Single-Cell Atlas of Spleen Remodeling Reveals Macrophage Subset-Driven ASFV Pathogenesis by Liyuan Wang, Shouzhang Sun, Lei Liu, Yun Chen, Haixue Zheng, Zhonglin Tang

“…Viral gene expression analysis revealed E165R as a central hub in viral replication networks, while host transcriptomics uncovered disruption of Netrin signaling pathways that may facilitate immune evasion. …”
Get full text

The spatial landscape of glial pathology and T cell response in Parkinson’s disease substantia nigra by Maxwell Ma, Fahad Paryani, Kelly Jakubiak, Shengnan Xia, Susumu Antoku, Adithya Kannan, Jaeseung Lee, Nacoya Madden, Shailesh Senthil Kumar, Juncheng Li, David Chen, Gunnar Hargus, Aayushi Mahajan, Xena Flowers, Ashley S. Harms, David Sulzer, James E. Goldman, Peter A. Sims, Osama Al-Dalahmah

“…Here, we employed single-nucleus RNAseq, spatial transcriptomics, and T cell receptor (TCR) sequencing to analyze T cell and glial cell states in post-mortem PD brain tissue. …”
Get full text

Preventive regulation of cellular heat stress injury by mung bean polyphenols revealed by multi-omics analysis by Yuchao Feng, Shu Zhang, Decheng Suo, Tianxin Fu, Xiaonan Li, Changyuan Wang, Xia Fan

“…Then mung bean polyphenols can exert heat stress preventive activity through the regulation of cellular oxidative damage and energy metabolism. This study provides a good idea for the research and development of dietary intervention products for heat stress.…”
Get full text

Pharmacoproteomic characterisation of human colon and rectal cancer by Martin Frejno, Riccardo Zenezini Chiozzi, Mathias Wilhelm, Heiner Koch, Runsheng Zheng, Susan Klaeger, Benjamin Ruprecht, Chen Meng, Karl Kramer, Anna Jarzab, Stephanie Heinzlmeir, Elaine Johnstone, Enric Domingo, David Kerr, Moritz Jesinghaus, Julia Slotta‐Huspenina, Wilko Weichert, Stefan Knapp, Stephan M Feller, Bernhard Kuster

“…Integration with proteomes of 90 CRC patients and matched transcriptomics data defined integrated CRC subtypes, highlighting cell lines representative of each tumour subtype. …”
Get full text

Natural genetic variation impacts expression levels of coding, non‐coding, and antisense transcripts in fission yeast by Mathieu Clément‐Ziza, Francesc X Marsellach, Sandra Codlin, Manos A Papadakis, Susanne Reinhardt, María Rodríguez‐López, Stuart Martin, Samuel Marguerat, Alexander Schmidt, Eunhye Lee, Christopher T Workman, Jürg Bähler, Andreas Beyer

“…The strains, methods, and datasets generated here provide a rich resource for future studies.…”
Get full text

Genetically Engineered Brain Organoids Recapitulate Spatial and Developmental States of Glioblastoma Progression by Matthew Ishahak, Rowland H. Han, Devi Annamalai, Timothy Woodiwiss, Colin McCornack, Ryan T. Cleary, Patrick A. DeSouza, Xuan Qu, Sonika Dahiya, Albert H. Kim, Jeffrey R. Millman

“…Single‐cell and spatial transcriptomic analyses revealed that these mutations disrupt normal neurodevelopment gene regulatory networks resulting in changes in cellular composition and spatial organization. …”
Get full text

The modulatory effect of oolong tea polyphenols on intestinal flora and hypothalamus gene expression in a circadian rhythm disturbance mouse model by Ruonan Yan, Chi-Tang Ho, Yanan Liu, Shengnan Zhan, Zufang Wu, Xin Zhang

“…The interaction between host circadian rhythm and gut microbes through the gut-brain axis provides new clues for tea polyphenols to improve host health. …”
Get full text

(Apo)Lipoprotein Profiling with Multi‐Omics Analysis Identified Medium‐HDL‐Targeting PSRC1 with Therapeutic Potential for Coronary Artery Disease by Yingmei Li, Sihan Wang, Ling Liu, Hao Cai, Yacan Huang, Mingjing Gao, Xiaogang Zhang, Qingqing Wu, Gaokun Qiu

“…The results provide strong evidence as well as mechanistic clues of PSRC1’s therapeutic potential for CAD.…”
Get full text

Multiparametric MRI along with machine learning predicts prognosis and treatment response in pediatric low-grade glioma by Anahita Fathi Kazerooni, Adam Kraya, Komal S. Rathi, Meen Chul Kim, Arastoo Vossough, Nastaran Khalili, Ariana M. Familiar, Deep Gandhi, Neda Khalili, Varun Kesherwani, Debanjan Haldar, Hannah Anderson, Run Jin, Aria Mahtabfar, Sina Bagheri, Yiran Guo, Qi Li, Xiaoyan Huang, Yuankun Zhu, Alex Sickler, Matthew R. Lueder, Saksham Phul, Mateusz Koptyra, Phillip B. Storm, Jeffrey B. Ware, Yuanquan Song, Christos Davatzikos, Jessica B. Foster, Sabine Mueller, Michael J. Fisher, Adam C. Resnick, Ali Nabavizadeh

“…This radiogenomic study in pLGGs provides a framework for the identification of high-risk patients who may benefit from targeted therapies.…”
Get full text

PPM1J regulates meat quality feature and glycerophospholipids composition in broiler by modulating protein dephosphorylation by Manting Ma, Xin Yang, Yanan Zhang, Shuang Wang, Chenglong Jin, Weiguang Xia, Wei Chen, Bolin Cai, Chuntian Zheng

