Chromatin network markers of leukemia N. Malod-Dognin, V. Pancaldi, A. Valencia, and N. Pržulj Bioinformatics 36: Issue Supplement_1, i455–i463, 2020.[doi]

J23.

Unveiling new disease, pathway, and gene associations via multi-scale neural networks
T. Gaudelet, N. Malod-Dognin, J. Sanchez-Valle, V. Pancaldi, A. Valencia, and N. Pržulj PLoS ONE15(4): e0231059, 2020.[doi]

J22.

Antiproliferative activity and mode of action analysis of novel amino and amido substituted phenantrene and naphtho[2,1-b]thiophene derivatives
N. Perin, V. Rep, I. Sović, Š. Juričić, D. Selgrad, M. Klobučar; N. Pržulj, C.L. Gupta, N. Malod-Dognin, S.K. Pavelić, M. Hranjec European Journal of Medicinal Chemistry185: 111833, 2019. [doi]

J21.

Graphlet Laplacians for topology-function and topology-disease relationships
S.F.L. Windels, N. Malod-Dognin, and N. Pržulj Bioinformatics 35(24): 5226–5234, 2019. [doi]

J20.

Towards a data-integrated cell N. Malod-Dognin, J. Petschnigg, S.F.L. Windels, J. Povh, H. Hemingway, R. Ketteler, and N. Pržulj Nature Communications10: 805, 2019. [doi]

J19.

Functional geometry of protein-protein interaction networks N. Malod-Dognin and N. Pržulj Bioinformatics35(19): 3727-3734, 2019. [doi]

J18.

Higher order molecular organisation as a source of biological function
T. Gaudelet, N. Malod-Dognin and N. Pržulj Bioinformatics34(17): i944-i953, 2018. Also conference C11. [doi]

Omics data complementarity underlines functional cross-communication in yeast N. Malod-Dognin and N. Pržulj Journal of Integrative Bioinformatics14(2), 2017. Also Conference paper C10. [pdf][doi]

J15.

Unified Alignment of Protein-Protein Interaction Networks N. Malod-Dognin, K. Ban and N. Pržulj Scientific Reports7:953, 2017. [pdf][doi]

J14.

Rebuttal to the Letter to the Editor in response to the paper: Proper evaluation of alignment-free network comparison methods
O.N. Yaveroğlu, N. Malod-Dognin, T. Milenković and N. Pržulj Bioinformatics33(7):1107-1109, 2017. [pdf][doi]

J13.

Graphlet-based Characterization of Directed Networks
A. Sarajlić, N. Malod-Dognin, O.N. Yaveroğlu and N. Pržulj Scientific Reports6:35098, 2016. [pdf][doi]

J12.

A global genetic interaction network maps a wiring diagram of cellular function
M. Costanzo, B. VanderSluis, E. N. Koch, A. Baryshnikova, C. Pons, G. Tan, W. Wang, M. Usaj, J. Hanchard, S. D. Lee, V. Pelechano, E. B. Styles, M. Billmann, J. van Leeuwen, N. van Dyk, Z.-Y. Lin, E. Kuzmin, J. Nelson, J. S. Piotrowski, T. Srikumar, S. Bahr, Y. Chen, R. Deshpande, C. F. Kurat, S. C. Li, Z. Li, M. M. Usaj, H. Okada, N. Pascoe, B.-J. San Luis, S. Sharifpoor, E. Shuteriqi, S. W. Simpkins, J. Snider, H. G. Suresh, Y. Tan, H. Zhu, N. Malod-Dognin, V. Janjic, N. Pržulj, O. G. Troyanskaya, I. Stagljar, T. Xia, Y. Ohya, A.-C. Gingras, B. Raught, M. Boutros, L. M. Steinmetz, C. L. Moore, A. P. Rosebrock, A. A. Caudy, C. L. Myers, B. Andrews and C. Boone Science353(6306):aaf1420, 2016. [pdf][doi]

J11.

Network Analytics in the age of Big Data
N. Pržulj and N. Malod-Dognin Science353(6295):aah3449, 2016. [pdf][doi]

J10.

Integrative Methods for Analysing Big Data in Precision Medicine
V. Gligorijević, N. Malod-Dognin and N. Pržulj Proteomics16(15):741-758, 2016. [pdf][doi]

J9.

FUSE: Multiple Network Alignment via Data Fusion
V. Gligorijević, N. Malod-Dognin and N. Pržulj Bioinformatics32(8):1195-1203, 2016. [pdf][doi]

J8.

