Works matching DE "GENE regulatory networks"

Results: 5000

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 plk1 Gene Regulatory Network Modeling Identifies Three Circuits for plk1 -mediated Genomic Instability Leading to Neoplastic Transformation.

Published in:

Life (2075-1729), 2025, v. 15, n. 5, p. 799, doi. 10.3390/life15050799

By:

Suescum-Holguín, Jeison F.;
Clavijo-Buriticá, Diana Carolina;
Carrillo-Borda, Edward Fabian;
Quimbaya, Mauricio Alberto

Publication type:

Article

Identification of Critical Molecular Pathways Induced by HDAC11 Overexpression in Cardiac Mesenchymal Stem Cells.

Published in:

Biomolecules (2218-273X), 2025, v. 15, n. 5, p. 662, doi. 10.3390/biom15050662

By:

Zhang, Chongyu;
Weintraub, Neal L.;
Tang, Yaoliang

Publication type:

Article

Synthesizing Time-Series Gene Expression Data to Enhance Network Inference Performance Using Autoencoder.

Published in:

Applied Sciences (2076-3417), 2025, v. 15, n. 10, p. 5768, doi. 10.3390/app15105768

By:

Anh, Cao-Tuan;
Kwon, Yung-Keun

Publication type:

Article

Bioinformatics analysis combined with experimental validation reveals the novel mechanisms of multi-targets of dapagliflozin attenuating diabetic liver injury.

Published in:

Frontiers in Endocrinology, 2025, p. 1, doi. 10.3389/fendo.2025.1519153

By:

Wang, Pengyu;
Sun, Zhen;
Lan, Qing;
Zhang, Shuo;
Song, Yan;
Yang, Leiming;
Chen, Mi;
Shen, Jianfen;
Huang, Qi;
Zhang, Youzhi

Publication type:

Article

Glypican-3 regulated epithelial mesenchymal transformation-related genes in osteosarcoma: based on comprehensive tumor microenvironment profiling.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1566061

By:

Zhang, Jiaming;
Wang, Wei

Publication type:

Article

Integrated Genomic and Transcriptomic Analysis Reveals a Transcription Factor Gene Set Facilitating Gonadal Differentiation in the Pacific Oyster Crassostrea gigas.

Published in:

Genes, 2025, v. 16, n. 5, p. 513, doi. 10.3390/genes16050513

By:

Shen, Yunwang;
Wang, Ziyi;
Jia, Yanglei;
Liu, Xiao

Publication type:

Article

Transcriptomic Analysis of Leaves from Two Maize Hybrids Under Heat Stress During the Early Generative Stage.

Published in:

Genes, 2025, v. 16, n. 5, p. 480, doi. 10.3390/genes16050480

By:

Zhang, Siqi;
Sun, Lei;
Ma, Chunhong;
Xu, Dajin;
Jiao, Bo;
Wang, Jiao;
Dong, Fushuang;
Yang, Fan;
Zhou, Shuo;
Yang, Qing;
Zhao, Pu

Publication type:

Article

Integration of bioinformatics and identification of the role of m6A genes in NAFLD.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0321757

By:

Ma, Jianguo;
Xu, Rongyi;
Li, Renlin;
Fu, Yangyang;
Xu, Jing;
Zhou, Lei;
Qi, Yan

Publication type:

Article

Identification of Cancer Associated Fibroblasts Related Genes Signature to Facilitate Improved Prediction of Prognosis and Responses to Therapy in Patients with Pancreatic Cancer.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 10, p. 4876, doi. 10.3390/ijms26104876

By:

Zhou, Yong;
Lu, Yanxi;
Czubayko, Franziska;
Chen, Jisheng;
Zheng, Shuwen;
Mo, Huaqing;
Liu, Rui;
Weber, Georg F.;
Grützmann, Robert;
Pilarsky, Christian;
David, Paul

Publication type:

Article

GSNCASCR: An R Package to Identify Differentially Co-Expressed Curated Gene Sets with Single-Cell RNA-Seq Data.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 10, p. 4771, doi. 10.3390/ijms26104771

By:

Gao, Shouguo;
Li, Haoran;
Wu, Zhijie;
Mizumaki, Hiroki;
Kajigaya, Sachiko;
Young, Neal S.

Publication type:

Article

Genetic, Transcriptomic, and Epigenomic Insights into Sjögren's Disease: An Integrative Network Investigation and Immune Diseases Comparison.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 10, p. 4637, doi. 10.3390/ijms26104637

By:

Enduru, Nitesh;
Manuel, Astrid M.;
Zhao, Zhongming

Publication type:

Article

PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome.

