Works matching DE "GENE regulatory networks"

Results: 5000

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

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

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

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

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

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

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

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

Body plan evolvability: The role of variability in gene regulatory networks.

Published in:

Journal of Bioinformatics & Computational Biology, 2024, v. 22, n. 3, p. 1, doi. 10.1142/S0219720024500112

By:

Spirov, Alexander V.;
Myasnikova, Ekaterina M.;
Holloway, David M.

Publication type:

Article

Author Index Volume 20 (2022).

Published in:: Journal of Bioinformatics & Computational Biology, 2022, v. 20, n. 6, p. 1, doi. 10.1142/S0219720022990013
Publication type:: Article

A network-based dynamic criterion for identifying prediction and early diagnosis biomarkers of complex diseases.

Published in:

Journal of Bioinformatics & Computational Biology, 2022, v. 20, n. 6, p. 1, doi. 10.1142/S0219720022500275

By:

Huang, Xin;
Su, Benzhe;
Wang, Xingyu;
Zhou, Yang;
He, Xinyu;
Liu, Bing

Publication type:

Article

Behavioral dynamics of bacteriophage gene regulatory networks.

Published in:

Journal of Bioinformatics & Computational Biology, 2022, v. 20, n. 5, p. 1, doi. 10.1142/S0219720022500214

By:

Melkus, Gatis;
Cerans, Karlis;
Freivalds, Karlis;
Lace, Lelde;
Zajakina, Darta;
Viksna, Juris

Publication type:

Article

Transcriptomic meta-analysis reveals biomarker pairs and key pathways in Tetralogy of Fallot.

Published in:

Journal of Bioinformatics & Computational Biology, 2022, v. 20, n. 4, p. 1, doi. 10.1142/S0219720022400042

By:

Charles, Sona;
Sreekumar, J;
Natarajan, Jeyakumar

Publication type:

Article

Identification of cancer-related module in protein–protein interaction network based on gene prioritization.

Published in:

Journal of Bioinformatics & Computational Biology, 2022, v. 20, n. 1, p. 1, doi. 10.1142/S0219720021500311

By:

Wu, Jingli;
Zhang, Qi;
Li, Gaoshi

Publication type:

Article

Author Index Volume 19 (2021).

Published in:: Journal of Bioinformatics & Computational Biology, 2021, v. 19, n. 6, p. 1, doi. 10.1142/S0219720021990018
Publication type:: Article

Incorporating biological networks into high-dimensional Bayesian survival analysis using an ICM/M algorithm.

Published in:

Journal of Bioinformatics & Computational Biology, 2021, v. 19, n. 5, p. 1, doi. 10.1142/S021972002150027X

By:

Pungpapong, Vitara

Publication type:

Article

Response of gene regulatory networks after infection of H3N2 virus.

Published in:

Journal of Bioinformatics & Computational Biology, 2021, v. 19, n. 4, p. 1, doi. 10.1142/S0219720021500177

By:

Deng, Shiguo;
Yuan, Qianshun;
Zhang, Jing;
Yang, Huijie

Publication type:

Article

Identifying protein complexes from protein–protein interaction networks based on the gene expression profile and core-attachment approach.

Published in:

Journal of Bioinformatics & Computational Biology, 2021, v. 19, n. 3, p. N.PAG, doi. 10.1142/S0219720021500098

By:

Noori, Soheir;
Al-A'Araji, Nabeel;
Al-Shamery, Eman

Publication type:

Article

Learning gene regulatory networks using gaussian process emulator and graphical LASSO.

Published in:

Journal of Bioinformatics & Computational Biology, 2021, v. 19, n. 3, p. N.PAG, doi. 10.1142/S0219720021500074

By:

Chatrabgoun, H.;
Soltanian, A. R.;
Mahjub, H.;
Bahreini, F.

Publication type:

Article

KFGRNI: A robust method to inference gene regulatory network from time-course gene data based on ensemble Kalman filter.

Published in:

Journal of Bioinformatics & Computational Biology, 2021, v. 19, n. 2, p. N.PAG, doi. 10.1142/S0219720021500025

By:

Pirgazi, Jamshid;
Olyaee, Mohammad Hossein;
Khanteymoori, Alireza

Publication type:

Article

Identification of deregulation mechanisms specific to cancer subtypes.

Published in:

Journal of Bioinformatics & Computational Biology, 2021, v. 19, n. 1, p. N.PAG, doi. 10.1142/S0219720021400035

By:

Champion, Magali;
Chiquet, Julien;
Neuvial, Pierre;
Elati, Mohamed;
Radvanyi, François;
Birmelé, Etienne

Publication type:

Article

Author Index Volume 18 (2020).

Published in:: Journal of Bioinformatics & Computational Biology, 2020, v. 18, n. 6, p. N.PAG, doi. 10.1142/S0219720020990012
Publication type:: Article

Comparison of gene regulatory networks to identify pathogenic genes for lymphoma.

Published in:

Journal of Bioinformatics & Computational Biology, 2020, v. 18, n. 5, p. N.PAG, doi. 10.1142/S0219720020500298

By:

Yu, Xiao;
Weng, Tongfeng;
Gu, Changgui;
Yang, Huijie

Publication type:

Article

Constructing gene regulatory networks from microarray data using non-Gaussian pair-copula Bayesian networks.

