Works matching DE "GENE regulatory networks"

Results: 5000

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

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

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

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

Identification of Common miRNAs Differentially Expressed in Periodontitis and Pancreatic Cancer.

Published in:

In Vivo, 2025, v. 39, n. 3, p. 1422, doi. 10.21873/invivo.13944

By:

SUNNETCI-AKKOYUNLU, DENIZ;
UGURTAS, CANSU;
KULCU-SARIKAYA, NURHAN;
OZER, TOLGAHAN;
CINE, NACI;
EREN-KESKIN, SEDA;
KANLI, AYLIN;
SAVLI, HAKAN

Publication type:

Article

Decoding serotonin: the molecular symphony behind depression.

Published in:

Frontiers in Cellular Neuroscience, 2025, p. 1, doi. 10.3389/fncel.2025.1572462

By:

Shu, Yue;
Tian, Lei;
Wang, Xing;
Meng, Tinyang;
Yu, Shouyang;
Li, Yulan

Publication type:

Article

Identification and Correlation of Novel Genes Associated with Progression of Alzheimer's Disease.

Published in:

Gene Expression (1052-2166), 2025, v. 24, n. 2, p. 84, doi. 10.14218/GE.2023.00143

By:

Arora, Tania;
Jain, Puneet;
Sharma, Harshita;
Prashar, Vikash;
Singh, Randeep;
Sharma, Arti;
Changotra, Harish;
Parkash, Jyoti

Publication type:

Article

ProgModule: A novel computational framework to identify mutation driver modules for predicting cancer prognosis and immunotherapy response.

Published in:

Journal of Translational Medicine, 2025, v. 23, n. 1, p. 1, doi. 10.1186/s12967-025-06497-0

By:

Li, Xiangmei;
Pan, Bingyue;
Zhao, Xilong;
Su, Yinchun;
Lai, Jiyin;
Li, Siyuan;
He, Yalan;
Wu, Jiashuo;
Han, Junwei

Publication type:

Article

Single-cell multi-omics delineates the dynamics of distinct epigenetic codes coordinating mouse gastrulation.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-025-11619-5

By:

Fu, Mingzhu;
Pang, Long;
Wu, Zhenwei;
Wang, Mei;
Jin, Jin;
Ai, Shanshan;
Li, Xin

Publication type:

Article

Targeting the HER2-ELF3-KRAS axis: a novel therapeutic strategy for KRAS<sup>G13D</sup> colorectal cancer.

Published in:

Molecular Cancer, 2025, v. 24, n. 1, p. 1, doi. 10.1186/s12943-025-02343-5

By:

Hwang, Soo-Yeon;
Seo, Yoojeong;
Park, Seojeong;
Kim, Seul-Ah;
Moon, Inhye;
Liu, Yi;
Kim, Seojeong;
Pak, Eun Seon;
Jung, Sehyun;
Kim, Hyeyoon;
Jeon, Kyung-Hwa;
Seo, Seung Hee;
Sung, Inyoung;
Lee, Heetak;
Park, So-Yeon;
Na, Younghwa;
Kim, Tae Il;
Kwon, Youngjoo

Publication type:

Article

Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 5, p. 1, doi. 10.1371/journal.pcbi.1012476

By:

Zhao, Wenjun;
Larschan, Erica;
Sandstede, Björn;
Singh, Ritambhara

Publication type:

Article

基于生物信息学分析双硫死亡相关基因在代谢相关脂肪性肝病中的作用.

Published in:

Journal of Xi'an Jiaotong University (Medical Sciences), 2025, v. 46, n. 2, p. 249, doi. 10.7652/jdyxb202502008

By:

熊永强;
王博;
王纪云;
李韧;
张澍

Publication type:

Article

Key gene screening and diagnostic model establishment for acute type a aortic dissection.

Published in:

Frontiers in Genetics, 2025, p. 1, doi. 10.3389/fgene.2025.1586880

By:

Pan, Yue;
Yu, Zhiming;
Qian, Xiaoyu;
Zhang, Xuesong;
Xue, Qun;
Xiao, Weizhang

Publication type:

Article

Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction.

Published in:

eLife, 2025, p. 1, doi. 10.7554/eLife.90668

By:

Poudel, Saugat;
Hyun, Jason;
Ying Hefner;
Monk, Jon;
Nizet, Victor;
Palsson, Bernhard O.