Published in:

Nature Structural & Molecular Biology, 2015, v. 22, n. 5, p. 362, doi. 10.1038/nsmb.3014

By:

Kroeze, Wesley K;
Sassano, Maria F;
Huang, Xi-Ping;
Lansu, Katherine;
McCorvy, John D;
Giguère, Patrick M;
Sciaky, Noah;
Roth, Bryan L

Publication type:

Article

Structural basis for RNA recognition in roquin-mediated post-transcriptional gene regulation.

Published in:

Nature Structural & Molecular Biology, 2014, v. 21, n. 8, p. 671, doi. 10.1038/nsmb.2855

By:

Schlundt, Andreas;
Heinz, Gitta A;
Janowski, Robert;
Geerlof, Arie;
Stehle, Ralf;
Heissmeyer, Vigo;
Niessing, Dierk;
Sattler, Michael

Publication type:

Article

Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs.

Published in:

Nature Structural & Molecular Biology, 2014, v. 21, n. 7, p. 585, doi. 10.1038/nsmb.2842

By:

Zheng, Grace X Y;
Do, Brian T;
Webster, Dan E;
Khavari, Paul A;
Chang, Howard Y

Publication type:

Article

Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysis.

Published in:

Nature Structural & Molecular Biology, 2012, v. 19, n. 8, p. 797, doi. 10.1038/nsmb.2336

By:

Hensel, Zach;
Feng, Haidong;
Han, Bo;
Hatem, Christine;
Wang, Jin;
Xiao, Jie

Publication type:

Article

Identification and Validation of Aging Related Genes Signature in Chronic Obstructive Pulmonary Disease.

Published in:

COPD: Journal of Chronic Obstructive Pulmonary Disease, 2024, v. 21, n. 1, p. 1, doi. 10.1080/15412555.2024.2379811

By:

Li, Tian-Tian;
Bai, Hong-Yan;
Zhang, Jing-Hong;
Kang, Xiu-He;
Qu, Yi-Qing

Publication type:

Article

Exploration of ferroptosis-related biomarkers with prognostic capability in RIF based on WGCNA.

Published in:

Journal of Assisted Reproduction & Genetics, 2025, v. 42, n. 3, p. 949, doi. 10.1007/s10815-024-03370-9

By:

Zhou, Tingting;
Zhang, Qian;
Yu, Wenhao;
Cui, Yuqian;
Yan, Junhao;
Ni, Tianxiang;
Fu, Xiaohua;
Li, Junwei

Publication type:

Article

Evaluation of the diagnostic utility of immune microenvironment-related biomarkers in endometriosis using multidimensional transcriptomic data.

Published in:

Journal of Assisted Reproduction & Genetics, 2024, v. 41, n. 11, p. 3213, doi. 10.1007/s10815-024-03261-z

By:

Tu, Qing;
Zhao, Ruiheng;
Lu, Ning

Publication type:

Article

Bioinformatic analysis of the role of immune checkpoint genes and immune infiltration in the pathogenesis and development of premature ovarian insufficiency.

Published in:

Journal of Assisted Reproduction & Genetics, 2024, v. 41, n. 6, p. 1619, doi. 10.1007/s10815-024-03120-x

By:

Zhang, Xiyan;
Wang, Ling;
Yang, Tongkun;
Kong, Li;
Wei, Luxiao;
Du, Jing

Publication type:

Article

lncRNA TTTY14 participates in the progression of repeated implantation failure by regulating the miR-6088/SEMA5A axis.

Published in:

Journal of Assisted Reproduction & Genetics, 2024, v. 41, n. 3, p. 727, doi. 10.1007/s10815-024-03032-w

By:

Yu, Lingzhu;
Ye, Jing;
Chen, Qiuju;
Hong, Qingqing

Publication type:

Article

Comprehensive analysis of lncRNA-miRNA-mRNA ceRNA network and key genes in granulosa cells of patients with biochemical primary ovarian insufficiency.

Published in:

Journal of Assisted Reproduction & Genetics, 2024, v. 41, n. 1, p. 15, doi. 10.1007/s10815-023-02937-2

By:

Liu, Biting;
Liu, Li;
Sulaiman, Zubaidan;
Wang, Chunyan;
Wang, Lian;
Zhu, Jihui;
Liu, Shupeng;
Cheng, Zhongping

Publication type:

Article

The effects of AdipoRon on cytochrome P450-related gene expression, acute steroidogenic regulatory protein, and structure of ovary in polycystic ovary syndrome model.

