Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models by Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I Jordan, Nir Yosef

“…Abstract As the number of single‐cell transcriptomics datasets grows, the natural next step is to integrate the accumulating data to achieve a common ontology of cell types and states. …”
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Transcriptomes That Confer to Plant Defense against Powdery Mildew Disease in Lagerstroemia indica by Xinwang Wang, Weibing Shi, Timothy Rinehart

“…The relative abundance of transcripts for 16 candidate DEGs (9 from CAB and 7 from NAT) detected by qRT-PCR showed general agreement with the abundances of the assembled transcripts in NAT. This study provided the first transcriptome analyses in L. indica. …”
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Single-cell transcriptomics uncovers key immune drivers of vaccine efficacy in cattle by Annaleise Wilson, Pâmela A. Alexandre, Aaron M. Brice, Brad C. Hine, Aaron Ingham, Thibault P. R. A. Legrand, Caroline Royle, Dominic Niemeyer, Antonio Reverter, Stuart E. Denman, Ryan J. Farr

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An integrated transcriptome, metabolome, and microbiome dataset of Populus under nutrient-poor conditions by Jiadong Wu, Dongyan He, Yue Wang, Sijia Liu, Yuxin Du, Haofei Wang, Shuxian Tan, Deqiang Zhang, Jianbo Xie

“…Here, we generated a comprehensive dataset, including 27 root transcriptomes, 27 root metabolomes, and 54 bulk or rhizosphere soil 16S rRNA amplicons across nine poplar species from four sections grown in nutrient-poor natural soil, along with eleven growth phenotype data. …”
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Revealing the Transcriptional and Metabolic Characteristics of Sebocytes Based on the Donkey Cell Transcriptome Atlas by Yu Tian, Shuqin Liu, Hongtao Shi, Jianjun Li, Xinglong Wan, Yujiang Sun, Huayun Li, Ning Cao, Zhixi Feng, Teng Zhang, Junjie Wang, Wei Shen

“…In summary, this work offers new insights into the unique metabolic patterns of donkey skin and provides a valuable resource for the conservation of donkey germplasm and the advancement of selective breeding programs.…”
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A new era in gammaherpesvirus transcriptomics: high-resolution profiling and model development by Kiran Fida, Brent A. Stanfield

“…., mSystems 10:e01678-24, 2025, https://doi.org/10.1128/msystems.01678-24) presents the first high-resolution, long-read transcriptomic atlas of Caviid gammaherpesvirus 1 (CaGHV-1), offering insights into its transcriptional complexity. …”
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Transcriptome Analysis of Gelatin Seed Treatment as a Biostimulant of Cucumber Plant Growth by H. T. Wilson, K. Xu, A. G. Taylor

“…Using mRNA sequencing based approach, transcriptomes of one- and two-week-old cucumber plants from gelatin capsule treated and nontreated seeds were characterized. …”
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Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response. by Monta Briviba, Laura Ansone, Ivars Silamikelis, Vita Rovite, Ilze Elbere, Laila Silamikele, Ineta Kalnina, Davids Fridmanis, Jelizaveta Sokolovska, Ilze Konrade, Valdis Pirags, Janis Klovins

“…We chose the RNA-Seq-based comparative transcriptomics approach to evaluate the systemic effect of metformin and highlight potential predictive biomarkers of metformin response in drug-naïve volunteers with type 2 diabetes in vivo. …”
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A deep proteome and transcriptome abundance atlas of 29 healthy human tissues by Dongxue Wang, Basak Eraslan, Thomas Wieland, Björn Hallström, Thomas Hopf, Daniel Paul Zolg, Jana Zecha, Anna Asplund, Li‐hua Li, Chen Meng, Martin Frejno, Tobias Schmidt, Karsten Schnatbaum, Mathias Wilhelm, Frederik Ponten, Mathias Uhlen, Julien Gagneur, Hannes Hahne, Bernhard Kuster

“…Abstract Genome‐, transcriptome‐ and proteome‐wide measurements provide insights into how biological systems are regulated. …”
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Deep Learning-Enabled Integration of Histology and Transcriptomics for Tissue Spatial Profile Analysis by Yongxin Ge, Jiake Leng, Ziyang Tang, Kanran Wang, Kaicheng U, Sophia Meixuan Zhang, Sen Han, Yiyan Zhang, Jinxi Xiang, Sen Yang, Xiang Liu, Yi Song, Xiyue Wang, Yuchen Li, Junhan Zhao

“…This enhancement enables more accurate gene expression analysis and aids in identifying prognostic marker genes, outperforming state-of-the-art deep learning methods with a total improvement of up to 49.72%. GIST provides a generalizable framework for integrating histology with spatial transcriptome analysis, revealing novel insights into spatial organization and functional dynamics.…”
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Transcriptomic landscape of Hras12V oncogene-induced hepatocarcinogenesis with gender disparity by Huaiyuan Di, Zhuona Rong, Nan Mao, Huiling Li, Jun Chen, Renwu Liu, Aiguo Wang

