scFocus: Detecting branching probabilities in single-cell data with SAC by Chunlin Chen, Zeyu Fu, Jiajia Yang, Huaqing Chen, Jiabao Huang, Shitian Qin, Chuhuai Wang, Xiaoqian Hu

“…This demonstrates its applicability on different types of datasets and showcases its potential in discovering biological changes due to experimental treatments through multi-batch dataset processing. Finally, an online analysis tool based on scFocus was developed, helping researchers and clinicians in the process and visualization of single-cell RNA sequencing data as well as the interpretation of these data through branch probabilities in a streamlined and intuitive way.…”
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Integrated single-cell sequencing for the development of a GJA4-based precision immuno-prognostic model in melanoma by Yantao Ding, Si Xie, Wenyang Nie, Yun Bai, Tianyu Yao, Yixiao Wang, Jiajie Chen, Bo Liang, Yi Zhou, Hui Cheng, Zaixing Wang, Shengxiu Liu

“…Methods: We conducted an analysis of RNA-seq and microarray data obtained from the TCGA and GEO databases, alongside single-cell RNA sequencing (scRNA-seq) data from glioma patients within the GEO repository. …”
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Reconstruction of the transmission history of RNA virus outbreaks using full genome sequences: foot-and-mouth disease virus in Bulgaria in 2011. by Begoña Valdazo-González, Lilyana Polihronova, Tsviatko Alexandrov, Preben Normann, Nick J Knowles, Jef M Hammond, Georgi K Georgiev, Fuat Özyörük, Keith J Sumption, Graham J Belsham, Donald P King

“…Improvements to sequencing protocols and the development of computational phylogenetics have opened up opportunities to study the rapid evolution of RNA viruses in real time. …”
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Use of next-generation sequencing in genomic studies of polyploid crops: cotton as an example by Zhu Qianhao, Danny Llewellyn, Iain Wilson

“…This article summarises the applications of NGS in cotton genomic studies, including genome sequencing and resequencing, transcriptomic analysis, small RNA sequencing and miRNA identification, and identification of single nucleotide polymorphisms. …”
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Application of high-throughput sequencing in citrus virus identification and analysis of population diversity by LI Xiang, YANG Jin, HUANG Aijun, ZHOU Jun, YI Long

“…For example, the complexity of data analysis and the need for bioinformatics knowledge limits its popularization and application in some areas; the high cost of sequencing is still a major obstacle for resource-limited areas. …”
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Interpretable and integrative analysis of single-cell multiomics with scMKL by Samuel D. Kupp, Ian A. VanGordon, Mehmet Gönen, Sadık Esener, Sebnem Ece Eksi, Çiğdem Ak

“…In this manuscript, we introduce an innovative method for single-cell analysis using Multiple Kernel Learning (scMKL), that merges the predictive capabilities of complex models with the interpretability of linear approaches, aimed at providing actionable insights from single-cell multiomics data. scMKL excels at classifying healthy and cancerous cell populations across multiple cancer types, utilizing data from single-cell RNA sequencing, ATAC sequencing, and 10x Multiome. …”
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Studying strands polarity of different viroids and their combinations in infected hop plants by Andrej SEČNIK, Sebastjan RADIŠEK, Nataša ŠTAJNER, Jernej JAKŠE

“…RNA-seq data indicate that viroids amplify until saturation further demonstrating plant's biological capacity. …”
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Deciphering the role of SEMA4A/MAPK signaling in sepsis: insights from Mendelian randomization, transcriptomic, single-cell sequencing analyses, and vitro experiments by Meng-Qin Pei, Yan-Ling Lin, Li-Ming Xu, Yu-Shen Yang, Zhen-Dong Sun, Ya-Fen Zeng, Gui-Dan Wang, He-Fan He, Li-Ying Yu, Li-Ying Yu

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to elucidate the functional pathways of core genes. Single-cell RNA sequencing (scRNA-seq) analysis was employed to evaluate gene expression profiles across various cell types in sepsis. …”
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Isoform analysis of heterozygous putative splicing variants at the allele level using nanopore long-read sequencing by Kokoro Ozaki, Takashi Irioka, Shohei Noma, Akira Machida, Moe Fukunaga, Tatsuro Murano, Chitose Takahashi, Michihira Tagami, Tsugumi Kawashima, Tomoko Hirata, Yuki Yasuoka, Hiroya Kuwahara, Toshiyuki Araki, Ken Yagi, Hidehiro Mizusawa, Kinya Ishikawa, Yasushi Okazaki, Takanori Yokota

“…Our aim was to analyze these variants by dividing cDNA or direct RNA nanopore long reads into two alleles, referencing whole-genome sequencing data containing allele-informative single nucleotide variants and then comparing the allele-separated reads using Full-Length Alternative Isoform analysis of RNA (FLAIR), a previously published bioinformatics tool for isoform analysis. …”
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An atlas of immune cell exhaustion in HIV-infected individuals revealed by single-cell transcriptomics by Shaobo Wang, Qiong Zhang, Hui Hui, Kriti Agrawal, Maile Ann Young Karris, Tariq M. Rana

