Works matching DE "GENE regulatory networks"

Results: 5000

Associative conditioning in gene regulatory network models increases integrative causal emergence.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-08411-2

By:

Pigozzi, Federico;
Goldstein, Adam;
Levin, Michael

Publication type:

Article

The engineering toolbox of Parageobacillus thermoglucosidasius.

Published in:

Applied Microbiology & Biotechnology, 2025, v. 109, n. 1, p. 1, doi. 10.1007/s00253-025-13508-z

By:

Millgaard, Marie;
Escher, Belinda;
Pogrebnyakov, Ivan;
Nielsen, Alex Toftgaard

Publication type:

Article

HBO1 determines epithelial-mesenchymal transition and promotes immunotherapy resistance in ovarian cancer cells.

Published in:

Cellular Oncology (2211-3428), 2025, v. 48, n. 4, p. 943, doi. 10.1007/s13402-025-01055-8

By:

Zhang, Cong;
Zhu, Jinmin;
Lin, Huaisong;
Zhang, Zhishuai;
Kang, Baoqiang;
Li, Fei;
Shan, Yongli;
Zhang, Yanqi;
Xing, Qi;
Gu, Jiaming;
Hu, Xing;
Cui, Yuanbin;
Huang, Jingxi;
Zhou, Tiancheng;
Mai, Yuchan;
Chen, Qianyu;
Mao, Rui;
Li, Peng;
Pan, Guangjin

Publication type:

Article

Transcriptomic profiling and bioinformatic insights into myocardial injury following aneurysmal subarachnoid hemorrhage.

Published in:

Frontiers in Neurology, 2025, p. 1, doi. 10.3389/fneur.2025.1492398

By:

Wu, Zuoli;
He, Wenbo;
Ye, Weihao;
Xu, Shang;
Wei, Shengwei;
Huang, Baozi;
Li, Pingping;
Tang, Yanyan;
Qin, Chao;
Liu, Ying;
Ye, Ziming

Publication type:

Article

Exploring ABHD5 as a Lipid-Related Biomarker in Idiopathic Pulmonary Fibrosis: Integrating Machine Learning, Bioinformatics, and In Vitro Experiments.

Published in:

Inflammation, 2025, v. 48, n. 3, p. 1176, doi. 10.1007/s10753-024-02107-1

By:

Liao, Yi;
Peng, Xiaying;
Yang, Yan;
Zhou, Guanghong;
Chen, Lijuan;
Yang, Yang;
Li, Hongyan;
Chen, Xianxia;
Guo, Shujin;
Zuo, Qiunan;
Zou, Jun

Publication type:

Article

A dataset of expression profile of certain microRNAs in Caenorhabditis elegans.

Published in:

Scientific Data, 2025, v. 12, n. 1, p. 1, doi. 10.1038/s41597-025-05486-8

By:

Gao, Yimeng;
Bai, Yuchuan;
Hu, Shipeng;
Tao, Zhiju;
Jiang, Yiru;
Zhao, Di

Publication type:

Article

Utilizing machine learning algorithms to identify biomarkers associated with Alzheimer's disease and ferroptosis-related genes.

Published in:

Technology & Health Care, 2025, v. 33, n. 4, p. 2041, doi. 10.1177/09287329251322278

By:

Wang, Di;
Lin, Chunsheng;
Liu, Gang;
Wang, Xin;
Han, Shengwang;
Han, Zengxin

Publication type:

Article

Role of Col1a2 and Postn in left ventricular noncompaction cardiomyopathy.

Published in:

Journal of Cardiothoracic Surgery, 2025, v. 20, n. 1, p. 1, doi. 10.1186/s13019-025-03509-4

By:

Liu, Huibing;
Meng, Ling-bing;
Liu, Qian

Publication type:

Article

Integrated transcriptomic and metabolomic analysis of flavonoid biosynthesis in cigar tobacco leaves under variable nitrogen regimes.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1589215

By:

Jia, Kai;
Shi, Juanjuan;
Bai, Lingli;
Wang, Xueren;
Wang, Yuemin;
Li, Xiangzhen;
Li, Wenqing;
Zheng, Chaoyuan

Publication type:

Article

Insights into the evolution and regulation of miRNAs from the view of their DNA replication temporal domains.

