Thrombospondin-I is a critical modulator in non-alcoholic steatohepatitis (NASH). by Jessica Min-DeBartolo, Franklin Schlerman, Sandeep Akare, Ju Wang, James McMahon, Yutian Zhan, Jameel Syed, Wen He, Baohong Zhang, Robert V Martinez

“…Comparison of transcriptomic profiles based on genotype suggested that peroxisome proliferator activated receptor alpha (PPARα) pathway and amino acid metabolism pathways are differentially expressed in TSP-1 null mice. …”
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Differential Cell Death Pathways Induced by Oxidative Stress in Multi-Organs of Amur Grayling (<i>Thymallus grubii</i>) Under Gradient Ammonia Stress by Cunhua Zhai, Yutao Li, Ruoyu Wang, Ying Zhang, Bo Ma

“…In addition, it was also demonstrated that ammonia nitrogen stress affected the composition of intestinal microbiota taxa. This study provides insights into the potential risks and hazards of ammonia stress on cold fish in natural waters and provides a reference for the environment control of the water quality in aquaculture.…”
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A comparative analysis of carcass traits and meat quality between Tibetan sheep and their three-way crossbred sheep by Yu Qiao, Deming Yang, Jishun Tang, Wei Zhang, Sheng Chen, Wenqiao Hui

“…These findings provide practical strategies for enhancing Tibetan lamb meat quality through crossbreeding optimization in high-altitude regions.…”
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Phosphatidylcholine Ameliorates Palmitic Acid‐Induced Lipotoxicity by Facilitating Endoplasmic Reticulum and Mitochondria Contacts in Intervertebral Disc Degeneration by Shuangshuang Tu, Yijun Dong, Chuanfu Li, Mingxin Jiang, Liqun Duan, Wenzhi Zhang, Xi Chen

“…These findings advance our understanding of IDD pathogenesis and provide a novel metabolic target for therapeutic development.…”
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Crosstalk with infant-derived Th17 cells, as well as exposure to IL-22 promotes maturation of intestinal epithelial cells in an enteroid model by Zohreh Sharafian, Zohreh Sharafian, Paula T. Littlejohn, Paula T. Littlejohn, Paula T. Littlejohn, Christina Michalski, Christina Michalski, James A. Sousa, James A. Sousa, Janelle Cheung, Mariana Hill, Mariana Hill, Hannah Piper, Kevan Jacobson, Kevan Jacobson, Pascal M. Lavoie, Pascal M. Lavoie, Joannie M. Allaire, Bruce A. Vallance, Bruce A. Vallance

“…We assessed morphological changes and conducted transcriptomics profiling via RNAseq.ResultsExposing enteroids to neonatal Th17-cells-derived conditioned media led to enhanced growth, maturation, and differentiation as compared to control media. …”
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Biomarker analysis from CheckMate 214: nivolumab plus ipilimumab versus sunitinib in renal cell carcinoma by Jin Yao, Thomas Powles, David F McDermott, Toni K Choueiri, Petra Ross-MacDonald, Simon Papillon-Cavanagh, Robert J Motzer, M Brent McHenry, Megan Wind-Rotolo, Ron Ammar, Yann-Alexandre Vano, Saurabh Gupta, Celine Han, Shruti S Saggi

“…Further validation may help to provide biomarker-driven precision treatment for patients with RCC.…”
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A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping by Pengfei Dong, Liting Song, Jaroslav Bendl, Ruth Misir, Zhiping Shao, Jonathan Edelstien, David A. Davis, Vahram Haroutunian, William K. Scott, Susanne Acker, Nathan Lawless, Gabriel E. Hoffman, John F. Fullard, Panos Roussos

“…Abstract Brain region- and cell-specific transcriptomic and epigenomic features are associated with heritability for neuropsychiatric traits, but a systematic view, considering cortical and subcortical regions, is lacking. …”
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In vitro and in vivo drug screens of tumor cells identify novel therapies for high‐risk child cancer by Loretta M S Lau, Chelsea Mayoh, Jinhan Xie, Paulette Barahona, Karen L MacKenzie, Marie Wong, Alvin Kamili, Maria Tsoli, Tim W Failes, Amit Kumar, Emily V A Mould, Andrew Gifford, Shu‐Oi Chow, Mark Pinese, Jamie I Fletcher, Greg M Arndt, Dong‐Anh Khuong‐Quang, Carol Wadham, Daniel Batey, Georgina Eden, Peter Trebilcock, Swapna Joshi, Stephanie Alfred, Anjana Gopalakrishnan, Aaminah Khan, Dylan Grebert Wade, Patrick A Strong, Elodie Manouvrier, Lisa T Morgan, Miriam Span, Jin Yi Lim, Roxanne Cadiz, Caitlin Ung, David M Thomas, Katherine M Tucker, Meera Warby, Geoffrey B McCowage, Luciano Dalla‐Pozza, Jennifer A Byrne, Federica Saletta, Andrew Fellowes, Stephen B Fox, Murray D Norris, Vanessa Tyrrell, Toby N Trahair, Richard B Lock, Mark J Cowley, Paul G Ekert, Michelle Haber, David S Ziegler, Glenn M Marshall

