Mapping the rapid growth of multi-omics in tumor immunotherapy: Bibliometric evidence of technology convergence and paradigm shifts by Huijing Dong, Xinmeng Wang, Yumin Zheng, Jia Li, Zhening Liu, Aolin Wang, Yulei Shen, Daixi Wu, Huijuan Cui

“…This study aims to fill the knowledge gap in systematically mapping the evolution of omics-driven tumor immunotherapy research through a bibliometric lens. While omics technologies (genomics, transcriptomics, proteomics, metabolomics)provide multidimensional molecular profiling, their synergistic potential with immunotherapy remains underexplored in large-scale trend analyses. …”
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Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets by Gonzalez Sergio Alberto, Rivarola Maximo, Ribone Andres, Lew Sergio, Paniego Norma

“…While methods and algorithms for transcriptome assembly are continually being developed and published, the quality of de novo assemblies using short reads depends on the complexity of the transcriptome and is limited by several types of errors. …”
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In silico analysis reveals distinct changes in markers of epithelial to mesenchymal transition in glioma subtypes by Nives Pećina-Šlaus, Alja Zottel, Željko Škripek, Borna Puljko, Fran Dumančić, Anja Bukovac, Ivana Jovčevska, Anja Kafka

“…The genes were additionally validated by gene expression on the GlioVis portal, STRING protein network analysis, survival analysis, and experimentally with qRT-PCR. …”
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Cis-regulation analysis of RNA m6A methylation and gene expression in colorectal cancer by Zhen-Liang Lin, Pan-Pan Yu, Bei-Lei Ye

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Identification and expression analysis of myo-inositol oxygenase gene family in Brassica napus L. by CHEN Shubing, XU Zishu, HUANG Qian, ZHANG Hui, ZHANG Kangni, DUAN Yi, SUN Yue’e, ZHOU Weijun, XU Ling

“…In this study, the genome-wide identification and expression pattern analysis of the MIOX family gene in Brassica napus L. …”
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Computational analysis of the functional impact of MHC-II-expressing triple-negative breast cancer by Yang Cui, Weihang Zhang, Xin Zeng, Yitao Yang, Sung-Joon Park, Kenta Nakai, Kenta Nakai

“…To understand the role of MHC-II-expressing tumor cells, we analyzed triple-negative breast cancer (TNBC), an aggressive subtype with poor prognosis and limited treatment options, using public bulk RNA-seq, single-cell RNA-seq, and spatial transcriptomics datasets. Our analysis revealed a distinct tumor subpopulation that upregulates MHC-II genes and actively interacts with immune cells. …”
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Comparative analysis of library preparation approaches for FFPE gene expression profiling and related recommendations by Sara Pignatta, Marcella Tazzari, Valentina Indio, Maria Maddalena Tumedei, Francesco Limarzi, Francesca Tauceri, Michela Tebaldi, Dalila Fanelli, Jenny Bulgarelli

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Comprehensive analysis of multi‐omics single‐cell data using the single‐cell analyst by Lu Pan, Bufu Tang, Xuan Zhang, Paolo Parini, Roman Tremmel, Joseph Loscalzo, Volker M. Lauschke, Bradley A. Maron, Paola Paci, Ingemar Ernberg, Nguan Soon Tan, Ákos Végvári, Zehuan Liao, Sundararaman Rengarajan, Roman Zubarev, Yuxuan Fan, Xu Zheng, Xinyue Jian, Ren Sheng, Zhenning Wang, Xuexin Li

“…It automates critical analysis steps, such as quality control, data processing, and phenotype‐specific analyses, while also offering interactive, publication‐ready visualizations. …”
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Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds by Yuting Zhang, Yunhao Liu, Zhanxiang Zong, Liang Guo, Wenhao Shen, Hu Zhao

“…Experimental validation reveals that four genes (BnaA09.PYRD, BnaA08.PSK1, BnaA08.SWI3, and BnaC02.LTP15) positively modulate oleic acid content while negatively impact erucic acid content. Comparative analysis of transcriptome profiles suggests that BnaA09.PYRD may influence fatty acid composition by regulating energy metabolism during seed development. …”
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Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis by Qiuting Deng, Pengfei Cai, Yingjie Luo, Zhongjin Zhang, Wen Ma, Zijie Huang, Xiaoya Chen, Shijie Hao, Weiguang Ma, Jiangshan Xu, Chunqing Wang, Mengnan Cheng, Xiumei Lin, Ru Zhou, Shanshan Duan, Junjie Chen, Ronghai Li, Xuyang Shi, Chang Liu, Liang Wu, Peng Gao, Jianting Li, Xiao Yang, Xiangdong Wang, Jun Xie, Longqi Liu, Yue Yuan, Chuanyu Liu

“…Here, we present high-throughput single-cell chromatin accessibility and transcriptome sequencing (HT-scCAT-seq), a method that simultaneously profiles transcriptome and chromatin accessibility. …”
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Comparative RNA-Seq analysis of differentially expressed genes in the sertoli cells of yak and cattle-yak by Xue-Mei Chen, Ming-Xiu Wang, Peng Zhang, Ke-Min Jing, Bing-Lin Yue, Zhi-Juan Wu, Zhi-Xin Chai, Xin-Rui Liu, Jin-Cheng Zhong, Xin Cai

