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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Pioneering the use of micro-biomarkers in oral cancer detection by Namrutha D Shekar, L. Kayal, N. Aravindha Babu, Mukesh Kumar Dharmalingam Jothinathan, Iadalin Ryntathiang

“…Therefore, this review underlines the position of omics technology which helps us understand the role of microbiome and possibly its contribution in cancer development. …”
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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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Biomarkers of inflammation and colorectal cancer risk by Yuting Li, Yuting Li, Yuting Li, Yuexin Luo, Yue Ran, Furong Lu, You Qin

“…In terms of screening, non-invasive methods like fecal occult blood tests (FOBTs) are widely used, and combining biomarkers with iFOBT shows potential. Multi-omics techniques, including genomics and microbiomics, offer new avenues for CRC diagnosis. …”
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Metataxonomics study of dental bioaerosols affected by waterline disinfection by Wachirakorn Poolkerd, Boonlased Swatasuk, Methanee Saengpitak, Sureeporn Muangsawat, Piriya Klankeo, Kittisak Thotsaporn, Ruchanee Salingcarnboriboon Ampornaramveth

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High antimony resistance strain Enterobacter sp. Z1 mediates biomineralization of antimony trioxide by Zijie Zhou, Hongbo Yu, Gejiao Wang, Mingshun Li, Kaixiang Shi

“…Z1 produced antimony trioxide (Sb2O3) via biomineralization during cultivation. Omics analysis revealed the upregulation of pyruvate metabolism and accumulation of DL-3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) in the presence of Sb(III).Using pyruvate as the sole carbon source in a chemically defined medium significantly enhanced Sb(III) biomineralization ratio from 20.8 % to 90.4 % compared with that using R2A medium. …”
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Inflammatory disease progression shapes nanoparticle biomolecular corona-mediated immune activation profiles by Jacob R. Shaw, Nicholas Caprio, Nhu Truong, Mehari Weldemariam, Anh Tran, Nageswara Pilli, Swarnima Pandey, Jace W. Jones, Maureen A. Kane, Ryan M. Pearson

“…NP coronas alter cell associations in a disease-dependent manner, induce differential co-stimulatory and co-inhibitory molecule expression, and influence cytokine release. Integrated multi-omics analysis of proteomics, lipidomics, metabolomics, and cytokine datasets highlight a set of differentially enriched TLR4 ligands that correlate with dynamic NP corona-mediated immune activation. …”
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Soil Alveolata diversity in the undisturbed steppe and wheat agrocenoses under different tillage by N. B. Naumova, P. A. Barsukov, O. A. Baturina, O. A. Rusalimova, M. R. Kabilov

“…The ITS-metabarcoding technique was used for the first time in the research of ciliates diversity; further studies, embracing diverse aspects of soil ciliates by combining -omics methodology with the traditional one, are needed to get a better insight on the ecological roles of the main ciliate taxa in the complex soil system.…”
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Tissue-resident immune cells: from defining characteristics to roles in diseases by Jia Li, Chu Xiao, Chunxiang Li, Jie He

“…The advancement of tissue-resolution technologies, such as single-cell sequencing and spatiotemporal omics, provides deeper insights into the cell morphology, characteristic markers, and dynamic transcriptional profiles of TRICs. …”
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A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population by Tindaro Bongiovanni, Marina Santiago, Kinga Zielinska, Jonathan Scheiman, Carolina Barsa, Ralf Jäger, Daniela Pinto, Fabio Rinaldi, Giammaria Giuliani, Tullio Senatore, Aleksandar D. Kostic

“…These improvements were associated with a significant decrease in D-ROMS (a marker of oxidative stress) and a significantly higher free-testosterone/cortisol ratio. Multi-omics analyses revealed specific changes in microbiome composition and function, potentially providing mechanistic insights into these observed effects. …”
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A review on bioremediation by microbial immobilization-an effective alternative for wastewater treatment by Frank Abimbola Ogundolie, Olorunfemi Oyewole Babalola, Charles Oluwaseun Adetunji, Christiana Eleojo Aruwa, Jacqueline Njikam Manjia, Taoheed Kolawole Muftaudeen

“…The potential integration of 'omics' technologies for enhancing and revealing new insights into bioremediation via cell immobilization is also discussed.…”
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