Integrated Connectedness for a New Representation of Biology

Project Information

ICON-BIO

Grant agreement ID: 770827

DOI 10.3030/770827

EC signature date 13 March 2018

Start date 1 April 2018

End date 30 April 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 2 000 000,00

EU contribution € 2 000 000,00

Coordinated by

BARCELONA SUPERCOMPUTING CENTER CENTRO NACIONAL DE SUPERCOMPUTACION
Spain

Publications

Peer reviewed articles (20)

Towards a data-integrated cell

Author(s): Noël Malod-Dognin, Julia Petschnigg, Sam F. L. Windels, Janez Povh, Harry Hemingway, Robin Ketteler, Nataša Pržulj
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-08797-8

Identifying cellular cancer mechanisms through pathway-driven data integration

Author(s): Sam F L Windels; Noël Malod-Dognin; Nataša Pržulj
Published in: instname:Universitat Politècnica de Catalunya (UPC), Issue 1, 2022, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac493

Four algorithms to solve symmetric multi-type non-negative matrix tri-factorization problem

Author(s): R. Hribar, T. Hrga, G. Papa, G. Petelin, J. Povh, N. Pržulj, V. Vukašinović
Published in: Journal of Global Optimization, Issue 82, 2021, ISSN 0925-5001
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10898-021-01074-3

Integrative Data Analytic Framework to Enhance Cancer Precision Medicine

Author(s): Thomas Gaudelet, Noël Malod-Dognin,Nataša Pržulj
Published in: Network and Systems Medicine, Issue 4, 2021, ISSN 2690-5949
Publisher: Mary Ann Liebert, Inc., publishers
DOI: 10.1089/nsm.2020.0015

Linear functional organization of the omic embedding space

Author(s): A Xenos, N Malod-Dognin, S Milinković, N Pržulj
Published in: Bioinfomatics, Issue 37, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab487

A phenotype driven integrative framework uncovers molecular mechanisms of a rare hereditary thrombophilia

Author(s): Noël Malod-Dognin ,Gaia Ceddia ,Maja Gvozdenov,Branko Tomić,Sofija Dunjić Manevski,Valentina Djordjević,Nataša Pržulj
Published in: PLoS ONE, 2023, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0284084

Unveiling new disease, pathway, and gene associations via multi-scale neural network

Author(s): Thomas Gaudelet, Noël Malod-Dognin, Jon Sánchez-Valle, Vera Pancaldi, Alfonso Valencia, Nataša Pržulj
Published in: PLOS ONE, Issue 15/4, 2020, Page(s) e0231059, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0231059

Graphlet eigencentralities capture novel central roles of genes in pathways

Author(s): Sam F. L Windels, Noël Malod-Dognin, Nataša Pržulj
Published in: PLOS ONE, Issue 17 (1), 2022, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0261676

Antiproliferative activity and mode of action analysis of novel amino and amido substituted phenantrene and naphtho[2,1-b]thiophene derivatives

Author(s): Perin, Nataša; Rep, Valentina; Sović, Irena; Juričić, Štefica; Selgrad, Danijel; Klobučar, Marko; Pržulj, Nataša; Gupta, Chhedi Lal; Malod-Dognin, Noël; Pavelić, Sandra Kraljević; Hranjec, Marijana
Published in: European Journal of Medicinal Chemistry, Issue 1, 2019, ISSN 0223-5234
Publisher: Elsevier BV
DOI: 10.1016/j.ejmech.2019.111833

Chromatin network markers of leukemia

Author(s): N Malod-Dognin, V Pancaldi, A Valencia, N Pržulj
Published in: Bioinformatics, Issue 36/Supplement_1, 2020, Page(s) i455-i463, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa445

Integrated Data Analysis Uncovers New COVID-19 Related Genes and Potential Drug Re-Purposing Candidates

Author(s): Alexandros Xenos; Noël Malod-Dognin; Carme Zambrana; Nataša Pržulj
Published in: International Journal of Molecular Sciences; Volume 24; Issue 2; Pages: 1431, Issue 1, 2023, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24021431

Probabilistic graphlets capture biological function in probabilistic molecular networks

Author(s): Sergio Doria-Belenguer, Markus K. Youssef, René Böttcher, Noël Malod-Dognin, Nataša Pržulj
Published in: Bioinformatics, Issue 36, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa812

Critical Review on Zeolite Clinoptilolite Safety and Medical Applications in vivo

Author(s): Sandra Kraljević Pavelić, Jasmina Simović Medica, Darko Gumbarević, Ana Filošević, Nataša Pržulj, Krešimir Pavelić
Published in: Frontiers in Pharmacology, Issue 9, 2018, ISSN 1663-9812
Publisher: Frontiers Media S.A.
DOI: 10.3389/fphar.2018.01350

Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets

Author(s): D A Salazar, N Pržulj, C F Valencia
Published in: Bioinformatics, Issue 37 (24), 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab579

Higher-order molecular organization as a source of biological function

Author(s): Thomas Gaudelet, Noël Malod-Dognin, Nataša Pržulj
Published in: Bioinformatics, Issue 34/17, 2018, Page(s) i944-i953, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty570

Big Data to Knowledge Analytics Reveals the Zika Virus Epidemic as Only One of Multiple Factors Contributing to a Year-Over-Year 28-Fold Increase in Microcephaly Incidence.

Author(s): Myriam Patricia Cifuentes; Clara Mercedes Suarez; Ricardo Cifuentes; Noel Malod-Dognin; Sam Windels; Jose Fernando Valderrama; Paul D. Juarez; R. Burciaga Valdez; Cynthia Colen; Charles Phillips; Aramandla Ramesh; Wansoo Im; Maureen Lichtveld; Charles Mouton; Nataša Pržulj; Darryl B. Hood
Published in: International Journal of Environmental Research and Public Health, 2022, ISSN 1660-4601
Publisher: MDPI
DOI: 10.3390/ijerph19159051

Classification in biological networks with hypergraphlet kernels

Author(s): Jose Lugo-Martinez, Daniel Zeiberg, Thomas Gaudelet, Noël Malod-Dognin, Natasa Przulj, Predrag Radivojac
Published in: Bioinformatics, Issue 37 (7), 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa768

Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates

Author(s): Carme Zambrana, Alexandros Xenos, René Böttcher, Noël Malod-Dognin, Nataša Pržulj
Published in: Scientific Reports, Issue 11, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-98289-x

Functional geometry of protein interactomes

Author(s): Noël Malod-Dognin, Nataša Pržulj
Published in: Bioinformatics, Issue Volume 35, Issue 19, 2019, Page(s) 3727–3734, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz146

Graphlet Laplacians for topology-function and topology-disease relationships

Author(s): Sam F L Windels, Noël Malod-Dognin, Nataša Pržulj
Published in: Bioinformatics, Issue 35/24, 2019, Page(s) 5226-5234, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz455