Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions by Zhenhua Zhang, Wenchao Li, Qiuyao Zhan, Michelle Aillaud, Javier Botey-Bataller, Martijn Zoodsma, Rob ter Horst, Leo A. B. Joosten, Christoph Bock, Leon N. Schulte, Cheng-Jian Xu, Mihai G. Netea, Marc Jan Bonder, Yang Li

“…We map genetic effects on gene expression (expression quantitative trait locus, eQTL) using single-cell transcriptomes of 152 samples from 38 healthy individuals, covering baseline state and lipopolysaccharide challenge either before or after Bacillus Calmette-Guerin vaccination. …”
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Ultra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases by Feng Xian, Malena Brenek, Christoph Krisp, Elisabeth Urbauer, Ranjith Kumar Ravi Kumar, Doriane Aguanno, Tharan Srikumar, Qixin Liu, Allison M. Barry, Bin Ma, Jonathan Krieger, Dirk Haller, Manuela Schmidt, David Gómez-Varela

“…Orthogonal validation using transcriptomic data from Crohn’s disease patients confirmed key host protein alterations. …”
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Understanding the Functionality of Probiotics on the Edge of Artificial Intelligence (AI) Era by Remziye Asar, Sinem Erenler, Dilara Devecioglu, Humeyra Ispirli, Funda Karbancioglu-Guler, Hale Inci Ozturk, Enes Dertli

“…To that end, this review provides an overview of the current knowledge on probiotics as well as next-generation probiotics. …”
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Perturbations in the microbiota-gut-brain axis shaped by social status loss by Ruijing Yang, Xin Wang, Jie Yang, Xingyu Zhou, Yiyuan Wu, Yifan Li, Yu Huang, Jianping Zhang, Ping Liu, Minghao Yuan, Xunmin Tan, Peng Zheng, Jing Wu

“…Weighted gene co-expression network analysis (WGCNA) reveals modules linked to forced loss in the gut microbiota, colon, PFC, and PFC interneurons, suggesting changes in the PI3K-Akt signaling pathway and the glutamatergic synapse. Our findings provide evidence for MGBA perturbations induced by social status loss, offering potential intervention targets for related brain disorders.…”
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Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2 by Christina N. Como, Rebecca O’Rourke, Caitlin Winkler, Danae Mitchell, Luuli Tran, David Lorberbaum, Lori Sussel, Santos Franco, Julie Siegenthaler

“…Our findings elucidate a previously unknown mechanism of how meningeal RA coordinates neocortical development and provide insight into how defects in meningeal development may cause neurodevelopmental disorders.…”
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Integrated bioinformatics and machine learning reveal key genes and immune mechanisms associated with uremia by Zhiyue Sun, Zhiqiang Ding, Xiaoyang Guo, Jiangtao Li, Daoyuan Ding, Bo Wen

“…In this study, we analyzed transcriptomic data from the GSE37171 dataset to identify genes associated with uremia. …”
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Longitudinal scRNA-seq of retinal organoids derived from Stargardt disease patient with ABCA4 mutation by Yingke Zhao, Yun Cheng, Ting Li, Jiawen Wu, Chenchen Li, Shenghai Zhang, Jihong Wu

“…By using iPSCs carrying most common variant in Chinese STGD patients, the dataset not only provides a powerful resource for studying STGD, but also offers novels insight into the developmental mechanisms underlying ABCA4-associated pathological changes in the retinal organoid system.…”
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Dual IRE1 RNase functions dictate glioblastoma development by Stéphanie Lhomond, Tony Avril, Nicolas Dejeans, Konstantinos Voutetakis, Dimitrios Doultsinos, Mari McMahon, Raphaël Pineau, Joanna Obacz, Olga Papadodima, Florence Jouan, Heloise Bourien, Marianthi Logotheti, Gwénaële Jégou, Néstor Pallares‐Lupon, Kathleen Schmit, Pierre‐Jean Le Reste, Amandine Etcheverry, Jean Mosser, Kim Barroso, Elodie Vauléon, Marion Maurel, Afshin Samali, John B Patterson, Olivier Pluquet, Claudio Hetz, Véronique Quillien, Aristotelis Chatziioannou, Eric Chevet

“…This study provides the first demonstration of a dual role of IRE1 downstream signaling in cancer and opens a new therapeutic window to abrogate tumor progression.…”
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Case Report: FAP+ fibroblasts and SPP1+ macrophages in SMARCA2-deficient while SMARCA4-preserved poorly differentiated lung adenocarcinoma: two case reports and multi-omics analysi... by Zhaoxuan Wang, Junying Wang, Shengmin Wang, Weijiao Xu, Yixiang Zhang

