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Items: 1 to 50 of 62

1.

Omics Data Complementarity Underlines Functional Cross-Communication in Yeast.

Malod-Dognin N, Pržulj N.

J Integr Bioinform. 2017 Jun 10;14(2). pii: /j/jib.2017.14.issue-2/jib-2017-0018/jib-2017-0018.xml. doi: 10.1515/jib-2017-0018.

2.

Unified Alignment of Protein-Protein Interaction Networks.

Malod-Dognin N, Ban K, Pržulj N.

Sci Rep. 2017 Apr 19;7(1):953. doi: 10.1038/s41598-017-01085-9.

3.

Systematic protein-protein interaction mapping for clinically relevant human GPCRs.

Sokolina K, Kittanakom S, Snider J, Kotlyar M, Maurice P, Gandía J, Benleulmi-Chaachoua A, Tadagaki K, Oishi A, Wong V, Malty RH, Deineko V, Aoki H, Amin S, Yao Z, Morató X, Otasek D, Kobayashi H, Menendez J, Auerbach D, Angers S, Pržulj N, Bouvier M, Babu M, Ciruela F, Jockers R, Jurisica I, Stagljar I.

Mol Syst Biol. 2017 Mar 15;13(3):918. doi: 10.15252/msb.20167430.

4.

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

Yaveroglu ÖN, Malod-Dognin N, Milenkovic T, Pržulj N.

Bioinformatics. 2017 Apr 1;33(7):1107-1109. doi: 10.1093/bioinformatics/btw388. No abstract available.

PMID:
28073757
5.

Graphlet-based Characterization of Directed Networks.

Sarajlić A, Malod-Dognin N, Yaveroğlu ÖN, Pržulj N.

Sci Rep. 2016 Oct 13;6:35098. doi: 10.1038/srep35098.

6.

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

Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, Tan G, Wang W, Usaj M, Hanchard J, Lee SD, Pelechano V, Styles EB, Billmann M, van Leeuwen J, van Dyk N, Lin ZY, Kuzmin E, Nelson J, Piotrowski JS, Srikumar T, Bahr S, Chen Y, Deshpande R, Kurat CF, Li SC, Li Z, Usaj MM, Okada H, Pascoe N, San Luis BJ, Sharifpoor S, Shuteriqi E, Simpkins SW, Snider J, Suresh HG, Tan Y, Zhu H, Malod-Dognin N, Janjic V, Przulj N, Troyanskaya OG, Stagljar I, Xia T, Ohya Y, Gingras AC, Raught B, Boutros M, Steinmetz LM, Moore CL, Rosebrock AP, Caudy AA, Myers CL, Andrews B, Boone C.

Science. 2016 Sep 23;353(6306). pii: aaf1420.

7.

NETWORK ANALYSIS. Network analytics in the age of big data.

Pržulj N, Malod-Dognin N.

Science. 2016 Jul 8;353(6295):123-4. doi: 10.1126/science.aah3449. No abstract available.

PMID:
27387938
8.

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

Gligorijević V, Malod-Dognin N, Pržulj N.

Pac Symp Biocomput. 2016;21:321-32.

9.

Integrative methods for analyzing big data in precision medicine.

Gligorijević V, Malod-Dognin N, Pržulj N.

Proteomics. 2016 Mar;16(5):741-58. doi: 10.1002/pmic.201500396. Review.

10.

Fuse: multiple network alignment via data fusion.

Gligorijević V, Malod-Dognin N, Pržulj N.

Bioinformatics. 2016 Apr 15;32(8):1195-203. doi: 10.1093/bioinformatics/btv731. Epub 2015 Dec 14.

11.

Methods for biological data integration: perspectives and challenges.

Gligorijević V, Pržulj N.

J R Soc Interface. 2015 Nov 6;12(112). pii: 20150571. doi: 10.1098/rsif.2015.0571. Review.

12.

Proper evaluation of alignment-free network comparison methods.

Yaveroğlu ÖN, Milenković T, Pržulj N.

Bioinformatics. 2015 Aug 15;31(16):2697-704. doi: 10.1093/bioinformatics/btv170. Epub 2015 Mar 24.

13.

L-GRAAL: Lagrangian graphlet-based network aligner.

Malod-Dognin N, Pržulj N.

Bioinformatics. 2015 Jul 1;31(13):2182-9. doi: 10.1093/bioinformatics/btv130. Epub 2015 Feb 28.

14.

Topology-function conservation in protein-protein interaction networks.

Davis D, Yaveroğlu ÖN, Malod-Dognin N, Stojmirovic A, Pržulj N.

