Works matching DE "GENE regulatory networks"

Results: 5000

Transcriptomic Reprogramming and Key Molecular Pathways Underlying Huanglongbing Tolerance and Susceptibility in Six Citrus Cultivars.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 15, p. 7359, doi. 10.3390/ijms26157359

By:

Chen, Xiaohong;
Fang, Fang;
Chen, Tingting;
Wu, Jinghua;
Zheng, Zheng;
Deng, Xiaoling

Publication type:

Article

Escalated Oxycodone Self-Administration Is Associated with Activation of Specific Gene Networks in the Rat Dorsal Striatum.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 15, p. 7356, doi. 10.3390/ijms26157356

By:

Wabreha, Ammanuel Y.;
McCoy, Michael T.;
Cadet, Jean Lud;
Daiwile, Atul P.

Publication type:

Article

The Evolution of Plant Hormones: From Metabolic Byproducts to Regulatory Hubs.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 15, p. 7190, doi. 10.3390/ijms26157190

By:

Kurepa, Jasmina;
Smalle, Jan

Publication type:

Article

Integrated Transcriptome and Metabolome Analyses Uncover Cholesterol-Responsive Gene Networks.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 15, p. 7108, doi. 10.3390/ijms26157108

By:

Zhang, Ruihao;
Sun, Qi;
Huang, Lixia;
Li, Jian

Publication type:

Article

Transcriptional programs underlying human monocyte differentiation and diversity Open Access.

Published in:

Journal of Leukocyte Biology, 2025, v. 117, n. 7, p. 1, doi. 10.1093/jleuko/qiaf058

By:

Komaravolu, Ravi K;
Araujo, Daniel J;
Hedrick, Catherine C;
Alimadadi, Ahmad

Publication type:

Article

Transcriptomic Comparison of Lissencephaly-related Genes: From Correlation to Clinical Relevance.

Published in:

Anatolian Journal of General Medical Research, 2025, v. 35, n. 2, p. 230, doi. 10.4274/anatoljmed.2025.92400

By:

Kuruoğlu, Aykut;
Polat, İpek;
Oktay, Yavuz

Publication type:

Article

Deciphering functional landscape and clinical implications of enhancer RNAs in lung adenocarcinoma.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-15485-9

By:

Li, Aike;
Zhang, Liguang;
Du, Xinsheng;
Dong, Yi;
Guo, Yan;
Zhao, Jiwei;
Fang, Xiuli;
Lin, Pingping

Publication type:

Article

Causality-aware graph neural networks for functional stratification and phenotype prediction at scale.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00567-1

By:

Triantafyllidis, Charalampos P.;
Aguas, Ricardo

Publication type:

Article

YAP charge patterning mediates signal integration through transcriptional co-condensates.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-62157-3

By:

Meyer, Kirstin;
Yserentant, Klaus;
Cheloor-Kovilakam, Rasmi;
Ruff, Kiersten M.;
Chung, Chan-I;
Shu, Xiaokun;
Huang, Bo;
Weiner, Orion D.

Publication type:

Article

Almost lost in translation: integrated transcriptome and proteome analyses for early Arabidopsis flower development Open Access.

Published in:

Journal of Experimental Botany, 2025, v. 76, n. 10, p. 2602, doi. 10.1093/jxb/eraf144

By:

Folter, Stefan de

Publication type:

Article

Dancing molecules: group A bZIPs and PEBPs at the heart of plant development and stress responses Open Access.

Published in:

Journal of Experimental Botany, 2025, v. 76, n. 8, p. 2081, doi. 10.1093/jxb/eraf034

By:

Martignago, Damiano;
Falavigna, Vítor da Silveira;
Coupland, George;
Conti, Lucio

Publication type:

Article

Gibberellins: extending the Green Revolution Open Access.

Published in:

Journal of Experimental Botany, 2025, v. 76, n. 7, p. 1837, doi. 10.1093/jxb/erae476

By:

Robil, Janlo M;
Awale, Prameela;
McSteen, Paula;
Best, Norman B

Publication type:

Article

Research progress on non-coding RNA regulatory networks and targeted therapy in diabetic nephropathy.

