Our Research Publications
We publish high-impact peer-reviewed research in leading journals across computational network biology, multi-omics integration, precision medicine, AI-driven systems biology, and network-based drug discovery.
All publications
2025
iTissue
Cold Spring Harbor Laboratory
·
08 Jun 2025
·
doi:10.1101/2025.06.04.657816
Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data
Bioinformatics
·
22 Mar 2025
·
doi:10.1093/bioinformatics/btaf122
Biological databases in the age of generative artificial intelligence.
Bioinformatics advances
·
20 Mar 2025
·
pmid:40177265
Simplicity within biological complexity
Bioinformatics Advances
·
06 Feb 2025
·
doi:10.1093/bioadv/vbae164
Author Correction, Systematic protein-protein interaction mapping for clinically relevant human GPCRs
Molecular systems biology
·
03 Feb 2025
·
doi:10.1093/bioadv/vbae164
2024
Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks
Bioinformatics
·
01 Nov 2024
·
doi:10.1093/bioinformatics/btae650
Simplifying complex machine learning by linearly separable network embedding spaces
arXiv
·
02 Oct 2024
·
doi:10.48550/arXiv.2410.01865
MONFIT: Multi-omics factorization-based integration of time-series data sheds light on Parkinson's disease
NAR Molecular Medicine
·
24 Sep 2024
·
doi:10.1093/narmme/ugae012
Current and future directions in network biology
Bioinformatics advances
·
14 Aug 2024
·
pmc:PMC11321866
Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing
Nucleic acids research
·
05 Jul 2024
·
pmc:PMC11223884
Bridging the Gap in Precision Medicine: TranSYS Training Programme for Next-Generation Scientists
Frontiers in Medicine
·
24 May 2024
·
doi:10.3389/fmed.2024.1348148
Graphlets correct for the topological information missed by random walks
arXiv
·
23 May 2024
·
doi:10.48550/arXiv.2405.14194
The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell
Bioinformatics advances
·
23 May 2024
·
pmc:PMC11142626
Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson's disease.
Scientific reports
·
14 May 2024
·
pmid:38744869
Graphlet-based higher-order network embeddings: the past, the present and the future
5th Belgrade Bioinformatics Conference
·
01 Jan 2024
·
graphlet-higherorder-2024
"Pan-viral" disease mechanisms unveil the sweet spot for therapeutic intervention
5th Belgrade Bioinformatics Conference
·
01 Jan 2024
·
panviral-2024
Towards a linearly organised embedding space of biological networks
5th Belgrade Bioinformatics Conference
·
01 Jan 2024
·
linear-embedding-2024
PCR-based nanopore sequencing method for characterizing short tandem repeat expansions
5th Belgrade Bioinformatics Conference
·
01 Jan 2024
·
pcr-nanopore-2024
Estimating the dimensionality of omics network embedding space
5th Belgrade Bioinformatics Conference
·
01 Jan 2024
·
dimspace-2024
INMTD: integrative clustering with 2D genotypes and 3D facial images in the presence of confounders
5th Belgrade Bioinformatics Conference
·
01 Jan 2024
·
inmtc-2024
2023
A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma.
Cancer gene therapy
·
07 Jul 2023
·
pmid:37420093
A phenotype driven integrative framework uncovers molecular mechanisms of a rare hereditary thrombophilia.
PloS one
·
25 Apr 2023
·
pmid:37098010
A functional analysis of omic network embedding spaces reveals key altered functions in cancer
Bioinformatics
·
21 Apr 2023
·
doi:10.1093/bioinformatics/btad281
Integrated Data Analysis Uncovers New COVID-19 Related Genes and Potential Drug Re-Purposing Candidates
International Journal of Molecular Sciences
·
11 Jan 2023
·
doi:10.3390/ijms24021431
2022
Identifying cellular cancer mechanisms through pathway-driven data integration
Bioinformatics (Oxford, England)
·
15 Sep 2022
·
pmc:PMC9477533
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
·
25 Jul 2022
·
pmc:PMC9331749
Graphlet eigencentralities capture novel central roles of genes in pathways.
PloS one
·
25 Jan 2022
·
pmid:35077468
2021
Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets.