L-GRAAL: Lagrangian Graphlet-based Network Aligner N. Malod-Dognin and N. Pržulj Bioinformatics31(13):2182-2189, 2015. [pdf][doi]

J7.

Topology-Function Conservation in Protein-Protein Interaction Networks
D. Davis, O.N. Yaveroğlu, N. Malod-Dognin, A. Stojmirovic and N. Pržulj Bioinformatics31(10):1632-1639, 2015. [pdf][doi]

J6.

Revealing the Hidden Language of Complex Networks
O.N. Yaveroğlu, N. Malod-Dognin, D. Davis, Z. Levnajic, V. Janjic, R. Karapandza, A. Stojmirovic and N. Pržulj Scientific Reports4:4547, 2014. [pdf][doi]

J5.

GR-Align: Fast and Flexible Alignment of Protein 3D Structures Using Graphlet Degree Similarity N. Malod-Dognin and N. Pržulj Bioinformatics30(9):1259-1265, 2014. [pdf][doi]

CSA: Comprehensive comparison of pairwise structural protein alignments
I. Wohlers, N. Malod-Dognin, R. Andonov and G.W. Klau Nucleic Acids Research40(W1):W303-W309, 2012. [pdf][doi]

Solving Maximum Clique Problem for Protein Structure Similarity N. Malod-Dognin, R. Andonov and N. Yanev Serdica Journal of Computing4(1):93-100, 2010. [pdf]

C11.

Higher order molecular organisation as a source of biological function
T. Gaudelet, N. Malod-Dognin and N. Pržulj European Conference on Computational Biology (ECCB), 2018. Also journal publication J18.

C10.

IB'17

Omics data complementarity underlines functional cross-communication in yeast N. Malod-Dognin and N. Pržulj Proceedings of the International Symposium on Integrative Bioinformatics, 2017. Also journal publication J16.

C9.

Patient-Specific Data Fusion for Cancer Stratification and Personalized Treatment
V. Gligorijević, N. Malod-Dognin and N. Pržulj Proceedings of the 21st Pacific Symposium on Biocomputing, p. 321-332, 2016. [pdf]

C8.

CSA : Comparaison compréhensible d'alignement de paires de structures de protéines
I. Wohlers, N. Malod-Dognin, R. Andonov, G.W. Klau Proceedings of JOBIM, p.201-208, 2012 (in french).

C7.

PRIB'11

Shape Matching by Localized Calculations of Quasi-isometric Subsets, with Applications to the Comparison of Protein Binding Patches
F. Cazals and N. Malod-Dognin Pattern Recognition in Bioinformatics, Lecture Notes in Computer Science, vol. 7036, p. 272-283, 2011. [pdf][doi][bib]

C6.

WABI'11

Using Dominances for Solving the Protein Family Identification Problem N. Malod-Dognin, M. Le Boudic-Jamin, P. Kamath, and R. Andonov Algorithms in Bioinformatics, Lecture Notes in Computer Science, vol. 6833, p. 201-212, 2011. [pdf][doi][bib]

C5.

Identification rapide de familles protéiques par dominance
M. Le Boudic-Jamin, N. Malod-Dognin, A. Cornu, J. Nicolas and R. Andonov Proceedings of the 12th Annual Congress of the French National Society of Operations Research and Decision Science (ROADEF), vol. 2, p.791-792, 2011 (in french).

C4.

SHREC'10

SHREC-10 Track: Protein Model Classification
L. Mavridis, V. Venkatraman, D. W. Ritchie, N. Morikawa, R. Andonov, A. Cornu, N. Malod-Dognin, J. Nicolas, M. Temerinac-Ott, M. Reisert, H. Burkhardt, A. Axenopoulos and P. Daras Eurographics Workshop on 3D Object Retrieval (3DOR), p. 117-124, 2010. [pdf][bib]

C3.

SEA'10

Maximum Clique in Protein Structure Comparison N. Malod-Dognin, R. Andonov and N. Yanev Experimental Algorithms, Lecture Notes in Computer Science, vol. 6049, p.106-117, 2010. [pdf][doi][bib]

C2.

WABI'08

An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem
R. Andonov, N. Yanev and N. Malod-Dognin Algorithms in Bioinformatics, Lecture Notes in Computer Science, vol. 5251, p. 162-173, 2008. [pdf][doi][bib]

C1.

