Integrative Computational Network Biology (ICONBI)

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2025

2024

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

Nucleic Acids Research

A. Maier, M. Hartung, M. Abovsky, K. Adamowicz, G. D. Bader, S. Baier, D. B. Blumenthal, J. Chen, M. L. Elkjaer, C. Garcia-Hernandez, M. Helmy, M. Hoffmann, I. Jurisica, M. Kotlyar, O. Lazareva, H. Levi, M. List, S. Lobentanzer, J. Loscalzo, N. Malod-Dognin, Q. Manz, J. Matschinske, M. Mee, M. Oubounyt, C. Pastrello, A. R. Pico, R. T. Pillich, J. M. Poschenrieder, D. Pratt, N. Pržulj, S. Sadegh, J. Saez-Rodriguez, S. Sarkar, G. Shaked, R. Shamir, N. Trummer, U. Turhan, R-S. Wang, O. Zolotareva, and J. Baumbach
Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson’s disease

Scientific Reports

K. Mihajlovic, G. Ceddia, N. Malod-Dognin, G. Novak, D. Kyriakis, A. Skupin, and N. Pržulj

2023

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

Bioinformatics

S. Doria-Belenguer, A. Xenos, G. Ceddia, N. Malod-Dognin, and N. Pržulj
A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

Cancer Gene Therapy

V. Gureghian, H. Herbst, I. Kozar, K. Mihajlovic, N. Malod-Dognin, G. Ceddia, C. Angeli, C. Margue, T. Randic, D. Philippidou, M. Tetsi Nomigni, A. Hemedan, L-C. Tranchevent, J. Longworth, M. Bauer, A. Badkas, A. Gaigneaux, A. Muller, M. Ostaszewski, F. Tolle, N. Pržulj, and S. Kreis
Integrated Data Analysis Uncovers New COVID-19 Related Genes and Potential Drug Re-Purposing Candidates

International Journal of Molecular Sciences

A. Xenos, N. Malod-Dognin, C. Zambrana, and N. Pržulj
A phenotype driven integrative framework uncovers molecular mechanisms of a rare hereditary thrombophilia

PLOS ONE

N. Malod-Dognin, G. Ceddia, M. Gvozdenov, B. Tomić, S. Dunjić Manevski, V. Djordjević, and N. Pržulj

2022

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

International Journal of Environmental Research and Public Health

M. PatriciaCifuentes, C. Mercedes Suarez, R. Cifuentes, N. Malod-Dognin, S. Windels, J. Fernando Valderrama, P. D. Juarez, B. R. Valdez, C. Colen, C. Phillips, A. Ramesh, W. Im, M. Lichtveld, C. Mouton, N. Pržulj, and D. B. Hood
Identifying cellular cancer mechanisms through pathway-driven data integration

Bioinformatics

S. F. L. Windels, N. Malod-Dognin, and N. Pržulj
Identifying cellular cancer mechanisms through pathway-driven data integration

Identifying cellular cancer mechanisms through pathway-driven data integration

S. F. L. Windels, N. Malod-Dognin, and N. Pržulj
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

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

M. PatriciaCifuentes, C. Mercedes Suarez, R. Cifuentes, N. Malod-Dognin, S. Windels, J. Fernando Valderrama, P. D. Juarez, B. R. Valdez, C. Colen, C. Phillips, A. Ramesh, W. Im, M. Lichtveld, C. Mouton, N. Pržulj, and D. B. Hood
Four algorithms to solve symmetric multi-type non-negative matrix tri-factorization problem

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

R. Hribar, T. Hrga, G. Papa, G. Petelin, J. Povh, N. Pržulj, and V. Vukašinović
Graphlet eigencentralities capture novel central roles of genes in pathways

PLOS ONE

S. F. L. Windels, N. Malod-Dognin, and N. Pržulj

2021

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

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

C. Zambrana, A. Xenos, R. Böttcher, N. Malod-Dognin, and N. Pržulj
Four algorithms to solve symmetric multi-type non-negative matrix tri-factorization problem

Journal of Global Optimization

R. Hribar, T. Hrga, G. Papa, G. Petelin, J. Povh, N. Pržulj, and V. Vukašinović
Integrative Data Analytic Framework to Enhance Cancer Precision Medicine

Network and Systems Medicine

T. Gaudelet, N. Malod-Dognin, and N. Pržulj
Linear functional organization of the omic embedding space

Bioinformatics

A. Xenos, N. Malod-Dognin, S. Milinković, and N. Pržulj
Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets

Bioinformatics

D. A. Salazar, N. Pržulj, and C. F. Valencia

2020

Classification in biological networks with hypergraphlet kernels

Bioinformatics

J. Lugo-Martinez, D. Zeiberg, T. Gaudelet, N. Malod-Dognin, N. Pržulj, and P. Radivojac
Antiproliferative activity and mode of action analysis of novel amino and amido substituted phenantrene and naphtho[2,1-b]thiophene derivatives

European Journal of Medicinal Chemistry

N. Perin, V. Rep, I. Sović, Š. Juričić, D. Selgrad, M. Klobučar, N. Pržulj, C. Lal Gupta, N. Malod-Dognin, S. Kraljević Pavelić, and M. Hranjec
national initiative in data science for health: an evaluation of the UK Farr Institute

International Journal of Population Data Science

H. Hemingway, R. Lyons, Q. Li, I. Buchan, J. Ainsworth, J. Pell, and A. Morris
Unveiling new disease, pathway, and gene associations via multi-scale neural network

PLOS ONE

T. Gaudelet, N. Malod-Dognin, J. Sánchez-Valle, V. Pancaldi, A. Valencia, and N. Pržulj
Chromatin network markers of leukemia

Bioinformatics

N. Malod-Dognin, V. Pancaldi, A. Valencia, and N. Pržulj
Probabilistic graphlets capture biological function in probabilistic molecular networks

Bioinformatics

S. Doria-Belenguer, M. K. Youssef, R. Böttcher, N. Malod-Dognin, and N. Pržulj

2019

Graphlet Laplacians for topology-function and topology-disease relationships

Bioinformatics

S. F. L. Windels, N. Malod-Dognin, and N. Pržulj
Analyzing Network Data in Biology and MedicineMachine Learning for Data Integration in Cancer Precision Medicine: Matrix Factorization Approaches
Analyzing Network Data in Biology and MedicineFrom Genetic Data to Medicine: From DNA Samples to Disease Risk Prediction in Personalized Genetic Tests
Analyzing Network Data in Biology and Medicine: An Interdisciplinary Textbook for Biological, Medical and Computational Scientists

Analyzing Network Data in Biology and Medicine: An Interdisciplinary Textbook for Biological, Medical and Computational Scientists
Analyzing Network Data in Biology and MedicineIntroduction to Graph and Network Theory
Analyzing Network Data in Biology and MedicineAnalysis of the Signatures of Cancer Stem Cells in Malignant Tumors Using Protein Interactomes and the STRING Database

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