RatDEGdb: a knowledge base of differentially expressed genes in the rat as a model object in biomedical research by I. V. Chadaeva, S. V. Filonov, K. A. Zolotareva, B. M. Khandaev, N. I. Ershov, N. L. Podkolodnyy, R. V. Kozhemyakina, D. A. Rasskazov, A. G. Bogomolov, E. Yu. Kondratyuk, N. V. Klimova, S. G. Shikhevich, M. A.  Ryazanova, L. A. Fedoseeva, О. Е. Redina, О. S. Kozhevnikova, N. A. Stefanova, N. G. Kolosova, A. L. Markel, M. P. Ponomarenko, Yu. D. Oshchepkov

“…RatDEGdb may be interesting first of all to human geneticists, molecular biologists, clinical physicians, genetic advisors as well as experts in biopharmaceutics, bioinformatics and personalized genomics. RatDEGdb is publicly available at https://www.sysbio.ru/RatDEGdb.…”
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IMA Genome – F19 by Janneke Aylward, Andi M. Wilson, Cobus M. Visagie, Joseph Spraker, Irene Barnes, Carla Buitendag, Callin Ceriani, Lina Del Mar Angel, Deanné du Plessis, Taygen Fuchs, Katharina Gasser, Daniella Krämer, WenWen Li, Kiara Munsamy, Anja Piso, Jenna-Lee Price, Byron Sonnekus, Chanel Thomas, Ariska van der Nest, Alida van Dijk, Alishia van Heerden, Nicole van Vuuren, Neriman Yilmaz, Tuan A. Duong, Nicolaas A. van der Merwe, Michael J. Wingfield, Brenda D. Wingfield

“…As a result, such data are increasingly becoming accessible to biologists outside of the field of bioinformatics. In contrast, access to training in the methods of genome assembly and annotation are not growing at a similar rate. …”
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Tangeretin alleviates sepsis-induced acute lung injury by inhibiting ferroptosis of macrophage via Nrf2 signaling pathway by Hui Zhang, Yan Wang, Shenghua Wang, Xiaomei Xue, Kai Huang, Dunfeng Xu, Lai Jiang, Siyuan Li, Yunqian Zhang

“…Besides, the levels of LPS-stimulated inflammatory factors IL-6, IL-1β and TNF-α were also decreased by tangeretin. RNA-seq and bioinformatics analysis demonstrated that tangeretin inhibited inflammatory response. …”
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Targeting deubiquitinase USP7-mediated stabilization of XPO1 contributes to the anti-myeloma effects of selinexor by Junying Wang, Mengping Chen, Jinxing Jiang, Yike Wan, Xin Li, Minyue Zhang, Fei Xiao, Lu Zhong, Hua Zhong, Zhaoyu Qin, Jian Hou

“…Immunoprecipitation coupled with mass spectrometry (IP-MS), bioinformatics analysis and ubiquitination assays, were employed to identify the molecular targets responsible for SEL-induced degradation of XPO1. shRNA-mediated knockdown assays and small molecule inhibitors of USP7 were utilized to disrupt the function of USP7. …”
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Assembly mechanisms, not species pool, shape β-diversity of soil methanotrophic communities in steppes of China by Yongping Kou, Zhe Feng, Huan Li, Yanjiao Liu, Yanjiao Liu, Lin Xu, Lin Xu, Xiangzhen Li

“…While biodiversity patterns across geographical gradients are often attributed both to local assembly processes and regional species pools, the distinct roles of these factors in shaping soil aerobic methanotrophic diversity remain underexplored.MethodsUsing amplicon sequencing and bioinformatics analysis, this study focuses on comparing the relative importance of species pool and community assembly processes in shaping soil methanotrophic communities across three distinct plateaus in China: the Loess Plateau, the Qinghai-Tibetan Plateau, and the Inner Mongolian Plateau. …”
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Sex differences in the associations of water, coffee and tea consumption with cardiovascular diseases: a prospective cohort study by Dandan Ke, Dandan Ke, Yueqing Wang, Yabing Hou, Weihao Shao, Jiawen Ke, Xiaoxuan Zhang, Hongxi Yang, Zhong He, Zuolin Lu

