Integrated Connectedness for a New Representation of Biology

Project Information

ICON-BIO

Grant agreement ID: 770827

DOI

10.3030/770827

Project closed

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

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (30)

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

Biological databases in the age of generative artificial intelligence

Author(s): Mihai Pop, Teresa K Attwood, Judith A Blake, Philip E Bourne, Ana Conesa, Terry Gaasterland, Lawrence Hunter, Carl Kingsford, Oliver Kohlbacher, Thomas Lengauer, Scott Markel, Yves Moreau, William S Noble, Christine Orengo, B F Francis Ouellette, Laxmi Parida, Natasa Przulj, Teresa M Przytycka, Shoba Ranganathan, Russell Schwartz, Alfonso Valencia, Tandy Warnow
Published in: Bioinformatics Advances, 2025, ISSN 2635-0041
Publisher: Oxford University Press (OUP)

The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell

Author(s): Sergio Doria-Belenguer, Alexandros Xenos, Gaia Ceddia, Noël Malod-Dognin, Nataša Pržulj
Published in: Bioinformatics Advances, Issue 4, 2024, ISSN 2635-0041
Publisher: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbae075

Simplicity within biological complexity

Author(s): Nataša Pržulj, Noël Malod-Dognin
Published in: Bioinformatics Advances, Issue 5, 2025, ISSN 2635-0041
Publisher: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbae164

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 functional analysis of omic network embedding spaces reveals key altered functions in cancer

Author(s): Sergio Doria-Belenguer, Alexandros Xenos, Gaia Ceddia, Noël Malod-Dognin, Nataša Pržulj
Published in: Bioinformatics, Issue 39, 2023, ISSN 1367-4811
Publisher: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btad281

Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson’s disease

Author(s): Katarina Mihajlović, Gaia Ceddia, Noël Malod-Dognin, Gabriela Novak, Dimitrios Kyriakis, Alexander Skupin, Nataša Pržulj
Published in: Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson’s disease, 2025, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1101/2023.12.12.570554

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

Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks

Author(s): Daniel Tello Velasco, Sam F. L. Windels, Mikhail Rotkevich, Noël Malod-Dognin, Nataša Pržulj
Published in: Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks, 2023, ISSN 1367-4811
Publisher: Oxford Academic
DOI: 10.1101/2023.10.27.564419

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

Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing

Author(s): Andreas Maier, Michael Hartung, Mark Abovsky, Klaudia Adamowicz, Gary D Bader, Sylvie Baier, David B Blumenthal, Jing Chen, Maria L Elkjaer, Carlos Garcia-Hernandez, Mohamed Helmy, Markus Hoffmann, Igor Jurisica, Max Kotlyar, Olga Lazareva, Hagai Levi, Markus List, Sebastian Lobentanzer, Joseph Loscalzo, Noel Malod-Dognin, Quirin Manz, Julian Matschinske, Miles Mee, Mhaned Oubounyt, Chiara Past
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) W481-W488, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae388

MONFIT: multi-omics factorization-based integration of time-series data sheds light on Parkinson’s disease

Author(s): Katarina Mihajlović, Noël Malod-Dognin, Corrado Ameli, Alexander Skupin, Nataša Pržulj
Published in: NAR Molecular Medicine, Issue 1, 2025, ISSN 2976-856X
Publisher: Oxford University Press (OUP)
DOI: 10.1093/narmme/ugae012

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

A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

Author(s): Vincent Gureghian, Hailee Herbst, Ines Kozar, Katarina Mihajlovic, Noël Malod-Dognin, Gaia Ceddia, Cristian Angeli, Christiane Margue, Tijana Randic, Demetra Philippidou, Milène Tetsi Nomigni, Ahmed Hemedan, Leon-Charles Tranchevent, Joseph Longworth, Mark Bauer, Apurva Badkas, Anthoula Gaigneaux, Arnaud Muller, Marek Ostaszewski, Fabrice Tolle, Nataša Pržulj, Stephanie Kreis
Published in: Cancer Gene Therapy, Issue 30, 2023, Page(s) 1330-1345, ISSN 0929-1903
Publisher: Nature Publishing Group
DOI: 10.1038/s41417-023-00640-z

Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data

Author(s): Z. Li, S. Windels, N. Malod-Dognin, S. M. Weinberg, M. L. Marazita, S. Walsh, M. D. Shriver, D. W. Fardo, P. Claes, N. Przulj, and K. Van Ste
Published in: Bioinformatics, 2025, ISSN 1367-4811
Publisher: Oxford University Press (OUP)

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

Monographic books (1)

Analyzing Network Data in Biology and Medicine

Author(s): Natasa Przulj
Published in: 2019
Publisher: Cambridge University Press
DOI: 10.1017/9781108377706

Other (3)

iTissue

Author(s): Carme Zambrana, Noel Malod-Dognin, Natasa Przulj
Published in: 2025
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.06.04.657816

Simplifying complex machine learning by linearly separable network embedding spaces

Author(s): A. Xenos, N. Malod-Dognin, and N. Przulj
Published in: arXiv, 2024
Publisher: Cornell University
DOI: 10.48550/arxiv.2410.01865

Graphlets correct for the topological information missed by random walks

Author(s): S Windels, N Malod-Dognin, and N. Przulj
Published in: arXiv, 2024
Publisher: Cornell University
DOI: 10.48550/arxiv.2405.14194