Works matching DE "RNA sequencing"

Results: 5000

Deciphering the tumor immune microenvironment: single-cell and spatial transcriptomic insights into cervical cancer fibroblasts.

Published in:

Journal of Experimental & Clinical Cancer Research (17569966), 2025, p. 1, doi. 10.1186/s13046-025-03432-5

By:

Lin, Zhiheng;
Zhou, Youwei;
Liu, Zhenran;
Nie, Wenyang;
Cao, Hengjie;
Li, Shengnan;
Li, Xuanling;
Zhu, Lijun;
Lin, Guangyao;
Ding, Yanyu;
Jiang, Yi;
Gu, Zuxi;
Xu, Lianwei;
Zhao, Zhijie;
Cai, Huabao

Publication type:

Article

DiSC: a statistical tool for fast differential expression analysis of individual-level single-cell RNA-seq data Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf327

By:

Zhang, Lujun;
Yang, Lu;
Ren, Yingxue;
Zhang, Shuwen;
Guan, Weihua;
Chen, Jun

Publication type:

Article

Brownian motion data augmentation: a method to push neural network performance on nanopore sensors Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf323

By:

Kipen, Javier;
Jaldén, Joakim

Publication type:

Article

Single cell RNA sequencing shows that cells expressing Sox9 postnatally populate most skeletal lineages in mouse bone.

Published in:

Journal of Bone & Mineral Research, 2025, v. 40, n. 6, p. 799, doi. 10.1093/jbmr/zjaf043

By:

Smith, Neal P;
Janton, Christopher;
Alcantara, Ana Clara Morellato;
George, Majd;
Mankongtreecheep, Kasidet;
Mao, Guping;
Villani, Alexandra-Chloé;
Kronenberg, Henry M

Publication type:

Article

An inducible mouse model of osteogenesis imperfecta type V reveals aberrant osteogenesis caused by Ifitm5 c.-14C>T mutation.

Published in:

Journal of Bone & Mineral Research, 2025, v. 40, n. 5, p. 577, doi. 10.1093/jbmr/zjaf022

By:

Tan, Zhijia;
Shek, Hiu Tung;
Li, Zeluan;
Xia, Linjian;
He, Yanni;
Chen, Peikai;
Wong, Janus Siu Him;
Gao, Bo;
Chan, Danny;
To, Michael Kai Tsun

Publication type:

Article

Intranasal Calcitriol Accelerates Improvement of Sinonasal Inflammation and Olfactory Impairment in Mice After Cessation of Chronic Cigarette‐Smoke Exposure.

Published in:

International Forum of Allergy & Rhinology, 2025, v. 15, n. 7, p. 680, doi. 10.1002/alr.23504

By:

Langerude, Logan;
McQuiston, Alex;
Atkinson, Carl;
Mulligan, Jennifer K.

Publication type:

Article

Immunoregulatory macrophages induced by mycobacterial nonpolar lipids.

Published in:

Journal of Immunology, 2025, v. 214, n. 5, p. 1059, doi. 10.1093/jimmun/vkae058

By:

Petrilli, Jéssica Dias;
Estevão, Paulo;
De Araújo, Luana Evangelista;
Muller, Igor;
Yoshinaga, Marcos Yukio;
Ramos, Pablo Ivan Pereira;
Chaves-Filho, Adriano Britto;
Horta, Thainá;
Sorgi, Carlos Arterio;
Miyamoto, Sayuri;
Riley, Lee;
Arruda, Sérgio;
Queiroz, Adriano

Publication type:

Article

Integrated transcriptomic and proteomic profiling of colonic tissue in interleukin-10-deficient mice.

Published in:

Scientific Data, 2025, v. 12, n. 1, p. 1, doi. 10.1038/s41597-025-05212-4

By:

Li, Lili;
Ma, Chunxiang;
Chen, Kexin;
Jia, Yongbin;
Wu, Yushan;
Lin, Hao;
Cheng, Rui;
Jiang, Mingshan;
Zeng, Zhen;
Chen, Jingjing;
Pang, Jiangmei;
Li, Jiaxin;
Zhang, Hu

Publication type:

Article

Morphological, immunohistochemical and molecular analysis of follicular dendritic cell sarcomas: L1CAM as a new diagnostic marker.