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Computational and in vitro evaluation of sumac-derived ©Rutan compounds towards Sars-CoV-2 Mpro inhibition by Muzaffar Kayumov, Parthiban Marimuthu, Parthiban Marimuthu, Jamoliddin Razzokov, Jamoliddin Razzokov, Jamoliddin Razzokov, Nurkhodja Mukhamedov, Nurkhodja Mukhamedov, Akmal Asrorov, Nodir S. Berdiev, Jamolitdin F. Ziyavitdinov, Ansor Yashinov, Ansor Yashinov, Yuliya Oshchepkova, Shavkat Salikhov, Sharafitdin Mirzaakhmedov

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High expression of SULF1 is associated with adverse prognosis in breast cancer brain metastasis by Yitong Li, Tingting Feng, Qinghong Wang, Yue Wu, Jue Wang, Wenlong Zhang, Qi Kong

“…Conclusions This study, through bioinformatics analysis, unveiled SULF1 as a potential target for treating breast cancer brain metastasis (BM).…”
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Mitochondrial dysfunction-driven AMPK-p53 axis activation underpins the anti-hepatocellular carcinoma effects of sulfane sulfur by Xue Zheng, Yuhua Luo, Rui Huo, Yiwen Wang, Youbang Chen, Mianrong Chen, Qi Zhao, Kexin Li, Hanyi Zhang, Xiaotong Li, Xiang Li, Hui Zhang, Zaopeng He, Li Huang, Chun-tao Yang

“…This study aimed to investigate the effects of PSCP on HCC and elucidate the underlying mechanisms. We utilized bioinformatics algorithms for clustering, function enrichment, feature screening and survival analysis on proteomic data from the Cancer Proteome Atlas (CPTAC) and transcriptomic data from the Cancer Genome Atlas (TCGA). …”
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Characterisation of clinical response and transcriptional profiling of proliferating CD8 T cells in the blood of cancer patients after PD-1 monotherapy or combination therapy by Peng Li, Haydn Kissick, Rebecca C Obeng, Tahseen H Nasti, Christiane S Eberhardt, Rafi Ahmed, Zhengjia Chen, Warren J Leonard, Suresh S Ramalingam, Andreas Wieland, Annapaola Mariniello, Jeffrey M Switchenko, Kylee Martens, Daniel Y Chang, Donald McGuire, Candace Daugherty, Yuzi Zhang, Rathi Pillai, Alice O Kamphorst

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Molecular and pharmacological heterogeneity of ETV6::RUNX1 acute lymphoblastic leukemia by Zhenhua Li, Huanbin Zhao, Wenjian Yang, Maud Maillard, Satoshi Yoshimura, Yu-Chih Hsiao, Xin Huang, Yoshihiro Gocho, Lauren Rowland, Anthony Brown, Landon Choi, Kristine R. Crews, Charles G. Mullighan, Samuel W. Brady, Cheng Cheng, Ti-Cheng Chang, Gang Wu, Mignon L. Loh, Allen Eng Juh Yeoh, Federico Antillon-Klussmann, Sima Jeha, Hiroto Inaba, Jiyang Yu, Ching-Hon Pui, Seth E. Karol, William E. Evans, Jun J. Yang

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The Multifaceted Roles of Myrrha in the Treatment of Breast Cancer: Potential Therapeutic Targets and Promises by Anwar Shams MD, MSc, PhD, Abdullah Ahmed Alzahrani, Taghreed A Ayash MSc, PhD, Shadi Tamur MD, FRCPC, FAAP, Majed AL-Mourgi MD, FRCS, FCCP, FACS

“…Results: Combining the results of network pharmacology with other bioinformatics databases suggests that myrrh’s active components exert anti-cancer effects by regulating genes involved in breast cancer pathogenesis, particularly PTGS2, EGFR, ESR2, MMP2, and JUN. …”
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The trend of phylogenetic and epitope variations of SARS-CoV-2 Omicron sub-lineages in Iran by Mehdi Shabani, Ahmad Nejati, Jila Yavarian, Jila Yavarian, Kaveh Sadeghi, Sevrin Zadheidar, Akram Sadat Ahmadi, Monire Ghadirali, Arghavan Zebardast, Adel Abedi, Mohammad Hossein Najmi, Nazanin-Zahra Shafiei-Jandaghi, Talat Mokhtari-Azad