“…Here, metabolomics and transcriptomics were used to systematically identify the genetic regulation of differences in meat flavor among different broiler. …”
Get full text

Microbiome in cancer metastasis: biological insights and emerging spatial omics methods by Marianne Meyers, Charlotte B. A. Stoffels, Gilles Frache, Elisabeth Letellier, Maureen Feucherolles

“…Biological models used to study metastasis are discussed to provide context for the further investigation of these interactions. …”
Get full text

Single-cell expression profiling of bat wing development by Xue Lyu, Jing Bai, Ji-Bin Jiang, Chang-Jie Sun, Peng Chen, Qi Liu, Yuan-Shuo Ma, Zhen Liu

“…Here, we use single-cell transcriptomic sequencing to map ~39,000 cells from the limbs of bats (Rhinolophus sinicus) at developmental stages Carnegie stages (CS) 16, 18, and 20. …”
Get full text

The Key Role and Mechanism of Oxidative Stress in Hypertrophic Cardiomyopathy: A Systematic Exploration Based on Multi-Omics Analysis and Experimental Validation by Sijie Zhang, Tianzhi Li, Shiyi Sun, Yujiao Jiang, Yuxin Sun, Yan Meng

“…This study systematically analysed HCM transcriptomic data using differential gene expression, weighted gene co-expression network analysis (WGCNA), and unsupervised consensus clustering to identify key genes and classify HCM subtypes. …”
Get full text

Integrated omics identifies molecular networks of brain-body interactions of brain injury by Yuan-Hong Deng, Hong Wang, Jia-Hang Zhang, Yu-Fei Wang, Meng-Yao Wang, Xin-Ru Pan, Yao-Dan Zhang, Yuan-Hui Gan, Yi He, Fang Xie, Xiao-Shuang Feng, Jia-Xin Xie, Bai-Tong Liu, Jiang-Tao Wang, Xin-Xiao Zhang, Peng-Fei Wang, Jie Li, Shu-Guang Yu, Qing-Wu Yang, Ming-Ze Bai, Yong Tang, Xiao-Yi Xiong

“…Through integrative analysis of multi-organ proteomic, metabolomic, and transcriptomic data following ischemic stroke, we identified dynamic molecular signatures across organs. …”
Get full text

Artificial intelligence and anti-cancer drugs' response by Xinrui Long, Kai Sun, Sicen Lai, Yuancheng Liu, Juan Su, Wangqing Chen, Ruhan Liu, Xiaoyu He, Shuang Zhao, Kai Huang

“…It provides a detailed exposition of the processes involved in data processing and model construction, examines the current challenges faced in this field and future development directions, with the aim of better advancing the progress of precision medicine.…”
Get full text

Prediction of post-treatment recurrence in early-stage breast cancer using deep-learning with mid-infrared chemical histopathological imaging by Abigail Keogan, Thi Nguyet Que Nguyen, Pascaline Bouzy, Nicholas Stone, Karin Jirstrom, Arman Rahman, William M. Gallagher, Aidan D. Meade

“…Prognostic assays which utilize bulk transcriptomics ignore the spatial context of the cellular material and are, therefore, of limited value in the development of mechanistic models. …”
Get full text

The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal genetic responses to tapping in rubber tree by Chaochao Li, Yuan Yuan, Zhiyi Nie, Tingkai Wu, Zhiyuan Wang, Jiangxia Qiao, Zhi Deng, Xiaobo Wang, Dong Xu, Xu Wang, Shuo Cao, Bingqin Li, Zewei An, Wenguan Wu, Zhongxin Jin, Huasun Huang, Wei Hu, Yongfeng Zhou, Han Cheng

“…We propose a model where JA-induced myelocytomatosis proteins 2 activate mevalonate kinase 1 expression, boosting MVA synthesis and rubber production. These findings provide insights into rubber tree genomics and its molecular response to tapping.…”
Get full text

Gene transcription, neurotransmitter, and neurocognition signatures of brain structural-functional coupling variability by Lin Jiang, Sarah Genon, Jiayu Ye, Yan Zhu, Guangying Wang, Runyang He, Pedro A. Valdes-Sosa, Feng Wan, Dezhong Yao, Simon B. Eickhoff, Debo Dong, Fali Li, Peng Xu

“…Collectively, SFC variability mapping provides a biologically plausible framework for understanding how SFC fluctuates over time to support macroscale neurocognitive specialization.…”
Get full text

Multi-platform omics analysis of Nipah virus infection reveals viral glycoprotein modulation of mitochondria by Gunner P. Johnston, Fikret Aydemir, Haewon Byun, Emmie de Wit, Kristie L. Oxford, Jennifer E. Kyle, Jason E. McDermott, Brooke L. Deatherage Kaiser, Cameron P. Casey, Karl K. Weitz, Heather M. Olson, Kelly G. Stratton, Natalie C. Heller, Viraj Upadhye, I. Abrrey Monreal, J. Lizbeth Reyes Zamora, Lei Wu, D.H. Goodall, David W. Buchholz, Joeva J. Barrow, Katrina M. Waters, Ruth N. Collins, Heinz Feldmann, Joshua N. Adkins, Hector C. Aguilar

“…This study identified changes in cellular components during NiV infection of human cells using a multi-platform, high-throughput transcriptomics, proteomics, lipidomics, and metabolomics approach. …”
Get full text

The caterpillar Manduca sexta brain shows changes in gene expression and protein abundance correlating with parasitic manipulation of behaviour by McMillan LEM, Herbison RH, Biron DG, A Barkhouse, DW Miller, N Raun, Adamo SA

“…Using proteomic, transcriptomic and qPCR studies, we discovered an increase in antimicrobial peptide gene expression and protein abundance in the host central nervous system at the time of wasp emergence, correlating with the change in host behaviour. …”
Get full text