Published in:

Histopathology, 2025, v. 87, n. 2, p. 258, doi. 10.1111/his.15458

By:

Schelbert, Selina;
Maurus, Katja;
Roth, Sabine;
Ott, German;
Kurz, Katrin S;
Mogler, Carolin;
Wollenberg, Barbara;
Linde, John;
Zamo, Alberto;
Anagnostopoulos, Ioannis;
Gramlich, Susanne;
Rosenwald, Andreas;
Gerhard‐Hartmann, Elena

Publication type:

Article

Early life microbiome disbalance impacts neuroendocrine outcomes in pre-pubertal mice in a sexually dimorphic manner.

Published in:

Frontiers in Microbiology, 2025, p. 1, doi. 10.3389/fmicb.2025.1504513

By:

Nankova, Bistra B.;
Hu, Furong;
LaGamma, Edmund F.

Publication type:

Article

Cardiac fibroblasts regulate myocardium and coronary vasculature development in the murine heart via the collagen signaling pathway.

Published in:

eLife, 2025, p. 1, doi. 10.7554/eLife.102305

By:

Yiting Deng;
Yuanhang He;
Juan Xu;
Haoting He;
Manling Zhang;
Guang Li

Publication type:

Article

Single-cell transcriptomics analysis reveals a disrupted NK-T cell interaction network in liver metastatic cancer.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-06241-0

By:

Wang, Xiaoshuang;
Wu, Zhongen;
Zhou, Yan;
Yang, Dehua;
Zhou, Qingtong;
Zhu, Di;
Wang, Ming-Wei;
Wang, Lu

Publication type:

Article

Exploring temperature-dependent transcriptomic adaptations in Yersinia pestis using direct cDNA sequencing by Oxford Nanopore Technologies.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-05662-1

By:

Robin, Brandon;
Baillez, Alexandre;
Le Guillouzer, Servane;
Lecoeur, Cécile;
Sebbane, Florent;
Bontemps-Gallo, Sébastien

Publication type:

Article

CXCL8 is essential for cervical cancer cell acquired radioresistance and acts as a promising therapeutic target in cervical cancer.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-05435-w

By:

Hu, Qinghong;
Zuo, Xiaoxiao;
Gu, Xiaobin;
Liu, Liya;
Tang, Ying;
Niu, Xiaomin;
Shi, Yonggang;
Han, Liping

Publication type:

Article

Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 7, p. 1, doi. 10.1371/journal.pcbi.1013179

By:

Vock, Isaac W.;
Mabin, Justin W.;
Machyna, Martin;
Zhang, Alexandra;
Hogg, J. Robert;
Simon, Matthew D.

Publication type:

Article

Single‑cell RNA sequencing reveals TMEM71 as an immunomodulatory biomarker predicting immune checkpoint blockade response in breast cancer.

Published in:

Discover Oncology, 2025, v. 16, n. 1, p. 1, doi. 10.1007/s12672-025-03068-z

By:

Li, Boyang;
Lin, Ruonan;
Hua, Yibo;
Ma, Binlin;
Chen, Yi

Publication type:

Article

Single-cell RNA sequencing reveals the potential role of estrogen in tuberous sclerosis complex related renal angiomyolipoma.

Published in:

Discover Oncology, 2025, v. 16, n. 1, p. 1, doi. 10.1007/s12672-025-02909-1

By:

Liu, Yi;
Wang, Wenda;
Zheng, Guoyang;
Xu, Weifeng;
Wang, Zhan;
Wang, Xu;
Liu, Jiang;
Qiu, Dongxu;
Li, Yanan;
Zhao, Yang;
Zhang, Yushi

Publication type:

Article

Caracterización molecular de microorganismos silvestres asociados a fermentaciones artesanales de cacao en el municipio de Los Andes, Nariño, Colombia.

Published in:

NOVA: Publicación Científica en Ciencias Biomédicas, 2025, v. 22, n. 44, p. 105, doi. 10.22490/24629448.9986

By:

Fernández Izquierdo, Pablo;
Martínez Muñoz, Julián Felipe;
Miramag Yaqueno, Kevin Mauricio;
Ortiz Benavides, Fedra

Publication type:

Article

Metabolomic and transcriptomic analyses provide insights into the red pigmentation in loquat (Eriobotrya japonica) peel.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1615281

By:

Zhang, Yaling;
Chen, Xiuping;
Su, Wenbing;
Deng, Chaojun;
Jiang, Jimou;
Zheng, Shaoquan

Publication type:

Article

A novel, rapid, and practical prognostic model for sepsis patients based on dysregulated immune cell lactylation.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1625311

By:

Li, Chang;
He, Mei;
Shi, PeiChi;
Yao, Lu;
Fang, XiangZhi;
Li, XueFeng;
Li, QiLan;
Yang, XiaoBo;
Xu, JiQian;
Shang, You

Publication type:

Article

A Comparison of Zero-Inflated Models for Modern Biomedical Data.