“…Furthermore, we perform a comprehensive multi-omics analysis of the transcriptomic cohort GSE31210 (n=226), the proteomic cohort from the study by Chen et al. …”
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Single-cell sequencing reveals transcriptional dynamics regulated by ERα in mouse ovaries. by Qicai Hu, Yiqian Gui, Congcong Cao, Jun Xie, Huiru Tang

“…<h4>Methods</h4>Single-cell RNA sequencing (scRNA-seq) was used to compare transcriptomes from individual ovarian cells in both wild type and αERKO mice. …”
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Graph-based pan-genome analysis reveals diversity of structural variations in native and commercial chicken by Yiming WANG, Zijia NI, Yinhua HUANG

“…Compared to the linear genome, the pan-genome provided significant improvements in the efficiency of structural variation identification. …”
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Identification and characterization of seminal fluid proteins in the Asian tiger mosquito, Aedes albopictus. by Kathryn E Boes, José M C Ribeiro, Alex Wong, Laura C Harrington, Mariana F Wolfner, Laura K Sirot

“…Despite the importance of Sfps on female reproductive behavior in mosquitoes and other insects, the identity of Sfps in Ae. albopictus has not previously been reported. We used transcriptomics and proteomics to identify 198 Sfps in Ae. albopictus. …”
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Widespread release of translational repression across Plasmodium's host-to-vector transmission event. by Kelly T Rios, James P McGee, Aswathy Sebastian, Sanjaya Aththawala Gedara, Robert L Moritz, Marina Feric, Sabrina Absalon, Kristian E Swearingen, Scott E Lindner

“…Together, these data provide a model for the essential translational control mechanisms that promote Plasmodium's efficient transmission from mammalian host to mosquito vector.…”
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Radiomics in glioma: emerging trends and challenges by Zihan Wang, Lei Wang, Yinyan Wang

“…Additionally, advanced imaging techniques, such as diffusion‐weighted imaging, perfusion‐weighted imaging, magnetic resonance spectroscopy, magnetic resonance fingerprinting, functional MRI, and positron emission tomography, can provide supplementary information for tumor characterization and classification. …”
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Mechanistic role of pyroptosis in Kawasaki disease: An integrative bioinformatics analysis of immune dysregulation, machine learning-based biomarker discovery, WGCNA, and drug repu... by Chen Wang, Qinchao Wu, Jie Chen, Jun Wang, Dan Li

“…In this study, we employed integrative bioinformatics approaches to investigate the mechanistic role of pyroptosis in KD. By analyzing transcriptomic datasets, we identified differentially expressed genes (DEGs) associated with pyroptosis and immune dysregulation. …”
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Lactylation modification in cancer: mechanisms, functions, and therapeutic strategies by Mengqi Lv, Yefei Huang, Yansu Chen, Kun Ding

“…The emergence of single-cell and spatial transcriptomics may offer valuable insights for selecting targets. …”
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Unveiling the functional nature of retrogenes in dinoflagellates by Ronie Haro, Renny Lee, Claudio H. Slamovits

“…We conducted a comprehensive search for retrogenes in dinoflagellate transcriptomes to uncover their functional nature and the processes underlying their redundancy. …”
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Systems approach for congruence and selection of cancer models towards precision medicine. by Jian Zou, Osama Shah, Yu-Chiao Chiu, Tianzhou Ma, Jennifer M Atkinson, Steffi Oesterreich, Adrian V Lee, George C Tseng

“…Here, we present Congruence Analysis and Selection of CAncer Models (CASCAM), a statistical and machine learning framework for authenticating and selecting the most representative cancer models in a pathway-specific manner using transcriptomic data. CASCAM provides harmonization between human tumor and cancer model omics data, systematic congruence quantification, and pathway-based topological visualization to determine the most appropriate cancer model selection. …”
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From barcodes to genomes: a new era of molecular exploration in bryophyte research by Anshul Dhyani, Shruti Kasana, Prem Lal Uniyal

“…Recent research involving plastomes, mitogenomes, and transcriptomes of various bryophyte species has provided insights into molecular changes and gene expression in response to environmental stressors. …”
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Metabolomics survey of uropathogenic bacteria in human urine by Carly C. Y. Chan, Ryan A. Groves, Thomas Rydzak, Ian A. Lewis

“…These metabolic classifications can be further subdivided on a species-to-species level.DiscussionThis survey provides a framework to understanding the metabolic activity of the diverse range of uropathogens and how these species use divergent metabolic strategies to occupy the same niche.…”
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