Genome-wide analysis and characterization of TPD1 family proteins in pearl millet (Cenchrus americanus): Insights into reproductive regulation and phytohormone responses. by Zainab M Almutairi

“…Seven transmembrane proteins (from 127 to 172 aa) comprising TPD1 domain were identified via genome-wide mining. Analysis of gene expression during developmental stages revealed high expression of four CaTPD1s in reproductive organs. …”
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Brain gliomas new transcriptomic discoveries from differentially expressed genes to therapeutic targets by Shiwen Pei, Zhiquan Jiang, Hongwei Cheng

“…We obtained two independent glioma datasets from the Gene Expression Omnibus database, processed and normalized them using R software, and evaluated the relationship between differentially expressed genes and glioma by differential expression, expression quantitative trait loci, and Mendelian randomization (MR) analyses. …”
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Dietary, Metabolic, and Potentially Environmental Modulation of the Lysine Acetylation Machinery by Go-Woon Kim, Goran Gocevski, Chao-Jung Wu, Xiang-Jiao Yang

“…Epigenetic changes play a key role in defining gene expression patterns under both normal and pathological conditions. …”
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INFORMATION SUPPORT OF RESEARCH ON TRANSCRIPTIONAL REGULATORY MECHANISMS: AN ONTOLOGICAL APPROACH by N. L. Podkolodnyy, E. V. Ignatieva, O. A. Podkolodnaya, N. A. Kolchanov

“…This paper presents approaches to building knowledge domain ontology, formalized description of the mechanisms of transcriptional regulation and the development of methods for integration of heterogeneous information on the features of the regulation of gene expression on this base. The pilot version of the knowledge base on the transcriptional regulation of eukaryotic genes includes: (1) description of basic terms related to transcription regulation and relationships between them; (2) hierarchical classification of transcription regulators; (3) classification of phases and steps of transcription; (4) a database of transcriptional regulators of three mammalian species (human, mouse, and rat); and (5) dictionaries for molecular processes involved in transcriptional regulation. …”
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Treatment of gouty lumbar spinal stenosis: a case report and bioinformatics analysis by Xiao Zhang, Wenbo Gu, Di Luo, Xi Zhu, Xusheng Li, Haifeng Yuan

“…In addition, in order to further investigate the deep mechanism of LSS associated with gout, we obtained the intersecting genes of the two diseases based on a machine learning approach by obtaining the dataset GSE113212 related to LSS from the Gene Expression Omnibus (GEO) database, and the genes related to gout from the human gene database. …”
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Transformation of brain myeloid cell populations by SIV in rhesus macaques revealed by multiomics by Xiaoke Xu, Meng Niu, Benjamin G. Lamberty, Katy Emanuel, Moses Jedd Facun Apostol, Howard S. Fox

“…Given the gaps in our knowledge on how these cells respond in vivo to CNS infection, we perform single-cell multiomic sequencing, including gene expression and ATAC-seq, on myeloid cells from the brains of rhesus macaques with SIV-induced encephalitis (SIVE) as well as uninfected controls. …”
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Spatiotemporal Pattern of Neuroinflammation After Impact-Acceleration Closed Head Injury in the Rat

“…Our study shows rapid induction of inflammatory gene expression that exceeds by far the primary impact site and might therefore contribute to tissue damage at remote sites.…”
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Upregulation of FOXO3 in New-Onset Type 1 Diabetes Mellitus by Magdalena Zurawek, Marta Fichna, Piotr Fichna, Maria Czainska, Natalia Rozwadowska

“…FOXO3 expression was estimated in peripheral blood mononuclear cells (PBMCs) from newly diagnosed T1DM pediatric patients (n=28) and age-matched healthy donors (n=27) by reahavel-time PCR and TaqMan gene expression assays. Expression analysis revealed significant upregulation of FOXO3 in T1DM (P=0.0005). …”
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Peripheral T-Cell Lymphoma: Review and Updates of Current Management Strategies by Tiffany Tang, Kevin Tay, Richard Quek, Miriam Tao, Soo Yong Tan, Leonard Tan, Soon Thye Lim

