Integrated Connectedness for a New Representation of Biology

Información del proyecto

ICON-BIO

Identificador del acuerdo de subvención: 770827

DOI

10.3030/770827

Proyecto cerrado

Fecha de la firma de la CE 13 Marzo 2018

Fecha de inicio 1 Abril 2018

Fecha de finalización 30 Abril 2025

Financiado con arreglo a

• EXCELLENT SCIENCE - European Research Council (ERC)

Coste total

€ 2 000 000,00

Aportación de la UE

€ 2 000 000,00

Coordinado por

BARCELONA SUPERCOMPUTING CENTER CENTRO NACIONAL DE SUPERCOMPUTACION
Spain

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Publicaciones

Peer reviewed articles (30)

Towards a data-integrated cell

Autores: Noël Malod-Dognin, Julia Petschnigg, Sam F. L. Windels, Janez Povh, Harry Hemingway, Robin Ketteler, Nataša Pržulj
Publicado en: Nature Communications, Edición 10/1, 2019, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-08797-8

Biological databases in the age of generative artificial intelligence

Autores: 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
Publicado en: Bioinformatics Advances, 2025, ISSN 2635-0041
Editor: Oxford University Press (OUP)

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

Autores: Sergio Doria-Belenguer, Alexandros Xenos, Gaia Ceddia, Noël Malod-Dognin, Nataša Pržulj
Publicado en: Bioinformatics Advances, Edición 4, 2024, ISSN 2635-0041
Editor: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbae075

Simplicity within biological complexity

Autores: Nataša Pržulj, Noël Malod-Dognin
Publicado en: Bioinformatics Advances, Edición 5, 2025, ISSN 2635-0041
Editor: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbae164

Identifying cellular cancer mechanisms through pathway-driven data integration

Autores: Sam F L Windels; Noël Malod-Dognin; Nataša Pržulj
Publicado en: instname:Universitat Politècnica de Catalunya (UPC), Edición 1, 2022, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btac493

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

Autores: R. Hribar, T. Hrga, G. Papa, G. Petelin, J. Povh, N. Pržulj, V. Vukašinović
Publicado en: Journal of Global Optimization, Edición 82, 2021, ISSN 0925-5001
Editor: Kluwer Academic Publishers
DOI: 10.1007/s10898-021-01074-3

Integrative Data Analytic Framework to Enhance Cancer Precision Medicine

Autores: Thomas Gaudelet, Noël Malod-Dognin,Nataša Pržulj
Publicado en: Network and Systems Medicine, Edición 4, 2021, ISSN 2690-5949
Editor: Mary Ann Liebert, Inc., publishers
DOI: 10.1089/nsm.2020.0015

Linear functional organization of the omic embedding space

Autores: A Xenos, N Malod-Dognin, S Milinković, N Pržulj
Publicado en: Bioinfomatics, Edición 37, 2021, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btab487

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

Autores: Sergio Doria-Belenguer, Alexandros Xenos, Gaia Ceddia, Noël Malod-Dognin, Nataša Pržulj
Publicado en: Bioinformatics, Edición 39, 2023, ISSN 1367-4811
Editor: 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

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

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

Autores: Noël Malod-Dognin ,Gaia Ceddia ,Maja Gvozdenov,Branko Tomić,Sofija Dunjić Manevski,Valentina Djordjević,Nataša Pržulj
Publicado en: PLoS ONE, 2023, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0284084

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

Autores: Thomas Gaudelet, Noël Malod-Dognin, Jon Sánchez-Valle, Vera Pancaldi, Alfonso Valencia, Nataša Pržulj
Publicado en: PLOS ONE, Edición 15/4, 2020, Página(s) e0231059, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0231059

Graphlet eigencentralities capture novel central roles of genes in pathways

Autores: Sam F. L Windels, Noël Malod-Dognin, Nataša Pržulj
Publicado en: PLOS ONE, Edición 17 (1), 2022, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0261676

Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks

Autores: Daniel Tello Velasco, Sam F. L. Windels, Mikhail Rotkevich, Noël Malod-Dognin, Nataša Pržulj
Publicado en: Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks, 2023, ISSN 1367-4811
Editor: 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

Autores: 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
Publicado en: European Journal of Medicinal Chemistry, Edición 1, 2019, ISSN 0223-5234
Editor: Elsevier BV
DOI: 10.1016/j.ejmech.2019.111833

