Bibliography

## 2016

## Scientific papers

Axenovich, M., Harant, J., Przybyło, J., Soták, Roman, Voigt, M., Weidelich, J. A note on adjacent vertex distinguishing colorings of graphs. Discrete applied mathematics: pages 7, 2016. URL

Bezegová, L'udmila, Lužar, Borut, Mockovčiaková, Martina, Soták, Roman, Škrekovski, Riste. Star edge coloring of some classes of graphs. Journal of graph theory: 1-10, 2016. URL

Govorčin, Jelena, Škrekovski, Riste, Vukašinović, Vida, VUKIČEVIĆ, Damir. A measure for a balanced workload and its extremal values. Discrete applied mathematics 200: 59-66, 2016. URL

Harutyunyan, Ararat, Naserasr, Reza, Petruševski, Mirko, Škrekovski, Riste, Sun, Qiang. Mapping planar graphs into the Coxeter graph. Discrete Mathematics 339 (2): 839-849, 2016. URL

Jendrol´, S., Maceková, M., Montassier, M., Soták, Roman. Optimal unavoidable sets of types of 3-paths for planar graphs of given girth. Discrete Mathematics 339 (2): 780-789, 2016. URL

Knor, Martin, Škrekovski, Riste, Tepeh, Aleksandra. Mathematical aspects of Wiener index. Ars mathematica contemporanea 11 (2): 327-325, 2016. URL

Knor, Martin, Škrekovski, Riste, Tepeh, Aleksandra. Some remarks on Wiener index of oriented graphs. Applied mathematics and computation 273: 631-636, 2016. URL

Krnc, Matjaž, Škrekovski, Riste. On Wiener inverse interval problem. MATCH Communications in Mathematical and in Computer Chemistry 75 (1): 71-80, 2016. URL

## Conference papers

Bučar, Jože, Povh, Janez, Žnidaršič, Martin. Sentiment classification of the Slovenian news texts. Proceedings of the 9th International Conference on Computer Recognition Systems (CORES 2015), Advances in intelligent systems and computing 403, Springer: 777-787, 2016. URL

Zelenika, Darko, Povh, Janez, Ženko, Bernard. Text detection in document images by machine learning algorithms. Proceedings of the 9th International Conference on Computer Recognition Systems (CORES 2015), Advances in intelligent systems and computing 403, Springer: 169-179, 2016. URL

## 2015

## Scientific papers

Andova, Vesna, Blenkuš, Domen, Došlić, Tomislav, Kardoš, František, Škrekovski, Riste. On diameter of nanotubical fullerene graphs. MATCH Communications in Mathematical and in Computer Chemistry 73 (2): 529-542. URL

Andova, Vesna, Kardoš, František, Škrekovski, Riste. Sandwiching saturation number of fullerene graphs. MATCH Communications in Mathematical and in Computer Chemistry 73 (2): 501-518, 2015. URL

Barnard, Luke, Mertik, Matej. Usability of visualization libraries for web browsers for use in scientific analysis. International journal of computer applications 121 (1): 1-5, 2015. URL

Cafuta, Kristijan, Klep, Igor, Povh, Janez. Rational sums of hermitian squares of free noncommutative polynomials. Ars mathematica contemporanea: 243-259, 2015. URL

Damij, Nadja, Levnajić, Zoran, Rejec Skrt, Vesna, Suklan, Jana. What motivates us for work?, Intricate web of factors beyond money and prestige. PloS one 10 (7): 1-13, 2015. URL

Dimitrov, Darko, Škrekovski, Riste. Comparing the irregularity and the total irregularity of graphs. Ars mathematica contemporanea 9 (1): 45-50. URL

Farkasová, Zuzana, Soták, Roman. Fractional and circular 1-defective colorings of outerplanar graphs. The Australasian journal of combinatorics: 63 (1): 1-11, 2015. URL