Published in:

Frontiers in Genetics, 2025, p. 1, doi. 10.3389/fgene.2025.1544802

By:

Wu, Xudong;
Liu, Tingting

Publication type:

Article

The human infertility single‐cell testis atlas (HISTA): an interactive molecular scRNA‐Seq reference of the human testis.

Published in:

Andrology, 2025, v. 13, n. 5, p. 1190, doi. 10.1111/andr.13637

By:

Mahyari, Eisa;
Vigh‐Conrad, Katinka A.;
Daube, Clément;
Lima, Ana C.;
Guo, Jingtao;
Carrell, Douglas T.;
Hotaling, James M.;
Aston, Kenneth I.;
Conrad, Donald F.

Publication type:

Article

Early transcriptional responses reveal cell type-specific vulnerability and neuroprotective mechanisms in the neonatal ischemic hippocampus.

Published in:

Acta Neuropathologica Communications, 2025, v. 13, n. 1, p. 1, doi. 10.1186/s40478-025-02062-4

By:

Ianevski, Aleksandr;
Cámara-Quílez, María;
Wang, Wei;
Suganthan, Rajikala;
Hildrestrand, Gunn;
Grini, Jonas Viken;
Døskeland, Dagny Sanden;
Ye, Jing;
Bjørås, Magnar

Publication type:

Article

Genetic and transcriptome analyses of the effect of genotype-by-environment interactions on Brassica napus seed oil content.

Published in:

Plant Cell, 2025, v. 37, n. 4, p. 1, doi. 10.1093/plcell/koaf062

By:

Han, Xu;
Wu, Xiaowei;
Zhang, Yawen;
Tang, Qingqing;
Zeng, Lingju;
Liu, Yunhao;
Xiang, Yuyan;
Hou, Keqin;
Fang, Shuai;
Lei, Weixia;
Li, Haojie;
Tang, Shan;
Zhao, Hu;
Peng, Yan;
Yao, Xuan;
Guo, Tingting;
Zhang, Yuan-Ming;
Guo, Liang

Publication type:

Article

scNucMap: mapping the nucleosome landscapes at single-cell resolution Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf324

By:

Xiang, Qianming;
Lai, Binbin

Publication type:

Article

BiGSM: Bayesian inference of gene regulatory network via sparse modelling Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf318

By:

Qin, Hang;
Garbulowski, Mateusz;
Sonnhammer, Erik L L;
Chatterjee, Saikat

Publication type:

Article

TRENDY: gene regulatory network inference enhanced by transformer Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf314

By:

Tian, Xueying;
Patel, Yash;
Wang, Yue

Publication type:

Article

Molecular mechanisms of s-methoprene-induced growth inhibition in Ephestia elutella (Hübner) (Lepidoptera: Pyralidae): insights from transcriptomic analysis Open Access.

Published in:

Journal of Insect Science, 2025, v. 25, n. 3, p. 1, doi. 10.1093/jisesa/ieaf035

By:

Huang, Chao;
Lü, Jianhua;
Bai, Chunqi;
Guo, Yafei;
Guo, Chao;
Song, Jizhen;
Xi, Jiaqin

Publication type:

Article

Generalized information criteria for personalized gene network inference.

Published in:

Frontiers in Genetics, 2025, p. 1, doi. 10.3389/fgene.2025.1583756

By:

Park, Heewon;
Imoto, Seiya;
Konishi, Sadanori

Publication type:

Article

Identification and validation of key genes involved in cellular senescence in multiple sclerosis using bioinformatics.

Published in:

Journal of Chinese Pharmaceutical Sciences, 2025, v. 34, n. 6, p. 530, doi. 10.5246/jcps.2025.06.040

By:

Xiaoqin Zhang;
Qiuhong Qin;
Xiaojie Li;
Jiangang Yang;
Jibin Ma;
Jianping Ren

Publication type:

Article

Joint analysis of transcriptome and metabolome on the accumulation mechanism of flavonoids in quinoa seedlings under flooding stress.

