Comparative Transcriptome Analysis of Sexual Differentiation in Male and Female Gonads of Nao-Zhou Stock Large Yellow Croaker (<i>Larimichthys crocea</i>) by Haojie Wang, Zirui Wen, Eric Amenyogbe, Jinghui Jin, Yi Lu, Zhongliang Wang, Jiansheng Huang

“…This study used Illumina high-throughput sequencing to sequence the transcriptome of the testes and ovaries of Nao-zhou stock large yellow croaker to identify genes and molecular functions related to sex determination. …”
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Transcriptomic analysis of non-leukemic cell subsets in azacytidine-responsive AML highlights pathways associated with adhesion, platelet aggregation, and angiogenesis in mice and... by Nancy D. Ebelt, Suvithanandhini Loganathan, Lara C. Avsharian, Edwin R. Manuel

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Epizootic shell disease induces systemic transcriptomic shifts in Homarus americanus, characterized by increased shell degradation and impaired energy metabolism across tissues by Minseo Kim, Dianjun Cao, Vincent Cavaleri, Kyudong Han, Kyudong Han, Kyudong Han, Seyoung Mun, Seyoung Mun, Seyoung Mun, Soo Jin Jeon

“…This study revealed tissue-specific transcriptomic responses to ESD in the American lobster, providing a foundation for elucidating the molecular mechanisms underlying disease progression.…”
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Evaluating two live-attenuated vaccines against Salmonella enterica serovar Reading in turkeys: reduced tissue colonization and cecal tonsil transcriptome responses by Melissa S. Monson, Manoj Gurung, Manoj Gurung, Bradley L. Bearson, Samuel J. Whelan, Samuel J. Whelan, Julian M. Trachsel, Torey Looft, Matthew J. Sylte, Shawn M.D. Bearson

“…Gene expression of intestinal transporters (such as SCNN1B and SLC10A2) and tight junction proteins was significantly decreased in the turkey cecal tonsil transcriptome at 2 DPI with S. Reading. Vaccination with either vaccine mitigated most cecal tonsil gene expression responses to S. …”
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Transcriptome Analysis and Functional Characterization of the <i>HvLRR_8-1</i> Gene Involved in Barley Resistance to <i>Pyrenophora graminea</i> by Wenjuan Yang, Ming Guo, Yan Li, Qinglan Yang, Huaizhi Zhang, Chengdao Li, Juncheng Wang, Yaxiong Meng, Xiaole Ma, Baochun Li, Lirong Yao, Hong Zhang, Ke Yang, Xunwu Shang, Erjing Si, Huajun Wang

“…This study represents the first comparative transcriptome analysis of barley varieties with differing responses to <i>Pg</i> infection, providing that <i>HvLRR_8-1</i> represents a promising candidate gene for improving durable resistance against <i>Pg</i> in cultivated barley.…”
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Integrating multiple “omics” analysis for plant metabolites and their functions by ZHOU Guoyan, HU Wangxiong, XU Jianhong, XUE Qingzhong

“…Glucosinolate (GSL) metabolic pathways provide a useful model system for the research of genome structure of the quantitative characters, while the genome-wide association studies (GWAS) fast become the preferred method for analyzing complex quantitative traits. …”
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The Human Pathology Atlas for deciphering the prognostic features of human cancersResearch in context by Meng Yuan, Cheng Zhang, Kalle Von Feilitzen, Martin Zwahlen, Mengnan Shi, Xiangyu Li, Hong Yang, Xiya Song, Hasan Turkez, Mathias Uhlén, Adil Mardinoglu

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Foodomics: A sustainable approach for the specific nutrition and diets for human health by Dipendra Kumar Mahato, Madhu Kamle, Shikha Pandhi, Surabhi Pandey, Akansha Gupta, Veena Paul, Rhythm Kalsi, Swati Agrawal, Dawrul Islam, Shubhra Khare, Ajey Singh, Pradeep Kumar, Safia Obaidur Rab, Mohd Saeed

“…Its applications span the food industry and human health, including efforts to combat malnutrition, provide dietary recommendations, and ensure food safety. …”
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Endochondral ossification of hindlimbs in embryonic development of Japanese Quail (Coturnix japonica) by Xuan Li, Yuxin Zhang, Hongfeng Zhao

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Comprehensive transcriptomic analysis reveals turnip mosaic virus infection and its aphid vector Myzus persicae cause large changes in gene regulatory networks and co-transcription... by Venura Herath, Clare L. Casteel, Jeanmarie Verchot

“…This study employed high-throughput transcriptomic and alternative splicing analysis to understand the separate and combined impacts on host gene expression in Arabidopsis thaliana by Myzus persicae (green peach aphid), and turnip mosaic virus (TuMV). …”
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Cross-species analysis of abiotic stress in hydroponic leafy crops reveals conserved regulatory networks and key divergences by Jia Min Lee, Jia Min Lee, Jong Ching Goh, Eugene Koh, Daniela Mutwil-Anderwald, Marek Mutwil, Marek Mutwil