Published in:

Frontiers in Endocrinology, 2025, p. 1, doi. 10.3389/fendo.2025.1625307

By:

Wang, Xiaxia;
Jing, Ruge;
Yang, Tong;
Shao, Ruiwen;
Yang, Fan;
Shi, Yangyang;
Yang, Xiujuan;
An, Dong;
Liang, Yonglin

Publication type:

Article

DualNetM: an adaptive dual network framework for inferring functional-oriented markers.

Published in:

BMC Biology, 2025, v. 23, n. 1, p. 1, doi. 10.1186/s12915-025-02367-9

By:

Dai, Bingjie;
Li, Hanshuang;
Wang, Peizhuo;
Hu, Pengwei;
Xing, Jixiang;
Hu, Yanan;
Xi, Qilemuge;
Zuo, Yongchun

Publication type:

Article

Spatial transcriptomics identifies SPARC as a prognostic marker in interstitial lung diseases.

Published in:

Journal of Pathology, 2025, v. 267, n. 1, p. 79, doi. 10.1002/path.6451

By:

Niitsu, Takayuki;
Kataoka, Toshiaki;
Fukushima, Kiyoharu;
Motooka, Daisuke;
Shichino, Shigeyuki;
Natsume‐Kitatani, Yayoi;
Kitamura, Hideya;
Niwa, Takashi;
Baba, Tomohisa;
Okuzaki, Daisuke;
Kumanogoh, Atsushi;
Akira, Shizuo;
Okudela, Koji;
Ogura, Takashi

Publication type:

Article

Integrative identification of key genes governing Verticillium wilt resistance in Gossypium hirsutum using machine learning and WGCNA.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1621604

By:

Lei, Yufeng;
Zhao, Jing;
Hou, Siyuan;
Xu, Fufeng;
Zhang, Chongbo;
Cai, Dongchen;
Cao, Xiaolei;
Yao, Zhaoqun;
Zhao, Sifeng

Publication type:

Article

Identification of key modules and hub genes for sepsis-induced myopathy using weighted gene co-expression network analysis.

Published in:

Frontiers in Genetics, 2025, p. 1, doi. 10.3389/fgene.2025.1607575

By:

Lin, Siming;
Cai, Kexin;
Chen, Ai;
Wu, Weibin;
Lian, Guili;
Feng, Shaodan;
Lin, Zhihong;
Xie, Liangdi

Publication type:

Article

Multi-trait GWAS for growth under contrasting thermal rearing conditions in rainbow trout (Oncorhynchus mykiss).

Published in:

Molecular Genetics & Genomics, 2025, v. 300, n. 1, p. 1, doi. 10.1007/s00438-025-02263-5

By:

Gallardo-Hidalgo, Jousepth;
Tapia, David A.;
Garcia, Baltasar F.;
Marin-Nahuelpi, Rodrigo;
Cáceres, Pablo;
Bassini, Liane N.;
Mastrochirico-Filho, Vito A.;
Araya, Carolina;
Yáñez, José M.

Publication type:

Article

Genome-wide CRISPR screen for human factors involved in alternative polyadenylation based on differential localization of CD47.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-14782-7

By:

Wuttinontananchai, Chayanin;
Yamamoto, Junichi;
Sakamoto, Satoshi;
Yamaguchi, Yuki

Publication type:

Article

Comparative physiological and transcriptomic analyses identify computationally predicted key genes and regulatory pathways in non-heading Chinese cabbage under heat stress.

Published in:

BMC Plant Biology, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12870-025-07120-6

By:

Liu, Wei;
Dai, Zhangyang;
Jia, Jingyi;
Li, Xiaofeng;
Zhu, Hongfang;
Kan, Xianzhao;
Zhu, Bo

Publication type:

Article

Integrative analysis of DEGs and regulatory networks in T2DM: identification of core genes and regulatory elements as novel therapeutic targets.

