An in silico-based approach to improve the efficacy and precision of drug REPurpOsing TRIALs for a mechanism-based patient cohort with predominant cerebro-cardiovascular phenotypes

Livrables

Publish an open pre-clinical biobank for pre-clinical animal models related commROCG and other disease phenotypes for both genders

Publish an open preclinical biobank for preclinical animal models related commROCG and other disease phenotypes for both genders

Project brochure and professional templates
Communication and dissemination plan

Software for detection of pathway co-enrichment for extracting of patient(group)-specific pathways also enriched in target sites of effective drugs
Drugome 1.0 network

Drugome 10 network

Diseasome 2.0 network

Publications

Non-canonical chemical feedback self-limits nitric oxide-cyclic GMP signaling in health and disease

Auteurs: Vu Thao-Vi Dao, Mahmoud H. Elbatreek, Martin Deile, Pavel I. Nedvetsky, Andreas Güldner, César Ibarra-Alvarado, Axel Gödecke, Harald H. H. W. Schmidt
Publié dans: Scientific Reports, Numéro 10/1, 2020, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-020-66639-w

On the Clinical Pharmacology of Reactive Oxygen Species

Auteurs: Ana I. Casas, Cristian Nogales, Hermann A. M. Mucke, Alexandra Petraina, Antonio Cuadrado, Ana I. Rojo, Pietro Ghezzi, Vincent Jaquet, Fiona Augsburger, Francois Dufrasne, Jalal Soubhye, Soni Deshwal, Moises Di Sante, Nina Kaludercic, Fabio Di Lisa, Harald H. H. W. Schmidt
Publié dans: Pharmacological Reviews, Numéro 72/4, 2020, Page(s) 801-828, ISSN 0031-6997
Éditeur: American Society for Pharmacology and Experimental Therapeutics
DOI: 10.1124/pr.120.019422

De Novo and Supervised Endophenotyping Using Network-Guided Ensemble Learning

Auteurs: Simon J. Larsen, Harald H.H.W. Schmidt, Jan Baumbach
Publié dans: Systems Medicine, Numéro 3/1, 2020, Page(s) 8-21, ISSN 2573-3370
Éditeur: Network and Systems Medicine
DOI: 10.1089/sysm.2019.0008

Cyclic GMP modulating drugs in cardiovascular diseases: mechanism-based network pharmacology

Auteurs: Alexandra Petraina, Cristian Nogales, Thomas Krahn, Hermann Mucke, Thomas F Lüscher, Rodolphe Fischmeister, David A Kass, John C Burnett, Jr, Adrian J Hobbs, Harald H H W Schmidt
Publié dans: Cardivascular Research, 2021, ISSN 1755-3245
Éditeur: Oxford Academic
DOI: 10.1093/cvr/cvab240

Online bias-aware disease module mining with ROBUST-Web

Auteurs: Suryadipto Sarkar, Marta Lucchetta, Andreas Maier, Mohamed M Abdrabbou, Jan Baumbach, Markus List, Martin H Schaefer, David B Blumenthal
Publié dans: Bioinformatics, Numéro Volume 39, Numéro 6, 2023, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btad345

Un-biased housekeeping gene panel selection for high-validity gene expression analysis

Auteurs: Casas, A.I., Hassan, A.A., Manz, Q. et al.
Publié dans: Sci Rep 12, 12324, 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-15989-8

Re-Addressing Dementia by Network Medicine and Mechanism-Based Molecular Endotypes

Auteurs: Pacheco Pachado, Mayra; Casas, Ana I.; Elbatreek, Mahmoud H.; Nogales, Cristian; Guney, Emre; Espay, Alberto J.; Schmidt, Harald H.H.W.
Publié dans: Journal of Alzheimer's Disease, Numéro vol. 96, no. 1, 2023, Page(s) pp. 47-56, 2023, ISSN 1387-2877
Éditeur: IOS Press
DOI: 10.3233/jad-230694

netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks

Auteurs: Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Muhammad Ahmad Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach, Gary D. Bader
Publié dans: F1000Research, Numéro 9, 2020, Page(s) 1239, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.26429.2

Endothelial reactive oxygen-forming NADPH oxidase 5 is a possible player in diabetic aortic aneurysm but not atherosclerosis

Auteurs: Florence Ho; Anna M. D. Watson; Mahmoud H. Elbatreek; Pamela W. M. Kleikers; Waheed Khan; Karly C. Sourris; Aozhi Dai; Jay Jha; Harald H. H. W. Schmidt; Karin A. M. Jandeleit-Dahm
Publié dans: Sci Rep 12, 11570, 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-15706-5