“…This study not only deepens our understanding of abiotic stress adaptation in hydroponic systems but also provides a critical foundation for breeding stress-resilient crops and developing smart agriculture solutions.…”
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Multimodal sequencing of neoadjuvant nivolumab treatment in hepatocellular carcinoma reveals cellular and molecular immune landscape for drug response by Fanhong Zeng, Qingyang Zhang, Yu-Man Tsui, Huanhuan Ma, Lu Tian, Abdullah Husain, Jingyi Lu, Joyce Man-Fong Lee, Vanilla Xin Zhang, Po-Man Li, Gary Cheuk-Hang Cheung, Tan-To Cheung, Daniel Wai-Hung Ho, Irene Oi-Lin Ng

“…We used spatially-resolved transcriptomics, single- and bulk-cell transcriptomics, and TCR clonotype analyses to examine the spatiotemporal dynamics of the effects of nivolumab. …”
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Spatiotemporal dynamics of early oogenesis in pigs by Wei Ge, Yi-Lin Niu, Yu-Kang Li, Li Li, Han Wang, Wen-Wen Li, Tian Qiao, Yan-Ni Feng, Yu-Qing Feng, Jing Liu, Jun-Jie Wang, Xiao-Feng Sun, Shun-Feng Cheng, Lan Li, Wei Shen

“…Conclusions Overall, our work provides insight into the spatial characteristics of early oogenesis and the regulatory role of ovarian microenvironments in germ cell fate within a spatial context.…”
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Identifying key palmitoylation-associated genes in endometriosis through genomic data analysis by Jinyan Kai, Jiaqi Su, Yinping You, Xiaoliang Liang, Haitao Huang, Jie Fang, Qiong Chen

“…Methods This study integrated transcriptomic analysis and Mendelian randomization (MR) to identify a causal gene set implicated in endometriosis. …”
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Potential effect of Wolbachia on virus restriction in the spider mite T. truncatus by Lucas Yago Melo Ferreira, João Pedro Nunes Santos, David Gabriel do Nascimento Souza, Lixsy Celeste Bernardez Orellana, Sabrina Ferreira de Santana, Anderson Gonçalves Sousa, Paula Luize Camargos Fonseca, Amanda Gabrielly Santana Silva, Vinicius Castro Santos, Isaque João da Silva de Faria, Roenick Proveti Olmo, Luis Gustavo Carvalho Pacheco, Marcio Gilberto Cardoso Costa, Carlos Priminho Pirovani, Anibal Ramadan Oliveira, Eric Roberto Guimarães Rocha Aguiar

“…However, the viral restriction phenotype vanishes in co-infected mites. Transcriptomics analysis of singly-infected mites revealed upregulation of piRNA and autophagy-related genes, while lipid metabolism processes-related genes were downregulated, indicating an endosymbiont-sharing mechanisms of viral interference. …”
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Reference genome and reproduction-focused transcriptome for the threatened alpine tree frog (Litoria verreauxii alpina) [version 1; peer review: 2 approved] by Laura Brannelly, Alexander S. Wendt

“…This study provides the first publicly available reference genome for the Litoria genus to assist in conservation and reproduction focused works in amphibian management.…”
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Evaluating the Effectiveness of Various Small RNA Alignment Techniques in Transcriptomic Analysis by Examining Different Sources of Variability Through a Multi-Alignment Approach by Xinwei Zhao, Eberhard Korsching

“…While the focus is on microRNA analysis, the templates provided can be adapted for all transcriptomic and genomic analyses. …”
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Use of the Puccinia sorghi haustorial transcriptome to identify and characterize AvrRp1-D recognized by the maize Rp1-D resistance protein. by Saet-Byul Kim, Ki-Tae Kim, Solhee In, Namrata Jaiswal, Gir-Won Lee, Seungmee Jung, Abigail Rogers, Libia F Gómez-Trejo, Sujan Gautam, Matthew Helm, Hee-Kyung Ahn, Hye-Young Lee, Quentin D Read, Jongchan Woo, Katerina L Holan, Steven A Whitham, Jonathan D G Jones, Doil Choi, Ralph Dean, Eunsook Park, Peter Balint-Kurti

“…Our research provides valuable insights into the molecular interactions driving resistance against common rust in maize.…”
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Integrative transcriptomic and proteomic analyses reveal that carbon metabolism and complement system of Madin Darby Bovine Kidney cells are affected by bovine coronavirus infectio... by Hui Zhang, Qisheng Yu, Rui Guo, Qing Zhu, Jin Yu, Zhaohui Zhang, Lan Lan, Cheng Tang, Changqing Yu, Bin Zhang

“…Conclusions The findings of this study provide the first report of the integrative transcriptomic and proteomic analyses of BCoV infection in MDBK cells. …”
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Reference-guided detection of the transcriptome reveals circular RNA-related competing endogenous RNA networks in response to three respiration pathogens in pig lungs by Qian Wu, Kun Du, Mao-qing Gu, Yu Xia, Miao Yin, Xian Li, Shu-ting Zhang, Hong Zhao, Zhang-lin Li, Xi-wen Chen

“…Key points: 1. Our study provided a comprehensive circRNA catalog of circRNAs in pig lungs and revealed the differences of circRNAs in response to three major respiration pathogens. 2. …”
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