Published in:

3 Biotech, 2025, v. 15, n. 9, p. 1, doi. 10.1007/s13205-025-04453-9

By:

Yadav, Madhu;
Akhter, Yusuf

Publication type:

Article

Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine.

Published in:

Genome Medicine, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13073-025-01502-z

By:

Hieromnimon, Hanna M.;
Dolezal, James;
Doytcheva, Kristina;
Howard, Frederick M.;
Kochanny, Sara;
Zhang, Zhenyu;
Grossman, Robert L.;
Tanager, Kevin;
Wang, Cindy;
Kather, Jakob Nikolas;
Izumchenko, Evgeny;
Cipriani, Nicole A.;
Fertig, Elana J.;
Pearson, Alexander T.;
Riesenfeld, Samantha J.

Publication type:

Article

Gene behaviors-based network enrichment analysis and its application to reveal immune disease pathways enriched with COVID-19 severity-specific gene networks Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 7, p. 1, doi. 10.1093/bioinformatics/btaf378

By:

Park, Heewon;
Imoto, Seiya;
Miyano, Satory

Publication type:

Article

Adversarial attack of sequence-free enhancer prediction identifies chromatin architecture Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 7, p. 1, doi. 10.1093/bioinformatics/btaf371

By:

Gafur, Jamil;
Lang, Olivia W;
Lai, William K M

Publication type:

Article

dbscATAC: a resource of single-cell super-enhancers/enhancers and gene markers derived from scATAC-seq data Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 7, p. 1, doi. 10.1093/bioinformatics/btaf364

By:

Li, Yingmei;
Ullah, Shahid;
Xian, Yumei;
Sun, Yazhou;
Zheng, Zilong;
Ma, Xiaoyu;
Shi, Ming;
Zhang, Changlin;
Li, Tian;
Zeng, Leli;
Chen, Jie;
Deng, Yubin Y B;
Wei, Fuxin;
Gao, Tianshun

Publication type:

Article

SPONGE: simple prior omics network GEnerator Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 7, p. 1, doi. 10.1093/bioinformatics/btaf320

By:

Hovan, Ladislav;
Kuijjer, Marieke L

Publication type:

Article

Integration of multi-source gene interaction networks and omics data with graph attention networks to identify novel disease genes Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 7, p. 1, doi. 10.1093/bioinformatics/btaf181

By:

Yang, Kaiyuan;
Cheng, Jiabei;
Cao, Shenghao;
Pan, Xiaoyong;
Shen, Hong-bin;
Cheng, Jin;
Yuan, Ye

Publication type:

Article

基于 WGCNA 鉴定大豆抗大豆花叶病毒NAC转录因子及其诱导表达分析.

Published in:

Biotechnology Bulletin, 2025, v. 41, n. 7, p. 95, doi. 10.13560/j.cnki.biotech.bull.1985.2025-0109

By:

牛景萍;
赵婧;
郭茜;
王书宏;
赵晋忠;
杜维俊;
殷丛丛;
岳爱琴

Publication type:

Article

Multi-omics dissection of CPNE1 reveals its prognostic value and immune-regulatory function in liver cancer.

Published in:

Discover Oncology, 2025, v. 16, n. 1, p. 1, doi. 10.1007/s12672-025-03366-6

By:

Liu, Liu;
Hong, He;
Zhang, Weiwei;
Li, Xiang;
Yao, Yuan;
Zhang, Zhengjun;
Li, Guangyao

Publication type:

Article

Integrated analysis of gene networks and cellular functions identifies novel heart failure biomarkers.

