Integrative Computational Network Biology (ICONBI)

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2022

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 spaceAbstractMotivationResultsAvailability and implementationSupplementary information

Bioinformatics

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

Bioinformatics

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

2020

Classification in biological networks with hypergraphlet kernelsAbstractMotivationResultsAvailability and implementationSupplementary information

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 leukemiaAbstractMotivationResultsAvailability and implementationSupplementary information

Bioinformatics

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

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
Analyzing Network Data in Biology and Medicine
Towards a data-integrated cell
Analyzing Network Data in Biology and Medicine. An Interdisciplinary Textbook for Biological, Medical and Computational Scientists

N. Pržulj
Functional geometry of protein interactomes

Bioinformatics

N. Malod-Dognin, and N. Pržulj
Towards a data-integrated cell

Nature Communications

N. Malod-Dognin, J. Petschnigg, S. F. L. Windels, J. Povh, H. Hemmingway, R. Ketteler, and N. Pržulj

2018

Graphlet Laplacians: graphlet-based neighbourhoods highlight topology-function and topology-disease relationships
Precision medicine ― A promising, yet challenging road lies ahead

Current Opinion in Systems Biology

N. Malod-Dognin, J. Petschnigg, and N. Pržulj
Higher-order molecular organization as a source of biological function

Bioinformatics

T. Gaudelet, N. Malod-Dognin, and N. Pržulj
Critical Review on Zeolite Clinoptilolite Safety and Medical Applications in vivo

Frontiers in Pharmacology

S. KraljevićPavelić, J. Simović Medica, D. Gumbarević, A. Filošević, N. Pržulj, and K. Pavelić

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