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Scientific publications

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Elias Farr, Daniel Dimitrov, Denes Turei, Christina Schmidt, Sebastian Lobentanzer, Aurelien Dugourd, Julio Saez-Rodriguez

MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions

https://doi.org/10.1101/2023.12.30.573715

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Ricardo Omar Ramirez Flores, Jan David Lanzer, Daniel Dimitrov, Britta Velten, Julio Saez-Rodriguez

Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease

https://doi.org/10.7554/eLife.93161

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Sonnal Lohia, Agnieszka Latosinska, Jerome Zoidakis, Manousos Makridakis, Harald Mischak, Griet Glorieux, Antonia Vlahou and Vera Jankowski

Glycosylation Analysis of Urinary Peptidome Highlights IGF2 Glycopeptides in Association with CKD

Int. J. Mol. Sci. 2023, 24(6), 5402; https://doi.org/10.3390/ijms24065402

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Mara Lauriola, Ricard Farré, Pieter Evenepoel, Saskia Adriana Overbeek and Björn Meijers

Food-Derived Uremic Toxins in Chronic Kidney Disease

Toxins 2023, 15(2), 116; https://doi.org/10.3390/toxins15020116

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Shruti Bhargava, Erik Merckelbach, Heidi Noels, Ashima Vohra and Joachim Jankowski

Homeostasis in the Gut Microbiota in Chronic Kidney Disease

Toxins 2022, 14(10), 648; https://doi.org/10.3390/toxins14100648

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Avra Melina Madella, Jeroen Van Bergenhenegouwen, Johan Garssen, Rosalinde Masereeuw, Saskia Adriana Overbeek

Microbial-Derived Tryptophan Catabolites, Kidney Disease and Gut Inflammation

PMID: 36136583 PMCID: PMC9505404 DOI: 10.3390/toxins14090645

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Chiara Favero,Laura Giordano,Silvia Maria Mihaila,Rosalinde Masereeuw,Alberto Ortiz and Maria Dolores Sanchez-Niño

Postbiotics and Kidney Disease

Toxins 2022, 14(9), 623; https://doi.org/10.3390/toxins14090623

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Daniel Dimitrov, Dénes Türei, Martin Garrido-Rodriguez, Paul L. Burmedi, James S. Nagai, Charlotte Boys, Ricardo O. Ramirez Flores, Hyojin Kim, Bence Szalai, Ivan G. Costa, Alberto Valdeolivas, Aurélien Dugourd & Julio Saez-Rodriguez 

Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

Nature Communications volume 13, Article number: 3224 (2022)

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Sonnal Lohia, Antonia Vlahou and Jerome Zoidakis

Microbiome in Chronic Kidney Disease (CKD): An Omics Perspective

Toxins 2022, 14, 176. DOI: 10.3390/toxins14030176

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Eva Harlacher, Julia Wollenhaupt, Constance C. F. M. J. Baaten, and Heidi Noels

Impact of Uremic Toxins on Endothelial Dysfunction in Chronic Kidney Disease: A Systematic Review

Int. J. Mol. Sci. 2022, 23(1), 531;

https://doi.org/10.3390/ijms23010531

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Annapaola Coppola, Carmela Vigorito, Patrizia Lombari, Yuselys García Martínez, Margherita Borriello, Francesco Trepiccione, Diego Ingrosso and Alessandra F. Perna

Uremic Toxin Lanthionine Induces Endothelial Cell Mineralization In Vitro

Biomedicines 2022, 10, 444.

https://doi.org/10.3390/biomedicines10020444

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Emmanouil Mavrogeorgis, Harald Mischak, Agnieszka Latosinska, Antonia Vlahou, Joost P. Schanstra, Justyna Siwy, Vera Jankowski, Joachim Beige and Joachim Jankowski 

Collagen-Derived Peptides in CKD: A Link to Fibrosis

Toxins 2022, 14, 10 10.3390/toxins14010010

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Emmanouil Mavrogeorgis, Harald Mischak, Agnieszka Latosinska, Justyna Siwy, Vera Jankowski and Joachim Jankowski

Reproducibility Evaluation of Urinary Peptide Detection Using CE-MS

Molecules 2021 , 26(23), 7260; https://doi.org/10.3390/molecules26237260

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Mieke Steenbeke, Sophie Valkenburg, Tessa Gryp, Wim Van Biesen, Joris R. Delanghe, Marijn M. Speeckaert and Griet Glorieux

Gut Microbiota and Their Derived Metabolites, a Search for Potential Targets to Limit Accumulation of Protein-Bound Uremic Toxins in Chronic Kidney Disease

Toxins 2021, 13, 809. https://doi.org/10.3390/toxins13110809

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Daniel Dimitrov, Dénes Türei, Charlotte Boys, James S. Nagai, Ricardo O. Ramirez Flores, Hyojin Kim, Bence Szalai, Ivan G. Costa, Aurélien Dugourd, Alberto Valdeolivas, Julio Saez-Rodriguez

Comparison of Resources and Methods to infer Cell-Cell Communication from Single-cell RNA Data

bioRxiv. 2021 doi: https://doi.org/10.1101/2021.05.21.445160

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Roman David Bülow, Daniel Dimitrov, Peter Boor & Julio Saez-Rodriguez 

How will artificial intelligence and bioinformatics change our understanding of IgA Nephropathy in the next decade?

Semin Immunopathol 43, 739–752 (2021). https://doi.org/10.1007/s00281-021-00847-y

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Chiara Favero, Sol Carriazo, Leticia Cuarental, Raul Fernandez-Prado, Elena Gomá-Garcés, Maria Vanessa Perez-Gomez, Alberto Ortiz, Beatriz Fernandez-Fernandez and Maria Dolores Sanchez-Niño

Phosphate, Microbiota and CKD

Nutrients. 2021 Apr 13;13(4):1273. doi: 10.3390/nu13041273. PMID: 33924419; PMCID: PMC8070653.

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Laura Giordano, Silvia Maria Mihaila, Hossein Eslami Amirabadi and Rosalinde Masereeuw

Microphysiological Systems to Recapitulate the Gut-Kidney Axis.

Trends in Biotechnology. 39.10.1016/j.tibtech.2020.12.001.

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