NOX5-induced uncoupling of endothelial NO synthase is a causal mechanism and theragnostic target of an age-related hypertension endotype

Auteurs: Mahmoud H. Elbatreek, Sepideh Sadegh, Elisa Anastasi, Emre Guney, Cristian Nogales, Tim Kacprowski, Ahmed A. Hassan, Andreas Teubner, Po-Hsun Huang, Chien-Yi Hsu, Paul M. H. Schiffers, Ger M. Janssen, Pamela W. M. Kleikers, Anil Wipat, Jan Baumbach, Jo G. R. De Mey, Harald H. H. W. Schmidt
Publié dans: PLOS Biology, Numéro 18/11, 2020, Page(s) e3000885, ISSN 1545-7885
Éditeur: PLOS Biology
DOI: 10.1371/journal.pbio.3000885

Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing

Auteurs: Sepideh Sadegh, Julian Matschinske, David B. Blumenthal, Gihanna Galindez, Tim Kacprowski, Markus List, Reza Nasirigerdeh, Mhaned Oubounyt, Andreas Pichlmair, Tim Daniel Rose, Marisol Salgado-Albarrán, Julian Späth, Alexey Stukalov, Nina K. Wenke, Kevin Yuan, Josch K. Pauling, Jan Baumbach
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-17189-2

Robust disease module mining via enumeration of diverse prize-collecting Steiner trees

Auteurs: Judith Bernett, Dominik Krupke, Sepideh Sadegh, Jan Baumbach, Sándor P Fekete, Tim Kacprowski, Markus List, David B Blumenthal
Publié dans: Bioinformatics, 2022, ISSN 1460-2059
Éditeur: Oxford Academics

Online in silico validation of disease and gene sets, clusterings, or subnetworks with DIGEST

Auteurs: Klaudia Adamowicz; Andreas Maier; Jan Baumbach; David Blumenthal
Publié dans: Briefings in Bioinformatics, Numéro Volume 23, Numéro 4, 2022, ISSN 1477-4054
Éditeur: Oxford University Press
DOI: 10.14293/s2199-1006.1.sor-.ppp32eqz.v1

Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond

Auteurs: Sepideh Sadegh; James Skelton; Elisa Anastasi; Andreas Maier; Klaudia Adamowicz; Anna Möller; Nils M. Kriege; Jaanika Kronberg; Toomas Haller; Tim Kacprowski; Anil Wipat; Jan Baumbach; David B. Blumenthal
Publié dans: Nat Commun, Numéro 14, 1662, 2023, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-023-37349-4

Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine

Auteurs: Blandine Comte, Jan Baumbach, Arriel Benis, José Basílio, Nataša Debeljak, Åsmund Flobak, Christian Franken, Nissim Harel, Feng He, Martin Kuiper, Juan Albino Méndez Pérez, Estelle Pujos-Guillot, Tadeja Režen, Damjana Rozman, Johannes A. Schmid, Jeanesse Scerri, Paolo Tieri, Kristel Van Steen, Sona Vasudevan, Steven Watterson, Harald H.H.W. Schmidt
Publié dans: Network and Systems Medicine, Numéro 3/1, 2020, Page(s) 67-90, ISSN 2690-5949
Éditeur: Mary Ann Liebert, Inc.
DOI: 10.1089/nsm.2020.0004

Network medicine for disease module identification and drug repurposing with the NeDRex platform

Auteurs: Sepideh Sadegh, James Skelton, Elisa Anastasi, Judith Bernett, David B. Blumenthal, Gihanna Galindez, Marisol Salgado-Albarrán, Olga Lazareva, Keith Flanagan, Simon Cockell, Cristian Nogales, Ana I. Casas, Harald H. H. W. Schmidt, Jan Baumbach, Anil Wipat & Tim Kacprowski
Publié dans: Nature Communications, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-27138-2

Molecular networks in Network Medicine: Development and applications

Auteurs: Edwin K. Silverman, Harald H. H. W. Schmidt, Eleni Anastasiadou, Lucia Altucci, Marco Angelini, Lina Badimon, Jean-Luc Balligand, Giuditta Benincasa, Giovambattista Capasso, Federica Conte, Antonella Di Costanzo, Lorenzo Farina, Giulia Fiscon, Laurent Gatto, Michele Gentili, Joseph Loscalzo, Cinzia Marchese, Claudio Napoli, Paola Paci, Manuela Petti, John Quackenbush, Paolo Tieri, Davide Viggiano,
Publié dans: Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2020, Page(s) e1489, ISSN 1939-5094
Éditeur: John Wiley and Sons Inc.
DOI: 10.1002/wsbm.1489

