Platelet‐derived apoptotic vesicles ameliorate nonalcoholic fatty liver disease by regulating lipid metabolism via apolipoprotein A‐II by Yuhe Jiang, Yike Liao, Zeying Wang, Lei Zhu, Yunsong Liu, Ping Zhang, Yuan Zhu, Wenyue Li, Yongsheng Zhou, Xiao Zhang

“…The results showed that PLT‐apoVs exhibited superior effects in diminishing lipid accumulation in liver induced by high‐fat diet than MSC‐apoVs. Through proteomic analysis, we defined and validated apolipoprotein A‐II (APOA2) as a regulator for apoV‐mediated MSC adipogenesis, which could be used as a target to enhance apoV therapeutic potential in the lipid metabolism biomedical field. …”
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NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface by Andrea Conte, Nicola Gulmini, Francesco Costa, Matteo Cartura, Felix Bröhl, Francesco Patanè, Francesco Filippini

“…Abstract Background Vaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens genome or proteome through computational analyses. When NERVE (New Enhanced RV Environment), the first RV software integrating tools to perform the selection of VCs, was released, it prompted further development in the field. …”
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Ginsenoside F1 administration promotes UCP1-dependent fat browning and ameliorates obesity-associated insulin resistance by Yuhan Meng, Weili Li, Chenxing Hu, Si Chen, Haiyang Li, Feifei Bai, Lujuan Zheng, Ye Yuan, Yuying Fan, Yifa Zhou

“…We also investigated the ability of F1 on energy metabolism in obesity-induced diabetic mice, including body weight, body composition and energy expenditure. The results of proteomics showed that F1 significantly up-regulated thermogenesis proteins and lipolytic proteins, but down-regulated fatty acid synthesis proteins. …”
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Transcription factor TCF4: structure, function, and associated diseases by R. R. Savchenko, N. A. Skryabin

“…The biological role of approximately 20 % of human proteins has not been established yet, and the molecular functions of the known part of the proteome remain poorly understood. This hinders progress in basic and applied biological and medical sciences, especially in treating hereditary diseases, which are caused by mutations and polymorphic variants in individual genes. …”
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Robust ensemble of handcrafted and learned approaches for DNA-binding proteins by Loris Nanni, Sheryl Brahnam

“…Purpose – Automatic DNA-binding protein (DNA-BP) classification is now an essential proteomic technology. Unfortunately, many systems reported in the literature are tested on only one or two datasets/tasks. …”
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A novel two-component system contributing the catabolism of c-di-GMP influences virulence in Aeromonas veronii by Chaolun Liu, Jia Shao, Xiang Ma, Yanqiong Tang, Juanjuan Li, Hong Li, Xue Chi, Zhu Liu

“…The roles of ArrS/ArrR in Aeromonas veronii were investigated using RT-qPCR, murine model, and proteomics.ResultsArrS and ArrR constituted a two-component system in Aeromonas veronii and were transcriptionally repressed by ArgR. …”
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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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A review of leishmaniasis: current knowledge and future directions of heterocyclic molecules by Tejaswini Masne, Dileep Kumar, Deepali Bansode

“…It emphasizes the importance of interdisciplinary research and integrating emerging technologies, such as genomics and proteomics, to identify new drug targets and strategies for disease control. …”
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Multi-modal investigation reveals pathogenic features of diverse DDX3X missense mutations. by Federica Mosti, Mariah L Hoye, Carla F Escobar-Tomlienovich, Debra L Silver

“…Here, we integrate transcriptomics, proteomics, and live imaging to demonstrate clinically diverse DDX3X missense mutations perturb neural development via distinct cellular and molecular mechanisms. …”
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The molecular view of mechanical stress of brain cells, local translation, and neurodegenerative diseases by T. M. Khlebodarova

“…In further consideration of the role of the local translation system in the development of neuropsychic and neurodegenerative diseases, an original hypothesis was put forward that one of the possible causes of synaptopathies is impaired proteome stability associated with mTOR hyperactivity and formation of complex dynamic modes of de novo protein synthesis in response to synapse-stimulating factors, including chronic mechanical stress.…”
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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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Cytoplasmic male sterility and prospects for its utilization in breeding, genetic studies and seed production of potato by I. N. Anisimova, T. A. Gavrilenko

