Scientific publications

Philipp Sven Lars Schäfer, Daniel Dimitrov, Eduardo J. Villablanca & Julio Saez-Rodriguez

Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system

Nature Immunology volume 25, pages405–417 (2024)

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

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

Mayra Alejandra Jaimes Campos, Emmanouil Mavrogeorgis, Agnieszka Latosinska, Susanne Eder, Lukas Buchwinkler, Harald Mischak, Justyna Siwy, Peter Rossing, Gert Mayer, Joachim Jankowski

Urinary peptide analysis to predict the response to blood pressure medication

Nephrology Dialysis Transplantation, gfad223,

https://doi.org/10.1093/ndt/gfad223

Emmanouil Mavrogeorgis, Tianlin He, Harald Mischak, Agnieszka Latosinska, Antonia Vlahou, Joost P Schanstra, Lorenzo Catanese, Kerstin Amann, Tobias B Huber, Joachim Beige, Harald D Rupprecht, Justyna Siwy

Urinary peptidomic liquid biopsy for non-invasive differential diagnosis of chronic kidney disease

Nephrology Dialysis Transplantation, Volume 39, Issue 3, March 2024, Pages 453–462, https://doi.org/10.1093/ndt/gfad200

Sonnal Lohia, Justyna Siwy, Emmanouil Mavrogeorgis, Susanne Eder, Stefanie Thöni, Gert Mayer, Harald Mischak, Antonia Vlahou, Vera Jankowski

Exploratory Study Analyzing the Urinary Peptidome of T2DM Patients Suggests Changes in ECM but Also Inflammatory and Metabolic Pathways Following GLP-1R Agonist Treatment

Int J Mol Sci 2023 Aug 31;24(17):13540. doi: 10.3390/ijms241713540

Sam Hobson, Emmanouil Mavrogeorgis, Tianlin He, Justyna Siwy, Thomas Ebert, Karolina Kublickiene, Peter Stenvinkel and Harald Mischak

Urine Peptidome Analysis Identifies Common and Stage-Specific Markers in Early Versus Advanced CKD

Proteomes 2023, 11(3), 25; https://doi.org/10.3390/proteomes11030025

Emmanouil Mavrogeorgis, Tianlin He, Harald Mischak, Agnieszka Latosinska, Antonia Vlahou, Joost P. Schanstra, Lorenzo Catanese, Kerstin Amann, Tobias B. Huber, Joachim Beige, Harald Rupprecht, Justyna Siwy

Uniform Manifold Approximation and Projection-based Assessment of Chronic Kidney Disease Aetiologies based on Urinary Peptidomics

doi: https://doi.org/10.1101/2023.05.19.23290228

Sonnal Lohia, Justyna Siwy, Emmanouil Mavrogeorgis, Susanne Eder, Stefanie Thoeni, Gert Mayer, Harald Mischak, Antonia Vlahou, Vera Jankowski

Effect of treatment with GLP-1R agonists on the urinary peptidome of T2DM patients

doi: https://doi.org/10.1101/2023.05.03.23289439

Hratch Baghdassarian, Daniel Dimitrov, Erick Armingol, Julio Saez-Rodriguez, Nathan E. Lewis

Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples

Biorxiv https://doi.org/10.1101/2023.04.28.538731

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

Giulia Ilaria Bagarolo, Robert Schierwagen, Wenyi Gu, Vera Jankowski, Josefin Soppert, Emona Barzakova, Federica Cascone, Olaf Tyc, Christiane Kuhl, Heidi Noels, Jonel Trebicka, Joachim Jankowski

Effect of the transjugular intrahepatic portosystemic shunt on peptidomics composition of peripheral plasma

https://doi.org/10.21203/rs.3.rs-2481443/v1

Yuselys García-Martínez, Margherita Borriello, Giovanna Capolongo, Diego Ingrosso and Alessandra F. Perna

The Gut Microbiota in Kidney Transplantation: A Target for Personalized Therapy?

Biology 2023, 12(2), 163;

https://doi.org/10.3390/biology12020163

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

Josefin Soppert, Elisa Fabiana Brandt, Nicole Maria Heussen, Emona Barzakova, Lars Mathias Blank, Lars Kuepfer, Mathias Walter Hornef, Jonel Trebicka, Joachim Jankowski, Marie-Luise Berres, Heidi Noels

Blood Endotoxin Levels as Biomarker of Nonalcoholic Fatty Liver Disease: A Systematic Review and Meta-analysis

DOI:https://doi.org/10.1016/j.cgh.2022.11.030

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

Piotr Bartochowski, Nathalie Gayrard, Stéphanie Bornes, Céline Druart, Angel Argilés, Magali Cordaillat-Simmons and Flore Duranton

Gut–Kidney Axis Investigations in Animal Models of Chronic Kidney Disease

Toxins 2022, 14(9), 626

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

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

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)

Rafael Stroggilos, Maria Frantzi, Jerome Zoidakis, Marika Mokou, Napoleon Moulavasilis, Emmanouil Mavrogeorgis, Anna Melidi, Manousos Makridakis, Konstantinos Stravodimos, Maria G. Roubelakis , Harald Mischak and Antonia Vlahou

Gene Expression Monotonicity across Bladder Cancer Stages Informs on the Molecular Pathogenesis and Identifies a Prognostic Eight-Gene Signature

Cancers 2022, 14(10), 2542;

https://doi.org/10.3390/cancers14102542

Raymond Vanholder, Sanjay K. Nigam, Stéphane Burtey and Griet Glorieux

What If Not All Metabolites from the Uremic Toxin Generating Pathways Are Toxic? A Hypothesis

Toxins 2022, 14(3), 221;

https://doi.org/10.3390/toxins14030221

Sonnal Lohia, Antonia Vlahou and Jerome Zoidakis

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

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

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

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

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

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

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

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

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.

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

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.

Griet Glorieux, Tessa Gryp and Alessandra Perna

Gut-Derived Metabolites and Their Role in Immune Dysfunction in Chronic Kidney Disease.

Toxins 2020, 12(4), 245; https://doi.org/10.3390/toxins12040245