cellular features in tumor-related adipose microenvironment of breast cancer patients with high BMI by Xiaoxiao Hu, Fang Jia, Lili Li, Wuzhen Chen, Leyi Zhang, Jun Pan, Sangsang Zhu, Zhen Wang, Jian Huang

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MTFAP: a comprehensive platform for predicting and analyzing master transcription factors by Jianyuan Zhou, Haojie Yu, Chunhui Lou, Min Yang, Yanshang Li, Qian Yang, Shuhan Li, Chunwang Ji, Song Li, Shuang Wang, Haotian Cao, Xuecang Li, Lian Liu

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PRC1 as an independent adverse prognostic factor in Wilms tumor via integrated bioinformatics and experimental validation by Yanping Wang, Hongjie Gao, Xuetian Li, Ding Li, Fan Huang, Yuqiang Sun, Xingjian Liu, Junli Yang, Fengyin Sun

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Identification of biomarkers for Laryngeal squamous cell carcinoma through Mendelian randomization and integrated bioinformatics analysis by Pengjian Zhang, Weizhang Chen, Kai Chen, Yuanhang Ye, Weijun Wu

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Protocol for interpretable and context-specific single-cell-informed deconvolution of bulk RNA-seq data by Daniele Malpetti, Francesca Mangili, Marco Bolis, Anna Rinaldi, David Legouis, Lorenzo Ruinelli, Pietro Cippà, Laura Azzimonti

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Protocol for deep-learning-driven cell type label transfer in single-cell RNA sequencing data by Zoe Zabetian, Jesus Gonzalez-Ferrer, Julian Lehrer, Vanessa D. Jonsson, Mircea Teodorescu, David Haussler, Mohammed A. Mostajo-Radji

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Comparative analysis of genotype imputation strategies for SNPs calling from RNA-seq by Kaixuan Guo, Zhanming Zhong, Haonan Zeng, Changliang Zhang, Teddy Tinashe Chitotombe, Jinyan Teng, Yahui Gao, Zhe Zhang

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Decoding pilocarpine biosynthesis and its roles in Pilocarpus microphyllus through a comparative transcriptomics approach by Mariane Brom Sobreiro, Giordano Bruno Soares-Souza, Leandro Magalhães, Débora de Morais Cordeiro, Michele Molina, Santelmo Vasconcelos, Yan Nunes Dias, Renato R. Moreira-Oliveira, Markus Gastauer, Silvio Ramos, Guilherme Oliveira, Cecílio Frois Caldeira, Amanda F. Vidal

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Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing by Diane Delobel, Hiromi Nishiyori-Sueki, Ilaria Nisoli, Hideya Kawaji, Pauline Robbe, Piero Carninci, Hazuki Takahashi

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