Distinctive chromosomal, mutational and transcriptional profiling in colon versus rectal cancers by Maria Teresa De Angelis, Antonia Rizzuto, Angela Amaddeo, Carlo Sagnelli, Niccolò Vono, Michela Reda, Valentina Lise, Luca Parrillo, Carmela De Marco, Donatella Malanga, Gianluca Santamaria, Giuseppe Viglietto

“…However, the most substantial divergence was observed in transcriptomic profiling, with 56% and 33% of DEGs (in CC and RC, respectively) that were tumor-type specific. …”
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Characterization of drug‐induced transcriptional modules: towards drug repositioning and functional understanding by Murat Iskar, Georg Zeller, Peter Blattmann, Monica Campillos, Michael Kuhn, Katarzyna H Kaminska, Heiko Runz, Anne‐Claude Gavin, Rainer Pepperkok, Vera van Noort, Peer Bork

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Multi-omics analysis links NFKB1 activation to poor immunosuppressive therapy response in acquired aplastic anemia by Nianbin Li, Ting Wang, Boyi Wang, Rong Fu

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Novel machine‐learning bioinformatics reveal distinct metabolic alterations for enhanced colorectal cancer diagnosis and monitoring by Rui Xu, Hyein Jung, Fouad Choueiry, Shiqi Zhang, Rachel Pearlman, Heather Hampel, Ning Jin, Jieli Li, Jiangjiang Zhu

“…Meanwhile, complementary transcriptomic data were also analyzed and integrated to further understand CRC metabolic dysregulations. …”
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Estradiol Reverses Ovariectomy-Induced Disruption of Hypothalamic Gene Expression and Behavior via Modulation of Gonadotropin Releasing Hormone and Calcium Signaling Pathways by Asim Muhammad, Mubashir Muhammad, Xiaohuan Chao, Chunlei Zhang, Jiahao Chen, Huan Yang, Shuhan Liu, Yuan Ding, Ziming Wang, Hongwei Bi, Wen Guo, Junhong Fan, Bo Zhou

“…OVX-induced neuroendocrine disruptions were partially reversed by E2 treatment, as evidenced by transcriptomic and behavioral outcomes. Pearson correlation analysis further linked gene expression patterns with phenotypic traits, providing insights into estrogen’s regulatory mechanisms in the hypothalamus. …”
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Multi‐omics profiling identifies TNFRSF18 as a novel marker of exhausted CD8⁺ T cells and reveals tumour‐immune dynamics in colorectal cancer by Tengfei Jia, Yingxi Guo, Xin meng Cheng, Zeyang Zhou, Xiaojiang Xu, Hebin Liu, Xiaodong Yang

“…Methods Tumour and adjacent tissues (20 samples total) from 6 CRC patients spanning diverse TNM stages were analyzed using integrated single‐cell transcriptomic profiling (scRNA‐seq), single‐cell T cell receptor/B cell receptor sequencing (scVDJ‐seq), and spatial transcriptomics. …”
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Antifungal Volatile Organic Compounds from <i>Talaromyces purpureogenus</i> CEF642^N: Insights from One Strain Many Compounds (OSMAC) Strategy for Controlling <i>Verticil... by Peng Li, Yalin Zhang, Hongjie Feng, Jinglong Zhou, Lihong Zhao, Heqin Zhu, Feng Wei, Zili Feng

“…These findings provide a foundation for future research aimed at identifying key genes involved in the eight-carbon volatile biosynthetic pathway.…”
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A genome-wide association study identifies a novel East Asian–specific locus for dementia with Lewy bodies in Japanese subjects by Risa Mitsumori, Yuya Asanomi, Takashi Morizono, Daichi Shigemizu, Shumpei Niida, Kouichi Ozaki

“…Conclusions This is the first GWAS for DLB in East Asians, and our findings provide new biological and clinical insights into the pathogenesis of DLB.…”
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Optimizing the Bioprocesses of Bacteriocin Production in <i>Lacticaseibacillus paracasei</i> HD1.7 by the “Acetate Switch”: Novel Insights into the Labor Division Between Energy Me... by Weige Yao, Rui Sun, Wen Zhang, Jie Kang, Zhenchao Wu, Liangyang Mao, Ying Yang, Shuo Li, Gang Song, Jingping Ge, Wenxiang Ping

“…Before and after the “acetate switch”, some metabolic pathways were significantly altered according to the transcriptomic analysis by HD1.7 and HD1.7-Δ<i>pta</i>. …”
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Endothelial Cpt1a Inhibits Neonatal Hyperoxia‐Induced Pulmonary Vascular Remodeling by Repressing Endothelial‐Mesenchymal Transition by Xiaoyun Li, Katy Hegarty, Fanjie Lin, Jason L. Chang, Amro Abdalla, Karthik Dhanabalan, Sergey O. Solomevich, Wenliang Song, Karim Roder, Chenrui Yao, Wenju Lu, Peter Carmeliet, Gaurav Choudhary, Phyllis A. Dennery, Hongwei Yao