“…Here, we investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from four healthy subjects (37,847 cells) and six HIV-infected donors (28,610 cells). …”
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APPLICATIONS OF TRANSCRIPTOMICS METHODS IN BREAST CANCER by Yeşim Gökmen Polar

“…Using TCGA and METABRIC cohorts, we identified immune-subtypes with better outcomes in triple negative breast cancer (TNBCs). Recently, single cell RNA-seq (sc-RNAseq) and spatial RNA-seq technologies have enabled analysis of single tumor cell phenotypes and intratumor heterogeneity. …”
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A dataset of chronic nicotine-induced genes in breast cancer cellsUniversity of California San Diego Library Digital Collections by Samson Mugisha, Shreyas Labhsetwar, Devam Dave, Richard Klemke, Jay S. Desgrosellier

“…To produce this dataset, we first performed single cell RNA sequencing from HCC38 cells chronically treated with vehicle or nicotine, followed by scanpy analysis to yield 6 discrete cell clusters at conservative resolution. …”
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WGCNA and single-cell analysis reveal ferroptosis-related gene signatures for hepatocellular carcinoma prognosis and therapy by Can Peng, Fujian Yan, Mingli Xu, Yueyue Zhao, Jiaxing Sun

“…We used single-cell RNA sequencing data to analyze the expression of these genes in different cell types. …”
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Single-cell transcriptomic analysis of the human vascular atlas provides new insights into vasorelaxation redundancy and heterogeneity by Elisa Avolio, Sarah F. Pearce, David Wambeke, Paolo Madeddu

“…However, it remains unknown whether vasorelaxant mediators reiterate this pattern.Working hypothesisThe expression of “sentinel” gene transcripts provides a first insight into angiotypic and organotypic heterogeneity of vasorelaxation.MethodsThe expression of NO- and PGI2-generating enzymes and potassium channels was evaluated by analyzing single-cell RNA-sequencing data derived from the Human Vascular Cell Atlas. …”
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Unveiling the therapeutic potential of senescence-related IQGAP2 in pancreatic Cancer through post-GWAS genomic and scRNA-seq analyses by Zilong Bai, Jiale Liang, Yuanhua Nie, Shilong Wang, Dongmin Chang

“…While cellular senescence has been linked to the advancement of various cancers, its specific role in PC is not well understood. Method We employed Mendelian randomization (MR) alongside single-cell RNA sequencing (scRNA-seq) to explore the involvement of senescence-associated genes (SAGs) in PC. …”
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Integrated transcriptomic and single-cell analysis reveals key immune-related genes and cellular crosstalk in the myocarditis microenvironment by Yuanqing Li, Shangfei He, Jun Wu, Shenrong Liu, Ruiming Liu, Yipeng Du, Dunzheng Han, Wenjie Luo, Zheng Huang, Pingzhen Yang

“…Subsequently, we integrated single-cell RNA sequencing data to explore different cell subpopulations through clustering analysis, utilizing GSEA, GSVA, and CellChat to examine their functions and interactions. …”
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Single-cell analysis of gene regulatory networks in the mammary glands of P4HA1-knockout mice. by Akshat Gupta, Lilin Huang, Jinpeng Liu, Ke Chen, Ren Xu, Wei Wu

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Cellular interactions and Ion channel signatures in atrial fibrillation remodeling: insights from single-cell analysis and machine learning by Bin He, Yan Cheng, Juan Wang, Ya Zhan, YanQun Liu

“…Although previous studies have offered insights into these changes, the cellular interactions involved in atrial structural remodeling and the ion channel marker genes associated with electrical remodeling in AF remain insufficiently elucidated.MethodsWe used single-cell RNA sequencing (scRNA-seq) to investigate the structural remodeling in AF at the cellular level. …”
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The Transcriptional Program of <i>Staphylococcus aureus</i> Phage K Is Affected by a Host <i>rpoC</i> Mutation That Confers Phage K Resistance by Rohit Kongari, Melissa D. Ray, Susan M. Lehman, Roger D. Plaut, Deborah M. Hinton, Scott Stibitz

“…However, in many cases, sequences upstream of late genes did not contain clear, complete, canonical promoter sequences, suggesting that factors in addition to host RNA polymerase are required for their expression. …”
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SPP1+ tumor-associated macrophages define a high-risk subgroup and inform personalized therapy in hepatocellular carcinoma by Wei-Xuan Xu, Ya-Mei Ye, Jia-Lin Chen, Xin-Ying Guo, Chen Li, Juan Luo, Lin-Bin Lu, Xiong Chen

“…Through multiple immunofluorescence, our findings were verified.ResultsHerein, integrating single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data, we established a novel TAM classification system based on mutually exclusive SPP1 and FOLR2 signatures. …”
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