Works matching DE "GENE regulatory networks"

Results: 5000

Identification of mitophagy-related biomarkers in severe acute pancreatitis: integration of WGCNA, machine learning algorithms and scRNA-seq.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1594085

By:

Xie, Xiaozhou;
Wang, Zheng;
Zhang, Haoyu;
Lu, Jiongdi;
Cao, Feng;
Li, Fei

Publication type:

Article

Identification and Analysis of Key miRNA for Sex Differentiation in Hermaphroditic Juglans mandshurica Maxim.

Published in:

Plant Molecular Biology Reporter, 2025, v. 43, n. 2, p. 777, doi. 10.1007/s11105-024-01510-0

By:

Li, Jingze;
Zhang, Mengmeng;
Wu, Jingwen;
Qin, Baiting;
Liu, ChunPing;
Zhang, Lijie

Publication type:

Article

Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation.

Published in:

Journal of Bioinformatics & Computational Biology, 2025, v. 23, n. 2, p. 1, doi. 10.1142/S0219720025500052

By:

Zhao, Na;
Liu, Haihong;
Yan, Fang

Publication type:

Article

Watkins wheat landraces decode nitrogen-driven biomass trade-offs: GWAS exposes root-shoot dialectics and elite landraces for resilient agriculture.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1603577

By:

Waheed, Abdul;
Iqbal, Muhammad Shahid;
Sarfraz, Zareen;
Hou, Junliang;
Wei, Yanping;
Song, Bo;
Cheng, Shifeng

Publication type:

Article

Comprehensive transcriptome analysis provides molecular insights into the heterosis-associated drought tolerance and reveals ZmbHLH137 that promotes drought tolerance in maize seedlings.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1565650

By:

Cao, Liru;
Zhang, Dongling;
Fahim, Abbas Muhammad;
Liu, Huafeng;
Zhang, Zhe;
Hu, Desheng;
Ye, Feiyu;
Ma, Chenchen;
Abou-Elwaf, Salah Fatouh;
Aboud, Nora M. Al;
Song, Yinghui;
Guo, Shulei;
Zhang, Qianjin;
Zhang, Xin;
Lu, Xiaomin

Publication type:

Article

Subregion-based radiomics analysis for predicting the histological grade of clear cell renal cell carcinoma.

Published in:

Frontiers in Oncology, 2025, p. 1, doi. 10.3389/fonc.2025.1554830

By:

Lv, Xue;
Dai, Xiao-Mao;
Zhou, Dai-Quan;
Yu, Na;
Hong, Yu-Qin;
Liu, Qiao

Publication type:

Article

Malignant epithelial cell marker–driven risk signature enables precise stratification in esophageal cancer.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1610991

By:

Zhang, Hao;
Cheng, Shizhao;
Xu, Yijun

Publication type:

Article

Single‐cell transcriptional profiling reveals cellular senescence and inflammatory persistence as key features of type 1 diabetes partial remission.

Published in:

Diabetes, Obesity & Metabolism, 2025, v. 27, n. 7, p. 3653, doi. 10.1111/dom.16384

By:

Xie, Ruiqiang;
Li, Tianhao;
Gao, Hong;
Xie, Chunguang;
Yuan, Haipo;
Feng, Zhijun

Publication type:

Article

Modular and signal-responsive transcriptional regulation using CRISPRi-aided genetic switches in Escherichia coli.

Published in:

Journal of Biological Engineering, 2025, v. 19, n. 1, p. 1, doi. 10.1186/s13036-025-00526-8

By:

Kim, Seong Keun;
Woo, Seung-Gyun;
Park, Jun-Hong;
Lee, Seung-Goo;
Lee, Dae-Hee

Publication type:

Article

Identification and Functional Investigation of Hub Genes Associated with Follicular Lymphoma.

Published in:

Biochemical Genetics, 2025, v. 63, n. 3, p. 2470, doi. 10.1007/s10528-024-10831-4

By:

Zhu, Yidong;
Jin, Xiaoyi;
Liu, Jun;
Yang, Wenzhong

Publication type:

Article

Landscape control for cell fate transitions.

Published in:

Communications Physics, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42005-025-02160-8

By:

Lv, Jinchao;
Zhang, Song;
Zhou, Wenjia;
Li, Chunhe

Publication type:

Article

Distinct type I and II interferon responses direct cortical and medullary thymic epithelial cell development.

