Advances in the application of multi-omics and machine learning technologies in sepsis research by Chen Pengpeng, Yang Jie, Jin Xinhao, Zhang Bo, Yang Suibi, Hong Yucai, Ni Hongying, Zhang Zhongheng

“…Chinese Multi-omics Advances in Sepsis (CMAISE) integrates multi-omics data, including genomics, proteomics, and metabolomics, to explore the molecular mechanisms and biomarkers of sepsis. …”
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Molecular and spatial analysis of tertiary lymphoid structures in Sjogren’s syndrome by Saba Nayar, Jason D. Turner, Saba Asam, Eanna Fennell, Matthew Pugh, Serena Colafrancesco, Onorina Berardicurti, Charlotte G. Smith, Joe Flint, Ana Teodosio, Valentina Iannizzotto, David H. Gardner, Joel van Roon, Ilya Korsunsky, Dawn Howdle, Roche Fibroblast Network Consortium, Andreas P. Frei, Kara G. Lassen, Simon J. Bowman, Wan-Fai Ng, Adam P. Croft, Andrew Filer, Benjamin A. Fisher, Christopher D. Buckley, Francesca Barone

“…Here we use combine single-cell RNA-sequencing, spatial transcriptomics and proteomics of minor salivary glands of patients with Sjogren’s disease and Sicca Syndrome, with ex-vivo functional studies to construct a cellular and spatial map of key components involved in the formation and function of tertiary lymphoid structures. …”
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Joint fluid multi-omics improves diagnostic confidence during evaluation of children with presumed septic arthritis by Yolanda Peña-López, Naureen G. Tareen, Bo Zhang, Indu Raman, Carlos A. Arana, Chengsong Zhu, Yang Liu, Pratibha Selvakumar, Nicolai S. C. van Oers, Simrat Morris, Lora V. Hooper, Lawson A. B. Copley, Prithvi Raj

“…A multi-omics strategy comprising metagenomic and proteomic technologies were undertaken for children diagnosed with presumed septic arthritis to advance clinical diagnoses and care for affected individuals. …”
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N88S seipin-related seipinopathy is a lipidopathy associated with loss of iron homeostasis by Mariana O. Ribeiro, Mafalda Oliveira, Verónica Nogueira, Vítor Costa, Vitor Teixeira

“…Methods Quantitative untargeted mass spectrometric proteomic and lipidomic analyses were conducted to examine changes in protein and lipid abundance in wild-type (WT) versus N88S seipin-expressing mutant cells. …”
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Genomic 8-oxoguanine modulates gene transcription independent of its repair by DNA glycosylases OGG1 and MUTYH by Tobias Obermann, Teri Sakshaug, Vishnu Vignesh Kanagaraj, Andreas Abentung, Mirta Mittelstedt Leal de Sousa, Lars Hagen, Antonio Sarno, Magnar Bjørås, Katja Scheffler

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A Systems Biology Overview on Human Diabetic Nephropathy: From Genetic Susceptibility to Post-Transcriptional and Post-Translational Modifications by Francesca Conserva, Loreto Gesualdo, Massimo Papale

“…We performed a systematic analysis of the most relevant studies investigating genetic susceptibility and specific transcriptomic, epigenetic, proteomic, and metabolomic patterns in order to summarize the most significant traits associated with the disease onset and progression. …”
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Absence of MCJ/DnaJC15 promotes brown adipose tissue thermogenesis by Beatriz Cicuéndez, Alfonso Mora, Juan Antonio López, Andrea Curtabbi, Javier Pérez-García, Begoña Porteiro, Daniel Jimenez-Blasco, Pedro Latorre-Muro, Paula Vo, Madison Jerome, Beatriz Gómez-Santos, Rafael Romero-Becerra, Magdalena Leiva, Elena Rodríguez, Marta León, Luis Leiva-Vega, Noemi Gómez-Lado, Jorge L. Torres, Lourdes Hernández-Cosido, Pablo Aguiar, Miguel Marcos, Martin Jastroch, Andreas Daiber, Patricia Aspichueta, Juan Pedro Bolaños, Jessica B. Spinelli, Pere Puigserver, José Antonio Enriquez, Jesús Vázquez, Cintia Folgueira, Guadalupe Sabio

“…Electron microscopy unveils changes in mitochondrial morphology resembling BAT activation. Proteomic analysis confirms these findings and suggests involvement of the eIF2α mediated stress response. …”
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Spatial transcriptomic analysis drives PET imaging of tight junction protein expression in pancreatic cancer theranostics by James Wang, Jai Woong Seo, Aris J. Kare, Martin Schneider, Mallesh Pandrala, Spencer K. Tumbale, Marina N. Raie, Gokce Engudar, Nisi Zhang, Yutong Guo, Xiaoxu Zhong, Sofia Ferreira, Bo Wu, Laura D. Attardi, Guillem Pratx, Andrei Iagaru, Ryan L. Brunsing, Gregory W. Charville, Walter G. Park, Katherine W. Ferrara

