Spatio-temporal models of synthetic genetic oscillators by Cicely K. Macnamara, Mark A. J. Chaplain

Subjects: “…gene regulatory networks…”
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The landscape of cell regulatory and communication networks in the human dental follicle by Jia-Ning Liu, Jia-Ning Liu, Jiong-Yi Tian, Lu Liu, Lu Liu, Yuan Cao, Yuan Cao, Xiao Lei, Xiao Lei, Xiao-Hui Zhang, Xiao-Hui Zhang, Zi-Qi Zhang, Zi-Qi Zhang, Jun-Xi He, Jun-Xi He, Chen-Xi Zheng, Chao Ma, Sheng-Feng Bai, Bing-Dong Sui, Fang Jin, Ji Chen, Ji Chen

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Review of Biological Network Data and Its Applications by Donghyeon Yu, MinSoo Kim, Guanghua Xiao, Tae Hyun Hwang

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In Silico Evolution of Gene Cooption in Pattern-Forming Gene Networks by Alexander V. Spirov, Marat A. Sabirov, David M. Holloway

“…Gene recruitment or cooption occurs when a gene, which may be part of an existing gene regulatory network (GRN), comes under the control of a new regulatory system. …”
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Understanding cancer from an evolutionary perspective: high-risk reprogramming of genome-damaged stem cells by Vladimir F. Niculescu

“…This shift is steered by genes housed within the ancestral genome compartment, pervasive across all metazoan genomes, encompassing humans, and governed by a premetazoic ancestral gene regulatory network. This work aims to highlight the emerging field of evolutionary cancer cell biology (ECCB), which points to the deep homology between cancer and protist life cycles tracing back to the common ancestor of amoebozoans, metazoans, and fungi (AMF). …”
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Data Mining Mycobacterium tuberculosis Pathogenic Gene Transcription Factors and Their Regulatory Network Nodes by Guangxin Yuan, Yu Bai, Yuhang Zhang, Guangyu Xu

“…Based on the differentially expressed gene, the transcriptional regulatory element databases (TRED) were integrated to construct the M. tuberculosis pathogenic gene regulatory network, and the correlation of the network genes with disease was analyzed with the DAVID online annotation tool. …”
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Single-cell chromatin accessibility landscape profiling reveals the diversity of epigenetic regulation in the rat nervous system by Peiyao Ma, Shanshan Duan, Wen Ma, Qiuting Deng, Yeya Yu, Peng Gao, Yue Yuan, Chuanyu Liu

“…To further investigate the gene regulatory network involved in spinal cord regeneration, we integrated our scATAC-seq data with published single-nucleus RNA-seq data from the spinal cord, and we identified more detailed regeneration related elements by drawing GRNs centered on the transcription factor Jun in the OPC. …”
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The GbbZIP41 transcription factor participates in terpene trilactones biosynthesis in Ginkgo biloba L. by Nuo Wang, Yi Tu, Sirui Zeng, Jiabao Ye, Weiwei Zhang, Feng Xu, Yongling Liao

“…However, there are few studies on the transcriptional modulation of TTLs biosynthesis and gene regulatory network of TTLs biosynthesis remains unclear. …”
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SEM-2/SoxC regulates multiple aspects of C. elegans postembryonic mesoderm development. by Marissa Baccas, Vanathi Ganesan, Amy Leung, Lucas R Pineiro, Alexandra N McKillop, Jun Liu

“…Furthermore, our work identified new interactions in the gene regulatory network (GRN) underlying C. elegans postembryonic development and adds to the general understanding of the structure-function relationship of SoxC proteins.…”
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Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry by Lydia Freddolino, Jamie Yang, Amir Momen-Roknabadi, Saeed Tavazoie

“…We provide experimental evidence for stochastic tuning in the adaptation of Saccharomyces cerevisiae to laboratory-engineered environments that are foreign to its native gene-regulatory network. Stochastic tuning operates locally at individual gene promoters, and its efficacy is modulated by perturbations to chromatin modification machinery.…”
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Temporal transcriptional profiling of host cells infected by a veterinary alphaherpesvirus using nanopore sequencing by Dóra Tombácz, Zoltán Maróti, Péter Oláh, Ákos Dörmő, Gábor Gulyás, Tibor Kalmár, Zsolt Csabai, Zsolt Boldogkői