Gregor, Petr, Škrekovski, Riste, Vukašinović, Vida. Rooted level-disjoint partitions of Cartesian products. Applied mathematics and computation 266: 244-258, 2015. URL

Hristovski, Dimitar, Dinevski, Dejan, Kastrin, Andrej, Rindflesch, Thomas C. Biomedical question answering using semantic relations. BMC bioinformatics 16 (6): pages 14, 2015. URL

Hornák, Mirko, Jendrol, Stanislav, Schiermeyer, Ingo, Soták, Roman. Rainbow numbers for cycles in plane triangulations. Journal of graph theory 78 (4): 248-257, 2015. URL

Jendrol´, S., MAceková, M., Soták, Roman. Note on 3-paths in plane graphs of girth 4. Discrete Mathematics 338 (9): 1643-1648, 2015. URL

Karafová, Gabriela, Soták, Roman. Generalized fractional total colorings of graphs. Discussiones mathematicae, Graph theory 35 (3): 463-473, 2015. URL

Kemnitz, Arnfried, Marangio, Massimiliano, Mihók, Peter, Oravcová, Janka, Soták, Roman. Generalized fractional and circular total colorings of graphs. Discussiones mathematicae, Graph theory 35 (3): 517-532, 2015. URL

Klep, Igor, Povh, Janez. Constrained trace-optimization of polynomials in freely noncommuting variables. Journal of global optimization, pages [24], 2015. URL

Knor, Martin, Lužar, Borut, Škrekovski, Riste. Sandwiching the (generalized) Randić index. Discrete applied mathematics 181: 160-166, 2015. URL

Knor, Martin, Škrekovski, Riste, Tepeh, Aleksandra. An inequality between the edge-Wiener index and the Wiener index of a graph. Applied mathematics and computation 269: 714-721, 2015. URL

Knor, Martin, Škrekovski, Riste, Tepeh, Aleksandra. Balaban index of cubic graphs. MATCH Communications in Mathematical and in Computer Chemistry 73 (2): 519-528, 2015. URL

Kranjc, Jaka, Lužar, Borut, Mockovčiaková, Martina, Soták, Roman. On a generalization of Thue sequences. The Electronic journal of combinatorics 22 (2): 1-14, 2015. URL

Krnc, Matjaž, Škrekovski, Riste. Centralization of transmission in networks. Discrete Mathematics 338 (338): 2412-2420, 2015. URL

Krnc, Matjaž, Škrekovski, Riste. Group centralization of network indices. Discrete applied mathematics 186: 147-157, 2015. URL

Levnajić, Zoran, Mezić, Igor. Ergodic theory and visualization. II, Fourier mesochronic plots visualize (quasi)periodic sets. Chaos 25 (5), 2015. URL

Lužar, Borut, Mockovčiaková, Martina, Soták, Roman, Škrekovski, Riste, Šugerek, Peter. l-facial edge colorings of graphs. Discrete applied mathematics 181: 193-200, 2015. URL

Lužar, Borut, Petruševski, Mirko, Škrekovski, Riste. Odd edge coloring of graphs. Ars mathematica contemporanea 9 (2): 277-287, 2015. URL

Lužar, Borut, Škrekovski, Riste. Counterexamples to a conjecture on injective colorings. Ars mathematica contemporanea 8 (2): 291-295, 2015. URL

Schiermeyer, Ingo, Soták, Roman. Rainbow numbers for graphs containing small cycles. Graphs and combinatorics 31 (6): 1985-1991, 2015. URL

Šubelj, Lovro, Bajec, Marko, Mileva-Boshkoska, Biljana, Kastrin, Andrej, Levnajić, Zoran. Quantifying the consistency of scientific databases. PloS one 10 (5): 1-16, 2015. URL

## Conference papers

Gologranc, Tanja, Jerebic, Janja, Kranjc, Jaka, Lužar, Borut, Mali, Luka, Povh, Janez, Bokal, Drago. On applying mathematical models of frequency assignment to Wi-Fi throughput optimization. 13th International Symposium on Operational Research in Slovenia (SOR15) proceedings: 137-142, 2015.

