Mushroom β-glucan and polyphenol formulations as natural immunity boosters and balancers: nature of the application by Maja Kozarski, Anita Klaus, Leo van Griensven, Dragica Jakovljevic, Nina Todorovic, Wan Abd Al Qadr Imad Wan-Mohtar, Jovana Vunduk

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Transcriptional regulation of suberin and its response to the environment by ZHOU Yue, AN Yongping, MA Rong, WANG Pei

“…[Prospect] Future research should focus on the key regulatory nodes of suberin biosynthesis, particularly exploring the factors that influence species-specific deposition of suberin in crops. By leveraging multi-omics approaches to elucidate its transport, assembly, and post-transcriptional regulation mechanisms, there is potential to provide new strategies for enhancing nutrient use efficiency and stress resistance in crop genetic improvement.…”
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Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species by Reilly Pidgeon, Sacha Mitchell, Michael Shamash, Layan Suleiman, Lharbi Dridi, Corinne F. Maurice, Bastien Castagner

“…Collectively, this work identifies Enterocloster species and the ucd operon as important contributors to uroA production and establishes a multi-omics framework to further our mechanistic understanding of polyphenol metabolism by the human gut microbiota.…”
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Impact of developmental state, p53 status, and interferon signaling on glioblastoma cell response to radiation and temozolomide treatment. by Artem Berezovsky, Oluwademilade Nuga, Indrani Datta, Kimberly Bergman, Thais Sabedot, Katherine Gurdziel, Susan Irtenkauf, Laura Hasselbach, Yuling Meng, Claudius Mueller, Emanuel F Petricoin, Stephen Brown, Neeraja Purandare, Sidhesh Aras, Tom Mikkelsen, Laila Poisson, Houtan Noushmehr, Douglas Ruden, Ana C deCarvalho

“…In this study, we employed an integrative multi-omics approach, including targeted proteomics, transcriptomics, genomics, and DNA methylation profiling, to investigate the response of a representative panel of GBM patient-derived cancer stem cells (CSCs) to astrocytic differentiation and RT and TMZ treatments. …”
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Subregional pedoclimatic conditions with contrasted UV-radiation shape host-microbiome and metabolome phenotypes in the grape berry by Viviana Martins, Cécile Abdallah, António Teixeira, Carolina Moreira, Márcio Nóbrega, Arnaud Lanoue, Hernâni Gerós

“…This study used integrative omics to address the response of key elements of the grapevine holobiont to contrasted pedoclimatic conditions found in distinct subregions of Douro Valley (Portugal). …”
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Drought Tolerance in Modern and Wild Wheat by Hikmet Budak, Melda Kantar, Kuaybe Yucebilgili Kurtoglu

“…Therefore, identification of candidate molecules or loci involved in drought tolerance is necessary, which is undertaken by “omics” studies and QTL mapping. In this sense, wild counterparts of modern varieties, specifically wild emmer wheat (T. dicoccoides), which are highly tolerant to drought, hold a great potential. …”
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Rehabilomics Strategies Enabled by Cloud-Based Rehabilitation: Scoping Review by Sejun Oh, SangHeon Lee

“… BackgroundRehabilomics, or the integration of rehabilitation with genomics, proteomics, metabolomics, and other “-omics” fields, aims to promote personalized approaches to rehabilitation care. …”
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Genome-wide transcriptomics revealed carbon source-mediated gamma-aminobutyric acid (GABA) production in a probiotic, Lactiplantibacillus pentosus 9D3 by Nachon Raethong, Pitakthai Chamtim, Roypim Thananusak, Kanyawee Whanmek, Chalat Santivarangkna

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Decoding the mechanisms behind second primary cancers by Meiyuan Zeng, Anqi Lin, Aimin Jiang, Zhengang Qiu, Hongman Zhang, Shifu Chen, Mingyan Xu, Zaoqu Liu, Quan Cheng, Jian Zhang, Peng Luo

“…Furthermore, potential applications of intratumoral microbes, single-cell multi-omics, and metabolomics in investigating SPC mechanisms are also discussed, providing new ideas for follow-up studies.…”
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How the Knowledge of Interactions between Meningococcus and the Human Immune System Has Been Used to Prepare Effective Neisseria meningitidis Vaccines by R. Gasparini, D. Panatto, N. L. Bragazzi, P. L. Lai, A. Bechini, M. Levi, P. Durando, D. Amicizia