Published in:

Science Immunology, 2025, v. 10, n. 107, p. 1, doi. 10.1126/sciimmunol.ado4720

By:

Mohammed, Abdulvasey;
Wang, Wenqing;
Arreola, Martin;
Solomon, Benjamin D.;
Slepicka, Priscila F.;
Hubka, Kelsea M.;
Nguyen, Hanh Dan;
Zheng, Zihao;
Chavez, Michael G.;
Yeh, Christine Y.;
Kim, Doo Kyung;
Ma, Michael R.;
Martin, Elisabeth;
Li, Li;
Pasca, Anca M.;
Winn, Virginia D.;
Gifford, Casey A.;
Kedlian, Veronika R.;
Park, Jong-Eun;
Khatri, Purvesh

Publication type:

Article

The potential role of biomarkers CD28 and PF4 in the pathogenesis of idiopathic pulmonary fibrosis and their impact on the prognosis: an immune microenvironment analysis.

Published in:

Hereditas, 2025, v. 162, n. 1, p. 1, doi. 10.1186/s41065-025-00464-x

By:

Yan, Li;
Li, Jiang-Han;
Zhang, Ai-Li;
Li, He;
Pang, Bo;
Meng, De-Yang;
Fu, Qian;
Du, Li-Juan;
Su, Yan

Publication type:

Article

Identification and validation of prognostic genes associated with T-cell exhaustion and macrophage polarization in breast cancer.

Published in:

Frontiers in Endocrinology, 2025, p. 1, doi. 10.3389/fendo.2025.1556496

By:

Cui, Fengqiang;
Yan, Changjiao;
Wu, Jiang;
Yang, Yuqing;
Yang, Jixin;
Luo, Jialing;
Li, Nanlin

Publication type:

Article

Dynamical mechanisms of growth-feedback effects on adaptive gene circuits.

Published in:

eLife, 2025, p. 1, doi. 10.7554/eLife.89170

By:

Ling-Wei Kong;
Wenjia Shi;
Xiao-Jun Tian;
Ying-Cheng Lai

Publication type:

Article

Single-cell transcriptome sequencing reveals new epithelial-stromal associated mesenchymal-like subsets in recurrent gliomas.

Published in:

Acta Neuropathologica Communications, 2025, v. 13, n. 1, p. 1, doi. 10.1186/s40478-025-02036-6

By:

Li, Jinwei;
Long, Shengrong;
Zhang, Yang;
Yu, Shuangqi;
Xu, Hongyu;
Liang, Rui;
Liu, Quan;
Zhang, Jinnan;
Li, Xiang;
Fu, Yixin;
Xin, Tao;
Wang, Yinyan

Publication type:

Article

Using Fisher's Method to Identify Enriched Gene Sets.

Published in:

Statistics in Biopharmaceutical Research, 2014, v. 6, n. 2, p. 154, doi. 10.1080/19466315.2014.888013

By:

Tryputsen, Volha;
Cabrera, Javier;
De Bondt, An;
Amaratunga, Dhammika

Publication type:

Article

Bioinformatics‑Based Analysis Reveals Diagnostic Biomarkers and Immune Landscape in Atopic Dermatitis.

Published in:

Clinical, Cosmetic & Investigational Dermatology, 2025, v. 18, p. 1071, doi. 10.2147/CCID.S510044

By:

Yang, Mingmei;
Zhang, Xiaolei;
Zhou, Chao;
Du, Yuanyun;
Zhou, Mengyuan;
Zhang, Wenting

Publication type:

Article

Does Bilirubin Have a Causal Relationship With Vitiligo? A Mendelian Randomization Study and Bioinformatics Analysis.

Published in:

Clinical, Cosmetic & Investigational Dermatology, 2025, v. 18, p. 1107, doi. 10.2147/CCID.S522604

By:

Xu, Danfeng;
Yin, Yinmeng;
Teng, Yan;
Huang, Youming;
Yu, Yong;
Tao, Xiaohua;
Fan, Yibin;
Ding, Xiaoxia

Publication type:

Article

Optimal Network Pairwise Comparison.

Published in:

Journal of the American Statistical Association, 2025, v. 120, n. 550, p. 1048, doi. 10.1080/01621459.2024.2393471

By:

Jin, Jiashun;
Ke, Zheng Tracy;
Luo, Shengming;
Ma, Yucong

Publication type:

Article

Shared hub genes in membranous nephropathy and kidney renal clear cell carcinoma: investigating molecular overlap and tumor progression.