Published in:

American Journal of Undergraduate Research, 2025, v. 22, n. 2, p. 49, doi. 10.33697/ajur.2025.141

By:

Beveridge, Max;
Goldstein, Zach;
Hee Cheol Chung

Publication type:

Article

Making sense of human colorectal cancer molecular subtypes: mice are stepping in.

Published in:

Cell Death Discovery, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41420-025-02594-7

By:

Green, Caleb;
Roccia, Pamela;
Rufini, Alessandro

Publication type:

Article

Spatially resolved C1QC+ macrophage-CD4+ T cell niche in colorectal cancer microenvironment: implications for immunotherapy response.

Published in:

Cell Discovery, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41421-025-00811-2

By:

Zhang, Hangyu;
Hong, Libing;
Dong, Zhen;
Xin, Shan;
Lin, Bo;
Cheng, Jinlin;
Tian, Weihong;
Li, Bin;
Wang, Jing;
Liu, Xiaoyan;
Liu, Chuan;
Jin, Yuzhi;
Feng, Yanzhi;
Su, Ge;
Sun, Xuqi;
Liu, Qiqi;
Dai, Xiaomeng;
Gao, Yang;
Tong, Zhou;
Liu, Lulu

Publication type:

Article

Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosis.

Published in:

Respiratory Research, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12931-025-03300-y

By:

Ferrini, Erica;
Bonfini, Costanza;
Marchese, Giovanna;
Buccardi, Martina;
Zoboli, Matteo;
Faccioli, Primetta;
Sverzellati, Nicola;
Villetti, Gino;
Ottonello, Simone;
Ravo, Maria;
Stellari, Franco F.

Publication type:

Article

Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithms.

Published in:

Journal of Translational Medicine, 2025, v. 23, n. 1, p. 1, doi. 10.1186/s12967-025-06733-7

By:

Li, Hanqi;
Zhang, Jiayi;
Shi, Yu;
Wang, Huanhuan;
Yang, Ruida;
Wu, Shaobo;
Li, Yue;
Yang, Xue;
Liu, Qingguang;
Sun, Liankang

Publication type:

Article

Exploring the interactome of the Staphylococcus aureus sRNA Srn_9342 identified a complex formation with RNAIII leading to the modulation of δ-hemolysin expression.

Published in:

BMC Microbiology, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12866-025-04113-1

By:

Bronsard, Julie;
Silard, Chloé;
Legros, Julie;
Germain-Amiot, Noëlla;
Hallier, Marc;
Augagneur, Yoann

Publication type:

Article

KLF13 promotes ferroptosis and chemosensitivity in lung adenocarcinoma.

Published in:

BMC Biology, 2025, v. 23, n. 1, p. 1, doi. 10.1186/s12915-025-02303-x

By:

Shi, Haochun;
Pan, Binyang;
Wu, Gujie;
Liang, Jiaqi;
Bian, Yunyi;
Shan, Guangyao;
Ren, Shencheng;
Bi, Guoshu;
Zhan, Cheng;
Guo, Weigang

Publication type:

Article

An ancient influenza genome from Switzerland allows deeper insights into host adaptation during the 1918 flu pandemic in Europe.

Published in:

BMC Biology, 2025, v. 23, n. 1, p. 1, doi. 10.1186/s12915-025-02282-z

By:

Urban, Christian;
Vrancken, Bram;
Patrono, Livia V.;
Düx, Ariane;
Le Vu, Mathilde;
Matthes, Katarina L.;
Burkhard-Koren, Nina Maria;
Widulin, Navena;
Schnalke, Thomas;
Carraro, Sabina;
Rühli, Frank;
Lemey, Philippe;
Staub, Kaspar;
Calvignac-Spencer, Sébastien;
Schuenemann, Verena J.

Publication type:

Article

CircERC1 facilitates chemoresistance through inhibiting pyroptosis and remodeling extracellular matrix in pancreatic cancer.