Published in:

Hereditas, 2025, v. 162, n. 1, p. 1, doi. 10.1186/s41065-025-00521-5

By:

Juncheng, Jiang;
Lei, Chen;
Hao, Lin;
Fei, Liang

Publication type:

Article

Screening and identification of muscle pericyte selective markers.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-14225-3

By:

Ruan, Jingsong;
Kang, Minkyung;
Wang, Rong;
Xuan, Wanling;
Cheng, Feng;
Yao, Yao

Publication type:

Article

Optimized network inference for immune diseased single cells.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1597862

By:

Tejero, Elena Merino;
Vaz, Dwain Jude;
Barturen, Guillermo;
Rivas-Torrubia, María;
Alarcón-Riquelme, Marta E.;
Kolch, Walter;
Matallanas, David

Publication type:

Article

E2F1 suppresses Epstein-Barr virus lytic reactivation through cellular and viral transcriptional networks.

Published in:

PLoS Pathogens, 2025, v. 21, n. 8, p. 1, doi. 10.1371/journal.ppat.1013410

By:

Biswas, Joyanta;
Ali, SK. Asif;
Malik, Samaresh;
Nag, Subhadeep;
Mukherjee, Piyali;
Saha, Abhik

Publication type:

Article

Efficient Extracellular Production of a-Amylase in Bacillus subtilis under the Influence of Xylose-Inducible Promoter.

Published in:

BioResources, 2025, v. 20, n. 3, p. 7728, doi. 10.15376/biores.20.3.7728-7737

By:

Farouk, Abd-El Aziem;
Aroob, Iqra;
Amjad, Quratulain;
Abdelmigid, Hala Mohamed;
Greiner, Ralf

Publication type:

Article

WGCNA and single-cell analysis reveal ferroptosis-related gene signatures for hepatocellular carcinoma prognosis and therapy.

Published in:

Discover Oncology, 2025, v. 16, n. 1, p. 1, doi. 10.1007/s12672-025-03335-z

By:

Peng, Can;
Yan, Fujian;
Xu, Mingli;
Zhao, Yueyue;
Sun, Jiaxing

Publication type:

Article

ABA-GA antagonism and modular gene networks cooperatively drive acquisition of desiccation tolerance in perilla seeds.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1624742

By:

Yang, Xiaohuan;
Chen, Minghao;
Liu, Mingwang;
Li, Bowen;
Sun, Zhichao;
Lu, Ailian;
Zhang, Sen;
Shi, Xinghai;
Ren, Jun;
Qin, Xiuzhen;
Ma, Jinhu

Publication type:

Article

Cross-species analysis of abiotic stress in hydroponic leafy crops reveals conserved regulatory networks and key divergences.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1613016

By:

Lee, Jia Min;
Goh, Jong Ching;
Koh, Eugene;
Mutwil-Anderwald, Daniela;
Mutwil, Marek

Publication type:

Article

Petri net modeling and simulation of post-transcriptional regulatory networks of human embryonic stem cell (hESC) differentiation to cardiomyocytes.

Published in:

Journal of Integrative Bioinformatics, 2025, v. 22, n. 1, p. 1, doi. 10.1515/jib-2024-0037

By:

Hansel-Fröse, Aruana F. F.;
Brinkrolf, Christoph;
Friedrichs, Marcel;
Dallagiovanna, Bruno;
Spangenberg, Lucia

Publication type:

Article

Multi-omics profiling of metastatic colorectal cancer reveals the transcriptional network of focal adhesion and immune suppression and the role of p-RPS6.

Published in:

Cancer Cell International, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12935-025-03924-6

By:

Jiang, Yimei;
Li, Zhe;
Zheng, Fang;
Jia, Wenqing;
Guo, Zichao;
Xu, Zhuoqing;
Huang, Chenhao;
Li, Zhiliang;
Wang, Changgang;
Liu, Kun;
Feng, Haoran;
Zhao, Ren;
Cheng, Xi

Publication type:

Article

基于WGCNA挖掘野生大豆耐镉关键基因.

Published in:

Biotechnology Bulletin, 2025, v. 41, n. 8, p. 124, doi. 10.13560/j.cnki.biotech.bull.1985.2024-1113

By:

朱丽娟;
张锴;
温晓蕾;
褚佳豪;
史凤玉;
王艳丽

Publication type:

Article

Activation of the mechanosensitive ion channels TRPV4 and PIEZO1 downregulates key regulatory systems in the chondrocyte mechanome.

