Works matching DE "TRANSCRIPTOMES"

Results: 5000

H<sub>2</sub>O<sub>2</sub> mediates transcriptome reprogramming during Soybean mosaic virus-induced callose deposition in soybean.

Published in:

Crop Journal (2095-5421), 2022, v. 10, n. 1, p. 262, doi. 10.1016/j.cj.2021.04.005

By:

Tianjie Sun;
Xizhe Sun;
Fukuan Li;
Nan Ma;
Mengxuan Wang;
Yan Chen;
Na Liu;
Yuan Jin;
Jie Zhang;
Chunyan Hou;
Chunyan Yang;
Dongmei Wang

Publication type:

Article

New transcriptomic insights in two RNAi wheat lines with the gliadins strongly down-regulated by two endosperm specific promoters.

Published in:

Crop Journal (2095-5421), 2022, v. 10, n. 1, p. 194, doi. 10.1016/j.cj.2021.04.009

By:

Marín-Sanz, Miriam;
Iehisa, Julio C. Masaru;
Barro, Francisco

Publication type:

Article

Dynamic patterns of the translatome in a hybrid triplet show translational fractionation of the maize subgenomes.

Published in:

Crop Journal (2095-5421), 2022, v. 10, n. 1, p. 36, doi. 10.1016/j.cj.2021.02.002

By:

Wanchao Zhu;
Sijia Chen;
Tifu Zhang;
Jia Qian;
Zi Luo;
Han Zhao;
Yirong Zhang;
Lin Li

Publication type:

Article

The use of transcriptomic data in developing biomarkers in breast cancer.

Published in:

Immunomedicine, 2024, v. 4, n. 1, p. 1, doi. 10.1002/imed.1051

By:

Albitar, Maher;
Goy, Andre;
Pecora, Andrew;
Graham, Deena;
McNamara, Donna;
Charifa, Ahmad;
IP, Andrew;
Ma, Wanlong;
Waintraub, Stanley

Publication type:

Article

A Bayesian hierarchical model with spatially varying dispersion for reference-free cell type deconvolution in spatial transcriptomics.

Published in:

Statistical Theory & Related Fields, 2025, v. 9, n. 2, p. 178, doi. 10.1080/24754269.2025.2495651

By:

Li, Xuan;
Tang, Yincai;
Ming, Jingsi;
Shi, Xingjie

Publication type:

Article

Transcriptome Analysis Reveals a Two-Gene Signature Links to Motor Progression and Alterations of Immune Cells in Parkinson's Disease.

Published in:

Journal of Parkinson's Disease, 2023, v. 13, n. 1, p. 25, doi. 10.3233/JPD-223454

By:

Li, Weimin;
Shen, Jiaqi;
Wu, Hao;
Lin, Lishan;
Liu, Yanmei;
Pei, Zhong;
Liu, Ganqiang

Publication type:

Article

Reclassifying NOBOX variants in primary ovarian insufficiency cases with a corrected gene model and a novel quantitative framework.

Published in:

Human Reproduction, 2025, v. 40, n. 6, p. 1220, doi. 10.1093/humrep/deaf058

By:

Veitia, Reiner A;
Cowles, Jamie D;
Caburet, Sandrine

Publication type:

Article

Plasma Transcriptome Profile Associated with Chronic Kidney Disease Progression.

Published in:

American Journal of Nephrology, 2025, v. 56, n. 3, p. 296, doi. 10.1159/000542707

By:

Srivastava, Anvesha;
Maienschein-Cline, Mark;
Amdur, Richard L.;
Susztak, Katalin;
Kopp, Jeffrey Burnett;
Cao, Haiming;
Shankaranarayanan, Divya;
Abdalla, Yoosif;
Pabalan, Ana;
Gombert, Michael;
Raj, Dominic

Publication type:

Article

A workflow for human health hazard evaluation using transcriptomic data and Key Characteristics-based gene sets.

Published in:

Toxicological Sciences, 2025, v. 205, n. 2, p. 310, doi. 10.1093/toxsci/kfaf036

By:

Tsai, Han-Hsuan D;
Oware, King D;
Wright, Fred A;
Chiu, Weihsueh A;
Rusyn, Ivan

Publication type:

Article

Single‐cell transcriptomes reveal spatiotemporal heat stress response in pearl millet leaves.

