Unveiling fine-scale spatial structures and amplifying gene expression signals in ultra-large ST slices with HERGAST by Yuqiao Gong, Xin Yuan, Qiong Jiao, Zhangsheng Yu

“…Abstract We propose HERGAST, a system for spatial structure identification and signal amplification in ultra-large-scale and ultra-high-resolution spatial transcriptomics data. To handle ultra-large spatial transcriptomics (ST) data, we consider the divide and conquer strategy and devise a Divide-Iterate-Conquer framework especially for spatial transcriptomics data analysis, which can also be adopted by other computational methods for extending to ultra-large-scale ST data analysis. …”
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Narciclasine enhances cisplatin-induced apoptotic cell death by inducing unfolded protein response-mediated regulation of NOXA and MCL1 by Ji Hae Lee, Seung Hee Seo, Jaegal Shim, Yong-Nyun Kim, Kyungsil Yoon

“…The synergistic effects of cisplatin and narciclasine were elucidated through transcriptomic analysis and subsequent validation of candidate molecules by regulating their expression. …”
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Identification of STAT3 signaling as a shared pathogenic signature in systemic lupus erythematosus, chronic obstructive pulmonary disease, and asthma by Arman Mokaram Doust Delkhah

“…Abstract While patients with systemic lupus erythematosus (SLE) have a higher risk of developing chronic obstructive pulmonary disease (COPD) and asthma, the underlying mechanisms have yet to be elucidated. …”
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Flexible integration of spatial and expression information for precise spot embedding via ZINB-based graph-enhanced autoencoder by Jiacheng Leng, Jiating Yu, Ling-Yun Wu, Hongyang Chen

“…Abstract Domain identification is a critical problem in spatially resolved transcriptomics data analysis, which aims to identify distinct spatial domains within a tissue that maintain both spatial continuity and expression consistency. …”
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Target of Rapamycin is involved in root hair development in Phaseolus vulgaris by Hugo Alberto Monreal Contreras, Manoj-Kumar Arthikala, Miguel Lara, Kalpana Nanjareddy

“…Transcriptomic analysis revealed differential expression of 148 P. vulgaris homologs of Arabidopsis thaliana root hair-related genes, with 63 genes downregulated and 85 upregulated. …”
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Advancing breast cancer circulating tumour cell research at the Institute of Oncology Ljubljana by Tanja Jesenko, Cvetka Grašič Kuhar, Živa Pišljar, Simona Miceska, Veronika Kloboves-Prevodnik, Maja Čemažar

“…In addition to evaluation of single CTCs and CTC clusters in ongoing clinical trials using currently established methods and the planned establishment of a translational platform in mouse models, we aim to expand the range of CTC studies in the future to include genomic and transcriptomic analysis. …”
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Differential behavior responses and genetic alteration underpinning exercise effectiveness in stress-susceptible mice by Dong-Joo Hwang, Ji-Eun Kim, Joon-Yong Cho, Jung-Hoon Koo, Yongchul Jang, Tae-Kyung Kim

“…A multidimensional behavior analysis revealed significant variability in VWR efficacy among individuals; while some mice showed substantial behavior phenotypic improvements (SES), others displayed limited/no benefits (SER). …”
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Multi-modal investigation reveals pathogenic features of diverse DDX3X missense mutations. by Federica Mosti, Mariah L Hoye, Carla F Escobar-Tomlienovich, Debra L Silver

“…We observe notable overlap amongst severe mutations, suggesting common mechanisms underlying altered cell fate and survival. Transcriptomic analysis and subsequent cellular investigation highlights new pathways associated with DDX3X missense variants, including upregulated DNA Damage Response. …”
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Sulfated dietary fiber protects gut microbiota from antibiotics by Fuqing Wu, Xiaoqian Annie Yu, David Angeles-Albores, Susan E. Erdman, Eric J. Alm

“…This protective effect is dependent on the structural integrity, molecular weight, and sulfur content of the polysaccharide. Transcriptomic analysis showed that while fucoidan had minimal impact on baseline gene expression, it counteracted about 60% of the genes induced by kanamycin, suggesting a potential inhibition of kanamycin. …”
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E2F1 suppresses Epstein-Barr virus lytic reactivation through cellular and viral transcriptional networks. by Joyanta Biswas, Sk Asif Ali, Samaresh Malik, Subhadeep Nag, Piyali Mukherjee, Abhik Saha

“…Targeting lytic reactivation offers a promising therapeutic avenue for EBV-associated cancers. Our genome-wide transcriptomic analysis reveals that E2F1 is transcriptionally activated during EBV latency but significantly suppressed during lytic reactivation. …”
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Dynamic metabolic regulation of histone modifications during the yeast metabolic cycle. by Bárbara Guzmán-Dinamarca, Raúl Conejeros, Marcelo Rivas-Astroza