Chromatin network markers of leukemia

Autores: N Malod-Dognin, V Pancaldi, A Valencia, N Pržulj
Publicado en: Bioinformatics, Edición 36/Supplement_1, 2020, Página(s) i455-i463, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btaa445

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

Autores: Alexandros Xenos; Noël Malod-Dognin; Carme Zambrana; Nataša Pržulj
Publicado en: International Journal of Molecular Sciences; Volume 24; Edición 2; Pages: 1431, Edición 1, 2023, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24021431

Probabilistic graphlets capture biological function in probabilistic molecular networks

Autores: Sergio Doria-Belenguer, Markus K. Youssef, René Böttcher, Noël Malod-Dognin, Nataša Pržulj
Publicado en: Bioinformatics, Edición 36, 2020, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btaa812

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

Autores: 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
Publicado en: Nucleic Acids Research, Edición 52, 2024, Página(s) W481-W488, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkae388

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

Autores: Katarina Mihajlović, Noël Malod-Dognin, Corrado Ameli, Alexander Skupin, Nataša Pržulj
Publicado en: NAR Molecular Medicine, Edición 1, 2025, ISSN 2976-856X
Editor: Oxford University Press (OUP)
DOI: 10.1093/narmme/ugae012

Critical Review on Zeolite Clinoptilolite Safety and Medical Applications in vivo

Autores: Sandra Kraljević Pavelić, Jasmina Simović Medica, Darko Gumbarević, Ana Filošević, Nataša Pržulj, Krešimir Pavelić
Publicado en: Frontiers in Pharmacology, Edición 9, 2018, ISSN 1663-9812
Editor: Frontiers Media S.A.
DOI: 10.3389/fphar.2018.01350

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

Autores: D A Salazar, N Pržulj, C F Valencia
Publicado en: Bioinformatics, Edición 37 (24), 2021, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btab579

Higher-order molecular organization as a source of biological function

Autores: Thomas Gaudelet, Noël Malod-Dognin, Nataša Pržulj
Publicado en: Bioinformatics, Edición 34/17, 2018, Página(s) i944-i953, ISSN 1367-4803
Editor: 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.

Autores: 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
Publicado en: International Journal of Environmental Research and Public Health, 2022, ISSN 1660-4601
Editor: MDPI
DOI: 10.3390/ijerph19159051

Classification in biological networks with hypergraphlet kernels

Autores: Jose Lugo-Martinez, Daniel Zeiberg, Thomas Gaudelet, Noël Malod-Dognin, Natasa Przulj, Predrag Radivojac
Publicado en: Bioinformatics, Edición 37 (7), 2020, ISSN 1367-4803
Editor: 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

Autores: 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
Publicado en: Cancer Gene Therapy, Edición 30, 2023, Página(s) 1330-1345, ISSN 0929-1903
Editor: 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

Autores: 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
Publicado en: Bioinformatics, 2025, ISSN 1367-4811
Editor: Oxford University Press (OUP)

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

Autores: Carme Zambrana, Alexandros Xenos, René Böttcher, Noël Malod-Dognin, Nataša Pržulj
Publicado en: Scientific Reports, Edición 11, 2021, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-021-98289-x

Functional geometry of protein interactomes

Autores: Noël Malod-Dognin, Nataša Pržulj
Publicado en: Bioinformatics, Edición Volume 35, Edición 19, 2019, Página(s) 3727–3734, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btz146

Graphlet Laplacians for topology-function and topology-disease relationships

Autores: Sam F L Windels, Noël Malod-Dognin, Nataša Pržulj
Publicado en: Bioinformatics, Edición 35/24, 2019, Página(s) 5226-5234, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btz455

Monographic books (1)

Analyzing Network Data in Biology and Medicine

Autores: Natasa Przulj
Publicado en: 2019
Editor: Cambridge University Press
DOI: 10.1017/9781108377706

Other (3)

iTissue

Autores: Carme Zambrana, Noel Malod-Dognin, Natasa Przulj
Publicado en: 2025
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.06.04.657816

Simplifying complex machine learning by linearly separable network embedding spaces

Autores: A. Xenos, N. Malod-Dognin, and N. Przulj
Publicado en: arXiv, 2024
Editor: Cornell University
DOI: 10.48550/arxiv.2410.01865

Graphlets correct for the topological information missed by random walks

Autores: S Windels, N Malod-Dognin, and N. Przulj
Publicado en: arXiv, 2024
Editor: Cornell University
DOI: 10.48550/arxiv.2405.14194