Disulfidptosis in pediatric AML: a multi-omics approach to risk stratification and potential therapeutic strategy by Yichen Lei, Jiasi Zhang, Yaqin Wang, Aiguo Liu

“…Using ssGSEA, we quantified PDC patterns across bulk and single-cell transcriptomes, revealing distinct molecular subtypes via unsupervised clustering. …”
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Potential Biomarkers for Predicting the Risk of Developing Into Long COVID After COVID‐19 Infection by Zhiyong Hou, Yu Ming, Jun Liu, Zhong Wang

“…ABSTRACT Background Long COVID, a heterogeneous condition characterized by a range of physical and neuropsychiatric presentations, can be presented with a proportion of COVID‐19‐infected individuals. Methods Transcriptomic data sets of those within gene expression profiles of COVID‐19, long COVID, and healthy controls were retrieved from the GEO database. …”
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MED19 alters AR occupancy and gene expression in prostate cancer cells, driving MAOA expression and growth under low androgen. by Hannah Weber, Rachel Ruoff, Michael J Garabedian

“…To delineate the mechanism, we determined the MED19 and AR transcriptomes and cistromes in control and MED19-overexpressing LNCaP cells. …”
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Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing. by Jeong-Hyeon Choi, Yajun Li, Juyuan Guo, Lirong Pei, Tibor A Rauch, Robin S Kramer, Simone L Macmil, Graham B Wiley, Lynda B Bennett, Jennifer L Schnabel, Kristen H Taylor, Sun Kim, Dong Xu, Arun Sreekumar, Gerd P Pfeifer, Bruce A Roe, Charles W Caldwell, Kapil N Bhalla, Huidong Shi

“…<h4>Conclusions/significance</h4>This study is the first to provide a large scale and comprehensive analysis of the DNA methylation sequence composition and distribution in the FL epigenome. …”
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Identifying genes associated with Sorafenib resistance in hepatocellular carcinoma to develop risk model by Kuan He, Hongyan Hui, Fang Zhou, Kai Liu, Xi Zhao, Jun Liu

“…Conclusion This study provides a comprehensive framework for understanding sorafenib resistance in HCC, alongside a validated prognostic model that holds potential for clinical application.…”
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Integrative machine learning and bioinformatics analysis to identify cellular senescence-related genes and potential therapeutic targets in ulcerative colitis and colorectal cancer by Tianle Xue, Yunpeng Chen, Xiaomeng Li, Zhixiang Zhou, Qiyang Chen

“…Furthermore, drug enrichment and molecular docking studies identified several promising therapeutic candidates targeting these senescence‐related genes.ConclusionThis study provides novel insights into the molecular interplay between cellular senescence and the UC-to-CRC transition. …”
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Yoda1 Inhibits TGFβ-Induced Cardiac Fibroblast Activation via a BRD4-Dependent Pathway by Perwez Alam, Sara M. Stiens, Hunter J. Bowles, Hieu Bui, Douglas K. Bowles

“…Intriguingly, Yoda1 was found to inhibit TGFβ-induced fibroblast activation through a Piezo1-independent mechanism. Transcriptomic analysis revealed that Yoda1 modulates fibroblast activation by altering gene expression pathways associated with fibrotic processes. …”
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A Maternal Gene Regulator CPEB2 Is Involved in Mating-Induced Egg Maturation in the <i>Cnaphalocrocis medinalis</i> by Yi Duan, Yueran Xiao, Guo Cai, Kepeng Wang, Chenfan Zhao, Pengcheng Liu

“…Liposome-mediated RNA interference targeting <i>CmCPEB2</i> resulted in a 52% reduction in transcript abundance, leading to significant defects in ovarian maturation, diminished vitellogenin deposition, and a 36.7% decline in fecundity. The transcriptomic analysis of RNAi-treated ovaries identified 512 differentially expressed genes, with downregulated genes enriched in chorion formation and epithelial cell development. …”
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Genome-wide identification, expression analysis, and stress response analysis of the RdbZIP gene family in Rhododendron delavayi by Mengxian Cai, Chunxing Sun, Junxing Yu, Jing Ou, Bin Zhu

“…Conclusion This study provides the first comprehensive characterization of the bZIP transcription factor family in Rhododendron delavayi, laying a foundational framework for functional studies of individual RdbZIP genes. …”
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Prediction of new candidate proteins and analysis of sub-modules and protein hubs associated with seed development in rice (Oryza sativa) using an ensemble network-based systems bi... by M. R. P. De Silva, J. W. J. K. Weeraman, S. Piyatissa, P. C. Fernando