Bioinformatics (Oxford, England)
·
11 Dec 2021
·
pmid:34375392
Linear functional organization of the omic embedding space
Bioinformatics (Oxford, England)
·
05 Nov 2021
·
pmc:PMC8570782
Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates.
Scientific reports
·
23 Sep 2021
·
pmid:34556735
Classification in biological networks with hypergraphlet kernels.
Bioinformatics (Oxford, England)
·
17 May 2021
·
pmid:32886115
2020
Probabilistic graphlets capture biological function in probabilistic molecular networks.
Bioinformatics (Oxford, England)
·
30 Dec 2020
·
pmid:33381834
Chromatin network markers of leukemia.
Bioinformatics (Oxford, England)
·
01 Jul 2020
·
pmid:32657405
Unveiling new disease, pathway, and gene associations via multi-scale neural network.
PloS one
·
06 Apr 2020
·
pmid:32251458
2019
Graphlet Laplacians for topology-function and topology-disease relationships.
Bioinformatics (Oxford, England)
·
15 Dec 2019
·
pmid:31192358
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
·
06 Nov 2019
·
pmid:31734024
Functional geometry of protein interactomes.
Bioinformatics (Oxford, England)
·
01 Oct 2019
·
pmid:30821317
Author Correction: Towards a data-integrated cell.
Nature communications
·
21 May 2019
·
pmid:31113941
Analyzing Network Data in Biology and Medicine
Cambridge University Press
·
18 Mar 2019
·
doi:10.1017/9781108377706
Towards a data-integrated cell
Nature communications
·
18 Feb 2019
·
pmc:PMC6379402
2018
Critical Review on Zeolite Clinoptilolite Safety and Medical Applications
Frontiers in pharmacology
·
27 Nov 2018
·
pmid:30538633
Higher-order molecular organization as a source of biological function.
Bioinformatics (Oxford, England)
·
01 Sep 2018
·
pmid:30423061
Precision medicine ― A promising, yet challenging road lies ahead
Current Opinion in Systems Biology
·
01 Feb 2018
·
doi:10.1016/j.coisb.2017.10.003
2017
Omics Data Complementarity Underlines Functional Cross-Communication in Yeast.
Journal of integrative bioinformatics
·
10 Jun 2017
·
pmid:28600905
Unified Alignment of Protein-Protein Interaction Networks.
Scientific reports
·
19 Apr 2017
·
pmid:28424527
Rebuttal to the Letter to the Editor in response to the paper: proper evaluation of alignment-free network comparison methods.
Bioinformatics (Oxford, England)
·
01 Apr 2017
·
pmid:28073757
Systematic protein-protein interaction mapping for clinically relevant human GPCRs.
Molecular systems biology
·
15 Mar 2017
·
pmid:28298427
2016
Graphlet-based Characterization of Directed Networks.
Scientific reports
·
13 Oct 2016
·
pmid:27734973
A global genetic interaction network maps a wiring diagram of cellular function.
Science (New York, N.Y.)
·
23 Sep 2016
·
pmid:27708008
NETWORK ANALYSIS. Network analytics in the age of big data.
Science (New York, N.Y.)
·
08 Jul 2016
·
pmid:27387938
Integrative methods for analyzing big data in precision medicine.
Proteomics
·
01 Mar 2016
·
pmid:26677817
PATIENT-SPECIFIC DATA FUSION FOR CANCER STRATIFICATION AND PERSONALISED TREATMENT.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
·
01 Jan 2016
·
pmid:26776197
Computational Methods for Integration of Biological Data
Europeanization and Globalization
·
01 Jan 2016
·
doi:10.1007/978-3-319-39349-0_8
2015
Fuse: multiple network alignment via data fusion.
Bioinformatics (Oxford, England)
·
14 Dec 2015
·
pmid:26668003
Methods for biological data integration: perspectives and challenges.
Journal of the Royal Society, Interface
·
06 Nov 2015
·
pmid:26490630
Proper evaluation of alignment-free network comparison methods.
Bioinformatics (Oxford, England)
·
24 Mar 2015
·
pmid:25810431
L-GRAAL: Lagrangian graphlet-based network aligner.
Bioinformatics (Oxford, England)
·
28 Feb 2015
·
pmid:25725498
Topology-function conservation in protein-protein interaction networks.
