Works matching DE "GENE regulatory networks"

Results: 5000

Editorial: Multi-omics strategies to analyze complex agronomic traits in plants, volume II.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1614041

By:

Tan, Guo-Fei;
Chen, Lin

Publication type:

Article

Integrative transcriptomic-physiological analysis deciphers nitrogen-mediated carbon reallocation balancing growth and flavonoid metabolism in Epimedium pubescens.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1539445

By:

Liu, Shangnian;
An, Xiaojing;
Xu, Chaoqun;
He, Dongmei;
Li, Xianen;
Chen, Caixia;
Guo, Baolin;
Xu, De;
Huang, Juan

Publication type:

Article

Bioinformatics and system biology approach to discover the common pathogenetic processes between COVID-19 and chronic hepatitis B.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0323708

By:

Ma, Xiao;
Huang, Tengda;
Song, Yujia;
Pan, Hongyuan;
Du, Ao;
Zhou, Xinyi;
Zeng, Yong;
Yuan, Kefei

Publication type:

Article

Analysis of Functional cis-Regulatory Elements Reveals Novel Transcriptional Regulatory Mechanisms in Gonadal Development.

Published in:

Sexual Development, 2024, v. 18, n. 1-6, p. 14, doi. 10.1159/000543594

By:

Kirino, Shizuka;
Nakagawa, Ryuichi;
Gau, Maki;
Takasawa, Kei;
Murakawa, Yasuhiro;
Kawaji, Hideya;
Hayashizaki, Yoshihide;
Morio, Tomohiro;
Kashimada, Kenichi

Publication type:

Article

Identification of shared mechanisms between Alzheimer's disease and atherosclerosis by integrated bioinformatics analysis.

Published in:

European Journal of Medical Research, 2025, v. 30, n. 1, p. 1, doi. 10.1186/s40001-025-02642-z

By:

Wang, Jukun;
Yao, Jing;
Wang, Zhe

Publication type:

Article

Single‐cell multiome reveals root hair‐specific responses to salt stress.

Published in:

New Phytologist, 2025, v. 246, n. 6, p. 2634, doi. 10.1111/nph.70160

By:

Liu, Qing;
Kang, Jingmin;
Du, Lin;
Liu, Zhaokun;
Liang, Hao;
Wang, Kailai;
He, Haijiao;
Zhang, Xiaonan;
Wang, Qifan;
Hong, Yiguo;
Cheng, Qi;
Liu, Xin;
Ma, Wei;
Zhao, Jianjun

Publication type:

Article

Genomic and transcriptomic insights into legume–rhizobia symbiosis in the nitrogen‐fixing tree Robinia pseudoacacia.

Published in:

New Phytologist, 2025, v. 246, n. 6, p. 2522, doi. 10.1111/nph.70101

By:

Hu, Bin;
Messerer, Maxim;
Haberer, Georg;
Lux, Thomas;
Marosi, Vanda;
Mayer, Klaus F. X.;
Oliphant, Kevin D.;
Kaufholdt, David;
Schulze, Jutta;
Kreth, Lana‐Sophie;
Jurgeleit, Jens;
Geffers, Robert;
Hänsch, Robert;
Rennenberg, Heinz

Publication type:

Article

Identification and validation of shared biomarkers and drug repurposing in psoriasis and Crohn's disease: integrating bioinformatics, machine learning, and experimental approaches.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1587705

By:

Li, Xiaolong;
Cao, Hui;
Niu, Mutian;
Liu, Qingbo;
Liang, Bin;
Hou, Junfeng;
Tu, Jian;
Gao, Jintao

Publication type:

Article

Identification of potential biomarkers and pathways related to major depressive disorder by integrated bioinformatic analysis and experimental validation.

Published in:

Asian Pacific Journal of Tropical Biomedicine, 2025, v. 15, n. 5, p. 200, doi. 10.4103/apjtb.apjtb_750_24

By:

Zeng, Ying;
Peng, Lu-Qi;
Zhang, Mei;
Zhong, Rong;
Nie, Ke-Chao;
Huang, Wei

Publication type:

Article

تجزیه و تحلیل مقایسه ای شبکه های هم بیان ژنی خانواده دی آسیل گلیسرول آسیل ترانسفراز (DGAT) در گاو و انسان.

Published in:

Animal Production Research, 2025, v. 14, n. 1, p. 19, doi. 10.22124/ar.2025.29572.1879

By:

عفت نصر اصفهانی;
سعید انصاری مهیا;
مصطفی قادری زفره

Publication type:

Article

Bioinformatics and In-Silico Findings Reveal Candidate Genes for Tetralogy of Fallot via Integrative Multi-Omics Data.

