Comprehensive multi‐tissue epigenome atlas in sheep: A resource for complex traits, domestication, and breeding by Deyin Zhang, Jiangbo Cheng, Xiaolong Li, Kai Huang, Lvfeng Yuan, Yuan Zhao, Dan Xu, Yukun Zhang, Liming Zhao, Xiaobin Yang, Zongwu Ma, Quanzhong Xu, Chong Li, Xiaojuan Wang, Chen Zheng, Defu Tang, Fang Nian, Xiangpeng Yue, Wanhong Li, Huibin Tian, Xiuxiu Weng, Peng Hu, Yuanqing Feng, Peter Kalds, Zhihua Jiang, Yunxia Zhao, Xiaoxue Zhang, Fadi Li, Weimin Wang

“…Here, we generated 92 transcriptomic and epigenomic data sets from nine major tissues, along with whole‐genome data from 2357 individuals across 29 breeds worldwide, and 4006 phenotypic data related to tail fat weight. …”
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An increase in reactive oxygen species underlies neonatal cerebellum repair by Anna Pakula, Salsabiel El Nagar, N Sumru Bayin, Jens Bager Christensen, Daniel Stephen, Adam James Reid, Richard P Koche, Alexandra L Joyner

“…Here, we investigate how the microenvironment of the injured cerebellum changes upon injury and contributes to the regenerative potential of normally gliogenic-NEPs and their adaptive reprogramming. Single-cell transcriptomic and bulk chromatin accessibility analyses of the NEPs from injured neonatal cerebella compared to controls show a temporary increase in cellular processes involved in responding to reactive oxygen species (ROS), a known damage-associated molecular pattern. …”
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Chirality‐Induced Hydroxyapatite Manipulates Enantioselective Bone‐Implant Interactions Toward Ameliorative Osteoporotic Osseointegration by Liang Yang, Jinzhou Du, Shengyang Jin, Shuyi Yang, Zhaowei Chen, Shiyang Yu, Cunyi Fan, Chao Zhou, Hongjiang Ruan

“…Moreover, as analyzed by transcriptomic RNA‐seq, a new discovery of down‐regulated IL‐17 signaling pathway is considered predominately responsible for the desired immunomodulation ability of L‐CHA. …”
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Single-cell sequencing and machine learning reveal the role of dioxin-interacting genes in HCC prognosis and immune microenvironment by Senyan Wang, Qi Liu, Xiaoyan Sun, Minghui Hou, Wenjuan Wei, Hao Song, Jing Xu, Danyang Lu, Jing Fu, Xiaofang Zhao, Hongyang Wang

“…These findings underscore the pivotal role of dioxin accumulation in liver cancer progression and provide a foundation for personalized treatment strategies and improved prognostic assessment.…”
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Comprehensive analysis of plasma cell heterogeneity and immune interactions in multiple myeloma by Shuang Qu, Zhihai Zheng, Xiaoling Guo, Jiaqi Mei, Sicong Jiang, Biyun Chen

“…This study focused on the role of plasma cells in multiple myeloma (MM) and the associated potential mechanisms. Transcriptomic data of MM and various gene sets from several public databases were downloaded for subsequent analyses. …”
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Stage-specific gene pair ratios highlight genes and mechanisms related to presymptomatic and symptomatic Multiple Myeloma by Grigoris Georgiou, George Minadakis, Nestoras Karathanasis, Kyriaki Savva, Efi Athieniti, Marilena M. Bourdakou, George M. Spyrou

“…The identification and progression/behaviour of molecular markers across stages remains a scientific challenge. This work aims to provide a holistic approach in the understanding of the disease progression through a computational approach, capable of characterising and distinguishing disease stages. …”
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The Regulatory Role of EvfG Through Coordinated Control of Flagellar Biosynthesis and Energy Metabolism in Porcine Extraintestinal Pathogenic <i>Escherichia coli</i> (ExPEC) by Bingbing Zong, Peiyi Wang, Wei Liu, Aihua Wu, Yong Xiao, Shulin Fu, Yinsheng Qiu, Yanyan Zhang, Wentong Liu

“…To further explore the reasons why the deletion of <i>evfG</i> affects the motility of PCN033, transcriptomic and metabolomic analyses were conducted. …”
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Genetic variations at BBX24 and MYB110a loci regulated anthocyanin accumulation in pear bud sports by Yuhao Gao, Hongxu Li, Zhiwei Wang, Huabai Xue, Jianzhao Li, Wenjie Yu, Jiaxin Zhang, Junbei Ni, Yuanwen Teng, Songling Bai

“…This work enhances understanding of coloration in red pears and provides a novel genomic resource for further studies on ‘Hongzaosu’ pear.…”
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Characterization and Expression Analysis of PUB Gene Family Involved in Drought Stress Response in Trifoliate Orange (<i>Poncirus trifoliata</i>) by Bobo Song, Sanpeng Jin, Xuchen Gong, Yong Liu, Dechun Liu, Li Yang, Wei Hu, Liuqing Kuang, Jie Song

“…This study provides a foundation for understanding the functional roles of <i>PUB</i> genes in trifoliate orange and offers insights for improving stress tolerance in citrus breeding programs.…”
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Topologically associating domains of chromatin on single-cell Hi-C data: a survey of bioinformatic tools and applications in the light of artificial intelligence by Hongqiang Lyu, Yao Li, Xinran Chen, Yuan Liu, Erhu Liu, Xiaoliang Cheng