Hristovski, Dimitar, Kastrin, Andrej, Rindflesch, Thomas C. Semantics-based cross-domain collaboration recommendation in the life sciences : preliminary results. IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2015) proceedings: 805-806, 2015.

Hristovski, Dimitar, Kastrin, Andrej, Dinevski, Dejan, Rindflesch, Thomas C. Towards implementing semantic literature-based discovery with a graph database. The Seventh International Conference on Advances in Databases, Knowledge, and Data Applications: 180-184, 2015. URL

Hristovski, Dimitar, Kastrin, Andrej, Dinevski, Dejan, Rindflesch, Thomas C. Constructing a graph database for semantic literature-based discovery. 15th World Congress on Health and Biomedical Informatics (MEDINFO 2015), 2015. URL

## 2014

## Scientific papers

Alizadeh, Yaser, Andova, Vesna, Klavžar, Sandi, Škrekovski, Riste. Wiener dimension: fundamental properties and (5,0)-nanotubical fullerenes. MATCH Communications in Mathematical and in Computer Chemistry 72 (1): 279-294, 2014. URL

Cranston, Daniel W., Škrekovski, Riste. Sufficient sparseness conditions for G [sup] 2 to be ([Delta] + 1)-choosable, when [Delta is greater than or equal to] 5. Discrete Applied Mathematics 162: 167-176, 2014. URL

Cvijovic, Marija, Pržulj, Nataša, et al. Bridging the gaps in systems biology. Molecular genetics and genomics 289 (5): 727-734, 2014. URL

Dickinson, Peter J. C., Povh, Janez. On an extension of Pólyaʼs Positivstellensatz. Journal of global optimization: 1-11, 2014. URL

Filipović, Aleksandra, Pržulj, Nataša, et al. Anti-nicastrin monoclonal antibodies elicit pleiotropic anti-tumour pharmacological effects in invasive breast cancer cells. Breast cancer research and treatment 148 (2): 455-463.

Gligorijević, Vladimir, Janjić, Vuk, Pržulj, Nataša. Integration of molecular network data reconstructs Gene Ontology. The 13th European conference on computational biology. Bioinformatics (Oxford. Print) 30 (17): 594-600, 2014. URL

Govorčin, Jelena, Škrekovski, Riste. On the connectivity of Cartesian product of graphs. Ars mathematica contemporanea 7 (2): 293-297, 2014. URL

Hriňáková, Katarína, Knor, Martin, Škrekovski, Riste, Tepeh, Aleksandra. A congruence relation for the Wiener index of graphs with a tree-like structure. MATCH Communications in Mathematical and in Computer Chemistry 72 (3): 791-806, 2014. URL

Hudák, Dávid, Lužar, Borut, Sotak, Roman, Škrekovski, Riste. Strong edge-coloring of planar graphs. Discrete Mathematics 324: 41-49, 2014. URL

Janjić, Vuk, Sharan, Roded, Pržulj, Nataša. Modelling the yeast interactome. Scientific reports 4, 2014. URL

Kaiser, Tomáš, Stehlík, Matěj, Škrekovski, Riste. Replication in critical graphs and the persistence of monomial ideals. Journal of combinatorial theory, Series A, 123 (1): 239-251, 2014. URL

Kastrin, Andrej, Rindflesch, Thomas C., Hristovski, Dimitar. Large-scale structure of a network of co-occurring MeSH terms : statistical analysis of macroscopic properties. PloS one 9 (7), 2014. URL

Kastrin, Andrej, Rindflesch, Thomas C., Hristovski, Dimitar. Link prediction on the semantic MEDLINE network : an approach to literature-based discovery. Lecture notes in artificial intelligence 8777: 135-143, 2014.