Published in:

Congenital Heart Disease, 2025, v. 20, n. 2, p. 213, doi. 10.32604/chd.2025.064950

By:

Shi, Jiawei;
Wang, Zhen;
Bai, Ying;
Li, Shiying;
Zhang, Xin;
Liu, Tianshu;
Hong, Liu;
Cui, Li;
Zhang, Yi;
Ma, Jing;
Liu, Juanjuan;
Zhang, Jing;
Cao, Haiyan;
Wang, Jing

Publication type:

Article

The molecular mechanism by which CTSB degrades FPN to disrupt macrophage iron homeostasis and promote the progression of atherosclerosis.

Published in:

Molecular & Cellular Biochemistry, 2025, v. 480, n. 6, p. 3889, doi. 10.1007/s11010-025-05228-9

By:

Qiu, Quanli;
Sun, Qiyu;
Yang, Jiaxin;
Yuan, Qingxin;
Wang, Ping;
Liu, Qingwei;
Cui, Zhenzhen;
Ma, Xiaowen;
Li, Min

Publication type:

Article

RNA epigenetic modifications: a new field of research in calcific aortic valve disease Free.

Published in:

Cardiovascular Research, 2025, v. 121, n. 1, p. 8, doi. 10.1093/cvr/cvae256

By:

Briend, Mewen;
Mathieu, Patrick

Publication type:

Article

Dual-responsive synthetic gene circuit for dynamic biologic drug delivery via inflammatory and circadian signaling pathways.

Published in:

Journal of Biological Engineering, 2025, v. 19, n. 1, p. 1, doi. 10.1186/s13036-025-00519-7

By:

Cimino, Amanda;
Pat, Fiona;
Oyebamiji, Omolabake;
Pham, Christine T.N.;
Herzog, Erik D.;
Guilak, Farshid

Publication type:

Article

A fast validation test of gene regulatory network models via the Fokker-Planck equation.

Published in:

Journal of Biological Physics, 2025, v. 51, n. 1, p. 1, doi. 10.1007/s10867-025-09681-x

By:

López-Paleta, Natalia;
Moreno-Barbosa, Eduardo;
Velázquez-Castro, Jorge

Publication type:

Article

Identification and Experimental Validation of Biomarkers Associated With Mitochondria and Macrophage Polarization in Sepsis.

Published in:

Emergency Medicine International, 2025, v. 2025, p. 1, doi. 10.1155/emmi/8755175

By:

She, Liping;
Deng, Xiaojing;
Bian, Yeping;
Cheng, Hui;
Xu, Jian;
Cirocchi, Roberto

Publication type:

Article

Bioinformatics analysis of comorbid mechanisms between ischemic stroke and end stage renal disease.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-01049-4

By:

Wang, Shuhong;
Li, Zhongda;
Wang, Xiao;
Zhou, Jiexue;
Meng, Shandong;
Zhuang, Jinyang;
Zhou, Yan;
Zhao, Qin;
Zhu, Chunli;
Zhang, Yusheng;
Shen, Sheng

Publication type:

Article

The identification and validation of histone acetylation-related biomarkers in depression disorder based on bioinformatics and machine learning approaches.

Published in:

Frontiers in Neuroscience, 2025, p. 1, doi. 10.3389/fnins.2025.1479616

By:

Zhang, Lu;
Lv, YuJing;
Ma, Mengqing;
Lv, Jile;
Chen, Jie;
Lei, Shang;
Man, Yi;
Xing, Guimei;
Wang, Yu

Publication type:

Article

Integrating single-cell sequencing and transcriptome analysis to unravel the mechanistic role of sialylation-related genes in sepsis-induced acute respiratory distress syndrome.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1528769

By:

Liu, Xiaobing;
Huang, Yake;
Zhang, Hao;
Yang, Xia;
Liu, Quanxing;
Dai, Jigang

Publication type:

Article

Identification of potential crucial genes and mechanisms associated with metabolically unhealthy obesity based on the gene expression profile.

Published in:

Frontiers in Genetics, 2025, p. 1, doi. 10.3389/fgene.2025.1540721

By:

Wang, Qingqing;
Wang, Silu;
Zhuang, Zhanyu;
Wu, Xueting;
Gao, Hongkun;
Zhang, Tianyi;
Zou, Guorong;
Ge, Xing;
Liu, Yapeng

Publication type:

Article

Identification immune-related hub genes in diagnosing atherosclerosis with ischemic stroke through comprehensive bioinformatics analysis and machine learning.