Isoform-selective NADPH oxidase inhibitor panel for pharmacological target validation

Auteurs: Vu Thao-Vi Dao, Mahmoud H. Elbatreek, Sebastian Altenhöfer, Ana I. Casas, Mayra P. Pachado, Christopher T. Neullens, Ulla G. Knaus, Harald H.H.W. Schmidt
Publié dans: Free Radical Biology and Medicine, Numéro 148, 2020, Page(s) 60-69, ISSN 0891-5849
Éditeur: Elsevier BV
DOI: 10.1016/j.freeradbiomed.2019.12.038

Cancer driver drug interaction explorer

Auteurs: Michael Hartung; Elisa Anastasi; Zeinab M Mamdouh; Cristian Nogales; Harald H H W Schmidt; Jan Baumbach; Olga Zolotareva; Markus List
Publié dans: Nucleic Acids Research, Numéro Volume 50, Numéro W1, 5 July 2022,, 2022, Page(s) Pages W138–W144, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkac384

Thromboinflammation in Brain Ischemia: Recent Updates and Future Perspectives

Auteurs: Simon F. De Meyer, PhD, Friederike Langhauser, PhD, Steffen Haupeltshofer, PhD, Christoph Kleinschnitz, MD, PhD, Ana I. Casas, PhD
Publié dans: Stroke, Numéro 53(5), 2022, Page(s) 1487-1499, ISSN 1524-4628
Éditeur: AHA/ASA Journals
DOI: 10.1161/strokeaha.122.038733

Network pharmacology: curing causal mechanisms instead of treating symptoms.

Auteurs: Nogales C, Mamdouh ZM, List M, Kiel C, Casas AI, and Schmidt HHHW.
Publié dans: Trends in Pharmacological Sciences, Numéro Vol. 43, No. 2, 2021, ISSN 1873-3735
Éditeur: Cell Press - Elsevier Inc.
DOI: 10.1016/j.tips.2021.11.004

NeDRex - an integrative and interactive network medicine platform for drug repurposing

Auteurs: Sadegh S et al.
Publié dans: Drgu Repurposing Central - Science Open, Numéro Conference name: RExPO22 Conference date: 2-3 September, 2022, 2022
Éditeur: Drgu Repurposing Central - Science Open
DOI: 10.14293/s2199-1006.1.sor-.pppy90r8.v1

A plug-and-play solution to bring network exploration and drug repurposing to biomedical web platforms

Auteurs: Maier A et al.
Publié dans: Drug Repurposing Central - Science Open, Numéro Conference name: RExPO22 Conference date: 2-3 September, 2022, 2022
Éditeur: Drug Repurposing Central - Science Open
DOI: 10.14293/s2199-1006.1.sor-.pppvbd8w.v1

Network pharmacology and drug repurposing pave the way for precision oncology

Auteurs: Mamdouh Z et al.
Publié dans: Drug Repurposing Central - Science Open, Numéro Conference name: RExPO22 Conference date: 2-3 September, 2022, 2022
Éditeur: Drug Repurposing Central - Science Open
DOI: 10.14293/s2199-1006.1.sor-.pppdgtlb.v1

Repurposing soluble guanylate cyclase stimulators from one to another isoform within the ROCG signalling module

Auteurs: Alexandra Petraina, Mahmoud H Elbatreek and Christin Elgert et al.
Publié dans: Drug Repurposing Central - ScienceOpen, Numéro Conference name: RExPO22 Conference date: 2-3 September, 2022, 2022
Éditeur: Drug Repurposing Central - ScienceOpen
DOI: 10.14293/s2199-1006.1.sor-.pppux7cj.v1

Nitric Oxide Synthase Inhibitors into the Clinic at Last

Auteurs: Vu Thao-Vi Dao, Mahmoud H. Elbatreek, Thomas Fuchß, Ulrich Grädler, Harald H. H. W. Schmidt, Ajay M. Shah, Alan Wallace, Richard Knowles
Publié dans: Reactive Oxygen Species - Network Pharmacology and Therapeutic Applications, Numéro 264, 2021, Page(s) 169-204, ISBN 978-3-030-68509-6
Éditeur: Springer International Publishing
DOI: 10.1007/164_2020_382

NOX Inhibitors: From Bench to Naxibs to Bedside

Auteurs: Mahmoud H. Elbatreek, Hermann Mucke, Harald H. H. W. Schmidt
Publié dans: Reactive Oxygen Species - Network Pharmacology and Therapeutic Applications, Numéro 264, 2021, Page(s) 145-168, ISBN 978-3-030-68509-6
Éditeur: Springer International Publishing
DOI: 10.1007/164_2020_387

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