Published in:

Journal of Bioinformatics & Computational Biology, 2020, v. 18, n. 4, p. N.PAG, doi. 10.1142/S0219720020500237

By:

Chatrabgoun, O.;
Hosseinian-Far, A.;
Daneshkhah, A.

Publication type:

Article

Network motif-based analysis of regulatory patterns in paralogous gene pairs.

Published in:

Journal of Bioinformatics & Computational Biology, 2020, v. 18, n. 3, p. N.PAG, doi. 10.1142/S0219720020400089

By:

Melkus, Gatis;
Rucevskis, Peteris;
Celms, Edgars;
Čerāns, Kārlis;
Freivalds, Karlis;
Kikusts, Paulis;
Lace, Lelde;
Opmanis, Mārtiņš;
Rituma, Darta;
Viksna, Juris

Publication type:

Article

BENIN: Biologically enhanced network inference.

Published in:

Journal of Bioinformatics & Computational Biology, 2020, v. 18, n. 3, p. N.PAG, doi. 10.1142/S0219720020400077

By:

Wonkap, Stephanie Kamgnia;
Butler, Gregory

Publication type:

Article

Introduction to the JBCB special issue on CSBio 2019.

Published in:

2020

By:

De Maria, Elisabetta;
Magnin, Morgan

Publication type:

Editorial

Exploring disease comorbidity in a module–module interaction network.

Published in:

Journal of Bioinformatics & Computational Biology, 2020, v. 18, n. 2, p. N.PAG, doi. 10.1142/S0219720020500109

By:

Hwang, Soyoun;
Lee, Taekeon;
Yoon, Youngmi

Publication type:

Article

Author Index Volume 17 (2019).

Published in:: Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 6, p. N.PAG, doi. 10.1142/S0219720019990014
Publication type:: Article

Integration of multi-omics data to mine cancer-related gene modules.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 6, p. N.PAG, doi. 10.1142/S0219720019500380

By:

Li, Peng;
Guo, Maozu;
Sun, Bo

Publication type:

Article

SIN-KNO: A method of gene regulatory network inference using single-cell transcription and gene knockout data.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 6, p. N.PAG, doi. 10.1142/S0219720019500355

By:

Wang, Huiqing;
Lian, Yuanyuan;
Li, Chun;
Ma, Yue;
Yan, Zhiliang;
Dong, Chunlin

Publication type:

Article

Protein function prediction from dynamic protein interaction network using gene expression data.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 4, p. N.PAG, doi. 10.1142/S0219720019500252

By:

Saha, Sovan;
Prasad, Abhimanyu;
Chatterjee, Piyali;
Basu, Subhadip;
Nasipuri, Mita

Publication type:

Article

Inference of genetic networks using random forests: Assigning different weights for gene expression data.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 4, p. N.PAG, doi. 10.1142/S021972001950015X

By:

Kimura, Shuhei;
Tokuhisa, Masato;
Okada, Mariko

Publication type:

Article

A sparse and decomposed particle swarm optimization for inferring gene regulatory networks based on fuzzy cognitive maps.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 4, p. N.PAG, doi. 10.1142/S0219720019500239

By:

Liu, Luowen;
Liu, Jing

Publication type:

Article

TIGRNCRN: Trustful inference of gene regulatory network using clustering and refining the network.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 3, p. N.PAG, doi. 10.1142/S0219720019500185

By:

Pirgazi, Jamshid;
Khanteymoori, Ali Reza;
Jalilkhani, Maryam

Publication type:

Article

Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 3, p. N.PAG, doi. 10.1142/S0219720019400079

By:

Matsubara, Teppei;
Ochiai, Tomoshiro;
Hayashida, Morihiro;
Akutsu, Tatsuya;
Nacher, Jose C.

Publication type:

Article

Relative sensitivity analysis of the predictive properties of sloppy models.

Published in:

Journal of Bioinformatics & Computational Biology, 2018, v. 16, n. 2, p. -1, doi. 10.1142/S0219720018400085

By:

Myasnikova, Ekaterina;
Spirov, Alexander

Publication type:

Article

The search of CAR, AhR, ESRs binding sites in promoters of intronic and intergenic microRNAs.

Published in:

Journal of Bioinformatics & Computational Biology, 2018, v. 16, n. 1, p. -1, doi. 10.1142/S0219720017500299

By:

Ovchinnikov, Vladimir Y.;
Antonets, Denis V.;
Gulyaeva, Lyudmila F.

Publication type:

Article

Recurrent neural network-based modeling of gene regulatory network using elephant swarm water search algorithm.

Published in:

Journal of Bioinformatics & Computational Biology, 2017, v. 15, n. 4, p. -1, doi. 10.1142/S0219720017500160

By:

Mandal, Sudip;
Saha, Goutam;
Pal, Rajat Kumar

Publication type:

Article

Chaos and hyperchaos in simple gene network with negative feedback and time delays.

Published in:

Journal of Bioinformatics & Computational Biology, 2017, v. 15, n. 2, p. -1, doi. 10.1142/S0219720016500426

By:

Khlebodarova, Tamara M.;
Kogai, Vladislav V.;
Fadeev, Stanislav I.;
Likhoshvai, Vitaly A.

Publication type:

Article