Knor, Martin, Lužar, Borut, Škrekovski, Riste, Gutman, Ivan. On Wiener index of common neighborhood graphs. MATCH Communications in Mathematical and in Computer Chemistry 72 (1): 321-332, 2014. URL

Knor, Martin, Mačaj, Martin, Potočnik, Primož, Škrekovski, Riste. Complete solution of equation W(L[sup]3(T)) = W(T) for the Wiener index of iterated line graphs of trees. Discrete Applied Mathematics 171: 90-103, 2014. URL

Knor, Martin, Mačaj, Martin, Potočnik, Primož, Škrekovski, Riste. Trees T satisfying W(L[sup]3(T)) = W(T). Filomat 28 (3): 551-556, 2014. URL

Knor, Martin, Potočnik, Primož, Škrekovski, Riste. Relationship between the edge-Wiener index and the Gutman index of a graph. Discrete Applied Mathematics 167: 197-201, 2014. URL

Kranjc, Jaka, Lužar, Borut, Mockovčiaková, Martina, Soták, Roman. Note on coloring of double disk graphs. Journal of global optimization 60 (4): 793-799, 2014. URL

Levnajić, Zoran, Pikovsky, Arkady. Untangling complex dynamical systems via derivative-variable correlations. Scientific reports 4: 2045-2322 (6 str.), 2014. URL

Lužar, Borut, Levnajić, Zoran, Povh, Janez, Perc, Matjaž. Community structure and the evolution of interdisciplinarity in Slovenia's scientific collaboration network. PloS one 9 (4): 1-5, 2014. URL

Malod-Dognin, Noël, Pržulj, Nataša. GR-Align : fast and flexible alignment of protein 3D structures using graphlet degree similarity. Bioinformatics 30 (9): 1259-1265, 2014. URL

Saraljić, Anida, Filipović, Aleksandra, Janjić, Vuk, Coonbres, Raoul Charles, PRŽULJ, Nataša. The role of genes co-amplified with nicastrin in breast invasive carcinoma. Breast cancer research and treatment 143 (2): 393-401, 2014. URL

Saraljić, Anida, Gligorijević, Vladimir, Radak, Djordje, Pržulj, Nataša. Network wiring of pleiotropic kinases yields insight into protective role of diabetes on aneurysm. Integrative biology 6 (11): 1049-1057. URL

Saraljić, Anida, Pržulj, Nataša. Survey of Network-Based Approaches to Research of Cardiovascular Diseases. BioMed research international, 2014. URL

Sun, Kai, Buchan, Natalie, Larminie, Chris, Pržulj, Nataša. The integrated disease network. Integrative biology 6 (11): 1069-1079, 2014. URL

Sun, Kai, Gonçalves, Joana P, Larminie, Chris, Pržulj, Nataša. Predicting disease associations via biological network analysis. BMC bioinformatics 15 (304): 1-13, 2014. URL

Škrekovski, Riste, Gutman, Ivan. Vertex version of the Wiener theorem. MATCH Communications in Mathematical and in Computer Chemistry 72 (1): 295-300, 2014. URL

Vukašinović, Vida, Šilc, Jurij, Škrekovski, Riste. Modeling acquaintance networks based on balance theory. International journal of applied mathematics and computer science 24 (3): 683-696, 2014. URL

Yaveroğlu, Ömer Nebil, Levnajić, Zoran, Pržulj, Nataša, et al. Revealing the Hidden Language of Complex Networks. Scientific reports 4: 2045-2322 (9. str), 2014. URL

Žitnik, Marinka, Janjić, Vuk, Larminie, Chris, Zupan, Blaž, Pržulj, Nataša. Discovering disease-disease associations by fusing systems-level molecular data. Scientific reports 3, 2014. URL

## Conference contributions

Andova, Vesna, Kardoš, František, Škrekovski, Riste. Diameter on some classes of fullerene graphs. Proceedings of the 6th International Conference on Information Technologies and Information Society (ITIS 2014): 163-168, 2014. URL