Published in:

Connective Tissue Research, 2025, v. 66, n. 4, p. 239, doi. 10.1080/03008207.2025.2498512

By:

Palmer, Daniel R.;
Nims, Robert;
Zhang, Bo;
Guilak, Farshid

Publication type:

Article

Distinct Lung Adenocarcinoma-Associated Microbiota Are Associated with Inflammatory Immune Landscapes and Tumor Cell Proliferation via LCIIAR–ISG15 Regulatory Networks.

Published in:

Cancer Management & Research, 2025, v. 17, p. 1315, doi. 10.2147/CMAR.S520098

By:

Liu, Shipu;
Zhang, Zijian

Publication type:

Article

Molecular mechanisms of cryoablation-mediated lung cancer suppression unveiled by non-coding RNA regulatory network profiling.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-14655-z

By:

Wang, Xiaofan;
Zhang, Mohan;
Liu, Dianna;
Lin, Shicheng;
Zhang, Yuxin;
Li, Quanwang

Publication type:

Article

Spectral divergence prioritizes key classes, genes, and pathways shared between substance use disorders and cardiovascular disease.

Published in:

Frontiers in Neuroscience, 2025, p. 1, doi. 10.3389/fnins.2025.1572243

By:

Castaneda, Everest;
Chesler, Elissa;
Baker, Erich

Publication type:

Article

Cross-species analysis of abiotic stress in hydroponic leafy crops reveals conserved regulatory networks and key divergences.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1613016

By:

Lee, Jia Min;
Goh, Jong Ching;
Koh, Eugene;
Mutwil-Anderwald, Daniela;
Mutwil, Marek

Publication type:

Article

Epiregulon: Single-cell transcription factor activity inference to predict drug response and drivers of cell states.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-62252-5

By:

Włodarczyk, Tomasz;
Lun, Aaron;
Wu, Diana;
Shi, Minyi;
Ye, Xiaofen;
Menon, Shreya;
Toneyan, Shushan;
Seidel, Kerstin;
Wang, Liang;
Tan, Jenille;
Chen, Shang-Yang;
Keyes, Timothy;
Chlebowski, Aleksander;
Waddell, Adrian;
Zhou, Wei;
Wang, Yangmeng;
Yuan, Qiuyue;
Guo, Yu;
Chen, Liang-Fu;
Daniel, Bence

Publication type:

Article

Drug repositioning based on mutual information for the treatment of Alzheimer's disease patients.

Published in:

Medical & Biological Engineering & Computing, 2025, v. 63, n. 8, p. 2249, doi. 10.1007/s11517-025-03325-x

By:

Cava, Claudia;
Castiglioni, Isabella

Publication type:

Article

Molecular mechanism of nano-vitamin A-mediated regulation of intramuscular fat deposition involving noncoding RNAs in pigs.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-025-11898-y

By:

Li, Meng;
Cai, Wenrun;
Li, Ruotong;
Zhao, Wenye;
Zhang, Jiaxin;
Rong, Xiaoyin;
Zhang, Ting;
Yang, Yang;
Li, Bugao;
Guo, Xiaohong

Publication type:

Article

Cross-species analysis of abiotic stress in hydroponic leafy crops reveals conserved regulatory networks and key divergences.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1613016

By:

Lee, Jia Min;
Goh, Jong Ching;
Koh, Eugene;
Mutwil-Anderwald, Daniela;
Mutwil, Marek

Publication type:

Article

Hsa_circ_0006834 represses intrahepatic cholangiocarcinoma proliferation through activating AMPK-mTOR pathway and autophagy via has-miR-637-NGFR network.

Published in:

PLoS ONE, 2025, v. 20, n. 8, p. 1, doi. 10.1371/journal.pone.0329847

By:

Wang, Ji;
Qi, Xinyue;
Zhao, Wangqian;
Hao, Ziyan;
Wang, Kehan;
Li, Yuting;
Wang, Yue;
Zhang, Yunshan

Publication type:

Article