New insights into markers for distinguishing neuroendocrine prostate cancer: evidence from single-cell analysis by Hailang Luo, Hailang Luo, Hailang Luo, Boyang Li, Boyang Li, Boyang Li, Meng Zhang, Meng Zhang, Meng Zhang, Hongqun Wang, Zongyao Hao, Zongyao Hao, Zongyao Hao, Qintao Ge, Qintao Ge, Chaozhao Liang, Chaozhao Liang, Chaozhao Liang

“…The identification of reliable biomarkers for NEPC is essential for early detection and intervention.MethodsWe combined single-cell and bulk transcriptome analysis to identify novel markers of NEPC. …”
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Characterization of Spectrin Family Genes and Their Evolutionary Roles in Domestication and Breeding of the Silkworm <i>Bombyx mori</i> by Kunpeng Lu, Chengyu Zhan, Jianghong Shen, Chao Zhi, Jun Deng, Kerui Lai, Minjin Han, Hai Hu, Xiaoling Tong, Fangyin Dai

“…This study elucidates the characterization and functional relevance of silkworm spectrin genes, providing insights into their roles in domestication and breeding.…”
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Reinstating plasticity and memory in a tauopathy mouse model with an acetyltransferase activator by Snehajyoti Chatterjee, Raphaelle Cassel, Anne Schneider‐Anthony, Karine Merienne, Brigitte Cosquer, Laura Tzeplaeff, Sarmistha Halder Sinha, Manoj Kumar, Piyush Chaturbedy, Muthusamy Eswaramoorthy, Stéphanie Le Gras, Céline Keime, Olivier Bousiges, Patrick Dutar, Petnoi Petsophonsakul, Claire Rampon, Jean‐Christophe Cassel, Luc Buée, David Blum, Tapas K Kundu, Anne‐Laurence Boutillier

“…At the transcriptional level, CSP‐TTK21 re‐established half of the hippocampal transcriptome in learning mice, likely through increased expression of neuronal activity genes and memory enhancers. …”
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Multi-omics investigation reveals unique markers in Klebsiella pneumoniae compared to closely related species by Lena-Sophie Swiatek, Kristin Surmann, Elias Eger, Justus U. Müller, Manuela Gesell Salazar, Stefan E. Heiden, Guido Werner, Nils-Olaf Hübner, Jürgen A. Bohnert, Karsten Becker, Uwe Völker, Michael Schwabe, Katharina Schaufler, Katharina Schaufler

“…We identified markers enriched in KP STs, providing a foundation for future investigations including their relevance for diagnostics.…”
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Genome-wide analysis of AP2/ERF transcription Factors in Cymbidium sinense reveals their impact on orchid diversity by Yong-Lu Wei, Jian-Peng Jin, Jian-Peng Jin, Jie Li, Qi Xie, Chu-Qiao Lu, Jie Gao, Gen-Fa Zhu, Feng-Xi Yang

“…GO enrichment and KEGG pathway analysis further elucidated these patterns. To validate transcriptome-based predictions, qRT-PCR analysis was performed on ten key CsAP2/ERF genes, showing high consistency with RNA-seq data. …”
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Identification and validation of efferocytosis-related biomarkers for the diagnosis of metabolic dysfunction-associated steatohepatitis based on bioinformatics analysis and machine... by Chenghui Cao, Chenghui Cao, Wenwu Liu, Xin Guo, Shuwei Weng, Yang Chen, Yonghong Luo, Shuai Wang, Botao Zhu, Botao Zhu, Yuxuan Liu, Yuxuan Liu, Daoquan Peng

“…Additionally, we conducted immune infiltration and single-cell transcriptome analyses in both MASH and control samples, providing insights into the immune cell landscape and cellular heterogeneity in these conditions.ResultsThis research pinpointed 39 genes exhibiting a robust correlation with efferocytosis in MASH. …”
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Xingxiao Pill Suppressed the Progression of Non-Small Cell Lung Cancer by Targeting SREBP1/FASN&amp;ndash;Induced Fatty Acid Biosynthesis via PI3K/AKT/mTOR Signaling Pathway by Zhou X, Hu X, Zhang Z, Lin S, Lin X, Zhou T, Bai Y, Hu K

“…Bioinformatics analysis and transcriptome sequencing identified XXP’s potential targets and mechanisms. …”
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Whole RNA-Seq Analysis Reveals Longitudinal Proteostasis Network Responses to Photoreceptor Outer Segment Trafficking and Degradation in RPE Cells by Rebecca D. Miller, Isaac Mondon, Charles Ellis, Anna-Marie Muir, Stephanie Turner, Eloise Keeling, Htoo A. Wai, David S. Chatelet, David A. Johnson, David A. Tumbarello, Andrew J. Lotery, Diana Baralle, J. Arjuna Ratnayaka

“…These findings show detailed evidence of transcriptome-level responses to cargo trafficking and processing in RPE cells.…”
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Multi-omics analyses of the heterogenous immune microenvironment in triple-negative breast cancer implicate UQCRFS1 potentiates tumor progression by Yuhui Tang, Aiqi Xu, Zhongbiao Xu, Jindong Xie, Wei Huang, Liulu Zhang, Yitian Chen, Lu Yang, Shasha Du, Kun Wang