Published in:

Discover Oncology, 2025, v. 16, n. 1, p. 1, doi. 10.1007/s12672-025-02701-1

By:

Hui, Peng;
Shuwen, Zhang

Publication type:

Article

Investigation of high fecundity genes by nanopore sequencing in sheep (Ovis aries) pituitary.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-025-11732-5

By:

Xiao, Xue;
Ji, Zhibin;
Wang, Tong;
Zhu, Dejie;
Li, Zhonghui;
Xu, Xinming;
Li, Fen

Publication type:

Article

Comparative Analyses Reveal Conserved and Modified Steps in the Testis Descent and Scrotum Development in Mouse and Opossum.

Published in:

Cells Tissues Organs, 2025, v. 214, n. 3, p. 155, doi. 10.1159/000541805

By:

Wakamatsu, Yoshio;
Takeda, Yawara;
Tamura, Koji;
Suzuki, Kunihiro;
Kiyonari, Hiroshi;
Yamada, Gen

Publication type:

Article

The Tumor‐Associated Neutrophils‐Related Signatures Predict Prognosis and Indicate Immune Landscape in Colorectal Carcinoma.

Published in:

Mediators of Inflammation, 2025, v. 2025, p. 1, doi. 10.1155/mi/7259278

By:

Wang, Ying;
Zhu, Yizhen;
Zeng, Yuling;
Gao, Shuhui;
Tang, Youcai;
Wei, Ming;
Giovarelli, Mirella

Publication type:

Article

Multi-omics and single-cell approaches reveal molecular subtypes and key cell interactions in hepatocellular carcinoma.

Published in:

Frontiers in Pharmacology, 2025, p. 1, doi. 10.3389/fphar.2025.1605162

By:

Zou, Xueqing;
Wang, Yongmei;
Luan, Mingyuan;
Zhang, Yizheng

Publication type:

Article

Toward precision oncology in LUAD: a prognostic model using single-cell sequencing and WGCNA based on a disulfidptosis relative gene signature.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1581915

By:

Li, Panpan;
Zhang, Han;
Sun, Limin;
Wu, Xiaojuan

Publication type:

Article

Deep and periventricular white matter hyperintensities exhibit differential metabolic profiles in arteriosclerotic cerebral small vessel disease: an untargeted metabolomics study.

Published in:

Frontiers in Neuroscience, 2025, p. 1, doi. 10.3389/fnins.2025.1607242

By:

Ye, Shisheng;
Feng, Kaiyan;
Zeng, Guofang;
Cai, Jiaxin;
Liang, Lijuan;
Chen, Jiaxin;
He, Qishan;
Mai, Jianhui;
Wu, Qiaoling;
Chen, Chunwan;
Huang, Haifeng;
Yuan, Li;
Chen, Hai;
Li, Yizhong;
Li, Hao;
Zhang, Xiong

Publication type:

Article

De novo variants disrupt an LDB1-regulated transcriptional network in congenital ventriculomegaly.

Published in:

Brain: A Journal of Neurology, 2025, v. 148, n. 5, p. 1817, doi. 10.1093/brain/awae395

By:

Allington, Garrett;
Mehta, Neel H;
Dennis, Evan;
Mekbib, Kedous Y;
Reeves, Benjamin;
Kiziltug, Emre;
Chen, Shuang;
Zhao, Shujuan;
Duy, Phan Q;
Saleh, Maha;
Ang, Lee C;
Fan, Baojian;
Nelson-Williams, Carol;
Moreno-de-Luca, Andrés;
Haider, Shozeb;
Lifton, Richard P;
Alper, Seth L;
McGee, Stephen;
Jin, Sheng Chih;
Kahle, Kristopher T

Publication type:

Article

In silico study identifies hub genes and regulatory network associated with the pathogenesis of Japanese encephalitis virus.

Published in:

Egyptian Journal of Medical Human Genetics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s43042-025-00729-0

By:

Kumar, Arvind;
Chand, Gyanendra Bahadur;
Azad, Gajendra Kumar

Publication type:

Article

Efficient structure learning of gene regulatory networks with Bayesian active learning.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06149-6

By:

Sándor, Dániel;
Antal, Péter

Publication type:

Article

IFI35 and IFIT3 are potentially important biomarkers for early diagnosis and treatment of esophageal squamous cell carcinoma: based on WGCNA and machine learning analysis.

