Predicting patient outcomes with gene-expression biomarkers from colorectal cancer organoids and cell lines by Alexandra Razumovskaya, Mariia Silkina, Mariia Silkina, Mariia Silkina, Andrey Poloznikov, Timur Kulagin, Maria Raigorodskaya, Nina Gorban, Anna Kudryavtseva, Maria Fedorova, Boris Alekseev, Alexander Tonevitsky, Alexander Tonevitsky, Alexander Tonevitsky, Sergey Nikulin, Sergey Nikulin, Sergey Nikulin

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Integrative profiling of lung cancer biomarkers EGFR, ALK, KRAS, and PD-1 with emphasis on nanomaterials-assisted immunomodulation and targeted therapy by Li Peng, Hongmei Li, Wencai Yan, Yingjie Liu, Haihao Zhu, Yingcai Hong

“…Transcriptomic analyses revealed significant overexpression of EGFR (2.8-fold), KRAS (2.3-fold), ALK (1.9-fold), and PDCD1 (2.1-fold) in NSCLC tissues (p < 0.01). qRT-PCR corroborated these findings, with H1975 cells displaying elevated EGFR (3.2-fold) and KRAS (2.4-fold), and H520 cells showing increased ALK (2.7-fold) and moderate PDCD1 expression.ConclusionThis integrative study combining structural modeling, molecular interaction analysis, and transcriptomic validation confirms EGFR, ALK, KRAS, and PD-1 supports their relevance as clinically actionable and structurally druggable biomarkers in NSCLC. …”
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A single-cell landscape of the regenerating spinal cord of zebrafish by Lei Yao, Xinyi Cai, Saishuai Yang, Yixing Song, Lingyan Xing, Guicai Li, Zhiming Cui, Jiajia Chen

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Organic Acids Metabolic Response and Transcription Factor Expression Changes of Highland Barley Seedlings Under Na₂SeO₃ Treatment by Xiaozhuo Wu, Huichun Xie, Jianxia Ma, Guigong Geng, Xiaoli Yang, Feng Qiao

“…Based on metabolomics, 30 differential metabolites of organic acids were screened from highland barley seedlings under Na₂SeO₃ treatment and showed positive correlationships with organic selenium, inorganic selenium, and total selenium in highland barley seedling leaves. Through transcriptome analysis, heatmap analysis on six major categories of transcription factors (bHLH, MYB, NAC, WRKY, GATA, and HSF) was performed. …”
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Transcriptional regulation of hormone signalling genes in black pepper in response to Phytophthora capsici by Chidambareswaren Mahadevan, K. Mohamed Shafi, B Nagarathnam, Manjula Sakuntala, Ramanathan Sowdhamini

“…This study employs RNA sequencing and transcriptome analysis to explore the defense mechanisms of P. nigrum against P. capsici. …”
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Host cellular transcriptional response to respiratory syncytial virus infection in HEp-2 cells: insights from cDNA microarray and quantitative PCR analyses by Manoj K. Pastey, Christopher Lupfer

“…Anti-apoptotic MCL1 increased ~11-fold, while pro-apoptotic caspase-4 showed a more modest 1.6-fold rise, indicating a complex regulation of cell death pathways. …”
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Multi-omics profiling reveals elevated CO2-enhanced tolerance of Trifolium repens L. to lead stress through environment-plant-microbiome interactions by Lei Wang, Sui Wang, Haifeng Su, Hongguang Cai, Yankun Song, Xiang Gong, Zhihui Sun, Jianhua Qu, Ying Zhang

“…These insights shed light on the plant stress responses under elevated CO2 and while contributing to a broader comprehension of plant-environment interactions.…”
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Inflammation and platelet hyperresponsiveness in coronary artery disease and the influence of Talin-1/αIIbβ3-mediated bidirectional signaling pathway by Shengnan Shi, Jiaming Gao, Yehao Zhang, Min Zhan, Zhanfei Tan, Peili Wang, Jianhua Fu, Jianxun Liu

“…BackgroundWhile platelet hyperreactivity constitutes an independent risk factor for major adverse cardiovascular events (MACEs) in coronary artery disease, its molecular underpinnings remain poorly characterized. …”
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Membrane transporter genes predict chemoradiotherapy response in patients with cervical cancer by Natália Gregório Custódio, Fábio Ribeiro Queiroz, Angelo Borges de Melo Neto, Brenda Martins Cavalcante, Laurence Rodrigues do Amaral, Telma Maria Rossi de Figueiredo Franco, Matheus de Souza Gomes, Vasco Ariston de Carvalho Azevedo, Letícia da Conceição Braga, Paulo Guilherme de Oliveira Salles, Wander de Jesus Jeremias

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Untargeted metabolomics-based study of extracts from Simarouba glauca plant parts for insecticidal effects against Spodoptera frugiperda by Komala G, Shanthi Mookiah, Murugan Marimuthu, Sujayanand G. K, Vellaikumar Sampathrajan, Preetha Gnanadhas, Kavitha Govindasamy, Prakash Kolanchi