Publication type:

Article

Machine learning-driven prediction model for cuproptosis-related genes in spinal cord injury: construction and experimental validation.

Published in:

Frontiers in Neurology, 2025, p. 1, doi. 10.3389/fneur.2025.1525416

By:

Zhou, Yimin;
Li, Xin;
Wang, Zixiu;
Ng, Liqi;
He, Rong;
Liu, Chaozong;
Liu, Gang;
Fan, Xiao;
Mu, Xiaohong;
Zhou, Yu

Publication type:

Article

Dissecting the role of bHLH transcription factors in the potato spindle tuber viroid (PSTVd)-tomato pathosystem using network approaches.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0318573

By:

Aviña-Padilla, Katia;
Zambada-Moreno, Octavio;
Jimenez-Limas, Marco A.;
Hammond, Rosemarie W.;
Hernández-Rosales, Maribel

Publication type:

Article

Temporal transcriptomic changes in the THY-Tau22 mouse model of tauopathy display cell type- and sex-specific differences.

Published in:

Acta Neuropathologica Communications, 2025, v. 13, n. 1, p. 1, doi. 10.1186/s40478-025-02013-z

By:

Ali, Muhammad;
Garcia, Pierre;
Lunkes, Laetitia P.;
Sciortino, Alessia;
Thomas, Melanie H.;
Heurtaux, Tony;
Grzyb, Kamil;
Halder, Rashi;
Skupin, Alexander;
Buée, Luc;
Blum, David;
Buttini, Manuel;
Glaab, Enrico

Publication type:

Article

Integrated transcriptomic and metabolomic analyses reveal regulatory networks governing hub metabolic pathways in Fraxinus hupehensis seeds during germination.

Published in:

Tree Physiology, 2025, v. 45, n. 4, p. 1, doi. 10.1093/treephys/tpaf032

By:

Wei, Yifan;
Deng, Jing;
Tang, Huan;
Xu, Jia;
Zhou, Mingqin;
Ye, Jiabao

Publication type:

Article

Identification of the shared gene signatures and biological mechanism in type 2 diabetes mellitus and hepatocellular carcinoma.

Published in:

Clinical & Experimental Hepatology, 2025, v. 11, n. 1, p. 34, doi. 10.5114/ceh.2025.148439

By:

Lin, Yuxi;
Liao, Jiasheng;
Chong, Yutian

Publication type:

Article

Comprehensive visceral transcriptome profiling of three pig breeds along altitudinal gradients in Yunnan.

Published in:

Scientific Data, 2025, v. 12, n. 1, p. 1, doi. 10.1038/s41597-025-05070-0

By:

Huo, Jinlong;
Liu, Zhipeng;
Zhang, Xia;
Li, Changyao;
Xiang, Decai;
Fu, Guowen;
Lin, Wan;
Wu, Lingxiang;
Gong, Shaorong;
Zhao, Jiading;
Wang, Zhen;
Wang, Xiaohong;
Xiao, Zhiping;
Hao, Fanfan;
Ren, Yue;
Sun, Yu H.;
Zhao, Guiying

Publication type:

Article

Evolution and comparison of the expression of TCP genes in the benincaseae and cucurbiteae tribes.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-99296-y

By:

Wang, Shuoshuo;
Li, Wenli;
Jin, Han

Publication type:

Article

Pilot study using a discrete mathematical approach for topological analysis and ssGSEA of gene expression in autosomal recessive polycystic kidney disease.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-99048-y

By:

Okui, Nobuo;
Hachiya, Tsuyoshi;
Horie, Shigeo

Publication type:

Article

CLEC7A 调节 PD-L1 促进卵巢癌生长的作用及机制研究.

Published in:

Journal of New Medicine, 2025, v. 56, n. 4, p. 361, doi. 10.12464/j.issn.0253-9802.2025-0056

By:

陈瑶;
孙思柏;
许俊;
何杰

Publication type:

Article

Genetic association between gene expression profiles in oligodendrocyte precursor cells and psychiatric disorders.