Modèle de PLNE pour la recherche de cliques de poids maximal N. Malod-Dognin, R. Andonov, N. Yanev and J-F. Gibrat Proceedings of the 9th Annual Congress of the French National Society of Operations Research and Decision Science (ROADEF), p. 307-308, 25/02/2008 (In french).

B02.

Machine Learning for Data Integration in Cancer Precision Medicine: Matrix Factorization Approaches N. Malod-Dognin, S. Windels and N. Pržulj Analyzing Network Data in Biology and Medicine, edited by N. Pržulj, Cambridge University Press, forthcoming, 2018

Protein Structure Comparison: From Contact Map Overlap Maximisation to Distance-based Alignment Search Tool
Ph.D. Thesis, University of Rennes 1, January 2010. [Full manuscript available on HAL/TEL]

15.

Towards a data-integrated cell N. Malod-Dognin, J. Petschnigg, S.F.L. Windels, J. Povh, H. Hemingway, R. Ketteler, and N. Pržulj ISMB-ECCB, Basel, Switzerland, July 21-25, 2019.

14.

Higher order molecular organisation as a source of biological function
T. Gaudelet, N. Malod-Dognin, and N. Pržulj ECCB, Athens, Greece, September 8-12, 2018.

13.

Towards higher-order modelling and integration of biological data for precision medicine N. Malod-Dognin 2nd Workshop on Biomedical data fusion and non-negative matrix factorization, Ljubljana, Slovenia, May 23-25, 2018.

12.

ECTB 2016

Towards higher-order modelling and integration of biological data for precision medicine N. Malod-Dognin, T. Gaudelet, S. Windels and N. Pržulj European Conference on Translational Bioinformatics, Barcelona, Spain, April 16-17, 2018.

11.

Data-Fusion for Cancer Patient Stratification and Personalised Treatment
V. Gligorijević, N. Malod-Dognin and N. Pržulj International Conference on Complex Networks and Their Applications, Lyon, France, November 29 - December 01, 2017.

10.

Hypergraphlets Give Insight into Multi-Scale Organisation of Molecular Networks
T. Gaudelet, N. Malod-Dognin, J. Lugo-Martinez, P. Radivojac and N. Pržulj International Conference on Complex Networks and Their Applications, Lyon, France, November 29 - December 01, 2017.

9.

Patient Specific Network Data Integration Enables Precision Medicine in Cancer
V. Gligorijevic, N. Malod-Dognin and N. Przulj Belgrade Bioinformatics Conference, Belgrade, Serbia, 20-24 June 2016.

8.

Network data integration enables precision medicine in cancer N. Malod-Dognin ECCB, Workshop 7, The Hague, Netherlands, September 3, 2016.

7.

GenMed 2016

Network Data Integration Enables Precision Medicine
V. Gligorijevic, N. Malod-Dognin and N. Przulj Summer School: Genomic Medicine, Portoroz, Slovenia, 3-7 May 2016.

6.

Topology-Function Conservation in Protein-Protein Interaction Networks
D. Davis, O.N. Yaveroglu, N. Malod-Dognin, A. Stojmirovic and N. Przulj International School and Conference on Network Science, Zaragoza, Spain, 1-5 June 2015.

5.

Revealing the Hidden Language of Complex Networks
O. N. Yaveroglu, N. Malod-Dognin, D. Davis, Z. Levnajic, V. Janjic, R. Karapandza, A. Stojmirovic, and N. Przulj International School and Conference on Network Science, Berkeley, California, USA, June 2-6, 2014.

4.

3Dsig'13

GrAlign: Fast Flexible Alignment of Protein 3D Structures N. Malod-Dognin and N. Przulj ISMB - 3DSig, Berlin, Germany, July 19-20, 2013.

3.

SFBBM-SFB'12

Stoichiometry Determination for Mass-spectrometry Data in Structural Proteomics N. Malod-Dognin and F. Cazals SFBBM-SFB congress, Grenoble, France, November 21-23, 2012.

2.

MICOM'09

Maximum clique approach to protein structure similarity N. Malod-Dognin, R. Andonov and N. Yanev MASSEE (mathematical society of south-east europe) International Congress On Mathematics, Ohrid, Macedonia, September 16-20, 2009.

1.

MMSC'09

Maximum clique approach to protein structure similarity N. Malod-Dognin, R. Andonov and N. Yanev International Workshop on Mathematical Modelling and Scientific Computations, Velingrad, Bulgaria, September 23-26, 2009.

20.

Towards a data-integrated cell N. Malod-Dognin, J. Petschnigg, S.F.L. Windels, J. Povh, H. Hemingway, R. Ketteler, and N. Pržulj ISMB-ECCB, Basel, Switzerland, July 21-25, 2019.

