SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution by Linbu Liao, Esha Madan, António M. Palma, Hyobin Kim, Amit Kumar, Praveen Bhoopathi, Robert Winn, Jose Trevino, Paul Fisher, Cord Herbert Brakebusch, Gahyun Kim, Junil Kim, Rajan Gogna, Kyoung Jae Won

“…Our test showed that SC2Spa performs well for various ST technologies and robust to spatial resolution. …”
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BSA-seq and transcriptome analyses reveal candidate gene associated with petiole color in papaya (Carica papaya L.) by Sisi Chen, Vincent N Michael, Sarah Brewer, Alan Chambers, Xingbo Wu

“…In this study, F1 and F2 populations generated from two breeding lines PR-2043 (green petiole) and T5-2562 (purple petiole) were used to evaluate the inheritance patterns of petiole color as well as determine genetic loci and genes involved in petiole pigmentation in papaya through bulk segregant analysis (BSA) and transcriptome sequencing. …”
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Single-cell protein-DNA interactomics and multiomics tools for deciphering genome regulation by Xiong Haiqing, Wang Runyu, He Aibin

“…The emergence of single-cell genomic and transcriptomic sequencing accelerates the development of single-cell epigenomic technologies, providing an unprecedented opportunity for decoding cell fate decisions largely encoded in the epigenome. …”
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A multi-omics technology to the study of lactic acid bacteria responses to environmental stress: the past, current and future trends by Yaqi Liu, Jingxian Sun, Xiaowen Liu, Mingpeng Zheng, Wen Ma, Gang Jin

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Interpretable and integrative analysis of single-cell multiomics with scMKL by Samuel D. Kupp, Ian A. VanGordon, Mehmet Gönen, Sadık Esener, Sebnem Ece Eksi, Çiğdem Ak

“…It outperforms existing methods while delivering interpretable results that identify key transcriptomic and epigenetic features, as well as multimodal pathways– that existing methods have failed to achieve, in breast, lymphatic, prostate, and lung cancers. …”
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Integrating Artificial Intelligence in Next-Generation Sequencing: Advances, Challenges, and Future Directions by Konstantina Athanasopoulou, Vasiliki-Ioanna Michalopoulou, Andreas Scorilas, Panagiotis G. Adamopoulos

“…Key applications of AI integration in NGS include variant calling, epigenomic profiling, transcriptomics, and single-cell sequencing, where AI models such as CNNs, RNNs, and hybrid architectures outperform traditional methods. …”
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PLOD3 as a novel oncogene in prognostic and immune infiltration risk model based on multi-machine learning in cervical cancer by Lingling Qiu, Xiuchai Qiu, Xiaoyi Yang

“…Furthermore, the model demonstrated notable variations in immune cell infiltration among risk categories, which shown regulatory T cells may be involved in immune suppression, and natural killer cells might have a limited effect in tumor clearance. Spatial transcriptomics and single-cell analyses further validated the model, uncovering tumor heterogeneity and distinct intercellular communication patterns associated with different risk levels. …”
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Age-specific effects of synthetic cannabinoids on cognitive function and hippocampal gene expression in mice: insights from behavioral and molecular correlates by Kaixi Li, Kaixi Li, Yuanyuan Chen, Yuanyuan Chen, Yawen Xu, Yawen Xu, Yuan Pang, Yongli Bao, Simeng Zhang, Simeng Zhang, Xuesong Shi, Xuesong Shi, Jingzhi Ran, Jingzhi Ran, Yanling Qiao, Yanling Qiao, Yanling Qiao, Yizhao Xu, Yizhao Xu, Yiming Wang, Bin Di, Bin Di, Peng Xu, Peng Xu

“…The increasing use of Synthetic cannabinoids (SCs) in adolescents and young adults poses significant medical and psychiatric risks, and previous reports have been dominated by single-age animal studies. Here, we first investigated the effects of a single exposure of the fourth-generation synthetic cannabinoid 4F-ABUTINACA on cognitive behaviors in adolescent (PND 28–35 days) and adult (PND 49–56 days) male mice in an animal model, followed by an age-specific systematic study by conducting a whole-gene transcriptomics study of hippocampal tissue in the brain. …”
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Unraveling the pathogenesis of Barrett’s esophagus and esophageal adenocarcinoma: the “omics” era by Alberto Barchi, Giuseppe Dell’Anna, Giuseppe Dell’Anna, Luca Massimino, Luca Massimino, Francesco Vito Mandarino, Edoardo Vespa, Edi Viale, Sandro Passaretti, Vito Annese, Vito Annese, Alberto Malesci, Alberto Malesci, Silvio Danese, Silvio Danese, Federica Ungaro

