List of works - Nataša Pržulj

2-Tree probe interval graphs have a large obstruction set

A framework for FPGA acceleration of large graph problems: Graphlet counting case study

A global genetic interaction network maps a wiring diagram of cellular function

scientific article

An integrative approach to modeling biological networks

scientific article published on 25 March 2010

Anti-nicastrin monoclonal antibodies elicit pleiotropic anti-tumour pharmacological effects in invasive breast cancer cells

scientific article

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

scientific article published on 06 November 2019

Author Correction: Towards a data-integrated cell

scientific article published on 21 May 2019

Biological function through network topology: a survey of the human diseasome

scientific article published on 8 September 2012

Biological network comparison using graphlet degree distribution

scientific article published in January 2007

Biological network comparison using graphlet degree distribution

Bridging the gaps in systems biology

scientific article published on 13 April 2014

C-GRAAL: common-neighbors-based global GRAph ALignment of biological networks

scientific article published on 10 January 2012

Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy

scientific article

Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis

scholarly article

Classification in biological networks with hypergraphlet kernels

scientific article published on 04 September 2020

Complementarity of network and sequence information in homologous proteins

scientific article published on 25 March 2010

Critical Review on Zeolite Clinoptilolite Safety and Medical Applications

article

Discovering disease-disease associations by fusing systems-level molecular data

scientific article

Dominating biological networks

scientific article

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

scientific article published in 2024

Erratum to: Anti-nicastrin monoclonal antibodies elicit pleiotropic anti-tumour pharmacological effects in invasive breast cancer cells.

scientific article published on 28 October 2014

Fitting a geometric graph to a protein-protein interaction network

scientific article published on 14 March 2008

From Topology to Phenotype in Protein–Protein Interaction Networks

Functional geometry of protein interactomes

scientific article published on 01 October 2019

Functional topology in a network of protein interactions

scientific article published in February 2004

Fuse: multiple network alignment via data fusion

scientific article

GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity.

scientific article

Genetic mapping of a leaf rust resistance gene in the former Yugoslavian barley landrace MBR1012

article

Geometric Local Structure in Biological Networks

Geometric de-noising of protein-protein interaction networks

scientific article (publication date: August 2009)

Geometric evolutionary dynamics of protein interaction networks.

scientific article published in January 2010

GraphCrunch 2: Software tool for network modeling, alignment and clustering

scientific article

GraphCrunch: a tool for large network analyses

scientific article

Graphlet Laplacians for topology-function and topology-disease relationships

scientific article published on 01 December 2019

Graphlet eigencentralities capture novel central roles of genes in pathways

scientific article published on 25 January 2022

Graphlet-based Characterization of Directed Networks

scientific article published on 13 October 2016

Graphlet-based measures are suitable for biological network comparison

scientific article published on 23 January 2013

Hereditary dominating pair graphs

High-throughput mapping of a dynamic signaling network in mammalian cells

scientific article (publication date: 11 March 2005)

Higher-order molecular organization as a source of biological function

scientific article published on 01 September 2018

Integration of molecular network data reconstructs Gene Ontology

scientific article

Integrative methods for analyzing big data in precision medicine

scientific article

Integrative network alignment reveals large regions of global network similarity in yeast and human

scientific article published on 16 March 2011

Introduction to the Special Issue on Biological Networks

L-GRAAL: Lagrangian graphlet-based network aligner

scientific article published on 28 February 2015

Learning the structure of protein-protein interaction networks.

scientific article published in January 2009

Methods for biological data integration: perspectives and challenges

scientific article

Modeling interactome: scale-free or geometric?

scientific article published on 29 July 2004

Modelling protein-protein interaction networks via a stickiness index

scientific article

Modelling the yeast interactome

scientific article published on 04 March 2014

NETWORK ANALYSIS. Network analytics in the age of big data

scientific article

Network topology reveals key cardiovascular disease genes

scientific article (publication date: 2013)

Network wiring of pleiotropic kinases yields insight into protective role of diabetes on aneurysm

scientific article

Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution

scientific article

Omics Data Complementarity Underlines Functional Cross-Communication in Yeast

scientific article published on 10 June 2017

Optimal network alignment with graphlet degree vectors

scientific article published on 30 June 2010

Optimized null model for protein structure networks.

scientific article

PATIENT-SPECIFIC DATA FUSION FOR CANCER STRATIFICATION AND PERSONALISED TREATMENT.

scientific article

Predicting disease associations via biological network analysis.

scientific article

Probabilistic graphlets capture biological function in probabilistic molecular networks

scientific article published on 01 December 2020

Proper evaluation of alignment-free network comparison methods

scientific article published on 24 March 2015

Protein complex prediction via cost-based clustering

scientific article published on 4 June 2004

Protein complex prediction with RNSC.

scientific article published in January 2012

Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets

scientific article

Protein‐protein interactions: Making sense of networks via graph‐theoretic modeling ⬇️

scientific article published on February 1, 2011

Random Graph Models and Their Application to Protein-Protein Interaction Networks

Rebuttal to the Letter to the Editor in response to the paper: proper evaluation of alignment-free network comparison methods.

scientific article published on 10 January 2017

Revealing the hidden language of complex networks.