Published in:

BMC Plant Biology, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12870-025-06867-2

By:

Wang, Xuqin;
Zhang, Ping;
Qin, Zhiwei;
Jiang, Guofei;
Bai, Yutao;
Zhang, Lingyuan;
Liu, Junna;
Li, Li;
Li, Hanxue;
Huang, Liubin;
Yang, Jie;
Xie, Yuming;
Zhou, Jianlong;
Xia, Huanyao;
Qin, Peng

Publication type:

Article

Analysing the loss of embryogenic competence in long-term cell lines of Solanum betaceum Cav.: involvement of miR827, phosphate and sugar.

Published in:

BMC Plant Biology, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12870-025-06786-2

By:

Cordeiro, Daniela;
Canhoto, Jorge;
Correia, Sandra

Publication type:

Article

OsMADS55 nuclear translocation enhances OsATL15‐mediated thiamethoxam uptake in rice for controlling the brown planthopper.

Published in:

New Phytologist, 2025, v. 247, n. 3, p. 1382, doi. 10.1111/nph.70234

By:

Xiao, Yuyan;
Li, Zepu;
Deng, Shuqi;
Wang, Keyi;
Huang, Tinghong;
Liu, Linchuan;
Li, Youzhi;
Akihiro, Takashi;
Jia, Chunsheng;
Lin, Fei;
Xu, Hanhong

Publication type:

Article

Bridging aging, immunity, and atherosclerosis: novel insights into senescence-related genes.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1557266

By:

Lu, Yan;
Yuan, Rong;
Xin, Qiqi;
Chen, Keji;
Cong, Weihong

Publication type:

Article

Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics.

Published in:

Frontiers in Genetics, 2025, p. 1, doi. 10.3389/fgene.2025.1567173

By:

Yang, Xiaojuan;
Duan, Yutao;
Qiu, Lei;
Huang, Xia;
Li, Fei

Publication type:

Article

Meta-analysis of probiotics metabolites in gastrointestinal tract and metabolic health.

Published in:

Frontiers in Cellular & Infection Microbiology, 2025, p. 1, doi. 10.3389/fcimb.2025.1619501

By:

Ma, Xiangning;
Zhang, Hongjun

Publication type:

Article

Epilepsy Gene Discovery Needs Another Big Leap Forward.

Published in:

Epilepsy Currents, 2025, v. 25, n. 3, p. 201, doi. 10.1177/15357597251325685

By:

Frankel, Wayne N.

Publication type:

Article

Machine learning-based integration identifies plasma cells-related gene signature ST6GAL1 in idiopathic pulmonary fibrosis.

Published in:

BMC Pulmonary Medicine, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12890-025-03696-9

By:

Lin, Fanjie;
Lin, Ken;
Li, Donglei;
Kong, Weiguo;
Zhuang, Jiayu;
He, Wei;
Wei, Xinguang;
Xiao, Tianchi;
Zu, Hao;
Zhang, Zili;
Lu, Wenju

Publication type:

Article

Comparative transcriptomic analysis reveals the important role of hepatic fatty acid metabolism in the acute heat stress response in chickens.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-025-11832-2

By:

Mei, Zi;
Song, Zhenquan;
Zhou, Haobo;
Zheng, Bin;
Xiong, Yiwei;
Sheng, Zheya;
Gong, Yanzhang

Publication type:

Article

Site- and cell-type-specific miRNA and mRNA genes and networks across the cortex, striatum, and hypothalamus.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-08371-7

By:

Zacharias, Amanda M.;
O'Connor, Ciara D.;
Topouza, Danai G.;
Fang, Zhi Yi;
Ghazinejad, Helia;
Chen, Hanlin;
Duan, Qingling;
Ghasemlou, Nader

Publication type:

Article

A cross-talk established by tumor-targeted cytokines rescues CAR T cell activity and engages host T cells against glioblastoma in mice.

Published in:

Science Translational Medicine, 2025, v. 17, n. 805, p. 1, doi. 10.1126/scitranslmed.ado9511

By:

Rossari, Federico;
Alvisi, Giorgia;
Cusimano, Melania;
Beretta, Stefano;
Birocchi, Filippo;
Ambrosecchia, Deborah I.;
Vitaloni, Ottavia;
Brombin, Chiara;
Rancoita, Paola Maria Vittoria;
Canu, Tamara;
Orofino, Giorgio;
Annoni, Andrea;
Gentner, Bernhard;
Squadrito, Mario Leonardo;
Genua, Marco;
Ostuni, Renato;
Merelli, Ivan;
Coltella, Nadia;
Naldini, Luigi