Published in:

Molecular Cancer, 2025, v. 24, n. 1, p. 1, doi. 10.1186/s12943-025-02385-9

By:

Zhang, Jian;
Lv, Shengnan;
Peng, Xinyu;
Liu, Huan;
Guo, Jianxiong;
Liu, Ziyu;
Chu, Tongjia;
Liu, Han;
Duan, Kehang;
Lou, Fengxiang;
Chi, Yubo;
Gao, Bing;
Liu, Yan;
Wei, Feng

Publication type:

Article

Benchmarking metabolic RNA labeling techniques for high-throughput single-cell RNA sequencing.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-61375-z

By:

Zhang, Xiaowen;
Peng, Mingjian;
Zhu, Jianghao;
Zhai, Xue;
Wei, Chaoguang;
Jiao, He;
Wu, Zhichao;
Huang, Songqian;
Liu, Mingli;
Li, Wenhao;
Yang, Wenyi;
Miao, Kai;
Xu, Qiongqiong;
Chen, Liangbiao;
Hu, Peng

Publication type:

Article

GPerturb: Gaussian process modelling of single-cell perturbation data.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-61165-7

By:

Xing, Hanwen;
Yau, Christopher

Publication type:

Article

Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-61149-7

By:

Hou, Jiawen;
Zhao, Wei;
Nie, Qing

Publication type:

Article

Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60882-3

By:

Guo, Pengfei;
Chen, Yufan;
Mao, Liran;
Cardilla, Angelysia;
Lee, Chin Nien;
Cui, Yan;
Jin, Dengge;
Hua, Yucong;
Xu, Xiaowei;
Deng, Yanxiang

Publication type:

Article

Structural mechanism of DDX39B regulation by human TREX-2 and a related complex in mRNP remodeling.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60547-1

By:

Clarke, Bradley P.;
Gao, Shengyan;
Mei, Menghan;
Xie, Dongqi;
Angelos, Alexia E.;
Vazhavilla, Ashley;
Hill, Pate S.;
Cagatay, Tolga;
Batten, Kimberly;
Shay, Jerry W.;
Xie, Yihu;
Fontoura, Beatriz M. A.;
Ren, Yi

Publication type:

Article

Deciphering the impact of intra-tumoral bacterial infiltration on multi-omics profiles in low-grade gliomas.

Published in:

Frontiers in Oncology, 2025, p. 1, doi. 10.3389/fonc.2025.1582068

By:

Li, Wenshu;
Zhu, Zixiang;
Li, Longyuan;
Wu, Xin;
Li, Jiaxuan;
Zhou, Yi;
Gu, Lingwen;
Vittal, Pranathi;
Chen, Zhouqing;
Wang, Zhong;
Guo, Lingchuan

Publication type:

Article

Decoding neuroinflammation in Alzheimer's disease: a multi-omics and AI-driven perspective for precision medicine.

Published in:

Frontiers in Immunology, 2025, p. 1, doi. 10.3389/fimmu.2025.1616899

By:

Lin, Shiyu;
Zhan, Yijun;
Wang, Ruiqi;
Pei, Jian

Publication type:

Article

Tumor-associated macrophage-based predictive and prognostic model for hepatocellular carcinoma.

Published in:

PLoS ONE, 2025, v. 20, n. 7, p. 1, doi. 10.1371/journal.pone.0325120

By:

Shang, Changquan;
He, Tiancong;
Zhang, Yi

Publication type:

Article

Identification of parthanatos-related molecular subtypes and development of prognostic risk models in ovarian cancer based on multi-omics analysis.

Published in:

Journal of Ovarian Research, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13048-025-01726-y

By:

Qi, Xiaoying;
Jiang, Changqing;
Wang, Ning;
Han, Yi;
Liu, Tingting;
Huang, Liying;
Yin, Guangjie

Publication type:

Article

Single cell RNA sequencing to identify an Immunogenic cell death related prognostic signature in intrahepatic cholangiocarcinoma.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-08602-1

By:

Sha, Bowen;
Tong, Fei;
Shu, Qinghua;
Wu, Miao;
Zhao, Liang;
Zhang, Yufeng

Publication type:

Article

Deciphering the temporal transcriptional landscape of human fetal leptomeninges.

Published in:

Brain: A Journal of Neurology, 2025, v. 148, n. 6, p. 2218, doi. 10.1093/brain/awae397

By:

Sun, Licheng;
Liu, Ping;
Guo, Jingjing;
Fang, Chuantao;
Li, Li;
Liu, Yi;
Tan, Yanfeng;
Zhang, Yi;
Zhao, Rui;
Zhang, Fayong;
Xiao, Jianbo;
Dong, Rui;
Ma, Shaojie;
Mei, Xinyu;
Qi, Dashi

Publication type:

Article

CALR regulates the proliferation and drug sensitivity of multiple myeloma cells through the BCL2 signaling pathway.