Published in:

Frontiers in Neurology, 2025, p. 1, doi. 10.3389/fneur.2025.1507855

By:

Zhang, Ming;
Tang, Li-Jun;
Long, Shi-Yu

Publication type:

Article

Mechanistic role of pyroptosis in Kawasaki disease: An integrative bioinformatics analysis of immune dysregulation, machine learning-based biomarker discovery, WGCNA, and drug repurposing insights.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0323597

By:

Wang, Chen;
Wu, Qinchao;
Chen, Jie;
Wang, Jun;
Li, Dan

Publication type:

Article

Neutrophil extracellular traps-related genes contribute to sepsis-associated acute kidney injury.

Published in:

BMC Nephrology, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12882-025-04126-y

By:

Shaoqun, Tang;
Xi, Yu;
Wei, Wang;
Yaru, Luo;
Shaoqing, Lei;
Zhen, Qiu;
Yanlin, Yang;
Qian, Sun;
Zhongyuan, Xia

Publication type:

Article

1 H-NMR Guided Isolation of Bioactive Compounds from Species of the Genus Piper.

Published in:

Molecules, 2025, v. 30, n. 9, p. 2020, doi. 10.3390/molecules30092020

By:

Oliveira, Celso R.;
Burroughs, Megan J.;
Richards, Lora A.;
Dyer, Lee A.;
Urbano-Muñoz, Federico;
Lee, Camryn;
Warner, Megan;
Dodson, Craig D.;
Wallace, Ian S.;
Jeffrey, Christopher S.

Publication type:

Article

MYCN as an oncogene in pediatric brain tumors.

Published in:

Frontiers in Oncology, 2025, p. 1, doi. 10.3389/fonc.2025.1584978

By:

Fernandez Garcia, Adriana;
Jackson, Jayden;
Iyer, Poorvi;
Oliver, Elissa G.;
Funato, Kosuke

Publication type:

Article

Comprehensive Single‐Cell RNA Sequencing Analysis of Cervical Cancer: Insights Into Tumor Microenvironment and Gene Expression Dynamics.

Published in:

International Journal of Genomics, 2025, v. 2025, p. 1, doi. 10.1155/ijog/5027347

By:

Shen, Xiaoting;
Sun, Huier;
Zhang, Shanshan;
Zhao, Songyun

Publication type:

Article

Combined Transcriptomic and Mendelian Randomisation Explores the Diagnostic Value of Ubiquitination-Related Genes in Sepsis.

Published in:

Journal of Inflammation Research, 2025, v. 18, p. 4709, doi. 10.2147/JIR.S489077

By:

Bai, Xue;
Liu, RuXing;
Tang, Yujiao;
Yang, LiTing;
Niu, Zesu;
Hu, Yi;
Zhang, Ling;
Chen, MengFei

Publication type:

Article

An Integrative Analysis of Transcriptome Combined with Machine Learning and Single-Cell RNA-Seq for the Common Biomarkers in Crohn's Disease and Kidney Stone Disease.

Published in:

Journal of Inflammation Research, 2025, v. 18, p. 4961, doi. 10.2147/JIR.S502513

By:

Zhu, Jiejie;
Du, Yishan;
Gao, Luyao;
Wang, Jiajia;
Mei, Qiao

Publication type:

Article

Transcriptome Analysis Reveals Association of E-Class AmMADS-Box Genes with Petal Malformation in Antirrhinum majus L.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 9, p. 4450, doi. 10.3390/ijms26094450

By:

Yang, Dongmei;
Chen, Yiwen;
He, Yutong;
Song, Jiayi;
Jiang, Ye;
Yang, Meiyun;
Zheng, Xingyan;
Wang, Li;
Hu, Huizhen

Publication type:

Article

Transduction of Lentiviral Vectors and ADORA3 in HEK293T Cells Modulated in Gene Expression and Alternative Splicing.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 9, p. 4431, doi. 10.3390/ijms26094431

By:

Qian, Yongqi;
Liu, Zhaoyu;
Liu, Qingqing;
Tian, Xiaojuan;
Mo, Jing;
Leng, Liang;
Wang, Can;
Xu, Guoqing;
Zhang, Sanyin;
Xie, Jiang

Publication type:

Article

Responses of Calligonum leucocladum to Prolonged Drought Stress Through Antioxidant System Activation, Soluble Sugar Accumulation, and Maintaining Photosynthetic Homeostasis.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 9, p. 4403, doi. 10.3390/ijms26094403

