Using transcripts to refine image based cell segmentation with FastReseg by Lidan Wu, Joseph M. Beechem, Patrick Danaher

“…Abstract Spatial transcriptomics (ST) faces persistent challenges in cell segmentation accuracy, which can bias biological interpretations in a spatial-dependent way. …”
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Recent developments in omics studies and artificial intelligence in depression and suicide by Qingzhong Wang, Yogesh Dwivedi

“…This data captures significant molecular-level changes, including alterations in gene transcripts, epigenomes, and proteins, effectively reflecting the biological state of the disease. This review provides a systematic overview of advancements in transcriptomics, non-coding RNA, and AI related to depression and suicide. …”
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Integrating Proteomics and GWAS to Identify Key Tissues and Genes Underlying Human Complex Diseases by Chao Xue, Miao Zhou

“…Methods: We compiled proteomic and paired transcriptomic data for 12,229 genes across 32 human tissues from the GTEx project. …”
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Multi-omics insights into growth and fruiting body development in the entomopathogenic fungus Cordyceps blackwelliae by Jia-Ni Li, Shu Zhang, Yong-Jie Zhang

“…These findings provide new insights into the molecular networks underlying C. blackwelliae growth and fruiting body formation.…”
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An in vitro neurobacterial interface reveals direct modulation of neuronal function by gut bacteria by Juan Lombardo-Hernandez, Jesús Mansilla-Guardiola, Riccardo Aucello, Cristian Botta, Maria Teresa García-Esteban, Antonio Murciano-Cespedosa, David Muñoz-Rodríguez, Elisa Quarta, Álvaro Mateos González, Carmen Juan-Llamas, Kalliopi Rantsiou, Stefano Geuna, Luca Cocolin, Celia Herrera-Rincon

“…Together, our results provide proof-of-concept for targeted neuronal responses induced by bacterial contact, offering key resources and transcriptomic data to advance the study of bacteria-driven neural modulation within the gut–brain axis.…”
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Multi-omics analysis of SFTS virus infection in Rhipicephalus microplus cells reveals antiviral tick factors by Marine J. Petit, Charlotte Flory, Quan Gu, Mazigh Fares, Douglas Lamont, Alan Score, Kelsey Davies, Lesley Bell-Sakyi, Pietro Scaturro, Benjamin Brennan, Alain Kohl

“…Collectively, our results provide insights into the antiviral responses of R. microplus vector cells and highlight critical SFTSV restriction factors, while enriching transcriptomic and proteomic resources for future research.…”
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Tracing the evolutionary and genetic footprints of atmospheric tillandsioids transition from land to air by Xiaolong Lyu, Ping Li, Liang Jin, Feng Yang, Boas Pucker, Chenhao Wang, Linye Liu, Meng Zhao, Lu Shi, Yutong Zhang, Qinrong Yang, Kuangtian Xu, Xiao Li, Zhongyuan Hu, Jinghua Yang, Jingquan Yu, Mingfang Zhang

“…In this study, we use the epiphytic Tillandsioideae subfamily of Bromeliaceae as model plants to explore their origin, evolution and diversification. We provide a comprehensive phylogenetic tree based on nuclear transcriptomic sequences, indicating that core tillandsioids originated approximately 11.3 million years ago in the Andes. …”
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Assessment of the new Next Generation Sequencing (NGS) tools to identify genes associated with tolerance to water deficit in sugarcane by John Jaime Riascos Arcos, Héctor Fabio Espitia Navarro, Jershon López Gerena

“…Also, it was possible to detect differences in expression levels of highly similar transcripts. Our results provide evidence that support the use of NGS technologies in transcriptomics studies in genetically complex species such as sugarcane.…”
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Multi-omics analysis constructs a novel neuroendocrine prostate cancer classifier and classification system by Junxiao Shen, Luyuan Lu, Zujie Chen, Wei Guo, Shuwen Wang, Ziqiao Liu, Xuke Gong, Yiming Qi, Ruyi Jin, Cheng Zhang

“…Multi-omics analysis included 19 bulk transcriptomics, 14 single-cell transcriptomics, 1 spatial transcriptomics, 16 published NE signatures and 10 cellular experiments combined with multiple machine learning algorithms to construct a novel NEPC classifier and classification. …”
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Spatial heterogeneity reveals an evolutionary signature predicting therapeutic response and clinical outcomes in hepatocellular carcinoma by Shangyi Luo, Li Liu, Yang Sun, Jian Shi, Yajing Zhang, Yajing Zhang, Yajing Zhang

“…However, it remains unexplored whether intra-tumoral transcriptomic differences can capture crucial information regarding HCC evolution and be utilized to derive a predictive signature for patient’s clinical trajectories.MethodsWe quantified transcriptomic heterogeneity using four multiregional HCC cohorts comprising 172 samples from 37 patients, and validated transcriptomic heterogeneity and spatial dynamics using multiregional single-cell transcriptomic profiling of 110,817 cells from 34 liver specimens. …”
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Investigating the Causality and Pathogenesis of Primary Sclerosing Cholangitis in Colorectal Cancer Through Mendelian Randomization and Bioinformatics by Jie Jiao, Honglei Wang, Danping Sun, Wenbin Yu