“…The computational analysis of TADs on single-cell Hi-C (scHi-C) data in the era of single-cell transcriptomics has received continuous attention since it may provide information beyond that on bulk Hi-C data. …”
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MYB regulation of GST/GT mediates red petal spot development in cotton by Sujun Zhang, Jie Chen, Tao Jiang, Haitao Wang, Xiao Cai, Cunjing Liu, Liyuan Tang, Xinghe Li, Yaqian Sun, Jianhong Zhang

“…Accordingly, comprehensively evaluating the influence of these candidates and their homologs on cotton coloration may provide a more in-depth understanding of cotton coloration, ultimately facilitating the breeding of more colorful cotton.…”
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FGFR4 p.Gly388Arg polymorphism in PBMCs of LAM patients: findings of a pilot study by Sinem Koc-Gunel, Sinem Koc-Gunel, Amy L. Ryan, Melanie Winter, Thomas O. F. Wagner, Thomas O. F. Wagner

“…Overall, this study provides a hypothesis-generating framework for future investigations into the genetic drivers of LAM beyond TSC2 mutations.…”
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Heterozygous deletion of exon 17 of the Kit gene impairs mouse spermatogenesis by attenuating MAPK-ERK signaling by Siyuan Lin, Min Yang, Weipeng Zhu, Changqi Yang, Yaosheng Chen, Peiqing Cong, Xiaohong Liu, Zuyong He

“…These findings verified the function of exon 17 in the Kit gene and provide a theoretical basis for improving the semen quality of dominant white pigs through correction of the splice mutation of KIT.…”
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Molecular, cellular, and developmental organization of the mouse vomeronasal organ at single cell resolution by Max Henry Hills, Limei Ma, Ai Fang, Thelma Chiremba, Seth Malloy, Allison R Scott, Anoja G Perera, C Ron Yu

“…We have generated single cell transcriptomic atlases of vomeronasal organs (VNO) from juvenile and adult mice. …”
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Identification and Application of a Novel Patulin Degrading Enzyme From Meyerozyma guilliermondii by Yu Zhang, Qianhua Zhao, Solairaj Dhanasekaran, Esa Abiso Godana, Yue Zhang, Xue Bai, Qiya Yang, Hongyin Zhang

“…Furthermore, site‐directed mutagenesis reveals the essential role of the catalytic triad (Ser174‐Tyr188‐Lys192) in MgSDR1 activity. This study provides an efficient methodology for screening PAT‐degrading enzymes and lays a theoretical foundation for the removal of mycotoxins in the food industry.…”
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The PP2A regulator IER5L supports prostate cancer progression by Jana R. Crespo, Natalia Martín-Martín, Saioa Garcia-Longarte, Jon Corres-Mendizabal, Onintza Carlevaris, Ianire Astobiza, Amaia Zabala-Letona, Marc Guiu, Mikel Azkargorta, Monika Gonzalez-Lopez, Nuria Macías-Cámara, Phuong Doan, Félix Elortza, Isabel Mendizabal, Jukka Westermarck, Roger R. Gomis, Amaia Ercilla, Arkaitz Carracedo

“…Mechanistically, we characterize the transcriptomic and proteomic landscapes of IER5L-silenced cells. …”
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SARS-CoV-2 pseudovirus dysregulates hematopoiesis and induces inflammaging of hematopoietic stem and progenitor cells by Dong-Hoon Chae, Hyun Sung Park, Kyoung-Myeon Kim, Aaron Yu, Jae Han Park, Mi-Kyung Oh, Soon Won Choi, Jaechul Ryu, Cynthia E. Dunbar, Hee Min Yoo, Kyung-Rok Yu

“…Treatment with nanographene oxide, an antiviral agent, partially mitigated the myeloid bias and inflammaging phenotype both in vitro and in vivo. These findings provide insights into the abnormal hematopoietic and immune effects of SARS-CoV-2 infection and highlight potential therapeutic interventions.…”
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Hypoxia-inducible factor-1α promotes tubulointerstitial fibrosis via the upregulation of Muc4 by Zhong-Tang Li, Xin-Hui Hu, Wei-Jie Ni, Zuo-Lin Li, Bi-Kun Huang, Yu Zhang, A-Feng Miao, Jing-Yuan Cao

“…Altogether, these results demonstrate that tubular HIF-1α promotes TIF by upregulating Muc4 transcription. Our findings provide novel insights into the molecular mechanism underlying HIF-1-mediated TIF.…”
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Pathways to chronic disease detection and prediction: Mapping the potential of machine learning to the pathophysiological processes while navigating ethical challenges by Ebenezer Afrifa‐Yamoah, Eric Adua, Emmanuel Peprah‐Yamoah, Enoch O. Anto, Victor Opoku‐Yamoah, Emmanuel Acheampong, Michael J. Macartney, Rashid Hashmi

“…The pathophysiology and management of chronic diseases have benefitted from emerging fields in molecular biology like genomics, transcriptomics, proteomics, glycomics, and lipidomics. …”
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Synergistic effects of ectoine and biostimulants combinations on tomato seedling growth and heat stress resilience by Yanyan Chen, Weimin Xu, Chuankun Han, Miao Zhang, Ying Chen, Yujia Ma, Xinjun Zhang, Huhu Liu, Wenna Zhang

“…The combined application of biostimulants demonstrated synergistic effects, enhancing multiple physiological pathways that contribute to plant heat stress adaptation. These findings provide valuable insights of the molecular mechanisms underlying biostimulant-induced growth promotion and stress resilience in tomato seedlings. …”
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