scientific article

Structure of brain functional networks

scientific article published in January 2009

Survey of network-based approaches to research of cardiovascular diseases

scientific article published on 20 March 2014

Systematic protein-protein interaction mapping for clinically relevant human GPCRs

scientific article published on 15 March 2017

Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data

scientific article (publication date: 6 March 2010)

The Core Diseasome

scientific article published in October 2012

The integrated disease network

scientific article

The role of genes co-amplified with nicastrin in breast invasive carcinoma.

scientific article published on 13 December 2013

The topology of the growing human interactome data

scientific article

Topological Characteristics of Molecular Networks

Topological network alignment uncovers biological function and phylogeny

scientific article published on 17 March 2010

Topology-function conservation in protein-protein interaction networks

scientific article published on 20 January 2015

Towards a data-integrated cell

scientific article published on 18 February 2019

Uncovering biological network function via graphlet degree signatures.

scientific article published on 14 April 2008

Unified Alignment of Protein-Protein Interaction Networks

scientific article

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

scientific article published on 06 April 2020

List of works by Nataša Pržulj

2-Tree probe interval graphs have a large obstruction set

A framework for FPGA acceleration of large graph problems: Graphlet counting case study

A global genetic interaction network maps a wiring diagram of cellular function

An integrative approach to modeling biological networks

Anti-nicastrin monoclonal antibodies elicit pleiotropic anti-tumour pharmacological effects in invasive breast cancer cells

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

Author Correction: Towards a data-integrated cell

Biological function through network topology: a survey of the human diseasome

Biological network comparison using graphlet degree distribution

Biological network comparison using graphlet degree distribution

Bridging the gaps in systems biology

C-GRAAL: common-neighbors-based global GRAph ALignment of biological networks

Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy

Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis

Classification in biological networks with hypergraphlet kernels

Complementarity of network and sequence information in homologous proteins

Critical Review on Zeolite Clinoptilolite Safety and Medical Applications

Discovering disease-disease associations by fusing systems-level molecular data

Dominating biological networks

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

Erratum to: Anti-nicastrin monoclonal antibodies elicit pleiotropic anti-tumour pharmacological effects in invasive breast cancer cells.

Fitting a geometric graph to a protein-protein interaction network

From Topology to Phenotype in Protein–Protein Interaction Networks

Functional geometry of protein interactomes

Functional topology in a network of protein interactions

Fuse: multiple network alignment via data fusion

GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity.

Genetic mapping of a leaf rust resistance gene in the former Yugoslavian barley landrace MBR1012

Geometric Local Structure in Biological Networks

Geometric de-noising of protein-protein interaction networks

Geometric evolutionary dynamics of protein interaction networks.

GraphCrunch 2: Software tool for network modeling, alignment and clustering

GraphCrunch: a tool for large network analyses

Graphlet Laplacians for topology-function and topology-disease relationships

Graphlet eigencentralities capture novel central roles of genes in pathways

Graphlet-based Characterization of Directed Networks

Graphlet-based measures are suitable for biological network comparison

Hereditary dominating pair graphs

High-throughput mapping of a dynamic signaling network in mammalian cells

Higher-order molecular organization as a source of biological function

Integration of molecular network data reconstructs Gene Ontology

Integrative methods for analyzing big data in precision medicine

Integrative network alignment reveals large regions of global network similarity in yeast and human

Introduction to the Special Issue on Biological Networks

L-GRAAL: Lagrangian graphlet-based network aligner

Learning the structure of protein-protein interaction networks.

Methods for biological data integration: perspectives and challenges

Modeling interactome: scale-free or geometric?

Modelling protein-protein interaction networks via a stickiness index

Modelling the yeast interactome

NETWORK ANALYSIS. Network analytics in the age of big data

Network topology reveals key cardiovascular disease genes

Network wiring of pleiotropic kinases yields insight into protective role of diabetes on aneurysm

Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution

Omics Data Complementarity Underlines Functional Cross-Communication in Yeast

Optimal network alignment with graphlet degree vectors

Optimized null model for protein structure networks.

PATIENT-SPECIFIC DATA FUSION FOR CANCER STRATIFICATION AND PERSONALISED TREATMENT.

Predicting disease associations via biological network analysis.

Probabilistic graphlets capture biological function in probabilistic molecular networks

Proper evaluation of alignment-free network comparison methods

Protein complex prediction via cost-based clustering

Protein complex prediction with RNSC.

Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets

Protein‐protein interactions: Making sense of networks via graph‐theoretic modeling ⬇️

Random Graph Models and Their Application to Protein-Protein Interaction Networks

Rebuttal to the Letter to the Editor in response to the paper: proper evaluation of alignment-free network comparison methods.

Revealing the hidden language of complex networks.

Structure of brain functional networks

Survey of network-based approaches to research of cardiovascular diseases

Systematic protein-protein interaction mapping for clinically relevant human GPCRs

Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data

The Core Diseasome

The integrated disease network

The role of genes co-amplified with nicastrin in breast invasive carcinoma.

The topology of the growing human interactome data

Topological Characteristics of Molecular Networks

Topological network alignment uncovers biological function and phylogeny

Topology-function conservation in protein-protein interaction networks