Core-genome guided novel therapeutic targets identification and chimeric vaccine designing against Rickettsia rickettsii by Fizza Arshad, Asifa Sarfraz, Muhammad Shehroz, Umar Nishan, Asia Perveen, Riaz Ullah, Mohamed A. Ibrahim, Mohibullah Shah

“…In order to find new therapeutic targets and create multiepitope vaccines, this study integrated subtractive proteomics with reverse vaccinology. The core genome of R. rickettsii was investigated, resulting in the identification of seven essential, human non-homologous proteins as potential drug targets, as well as four antigenic, non-allergenic proteins suitable for vaccine development. …”
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Potential biomarkers for predicting the risk of thyroid cancer in immunosenescence: a population-based and externally validated multi omics study by Qian Li, Yuanyuan Zhao, Jiawei Yan, Chao He

“…Subsequently, we conducted a meta-analysis on the relationship between Hannum DNA methylation age and thyroid cancer risk, which identified 138 potential risk loci through FUMA. Additionally, proteomics and transcriptomics collectively identified 6 potential targets related to immunosenescence and thyroid cancer. …”
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Potential Pathways Involved in Elaidic Acid Induced Atherosclerosis in Human Umbilical Vein Endothelial Cells by Huahong Yu, Xiangmei Li, Zhongshang Liang, Bin Qiu, Siguang Li, Ting Luo, Jing Li, Hongyan Li, Zeyuan Deng

“…In the presented study, two-dimensional electrophoresis based proteomics was used to discover the role of elaidic acid in atherosclerosis. …”
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Exploring the Mesenchymal Stem Cell Secretome for Corneal Endothelial Proliferation by Bert Van den Bogerd, Nadia Zakaria, Steffi Matthyssen, Carina Koppen, Sorcha Ní Dhubhghaill

“…Specific identification of the underlying proteins using proteomics could render a bioactive protein that can be used for ex vivo expansion of cells or as an in vivo drug to treat early corneal endothelial damage.…”
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Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq by Shintaro Funasaki, Yuri Miyamura, Shunsuke Kamei, Akhinur Rahman, Masaya Yamazaki, Shingo Usuki, Keiichiro Yasunaga, Yorifumi Satou, Hiroto Ohguchi, Takashi Minami

“…This scalable protocol is also applicable to diverse omics studies, including proteomics and metabolomics.For complete details on the use and execution of this protocol, please refer to Miyamura et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.…”
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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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A ribosome-associating chaperone mediates GTP-driven vectorial folding of nascent eEF1A by Ibrahim M. Sabbarini, Dvir Reif, Kibum Park, Alexander J. McQuown, Anjali R. Nelliat, Charlotte Trejtnar, Volker Dötsch, Eugene I. Shakhnovich, Andrew W. Murray, Vladimir Denic

“…Here, we use AlphaPulldown to identify Ypl225w (also known as Chp1, Chaperone 1 for eEF1A) as a conserved yeast protein predicted to stabilize the N-terminal, GTP-binding (G) domain of eEF1A against its misfolding propensity, as predicted by computational simulations and validated by microscopy analysis of ypl225wΔ cells. Proteomics and biochemical reconstitution reveal that Ypl225w functions as a co-translational chaperone by forming dual interactions with the eEF1A G domain nascent chain and the UBA domain of ribosome-bound nascent polypeptide-associated complex (NAC). …”
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Allergen degradation of bee pollen by lactic acid bacteria fermentation and its alleviatory effects on allergic reactions in BALB/c mice by Shuting Yin, Qiangqiang Li, Yuxiao Tao, Enning Zhou, Kun Wang, Wanwen Chen, Xiangxin Li, Liming Wu

“…Four novel allergens (glutaredoxin, oleosin-B2, catalase and lipase) were identified with significant decreases in LAB-fermented BP (FBP) than natural BP by proteomics. Meanwhile, metabolomics analysis showed significant increases of 28 characteristic oligopeptides and amino acids in FBP versus BP, indicating the degradation of LAB on allergens. …”
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Profiling endogenous airway proteases and antiproteases and modeling proteolytic activation of Influenza HA using in vitro and ex vivo human airway surface liquid samples. by Stephanie A Brocke, Boris Reidel, Camille Ehre, Meghan E Rebuli, Carole Robinette, Kevin D Schichlein, Christian A Brooks, Ilona Jaspers

“…The airway proteolytic environment likely contains redundant antiproteases and proteases with diverse catalytic mechanisms, however a proteomic profile of these enzymes and inhibitors in airway samples has not been reported. …”
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Synthesis of Alkyl α-Amino-benzylphosphinates by the Aza-Pudovik Reaction; The Preparation of the Butyl Phenyl-<i>H</i>-phosphinate Starting P-Reagent by Bence Bajusz, Dorka Nagy, Regina Tóth, Zsuzsanna Szalai, Ágnes Gömöry, Angéla Takács, László Kőhidai, György Keglevich