19.

Unveiling new disease, pathway, and gene associations via multi-scale neural networks
T. Gaudelet, N. Malod-Dognin, J. Sanchez-Valle, V. Pancaldi, A. Valencia, and N. Pržulj ISMB-ECCB, Basel, Switzerland, July 21-25, 2019.

18.

Functional geometry of protein-protein interaction networks N. Malod-Dognin and N. Pržulj ECCB, Athens, Greece, September 8-12, 2018.

17.

Graphlet Laplacians: linking local wiring patterns in network neighbourhoods to biological function
S.F.L. Windels, N. Malod-Dognin and N. Pržulj ECCB, Athens, Greece, September 8-12, 2018.

16.

Higher-order modelling and integration of biological data for precision medicine N. Malod-Dognin, T. Gaudelet, S.F.L Windels and N. Pržulj International School and Conference on Network Science, Satellite Symposium on Network Medicine, Paris, France, June 11-15, 2018.

15.

Network analysis of Brazil's 2016 Zika-related incidence of microcephaly reveals misestimation of the outbreak and multiple contributing factors
M.P. Cifuentes, C.M. Suarez, S.F.L. Windels, R. Cifuentes, N. Doogan, J.F. Valderrama, N. Malod-Dognin, D. Hood and N. Pržulj International Conference on Complex Networks and Their Applications, Lyon, France, November 29 - December 01, 2017.

14.

Ulign: Unified Alignment of Protein-Protein Interaction Networks N. Malod-Dognin, K. Ban and N. Pržulj ISMB-ECCB, Prague, Czech Republic, July 21-25, 2017.

13.

Hypergraphlets Give Insight into Multi-Scale Organisation of Molecular Networks
T. Gaudelet, N. Malod-Dognin, J. Lugo-Martinez, P. Radivojac and N. Pržulj ISMB-ECCB, Prague, Czech Republic, July 21-25, 2017.

12.

A network analysis of the incidence pattern of microcephaly in the context of Zika Virus Infection
M.P. Cifuentes, C.M. Suarez, S.F.L. Windels, R. Cifuentes, N. Doogan, J.F. Valderrama, N. Malod-Dognin, D. Hood and N. Pržulj ISMB-ECCB, Prague, Czech Republic, July 21-25, 2017.

11.

Patient-Specific Data Fusion for Cancer Stratification and Personalized Treatment
V. Gligorijević, N. Malod-Dognin and N. Pržulj Pacific Symposium on Biocomputing, Big Island, Hawaii, January 4-8, 2016.

10.

FUSE: Multiple Network Alignment via Data Fusion
V. Gligorijević, N. Malod-Dognin and N.Pržulj ISMB-ECCB, Dublin, Ireland, July 10-14, 2015.

9.

L-GRAAL: Lagrangian Graphlet-based Network Aligner N. Malod-Dognin and N. Pržulj ECCB, Strasbourg, France, September 7-10, 2014.

8.

Topology-Function Conversion in Protein-Protein Interaction Networks
D. Davis, O.N. Yaveroğlu, N. Malod-Dognin, A. Stojmirovic and N. Pržulj ECCB, Strasbourg, France, September 7-10, 2014.

6-7.

ISMB-ECCB'13 3Dsig'13

GrAlign: Fast Flexible Alignment of Protein 3D Structures N. Malod-Dognin and N. Pržulj ISMB-ECCB, Berlin, Germany, July 21-23, 2013. 3Dsig, Berlin, Germany, July 19-20, 2013.

5.

GTBio'12

On the Stoichiometry Determination Problem for Mass Spectrometry Data
D. Agarwal, N. Malod-Dognin and F. Cazals GTBio; Montpellier, France, April 3-6, 2012.

2-4.

GTBio'12 GGMM'11 PRIB'11

On the Morphology of Protein Binding Patches N. Malod-Dognin and F.Cazals GTBio; Montpellier, France, April 3-6, 2012. The 17th GGMM congress; La Rochelle, France, May 30 to June 1, 2011. PRIB; Delft, The Netherlands, November 2-4, 2011. Best poster award

1.

ESF-EMBO'10

Protein Structure Comparison: A Generic Framework N. Malod-Dognin, R. Andonov and N. Yanev ESF-EMBO Symposium on Molecular Perspectives on Protein-Protein Interactions; Sant Feliu de Guixols, Spain, November 14-19, 2010.