Published in:

Frontiers in Psychiatry, 2025, p. 1, doi. 10.3389/fpsyt.2025.1566155

By:

Kondo, Reon;
Kimura, Hiroki;
Ikeda, Masashi

Publication type:

Article

A potential XGBoost Diagnostic Score for Staphylococcus aureus bloodstream infection.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1574003

By:

Shi, Junhong;
Chen, Lan;
Yuan, Xinru;
Yang, Jinjin;
Xu, Yanlei;
Shen, Li;
Huang, Yu;
Wang, Bingjie;
Yu, Fangyou

Publication type:

Article

Multi-omics identification of a polyamine metabolism related signature for hepatocellular carcinoma and revealing tumor microenvironment characteristics.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1570378

By:

Yu, Yuexi;
Liu, Huiru;
Liu, Kaipeng;
Zhao, Meiqi;
Zhang, Yiyan;
Jiang, Runci;
Wang, Fengmei

Publication type:

Article

Comprehensive analysis of plasma cell heterogeneity and immune interactions in multiple myeloma.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1549742

By:

Qu, Shuang;
Zheng, Zhihai;
Guo, Xiaoling;
Mei, Jiaqi;
Jiang, Sicong;
Chen, Biyun

Publication type:

Article

Multifaceted Evolution of the PhoPQ Two‐Component System in Salmonella enterica Enhanced the Expression of Horizontally Acquired Virulence Genes.

Published in:

Molecular Microbiology, 2025, v. 123, n. 5, p. 464, doi. 10.1111/mmi.15355

By:

Barretto, Luke A. F.;
Fowler, Casey C.

Publication type:

Article

Transcriptome insights into newcastle disease virus-mediated eradication of cholangiocarcinoma cells.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0322307

By:

Thanyaphoo, Suphannee;
Sae-Lee, Chanachai;
Thaopech, Wilasinee;
Amornrit, Warisa;
Junking, Mutita;
Yenchitsomanus, Pa-thai;
Poungvarin, Naravat

Publication type:

Article

Examination of the lung and lymphoid tissue mRNA transcriptome response in dairy calves following experimental challenge with bovine alphaherpesvirus one (BoHV-1).

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0319575

By:

O'Donoghue, Stephanie;
Earley, Bernadette;
Johnston, Dayle;
Finnie, Matthew S.;
Cosby, S. Louise;
Lemon, Ken;
McMenamy, Michael J.;
Taylor, Jeremy F.;
Kim, Jae Woo;
Morris, Derek W.;
Waters, Sinéad M.

Publication type:

Article

Response of different cotton genotypes to salt stress and re-watering.

Published in:

BMC Plant Biology, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12870-025-06534-6

By:

Zhao, Kang;
Yang, Tao;
Pang, Bo;
Wang, Honggang;
Yang, Zhining;
Liang, Weiwei;
Rui, Cun;
Gao, Wengwei

Publication type:

Article

Circular RNAs in endometriosis analyzed through RNA sequencing and bioinformatics for expression profile.

Published in:

PeerJ, 2025, p. 1, doi. 10.7717/peerj.19298

By:

Yue, Yan;
Qian, Jing;
Gui, Dandan;
Lu, Bin

Publication type:

Article

Prognostic value and immunotherapy analysis of immune cell-related genes in laryngeal cancer.

Published in:

PeerJ, 2025, p. 1, doi. 10.7717/peerj.19239

By:

Zhang, Sen;
Pan, Jianrui;
Guo, Huina;
Guan, Xiaoya;
Yan, Chenxu;
Ji, Lingling;
Wu, Xiansha;
Huangfu, Hui

Publication type:

Article

Non-Coding RNAs and Their Regulatory Systems: Evolutionary Origin and Putative Link with Ribozymes.

Published in:

Journal of Evolutionary Biochemistry & Physiology, 2025, v. 61, n. 2, p. 460, doi. 10.1134/S0022093025020073

By:

Markelov, V. A.;
Akhmadishina, L. Z.;
Solntsev, V. A.;
Danilko, K. V.;
Korytina, G. F.

