Publications by authors named "Danny Incarnato"

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Low butyrate concentrations exert anti-inflammatory and high concentrations exert pro-inflammatory effects on macrophages.
Muwei Jiang, Danny Incarnato, Rutger Modderman, Aina Altimira Lazaro, Iris H Jonkers

J Nutr Biochem· October 2025

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Nucleotide dependency analysis of genomic language models detects functional elements.
Pedro Tomaz da Silva, Alexander Karollus, Johannes Hingerl, Gihanna Sta Teresa Galindez, Nils Wagner, Danny Incarnato

Nat Genet· October 2025

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Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.
Ivana Borovská, Chundan Zhang, Sarah-Luisa J Dülk, Edoardo Morandi, Marta F S Cardoso, Danny Incarnato

Nat Biotechnol· July 2025

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Structural and biophysical dissection of RNA conformational ensembles.
Steve L Bonilla, Alisha N Jones, Danny Incarnato

Curr Opin Struct Biol· October 2024

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RNA dynamics from experimental and computational approaches.
Giovanni Bussi, Massimiliano Bonomi, Paraskevi Gkeka, Michael Sattler, Hashim M Al-Hashimi, Danny Incarnato

Structure· September 2024

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SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data.
Niek R Scholten, Dennis Haandrikman, Joshua O Tolhuis, Edoardo Morandi, Danny Incarnato

Nucleic Acids Res· July 2024

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Sequencing-based analysis of RNA structures in living cells with 2A3 via SHAPE-MaP.
Danny Incarnato

Methods Enzymol· November 2023

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Investigating the NRAS 5' UTR as a target for small molecules.
Sumirtha Balaratnam, Zachary R Torrey, David R Calabrese, Michael T Banco, Kamyar Yazdani, Danny Incarnato

Cell Chem Biol· June 2023

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p140Cap inhibits β-Catenin in the breast cancer stem cell compartment instructing a protective anti-tumor immune response.
Vincenzo Salemme, Mauro Vedelago, Alessandro Sarcinella, Federico Moietta, Alessio Piccolantonio, Danny Incarnato

Nat Commun· May 2023

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mA-driven SF3B1 translation control steers splicing to direct genome integrity and leukemogenesis.
Maciej Cieśla, Phuong Cao Thi Ngoc, Sowndarya Muthukumar, Gabriele Todisco, Magdalena Madej, Danny Incarnato

Mol Cell· April 2023

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Probing the dynamic RNA structurome and its functions.
Robert C Spitale, Danny Incarnato

Nat Rev Genet· March 2023

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5-Ethynyluridine: A Bio-orthogonal Uridine Variant for mRNA-Based Therapies and Vaccines.
Sjors Maassen, Britt Coenen, Sara Dulk, Martijn van der Werff, Harry Warner, Danny Incarnato

Chembiochem· March 2023

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DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells.
Andrea Lauria, Guohua Meng, Valentina Proserpio, Stefania Rapelli, Mara Maldotti, Danny Incarnato

Nat Commun· January 2023

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Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data.
Sharon Aviran, Danny Incarnato

J Mol Biol· September 2022

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Specific transcriptional programs differentiate ICOS from CD28 costimulatory signaling in human Naïve CD4 T cells.
Casimiro Luca Gigliotti, Elena Boggio, Francesco Favero, Danny Incarnato, Claudio Santoro

Front Immunol· September 2022

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Hmga2 protein loss alters nuclear envelope and 3D chromatin structure.
Giuseppina Divisato, Andrea M Chiariello, Andrea Esposito, Pietro Zoppoli, Federico Zambelli, Danny Incarnato

BMC Biol· August 2022

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STAT3 induces breast cancer growth via ANGPTL4, MMP13 and STC1 secretion by cancer associated fibroblasts.
Lidia Avalle, Laura Raggi, Emanuele Monteleone, Aurora Savino, Daniele Viavattene, Danny Incarnato

Oncogene· March 2022

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The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7.
Mara Maldotti, Andrea Lauria, Francesca Anselmi, Ivan Molineris, Annalaura Tamburrini, Danny Incarnato

Nucleic Acids Res· March 2022

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SHAPE-guided RNA structure homology search and motif discovery.
Edoardo Morandi, Martijn J van Hemert, Danny Incarnato

Nat Commun· March 2022

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A synthetic RNA-based biosensor for fructose-1,6-bisphosphate that reports glycolytic flux.
Alvaro Darío Ortega, Vakil Takhaveev, Silke Roelie Vedelaar, Yi Long, Neus Mestre-Farràs, Danny Incarnato

Cell Chem Biol· November 2021

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A chemical probe based on the PreQ metabolite enables transcriptome-wide mapping of binding sites.
Sumirtha Balaratnam, Curran Rhodes, Desta Doro Bume, Colleen Connelly, Christopher C Lai, Danny Incarnato

Nat Commun· October 2021

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RNA Framework for Assaying the Structure of RNAs by High-Throughput Sequencing.
Tycho Marinus, Danny Incarnato

Methods Mol Biol· June 2021

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HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness.
Jessica Sy Ho, Federico Di Tullio, Megan Schwarz, Diana Low, Danny Incarnato

Elife· June 2021

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RNA Post-Transcriptional Modification Mapping Data Analysis Using RNA Framework.
Ilaria Manfredonia, Danny Incarnato

Methods Mol Biol· June 2021

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Oncogenic translation directs spliceosome dynamics revealing an integral role for SF3A3 in breast cancer.
Maciej Cieśla, Phuong Cao Thi Ngoc, Eugenia Cordero, Álvaro Sejas Martinez, Mikkel Morsing, Danny Incarnato

Mol Cell· April 2021

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