“…The public spatial transcriptome, proteome data and qRT-PCR, western blotting experiments were exploited to corroborate UQCRFS1 expression in RNA and protein levels. …”
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Omics technologies accelerating research progress in yams by Yahui Chen, Hamza Tariq, Danyu Shen, Jinding Liu, Daolong Dou

“…The development of omics technologies provides an effective means for mining functional genes and exploring related molecular mechanisms in yams. …”
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Title not available by Jessica A. Zapata-García

“…Conclusion: This study provides novel information leading to the conclusion that the LSC profiles analyzed in this work exhibit divergent transcriptomic regulation that may benefit chemoresistant capacity in the context of myeloid leukemia. …”
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Diagnostic potential of genomic blood biomarkers of pulmonary fibrosis in a prospective cohort. by Daniel He, Casey P Shannon, Jeremy A Hirota, Kjetil Ask, Christopher J Ryerson, Scott J Tebbutt

“…Taken together, this pilot study provides support for the use of the peripheral transcriptome in identifying diagnostic biomarkers of ILD with biological relevance.…”
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Microtubule mechanotransduction refines cytomegalovirus interactions with and remodeling of host chromatin by Celeste D. Rosencrance, Derek Walsh

“…Abstract Human cytomegalovirus extensively alters nuclear organization and the cellular transcriptome, yet understanding of these genome-wide events remains relatively limited. …”
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HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data. by Evan Gorstein, Rosa Aghdam, Claudia Solís-Lemus

“…Here, we empirically study the behavior of this algorithm on simulated and real examples of three types of data that are common in modern biology: transcriptome, genome-wide association, and microbiome data. …”
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A secreted proteomic footprint for stem cell pluripotency. by Philip A Lewis, Edina Silajdžić, Helen Smith, Nicola Bates, Christopher A Smith, Fabrizio E Mancini, David Knight, Chris Denning, Daniel R Brison, Susan J Kimber

“…We identified a distinct proteomic footprint associated with early loss of pluripotency in both hPSC lines, and a strong correlation with changes in the transcriptome. We demonstrate that multiplexing of four E8- against four E6- enriched secretome biomarkers provides a robust, diagnostic metric for the pluripotent state. …”
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High‐throughput sequencing for biology and medicine by Wendy Weijia Soon, Manoj Hariharan, Michael P Snyder

“…In this review, we discuss these innovative new approaches—including ever finer analyses of transcriptome dynamics, genome structure and genomic variation—and provide an overview of the new insights into complex biological systems catalyzed by these technologies. …”
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Genome-wide identification and expression of the HB gene family during overwintering in Korla pear (Pyrus sinkiangensis) by LIU Xiaoyan, WANG Lijuan, YANG Shenghui, LUO Guanghong, ZHU Jianbo

“…This study aims to elucidate the expression patterns and regulatory mechanisms of HB gene family members in Pyrus sinkiangensis during the overwintering process, providing a theoretical foundation for further exploration of the biological functions of the HB gene family in this species. …”
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Identification of potential key targets and mechanisms underlying cleft palate induced by tobacco smoke exposure through multi-omics integrated Mendelian randomization analysis by Yuxin Lin, Xiaoping Zhong, Zhengyuan Chi, Hui Li, Rui Han, Hao Li, Shukai Zheng, Shijie Tang, Jiasheng Chen

“…Although the mechanisms underlying TS-induced CP remain incompletely understood, this study provides novel insights by integrating multi-omics with Mendelian Randomization (MR) analyses. …”
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Effects of sun shading on anthocyanin components and the expression of genes related to anthocyanin synthesis in Marselan grape by FU Dongyan, WANG Lei, ZHANG Longsheng

“…During the complete veraison stage and shading during the harvesting stage, the expression levels of PAL, CHS3, F3’H, F3’5’H, UFGT, GST4 and MYB90 genes were upregulated compared to other treatments during the harvesting stage. qRT-PCR analysis revealed that among the 15 screened genes, the expression levels of CHI, F3H, F3’5’H, F3’H, DFR, LDOX, UFGT and OMT showed inconsistent trends with transcriptome sequencing in each treatment, while the changes in other genes were consistent with transcriptome sequencing results. …”
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Characterization of Superoxide Dismutase (SOD) Gene Family and Their Responses to Salinity Stress and Fruit Development in Octoploid Strawberry by Yunting Zhang, Yan Chen, Weiliang Gao, Su Tian, Bangyu Lin, Xianjie Gu, Yuanxiu Lin, Mengyao Li, Yan Wang, Wen He, Yong Zhang, Qing Chen, Ya Luo, Xiaorong Wang, Haoru Tang

“…This study provides a basis for further exploration of the function of the <i>FaSOD</i> gene family in strawberry and provides candidate <i>FaSOD</i> genes for enhancing salinity tolerance and regulating fruit development and ripening.…”
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