Annotation of protein-coding genes in 49 diatom genomes from the Bacillariophyta clade by Natalia Nenasheva, Clara Pitzschel, Cynthia N. Webster, Alexander J. Hart, Jill L. Wegrzyn, Mia M. Bengtsson, Katharina J. Hoff

“…For gene prediction, BRAKER2 was employed in the absence of transcriptomic data, while BRAKER3 was utilised when transcriptome short read data were available from the Sequence Read Archive. …”
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Developmental features and unique characteristics of peptide-specific PLZF+ innate-like T cells in mice by Ahmed Hassan, Nico Heise, Anja Schimrock, Stefanie Willenzon, Inga Ravens, Reinhold Förster, Hristo Georgiev

“…Yet there are no present studies providing clues into the developmental features of PILT cells at a transcriptome level. …”
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Absence of fibroin H sequences and a significant divergence in the putative fibroin L homolog in Neomicropteryx cornuta (Micropterigidae) silk by Yume Imada, Lenka Rouhova, Martina Zurovcova, Miluse Hradilova, Sarka Podlahova, Hana Sehadova, Michal Zurovec

“…Abstract Micropterigidae is regarded as the sister group of all the other Lepidoptera, providing important insights into the evolution of Lepidoptera. …”
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Fungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifolia. by Niklaus Zemp, Raquel Tavares, Alex Widmer

“…These genes were overall down-regulated in females and up-regulated in males, causing, respectively, a defeminization in infected females and a feminization of the transcriptome in infected males. Our results reveal strong sex-specific responses to pathogen infection in a dioecious plant and provide a link between pathogen-induced changes in sex-biased gene expression and sexual dimorphism.…”
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Chromatin-focused genetic and chemical screens identify BRPF1 as a targetable vulnerability in Taxol-resistant triple-negative breast cancer by Ozlem Yedier-Bayram, Ahmet Cingöz, Ebru Yilmaz, Ali Cenk Aksu, Beril Esin, Nareg Degirmenci, Ayse Derya Cavga, Beyza Dedeoğlu, Buse Cevatemre, Hamzah Syed, Martin Philpott, Adam P. Cribbs, Udo Oppermann, Nathan A. Lack, Ceyda Acilan, Tamer T. Onder, Tugba Bagci-Onder

“…These cells exhibited reduced growth rates, altered morphology and evasion of apoptosis. Transcriptome analysis uncovered elevated ABCB1 expression and multidrug-resistant phenotype in these resistant cells. …”
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Single-Cell RNA Sequencing and Combinatorial Approaches for Understanding Heart Biology and Disease by Le Wang, Bo Jin

“…Compared with single-dimensional inspections, the combination of transcriptomes with spatial dimensions and other omics can provide a comprehensive understanding of single-cell functions, microenvironment, dynamic processes, and their interrelationships. …”
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A Survey of the ATP-Binding Cassette (ABC) Gene Superfamily in the Salmon Louse (Lepeophtheirus salmonis). by Greta Carmona-Antoñanzas, Stephen N Carmichael, Jan Heumann, John B Taggart, Karim Gharbi, James E Bron, Michaël Bekaert, Armin Sturm

“…Searches of both genome and transcriptome allowed the identification of a total of 33 genes / transcripts coding for ABC proteins, of which 3 were represented only in the genome and 4 only in the transcriptome. …”
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Comparative toxicotranscriptomics of longterm cypermethrin exposure to aquacultured fish Labeo catla (Catla) by Basanta Kumar Das, Satabdi Ganguly, Anupam Adhikari, Subhasree Subhasmita Raut, Smruti Priyambada Pradhan, Subir Kumar Nag, Kavita Kumari, Vikash Kumar

“…A total of 2665 and 18,020 unigenes and 333 and 454 DEGs were identified in the brain and liver transcriptome, respectively. DEGs associated with MAPK signaling and apoptosis pathways were co-expressed in both brain and liver transcriptome, according to pathway enrichment analysis. …”
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Cell cycle- and cancer-associated gene networks activated by Dsg2: evidence of cystatin A deregulation and a potential role in cell-cell adhesion. by Abhilasha Gupta, Daniela Nitoiu, Donna Brennan-Crispi, Sankar Addya, Natalia A Riobo, David P Kelsell, Mỹ G Mahoney

“…Cell-cell adhesion is paramount in providing and maintaining multicellular structure and signal transmission between cells. …”
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Dietary exposure of the water flea Daphnia galeata to microcystin-LR by Eun-jeong Kim, Donggu Jeon, Yeon-jeong Park, Hyunmin Woo, Seong-il Eyun