Publication type:

Article

Integrating bioinformatics and machine learning to investigate the mechanisms by which three major respiratory infectious diseases exacerbate heart failure.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-07090-7

By:

Yu, Yiding;
Han, Quancheng;
Zhang, Juan;
Shi, Jingle;
Yuan, Huajing;
Xue, Yitao;
Li, Yan

Publication type:

Article

Exploring the molecular mechanisms of comorbidity between thyroid cancer and breast cancer through multi-omics data.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-06566-w

By:

Yang, Rui;
Li, Jiayi;
Zhang, Hongyang;
Liu, Huan;
Lian, Bin;
Li, Jinping

Publication type:

Article

Identification and verification of oxidative stress-related genes in the diagnosis of osteoporosis.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-06118-2

By:

Liu, Zhenchuan;
Yang, Xu;
Wang, Zexin;
Li, Qi;
Gu, Hanwen;
Meng, Qunbo;
Zhang, Yuanqiang

Publication type:

Article

Building a Hand-Curated ceRNET for Endometrial Cancer, Striving for Clinical as Well as Medicolegal Soundness: A Systematic Review.

Published in:

Non-Coding RNA, 2025, v. 11, n. 3, p. 34, doi. 10.3390/ncrna11030034

By:

Piergentili, Roberto;
Sechi, Stefano;
De Paola, Lina;
Zaami, Simona;
Marinelli, Enrico

Publication type:

Article

Integrating Equation Coding with Residual Networks for Efficient ODE Approximation in Biological Research.

Published in:

Mathematical & Computational Applications, 2025, v. 30, n. 3, p. 47, doi. 10.3390/mca30030047

By:

Yi, Ziyue

Publication type:

Article

A novel gene signature for forecasting time to next relapse in multiple sclerosis using peripheral blood mononuclear cells.

Published in:

BMC Neurology, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12883-025-04231-3

By:

Zhang, Huimin;
Yang, Jiahui;
Zhang, Xiaobo;
Wu, Chaoyi;
Zhao, Zhen;
Yang, Ming;
Wu, Zhaoping

Publication type:

Article

Transcriptome and co-expression network analysis reveal the genetic basis of cell wall components in maize stalks.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-025-11816-2

By:

He, Yao;
Deng, Zhike;
He, Shijiang;
Qi, Zhaojie;
Chang, Hengshuo;
Liu, Peng;
Chen, Zhong;
Zou, Chaoying;
Shen, Yaou;
Ma, Langlang

Publication type:

Article

RNA binding protein HuR regulated by OIP5-AS1 may be involved in maternal transcript degradation during the human maternal-to-zygotic transition.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-025-11807-3

By:

Liu, Yan-na;
Li, Ke-Yi;
Wei, Hao;
Li, Wen-xiu;
Zhang, Yue-hua;
Qiu, Jia-jun;
Zeng, Fanyi;
Yan, Jing-bin

Publication type:

Article

Interplay of light and nitrogen for plant growth and development.

Published in:

Crop Journal (2095-5421), 2025, v. 13, n. 3, p. 641, doi. 10.1016/j.cj.2025.01.005

By:

Chenlong Guan;
Dong Zhang;
Chengcai Chu

Publication type:

Article

Amino acid derivatives as regulatory molecules: Mechanisms in plant growth and stress tolerance.

Published in:

Crop Journal (2095-5421), 2025, v. 13, n. 3, p. 668, doi. 10.1016/j.cj.2025.04.005

By:

Ning Ouyang;
Wenjuan Hu;
Jieqiong Meng;
Bo Wang

Publication type:

Article

The Root Development Genes (RDGs) Network in Brassica napus and the Role of BnaSHR-6 in Response to Low Nitrogen.

Published in:

Plants (2223-7747), 2025, v. 14, n. 12, p. 1842, doi. 10.3390/plants14121842

By:

Chen, Xingying;
Zhou, Sining;
Ye, Shuang;
Chen, Zhuo;
Wu, Zexuan;
Liu, Shiying;
Hu, Liping;
Yang, Xiwen;
Yang, Xiaoya;
He, Peiji;
Qian, Xingzhi;
Wan, Huafang;
Zhang, Ti;
Ying, Nengwen;
Zhao, Huiyan;
Li, Jiana;
Qu, Cunmin;
Du, Hai

Publication type:

Article

Exploring the Genetic Networks of HLB Tolerance in Citrus: Insights Across Species and Tissues.

