Publications by authors named "Fidel Ramirez"

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Cross-disease integration of single-cell RNA sequencing data from lung myeloid cells reveals TAM signature in model.
Catarina Pinto, Jakub Widawski, Sophie Zahalka, Barbara Thaler, Linda C Schuster

Oncoimmunology· December 2025

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Common and rare variant analyses reveal genetic factors underlying idiopathic pulmonary fibrosis and its shared aetiology with severe COVID-19.
Athanasios Kousathanas, Christopher A Odhams, James Cook, Yao Hu, Stephan Klee, Fidel Ramirez

EBioMedicine· December 2025

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JUNB O-GlcNAcylation-Mediated Promoter Accessibility of Metabolic Genes Modulates Distinct Epithelial Lineage in Pulmonary Fibrosis.
Marie-Therese Bammert, Meshal Ansari, Leoni Haag, Zuhdi Ahmad, Victoria Schröder, Fidel Ramirez

Adv Sci (Weinh)· February 2025

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Spatial transcriptomic characterization of pathologic niches in IPF.
Christoph H Mayr, Diana Santacruz, Sebastian Jarosch, Marina Bleck, John Dalton, Fidel Ramirez

Sci Adv· August 2024

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Transcriptomic and Proteomic Changes Driving Pulmonary Fibrosis Resolution in Young and Old Mice.
Jelena Weckerle, Christoph H Mayr, Katrin Fundel-Clemens, Bärbel Lämmle, Lukasz Boryn, Fidel Ramirez

Am J Respir Cell Mol Biol· October 2023

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Antifibrotic Drug Nintedanib Inhibits CSF1R to Promote IL-4-associated Tissue Repair Macrophages.
Carolin K Watson, Daniela Schloesser, Katrin Fundel-Clemens, Carmen Lerner, Svenja Gabler, Fidel Ramirez

Am J Respir Cell Mol Biol· April 2023

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miR449 Protects Airway Regeneration by Controlling AURKA/HDAC6-Mediated Ciliary Disassembly.
Merit Wildung, Christian Herr, Dietmar Riedel, Cornelia Wiedwald, Alena Moiseenko

Int J Mol Sci· July 2022

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CD206+ tumor-associated macrophages cross-present tumor antigen and drive antitumor immunity.
Madhura Modak, Ann-Kathrin Mattes, Daniela Reiss, Wioletta Skronska-Wasek, Rebecca Langlois, Fidel Ramirez

JCI Insight· June 2022

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Automation enables high-throughput and reproducible single-cell transcriptomics library preparation.
David Kind, Praveen Baskaran, Fidel Ramirez, Martin Giner, Michael Hayes

SLAS Technol· April 2022

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pyGenomeTracks: reproducible plots for multivariate genomic datasets.
Lucille Lopez-Delisle, Leily Rabbani, Joachim Wolff, Vivek Bhardwaj, Rolf Backofen

Bioinformatics· April 2021

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A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.
Mehmet Tekman, Bérénice Batut, Alexander Ostrovsky, Christophe Antoniewski, Dave Clements, Fidel Ramirez

Gigascience· October 2020

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Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling.
Gina Renschler, Gautier Richard, Claudia Isabelle Keller Valsecchi, Sarah Toscano, Laura Arrigoni

Genes Dev· November 2019

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Monoclonal Antibodies Against the Capsular Polysaccharides A, C, Y, W, and X of Neisseria meningitidis: A Platform for the Quality Control of Meningococcal Vaccines.
Elizabeth González, Fátima Reyes, Oscar Otero, Frank Camacho, Maribel Cuello

Methods Mol Biol· September 2019

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CAPRI enables comparison of evolutionarily conserved RNA interacting regions.
Amol Panhale, Florian M Richter, Fidel Ramírez, Maria Shvedunova, Thomas Manke

Nat Commun· June 2019

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RELACS nuclei barcoding enables high-throughput ChIP-seq.
Laura Arrigoni, Hoor Al-Hasani, Fidel Ramírez, Ilaria Panzeri, Devon Patrick Ryan

Commun Biol· December 2018

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A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains.
Abdulrahman Salhab, Karl Nordström, Gilles Gasparoni, Kathrin Kattler, Peter Ebert, Fidel Ramirez

Genome Biol· September 2018

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Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.
Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler

Nucleic Acids Res· July 2018

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GOATOOLS: A Python library for Gene Ontology analyses.
D V Klopfenstein, Liangsheng Zhang, Brent S Pedersen, Fidel Ramírez, Alex Warwick Vesztrocy

Sci Rep· July 2018

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Community-Driven Data Analysis Training for Biology.
Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj

Cell Syst· June 2018

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High-resolution TADs reveal DNA sequences underlying genome organization in flies.
Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A Grüning

Nat Commun· January 2018

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deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert

Nucleic Acids Res· July 2016

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Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation.
Sarantis Chlamydas, Herbert Holz, Maria Samata, Tomasz Chelmicki, Plamen Georgiev

Nat Struct Mol Biol· June 2016

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High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila.
Fidel Ramírez, Thomas Lingg, Sarah Toscano, Kin Chung Lam, Plamen Georgiev

Mol Cell· October 2015

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A novel monoclonal antibody to Neisseria meningitidis serogroup X capsular polysaccharide and its potential use in quantitation of meningococcal vaccines.
Fátima Reyes, Oscar Otero, Frank Camacho, Nevis Amin, Fidel Ramírez

Biologicals· November 2014

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Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells.
Aydan Bulut-Karslioglu, Inti A De La Rosa-Velázquez, Fidel Ramirez, Maxim Barenboim, Megumi Onishi-Seebacher

Mol Cell· July 2014

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