Published in:

Journal of Assisted Reproduction & Genetics, 2023, v. 40, n. 10, p. 2453, doi. 10.1007/s10815-023-02900-1

By:

Hazrati, Pegah;
Ramezani, Mahdi;
Ahmadimoghaddam, Davoud;
Asl, Sara Soleimani;
Artimani, Tayebe

Publication type:

Article

Novel variations in spermatogenic transcription regulators RFX2 and TAF7 increase risk of azoospermia.

Published in:

Journal of Assisted Reproduction & Genetics, 2021, v. 38, n. 12, p. 3195, doi. 10.1007/s10815-021-02352-5

By:

Pal, Samudra;
Paladhi, Pranab;
Dutta, Saurav;
Bose, Gunja;
Ghosh, Papiya;
Chattopadhyay, Ratna;
Chakravarty, Baidyanath;
Saha, Indranil;
Ghosh, Sujay

Publication type:

Article

An in silico model using prognostic genetic factors for ovarian response in controlled ovarian stimulation: A systematic review.

Published in:

Journal of Assisted Reproduction & Genetics, 2021, v. 38, n. 8, p. 2007, doi. 10.1007/s10815-021-02141-0

By:

Eisele, B. S.;
Silva, G. C. Villalba;
Bessow, C.;
Donato, R.;
Genro, V. K.;
Cunha-Filho, J. S.

Publication type:

Article

Duplications in 19p13.3 are associated with male infertility.

Published in:

Journal of Assisted Reproduction & Genetics, 2019, v. 36, n. 10, p. 2171, doi. 10.1007/s10815-019-01547-1

By:

Singh, Vertika;
Bala, Renu;
Chakraborty, Arijit;
Rajender, Singh;
Trivedi, Sameer;
Singh, Kiran

Publication type:

Article

Compromised global embryonic transcriptome associated with advanced maternal age.

Published in:

Journal of Assisted Reproduction & Genetics, 2019, v. 36, n. 5, p. 915, doi. 10.1007/s10815-019-01438-5

By:

McCallie, Blair R.;
Parks, Jason C.;
Trahan, G. Devon;
Jones, Kenneth L.;
Coate, Breanne D.;
Griffin, Darren K.;
Schoolcraft, William B.;
Katz-Jaffe, Mandy G.

Publication type:

Article

Preface.

Published in:

2019

By:

Lozano, Jose A.;
Tang, Ke;
Yao, Xin

Publication type:

Editorial

Reconstructing gene regulatory networks with a memetic-neural hybrid based on fuzzy cognitive maps.

Published in:

Natural Computing, 2019, v. 18, n. 2, p. 301, doi. 10.1007/s11047-016-9547-4

By:

Chi, Yaxiong;
Liu, Jing

Publication type:

Article

Scaling up genetic circuit design for cellular computing: advances and prospects.

Published in:

Natural Computing, 2018, v. 17, n. 4, p. 833, doi. 10.1007/s11047-018-9715-9

By:

Xiang, Yiyu;
Dalchau, Neil;
Wang, Baojun

Publication type:

Article

Ecological effects of cellular computing in microbial populations.

Published in:

Natural Computing, 2018, v. 17, n. 4, p. 811, doi. 10.1007/s11047-018-9708-8

By:

Baskerville, Maia;
Biro, Arielle;
Blazanin, Mike;
Chang, Chang-Yu;
Hallworth, Amelia;
Sonnert, Nicole;
Vila, Jean C. C.;
Sanchez, Alvaro

Publication type:

Article

Foreword: asynchronous behavior of cellular automata and discrete models.

Published in:

Natural Computing, 2015, v. 14, n. 4, p. 505, doi. 10.1007/s11047-015-9524-3

By:

Dennunzio, Alberto;
Formenti, Enrico;
Mauri, Giancarlo;
Worsch, Thomas

Publication type:

Article

Minimization and equivalence in multi-valued logical models of regulatory networks.

Published in:

Natural Computing, 2015, v. 14, n. 4, p. 555, doi. 10.1007/s11047-015-9525-2

By:

Streck, Adam;
Lorenz, Therese;
Siebert, Heike

Publication type:

Article

A genome analysis based on repeat sharing gene networks.

Published in:

Natural Computing, 2015, v. 14, n. 3, p. 403, doi. 10.1007/s11047-014-9437-6

By:

Castellini, Alberto;
Franco, Giuditta;
Milanese, Alessio

Publication type:

Article

Genome-wide identification and transcriptional expression profiles of the transcription factor WRKY in Gentiana macrophylla.