Published in:

Plants (2223-7747), 2025, v. 14, n. 12, p. 1792, doi. 10.3390/plants14121792

By:

Machado, Rodrigo;
Moschen, Sebastián;
Conti, Gabriela;
González, Sergio A.;
Rivarola, Máximo;
Gómez, Claudio;
Hopp, Horacio Esteban;
Fernández, Paula

Publication type:

Article

Transcriptome and Metabolome Analyses of Taxus chinensis var. mairei Tissues Provide New Insights into the Regulation of Paclitaxel Biosynthesis.

Published in:

Plants (2223-7747), 2025, v. 14, n. 12, p. 1775, doi. 10.3390/plants14121775

By:

Jiang, Luyuan;
Li, Yanyan;
Jiang, Xiaoyang;
Shao, Fenjuan;
Wu, Wenli;
Xu, Fan;
Wilson, Iain;
Hoffman, Angela;
Yang, Yanfang;
Qiu, Deyou

Publication type:

Article

Thresholds and Trade-Offs: Fire Severity Modulates Soil Microbial Biomass-Function Coupling in Taiga Forests, Northeast of China.

Published in:

Microorganisms, 2025, v. 13, n. 6, p. 1318, doi. 10.3390/microorganisms13061318

By:

Qu, Huijiao;
Jiang, Siyu;
Cheng, Zhichao;
Wei, Dan;
Yang, Libin;
Zhou, Jia

Publication type:

Article

Comparative Genomics of Sigma Factors in Acidithiobacillia Sheds Light into the Transcriptional Regulatory Networks Involved in Biogeochemical Dynamics in Extreme Acidic Environments.

Published in:

Microorganisms, 2025, v. 13, n. 6, p. 1199, doi. 10.3390/microorganisms13061199

By:

Sepúlveda-Rebolledo, Pedro;
González-Rosales, Carolina;
Dopson, Mark;
Pérez-Rueda, Ernesto;
Holmes, David S.;
Valdés, Jorge H.

Publication type:

Article

Super-Enhancers in Placental Development and Diseases.

Published in:

Journal of Developmental Biology, 2025, v. 13, n. 2, p. 11, doi. 10.3390/jdb13020011

By:

Rosario, Gracy X.;
Brown, Samuel;
Karmakar, Subhradip;
Rumi, Mohammad A. Karim;
Nayak, Nihar R.

Publication type:

Article

Butyrate Selectively Targets Super‐Enhancers and Transcriptional Networks Associated with Human Mast Cell Function.

Published in:

European Journal of Immunology, 2025, v. 55, n. 6, p. 1, doi. 10.1002/eji.202451680

By:

Folkerts, Jelle;
de Bruijn, Marjolein J. W.;
van IJcken, Wilfred F. J.;
Hendriks, Rudi W.;
Stadhouders, Ralph

Publication type:

Article

Editorial: Crop domestication and selection: an evolutionary view affecting the development of agronomic traits.

Published in:

2025

By:

Beernink, Bliss M.;
An, Hong;
Neik, Ting Xiang;
Lei, Li

Publication type:

Editorial

Comparative transcriptome and metabolome profiling unveil genotype-specific strategies for drought tolerance in cotton.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1610552

By:

Han, Aixia;
Fu, Wanwan;
Liusui, Yunhao;
Zhong, Xingyue;
Zhang, Xin;
Wang, Ziyu;
Li, Yuanxin;
Zhang, Jingbo;
Guo, Yanjun

Publication type:

Article

Gut microbiota orchestrates skeletal muscle development and metabolism in germ-free and SPF pigs.

Published in:

Frontiers in Microbiology, 2025, p. 1, doi. 10.3389/fmicb.2025.1615884

By:

Li, Zhengjie;
Wen, Mingxing;
Tang, Chuang;
Chen, Shuangshuang;
Tang, Die;
Zhang, Jinwei;
Sun, Jing;
Ge, Liangpeng;
Long, Keren;
Lu, Lu;
Jin, Long;
Li, Mingzhou;
Li, Xuewei;
Ma, Jideng

Publication type:

Article