Published in:

New Phytologist, 2025, v. 247, n. 2, p. 637, doi. 10.1111/nph.70232

By:

Jin, Yarong;
Yan, Haidong;
Zhu, Xin;
Yang, Yuchen;
Jia, Jiyuan;
Sun, Min;
Najeeb, Atiqa;
Luo, Jinchan;
Wang, Xiaoshan;
He, Min;
Xu, Bin;
Li, Xiang;
Luo, Ziliang;
Mao, Chunli;
Huang, Dejun;
Nie, Gang;
Feng, Guangyan;
Xie, Zheni;
Zhang, Xinquan;
Luo, Lin

Publication type:

Article

Comparative transcriptomics in B73-teosinte near-isogenic maize lines reveals key defense signaling and phytoalexins in response to Cercospora zeina infection.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1580016

By:

Sun, Xiaomeng;
Zhang, Ruiyu;
Wang, Zongping;
Zhang, Haotian;
Wen, Hairun;
Zhang, Junli;
Yu, Naibin;
Wang, Zhe;
Tai, Huanhuan;
Yang, Qin

Publication type:

Article

DSCT: a novel deep-learning framework for rapid and accurate spatial transcriptomic cell typing.

Published in:

National Science Review, 2025, v. 12, n. 5, p. 1, doi. 10.1093/nsr/nwaf030

By:

Xu, Yiheng;
Yu, Bin;
Chen, Xuan;
Peng, Aibing;
Tao, Quyuan;
He, Youzhe;
Wang, Yueming;
Li, Xiao-Ming

Publication type:

Article

Sequence Diversity and Encoded Enzymatic Differences of Monocistronic L1 ORF2 mRNA Variants in the Aged Normal and Alzheimer's Disease Brain.

Published in:

Journal of Neuroscience, 2025, v. 45, n. 25, p. 1, doi. 10.1523/JNEUROSCI.2298-24.2025

By:

Nicodemus, Juliet;
Liu, Christine S.;
Ransom, Linnea;
Tan, Valerie;
Romanow, William;
Jimenez, Natalia;
Chun, Jerold

Publication type:

Article

Altered cerebral functional activity and its associated genetic profiles underlying chronic insomnia disorder before and after treatment.

Published in:

World Journal of Biological Psychiatry, 2025, v. 26, n. 5, p. 211, doi. 10.1080/15622975.2025.2503938

By:

Zhang, Leyi;
Guo, Zhiguo;
Han, Yiding;
Yan, Haohao;
Lv, Dongsheng;
Yao, Ping;
Zhao, Jingping;
Chen, Lixia;
Guo, Wenbin

Publication type:

Article

Cytomegalic parvalbumin neurons in fetal cases of hemimegalencephaly.

Published in:

Epilepsia (Series 4), 2025, v. 66, n. 6, p. 2099, doi. 10.1111/epi.18325

By:

Gelot, Antoinette‐Bernabe;
Draia‐Nicolau, Tangra Ondina;
Mathieu, Rémi;
Silvagnoli, Lucas;
Watrin, Françoise;
Cardoso, Carlos;
Manent, Jean‐Bernard;
de Chevigny, Antoine;
Represa, Alfonso

Publication type:

Article

Microbiome in cancer metastasis: biological insights and emerging spatial omics methods.

Published in:

Frontiers in Cellular & Infection Microbiology, 2025, p. 1, doi. 10.3389/fcimb.2025.1559870

By:

Meyers, Marianne;
Stoffels, Charlotte B. A.;
Frache, Gilles;
Letellier, Elisabeth;
Feucherolles, Maureen

Publication type:

Article

Single-nucleus transcriptomics of wing sexual dimorphism and scale cell specialization in sulphur butterflies.

Published in:

PLoS Biology, 2025, v. 23, n. 6, p. 1, doi. 10.1371/journal.pbio.3003233

By:

Loh, Ling S.;
Hanly, Joseph J.;
Carter, Alexander;
Chatterjee, Martik;
Tsimba, Martina;
Shodja, Donya N.;
Livraghi, Luca;
Day, Christopher R.;
Reed, Robert D.;
McMillan, W. Owen;
Wray, Gregory A.;
Martin, Arnaud

Publication type:

Article

In‐frame insertions of SOX10 are highly enriched and characterize a distinct transcriptomic profile in gastrointestinal schwannomas.