“…Conclusions These findings, including the identified hub proteins and sub-modules, provide a better understanding of the PPI interaction landscape governing seed development in rice. …”
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Using machine learning to discover DNA metabolism biomarkers that direct prostate cancer treatment by Ali Shakeri Abroudi, Melika Djamali, Hossein Azizi

“…We performed an integrative analysis using transcriptomic data from the TCGA cohort and external validation datasets. …”
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Trem2 regulates microglial migratory responses via type I interferon signaling during photoreceptor degeneration by Jincan He, Wenchuan Zhou, Jing Li

“…Microglia were purified with CD11b MicroBeads. Transcriptomic profiles of the whole retina were generated and analyzed. …”
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Seed priming and abiotic stress tolerance in carrot: Unraveling the mechanisms of improved germination. by Marcin Nowicki, Marzena Nowakowska, Katarzyna Nowak, Wojciech Szczechura, Piotr Kaminski

“…Future research integrating omics approaches (e.g., transcriptomics, proteomics, metabolomics) will provide deeper insights into the molecular mechanisms that regulate stress tolerance, to aid in the development of more resilient carrot varieties suitable for cultivation under adverse environmental conditions.…”
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Drought-induced molecular changes in crown of various barley phytohormone mutants by Anetta Kuczyńska, Martyna Michałek, Piotr Ogrodowicz, Michał Kempa, Natalia Witaszak, Michał Dziurka, Damian Gruszka, Agata Daszkowska-Golec, Iwona Szarejko, Paweł Krajewski, Krzysztof Mikołajczak

“…Overall, the present study provides novel insights into the molecular drought-induced responses that occur in barley crowns.…”
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VPS26A as a Prognostic Biomarker and Therapeutic Target in Liver Hepatocellular Carcinoma: Insights from Comprehensive Bioinformatics Analysis by Hye-Ran Kim, Jongwan Kim

“…Functional enrichment and co-expression analyses revealed that VPS26A serves as a central regulator of the LIHC transcriptomic landscape, with positively correlated gene sets linked to poor prognosis. …”
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Comprehensive analysis of the microbial consortium in the culture of flagellate Monocercomonoides exilis by Alejandro Jiménez-González, Sebastian Cristian Treitli, Priscila Peña-Diaz, Anna Janovská, Vladimír Beneš, Petr Žáček, Vladimír Hampl

“…In this study, we used metagenomic sequencing, transcriptomics, and metabolomics to characterize the microbial consortium that supports the growth of M. exilis. …”
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Chromosome number variation and phylogenetic divergence of East Asian Cirsium sect. Onotrophe subsect. Nipponocirsium (Compositae), with a new species from Taiwan by Chih-Yi Chang, Pei-Chun Liao, Hsy-Yu Tzeng, Junko Kusumi, Zhi-Hui Su, Yen-Hsueh Tseng

“…Nipponocirsium and underscore the importance of integrating transcriptomic data in phylogenetic studies. This study provides a comprehensive framework for further investigations into the genetic diversity and adaptive mechanisms of this ecologically vital group.…”
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ZC3H12D gene expression exhibits dual effects on the development and progression of lung adenocarcinoma by Yuansi Zheng, Yuhuan Zhang, Jieyi Li, Ying Su

“…Multi-omics analyses integrated ZC3H12D transcriptomic (511 tumors vs 59 normals), proteomic (74 tumors vs 69 normals), and single-cell RNA-seq data (15 tumors vs 11 normals). …”
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Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia by Maxat Kulmanov, Saeideh Ashouri, Yang Liu, Marwa Abdelhakim, Ebtehal Alsolme, Masao Nagasaki, Yasuyuki Ohkawa, Yutaka Suzuki, Rund Tawfiq, Katsushi Tokunaga, Toshiaki Katayama, Malak S. Abedalthagafi, Robert Hoehndorf, Yosuke Kawai

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Immune composition of the mononuclear cell fraction of human umbilical cord blood by Karen Kikuta, Esmond Lee, Esmond Lee, Esmond Lee, Talia Menezes, Hannah Fung, Alvaro Amorin, Aditi Agrawal, Theodore L. Roth, Matthew Porteus, Matthew Porteus, Matthew Porteus

“…Overall, our findings provide a robust characterization of MNC UCB immune subsets and insights into how immune function develops from birth to adulthood.…”
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