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Somatic copy number deletion of chromosome 22q in papillary thyroid carcinoma by Olivia W Lee, Danielle M Karyadi, Stephen W Hartley, Weyin Zhou, Mitchell J Machiela, Shahriar A Zamani, Liudmyla Yu Zurnadzhy, John N Weinstein, Young Joo Park, Jeong-Sun Seo, Gerry A Thomas, Tetiana I Bogdanova, Mykola D Tronko, Lindsay M Morton, Stephen J Chanock

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Detection of 5 Kinds of Genes Related to Plasmid-Mediated Quinolone Resistance in Four Species of Nonfermenting Bacteria with 2 Drug Resistant Phenotypes by De-Song Ming, Qing-Qing Chen, Xiao-Ting Chen

“…Sequence alignment was carried out using the bioinformatics technique. Results. Of 19 strains tested, 8 strains carried acc(6′)-Ib-cr and 6 of them were of pandrug resistance phenotype (3 Ab strains, 2 Pa strains, and 1 Sm strain). …”
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High-throughput untargeted metabolomics reveals metabolites and metabolic pathways that differentiate two divergent pig breeds by S. Bovo, M. Bolner, G. Schiavo, G. Galimberti, F. Bertolini, S. Dall’Olio, A. Ribani, P. Zambonelli, M. Gallo, L. Fontanesi

“…The molecular data were analysed using a bioinformatics pipeline specifically designed for identifying differentially abundant metabolites between the two breeds in a robust and statistically significant manner, including the Boruta algorithm, which is a Random Forest wrapper, and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) for feature selection. …”
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SUMO-Specific Peptidase 5 Promotes Oesophageal Squamous Cell Carcinoma Growth through the NF-κB-SLC1A3 Axis by Chaoxiang Du, Yunfan Hu, Xinyu Yang, Zhe Zhang, Jianmin Gu, Tao Zhang, Renfeng Wang, Shaoyuan Zhang, Lijie Tan, Guiping Yu

“…Further RNA-seq comparisons between short hairpin SENP5 (shSENP5)- and short hairpin negative control (shNC)-transfected ESCC cell lines were conducted, and the nuclear factor kappa B (NF-κB)—SLC1A3 axis was identified through bioinformatics analysis. The correlation of SENP5 with signalling pathway components was validated via real-time quantitative PCR (qPCR), western blotting (WB), and immunoprecipitation. …”
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Genome-Wide Comprehensive Identification and In Silico Characterization of Lectin Receptor-Like Kinase Gene Family in Barley (Hordeum vulgare L.) by Fee Faysal Ahmed, Farah Sumaiya Dola, Md Shohel Ul Islam, Fatema Tuz Zohra, Nasrin Akter, Shaikh Mizanur Rahman, Md. Abdur Rauf Sarkar

“…Therefore, in this study, integrated bioinformatics tools were used to identify and characterize the LecRLK gene family in barley. …”
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The miR-1269a/PCDHGA9/CXCR4/β-catenin pathway promotes colorectal cancer invasion and metastasis by Haitao Mei, Qingshan Luo, Junyong Weng, Jialing Hao, Jinfeng Cai, Runkai Zhou, Ce Bian, Yingzi Ye, Shengzheng Luo, Yugang Wen

“…Differential gene expression from high-throughput sequencing was analyzed using ingenuity pathway analysis (IPA) to explore the biological functions of PCDHGA9 and its potential regulated genes. Bioinformatics tools were employed to explore potential upstream regulatory microRNAs of PCDHGA9. …”
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Relieving Sore Throat Formula Exerts a Therapeutic Effect on Pharyngitis through Immunoregulation and NF-κB Pathway by Yushi Ding, Suyun Yu, Zhonghong Wei, Rui Deng, Peng Chen, Yifan Sun, Qi Jia, Xiaoman Li, Yuanyuan Wu, Wenxing Chen, Kurt S. Zanker, Aiyun Wang, Yin Lu

“…We combined multiple methods including bioinformatics data digging, network pharmacology analysis, and pathway analysis to predict the potential target of RSTF. …”
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