Published in:

Journal of Pathology, 2025, v. 266, n. 3, p. 268, doi. 10.1002/path.6426

By:

Lee, Pei‐Hang;
Huang, Shih‐Chiang;
Lee, Jen‐Chieh;
Li, Sung‐Chou;
Tsai, Jen‐Wei;
Chang, Yi‐Ming;
Kao, Yu‐Chien;
Fan, Wen‐Lang;
Chang, Ching‐Di;
Chen, Hui‐Chun;
Li, Chih‐Hao;
Hu, Chia‐Fa;
Liu, Ting‐Ting;
Wu, Pao‐Shu;
Nam, Mann‐Hua;
Yu, Shih‐Chen;
Wang, Jui‐Chu;
Huang, Hsuan‐Ying

Publication type:

Article

Comparative transcriptomics of salivary basal cell adenoma and adenocarcinoma sustain linear neoplastic evolution and intertumor heterogeneity: classification and biological implications.

Published in:

Journal of Pathology, 2025, v. 266, n. 3, p. 258, doi. 10.1002/path.6424

By:

Mitani, Yoshitsugu;
Al‐Maghrabi, Haneen;
Karpinets, Tatiana V;
Relator, Raissa T;
Hilder, Lauren;
Chen, Irene Y;
Goepfert, Ryan P;
Bell, Diana;
Zhang, Jianhua;
Ferrarotto, Renata;
El‐Naggar, Adel K

Publication type:

Article

The Polarization of Macrophages Regulated by KCNG3 via the Activation of ASK1 Mediated by Potassium Ion Efflux.

Published in:

Cell Biology International, 2025, v. 49, n. 7, p. 810, doi. 10.1002/cbin.70022

By:

Zhang, Shuting;
Xin, Yanlong;
Yang, Yu;
Zhang, Yan;
Geng, Jing

Publication type:

Article

OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf279

By:

McLaughlin, James;
Lagrimas, Josh;
Iqbal, Haider;
Parkinson, Helen;
Harmse, Henriette

Publication type:

Article

TissueViewer: a web-based multiplexed image viewer Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf246

By:

IJzendoorn, David Gerardus Pieter van;
Matusiak, Magdalena;
West, Rob;
van de Rijn, Matt

Publication type:

Article

m2ST: dual multi-scale graph clustering for spatially resolved transcriptomics Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf221

By:

Zhang, Wei;
Zhang, Ziqi;
Yang, Hailong;
Zhang, Te;
Jiang, Shu;
Qiao, Ning;
Deng, Zhaohong;
Pan, Xiaoyong;
Shen, Hong-Bin;
Yu, Dong-Jun;
Wang, Shitong

Publication type:

Article

De novo clustering of large long-read transcriptome datasets with isONclust3 Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf207

By:

Petri, Alexander J;
Sahlin, Kristoffer

Publication type:

Article

ROICellTrack: a deep learning framework for integrating cellular imaging modalities in subcellular spatial transcriptomic profiling of tumor tissues Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf152

By:

Song, Xiaofei;
Yu, Xiaoqing;
Moran-Segura, Carlos M;
Xu, Hongzhi;
Li, Tingyi;
Davis, Joshua T;
Vosoughi, Aram;
Grass, G Daniel;
Li, Roger;
Wang, Xuefeng

Publication type:

Article

Candida albicans : a historical overview of investigations into an important human pathogen.

Published in:

Canadian Journal of Microbiology, 2025, v. 71, p. 1, doi. 10.1139/cjm-2025-0036

By:

Shrivastava, Manjari;
Whiteway, Malcolm

Publication type:

Article

A multi-type programmed cell death gene signature predicts survival and reveals therapeutic targets in osteosarcoma.

Published in:

Discover Oncology, 2025, v. 16, n. 1, p. 1, doi. 10.1007/s12672-025-02944-y

By:

Wu, Chunyang

Publication type:

Article

RIDDEN: Data-driven inference of receptor activity from transcriptomic data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013188

By:

Barsi, Szilvia;
Varga, Eszter;
Dimitrov, Daniel;
Saez-Rodriguez, Julio;
Hunyady, László;
Szalai, Bence

Publication type:

Article

Leucocalocybe mongolica Fungus Enhances Rice Growth by Reshaping Root Metabolism, and Hormone-Associated Pathways.

Published in:

Rice (19398425), 2025, v. 18, n. 1, p. 1, doi. 10.1186/s12284-025-00813-4

By:

Duan, Mingzheng;
Tao, Ming;
Wei, Fuhan;
Liu, Honggao;
Han, Sirui;
Feng, Jieming;
Ran, Qiuyue;
Duan, Xiande;
He, Zhifang;
Yang, Shunqiang;
Rao, Muhammad Junaid

Publication type:

Article

Transcriptomic and metabonomic profiling unveils the mechanism of Tartary buckwheat and kiwi co-fermentation products in hyperlipidemia treatment.

