Papers matching “transcriptome annotation” 38
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GeneSurfer enables transcriptome-wide exploration and annotation of gene co-expression modules in 3D spatial transcriptomics data2025 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Ximaine R. van der Burg, Louise van der Weerd, Thomas Höllt, +1 more
1citations -
SwarmMAP: swarm learning for decentralized cell type annotation in single cell sequencing data2026 npj Systems Biology and Applications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Oliver Lester Saldanha, Vivien Goepp, Hyojin Kim, Jie Fu Zhu, Rafael Kramann, Sikander Hayat, +1 more
2citations -
Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information2020 Nature Communications article Biochemistry, Genetics and Molecular Biology RNA Research and Splicing Open access
Sebastian Guelfi, Karishma D’Sa, Juan Antonio Botía, Jana Vandrovcová, Regina Hertfelder Reynolds, David Zhang, +94 more
39citations -
Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering2026 Nature Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jieran Sun, Kirti Biharie, Peiying Cai, Niklas Müller‐Bötticher, Paul Kießling, Meghan A. Turner, +47 more
9citations -
Analytical choices drive toxicogenomic potency estimates: a systematic evaluation of transcriptomic points of departure2026 Toxicological Sciences article Biochemistry, Genetics and Molecular Biology Carcinogens and Genotoxicity Assessment Open access
Imke B. Bruns, Dayna R. Schultz, Emmanuel Demuynck, Friedel Dewulf, Ioannis Theologidis, Steven J. Kunnen, +12 more
0citations -
A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery2023 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Claudio Novella-Rausell, Magda Grudniewska, Dorien J.M. Peters, Ahmed Essam Mahfouz
38citations -
Non-target molecular network and putative genes of flavonoid biosynthesis in Erythrina velutina Willd., a Brazilian semiarid native woody plant2022 Frontiers in Plant Science article Biochemistry, Genetics and Molecular Biology Plant Gene Expression Analysis Open access
Daisy Sotero Chacon, Marlon Dias Mariano Santos, Bernardo Bonilauri, Johnatan Vilasboa, Cibele Tesser da Costa, Ivanice Bezerra da Silva, +18 more
12citations -
Short-term test for the toxicogenomic assessment of ecotoxic modes of action in Myriophyllum spicatum2024 The Science of The Total Environment article Environmental Science Environmental Toxicology and Ecotoxicology Open access
Jost Hanfland, Joëlle Lousberg, Benedikt Ringbeck, Christoph Schäfers, Karsten Schlich, Sebastian Eilebrecht
5citations -
The Cell Ontology in the age of single-cell omics2026 eScholarship (California Digital Library) article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat, Caroline Eastwood, Brian D. Aevermann, Alida Avola, +29 more
7citations -
Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages2020 Environmental Microbiology article Environmental Science Bacteriophages and microbial interactions Open access
Cédric Lood, Katarzyna M. Danis-Wlodarczyk, Bob G. Blasdel, Ho Bin Jang, Dieter Vandenheuvel, Yves Briers, +4 more
52citations -
Capsicum Leaves under Stress: Using Multi-Omics Analysis to Detect Abiotic Stress Network of Secondary Metabolism in Two Species2022 Antioxidants article Agricultural and Biological Sciences Plant Stress Responses and Tolerance Open access
Julia J. Reimer, Basel Shaaban, Noud Drummen, Sruthy Sanjeev Ambady, Franziska Genzel, Gernot Poschet, +3 more
26citations -
Utilizing rat kidney gene co-expression networks to enhance safety assessment biomarker identification and human translation2025 iScience article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Steven J. Kunnen, Giulia Callegaro, Jeffrey J. Sutherland, Panuwat Trairatphisan, Hugo W van Kessel, Lukas S. Wijaya, +11 more
7citations -
MASI enables fast model-free standardization and integration of single-cell transcriptomics data2023 Communications Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Rafael Kramann, Rachel Patton McCord, Sikander Hayat
4citations -
Trypanosoma cruzi cell atlas as a single-cell resource for understanding parasite population heterogeneity and differentiation2026 Nature Communications article Medicine Trypanosoma species research and implications Open access
Ross F Laidlaw, Marta García-Sánchez, Juliana da Silva Pacheco, Luciana S. Paradela, Thomas D. Otto, Manu De Rycker
10citations -
Systematic assessment of transcriptomic and phenotypic biological profiling for mechanism-based hazard assessment using target-annotated reference chemicals in renal proximal tubular epithelial cells2026 Archives of Toxicology article Pharmacology, Toxicology and Pharmaceutics Computational Drug Discovery Methods Open access
Hugo W van Kessel, Marlene Wedler, Palle Steen Helmke, Dace Zigure, Stephen Ferguson, Joshua Harrill, +5 more
2citations -
The local cellular response to Human Papillomavirus focuses on basal layer restoration as visualized in situ by specific cellular neighborhoods near infected cells
Roderick C. Slieker, Ziena Abdulrahman, Saskia J A M Santegoets, Mariëtte I.E. van Poelgeest, Marij J.P. Welters, Sjoerd H. van der Burg
0citations -
Systematic comparison of temporal hepatotoxicant-induced gene network responses across 3 liver test systems2026 Toxicological Sciences article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Tamara Y Danilyuk, Marou Schouten, Elsje J Burgers, Barira Islam, Joost B. Beltman, Peter Bouwman, +2 more
0citations -
Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex2020 Molecular Plant article Biochemistry, Genetics and Molecular Biology Plant Gene Expression Analysis Open access
Takayuki Tohge, Federico Scossa, Regina Wendenburg, Pierre Frasse, Ilse Balbo, Mutsumi Watanabe, +10 more
108citations