“…While cancer-associated fibroblasts and integrins have been proposed as targets for imaging of pancreatic ductal adenocarcinoma (PDAC), herein, spatial transcriptomics and proteomics of human surgical samples are applied to select PDAC targets. …”
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Machine learning and multi-omics in precision medicine for ME/CFS by Katherine Huang, Brett A. Lidbury, Natalie Thomas, Paul R. Gooley, Christopher W. Armstrong

“…In this review, we explore how machine learning and multi-omics (genomics, transcriptomics, proteomics, and metabolomics) can transform precision medicine in ME/CFS research and healthcare. …”
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Phenotypic alterations in articulating joint cells: Role of mechanically loaded MSC secretome by Yann D. Ladner, Ursula Menzel, Keith Thompson, Angela R. Armiento, Martin J. Stoddart

“…Previously, we employed a small-panel microarray to demonstrate differences within conditioned medium (CM) of MSCs that were mechanically stimulated within a joint-mimicking bioreactor and their unloaded controls.This study analyzed the proteomic content within CM from 4 week mechanically loaded MSCs with a larger protein microarray. …”
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Identification of Osteosarcoma-Related Specific Proteins in Serum Samples Using Surface-Enhanced Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry by Jianli Gu, Jitian Li, Manyu Huang, Zhiyong Zhang, Dongsheng Li, Guoying Song, Xingpo Ding, Wuyin Li

“…Two proteins showed a significantly different expression in OS serum samples from control groups. Proteomic profiles and external leave-one-out cross-validation analysis showed that the correct rate of allocation, the sensitivity, and the specificity of diagnosis were 100%. …”
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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). Here, we review the molecular biology of the infectious agent and, in particular, its interactions with the immune system, focusing on both the innate and the adaptive responses. …”
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Colistin Resistance and Management of Drug Resistant Infections by Juhi Sharma, Divakar Sharma, Amit Singh, Kumari Sunita

“…Researchers focus on the most advanced genomics (whole genome sequencing), proteomics, and bioinformatics approaches to explore the question of colistin resistance. …”
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Classifications of triple-negative breast cancer: insights and current therapeutic approaches by Ziqi Chen, Yumeng Liu, Minchuan Lyu, Chi Ho Chan, Meiheng Sun, Xin Yang, Shuangying Qiao, Zheng Chen, Sifan Yu, Meishen Ren, Aiping Lu, Ge Zhang, Fangfei Li, Yuanyuan Yu

“…Additionally, TNBC exhibits significant heterogeneity at histopathological, proteomic, transcriptomic, and genomic levels, further complicating the development of effective treatments. …”
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<i>Pseudomonas aeruginosa pqs</i> Quorum Sensing Mediates Interaction with <i>Mycobacterium abscessus</i> In Vitro by Yun Long, Zhi Li, Menglu Li, Peiyi Lu, Yujia Deng, Pengyao Wu, Xue Li, Gangjian Qin, Jiamin Huang, Wenying Gao, Guobao Li, Tianyuan Jia, Liang Yang

“…In this study, we first demonstrated that <i>P. aeruginosa</i> inhibits the growth of <i>M. abscessus</i> by iron chelating via <i>pqs</i> quorum sensing. Next, through proteomic analysis, we discovered that the PQS molecule significantly changed a large amount of protein expression in <i>M. abscessus</i>, including proteins involved in the type VII secretion system and iron homeostasis. …”
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Psychrophilic Enzymes: From Folding to Function and Biotechnology by Georges Feller

“…Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. …”
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Metabonomics Research Progress on Liver Diseases by Mengqian Yu, Ying Zhu, Qingwei Cong, Chunyan Wu

“…Metabolomics as the new omics technique develops after genomics, transcriptomics, and proteomics and has rapid development at present. Liver diseases are worldwide public health problems. …”
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Non-histone lactylation: unveiling its functional significance by Pusong Shi, Yongjie Ma, Yongjie Ma, Yongjie Ma, Yongjie Ma, Yongjie Ma, Shaolu Zhang, Shaolu Zhang, Shaolu Zhang, Shaolu Zhang, Shaolu Zhang

“…Recently, high-throughput proteomics studies have identified a large number of lactylated proteins and sites, revealing their global regulatory role in disease development. …”
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Applications of liposomes and lipid nanoparticles in cancer therapy: current advances and prospects by Zhe Cheng, Huichao Huang, Meilong Yin, Huaizheng Liu

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Multilevel plasticity and altered glycosylation drive aggressiveness in hypoxic and glucose-deprived bladder cancer cells by Andreia Peixoto, Dylan Ferreira, Andreia Miranda, Marta Relvas-Santos, Rui Freitas, Tim S. Veth, Andreia Brandão, Eduardo Ferreira, Paula Paulo, Marta Cardoso, Cristiana Gaiteiro, Sofia Cotton, Janine Soares, Luís Lima, Filipe Teixeira, Rita Ferreira, Carlos Palmeira, Albert J.R. Heck, Maria José Oliveira, André M.N. Silva, Lúcio Lara Santos, José Alexandre Ferreira

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