Published in:

Frontiers in Pharmacology, 2025, p. 1, doi. 10.3389/fphar.2025.1572593

By:

Guohui, Nan;
Tingna, Xie;
Qinghui, He;
Hongchun, Yu;
Jing, Peng;
Shiyin, Jiang;
Li, Li;
Huawei, Yuan;
Daijing, Wei;
Qi, Wu

Publication type:

Article

Correction to: "GnRH—Gonadotropes Interactions Revealed by Pituitary Single-cell Transcriptomics in Zebrafish" Open Access.

Published in:: Endocrinology, 2025, v. 166, n. 7, p. 1, doi. 10.1210/endocr/bqaf098
Publication type:: Article

Sparse deconvolution of cell type medleys in spatial transcriptomics.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013169

By:

Erdogan, Nuray Sogunmez;
Eroglu, Deniz

Publication type:

Article

Construction and validation of a chemokine-related gene signature associated with prognosis, clinical significance, and immune microenvironment characteristics in cervical cancer.

Published in:

Discover Oncology, 2025, v. 16, n. 1, p. 1, doi. 10.1007/s12672-025-02973-7

By:

Huang, Tianjiao;
Cao, Renshuang;
Gao, Cong;
Luo, Jie;
Zhou, Zhiyu;
Ma, Kun

Publication type:

Article

Screening and validation of key microRNAs regulating muscle development in Hanper sheep.

Published in:

PLoS ONE, 2025, v. 20, n. 6, p. 1, doi. 10.1371/journal.pone.0325054

By:

Zhi, Yunxia;
Hu, Boxin;
Tian, Shujun;
Bai, Ying;
Chen, Xiaoyong

Publication type:

Article

From spots to cells: Cell segmentation in spatial transcriptomics with BOMS.

Published in:

PLoS ONE, 2025, v. 20, n. 6, p. 1, doi. 10.1371/journal.pone.0311458

By:

Kamboj, Ocima;
Park, Jeongbin;
Stegle, Oliver;
Hamprecht, Fred A.

Publication type:

Article

基于比较转录组学揭示青海湖裸鲤耐盐碱关键基因和潜在作用机制.

Published in:

Journal of Dalian Ocean University, 2025, v. 40, n. 2, p. 223, doi. 10.16535/j.cnki.dlhyxb.2024-200

By:

严青春;
李长忠;
王丽楠;
杨颖;
李昭楠;
梁天秀;
金文杰;
陈艳霞

Publication type:

Article

Genomic signatures associated with recurrent scale loss in cyprinid fish.

Published in:

Integrative Zoology, 2025, v. 20, n. 3, p. 535, doi. 10.1111/1749-4877.12851

By:

DING, Yongli;
ZOU, Ming;
GUO, Baocheng

Publication type:

Article

Revealing VCAN as a Potential Common Diagnostic Biomarker of Renal Tubules and Glomerulus in Diabetic Kidney Disease Based on Machine Learning, Single-Cell Transcriptome Analysis and Mendelian Randomization.

Published in:

Diabetes & Metabolism Journal, 2025, v. 49, n. 3, p. 407, doi. 10.4093/dmj.2024.0233

By:

Li Jiang;
Jie Jian;
Xulin Sai;
Xiai Wu

Publication type:

Article

Combining Transcriptome and Hormone-Targeted Metabolome Analyses to Dissect the Regulatory Mechanisms Underlying Wheat Peduncle Elongation.

Published in:

Plants (2223-7747), 2025, v. 14, n. 11, p. 1611, doi. 10.3390/plants14111611

By:

Hao, Huifang;
Chen, Lu;
Cao, Zhiyang;
Jin, Xiujuan;
Guo, Feng;
Shi, Zerui;
Yang, Jinwen;
Lu, Juan;
Sun, Daizhen

Publication type:

Article

Multi-Omics Joint Analysis of Molecular Mechanisms of Compound Essential Oils Inhibiting Spoilage Yeast in Paocai.

Published in:

Foods, 2025, v. 14, n. 11, p. 1998, doi. 10.3390/foods14111998

By:

Wu, Xinyi;
Zhu, Zhiyan;
Tian, Hao;
Liu, Li;
Li, Xuerui;
Pan, Jun;
Hu, Yifan;
Niu, Zhirui;
Wang, Hanmo;
Liu, Xiuwei

Publication type:

Article

The Mechanism of Seed Priming with Abscisic Acid for Enhancing Cuticle Deposition Under Drought Stress: Phenotypic and Transcriptomic Insights.