Bioinformatics (Oxford, England)
·
20 Jan 2015
·
pmid:25609797
ergm.graphlets: A Package for ERG Modeling Based on Graphlet Statistics
Journal of Statistical Software
·
01 Jan 2015
·
doi:10.18637/jss.v065.i12
2014
The integrated disease network.
Integrative biology : quantitative biosciences from nano to macro
·
01 Nov 2014
·
pmid:25133803
Network wiring of pleiotropic kinases yields insight into protective role of diabetes on aneurysm.
Integrative biology : quantitative biosciences from nano to macro
·
01 Nov 2014
·
pmid:25098752
Anti-nicastrin monoclonal antibodies elicit pleiotropic anti-tumour pharmacological effects in invasive breast cancer cells.
Breast cancer research and treatment
·
24 Sep 2014
·
pmid:25248409
Predicting disease associations via biological network analysis.
BMC bioinformatics
·
17 Sep 2014
·
pmid:25228247
Integration of molecular network data reconstructs Gene Ontology.
Bioinformatics (Oxford, England)
·
01 Sep 2014
·
pmid:25161252
The topology of the growing human interactome data.
Journal of integrative bioinformatics
·
23 Jun 2014
·
pmid:24953453
Bridging the gaps in systems biology.
Molecular genetics and genomics : MGG
·
13 Apr 2014
·
pmid:24728588
Revealing the hidden language of complex networks.
Scientific reports
·
01 Apr 2014
·
pmid:24686408
Survey of network-based approaches to research of cardiovascular diseases.
BioMed research international
·
20 Mar 2014
·
pmid:24772427
Modelling the yeast interactome.
Scientific reports
·
04 Mar 2014
·
pmid:24589662
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity.
Bioinformatics (Oxford, England)
·
17 Jan 2014
·
pmid:24443377
2013
The role of genes co-amplified with nicastrin in breast invasive carcinoma.
Breast cancer research and treatment
·
13 Dec 2013
·
pmid:24337538
Discovering disease-disease associations by fusing systems-level molecular data.
Scientific reports
·
15 Nov 2013
·
pmid:24232732
Network topology reveals key cardiovascular disease genes.
PloS one
·
15 Aug 2013
·
pmid:23977067
Graphlet-based measures are suitable for biological network comparison.
Bioinformatics (Oxford, England)
·
23 Jan 2013
·
pmid:23349212
2012
The Core Diseasome.
Molecular bioSystems
·
01 Oct 2012
·
pmid:22820726
Biological function through network topology: a survey of the human diseasome.
Briefings in functional genomics
·
08 Sep 2012
·
pmid:22962330
C-GRAAL: common-neighbors-based global GRAph ALignment of biological networks.
Integrative biology : quantitative biosciences from nano to macro
·
10 Jan 2012
·
pmid:22234340
Protein complex prediction with RNSC.
Methods in molecular biology (Clifton, N.J.)
·
01 Jan 2012
·
pmid:22144160
2011
A framework for FPGA acceleration of large graph problems: Graphlet counting case study
2011 International Conference on Field-Programmable Technology
·
01 Dec 2011
·
doi:10.1109/FPT.2011.6132667
Introduction to the Special Issue on Biological Networks
Internet Mathematics
·
28 Nov 2011
·
doi:10.1080/15427951.2011.621769
Random Graph Models and Their Application to Protein–Protein Interaction Networks
Handbook of Statistical Systems Biology
·
12 Sep 2011
·
doi:10.1002/9781119970606.ch14
Dominating biological networks.
PloS one
·
26 Aug 2011
·
pmid:21887225
Topological Characteristics of Molecular Networks
Functional Coherence of Molecular Networks in Bioinformatics
·
24 Aug 2011
·
doi:10.1007/978-1-4614-0320-3_2
Evidence for network evolution in an Arabidopsis interactome map.
Science (New York, N.Y.)
·
29 Jul 2011
·
pmid:21798944
Integrative network alignment reveals large regions of global network similarity in yeast and human.
Bioinformatics (Oxford, England)
·
16 Mar 2011
·
pmid:21414992
Protein-protein interactions: making sense of networks via graph-theoretic modeling.
BioEssays : news and reviews in molecular, cellular and developmental biology
·
01 Feb 2011
·
pmid:21188720
GraphCrunch 2: Software tool for network modeling, alignment and clustering.
