stDyer enables spatial domain clustering with dynamic graph embedding by Ke Xu, Yu Xu, Zirui Wang, Xin Maizie Zhou, Lu Zhang

“…Abstract Spatially resolved transcriptomics (SRT) data provide critical insights into gene expression patterns within tissue contexts, necessitating effective methods for identifying spatial domains. …”
Get full text

Single-cell and spatial atlas of glioblastoma heterogeneity: characterizing the PCLAF+ subtype and YEATS4’s oncogenic role by Siqi Ma, Yuwei Sun, Shaowei Zheng, Yilong Fu, Liangyu Wang, Dun Liu, Henan Jiao, Xuqiang Zhu, Xueyuan Li, Dongming Yan, Di Chen, Zi Ye

“…Spatial transcriptomics integrated Multimodal Intersection Analysis, TransferData, and Robust Cell Type Decomposition techniques to characterize the spatial distribution patterns of key cell subtypes. …”
Get full text

Multi-omics approaches reveal the mechanisms underlying the interaction between cyst fluid of Echinococcus granulosus and host immune cells by Rongdong He, Rongdong He, Ruofeng Yan, Yuanchun Shi, Aili Aierken, Xue Zhang, Hao Wen, Hao Wen, Kalibixiati Aimulajiang

“…These metabolites were primarily enriched in metabolic pathways such as beta-Alanine metabolism and Pyrimidine metabolism. Transcriptome analysis identified 16,694 differentially expressed genes, highlighting necroptosis and TGF-β signaling as top pathways, where Hgf and Myof were potential diagnostic markers.ConclusionsMetabolomics and transcriptomics analyses help identify potential candidate genes and provide diagnostic tools for future research and the discovery of new therapeutic targets. …”
Get full text

Impact of Arsenic Stress on the Antioxidant System and Photosystem of <i>Arthrospira platensis</i> by Jiawei Liu, Jie Du, Di Wu, Xiang Ji, Xiujuan Zhao

“…This study investigated the growth and resistance mechanisms of <i>A. platensis</i> under As³⁺ stress by measuring physiological and biochemical indices, conducting transcriptome sequencing, and validating the results through qPCR. …”
Get full text

Spatial gene regulatory networks driving cell state transitions during human liver disease by Nigel L Hammond, Syed Murtuza Baker, Sokratia Georgaka, Ali Al-Anbaki, Elliot Jokl, Kara Simpson, Rosa Sanchez-Alvarez, Varinder S Athwal, Huw Purssell, Ajith K Siriwardena, Harry V M Spiers, Mike J Dixon, Leoma D Bere, Adam P Jones, Michael J Haley, Kevin N Couper, Nicoletta Bobola, Andrew D Sharrocks, Neil A Hanley, Magnus Rattray, Karen Piper Hanley

“…This combined approach provides a spatial atlas of gene regulation and defines molecular signatures associated with liver disease for targeted therapeutics or as early diagnostic markers of progressive liver disease.…”
Get full text

Aortic valve-specific genes dysregulated in calcific aortic valve stenosis as potential biomarkers and therapeutic targets by Pardis Zamani, Ursula Houessou, Hasanga D. Manikpurage, Zhonglin Li, Manel Dahmene, Nathalie Gaudreault, François Dagenais, Marie-Annick Clavel, Philippe Pibarot, Benoit J. Arsenault, Patrick Mathieu, Yohan Bossé, Sébastien Thériault

Get full text

Characterization and Multi-Omics Basis of Biofilm Formation by <i>Lactiplantibacillus plantarum</i> by Ruitang Ma, Dong Zhao, Rongqing Zhou, Jia Zheng, Chongde Wu

Get full text

How “Omics” Studies Contribute to a Better Understanding of Fuchs’ Endothelial Corneal Dystrophy by Erika Prašnikar, Spela Stunf Pukl

“…In this review, we gathered genome-wide studies (n = 31) and sorted them according to genomics (n = 9), epigenomics (n = 3), transcriptomics (n = 15), proteomics (n = 3) and metabolomics (n = 1) levels to characterize progress in understanding FECD. …”
Get full text

Multi-omics analysis reveals the specific role of biocontrol reagents against tomato bacterial wilt by Xin-Qiao Du, Tian-Xiao Sun, Wu-Lin Xu, Tang Zhu, Qiang Wang, Pei-Wen Gu, Jiang Lu

“…In this study, we employed a combination of amplicon sequencing, transcriptomics, and metabolomics analysis to investigate how Bacillus velezensis and Pseudomonas fluorescens affect the defense responses against R. solanacearum in tomato. …”
Get full text

A comprehensive transcriptional reference for severity and progression in spinal cord injury reveals novel translational biomarker genes by Rubén Grillo-Risco, Marta R. Hidalgo, Beatriz Martínez-Rojas, Victoria Moreno-Manzano, Francisco García-García