Publication type:

Article

scMUG: deep clustering analysis of single-cell RNA-seq data on multiple gene functional modules.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 2, p. 1, doi. 10.1093/bib/bbaf138

By:

Liang, De-Min;
Du, Pu-Feng

Publication type:

Article

AttentionGRN: a functional and directed graph transformer for gene regulatory network reconstruction from scRNA-seq data.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 2, p. 1, doi. 10.1093/bib/bbaf118

By:

Gao, Zhen;
Su, Yansen;
Tang, Jin;
Jin, Huaiwan;
Ding, Yun;
Cao, Rui-Fen;
Wei, Pi-Jing;
Zheng, Chun-Hou

Publication type:

Article

Inferring gene regulatory networks from time-series scRNA-seq data via GRANGER causal recurrent autoencoders.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 2, p. 1, doi. 10.1093/bib/bbaf089

By:

Chen, Liang;
Dautle, Madison;
Gao, Ruoying;
Zhang, Shaoqiang;
Chen, Yong

Publication type:

Article

MulNet: a scalable framework for reconstructing intra- and intercellular signaling networks from bulk and single-cell RNA-seq data.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 2, p. 1, doi. 10.1093/bib/bbaf081

By:

Han, Mingfei;
Chen, Xiaoqing;
Li, Xiao;
Ma, Jie;
Chen, Tao;
Yang, Chunyuan;
Wang, Juan;
Li, Yingxing;
Guo, Wenting;
Zhu, Yunping

Publication type:

Article

The ESCRT protein CHMP5 promotes T cell leukemia by enabling BRD4-p300-dependent transcription.

Published in:

Nature Communications, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41467-025-59504-9

By:

Umphred-Wilson, Katharine;
Ratnayake, Shashikala;
Tang, Qianzi;
Wang, Rui;
Chaudhary, Sneha Ghosh;
Ballachanda, Devaiah N.;
Trichka, Josephine;
Wisniewski, Jan;
Zhou, Lan;
Chen, Qingrong;
Meerzaman, Daoud;
Singer, Dinah S.;
Adoro, Stanley

Publication type:

Article

Covariance Matrix Estimation for High-Throughput Biomedical Data with Interconnected Communities.

Published in:

American Statistician, 2024, v. 78, n. 4, p. 401, doi. 10.1080/00031305.2024.2329681

By:

Yang, Yifan;
Chen, Chixiang;
Chen, Shuo

Publication type:

Article

Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris.

Published in:

PLoS Biology, 2016, v. 14, n. 3, p. 1, doi. 10.1371/journal.pbio.1002391

By:

Israel, Jennifer W.;
Martik, Megan L.;
Byrne, Maria;
Raff, Elizabeth C.;
Raff, Rudolf A.;
McClay, David R.;
Wray, Gregory A.

Publication type:

Article

A Window into the Workings of the Segmentation Clock.

Published in:

PLoS Biology, 2012, v. 10, n. 7, p. 1, doi. 10.1371/journal.pbio.1001366

By:

Weaver, Janelle

Publication type:

Article

Precise Temporal Modulation in the Response of the SOS DNA Repair Network in Individual Bacteria.

Published in:

PLoS Biology, 2005, v. 3, n. 6, p. 1, doi. 10.1371/journal.pbio.0030238

By:

Friedman, Nir;
Vardi, Shuki;
Ronen, Michal;
Alon, Uri;
Stavans, Joel

Publication type:

Article

Linking Disulfide Levels and NAD+ Metabolism with Alzheimer's Disease for Diagnostic Modeling and Target Drug Analysis.

Published in:

Journal of Integrative Neuroscience, 2024, v. 23, n. 4, p. 1, doi. 10.31083/j.jin2304085

By:

Yanbing Wang;
Lining Su;
Yongcai Zhang;
Huiping Wei

Publication type:

Article

Bioinformatic Analysis and Experimental Validation of Ubiquitin-Proteasomal System-Related Hub Genes as Novel Biomarkers for Alzheimer's Disease.

Published in:

Journal of Integrative Neuroscience, 2023, v. 22, n. 6, p. 1, doi. 10.31083/j.jin2206138

By:

Yuting Zhang;
Jie Wu;
Guoxing You;
Wenjie Guo;
Yupeng Wang;
Zhiyong Yu;
Yan Geng;
Qinghua Zhong;
Jie Zan;
Linbo Zheng

Publication type:

Article

Author index Volume 22 (2024).

Published in:: Journal of Bioinformatics & Computational Biology, 2024, v. 22, n. 6, p. 1, doi. 10.1142/S0219720024990014
Publication type:: Article