“…The implementation of transcriptomic and proteomic analysis, even at the single-cell level, has widened the horizons, complementing the genomic alterations with their transcriptional and translational bond. …”
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Global Transcriptome Analysis Reveals Distinct Aluminum-Tolerance Pathways in the Al-Accumulating Species Hydrangea macrophylla and Marker Identification. by Haixia Chen, Changping Lu, Hui Jiang, Jinhui Peng

“…The assembly of hydrangea transcriptome provides a rich source for gene identification and mining molecular markers, including single nucleotide polymorphism (SNP) and simple sequence repeat (SSR). …”
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Biomarkers and potential therapeutic targets driving progression of non-alcoholic steatohepatitis to hepatocellular carcinoma predicted through transcriptomic analysis by Hui Fan, Rong Wang, Bin Wen, Jing Xiong

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scFocus: Detecting branching probabilities in single-cell data with SAC by Chunlin Chen, Zeyu Fu, Jiajia Yang, Huaqing Chen, Jiabao Huang, Shitian Qin, Chuhuai Wang, Xiaoqian Hu

“…Single-cell transcriptomics captures cell differentiation trajectories through changes in gene expression intensity. …”
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Detection by Single-Cell RNA Sequencing of Virally Mediated Skin Diseases by Linda Zhou, Thomas H. Leung

“…However, their role and precise mechanism of action in other skin diseases remain unknown. We describe a single-cell RNA-sequencing–based strategy to interrogate human skin biopsies for viral transcripts, permitting detection of viral infection within a sample, single-cell resolution of virally infected cells and identification of subsequent transcriptomic perturbations. …”
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An annotated CNS transcriptome of the medicinal leech, Hirudo verbana: De novo sequencing to characterize genes associated with nervous system activity. by Adam J Northcutt, Eva K Fischer, Joshua G Puhl, Karen A Mesce, David J Schulz

“…Here, we generated the first de novo transcriptome assembly from the entire central nervous system of Hirudo verbana, with the goal of providing a molecular resource, as well as to lay the foundation for a comprehensive discovery of genes fundamentally important for neural function. …”
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Integrated transcriptomics and machine learning reveal REN as a dual regulator of tumor stemness and NK cell evasion in Wilms tumor progression by Qingfei Cao, Junyi Li, Yunfei Zou, Changwen Xu, Huihui Tang, Meixue Chen

“…Tumor stemness and immune evasion mechanisms are implicated in poor clinical outcomes, yet the molecular drivers underpinning these processes remain inadequately understood.MethodsWe employed an integrative approach combining single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, bulk RNA-seq, and advanced machine learning techniques to uncover molecular regulators of tumor behavior in WT. …”
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Single-cell spatial atlas of smoking-induced changes in human gingival tissues by Yong Zhang, Zongshan Shen, Jiayu Yang, Junxian Ren, Chi Zhang, Lingping Tan, Li Gao, Chuanjiang Zhao

“…Recent advances in spatial transcriptomics have enabled a deeper exploration of the periodontal tissue microenvironment at single-cell resolution, offering new opportunities to investigate these mechanisms. …”
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Single-Cell RNA Sequencing and Combinatorial Approaches for Understanding Heart Biology and Disease by Le Wang, Bo Jin

“…In this review, we will introduce the latest advances in cardiac health and disease at single-cell resolution; single-cell detection methods that can be used for transcriptome, genome, epigenome, and proteome analysis; single-cell multi-omics; as well as their future application prospects.…”
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Understanding Atherosclerotic Plaque Cellular Composition: Recent Advances Driven by Single Cell Omics by Esra Cetin, Anne-Catherine Raby

“…With the development of single-cell transcriptomic and proteomic technologies, a previously inconceivable wealth of data has been generated in an attempt to better understand the pathophysiology of the disease and identify novel avenues for the development of targeted therapeutic interventions. …”
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Integrating Mendelian randomization and multi-transcriptomic analyses to unveil the genetic association risk of regulatory T cell-mediated free cholesterol and gastric cancer by Fanyu Peng, Haitao Liu, Yesong Guo, Jing Wen, Yizhi Ge, Yanhong Luo

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The Maltase Involved in Starch Metabolism in Barley Endosperm Is Encoded by a Single Gene. by Vasilios M E Andriotis, Gerhard Saalbach, Robbie Waugh, Robert A Field, Alison M Smith

“…It has been proposed that maltase may be involved directly in starch granule degradation as well as in maltose hydrolysis. The aim of our work was to discover the nature of maltase in barley endosperm. …”
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