“…Abstract The genesis of hepatocellular carcinoma (HCC) is closely related to male factors and hyper-activated Ras signals. A transcriptomic database was established via RNA-Seq of HCC (T) and the adjacent precancerous liver tissue (P) of Hras12V transgenic mice (Ras-Tg, HCC model) and the normal liver tissue of wild-type mice (W) of both sexes. …”
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Transcriptomic analysis of bone transport reveals different functions between both ends by Maochun Wang, Jiao Zhang, Chongxu Qiao, Shunchao Yan, Weicheng Gao, Guoping Wu

“…Notably, 15 DEGs were shared between the TE and CE groups, with consistent expression trends, suggesting partially overlapping molecular mechanisms in bone healing under different mechanical ends.ConclusionThese findings provided insights into the distinct and shared molecular pathways involved in bone regeneration during bone transport and could inform targeted therapeutic strategies to enhance bone healing.…”
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Insights into the molecular mechanisms of browning tolerance in luffa: a transcriptome and metabolome analysis by Shan Wu, Miao Sun, Huashan Lian

“…These findings provide a theoretical foundation for further investigation into the molecular mechanisms underlying luffa browning and offer potential targets for genetic improvement or breeding strategies to enhance luffa quality.…”
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Characteristics of transcriptome and chromatin accessibility in the peripheral blood after acute hypoxia exposure by Kuo Zeng, Pei-ru Yuan, Jin-feng Xuan, Lai-xi Zhao, Xiao-na Li, Jun Yao, Dong Zhao

“…Conclusions Our results can provide the reference for the early response of the organism to hypoxic adaptation.…”
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Spatial transcriptomics reveals regionally altered gene expression that drives retinal degeneration by Ulrike Schumann, Lixinyu Liu, Riemke Aggio-Bruce, Adrian V. Cioanca, Artur Shariev, Michele C. Madigan, Krisztina Valter, Jiayu Wen, Riccardo Natoli

“…We identify regionally distinct transcriptomes, with higher expression of immunity related genes in the superior retina. …”
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Transcriptome analysis unveils survival strategies of Streptococcus parauberis against fish serum. by Yoonhang Lee, Nameun Kim, HyeongJin Roh, Ahran Kim, Hyun-Ja Han, Miyoung Cho, Do-Hyung Kim

“…These results indicate that S. paraubers can resist and evade the humoral immune responses of fish. The transcriptomic data obtained in this study provide a better understanding of the mode of action of S. parauberis in fish.…”
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Transcriptomic Analysis Reveals the Biosynthesis Mechanism of Coixol Under Salicylic Acid Treatment by Yao Wang, Hanli Ye, Xuqin Luo, Ziwei Li, Chuanqi Zheng, Dali Sun

“…The biosynthesis pathway of coixol was determined by high-throughput transcriptome sequencing analysis and the genes were then verified by qRT-PCR. …”
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Universal receptive system as a novel regulator of transcriptomic activity of Staphylococcus aureus by George Tetz, Kristina Kardava, Maria Vecherkovskaya, Alireza Khodadadi-Jamayran, Aristotelis Tsirigos, Victor Tetz

“…To this end, transcriptomic analysis of S. aureus MSSA VT209 was performed following the destruction of TezRs. …”
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Inferring causal metabolic signals that regulate the dynamic TORC1‐dependent transcriptome by Ana Paula Oliveira, Sotiris Dimopoulos, Alberto Giovanni Busetto, Stefan Christen, Reinhard Dechant, Laura Falter, Morteza Haghir Chehreghani, Szymon Jozefczuk, Christina Ludwig, Florian Rudroff, Juliane Caroline Schulz, Asier González, Alexandre Soulard, Daniele Stracka, Ruedi Aebersold, Joachim M Buhmann, Michael N Hall, Matthias Peter, Uwe Sauer, Jörg Stelling

“…Our inference method identified putative downstream targets of TORC1 and putative metabolic inputs of TORC1, including the hypothesized glutamine signal. The work provides a basis for further mechanistic studies of nitrogen metabolism and a general computational framework to study cellular processes.…”
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Transcriptome‐wide analysis of circRNA and RBP profiles and their molecular relevance for GBM by Julia Latowska‐Łysiak, Żaneta Zarębska, Marcin P. Sajek, Adriana Grabowska, Alessia Buratin, Paweł Głodowicz, Julia O. Misiorek, Konrad Kuczyński, Stefania Bortoluzzi, Marek Żywicki, Jan G. Kosiński, Agnieszka Rybak‐Wolf, Rafał Piestrzeniewicz, Anna M. Barciszewska, Katarzyna Rolle

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