“…Overall, we present a transcriptomic reference and provide a comprehensive framework for assessing SCI considering severity and time perspectives, all integrated into a user-friendly tool. …”
Get full text

Current state and future prospects of spatial biology in colorectal cancer by Francisco G. Carranza, Fernando C. Diaz, Maria Ninova, Enrique Velazquez-Villarreal, Enrique Velazquez-Villarreal

“…Spatial transcriptomics enables high-resolution mapping of the whole transcriptome. …”
Get full text

Quantification and discovery of sequence determinants of protein‐per‐mRNA amount in 29 human tissues by Basak Eraslan, Dongxue Wang, Mirjana Gusic, Holger Prokisch, Björn M Hallström, Mathias Uhlén, Anna Asplund, Frederik Pontén, Thomas Wieland, Thomas Hopf, Hannes Hahne, Bernhard Kuster, Julien Gagneur

“…Here, we quantified PTR ratios for 11,575 proteins across 29 human tissues using matched transcriptomes and proteomes. We estimated by regression the contribution of known sequence determinants of protein synthesis and degradation in addition to 45 mRNA and 3 protein sequence motifs that we found by association testing. …”
Get full text

Analysis of the Differences Among <i>Camellia oleifera</i> Grafting Combinations in Its Healing Process by Zhilong He, Ying Zhang, Chengfeng Xun, Zhen Zhang, Yushen Ma, Xin Wei, Zhentao Wan, Rui Wang

“…The identified molecular markers not only advance our understanding of grafting mechanisms in woody plants but also provide valuable targets for future breeding programs aimed at improving grafting success rates in this important oil crop.…”
Get full text

Integrated miRNA Signatures: Advancing Breast Cancer Diagnosis and Prognosis by Maria Samara, Eleni Thodou, Marina Patoulioti, Antigoni Poultsidi, Georgia Eleni Thomopoulou, Antonis Giakountis

“…We have designed a computational approach combining transcriptome profiling, survival analyses, and diagnostic power calculations from 1165 patients with breast invasive carcinoma from The Cancer Genome Atlas (TCGA-BRCA). …”
Get full text

Insights of Phaseolus vulgaris’ response to infection by Uromyces appendiculatus using an RNA-seq approach by Penny Makhumbila, Molemi Rauwane, Hangwani Muedi, Sandiswa Figlan

Get full text

Physiological and Multi-Omics Analysis in Leaves of <i>Solanum americanum</i> in Response to Cd Toxicity by Jiao Zhou, Jun-Gang Zhu, Peng Xiao, Kai-Lu Wang, Qian Xu, Meng-Xi Wu, Yuan-Zhi Pan

“…This comprehensive study will provide detailed molecular-scale insights into the Cd response mechanisms in <i>S. americanum</i>.…”
Get full text

Molecular mechanisms and horticultural implications of temperature-induced color variation in Stropharia rugosoannulata mushrooms by Shen Meng, Yan Jing, Wang Ruisen, Quan Xinhua, Yuan Ye, Yao Xiangtan, Jin Qunli

“…This study integrated metabolomic and transcriptomic approaches to identify key metabolites and genes associated with the transition of cap color from white to wine-red under different temperature conditions. …”
Get full text

Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies by Scott J. Dos Santos, Clara Copeland, Jean M. Macklaim, Gregor Reid, Gregory B. Gloor

“…Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into the functions which are actively expressed and differential between states of health and disease. …”
Get full text

Gene expression analysis of primary graft dysfunction in adult heart transplant recipients: A cohort study by Samuel Padovani Steffen, MD, Alvaro Monteiro Perazzo, MD, MSc, Shirlyne Fabianni Dias Gaspar, MD, Ronaldo Honorato Barros Santos, MD, Domingos Dias Lourenço Filho, MD, PhD, Alexandre da Costa Pereira, MD, PhD, Luis Fernando B. da Costa Seguro, MD, PhD, Fabiana G. Marcondes-Braga, MD, PhD, Fernando Bacal, MD, PhD, Jose Eduardo Krieger, MD, PhD, Fabio Antonio Gaiotto, MD, PhD, Fabio Biscegli Jatene, MD, PhD

“…Many centers are studying PGD’s pathophysiology through epidemiological, biomarker, and transcriptome analyses. This study aims to evaluate, via transcriptomic analysis of myocardial biopsies, the gene expression profile of patients with PGD and compare it with those without PGD. …”
Get full text

High soybean dietary supplementation with quercetin improves antioxidant capacity of spotted sea bass Lateolabrax maculatus by Longhui Liu, Yanbo Zhao, Zhangfan Huang, Zhongying Long, Huihui Qin, Hao Lin, Sishun Zhou, Lumin Kong, Jianrong Ma, Yi Lin, Zhongbao Li

“…A total of 540 spotted sea bass were randomly allocated into 6 groups and provided with diets that corresponded to their respective groups for a duration of 56 days. …”
Get full text