Bioinformatics. 2015 May 15;31(10):1632-9. doi: 10.1093/bioinformatics/btv026. Epub 2015 Jan 20.

15.

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

Filipović A, Lombardo Y, Faronato M, Abrahams J, Aboagye E, Nguyen QD, d'Aqua BB, Ridley A, Green A, Rahka E, Ellis I, Recchi C, Przulj N, Sarajlić A, Alattia JR, Fraering P, Deonarain M, Coombes RC.

Breast Cancer Res Treat. 2014 Nov;148(2):455-62. doi: 10.1007/s10549-014-3119-z. Epub 2014 Sep 24. Erratum in: Breast Cancer Res Treat. 2014 Nov;148(2):463. Fronato, Monica [corrected to Faronato, Monica].

16.

Predicting disease associations via biological network analysis.

Sun K, Gonçalves JP, Larminie C, Przulj N.

BMC Bioinformatics. 2014 Sep 17;15:304. doi: 10.1186/1471-2105-15-304.

17.

Integration of molecular network data reconstructs Gene Ontology.

Gligorijević V, Janjić V, Pržulj N.

Bioinformatics. 2014 Sep 1;30(17):i594-600. doi: 10.1093/bioinformatics/btu470.

18.

The integrated disease network.

Sun K, Buchan N, Larminie C, Pržulj N.

Integr Biol (Camb). 2014 Nov;6(11):1069-79. doi: 10.1039/c4ib00122b.

PMID:
25133803
19.

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

Sarajlić A, Gligorijević V, Radak D, Pržulj N.

Integr Biol (Camb). 2014 Nov;6(11):1049-57. doi: 10.1039/c4ib00125g.

PMID:
25098752
20.

The topology of the growing human interactome data.

Janjić V, Pržulj N.

J Integr Bioinform. 2014 Jun 23;11(2):238. doi: 10.2390/biecoll-jib-2014-238.

PMID:
24953453
21.

The Topology of the Growing Human Interactome Data.

Janjić V, Pržulj N.

J Integr Bioinform. 2014 Jun 1;11(2):27-42. doi: 10.1515/jib-2014-238.

PMID:
29220943
22.

Survey of network-based approaches to research of cardiovascular diseases.

Sarajlić A, Pržulj N.

Biomed Res Int. 2014;2014:527029. doi: 10.1155/2014/527029. Epub 2014 Mar 20. Review.

23.

Bridging the gaps in systems biology.

Cvijovic M, Almquist J, Hagmar J, Hohmann S, Kaltenbach HM, Klipp E, Krantz M, Mendes P, Nelander S, Nielsen J, Pagnani A, Przulj N, Raue A, Stelling J, Stoma S, Tobin F, Wodke JA, Zecchina R, Jirstrand M.

Mol Genet Genomics. 2014 Oct;289(5):727-34. doi: 10.1007/s00438-014-0843-3. Epub 2014 Apr 13. Review.

PMID:
24728588
24.

Revealing the hidden language of complex networks.

Yaveroğlu ÖN, Malod-Dognin N, Davis D, Levnajic Z, Janjic V, Karapandza R, Stojmirovic A, Pržulj N.

Sci Rep. 2014 Apr 1;4:4547. doi: 10.1038/srep04547.

25.

Modelling the yeast interactome.

Janjić V, Sharan R, Pržulj N.

Sci Rep. 2014 Mar 4;4:4273. doi: 10.1038/srep04273.

26.

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

Malod-Dognin N, Pržulj N.

Bioinformatics. 2014 May 1;30(9):1259-65. doi: 10.1093/bioinformatics/btu020. Epub 2014 Jan 17.

PMID:
24443377
27.

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

Sarajlić A, Filipović A, Janjić V, Coombes RC, Pržulj N.

Breast Cancer Res Treat. 2014 Jan;143(2):393-401. doi: 10.1007/s10549-013-2805-6. Epub 2013 Dec 13.

PMID:
24337538
28.

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

Žitnik M, Janjić V, Larminie C, Zupan B, Pržulj N.

Sci Rep. 2013 Nov 15;3:3202. doi: 10.1038/srep03202.

29.

Network topology reveals key cardiovascular disease genes.

Sarajlić A, Janjić V, Stojković N, Radak D, Pržulj N.

PLoS One. 2013 Aug 15;8(8):e71537. doi: 10.1371/journal.pone.0071537. eCollection 2013.

30.

Graphlet-based measures are suitable for biological network comparison.

Hayes W, Sun K, Pržulj N.