“…We also explored whether gene co-expression could be a result of their collective regulation by upstream transcription factors using the Gene Regulatory Network database. Finally, our differential transcript usage (DTU) analysis identified a number of genes that exhibited altered proportions of transcript isoforms in comparison to non-infected cells. …”
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A dynamic co-expression approach reveals Gins2 as a potential upstream modulator of HNSCC metastasis by Nasibeh Khayer, Samira Shabani, Maryam Jalessi, Mohammad Taghi Joghataei, Frouzandeh Mahjoubi

“…Subsequently, the biologically relevant triples from statistically significant ones were defined through gene set enrichment analysis and reconstruction of the gene regulatory network. Finally, the validity of biologically relevant triplets was assessed at the protein level. …”
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The proneural transcription factor Atoh1 promotes odontogenic differentiation in human dental pulp stem cells (DPSCs) by Camila Sabatini, Huey-Jiun Lin, Galib Ovik, Richard Hall, Techung Lee

“…The functional versatility of Atoh1 prompted us to test the possibility that Atoh1 may intersect the dental pulp stem cell (DPSC) gene regulatory network governing odontogenic differentiation. …”
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Discovery of mutated oncodriver genes associated with glioblastoma originated from stem cells of subventricular zone through whole exome sequence profile analysis, and drug repurpo... by Arnob Sarker, Burhan Uddin, Reaz Ahmmed, Sabkat Mahmud, Alvira Ajadee, Md. Al Amin Pappu, Md. Abdul Aziz, Md. Nurul Haque Mollah

“…Then molecular mechanisms of GBM development were investigated by these three overexpressed driver genes through gene ontology (GO), KEGG-pathways, Gene regulatory network (GRN) and mutation analysis. Finally, overexpressed oncodriver genes guided top-ranked six drug agents (Irinotecan, Imatinib, etoposide, pazopanib, trametinib and cabozanitinib) were recommended against GBM through molecular docking study. …”
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Inference of a three-gene network underpinning epidermal stem cell development in Caenorhabditis elegans by Alicja Brożek, Arianna Ceccarelli, Andreas Christ Sølvsten Jørgensen, Mark Hintze, Vahid Shahrezaei, Michalis Barkoulas

“…Summary: Gene regulatory networks are crucial in cellular decision-making, making the inference of their architecture essential for understanding organismal development. …”
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Expression of cell-wall related genes is highly variable and correlates with sepal morphology by Hartasánchez, Diego A., Kiss, Annamaria, Battu, Virginie, Soraru, Charline, Delgado-Vaquera, Abigail, Massinon, Florian, Brasó-Vives, Marina, Mollier, Corentin, Martin-Magniette, Marie-Laure, Boudaoud, Arezki, Monéger, Françoise

“…Taking the sepal of Arabidopsis as a model, we investigated whether we can use variability of gene expression alongside variability of organ morphology to identify gene regulatory networks potentially involved in organ size and shape determination. …”
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An overview of the human immune system and the role of interferon regulatory factors (IRFs) by Ashwinder Kaur, Chee-Mun Fang

“…To deploy effective immune responses, immune systems comprise various cells and molecules that communicate with each other via signaling pathways coordinated by gene regulatory networks. The interferon regulatory factors (IRFs) are critical regulators of both the immune system’s development and activation of different cells. …”
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Protocol for predicting the single-cell network-based gene activity landscape during human B cell development by Xin Huang, Xuetong Hou, Yizhen Li, Jun J. Yang, Jiyang Yu

“…Summary: Owing to inconsistencies in human B cell classification and the difficulty in distinguishing heterogeneous subpopulations, we present a protocol to construct gene regulatory networks and gene activity landscapes for human B cell developmental stages. …”
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Verification and Optimal Control of Context-Sensitive Probabilistic Boolean Networks Using Model Checking and Polynomial Optimization by Koichi Kobayashi, Kunihiko Hiraishi

“…One of the significant topics in systems biology is to develop control theory of gene regulatory networks (GRNs). In typical control of GRNs, expression of some genes is inhibited (activated) by manipulating external stimuli and expression of other genes. …”
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A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators by Yuji Ke, Vincent Pujol, Jasper Staut, Lotte Pollaris, Ruth Seurinck, Thomas Eekhout, Carolin Grones, Maite Saura-Sanchez, Michiel Van Bel, Marnik Vuylsteke, Andrea Ariani, Christophe Liseron-Monfils, Klaas Vandepoele, Yvan Saeys, Bert De Rybel

“…These results allowed us to predict evolutionarily conserved tissue-specific markers and generate cell type-specific gene regulatory networks for root tissues of wheat and the other species used in our analysis. …”
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