Published in:

Agriculture; Basel, 2025, v. 15, n. 11, p. 1124, doi. 10.3390/agriculture15111124

By:

Yao, Luhua;
Li, Sennan;
Zhou, Nana;
Guo, Yanjun

Publication type:

Article

Unveiling the Therapeutic Potential of Baicalin in Intervertebral Disc Degeneration: Integrative Bulk and Single-Cell Transcriptome Analysis with Experimental Validation of PANoptosis Inhibition.

Published in:

Journal of Inflammation Research, 2025, v. 18, p. 6963, doi. 10.2147/JIR.S519179

By:

Wang, Xiaoqiang;
Gao, Silong;
Zhou, Daqian;
Cai, Weiye;
Lv, Jiale;
Wei, Zhangchao;
Song, Chao;
Shan, Xubin;
Liu, Zongchao

Publication type:

Article

Muscone Ameliorates High-Altitude Hypoxia Gastrointestinal Stress via Modulation of Lactobacillus Murinus and Mitochondrial Metabolism.

Published in:

Journal of Inflammation Research, 2025, v. 18, p. 6683, doi. 10.2147/JIR.S521991

By:

Zeng, Jin;
Yin, Xinxin;
Pang, Yidan;
Zhang, Jinglei;
Xie, Changpeng;
Chen, Siai;
Zhang, Liping;
Li, Xuejing;
Pan, YuanMing;
An, Juan

Publication type:

Article

Transcriptomic analysis reveals shared deregulated neutrophil responses in COVID-19 and idiopathic pulmonary fibrosis.

Published in:

Respiratory Research, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12931-025-03180-2

By:

Divolis, Georgios;
Synolaki, Evgenia;
Tringidou, Rodoula;
Tzouvelekis, Argyrios;
Boumpas, Dimitrios T.;
Skendros, Panagiotis;
Galani, Ioanna-Evdokia

Publication type:

Article

scDown: A Pipeline for Single-Cell RNA-Seq Downstream Analysis.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 11, p. 5297, doi. 10.3390/ijms26115297

By:

Sun, Liang;
Ma, Qianyi;
Cai, Chunhui;
Labaf, Maryam;
Jain, Ashish;
Dias, Caroline;
Rockowitz, Shira;
Sliz, Piotr

Publication type:

Article

Integrated Transcriptomic and Metabolomic Analysis Reveals the Regulation Network of CEBiP in Rice Defense Against Magnaporthe oryzae.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 11, p. 5194, doi. 10.3390/ijms26115194

By:

Zheng, Qi;
Bao, Jiandong;
Li, Lin;
Shen, Zifang;
Wang, Jiaoyu;
Daskalov, Asen;
Zhu, Xueming;
Lin, Fucheng

Publication type:

Article

Evolutionary Transcriptomics of Cancer Development.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 11, p. 5041, doi. 10.3390/ijms26115041

By:

Ivanov, Roman;
Afonnikov, Dmitry;
Matushkin, Yury;
Lashin, Sergey

Publication type:

Article

RNA Through Time: From the Origin of Life to Therapeutic Frontiers in Transcriptomics and Epitranscriptional Medicine.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 11, p. 4964, doi. 10.3390/ijms26114964

By:

Martínez-Campos, Cecilia;
Lanz-Mendoza, Humberto;
Cime-Castillo, Jorge A.;
Peralta-Zaragoza, Óscar;
Madrid-Marina, Vicente

Publication type:

Article

Short- and Long-Term Endothelial Inflammation Have Distinct Effects and Overlap with Signatures of Cellular Senescence.

Published in:

Cells (2073-4409), 2025, v. 14, n. 11, p. 806, doi. 10.3390/cells14110806

By:

Belakova, Barbora;
Basílio, José;
Campos-Medina, Manuel;
Sommer, Anna F. P.;
Gielecińska, Adrianna;
Resch, Ulrike;
Schmid, Johannes A.

Publication type:

Article

A Case‐Driven Multi‐Omics Analysis for Longitudinal Ibrutinib Response Evaluation of Patients With Chronic Lymphocytic Leukemia.

Published in:

European Journal of Haematology, 2025, v. 114, n. 6, p. 973, doi. 10.1111/ejh.14397

By:

Veyhe, Sólja Remisdóttir;
Hansen, Marcus Høy;
Cédile, Oriane;
Møller, Michael Boe;
Nielsen, Mie Kiszka;
Thomassen, Mads;
Juul‐Jensen, Karen;
Frederiksen, Henrik;
Dybkær, Karen;
Nyvold, Charlotte Guldborg

Publication type:

Article