“…Gas chromatography–tandem mass spectrometry identified key metabolites, including gamma-sitosterol and lanosta-8,24-dien-3-one, with distinct metabolic signatures in bark extracts, as revealed by principal component analysis and clustering techniques. Transcriptomic analysis using RNA sequencing and differential gene expression profiling identified 734 genes with significant expression changes, implicating disruptions in metabolic and signaling pathways associated with insect mortality and feeding deterrence. …”
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Advancing precision antibody-drug conjugate therapy: unique proteogenomic profiles of tumor subsets in non-small cell lung cancer by Edwin Lin, Ying-Chun Lo, Vivek Subbiah, Rajat Thawani, Aakash Desai

“…This study utilized transcriptomics and proteomics to characterize NSCLC subtypes with distinct ADC target expression profiles. …”
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Fenaminosulf Promotes Growth and Gall Formation in <i>Zizania latifolia</i> Through Modulation of Physiological and Molecular Pathways by Chaohong Ding, Ruifang Ma, Liqiu Wang, Xinyan Lan, Limin Chen, Jinxing Zhu, Lailiang Wang

“…In contrast, higher FM concentrations (2.5 g/L and 5 g/L) inhibited vegetative growth but significantly enhanced gall formation, particularly at 2.5 g/L, indicating that FM can redirect plant resources or alter susceptibility to favor the fungal interaction under specific conditions. Transcriptomic analysis provided mechanistic insights, revealing extensive gene expression reprogramming, especially under high FM treatment (5 g/L). …”
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Single-dose VSV-based vaccine protects cynomolgus macaques from disease after Taï Forest virus infection by Paige Fletcher, Kyle L. O’Donnell, Brianna M. Doratt, Delphine C. Malherbe, Chad S. Clancy, Joseph F. Rhoderick, Friederike Feldmann, Patrick W. Hanley, Thomas G. Ksiazek, Thomas W. Geisbert, Ilhem Messaoudi, Andrea Marzi

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The role of cytokine licensing in shaping the therapeutic potential of wharton’s jelly MSCs: metabolic shift towards immunomodulation at the expense of differentiation by Olena Rogulska, Eliska Vavrinova, Irena Vackova, Jarmila Havelkova, Klara Gotvaldova, Pavel Abaffy, Sarka Kubinova, Michal Sima, Pavel Rossner, Lucie Bacakova, Pavla Jendelova, Katarina Smolkova, Yuriy Petrenko

“…Methods WJ-MSCs were expanded and exposed to TNF-α and IFN-γ (10 ng/ml each) for 24 h. Transcriptomic analysis was performed using RNA sequencing to identify differentially expressed genes related to immune modulation and lineage commitment. …”
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The Dysregulation of Tuning Receptors and Transcription Factors in the Antennae of <i>Orco</i> and <i>Ir8a</i> Mutants in <i>Aedes aegypti</i> Suggests a Chemoreceptor Regulatory M... by Matthew M. Cooke, Michael S. Chembars, Ronald Jason Pitts

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Depot-specific metabolic and inflammatory profiles in perirenal and renal sinus adipose tissue by Maria J. Pereira, Argyri Mathioudaki, Susanne Hetty, Amir Sedigh, Jan W. Eriksson, Maria K. Svensson

“…Of 1113 significantly differentially expressed genes (DEGs) (PRAT: 571 down- and 542 upregulated), thermogenic and metabolic genes (UCP1, CIDEA, and CKMT1B) were enriched in PRAT, while inflammation-related genes (NFKBIA, BIRC3, and IRF1) in RSAT. …”
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Autoencoder techniques for survival analysis on renal cell carcinoma. by Iñigo Sanz Ilundain, Laura Hernández-Lorenzo, Cristina Rodríguez-Antona, Jesús García-Donas, José L Ayala

“…Thus, identifying molecular predictors of survival (like genetic alterations or transcriptomic patterns of gene expression) is one of the most relevant fields in current research. …”
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Temporal analysis of doxorubicin-induced cardiac toxicity and hypertrophy by Yu-Te Lin, Yi-Ju Lee, Wen-Wei Tseng, Zih-Hua Chen, Huai-Ching Hsieh, Ko-Hong Lin, Jin-Yu Su, An-Chi Wei

“…In this study, we collected time-course transcriptomics and metabolomics data from the human cardiomyocyte cell line AC16, which we analyzed along with curated public transcriptomics data on DOX-induced toxicity. …”
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Advances in the application of multi-omics analysis in skin aging by Boquan Long, Boquan Long, Weitian Pan, Shuozhong Wu, Qianye Nong, Wenhui Li, Siqi Chen, Siqi Chen, Hongwei Guo

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The impact of dropouts in scRNAseq dense neighborhood analysis by Alisa Pavel, Manja Gersholm Grønberg, Line H. Clemmensen

“…Single cell RNA sequencing (scRNAseq) provides the possibility to investigate transcriptomic profiles on a single cell level. However, the data show unique challenges in comparison to bulk transcriptomic data, one being high dropout rates, which yields high sparsity data. …”
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