“…In the last decades, tremendous advancement in dissecting the mechanisms of pathogenicity of Neisseria meningitidis at a molecular level has been achieved, exploiting converging approaches of different disciplines, ranging from pathology to microbiology, immunology, and omics sciences (such as genomics and proteomics). …”
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Perspectives on Clinical Informatics: Integrating Large-Scale Clinical, Genomic, and Health Information for Clinical Care by In Young Choi, Tae-Min Kim, Myung Shin Kim, Seong K. Mun, Yeun-Jun Chung

“…Bioclinical data warehouses integrating heterogeneous patient-related clinical or omics data should be considered. The representative standardization effort by the Clinical Bioinformatics Ontology (CBO) aims to provide uniquely identified concepts to include molecular pathology terminologies. …”
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Dynamic changes of peptidome and release of polysaccharide in sea cucumber (Apostichopus japonicus) hydrolysates depending on enzymatic hydrolysis approaches by Yanchao Wang, Yan Song, Yaoguang Chang, Yanyan Liu, Guangning Chen, Changhu Xue

“…Here, inspired by the clarification of Apostichopus japonicus genome, we investigated the enzymatic hydrolysis of sea cucumber body wall by using the omics strategy. Shared proteins, including major yolk proteins, collagens, extracellular matrix glycoproteins and muscle proteins, were released from the body wall by different hydrolysis condition. …”
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A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens by Gina Bouchard, Weiruo Zhang, Ilayda Ilerten, Irene Li, Asmita Bhattacharya, Yuanyuan Li, Winston Trope, Joseph B. Shrager, Calvin Kuo, Michael G. Ozawa, Amato J. Giaccia, Lu Tian, Sylvia K. Plevritis

“…Abstract Spatial omics is enabling unprecedented tissue characterization, but the ability to adequately compare spatial features across samples under different conditions is lacking. …”
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Somatic Mutaome Profile in Human Cancer Tissues by Nayoung Kim, Yourae Hong, Doyoung Kwon, Sukjoon Yoon

“…The Cancer Genome Atlas database includes large amounts of sequencing and omics data generated from diverse human cancer tissues. …”
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Contrastive-learning of language embedding and biological features for cross modality encoding and effector prediction by Yue Peng, Junze Wu, Yi Sun, Yuanxing Zhang, Qiyao Wang, Shuai Shao

“…Furthermore, integrating omics data via CLEF framework enhances protein representations to illustrate effector-effector interactions and determine in vivo colonization-essential genes. …”
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Understanding integrative approach of translational bioinformatics on cardiovascular disease: Myocardial Ischemia by Yeswanth Ranganathan, Saayaa Nazar, Ravi Shankar Krishnan, Yuvaraj Dinakarkumar, Vijayalakshmi Varadarajan, Lenita Sebastian, Brindha Rethinam

“…Conclusions Combining clinical and omics data using translational bioinformatics is critical for refining treatment regimens and speeding up medication repurposing. …”
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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

“…Abstract Pseudomyxoma peritonei (PMP), a rare condition characterized by mucinous ascites in the peritoneal cavity, often leads to a poor prognosis. However, omics profiling of this disease remains significantly underexplored. …”
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NTHi killing activity is reduced in COPD patients and is associated with a differential microbiome by Vancheswaran Gopalakrishnan, Ben Sparklin, Jung Hwan Kim, Jerome Bouquet, Margaret Kehl, Tara Kenny, Christopher Morehouse, Carolina Caceres, Paul Warrener, Ventzislava A. Hristova, Susan Wilson, Harini Shandilya, Arnita Barnes, Alexey Ruzin, Junmin Wang, Lisa Oberg, Bastian Angermann, Christopher McCrae, Adam Platt, Daniel Muthas, Sonja Hess, Christine Tkaczyk, Bret R. Sellman, Kristoffer Ostridge, Maria G. Belvisi, Tom M. A. Wilkinson, Karl J. Staples, Antonio DiGiandomenico, on behalf of the MICA II Study Group

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Integrative genetics and multiomics analysis reveal mechanisms and therapeutic targets in vitiligo highlighting JAK STAT pathway regulation of CTSS by Zi-yue Dong, Ming-jie He, Yong-kai Yu, Fang Wang, Peng-yuan Zhao, De-long Ran, De-shuang Fu, Qing He, Run-ping Yang, Jiang-an Zhang

“…Integrating multiple layers of omics data can provide a comprehensive view of disease pathogenesis and identify potential therapeutic targets. …”
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Metadag: a web tool to generate and analyse metabolic networks by Pere Palmer-Rodríguez, Ricardo Alberich, Mariana Reyes-Prieto, José A. Castro, Mercè Llabrés

“…Abstract Background MetaDAG is a web-based tool developed to address challenges posed by big data from omics technologies, particularly in metabolic network reconstruction and analysis. …”
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