By:

Yang, Fang;
Lv, Guanghui

Publication type:

Article

Identification and Exploration of Pyroptosis-Related Genes in Macrophage Cells Reveal Necrotizing Enterocolitis Heterogeneity Through Single-Cell and Bulk-Sequencing.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 9, p. 4036, doi. 10.3390/ijms26094036

By:

Zhang, Peipei;
Li, Ying;
Xu, Panpan;
Zou, Peicen;
Sheng, Sihan;
Xiao, Ruiqi;
Xu, Pu;
Chen, Ying;
Du, Yue;
Ma, Lishuang;
Wang, Yajuan

Publication type:

Article

Exploring the Role of Circadian Rhythm-Related Genes in the Identification of Sepsis Subtypes and the Construction of Diagnostic Models Based on RNA-seq and scRNA-seq.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 9, p. 3993, doi. 10.3390/ijms26093993

By:

Wang, Xuesong;
Guo, Zhe;
Wang, Ziwen;
Wang, Xinrui;
Xia, Yuxiang;
Wu, Dishan;
Wang, Zhong

Publication type:

Article

Dual Disruption of EGFR/PI3K Signaling: IGF2BP2 Targeting Reverses Anti-EGFR Resistance in CAFs-Infiltrated Oral Squamous Cell Carcinoma.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 9, p. 3941, doi. 10.3390/ijms26093941

By:

Hu, Yaying;
Zhu, Tianshuang;
Nong, Sheng;
Sun, Yanan;
Li, Yiwei;
Pan, Junchen;
Ma, Jiyuan;
Zhang, Jiali

Publication type:

Article

ABA Enhances Drought Resistance During Rapeseed (Brassica napus L.) Seed Germination Through the Gene Regulatory Network Mediated by ABA Insensitive 5.

Published in:

Plants (2223-7747), 2025, v. 14, n. 9, p. 1276, doi. 10.3390/plants14091276

By:

Luo, Dan;
Huang, Qian;
Chen, Manyi;
Li, Haibo;
Lu, Guangyuan;
Feng, Huimin;
Lv, Yan

Publication type:

Article

The Transcriptome Analysis Provides New Insights into Signaling for Bamboo Shoot Development of Sympodial Bamboo.

Published in:

Foods, 2025, v. 14, n. 9, p. 1647, doi. 10.3390/foods14091647

By:

Hu, Shunkai;
Dong, Mengran;
Guo, Qirong

Publication type:

Article

Comparative Proteome and Weighted Gene Co-Expression Network Analyses Uncover the Mechanism of Wheat Grain Protein Accumulation in Response to Nitrogen Fertilizer Application.

Published in:

Foods, 2025, v. 14, n. 9, p. 1481, doi. 10.3390/foods14091481

By:

Xu, Beiming;
Jia, Yuku;
Feng, Jianchao;
Yang, Yang;
Ma, Geng;
Zhang, Yanfei;
Xie, Yingxin;
Ma, Dongyun

Publication type:

Article

The Mitochondrial Metabolism Gene ECH1 Was Identified as a Novel Biomarker for Diabetic Nephropathy: Using Bioinformatics Analysis and Experimental Confirmation.

Published in:

Diabetes, Metabolic Syndrome & Obesity: Targets & Therapy, 2025, v. 18, p. 1087, doi. 10.2147/DMSO.S494644

By:

Miao, Yan;
Yan, Lei;
Cao, Huixia;
Jiao, Xiaojing;
Shao, Fengmin

Publication type:

Article

STAT3, MYC, and EBNA1 cooperate through a ZC3H18 transcriptional network to regulate survival and proliferation of EBV-positive lymphomas.

Published in:

PLoS Pathogens, 2025, v. 21, n. 5, p. 1, doi. 10.1371/journal.ppat.1013166

By:

Xu, Huanzhou;
Koganti, Siva;
Li, Chenglong;
McIntosh, Michael T.;
Bhaduri-McIntosh, Sumita

Publication type:

Article

Transcriptomics-based exploration of ubiquitination-related biomarkers and potential molecular mechanisms in laryngeal squamous cell carcinoma.

Published in:

BMC Medical Genomics, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s12920-025-02148-x

By:

Chen, Qiu;
Wu, Zhimin;
Ma, Yifei

Publication type:

Article

Construction of a Prognostic Model for Cervical Cancer Related to lncRNA Based on Differential Co-expression Network and Functional Study of Key Gene EGFR-AS1.