“…Sertoli cells were subjected to transcriptome sequencing, GO analysis, KEGG analysis and differentially expressed gene were validated by RT-qPCR and Western blotting. …”
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Integrative bioinformatics analysis and experimental validation reveals key genes and regulatory mechanisms in the development of gout by Ye Yuan, Zhiqiang Gao, Jianhong Chen, Yuejing Liu, Jingguo Zhou

“…This study aimed to identify key genes and elucidate regulatory mechanisms underlying gout development through bioinformatics analysis combined with experimental validation.MethodsTranscriptome dataset GSE160170 and single-cell dataset GSE211783 were analyzed using differential expression analysis and weighted gene co-expression network analysis (WGCNA). …”
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Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis. by Venkata Suresh Bonthala, Katie Mayes, Joanna Moreton, Martin Blythe, Victoria Wright, Sean Tobias May, Festo Massawe, Sean Mayes, Jamie Twycross

“…Therefore, in this study we developed a computational pipeline to identify and analyze the genes and gene modules associated with low temperature stress responses in bambara groundnut using the cross-species microarray technique (as bambara groundnut has no microarray chip) coupled with network-based analysis. Analyses of the bambara groundnut transcriptome using cross-species gene expression data resulted in the identification of 375 and 659 differentially expressed genes (p<0.01) under the sub-optimal (23°C) and very sub-optimal (18°C) temperatures, respectively, of which 110 genes are commonly shared between the two stress conditions. …”
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Comparative Analysis of Proximal Tubule Cell Sources for In Vitro Studies of Renal Proximal Tubule Toxicity by Courtney Sakolish, Han-Hsuan D. Tsai, Hsing-Chieh Lin, Piyush Bajaj, Remi Villenave, Stephen S. Ferguson, Jason P. Stanko, Richard A. Becker, Philip Hewitt, Weihsueh A. Chiu, Ivan Rusyn

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Impact of aging on gene expression in human oocytes: a comparative analysis of young and older patients by Raoul Orvieto, Omri Nayshool, Louisa Cohen, Yuval Yung, Adva Aizer, Efrat Glick Saar, Dan Dominissini

“…In addition, single human oocyte transcriptome analysis at both germinal vesicle (GV) and MII stages revealed distinct stage-dependent pathways impacted by aging, with a decrease in mitochondrial-related transcripts from GV to MII oocytes, and a much greater reduction in MII oocytes with advanced age. …”
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Inflammatory factor CCL2 enhances the interaction between monocyte-macrophage cells and liver parenchymal cells to promote liver inflammation and fibrosis in biliary atresia by Xin Li, Shaowen Liu, Tengfei Li, Qianhui Yang, Yuqiang Chen, Yu Meng, Zhiru Wang, Yilin Zhao, Shujian Zhang, Liang Ge, Alimujiang Abudureyimu, Jianghua Zhan

“…Single-cell RNA sequencing (scRNA-seq), spatial transcriptomics (ST), and Mendelian randomization (MR) were integrated for analysis. …”
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A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data by Teresa Rubio, Maria Chernigovskaya, Susanna Marquez, Cristina Marti, Paula Izquierdo-Altarejos, Amparo Urios, Carmina Montoliu, Vicente Felipo, Ana Conesa, Victor Greiff, Sonia Tarazona

“…However, many non-targeted RNA-seq experiments also contain reads of TCR genes, which could be leveraged for TCR expression analysis while reducing sample requirements and costs. …”
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Functional analysis of lncRNAs in lipid metabolism of fat and lean line broiler embryonic livers by Huili Zhang, Xuanming Cao, Youdong Wang, Bohan Cheng, Li Leng, Peng Luan, Zhiping Cao, Yumao Li, Xue Bai

“…This study revealed that, compared to lean line broiler embryos, fat line broiler embryos showed upregulated gene expression related to de novo fatty acid synthesis, glycerol-3-phosphate synthesis, triglyceride synthesis, and the degradation of both fatty acids and cholesterol. Through transcriptome analysis and functional validation, lncRNA1926 and lncRNA3223 were identified as key regulators of lipid metabolism in broiler embryo livers. …”
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Graph-based pan-genome analysis reveals diversity of structural variations in native and commercial chicken by Yiming WANG, Zijia NI, Yinhua HUANG

“…The emergence of next-generation sequencing has enabled precise analysis of single nucleotide polymorphisms and insertions/deletions in chicken, while third-generation sequencing achieves the accurate structural variant identification. …”
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The bioactive sphingolipid playbook. A primer for the uninitiated as well as sphingolipidologists by Yusuf A. Hannun, Alfred H. Merrill, Jr., Chiara Luberto

“…Thus, it is not surprising that untargeted genetic/transcriptomic/pharmacologic/metabolomic screens have uncovered changes in sphingolipids and sphingolipid genes/proteins while studying physiological and pathological processes. …”
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