“…Conclusion: Our MR study provides evidence that genetic susceptibility to PSC is significantly associated with an increased risk of colorectal cancer in European populations. …”
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Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses by Aurelien Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Attila Gabor, Kristina B. Emdal, Vitor Vieira, Dorte B. Bekker‐Jensen, Jennifer Kranz, Eric.M.J. Bindels, Ana S.H. Costa, Abel Sousa, Pedro Beltrao, Miguel Rocha, Jesper V. Olsen, Christian Frezza, Rafael Kramann, Julio Saez‐Rodriguez

“…Abstract Multi‐omics datasets can provide molecular insights beyond the sum of individual omics. …”
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Molecular characterization of Pseudomyxoma peritonei with single-cell and bulk RNA sequencing by Ye Jin Ha, Seong-Hwan Park, Seon-Kyu Kim, Ka Hee Tak, Jeong-Hwan Kim, Chan Wook Kim, Yong Sik Yoon, Seon-Young Kim, Jong Lyul Lee

“…Here, we present single-cell transcriptomic profiling of five PMP cases to identify cell type-specific gene features associated with PMP pathogenesis. …”
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The genome of a sea spider corroborates a shared Hox cluster motif in arthropods with a reduced posterior tagma by Nikolaos Papadopoulos, Siddharth S. Kulkarni, Christian Baranyi, Bastian Fromm, Emily V. W. Setton, Prashant P. Sharma, Andreas Wanninger, Georg Brenneis

“…Due to the lack of high-quality genomic and transcriptomic resources, however, this potential remains largely unexplored. …”
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Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis by Tomoya Kujirai, Junko Kato, Kyoka Yamamoto, Seiya Hirai, Takeru Fujii, Kazumitsu Maehara, Akihito Harada, Lumi Negishi, Mitsuo Ogasawara, Yuki Yamaguchi, Yasuyuki Ohkawa, Yoshimasa Takizawa, Hitoshi Kurumizaka

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Unraveling the Multi-Omic Landscape of Extracellular Vesicles in Human Seminal Plasma by Laura Governini, Alesandro Haxhiu, Enxhi Shaba, Lorenza Vantaggiato, Alessia Mori, Marco Bruttini, Francesca Loria, Natasa Zarovni, Paola Piomboni, Claudia Landi, Alice Luddi

“…Bioinformatic tools were applied for functional omics analysis; the integration of proteomic and transcriptomic data provided a comprehensive understanding of the cargo content and regulatory networks present in EVs. …”
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Chronic stress in mice: how gut bacteria influence gene activity in key brain neurons by Wenxia Jiang, Yifan Li, Jie Yang, Xunmin Tan, Ruimin Tian, Guojing Ma, Jing Wu, Jianping Zhang, Yu Huang, Ping Liu, Minghao Yuan, Xiaodong Song, Leyao Luo, Xingyu Zhou, Hongzhou Zuo, Ma-Li Wong, Julio Licino, Peng Zheng

“…Additionally, single-nucleus RNA sequencing (snRNA-seq) was used to compare the transcriptomic changes in the hypothalamus of these three groups. …”
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Integrative Spatial Proteomics and Single-Cell RNA Sequencing Unveil Molecular Complexity in Rheumatoid Arthritis for Novel Therapeutic Targeting by Xue Wang, Fei Wang, Archana S. Iyer, Heather Knight, Lori J. Duggan, Yingli Yang, Liang Jin, Baoliang Cui, Yupeng He, Jan Schejbal, Lucy A. Phillips, Bohdan P. Harvey, Sílvia Sisó, Yu Tian

“…By combining high-resolution spatial proteomics and transcriptomic analyses, we provide novel insights into the molecular mechanisms driving RA, and highlight potential protein targets for therapeutic intervention. …”
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The role of multiomics in revealing the mechanism of skin repair and regeneration by Shaoyan Shi, Xuehai Ou, Jafeng Long, Xiqin Lu, Siqi Xu, Gang Li

“…While genomic studies identify the genetic basis of wound healing, transcriptomics and proteomics uncover the dynamic changes in gene and protein expression, and metabolomics provides a snapshot of metabolic alterations associated with wound healing. …”
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Using DIMet for Differential Analysis of Labeled Metabolomics Data: A Step-by-step Guide Showcasing the Glioblastoma Metabolism by Johanna Galvis, Joris Guyon, Thomas Daubon, Macha Nikolski

“…In this protocol, we encourage the researchers to use SIRM and transcriptomics data and to perform the downstream analysis using our software tool DIMet. …”
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