A comprehensive assessment using multiple factors based on HAS-Flow analysis predicts ATL development and progression by Hideaki Nakamura, Tatsuro Watanabe, Akemi Sato, Atsushi Kawaguchi, Kaoru Uchimaru, Yorifumi Satou, Eisaburo Sueoka

Get full text

Comprehensive analysis of inhibin-β A as a potential biomarker for gastrointestinal tract cancers through bioinformatics approaches by Rohit Kumar Verma, Prashant Kumar Srivastava, Ashutosh Singh

“…DNA methylation, immune infiltration, functional enrichment analysis, the genes associated with INHBA, and survival analysis in all TCGA GI tract cancers have been extensively analyzed. …”
Get full text

Identification of genes associated with dissociation of cognitive performance and neuropathological burden: Multistep analysis of genetic, epigenetic, and transcriptional data. by Charles C White, Hyun-Sik Yang, Lei Yu, Lori B Chibnik, Robert J Dawe, Jingyun Yang, Hans-Ulrich Klein, Daniel Felsky, Alfredo Ramos-Miguel, Konstantinos Arfanakis, William G Honer, Reisa A Sperling, Julie A Schneider, David A Bennett, Philip L De Jager

“…<h4>Conclusions</h4>Through a multistep analysis of cognitive, neuropathological, genomic, epigenomic, and transcriptomic data, we identified ENC1 and UNC5C as genes with convergent genetic, epigenetic, and transcriptomic evidence supporting a potential role in the dissociation of cognition and neuropathology in an aging population, and we expanded our understanding of the TMEM106B haplotype that is protective against TDP-43 proteinopathy.…”
Get full text

Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet by Wei Luo, Min Sun, Ailing Zhang, Chuang Lin, Yarong Jin, Xiaoshan Wang, Linkai Huang

“…It serves as a staple food for millions, while also being utilized as forage and an energy crop. …”
Get full text

Shared blood gene signature in lung adenocarcinoma and microbial lung infections: a bioinformatic analysis and in silico validation by Milad Sheervalilou, Mostafa Ghanei, Masoud Arabfard

“…Abstract Background Microbial lung infections may promote development of lung cancer through overlapping molecular mechanisms. This analysis aimed to identify a co-regulated peripheral blood gene signature in lung adenocarcinoma (LUAD) and microbial lung infections. …”
Get full text

Identification and phylogenetic analysis of Nairobi sheep disease virus from Haemaphysalis longicornis ticks in Shandong Province, China by Yunxiao Wang, Ruiling Zhang, Xiurong Wang, Xudong Zhang, Zhong Zhang, Michael J. Carr, Guangfu Yu, Hong Zhou, Weifeng Shi

“…In the present study, a total of 343 ticks (Haemaphysalis longicornis) were collected in Shandong province, China in 2020, and pooled into 16 libraries. Analysis of the meta-transcriptomic sequencing data identified NSDV strains SDWL07, SDWL08, and SDWL16 from three pools. …”
Get full text

Molecular analysis highlights TREM2 as a discriminating biomarker for patients suffering from pancreatic ductal adenocarcinoma by Dimitrios Papakonstantinou, Haiding Wang, Mohamed-Amine Bani, Kevin Mulder, Garett Dunsmore, Alice Boilève, Gérôme Jules-Clément, Leonardo Panunzi, Leslie Robert de Sousa, Carlos de la Calle Fabregat, Marc Deloger, Nicolas Signolle, Grégoire Gessain, Sergey I Nikolaev, Michel Ducreux, Antoine Hollebecque, Florent Ginhoux, Camille Blériot

Get full text

Identification of GiOMT gene family in Glycyrrhiza inflata bat and expression analysis under UV-B stresses by Caijuan Li, Hao Li, Yufan Liang, Rong Miao, Ziliang Liu, Sijin Chen, Dan Zhang, Cuiling Wang, Jiling Wu, Xiangyan Zhou, Mengfei Li

“…Phylogenetic relationships showed that the OMT genes of three species, G. inflata, Arabidopsis and alfalfa, were distributed in three taxa, while the GiOMT genes were distributed in taxa I and II. …”
Get full text

Integrative multi-omics analysis reveals the interaction mechanisms between gut microbiota metabolites and ferroptosis in rheumatoid arthritis by Lifang Liang, Lifang Liang, Lifang Liang, Huaguo Liang, Min He, Min He, Min He, Huiling Zhang, Huiling Zhang, Huiling Zhang, Peifeng Ke, Peifeng Ke, Peifeng Ke

“…To systematically investigate the regulatory relationship between key ferroptosis genes and gut metabolites in RA, this study employed an integrative multi-omics approach combined with machine learning algorithms and single-cell transcriptomic data, identifying and validating GPX3 and MYC as potential critical ferroptosis regulators in RA.Methods and resultsFirst, 16 candidate genes were obtained by intersecting WGCNA, differential expression analysis results, and targets related to ferroptosis and gut microbiota. …”
Get full text