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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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The Synthesis, Crystal Structure, Modification, and Cytotoxic Activity of α-Hydroxy-Alkylphosphonates by Zsuzsanna Szalai, Anna Sára Kis, Angéla Takács, László Kőhidai, Konstantin Karaghiosoff, Mátyás Czugler, László Drahos, György Keglevich

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INSIHGT: an accessible multi-scale, multi-modal 3D spatial biology platform by Chun Ngo Yau, Jacky Tin Shing Hung, Robert A. A. Campbell, Thomas Chun Yip Wong, Bei Huang, Ben Tin Yan Wong, Nick King Ngai Chow, Lichun Zhang, Eldric Pui Lam Tsoi, Yuqi Tan, Joshua Jing Xi Li, Yun Kwok Wing, Hei Ming Lai

“…With INSIHGT, we map undescribed podocyte-to-parietal epithelial cell microfilaments in mouse glomeruli and neurofilament-intensive inclusion bodies in the human cerebellum, and identify NPY-proximal cell types defined by spatial morpho-proteomics in mouse hypothalamus. We anticipate that INSIHGT can form the foundations for 3D spatial multi-omics technology development and holistic systems biology studies.…”
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Investigating the role of intratumoral Streptococcus mitis in gastric cancer progression: insights into tumor microenvironment by Ping Yang, Gaoli Liang, Yangyue Ni, Xiaojie Chu, Xiaoshan Zhang, Zhongyu Wang, Adeel Khan, Fangfang Jin, Han Shen, Miao Li, Zhipeng Xu

“…Here, using 16 S rRNA sequencing, tumor tissue proteomics and serum cytokines analysis, we identified enrichment of specific microbial communities within tumors of gastric cancer patients, possibly affecting the tumor microenvironment by immune modulation, metabolic processes, and inflammatory responses. …”
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A graph neural network approach for hierarchical mapping of breast cancer protein communities by Xiao Zhang, Qian Liu

“…Results Using a large amount of publicly available proteomics data, we created a hierarchical tree for breast cancer protein communities using a novel hierarchical graph neural network, with the supervision of gene ontology terms and assistance of a pre-trained deep contextual language model. …”
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Sensory Diet Program Through In-Person and Tele-Occupationa Therapy in Children with Autism Spectrum Disorder: A Single-Blind Randomized Controlled Trial by Simin Dehghani, Marzieh Pashmdarfard, Zahra Pashazadeh Azari, Alireza Akbarzadeh Baghban, Sima Dehghani, Navid Mirzakhani Araghi

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The pathomechanism of bone marrow edema in the femoral head necrosis with pericollapse stage by Liang Mo, Zhangzheng Wang, Mengyu Jiang, Chi Zhou, Chao Ma, Yinuo Fan, Wei He, Zhenqiu Chen, Yuhao Liu

“…Meanwhile, data-independent Acquisition (DIA) proteomics technology was utilized to identify differentially expressed proteins (DEPs) within bone tissue. 141, 299 and 852 DEPs were identified in femoral neck, necrotic and sclerotic regions, respectively. …”
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The genomic architecture of circulating cytokine levels points to drug targets for immune-related diseases by Marek J. Konieczny, Murad Omarov, Lanyue Zhang, Rainer Malik, Tom G. Richardson, Sebastian-Edgar Baumeister, Jürgen Bernhagen, Martin Dichgans, Marios K. Georgakis

“…Drug target cis-MR using 2 independent proteomics datasets paired with colocalization revealed G-CSF/CSF-3 and CXCL9/MIG as potential causal mediators of asthma and Crohn’s disease, respectively, but also a potentially protective role of TNF-b in multiple sclerosis. …”
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An Innovative Method to Identify Autoantigens Expressed on the Endothelial Cell Surface: Serological Identification System for Autoantigens Using a Retroviral Vector and Flow Cytom... by Tsuyoshi Shirai, Hiroshi Fujii, Masao Ono, Ryu Watanabe, Tomonori Ishii, Hideo Harigae

“…For identification of autoantigens, proteomics and expression library analyses have been performed for many years with some success. …”
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Innovative applications and future trends of multiparametric PET in the assessment of immunotherapy efficacy by Tingting Qiao, Tingting Qiao, Zhaoping Cheng, Yanhua Duan

“…The integration of multi-omics data (including genomics and proteomics) with PET imaging enhanced the sensitivity and accuracy of efficacy prediction. …”
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