“…These findings offer insights into how organisms respond to ecotoxic stimuli, providing valuable information for understanding adaptation or defense pathways.…”
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Pseudomonas plecoglossicida infection induces neutrophil autophagy-driven NETosis in large yellow croaker Larimichthys crocea by Jia-Feng Cao, Jia-Feng Cao, Jia-Feng Cao, Jiong Chen, Jiong Chen, Jiong Chen

“…To further explore the underlying mechanism, we performed transcriptome analysis and western blotting, which revealed that P. plecoglossicida triggers NETosis through activation of the autophagy pathway. …”
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The transcriptional landscape of Rhizoctonia solani AG1-IA during infection of soybean as defined by RNA-seq. by Tanya R Copley, Raj Duggavathi, Suha Jabaji

“…Overall, this study provides the first insights into R. solani AG1-IA transcriptome responses to soybean invasion providing beneficial information for future targeted control methods of this successful pathogen.…”
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Identification of ECE2 signaling in promoting non-small lung cancer progression through ET1/YAP1/MAGEA3 axis by Huaiqing Xiao, Jiawei Ni, Qun Yu

“…Inhibiting ET1 signaling markedly enhanced the anticancer effectiveness of paclitaxel (PTX), providing a promising approach for managing NSCLC.…”
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Human lncRNAs NEAT1 and MALAT1 regulate the tumor microenvironment in lung cancer PDX models in athymic nude mice by Min-Shiau Hsieh, Meng-Xian Lin, Bing-Ying Ho, Jong-Kai Hsiao

“…This model allowed for the analysis of microenvironments through whole transcriptome sequencing to assess gene expression variations across different passages of the PDX model. …”
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Comparison of Nucleosome Landscapes Between Porcine Embryonic Fibroblasts and GV Oocytes by Minjun Zhao, Shunran Zhao, Zhaoqi Pang, Chunhui Jia, Chenyu Tao

“…Next, we reanalyzed the currently published transcriptome of fully grown GV oocytes and PEF, and a total of 51 genes in BF and 80 genes in PEF were identified as being uniquely expressed. …”
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Exploration of the clinicopathological and prognostic significance of BRCA1 in gastric cancer by Hongrong Zhang, Qi Xu, Hongxing Kan, Yinfeng Yang, Yunquan Cai

“…This is one of the initial comprehensive analysis involving MR and multidimensional approaches; it revealed the significant role of BRCA1 in GC, providing new ideas on drugs and targets for GC clinical treatment.…”
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Molecular mechanisms of cryoablation-mediated lung cancer suppression unveiled by non-coding RNA regulatory network profiling by Xiaofan Wang, Mohan Zhang, Dianna Liu, Shicheng Lin, Yuxin Zhang, Quanwang Li

“…We conducted the first transcriptome-based investigation of cryoablation’s anti-tumor mechanisms using the Lewis lung carcinoma (LLC) model. …”
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Let-7f-5p Modulates Lipid Metabolism by Targeting Sterol Regulatory Element-Binding Protein 2 in Response to PRRSV Infection by Dongfeng Jiang, Liyu Yang, Xiangge Meng, Qiuliang Xu, Xiang Zhou, Bang Liu

“…The findings demonstrate that let-7f-5p modulates lipogenesis by targeting SREBP2, providing novel insights into miRNA-mediated PRRSV pathogenesis and offering a potential antiviral therapeutic target.…”
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A new perspective on macrophage-targeted drug research: the potential of KDELR2 in bladder cancer immunotherapy by Zhiyi Zhao, Hongling Jia, Zhou Sun, Yumeng Li, Lingyun Liu

“…IntroductionBladder cancer was recognized as one of the most common malignant tumors in the urinary system, and treatment options remained largely limited to conventional surgery, radiotherapy, and chemotherapy, which limited patient benefits.MethodsResearchers constructed an RNA transcriptome map of bladder cancer by integrating single-cell RNA sequencing and clinical data, identifying potential molecular targets for diagnosis and treatment. …”
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G3DC: A Gene-Graph-Guided Selective Deep Clustering Method for Single Cell RNA-seq Data by Shuqing He, Jicong Fan, Tianwei Yu

“…Analyzing single-cell transcriptome allows the identification of heterogeneous cell groups, cellular-level regulations, and the trajectory of cell development. …”
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