State of the Art of Fuzzy Methods for Gene Regulatory Networks Inference by Tuqyah Abdullah Al Qazlan, Aboubekeur Hamdi-Cherif, Chafia Kara-Mohamed

“…To address one of the most challenging issues at the cellular level, this paper surveys the fuzzy methods used in gene regulatory networks (GRNs) inference. GRNs represent causal relationships between genes that have a direct influence, trough protein production, on the life and the development of living organisms and provide a useful contribution to the understanding of the cellular functions as well as the mechanisms of diseases. …”
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THE MAMMALIAN CIRCADIAN CLOCK: GENE REGULATORY NETWORK AND THEIR COMPUTER ANALYSIS by O. A. Podkolodnaya, N. N. Podkolodnaya, N. L. Podkolodnyy

“…This paper presents the results of the reconstruction and analysis of gene regulatory network of the circadian clock in mammals. …”
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Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells by Szabolcs Éliás, Angelika Schmidt, David Gomez-Cabrero, Jesper Tegnér

“…By combining information about mRNA expression, DNA accessibility, and predicted transcription factor binding, we reconstructed directed gene regulatory networks connecting transcription factors to their targets, which comprise putative key regulators of human GM-CSF-positive CD4 T cells as well as memory CD4 T cells. …”
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A Review of Integration Strategies to Support Gene Regulatory Network Construction by Hailin Chen, Vincent VanBuren

“…Gene regulatory network (GRN) construction is a central task of systems biology. …”
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Integrating Prior Knowledge Using Transformer for Gene Regulatory Network Inference by Guangzheng Weng, Patrick Martin, Hyobin Kim, Kyoung Jae Won

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Reconstruction of gene regulatory networks from single cell transcriptomic data by M. A. Rybakov, N. A. Omelyanchuk, E. V. Zemlyanskaya

Subjects: “…gene regulatory network…”
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Construction of Gene Regulatory Networks Using Recurrent Neural Networks and Swarm Intelligence by Abhinandan Khan, Sudip Mandal, Rajat Kumar Pal, Goutam Saha

“…We have proposed a methodology for the reverse engineering of biologically plausible gene regulatory networks from temporal genetic expression data. …”
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A posterior probability approach for gene regulatory network inference in genetic perturbation data by William Chad Young, Adrian E. Raftery, Ka Yee Yeung

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A GENE REGULATORY NETWORK MODEL FOR VERNALIZATION AND SEASONAL FLOWERING RESPONSE IN WINTER WHEAT AND BARLEY by I. L. Stepanenko, O. G. Smirnova, I. I. Titov

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Insufficient gene expression and lost gene regulatory network may underlie the mechanism of Hirschsprung Disease in 5p–syndrome by Yizhao Luan, Peng Li, Yuanyuan Luo, Hong Zhang, Xiaochun Zhu, Yan Zhang, Aihua Yin, Qiang Wu, Chengwei Chai

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Integrated transcriptomic and metabolomic analyses reveal critical gene regulatory network in response to drought stress in Dendrobium nobile Lindl by Chaoyan Lv, Ya He, Zaiqian Jiang, Wenjia Hu, Mei Zhang

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Covariate-adjusted construction of gene regulatory networks using a combination of generalized linear model and penalized maximum likelihood. by Omid Chatrabgoun, Alireza Daneshkhah, Parisa Torkaman, Mark Johnston, Nader Sohrabi Safa, Ali Kashif Bashir

“…Many machine learning techniques have been used to construct gene regulatory networks (GRNs) through precision matrix that considers conditional independence among genes, and finally produces sparse version of GRNs. …”
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Reconstruction and analysis of the gene regulatory network for cell wall function in <i>Arabidopsis thaliana</i> L. leaves in response to water deficit by A. R. Volyanskaya, E. A. Antropova, U. S. Zubairova, P. S. Demenkov, A. S. Venzel, Y. L. Orlov, A. A. Makarova, T. V. Ivanisenko, T. A. Gorshkova, A. R. Aglyamova, N. A. Kolchanov, M. Chen, V. A.  Ivanisenko

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The role of feedback in the formation of morphogen territories by David Iron, Adeela Syed, Heidi Theisen, Tamas Lukacsovich, Mehrangiz Naghibi, Lawrence J. Marsh, Frederic Y. M. Wan, Qing Nie

Subjects: “…gene regulatory network…”
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Multi-omics analysis reveals distinct gene regulatory mechanisms between primary and organoid-derived human hepatocytes by Haoyu Wu, Annie S. P. Yang, Suzan Stelloo, Floris J. M. Roos, René H. M. te Morsche, Anne H. Verkerk, Maria V. Luna-Velez, Laura Wingens, Johannes H. W. de Wilt, Robert W. Sauerwein, Klaas W. Mulder, Simon J. van Heeringen, Monique M. A. Verstegen, Luc J. W. van der Laan, Hendrik Marks, Richárd Bártfai

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Critical transitions in a model of a genetic regulatory system by Jesse Berwald, Marian Gidea

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Comprehensive transcriptomic analysis reveals turnip mosaic virus infection and its aphid vector Myzus persicae cause large changes in gene regulatory networks and co-transcription of alternative spliced mRNAs in Arabidopsis thaliana by Venura Herath, Clare L. Casteel, Jeanmarie Verchot

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WWTR1-AS1 LncRNA as a Novel Potential Diagnostic and Prognostic Biomarker in Breast Cancer by Mohadese Safabakhsh, Sohrab Boozarpour, Kamran Ghaedi, Mina Lashkarboloki, Shaaban Ghalandarayeshi

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PlantReg: the reconstruction of links between transcription factor regulatory networks and biological processes under their control by V. V. Lavrekha, N. A. Omelyanchuk, A. G. Bogomolov, E. V. Zemlyanskaya

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Control of Cellular Differentiation Trajectories for Cancer Reversion by Jeong‐Ryeol Gong, Chun‐Kyung Lee, Hoon‐Min Kim, Juhee Kim, Jaeog Jeon, Sunmin Park, Kwang‐Hyun Cho

Subjects: “…Boolean gene regulatory network model…”
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