Bioinformatics. 2013 Feb 15;29(4):483-91. doi: 10.1093/bioinformatics/bts729. Epub 2013 Jan 23.

PMID:
23349212
31.

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

Janjić V, Pržulj N.

Brief Funct Genomics. 2012 Nov;11(6):522-32. doi: 10.1093/bfgp/els037. Epub 2012 Sep 8.

PMID:
22962330
32.

The Core Diseasome.

Janjić V, Pržulj N.

Mol Biosyst. 2012 Oct;8(10):2614-25. doi: 10.1039/c2mb25230a.

PMID:
22820726
33.

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

Memišević V, Pržulj N.

Integr Biol (Camb). 2012 Jul;4(7):734-43. doi: 10.1039/c2ib00140c. Epub 2012 Jan 10.

PMID:
22234340
34.

Protein complex prediction with RNSC.

King AD, Pržulj N, Jurisica I.

Methods Mol Biol. 2012;804:297-312. doi: 10.1007/978-1-61779-361-5_16.

PMID:
22144160
35.

Dominating biological networks.

Milenković T, Memišević V, Bonato A, Pržulj N.

PLoS One. 2011;6(8):e23016. doi: 10.1371/journal.pone.0023016. Epub 2011 Aug 26.

36.

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

Kuchaiev O, Przulj N.

Bioinformatics. 2011 May 15;27(10):1390-6. doi: 10.1093/bioinformatics/btr127. Epub 2011 Mar 16.

PMID:
21414992
37.

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

Kuchaiev O, Stevanović A, Hayes W, Pržulj N.

BMC Bioinformatics. 2011 Jan 19;12:24. doi: 10.1186/1471-2105-12-24.

38.

Protein-protein interactions: making sense of networks via graph-theoretic modeling.

Pržulj N.

Bioessays. 2011 Feb;33(2):115-23. doi: 10.1002/bies.201000044. Review.

PMID:
21188720
39.

Optimal network alignment with graphlet degree vectors.

Milenković T, Ng WL, Hayes W, Przulj N.

Cancer Inform. 2010 Jun 30;9:121-37.

40.

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

Ho H, Milenković T, Memisević V, Aruri J, Przulj N, Ganesan AK.

BMC Syst Biol. 2010 Jun 15;4:84. doi: 10.1186/1752-0509-4-84.

41.

An integrative approach to modeling biological networks.

Memisevic V, Milenkovic T, Przulj N.

J Integr Bioinform. 2010 Mar 25;7(3). doi: 10.2390/biecoll-jib-2010-120.

PMID:
20375453
42.

Complementarity of network and sequence information in homologous proteins.

Memisevic V, Milenkovic T, Przulj N.

J Integr Bioinform. 2010 Mar 25;7(3). doi: 10.2390/biecoll-jib-2010-135.

PMID:
20375452
43.

Topological network alignment uncovers biological function and phylogeny.

Kuchaiev O, Milenkovic T, Memisevic V, Hayes W, Przulj N.

J R Soc Interface. 2010 Sep 6;7(50):1341-54. doi: 10.1098/rsif.2010.0063. Epub 2010 Mar 17.

44.

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

Kaake RM, Milenković T, Przulj N, Kaiser P, Huang L.

J Proteome Res. 2010 Apr 5;9(4):2016-29. doi: 10.1021/pr1000175.

45.

Structure of brain functional networks.

Kuchaiev O, Wang PT, Nenadic Z, Przulj N.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:4166-70. doi: 10.1109/IEMBS.2009.5333938.

PMID:
19964621
46.

Geometric evolutionary dynamics of protein interaction networks.

Przulj N, Kuchaiev O, Stevanović A, Hayes W.

Pac Symp Biocomput. 2010:178-89.

47.

Geometric de-noising of protein-protein interaction networks.

Kuchaiev O, Rasajski M, Higham DJ, Przulj N.

PLoS Comput Biol. 2009 Aug;5(8):e1000454. doi: 10.1371/journal.pcbi.1000454. Epub 2009 Aug 7.

48.

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

Milenkovic T, Memisevic V, Ganesan AK, Przulj N.

J R Soc Interface. 2010 Mar 6;7(44):423-37. doi: 10.1098/rsif.2009.0192. Epub 2009 Jul 22.

49.

Optimized null model for protein structure networks.

Milenković T, Filippis I, Lappe M, Przulj N.

PLoS One. 2009 Jun 26;4(6):e5967. doi: 10.1371/journal.pone.0005967.

50.

Learning the structure of protein-protein interaction networks.

Kuchaiev O, Przulj N.

Pac Symp Biocomput. 2009:39-50.

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