Published in:

Frontiers in Genetics, 2025, p. 1, doi. 10.3389/fgene.2025.1583202

By:

Wu, Hao;
Yang, Liang;
Weng, Xiaokun

Publication type:

Article

Exploring hypoxia-related genes in spinal cord injury: a pathway to new therapeutic targets.

Published in:

Frontiers in Molecular Neuroscience, 2025, p. 1, doi. 10.3389/fnmol.2025.1565430

By:

Cheng, Shihuan;
Li, Le;
Xu, Mengmeng;
Ma, Ningyi;
Zheng, Yinhua

Publication type:

Article

Comparative transcriptomic and proteomic analyses of hypoxia response in wild and cultivated tomato roots.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-025-11653-3

By:

Zhang, Zhihan;
Hou, Yabing;
Yin, Hao;
Lu, Song;
Liu, Daliang;
Cheng, Lin;
Yu, Houlin;
Li, Tao;
Zhao, Yiyong

Publication type:

Article

Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06174-5

By:

Yousefian, Maryam;
Frank, Anna-Simone;
Weber, Marcus;
Röblitz, Susanna

Publication type:

Article

Transposable Elements Drive Regulatory and Functional Innovation of F-box Genes Open Access.

Published in:

Molecular Biology & Evolution, 2025, v. 42, n. 5, p. 1, doi. 10.1093/molbev/msaf097

By:

Almeida, Miguel Vasconcelos;
Li, Zixin;
Rebelo-Guiomar, Pedro;
Dallaire, Alexandra;
Fiedler, Lukáš;
Price, Jonathan L;
Sluka, Jan;
Liu, Xiaodan;
Butter, Falk;
Rödelsperger, Christian;
Miska, Eric A

Publication type:

Article

Regulatory significance of terminator: A systematic approach for dissecting terminator-mediated enhancement of upstream mRNA stability.

Published in:

Synthetic & Systems Biotechnology, 2025, v. 10, n. 1, p. 326, doi. 10.1016/j.synbio.2024.11.006

By:

Jia-Wei Ren;
Jin-Peng Zhang;
Zi-Lun Mei;
Jia-Yi Shao;
Guo-Qiang Xu;
Hui Li;
Jin-Song Gong;
Xiao-Mei Zhang;
Jin-Song Shi;
Xiao-juan Zhang;
Zheng-hong Xu

Publication type:

Article

Engineering transcriptional regulatory networks for improving second-generation fuel ethanol production in Saccharomyces cerevisiae.

Published in:

Synthetic & Systems Biotechnology, 2025, v. 10, n. 1, p. 207, doi. 10.1016/j.synbio.2024.10.006

By:

Dongming Sun;
Longhao Wu;
Xiaocong Lu;
Chenhao Li;
Lili Xu;
Hongxing Li;
Deyun He;
Aiqun Yu;
Tao Yu;
Jianzhi Zhao;
Hongting Tang;
Xiaoming Bao

Publication type:

Article

Regulatory Network of Spinach Under Salt Stress: An Integrated Study of Long Non-coding RNAs and mRNAs.

Published in:

Journal of Plant Growth Regulation, 2025, v. 44, n. 5, p. 2298, doi. 10.1007/s00344-024-11546-x

By:

Mehralizade, Zahra;
Soorni, Aboozar;
Meratian Esfahani, Sepehr

Publication type:

Article

Mining Key Drought-Resistant Genes of Upland Cotton Based on RNA-Seq and WGCNA Analysis.

Published in:

Plants (2223-7747), 2025, v. 14, n. 10, p. 1407, doi. 10.3390/plants14101407

By:

Zhang, Hu;
Zhang, Wen;
Tang, Yu;
Guo, Yuantao;
Wang, Jinsheng;
Gao, Wenju;
Zeng, Qingtao;
Chen, Quanjia;
Chen, Qin

Publication type:

Article

Genome Mining Reveals Rifamycin Biosynthesis in a Taklamakan Desert Actinomycete.

Published in:

Microorganisms, 2025, v. 13, n. 5, p. 1068, doi. 10.3390/microorganisms13051068

By:

Luo, Xinrong;
Liu, Zhanwen;
Luo, Xiaoxia;
Xia, Zhanfeng;
Wan, Chuanxing;
Wang, Haoxin;
Zhang, Lili

Publication type:

Article

Multiple Transcriptomic Networks Regulate the Callus Development Process in Panax ginseng.