“…Screens also provided orthogonal proof of drug efficacy suggested by molecular analyses and negative results for some molecular findings. …”
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Leucocalocybe mongolica Fungus Enhances Rice Growth by Reshaping Root Metabolism, and Hormone-Associated Pathways by Mingzheng Duan, Ming Tao, Fuhan Wei, Honggao Liu, Sirui Han, Jieming Feng, Qiuyue Ran, Xiande Duan, Zhifang He, Shunqiang Yang, Muhammad Junaid Rao

“…These findings demonstrate the potential of LY9 as a sustainable soil amendment for improving rice productivity and provide valuable insights into the molecular basis of plant-fungal interactions in agricultural systems.…”
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Luminal epithelial cells integrate variable responses to aging into stereotypical changes that underlie breast cancer susceptibility by Rosalyn W Sayaman, Masaru Miyano, Eric G Carlson, Parijat Senapati, Arrianna Zirbes, Sundus F Shalabi, Michael E Todhunter, Victoria E Seewaldt, Susan L Neuhausen, Martha R Stampfer, Dustin E Schones, Mark A LaBarge

“…We generated and analyzed transcriptomes from primary luminal epithelial and myoepithelial cells from younger &lt;30 (y)ears old and older &gt;55 y women. …”
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Maternal plasma extracellular vesicles tsRNA as potential biomarkers for assessing preterm labor risk by Xinrui Sun, Ying Feng, Liang Xie, Yilun Wu, Jia Mao, Yi Zhang, Linyu Zhang, Xin Yuan, Jiangping Ni, Xue Xiao, Hanmin Liu, Li Dai, Fang Ma

“…Functional assays were used to assess the impact of tsRNA1 (tRNA-Gly-GCC-5p-tRF-921) on extravillous trophoblast (EVT) function, including apoptosis, migration, invasion, and endothelial-like tube formation in HTR8/SVneo cells. Transcriptomic sequencing was conducted to identify tsRNA1-mediated pathways, and DNA methylation patterns were predicted based on the transcriptomic data. …”
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Interactions with native microbial keystone taxa enhance the biocontrol efficiency of Streptomyces by Tianyu Sun, Hongwei Liu, Ningqi Wang, Mingcong Huang, Samiran Banerjee, Alexandre Jousset, Yangchun Xu, Qirong Shen, Shimei Wang, Xiaofang Wang, Zhong Wei

“…These findings highlight the significance of intricate microbial interactions within the microbiome in regulating plant diseases and provide a theoretical foundation for devising efficacious biocontrol strategies in sustainable agriculture. …”
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OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data. by Raga Krishnakumar, Anne M Ruffing

“…A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. …”
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Current state and prospects of protoplast technology and potato somatic hybridization (review) by O. B. Polivanova, A. S. Egorova, A. B. Sivolapova, S. V. Goryunova

“…In this review, the prospects for the use of this technology in modern potato breeding are considered. Genomic, transcriptomic, and proteomic studies provide further insight into the fundamental processes underlying the somatic hybrids formation, such as cell wall formation, chromosomal rearrangements in fusion products, regeneration, and also make a significant contribution to understanding the processes of genome stabilization. …”
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Trajectory inference from single-cell genomics data with a process time model. by Meichen Fang, Gennady Gorin, Lior Pachter

“…Single-cell transcriptomics experiments provide gene expression snapshots of heterogeneous cell populations across cell states. …”
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Metabolomics analysis and mRNA/miRNA profiling reveal potential cardiac regulatory mechanisms in Yili racehorses under different training regimens. by Tongliang Wang, Jun Meng, Xuan Peng, Jinlong Huang, Yunjiang Huang, Xinxin Yuan, Xueyan Li, Xixi Yang, Xiaokang Chang, Yaqi Zeng, Xinkui Yao

“…This study combined echocardiographic, transcriptomic, and metabolomic analyses to explore these relationships in high-level, average, and untrained Yili horses. …”
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Comprehensive analysis of poly(A) tails in mouse testes and ovaries using Nanopore Direct RNA Sequencing by Agnieszka Czarnocka-Cieciura, Michał Brouze, Natalia Gumińska, Seweryn Mroczek, Olga Gewartowska, Paweł S. Krawczyk, Andrzej Dziembowski

“…Moreover, gametogenesis, especially oogenesis, represents a unique instance of the complexity of poly(A) tails metabolism, with oocyte-specific waves of cytoplasmic polyadenylation. In this context, we provide a comprehensive transcriptomic dataset focusing on mRNA poly(A) tail composition and dynamics in murine testes and ovaries. …”
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Advances in modeling cellular state dynamics: integrating omics data and predictive techniques by Sungwon Jung

“…We highlight how these approaches integrated with various omics data such as transcriptomics, and single-cell RNA sequencing could be used to capture and predict cellular behavior and transitions. …”
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Olfactory sensory neurons transiently express multiple olfactory receptors during development by Longzhi Tan, Qian Li, X Sunney Xie

“…Here, we directly tested this rule by single‐cell transcriptomic sequencing of 178 cells from the main olfactory epithelium of adult and newborn mice. …”
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Post-genomic approaches to understanding interactions between fungi and their environment by R.P. de Vries, I. Benoit, G. Doehlemann, T. Kobayashi, J.K. Magnuson, E.A. Panisk, S.E. Baker, M.-H. Lebrun

“…Based on a Special Interest Group session held during IMC9, this paper provides examples of the recent advances in using (post- )genomic approaches to better understand fungal interactions with their environments.…”
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