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Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data by Marco Stock, Corinna Losert, Matteo Zambon, Niclas Popp, Gabriele Lubatti, Eva Hörmanseder, Matthias Heinig, Antonio Scialdone

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Transcriptional Responses of In Vitro Blood–Brain Barrier Models to Shear Stress by Koji L. Foreman, Benjamin D. Gastfriend, Moriah E. Katt, Sean P. Palecek, Eric V. Shusta

“…We utilized RNA sequencing to analyze the transcriptome of primary cultured rat brain microvascular endothelial cells (BMECs), as well as three human induced pluripotent stem cell-derived models. …”
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Ocean acidification induces changes in circadian alternative splicing profiles in a coral reef fish by Sneha Suresh, Michael Jarrold, Timothy Ravasi, Philip L. Munday, Celia Schunter

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Single cell atlas of canine natural killer cells identifies distinct circulating and tissue resident gene profiles by Aryana M. Razmara, Marshall Lammers, Sean J. Judge, William J. Murphy, Cameron E. Gaskill, William T.N. Culp, Alicia A. Gingrich, Zachary S. Morris, Robert B. Rebhun, C. Titus Brown, David M. Vail, Michael S. Kent, Robert J. Canter

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Pathogenicity and host-interacting mechanisms of enterogenic Enterobacter cancerogenus in silkworm by Meng Luo, Linhui Lai, Zailin Wu, Zailin Wu, Zailin Wu, Xiaoli Ren, Xiaoli Ren, Xiaoli Ren, Jiacheng Zhao, Jiacheng Zhao, Jiacheng Zhao, Hongmei Liu, Hongmei Liu, Hongmei Liu, Yaohang Long, Yaohang Long, Yaohang Long

“…ECL7 also stimulated the expression of genes related to the Toll and IMD immune signaling pathways, resulting in the upregulation of antimicrobial peptide–related differentially expressed genes (DEGs). Furthermore, transcriptomic analysis revealed an upregulation of DEGs associated with oxidative stress in response to ECL7 infection.DiscussionThis study provides valuable insights into the molecular mechanisms underlying the interaction between E. cancerogenus and silkworms. …”
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Resiquimod induces a mixed Th1 and Th2 response via STAT1 and STAT3 signalling in chickens by Deepthi Kappala, Saravanan Ramakrishnan, Patel Nikunjkumar Prakashbhai, Abinaya Kaliappan, Prasad Thomas, Jörg Linde, Mithilesh Singh, Sohini Dey, Madhan Mohan Chellappa

“…These insights provide a foundation for optimizing R-848 as an immunomodulatory agent in avian species.…”
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The role of JPT1 in hepatocellular carcinoma: tumor progression, microtubule dynamics regulation, and potential mechanisms within the immune microenvironment by Yipin Lu, Peng Xu, Sha Li, Jie Yao

“…Differentially expressed gene (DEG) analysis, functional enrichment analysis (GSEA and KEGG), and spatial transcriptomics were utilized to explore the biological functions and mechanisms of JPT1 in tumor biology. …”
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Omics data integration analysis identified new biological insights into chronic antibody-mediated rejection (CAMR) by Maurizio Bruschi, Simona Granata, Francesca Leone, Laura Barberio, Giovanni Candiano, Paola Pontrelli, Andrea Petretto, Martina Bartolucci, Sonia Spinelli, Loreto Gesualdo, Gianluigi Zaza

“…CHI3L1, previously associated with the severity of tissue damage in kidney diseases, was up-regulated in CAMR in both transcriptomics and proteomics, while SERPING1, a serine esterase inhibitor that blocks the classical and lectin pathway of complement, was up-regulated in CAMR in transcriptomics but down-regulated in proteomics. …”
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Inflammatory profiling and immune cell infiltration in dysthyroid optic neuropathy: insights from bulk RNA sequencing by Qintao Ma, Yuanping Hai, Yongbo Duan, Genfeng Yu, Cheng Song, ShengAi Huang, Anqi Huang, Yan Zhu, Yongzhi Shen, Zimeng Huang, Xiao Wang, Lan Liu, Thomas Efferth, Huiyu Guo, Yi Wang, Yi Wang, Jie Shen

“…The identified IRDGs and their associated pathways provide novel insights for innovative diagnostic and therapeutic strategies.…”
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A systems‐level study reveals host‐targeted repurposable drugs against SARS‐CoV‐2 infection by Fangyuan Chen, Qingya Shi, Fen Pei, Andreas Vogt, Rebecca A Porritt, Gustavo Garcia, Angela C Gomez, Mary Hongying Cheng, Mark E Schurdak, Bing Liu, Stephen Y Chan, Vaithilingaraja Arumugaswami, Andrew M Stern, D Lansing Taylor, Moshe Arditi, Ivet Bahar

“…These novel findings provide new paths for broadening the repertoire of compounds pursued as therapeutics against COVID‐19.…”
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