Publications by authors named "Ivan Costa"

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PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories.
Mingbo Cheng, Jitske Jansen, Katharina C Reimer, Vincent P Grande, James S Nagai, Ivan G Costa

Nat Methods· November 2025

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Pathology-oriented multiplexing enables integrative disease mapping.
Malte Kuehl, Yusuke Okabayashi, Milagros N Wong, Lukas Gernhold, Gabriele Gut, Ivan Costa

Nature· August 2025

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CREB regulates Foxp3ST-2 T with enhanced IL-10 production.
Sudheendra Hebbar Subramanyam, Judit Turyne Hriczko, Saskia Schulz, Thomas Look, Tannaz Goodarzi, Ivan Costa

Front Immunol· August 2025

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Inhibiting the alarmin-driven hematopoiesis-stromal cell crosstalk in primary myelofibrosis ameliorates bone marrow fibrosis.
Hélène F E Gleitz, Stijn N R Fuchs, Inge A M Snoeren, Charlotte Boys, James Nagai, Ivan G Costa

Hemasphere· August 2025

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PILOT-GM-VAE: patient-level analysis of single-cell disease atlas with optimal transport of Gaussian mixture variational autoencoders.
Mehdi Joodaki, Mina Shaigan, Samaneh Samiei, James Nagai, Tiago Maié, Ivan G Costa

Brief Bioinform· August 2025

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Deep Learning Reveals Liver MRI Features Associated With PNPLA3 I148M in Steatotic Liver Disease.
Yazhou Chen, Benjamin P M Laevens, Teresa Lemainque, Gustav Anton Müller-Franzes, Tobias Seibel, Ivan G Costa

Liver Int· July 2025

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Severity Classification of Functional Impairment Based on ICF Qualifiers: A New Proposal for Assessing Individuals With Pulmonary Hypertension.
Jonathan Dalavina, Ivan Peres Costa, Etiene FarahTeixeira de Carvalho, Jonathan Luiz Silva, Soraia Micaela Silva

Physiother Res Int· July 2025

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scACCorDiON: a clustering approach for explainable patient level cell-cell communication graph analysis.
James S Nagai, Tiago Maié, Michael T Schaub, Ivan G Costa

Bioinformatics· May 2025

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Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions.
Giulia Cesaro, James Shiniti Nagai, Nicolò Gnoato, Alice Chiodi, Gaia Tussardi, Ivan G Costa

Brief Bioinform· May 2025

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Deciphering the complex clonal heterogeneity of polycythemia vera and the response to interferon alfa.
Milena Kalmer, Martin Grasshoff, Tiago Maié, Kristina Pannen, Marcelo A S Toledo, Ivan G Costa

Blood Adv· April 2025

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Weighted 2D-kernel density estimations provide a new probabilistic measure for epigenetic age.
Juan-Felipe Perez-Correa, Thomas Stiehl, Riccardo E Marioni, Janie Corley, Simon R Cox, Ivan G Costa

Genome Biol· April 2025

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infection accelerates postnatal maturation of the intestinal epithelium.
Stefan Schlößer, Anna-Lena Ullrich, Nastaran Fazel Modares, Matthias A Schmitz, Johannes Schöneich, Ivan G Costa

Proc Natl Acad Sci U S A· January 2025

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A ONECUT1 regulatory, non-coding region in pancreatic development and diabetes.
Sarah Merz, Valérie Senée, Anne Philippi, Franz Oswald, Mina Shaigan, Ivan G Costa

Cell Rep· November 2024

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Cancer-associated fibroblasts reveal aberrant DNA methylation across different types of cancer.
Marco Schmidt, Tiago Maié, Thorsten Cramer, Ivan G Costa, Wolfgang Wagner

Clin Epigenetics· November 2024

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SIngle cell level Genotyping Using scRna Data (SIGURD).
Martin Grasshoff, Milena Kalmer, Nicolas Chatain, Kim Kricheldorf, Angela Maurer, Ivan G Costa

Brief Bioinform· September 2024

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Comparison of the effectiveness of the helmet interface using flow meters versus the mechanical ventilator for non-invasive ventilation in patients with coronavirus disease 2019. Controlled and randomized clinical trial.
Fernanda Dos Reis Ferreira, João Carlos Ferrari Correa, Eduardo Storopoli, Diego Restivo Faria, Karina Cassaro, Ivan Peres Costa

Arch Med Sci· May 2024

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tRigon: an R package and Shiny App for integrative (path-)omics data analysis.
David L Hölscher, Michael Goedertier, Barbara M Klinkhammer, Patrick Droste, Ivan G Costa

BMC Bioinformatics· March 2024

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Lineage tracing reveals transient phenotypic adaptation of tubular cells during acute kidney injury.
Marc Buse, Mingbo Cheng, Vera Jankowski, Michaela Lellig, Viktor Sterzer, Ivan G Costa

iScience· March 2024

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Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT).
Mehdi Joodaki, Mina Shaigan, Victor Parra, Roman D Bülow, Christoph Kuppe, Ivan G Costa

Mol Syst Biol· February 2024

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Proinflammatory phenotype of iPS cell-derived JAK2 V617F megakaryocytes induces fibrosis in 3D in vitro bone marrow niche.
Niclas Flosdorf, Janik Böhnke, Marcelo A S de Toledo, Niklas Lutterbach, Vanesa Gómez Lerma, Ivan G Costa

Stem Cell Reports· February 2024

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Non-canonical Hedgehog signaling mediates profibrotic hematopoiesis-stroma crosstalk in myeloproliferative neoplasms.
Jessica E Pritchard, Juliette E Pearce, Inge A M Snoeren, Stijn N R Fuchs, Katrin Götz, Ivan G Costa

Cell Rep· January 2024

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Enhanced fatty acid oxidation through metformin and baicalin as therapy for COVID-19 and associated inflammatory states in lung and kidney.
Verónica Miguel, Carlos Rey-Serra, Jessica Tituaña, Belén Sirera, Elena Alcalde-Estévez, Ivan G Costa

Redox Biol· December 2023

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Targeted DNA Methylation Analysis Facilitates Leukocyte Counts in Dried Blood Samples.
Wouter H G Hubens, Tiago Maié, Matthis Schnitker, Ledio Bocova, Deepika Puri, Ivan G Costa

Clin Chem· November 2023

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Mapping cardiac remodeling in chronic kidney disease.
Nadine Kaesler, Mingbo Cheng, James Nagai, James O'Sullivan, Fabian Peisker, Ivan Costa

Sci Adv· November 2023

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EphrinA5 regulates cell motility by modulating Snhg15/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter.
Can Bora Yildiz, Tathagata Kundu, Julia Gehrmann, Jannis Koesling, Amin Ravaei, Ivan G Costa

Epigenetics Chromatin· October 2023

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