Papers matching “transcriptome annotation” 90
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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 -
Advances and challenges in cell–cell communication inference: a comprehensive review of tools, resources, and future directions2025 Briefings in Bioinformatics review Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Giulia Cesaro, James Shiniti Nagai, Gnoato Nicolò, Alice Chiodi, Gaia Tussardi, Vanessa Klöker, +6 more
48citations -
MPN with multiple driver clones show distinct patterns of therapy response and progression - “MPN double driver”2025 Blood conference-abstract Medicine Myeloproliferative Neoplasms: Diagnosis and Treatment Open access
Kirsi Marjaana Manz, Tina M. Schnoeder, Francesca Palandri, Filippo Branzanti, Heike Luise Pahl, Martin Grießhammer, +20 more
3citations -
CEACAM6 Promotes Lung MetastasisviaEnhancing Proliferation, Migration and Suppressing Apoptosis of Prostate Cancer Cells2024 Cancer Genomics & Proteomics article Medicine Prostate Cancer Treatment and Research Open access
Alireza Azizi Saraji, Janine Stegmann-Frehse, Duan Kang, Anne Offermann, GEVORG SHAGHOYAN, Danny David Jonigk, +4 more
3citations -
Refining the transcriptional landscapes for distinct clades of virulent phages infecting pseudomonas aeruginosa2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Environmental Science Bacteriophages and microbial interactions Open access
Leena Putzeys, Laura Wicke, Maarten Boon, Vera van Noort, Jörg Vogel, Rob Lavigne
1citations -
D18-09 The Multiorgan Multicenter Spatial Transcriptomics Atlas Reveals Layered Granuloma Architecture and Cellular Programs Driving Sarcoidosis2026 American Journal of Respiratory and Critical Care Medicine article Medicine Sarcoidosis and Beryllium Toxicity Research
Jannik Ruwisch, Leonard Christian, Stephan Traidl, J Dietrich, J-C Kamp, Janis Casper, +19 more
0citations -
Analysis of pre-symptomatic Drosophila models for ALS and SMA reveals convergent impact on functional protein complexes linked to neuro-muscular degeneration2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Amyotrophic Lateral Sclerosis Research Open access
Marina L. García‐Vaquero, Barbara Flix, Marcelo Henrique Neves Pereira, Lucile Palin, Tânia Monteiro Marques, Francisco Rodrigues Pinto, +4 more
0citations -
Image-guided alignment of consecutive multi-modal tissue slides2026 Cell Reports Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Benedetta Manzato, Claudio Novella-Rausell, Gangqi Wang, Nina Ogrinc, Rosalie G. J. Rietjens, Marleen E Jacobs, +3 more
0citations -
EchoGO validation bundle: frozen materials for cross-species consensus enrichment in transcriptomic interpretation2026 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Camilo Escobar-Sierra, Felix Langschied, Angelina Miller, Pedro A. Inostroza
0citations -
Identification of Hypoxia Induced Metabolism Associated Genes in Pulmonary Hypertension2021 Frontiers in Pharmacology article Medicine Pulmonary Hypertension Research and Treatments Open access
Yangyang He, Xinmei Xie, Hongda Zhang, Jue Ye, Selin Gencer, Emiel P. C. van der Vorst, +6 more
30citations -
Explainable multi-view framework for dissecting intercellular signaling from highly multiplexed spatial data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jovan Tanevski, Ricardo O. Ramirez Flores, Attila Gábor, Denis Schapiro, Julio Sáez-Rodríguez
28citations -
The shifting lipidomic landscape of blood monocytes and neutrophils during pneumonia2024 JCI Insight article Biochemistry, Genetics and Molecular Biology Sphingolipid Metabolism and Signaling Open access
Alex R. Schuurman, Osoul Chouchane, Joe M. Butler, Hessel Peters Sengers, Sebastiaan C M Joosten, Xanthe Brands, +16 more
11citations -
Chromosome-Level Genome Assembly of the Cape Cliff Lizard (Hemicordylus capensis)2023 Genome Biology and Evolution article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Henrique G. Leitão, Genevieve Diedericks, Chris Broeckhoven, Simon Baeckens, Hannes Svardal
7citations -
Roles for the long non-coding RNA Pax6os1 / PAX6-AS1 in pancreatic beta cell identity and function2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Pancreatic function and diabetes Open access
Livia López–Noriega, Rebecca Callingham, Aida Martínez-Sánchez, Sameena Nawaz, Grazia Pizza, Nejc Haberman, +13 more
6citations