“…The main results of research on molecular mechanisms of CMS and fertility restoration obtained in the post-genomic era for various plant species using methods of transcriptomic and proteomic analyses are provided. As in many plant species, cytoplasmic male sterility in potato is of hybrid origin. …”
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Effect of Dietary Cholesterol, Phytosterol, and Docosahexaenoic Acid on Astaxanthin Absorption and Retention in Rainbow Trout by Yang Jin, Keshuai Li, Jon Olav Vik, Marie Hillestad, Rolf Erik Olsen

“…On the other hand, the transcriptomic and proteomic analyses found no changes of genes or proteins involved in Ax absorption, transport, or excretion in fish fed PS or DHA diets as compared to the control diet. …”
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Endothelial Progenitor Cell Migration-Enhancing Factors in the Secretome of Placental-Derived Mesenchymal Stem Cells by Witchayaporn Kamprom, Pakpoom Kheolamai, Yaowalak U-Pratya, Aungkura Supokawej, Methichit Wattanapanitch, Chuti Laowtammathron, Sittiruk Roytrakul, Surapol Issaragrisil

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The histone methyltransferase DOT1B is dispensable for stage differentiation and macrophage infection of Leishmania mexicana by Nicole Eisenhuth, Elisa Theres Rauh, Melina Mitnacht, Andrea Debus, Ulrike Schleicher, Falk Butter, Katerina Pruzinova, Petr Volf, Christian J. Janzen

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Gut microbiota drives colon cancer risk associated with diet: a comparative analysis of meat-based and pesco-vegetarian diets by Carlotta De Filippo, Sofia Chioccioli, Niccolò Meriggi, Antonio Dario Troise, Francesco Vitali, Mariela Mejia Monroy, Serdar Özsezen, Katia Tortora, Aurélie Balvay, Claire Maudet, Nathalie Naud, Edwin Fouché, Charline Buisson, Jacques Dupuy, Valérie Bézirard, Sylvie Chevolleau, Valérie Tondereau, Vassilia Theodorou, Claire Maslo, Perrine Aubry, Camille Etienne, Lisa Giovannelli, Vincenzo Longo, Andrea Scaloni, Duccio Cavalieri, Jildau Bouwman, Fabrice Pierre, Philippe Gérard, Françoise Guéraud, Giovanna Caderni

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Identification of GBN5 as a molecular biomarker of pan-cancer species by integrated multi-omics analysis by Qian Guo, Xinxin Zhong, Zihan Dang, Baiquan Zhang, Zixin Yang

“…Materials and methods We employed a multi-omics approach, including transcriptomic, genomic, proteomic, single-cell cytomic, spatial transcriptomic, and genomic data, to explore the prognostic value and potential oncogenic mechanisms of GBN5 across pan-cancers from multiple perspectives. …”
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Methods of yeast genome editing by A. S. Rozanov, V. N. Shlyahtun, L. A. Tekutieva, O. M. Son, S. V. Sizova, S. E. Peltek

“…Many high­throughput methods were developed in the second decade of the XXI century, including those used in genomics, transcriptomics, proteomics, metabolomics, interactomics, etc. Modern bioinformatic databases now allow one to rapidly process the increasing flow of information and model cellular processes. …”
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Genetics of aging and longevity by A. A. Moskalev, E. N. Proshkina, A. A. Belyi, I. A. Solovyev

“…Genes and signaling pathways that regulate stress response, metabolism, growth of cells and organism, maintaining of genome and proteome integrity, qualitative and quantitative mitochondria composition, inflammatory response, apoptosis and selection of viable cells, as well as circadian rhythms were considered. …”
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Palmitic Acid Accelerates Endothelial Cell Injury and Cardiovascular Dysfunction via Palmitoylation of PKM2 by Yu He, Senlin Li, Lujing Jiang, Kejue Wu, Shanshan Chen, Linjie Su, Cui Liu, Peiqing Liu, Wenwei Luo, Shilong Zhong, Zhuoming Li

“…In endothelial cells, inhibition of palmitoylation bypalmitoyl‐transferase inhibitor 2‐BP eliminates PA‐induced endothelial injury, whereas promotion of palmitoylation by depalmitoylase inhibitor ML349 exacerbates the harmful effect of PA. Palmitoyl‐proteomics analysis identifies pyruvate kinase isozyme type M2 (PKM2) as the palmitoylated protein responsible for PA‐induced endothelial injury, and Cys31 as the predominant palmitoylated site. …”
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