BMC bioinformatics
·
19 Jan 2011
·
pmid:21244715
2010
Optimal network alignment with graphlet degree vectors.
Cancer informatics
·
30 Jun 2010
·
pmid:20628593
Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets.
BMC systems biology
·
15 Jun 2010
·
pmid:20550706
Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy.
Journal of proteome research
·
05 Apr 2010
·
pmid:20170199
Complementarity of network and sequence information in homologous proteins.
Journal of integrative bioinformatics
·
25 Mar 2010
·
pmid:20375452
An integrative approach to modeling biological networks.
Journal of integrative bioinformatics
·
25 Mar 2010
·
pmid:20375453
Topological network alignment uncovers biological function and phylogeny.
Journal of the Royal Society, Interface
·
17 Mar 2010
·
pmid:20236959
Biological network comparison using graphlet degree distribution
Bioinformatics
·
03 Mar 2010
·
doi:10.1093/bioinformatics/btq091
Geometric evolutionary dynamics of protein interaction networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
·
01 Jan 2010
·
pmid:19908370
From Topology to Phenotype in Protein–Protein Interaction Networks
Network Science
·
01 Jan 2010
·
doi:10.1007/978-1-84996-396-1_3
2009
Geometric de-noising of protein-protein interaction networks.
PLoS computational biology
·
07 Aug 2009
·
pmid:19662157
Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data.
Journal of the Royal Society, Interface
·
22 Jul 2009
·
pmid:19625303
Optimized null model for protein structure networks.
PloS one
·
26 Jun 2009
·
pmid:19557139
Structure of brain functional networks.
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
·
01 Jan 2009
·
pmid:19964621
Learning the structure of protein-protein interaction networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
·
01 Jan 2009
·
pmid:19209694
2008
Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis.
Proceedings of the National Academy of Sciences of the United States of America
·
29 Aug 2008
·
pmid:18757749
Uncovering biological network function via graphlet degree signatures.
Cancer informatics
·
14 Apr 2008
·
pmid:19259413
Fitting a geometric graph to a protein-protein interaction network.
Bioinformatics (Oxford, England)
·
14 Mar 2008
·
pmid:18344248
GraphCrunch: a tool for large network analyses.
BMC bioinformatics
·
30 Jan 2008
·
pmid:18230190
2007
Geometric Local Structure in Biological Networks
2007 IEEE Information Theory Workshop
·
01 Sep 2007
·
doi:10.1109/ITW.2007.4313108
Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution.
PLoS computational biology
·
01 Jul 2007
·
pmid:17616981
Biological network comparison using graphlet degree distribution.
Bioinformatics (Oxford, England)
·
15 Jan 2007
·
pmid:17237089
2006
Modelling protein-protein interaction networks via a stickiness index.
Journal of the Royal Society, Interface
·
22 Oct 2006
·
pmid:16971339
Efficient estimation of graphlet frequency distributions in protein-protein interaction networks.
Bioinformatics (Oxford, England)
·
01 Feb 2006
·
pmid:16452112
2005
2-Tree probe interval graphs have a large obstruction set
Discrete Applied Mathematics
·
01 Sep 2005
·
doi:10.1016/j.dam.2004.06.015
High-throughput mapping of a dynamic signaling network in mammalian cells.
Science (New York, N.Y.)
·
11 Mar 2005
·
pmid:15761153
2004
Modeling interactome: scale-free or geometric?
Bioinformatics (Oxford, England)
·
29 Jul 2004
·
pmid:15284103
Protein complex prediction via cost-based clustering.
Bioinformatics (Oxford, England)
·
04 Jun 2004
·
pmid:15180928
Functional topology in a network of protein interactions.
Bioinformatics (Oxford, England)
·
12 Feb 2004
·
pmid:14960460
Hereditary dominating pair graphs
Discrete Applied Mathematics
·
01 Jan 2004
·
doi:10.1016/S0166-218X(03)00304-4
1998
Minimum Average Time Broadcast Graphs
Parallel Processing Letters
·
01 Jun 1998
·
doi:10.1142/s012962649800016x
Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation
Lecture Notes in Computer Science
·
·
doi:10.1007/978-3-540-73060-6_1