Characterization, Expression Profile Analysis, and Functional Prediction of <i>UGP</i> Gene Family in <i>Dendrocalamus brandisii</i> by He Li, Chongyang Wu, Xiangyi Li, Junlei Xu, Zhanchao Cheng, Jian Gao

“…This study identified and characterized the <i>DbUGP</i> gene family using the whole genome and transcriptome data of <i>D. brandisii</i>, in conjunction with whole genome data from 10 additional species through sequence alignment, phylogenetic analysis, gene structure and motif exploration, protein structure prediction, and expression profiling. …”
Get full text

Subcellular localization and expression analysis of MlSOC1 genes during flower bud differentiation period in Magnolia liliflora by XUAN Lingjuan, CHENG Shaoyu, DAI Mengyi, WANG Zhuowei, SHEN Yamei

“…Both of these two MlSOC1 genes contained highly conservative SOC1 motifs, which indicated that the genes belong to the SOC1/TM3 subfamily. Phylogenetic tree analysis showed that MlSOC1-1 was closely related to SOC1 homologous gene of M. praecocissima, while MlSOC1-2 was closely related to SOC1 homologous gene of M. virginiana. …”
Get full text

Integrative bioinformatics frameworks for abdominal aortic aneurysm using GWAS meta-analysis, biological network construction, and structural modeling by Pakorn Sagulkoo, Hathaichanok Chuntakaruk, Apichat Suratanee, Kitiporn Plaimas, Nuttinee Teerakulkittipong

“…We identified 74 DEGs through eQTL and TWAS analyses, with PPI network analysis highlighting CD40 and LRP1 as key proteins. …”
Get full text

Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes associated with breast cancer risk. by Joshua D Hoffman, Rebecca E Graff, Nima C Emami, Caroline G Tai, Michael N Passarelli, Donglei Hu, Scott Huntsman, Dexter Hadley, Lancelote Leong, Arunabha Majumdar, Noah Zaitlen, Elad Ziv, John S Witte

Get full text

Aux/IAA gene family identification and analysis reveals roles in flower opening and abiotic stress response in Osmanthus fragrans by Shanshan Cao, Yong Ye, Zifei Zheng, Shiwei Zhong, Yiguang Wang, Zheng Xiao, Qiu Fang, Jinping Deng, Hongbo Zhao, Bin Dong

“…Through transcriptome and expression pattern analysis, we found that the majority of OfIAA genes were expressed in the stem tissue. …”
Get full text

Reveal the mechanism of hepatic oxidative stress in mice induced by photo-oxidation milk using multi-omics analysis techniques by Sijia Tan, Qiangqiang Li, Can Guo, Sumeng Chen, Afaf Kamal-Eldin, Gang Chen

“…Objectives: This study employs multi-omics analysis techniques to elucidate the mechanisms by which photo-oxidized milk induces oxidative stress in the liver. …”
Get full text

Selenium exposure on breast cancer risk and progression: Comprehensive analysis identifies MSRB1 as a novel therapeutic target by Jingsong Cheng, Diyuan Zhang, Ningxi Wang, Ziheng Zheng, Cong Zhang, Nanting Chen, Yuanyuan Wan, Xue Chen, Qingyao Yin, Xinyi Zhu, Yu Zhao, Liming Yi, Na Sun

Get full text

Immunoregulatory programs in anti‐N‐methyl‐D‐aspartate receptor encephalitis identified by single‐cell multi‐omics analysis by Xinhui Li, Yicong Xu, Weixing Zhang, Zihao Chen, Dongjie Peng, Wenxu Ren, Zhongjie Tang, Huilu Li, Jin Xu, Yaqing Shu

“…Methods Peripheral blood mononuclear cells (PBMCs) from patients in the acute phase of anti‐NMDARE and healthy controls were sequenced using single‐cell joint profiling of transcriptome and chromatin accessibility. Differential gene expression analysis, transcription factor activity profiling, and cell‐cell communication modeling were performed to elucidate the immune mechanisms underlying the disease. …”
Get full text

Genome-Wide Identification and Expression Analysis of the <i>PsTPS</i> Gene Family in <i>Pisum sativum</i> by Hao Yuan, Baoxia Liu, Guwen Zhang, Zhijuan Feng, Bin Wang, Yuanpeng Bu, Yu Xu, Zhihong Sun, Na Liu, Yaming Gong

“…Phylogenetic analysis delineated evolutionary relationships, while gene structure analysis revealed compositional insights, and motif analysis provided functional insights. …”
Get full text

Vascular-type heterogeneity is associated with differential gene expression profiles of endothelial cells under shear stress by Allaura A. Cox, Christopher James Ng

Get full text

Disulfidptosis in pediatric AML: a multi-omics approach to risk stratification and potential therapeutic strategy by Yichen Lei, Jiasi Zhang, Yaqin Wang, Aiguo Liu

“…Machine learning deciphered the biological networks underlying disulfidptosis, while in vitro experiments were performed to further validate. …”
Get full text