“…We developed a novel approach integrating flux analysis with transcriptomic data to investigate the production fluxes of acetyl-CoA and SAM and their influence on histone marks H3K9Ac and H3K4me3. …”
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Novel Classification of Peroneal Tendon Disease Reveals Cellular and Molecular Phenotypes of the Tenosvnovium by Julia Matthias MD, Michael A. David PhD, Sara E. Buckley DO, Daniel J. Ross MD, Nathaniel Zona BA, Michael A. Hewitt B.A., Joshua Metzl MD, Daniel K. Moon MD, MS, MBA, Courtney Grimsrud MD, Douglas J. Adams PhD, Michael Zuscik PhD, Kenneth Hunt MD

“…For RNA-seq, standard Gene Ontology (GO) analysis was used to identify enriched gene pathways. …”
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Calcium overload via PVT1 reprograms neutrophil fate and constrains gastric cancer progression by Dong Wang, Yunlong Li, Xiaoyu Peng, Lulu Zhang, Ying Zhang, Xue Guan, Xiao Liang, Songbin Fu, Jingcui Yu

“…Functional validation through in vitro and in vivo models demonstrated PVT1’s oncogenic role, while transcriptomic profiling further decoded neutrophil activation mechanisms regulated by PVT1. …”
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Optimized Protocol for Linear RNA Amplification and Application to Gene Expression Profiling of Human Renal Biopsies by A. Scherer, A. Krause, J.R. Walker, S.E. Sutton, D. Serón, F. Raulf, M.P. Cooke

“…Gene expression analysis using high-density cDNA or oligonucleotide arrays is a rapidly emerging tool for transcriptomics, the analysis of the transcriptional state of a cell or organ. …”
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Identification of ulcerative colitis diagnostic markers from differentially expressed genes shared with Hirschsprung disease by Wei Zuo, Zhengguang Wang

“…Pearson correlation analysis evaluated the relationship between immune cell infiltration and feature genes, while a Protein-Protein Interaction (PPI) network examined interactions with related proteins. …”
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Japanese encephalitis virus-associated human microglia induce cell death of human microvascular endothelial cells in receptor-independent infection by Isabelle Fellay, Pauline Blanc, Alexey Larionov, Léa Schlunke, Léa Schlunke, Luis Filgueira, Nils Lannes

“…While the CX3CR1-CX3CL1 axis was inefficient in blocking virus rescue and protecting endothelial cell from cell death, transcriptomics analysis identified Tumour Necrosis Factor-related apoptosis inducing ligand and receptors as potential key player leading to endothelial cell death.DiscussionOverall, our findings demonstrate that human microvascular endothelial cells supply virus propagation and Japanese encephalitis virus-associated microglia greatly contribute to endothelial cell death, an important component of the blood brain barrier integrity. …”
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Dose-dependent dual effects of HDAC inhibitors on glial inflammatory response by Samantha Mancino, Mariaserena Boraso, Andrea Galmozzi, Melania Maria Serafini, Emma De Fabiani, Maurizio Crestani, Barbara Viviani

“…To better understand the dual effects of SAHA, transcriptomic analysis of glial cells was conducted in the presence of LPS and low and high SAHA concentrations (100 nM or 5 µM). …”
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Explainable machine learning reveals ribosome biogenesis biomarkers in preeclampsia risk prediction by Jingjing Chen, Dan Zhang, Chengxiu Zhu, Lin Lin, Kejun Ye, Ying Hua, Mengjia Peng

“…SHapley Additive exPlanations interpretability analysis revealed SUV39H1 as the dominant risk contributor, while GLUL exhibited a protective effect. …”
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Intercropping Forage Mulberry Benefits Nodulation and Growth of Soybeans by Xinjie Feng, Minghui Zhong, Xuexian Zhao, Xiuli Zhang, Yanbo Hu, Huihui Zhang

“…The aim was to explore the effects of this intercropping on soybean growth and yield. We used transcriptomics, redundancy analysis, and structural equation modeling to evaluate soybean growth, yield, and nodulation; results showed that intercropping did not adversely affect plant height or stem diameter but increased chlorophyll content, photosynthetic rate, leaf area, and yield of soybean. …”
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Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts by Infanta Eden M., Umashankar Vetrivel

“…Dual RNA-Seq technology has significantly advanced the study of biological interactions between two organisms by allowing parallel transcriptomic analysis. Existing analysis methods employ various combinations of open-source bioinformatics tools to process dual RNA-Seq data. …”
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