“…Nevertheless, there has been development in the understanding of T-cell lymphomas and how they should be managed; FDG-PET emerges as an increasingly important tool in diagnosis, gene-expression signatures may aid with prognostication in the future, and novel therapies are currently being studied to improve outcomes in T-cell lymphomas. …”
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Searching for the cellular underpinnings of the selective vulnerability to tauopathic insults in Alzheimer’s disease by Justin Torok, Pedro D. Maia, Chaitali Anand, Ashish Raj

“…Further, cell-type distributions were more predictive of end-time-point tau pathology than AD-risk-gene expression. Using gene ontology analysis, we found that the genes that are directly correlated to tau pathology are functionally distinct from those that constitutively embody the vulnerable cells. …”
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Identification of a comprehensive set of transcriptional regulators involved in the long-term survivability of Escherichia coli in soil by Soma Nakamoto, Ikki Kobayashi, Koichi Watanabe, Takeru Kikuta, Sousuke Imamura, Tomohiro Shimada

“…To adapt to environmental changes, bacteria alter their gene expression patterns using transcriptional regulators such as sigma factors. …”
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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

“…Starting from a minimal 2-gene network, insufficient for fitting the Drosophila gene expression patterns, we find a general trend of coopting available genes into the GRN, in order to better fit the data. …”
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Integrating Prior Knowledge Using Transformer for Gene Regulatory Network Inference by Guangzheng Weng, Patrick Martin, Hyobin Kim, Kyoung Jae Won

“…By combining LLMs ability to distillate biological knowledge from text and deep learning methodologies capturing complex patterns in gene expression data, GRNPT overcomes the limitations of traditional GRN inference methods and enables more accurate and comprehensive understanding of gene regulatory dynamics.…”
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PLncWX: A Machine-Learning Algorithm for Plant lncRNA Identification Based on WOA-XGBoost by Fei Guo, Zhixiang Yin, Kai Zhou, Jiasi Li

“…Studies have shown that lncRNAs can regulate gene expression at the epigenetic, transcriptional, and posttranscriptional levels, which are not only closely related to the occurrence, development, and prevention of human diseases, but also can regulate plant flowering and participate in plant abiotic stress responses such as drought and salt. …”
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Hydrogenotrophic methanogenesis at 7–12 mbar by Methanosarcina barkeri under simulated martian atmospheric conditions by Rachel L. Harris, Andrew C. Schuerger

“…Transcriptomics reveal that low total pressure and temperature did not significantly impact gene expression, highlighting the resilience of M. barkeri. …”
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MicroRNAs in Diabetic Kidney Disease by Rong Li, Arthur C. K. Chung, Xueqing Yu, Hui Y. Lan

“…The discovery of microRNAs had lead to a new era of post-transcriptional regulators of gene expression. Studies from cells, experimental animal models and patients under diabetic conditions demonstrate that expression patterns of microRNAs are altered during the progression of diabetic kidney disease. …”
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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... by Venura Herath, Clare L. Casteel, Jeanmarie Verchot

“…This study also shows that gene expressions are regulated through alternative pre-mRNA splicing and the use of alternative transcription start and termination sites. …”
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Severe, but not moderate asthmatics share blood transcriptomic changes with post-traumatic stress disorder and depression. by Sandor Haas-Neill, Anna Dvorkin-Gheva, Paul Forsythe

“…Our analysis revealed that commonalities in blood transcriptomic changes were only found between the severe form of asthma and mood disorders. Gene expression commonly regulated in PTSD and severe asthma, included ORMDL3 a gene known to be associated with asthma risk and STX8, which is involved in TrkA signaling. …”
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Continuous Delivery of D-Luciferin by Implanted Micro-osmotic Pumps Enables True Real-Time Bioluminescence Imaging of Luciferase Activity in Vivo by Shimon Gross, Ute Abraham, Julie L. Prior, Erik D. Herzog, David Piwnica-Worms

“…Bioluminescence imaging (BLI) of luciferase reporters in small animal models offers an attractive approach to monitor regulation of gene expression, signal transduction, and protein-protein interactions, as well as following tumor progression, cell engraftment, infectious pathogens, and target-specific drug action. …”
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Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana Genome by Rajesh Mehrotra, Amit Yadav, Purva Bhalothia, Ratna Karan, Sandhya Mehrotra

“…Transcription control of gene expression depends on a variety of interactions mediated by the core promoter region, sequence specific DNA-binding proteins, and their cognate promoter elements. …”
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