Published in:

Journal of Cancer, 2025, v. 16, n. 7, p. 2321, doi. 10.7150/jca.108429

By:

Kailong Du;
Qian Chen;
Hui Fan;
Yunlong Lei;
Jian Zhang

Publication type:

Article

Structural Dynamics, Evolutionary Significance, and Functions of Really Interesting New Gene Proteins in Ubiquitination and Plant Stress: A Review.

Published in:

DNA & Cell Biology, 2025, v. 44, n. 5, p. 214, doi. 10.1089/dna.2025.0002

By:

Agarwal, Parinita;
Chittora, Anjali;
Verma, Ayushi;
Agarwal, Pradeep K.

Publication type:

Article

Development of a prognostic model for osteosarcoma based on macrophage polarization-related genes using machine learning: implications for personalized therapy.

Published in:

Clinical & Experimental Medicine, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10238-024-01530-w

By:

Zeng, Jin;
Wang, Dong;
Tong, ZhaoChen;
Li, ZiXin;
Wang, GuoWei;
Du, YuMeng;
Li, Jinsong;
Miao, Jinglei;
Chen, Shijie

Publication type:

Article

Integrating genomics and transcriptomics reveals candidate genes affecting loin muscle area in Huaxi cattle.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0322026

By:

Xue, Qingqing;
Du, Lili;
Deng, Tianyu;
Liang, Mang;
Li, Keanning;
Qian, Li;
Qiu, Shiyuan;
Chen, Yan;
Gao, Xue;
Xu, Lingyang;
Wang, Zezhao;
Zheng, Caihong;
Zhang, Lupei;
Li, Junya;
Gao, Huijiang

Publication type:

Article

Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00522-0

By:

López-Sánchez, Patricio;
Ávila-Moreno, Federico;
Hernández-Lemus, Enrique;
Kuijjer, Marieke L.;
Espinal-Enríquez, Jesús

Publication type:

Article

Identification and Validation of Tryptophan Metabolism–Related Genes in Diabetic Kidney Disease and Construction of a Clinical Prediction Model.

Published in:

Journal of Diabetes Research, 2025, v. 2025, p. 1, doi. 10.1155/jdr/2736801

By:

Liu, Shaojie;
Jiang, Qingqing;
Li, Wenli;
Shi, Jinbao;
Wu, Binxuan;
Xiong, Man;
Huang, Liuying;
Ahmed, Syed Anees

Publication type:

Article

Integrative bioinformatic analysis identifies differentially expressed gene targets as potential biomarkers for anaplastic thyroid cancer.

Published in:

Journal of the Egyptian National Cancer Institute, 2025, v. 37, n. 1, p. 1, doi. 10.1186/s43046-025-00282-2

By:

Treviño-Juarez, Angel Sebastian;
Gonzalez-Gonzalez, Jose Gerardo;
Rodriguez-Gutierrez, Rene;
Sanchez-Garcia, Adriana;
Gonzalez-Velazquez, Camilo Daniel

Publication type:

Article

Decoding microRNA arm switching: a key to evolutionary innovation and gene regulation.

Published in:

Cellular & Molecular Life Sciences, 2025, v. 82, n. 1, p. 1, doi. 10.1007/s00018-025-05663-3

By:

Pinhal, Danillo;
Gonçalves, Leandro de B.;
Campos, Vinícius F.;
Patton, James G.

Publication type:

Article

KAT5 regulates neurodevelopmental states associated with G0-like populations in glioblastoma.

Published in:

Nature Communications, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41467-025-59503-w

By:

Mihalas, Anca B.;
Arora, Sonali;
O'Connor, Samantha A.;
Feldman, Heather M.;
Cucinotta, Christine E.;
Mitchell, Kelly;
Bassett, John;
Kim, Dayoung;
Jin, Kang;
Hoellerbauer, Pia;
Delegard, Jennifer;
Ling, Melissa;
Jenkins, Wesley;
Kufeld, Megan;
Corrin, Philip;
Carter, Lucas;
Tsukiyama, Toshio;
Aronow, Bruce;
Plaisier, Christopher L.;
Patel, Anoop P.

Publication type:

Article

The assembly of a Malus sieversii regulatory network reveals gene resistance against Alternaria alternata f. sp. mali when colonized by Trichoderma biofertilizer.

Published in:

Journal of Plant Research, 2025, v. 138, n. 3, p. 483, doi. 10.1007/s10265-025-01622-y

By:

Ji, Shida;
Li, Dechen;
Yao, Jin;
Liu, Bin;
Han, Jing;
Wang, Yucheng;
Liu, Zhihua

Publication type:

Article