Published in:

Molecular Biology Reports, 2025, v. 52, n. 1, p. 1, doi. 10.1007/s11033-025-10749-z

By:

Wang, Yin;
Hu, Xiaoli;
Song, Yaqi;
Ruan, Qianqi;
Bai, Xiaoteng;
Du, Juan

Publication type:

Article

Single-cell RNA sequencing analysis of intrahepatic cholangiocarcinoma reveals SPP1 facilitates disease progression via interaction with CD4+ T cells.

Published in:

Oncology Letters, 2025, v. 30, n. 2, p. N.PAG, doi. 10.3892/ol.2025.15135

By:

Lin, Xian;
Peng, Huanyan;
Liu, Ke;
Chen, Wenqi;
Shao, Ximing;
Ning, Chun;
Li, Hongchang;
Yang, Dongye

Publication type:

Article

Photosynthesis genes modulate cadmium tolerance in the freshwater alga Closterium acutum revealed by transcriptome analysis.

Published in:

Journal of Applied Phycology, 2025, v. 37, n. 3, p. 1951, doi. 10.1007/s10811-025-03486-0

By:

Shin, Jeongmin;
Kim, Han-Sol;
Bui, Quynh Thi Nhu;
Kim, Taehee;
Ki, Jang-Seu

Publication type:

Article

Role of Compensatory miRNA Networks in Cognitive Recovery from Heart Failure.

Published in:

Non-Coding RNA, 2025, v. 11, n. 3, p. 45, doi. 10.3390/ncrna11030045

By:

Gisa, Verena;
Islam, Md Rezaul;
Lbik, Dawid;
Hofmann, Raoul Maximilian;
Pena, Tonatiuh;
Krüger, Dennis Manfred;
Burkhardt, Susanne;
Schütz, Anna-Lena;
Sananbenesi, Farahnaz;
Toischer, Karl;
Fischer, Andre

Publication type:

Article

Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer.

Published in:

Non-Coding RNA, 2025, v. 11, n. 3, p. 38, doi. 10.3390/ncrna11030038

By:

Antunes-Ferreira, Mafalda;
Glogovitis, Ilias;
Fortunato, Diogo;
D'Ambrosi, Silvia;
Saborit, Mariona Colom;
Yahubyan, Galina;
Baev, Vesselin;
Hackenberg, Michael;
Zarovni, Natasa;
Wurdinger, Thomas;
Koppers-Lalic, Danijela

Publication type:

Article

An insight into COVID-19 host immunity at single-cell resolution.

Published in:

International Reviews of Immunology, 2025, v. 44, n. 4, p. 180, doi. 10.1080/08830185.2024.2443420

By:

Ghosh, Supratim;
Chatterjee, Ankita;
Maitra, Arindam

Publication type:

Article

Endometrial microbiome in reproductive failure: The possibility of metagenomic analysis.

Published in:

Clinical & Experimental Reproductive Medicine, 2025, v. 52, n. 2, p. 107, doi. 10.5653/cerm.2024.07171

By:

Han, Ae Ra

Publication type:

Article

Novel insights into the Leishmania infantum transcriptome diversity of protein-coding and non-coding sequences in both stages of parasite development using nanopore direct RNA sequencing.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-025-11767-8

By:

Emond-Rheault, Jean-Guillaume;
Ferreira, Gabriel Reis;
Lavoie-Ouellet, Camille;
Smith, Martin A.;
Papadopoulou, Barbara

Publication type:

Article

Integrated bulk and single-cell RNA sequencing reveals a cuproptosis-related LncRNA prognostic signature in neuroblastoma.

Published in:

BMC Cancer, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12885-025-14463-8

By:

Chen, Ke;
Wang, Jing;
Yang, Shimin;
Xiao, Jun;
Wu, Luyao;
Li, Zejian;
Zhao, Xiang;
Chen, Xuyong;
Li, Honglin;
Feng, Jiexiong;
Meng, Xinyao

Publication type:

Article

Sulforaphane induces cell morphology change and cell apoptosis by activating endoplasmic reticulum stress in glioblastoma.

Published in:

BMC Cancer, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12885-025-14378-4

By:

Li, Nan;
Jiang, Yan;
Wang, Ajun;
Jiang, Tongchao;
Dai, Huimin;
Xia, Chengyu;
Jiang, Tongcui

Publication type:

Article