Published in:

Molecular Biology Reports, 2025, v. 52, n. 1, p. 1, doi. 10.1007/s11033-025-10452-z

By:

Gu, Xiaohui;
Zhou, Lipan;
Pu, Yang;
Jiang, Fan;
Yang, Li;
Zhang, Tianyi;
Zhou, Tao;
Wang, Xumei

Publication type:

Article

Expression level of miR-548aa in tissue samples of patients with colorectal cancer.

Published in:

Molecular Biology Reports, 2025, v. 52, n. 1, p. 1, doi. 10.1007/s11033-025-10225-8

By:

Arabzadeh, AmirAhmad;
Farzollahpour, Morteza;
Seyedsadegi, Mirsalim;
Pourfarzi, Farhad;
Ghodsinezhad, Vadieh;
Bandehagh, Helia;
Pahlavan, Yasamin

Publication type:

Article

Identification of genes related to ribosomal proteins in colorectal cancer: exploring their potential as biomarkers, prognostic indicators, and therapeutic targets.

Published in:

Molecular Biology Reports, 2024, v. 51, n. 1, p. 1, doi. 10.1007/s11033-024-09522-5

By:

Salehinia, Negin;
Mohammad Al-Mosawi, Aseel Kamil;
Al-Moussawi, Duaa Kamel;
Sadeghi, Ensieh Sagheb;
Zamani, Atefeh;
Mahdevar, Mohammad

Publication type:

Article

Characterization and expression profiles of the ZmLBD gene family in Zea mays.

Published in:

Molecular Biology Reports, 2024, v. 51, n. 1, p. 1, doi. 10.1007/s11033-024-09483-9

By:

Hao, Lidong;
Li, Shifeng;
Dai, Jun;
Wang, Li;
Yan, Zhibin;
Shi, Yunqiang;
Zheng, Meiyu

Publication type:

Article

Exploring the role of interleukin 11 in cancer progression, patient survival, and therapeutic insights.

Published in:

Molecular Biology Reports, 2024, v. 51, n. 1, p. 1, doi. 10.1007/s11033-024-09358-z

By:

Hassani, Mahsa;
Mahdevar, Mohammad;
Peymani, Maryam

Publication type:

Article

The identification of signature genes and their relationship with immune cell infiltration in age-related macular degeneration.

Published in:

Molecular Biology Reports, 2024, v. 51, n. 1, p. 1, doi. 10.1007/s11033-023-08969-2

By:

Chen, Jinquan;
Zhao, Long;
Zhang, Longbin;
Luo, Yiling;
Jiang, Yuling;
H, Peng

Publication type:

Article

Optimizing model-agnostic random subspace ensembles.

Published in:

Machine Learning, 2024, v. 113, n. 2, p. 993, doi. 10.1007/s10994-023-06427-5

By:

Huynh-Thu, Vân Anh;
Geurts, Pierre

Publication type:

Article

Ensembles of extremely randomized predictive clustering trees for predicting structured outputs.

Published in:

Machine Learning, 2020, v. 109, n. 11, p. 2213, doi. 10.1007/s10994-020-05894-4

By:

Kocev, Dragi;
Ceci, Michelangelo;
Stepišnik, Tomaž

Publication type:

Article

Exploiting causality in gene network reconstruction based on graph embedding.

Published in:

Machine Learning, 2020, v. 109, n. 6, p. 1231, doi. 10.1007/s10994-019-05861-8

By:

Pio, Gianvito;
Ceci, Michelangelo;
Prisciandaro, Francesca;
Malerba, Donato

Publication type:

Article

Modeling the effect of transcriptional noise on switching in gene networks in a genetic bistable switch.

Published in:

Journal of Biological Physics, 2015, v. 41, n. 3, p. 235, doi. 10.1007/s10867-015-9375-2

By:

Chaudhury, Srabanti

Publication type:

Article

Identification of genes responsible for stress resistance in fusarium oxysporum- inoculated flax seedlings using weighted gene co-expression network analysis.

Published in:

European Journal of Plant Pathology, 2022, v. 163, n. 3, p. 513, doi. 10.1007/s10658-022-02497-8

By:

He, Rui;
Chang, Yingdong;
Wang, Jianming

Publication type:

Article

Gene co-expression network for Xanthomonas-challenged cassava reveals key regulatory elements of immunity processes.

Published in:

European Journal of Plant Pathology, 2019, v. 153, n. 4, p. 1083, doi. 10.1007/s10658-018-01628-4

By:

Gómez-Cano, Fabio;
Soto, Johana;
Restrepo, Silvia;
Bernal, Adriana;
López-Kleine, Liliana;
López, Camilo Ernesto

Publication type:

Article