Published in:

Agronomy, 2025, v. 15, n. 5, p. 1244, doi. 10.3390/agronomy15051244

By:

Kim, Jaewook;
Lee, Jung-Woo;
Jo, Ick-Hyun

Publication type:

Article

Comparative Transcriptome Analysis of Susceptible and Resistant Rutaceae Plants to Huanglongbing.

Published in:

Agronomy, 2025, v. 15, n. 5, p. 1218, doi. 10.3390/agronomy15051218

By:

Liao, Huihong;
Liu, Fuping;
Wang, Xi;
Huang, Hongming;
Huang, Qichun;
Wang, Nina;
Wei, Chizhang

Publication type:

Article

Transcriptomic Profiling of Heat-Treated Oriental Lily Reveals LhERF109 as a Positive Regulator of Anthocyanin Accumulation.

Published in:

Agronomy, 2025, v. 15, n. 5, p. 1071, doi. 10.3390/agronomy15051071

By:

Zhou, Mei;
Zeng, Lijia;
Li, Fan;
Jin, Chunlian;
Zhu, Jungang;
Yong, Xue;
Wu, Mengxi;
Jiang, Beibei;
Jia, Yin;
Yuan, Huijuan;
Wang, Jihua;
Pan, Yuanzhi

Publication type:

Article

Hippocampal Transcriptome Analysis in a Mouse Model of Chronic Unpredictable Stress Insomnia.

Published in:

Biomedicines, 2025, v. 13, n. 5, p. 1205, doi. 10.3390/biomedicines13051205

By:

Zhang, Shuo;
Tong, Changqing;
Cao, Na;
Tian, Dong;
Du, Linshan;
Xu, Ya;
Wang, Weiguang;
Chen, Zijie;
Zhai, Shuangqing

Publication type:

Article

Assessment of NUDT5 in Endometrial Carcinoma: Functional Insights, Prognostic and Therapeutic Implications.

Published in:

Biomedicines, 2025, v. 13, n. 5, p. 1136, doi. 10.3390/biomedicines13051136

By:

Yu, Hongfei;
Zu, Lingling;
Zang, Yuqin;
Teng, Fei;
Wang, Tao;
Wu, Ming;
Wang, Yingmei;
Xue, Fengxia

Publication type:

Article

Artificial Intelligence in Advancing Algal Bioactive Ingredients: Production, Characterization, and Application.

Published in:

Foods, 2025, v. 14, n. 10, p. 1783, doi. 10.3390/foods14101783

By:

Guo, Bingbing;
Lu, Xingyu;
Jiang, Xiaoyu;
Shen, Xiao-Li;
Wei, Zihao;
Zhang, Yifeng

Publication type:

Article

Transcriptomic Profiling Uncovers Molecular Basis for Sugar and Acid Metabolism in Two Pomegranate (Punica granatum) Varieties.

Published in:

Foods, 2025, v. 14, n. 10, p. 1755, doi. 10.3390/foods14101755

By:

Ke, Ding;
Zhang, Yilong;
Teng, Yingfen;
Zhao, Xueqing

Publication type:

Article

MultiGNN: A Graph Neural Network Framework for Inferring Gene Regulatory Networks from Single-Cell Multi-Omics Data.

Published in:

Computation, 2025, v. 13, n. 5, p. 124, doi. 10.3390/computation13050124

By:

Liu, Dongbo;
Chen, Hao;
Wang, Jianxin;
Wang, Yeru

Publication type:

Article

The Key Role and Mechanism of Oxidative Stress in Hypertrophic Cardiomyopathy: A Systematic Exploration Based on Multi-Omics Analysis and Experimental Validation.

Published in:

Antioxidants, 2025, v. 14, n. 5, p. 557, doi. 10.3390/antiox14050557

By:

Zhang, Sijie;
Li, Tianzhi;
Sun, Shiyi;
Jiang, Yujiao;
Sun, Yuxin;
Meng, Yan

Publication type:

Article

Bioinformatics prediction of function of T-cell exhaustion related genes in ischemic stroke.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-03724-y

By:

Gao, Yajun;
Bai, Ruyu;
Gao, Bo;
Li, Ma

Publication type:

Article