Barišić, Renato, Bučar, Jože. Machine learning in classification of news portal articles. Proceedings of the 6th International Conference on Information Technologies and Information Society (ITIS 2014): 29-32, 2014. URL

Bučar, Jože, Povh, Janez. Case study : web clipping and sentiment analysis. Proceedings of the 6th International Conference on Information Technologies and Information Society (ITIS 2014): 75-80, 2014. URL

Dobrovoljc, Andrej. An approach to predict malicious threats. Proceedings of the 6th International Conference on Information Technologies and Information Society (ITIS 2014): 33-39, 2014. URL

Dobrovoljc, Andrej, Perko, Tomaž, Bučar, Jože. Information security culture of online banking users. Proceedings of the 6th International Conference on Information Technologies and Information Society (ITIS 2014): 120-126, 2014. URL

Dobrovoljc, Andrej, Zelenika, Darko, Pezdirc, Robert, Novosel, Helena, Kegljevič, Simon, Povh Janez, Ženko, Bernard, Tomas, Božo. Automatic invoice capture in small and medium-sized Slovenian enterprises : final report. Proceedings of the 6th International Conference on Information Technologies and Information Society (ITIS 2014): 104-111, 2014. URL

Govorčin, Jelena, Škrekovski, Riste. Extremal graphs with respect to vertex betweenness for certain graph families. Proceedings of the 6th International Conference on Information Technologies and Information Society (ITIS 2014): 154-162, 2014. URL

Kastrin, Andrej, Hristovski, Dimitar. Learning links in MeSH co-occurrence network : preliminary results. Think mind : DBKDA 2014, 161-164, 2014. URL

Kastrin, Andrej, Rindflesch, Thomas C., Hristovski, Dimitar. Link prediction in a MeSH co-occurrence network : preliminary. E-health - for continuity of care : proceedings of the MIE2014 205: 579-583, 2014. URL

Kastrin, Andrej, Hristovski, Dimitar. Napovedovanje povezav v omrežju MeSH deskriptorjev = Modeling links in MeSH descriptor network. Boljše informacije za več zdravja : zbornik prispevkov z recenzijo: 84-88, 2014.

Lužar, Borut, Petruševski, Mirko, Škrekovski, Riste. On parity and weak-parity edge-colorings. Proceedings of the 6th International Conference on Information Technologies and Information Society (ITIS 2014): 175-181, 2014. URL

Mesojedec, Uroš, Levnajić, Zoran. Assessing the potentials of cloud-native applications. Proceedings of the 6th International Conference on Information Technologies and Information Society (ITIS 2014): 62-67, 2014. URL

Zorko, Albert, Levnajić, Zoran. Diagnosing mental disorders as a result of changes in the autonomic nervous system function. Proceedings of the 6th International Conference on Information Technologies and Information Society (ITIS 2014): 90-96, 2014. URL

## 2013

## Scientific papers

Andova, Vesna, Knor, Martin, Potočnik, Primož, Škrekovski, Riste. On a variation of Randić index. Australasian journal of combinatorics 56: 61-75, 2013. URL

Andova, Vesna, Škrekovski, Riste. Diameter of fullerene graphs with full icosahedral symmetry. MATCH Communications in Mathematical and in Computer Chemistry 70 (1): 205-220, 2013. URL

Burgdorf, Sabine, Cafuta, Kristijan, Klep, Igor, Povh, Janez. Algorithmic aspects of sums of Hermitian squares of noncommutative polynomials. Computational optimization and applications 55 (1): 137-153, 2013. URL

Burgdorf, Sabine, Cafuta, Kristijan, Klep, Igor, Povh, Janez. The tracial moment problem and trace-positive polynomials. Mathematical programming 137 (1/2): 557-578, 2013. URL

Dickinson, Peter J. C., Eichfelder, Gabriele, Povh, Janez. Erratum to : on the set-semidefinite representation of nonconvex quadratic programs over arbitrary feasible sets. Optimization letters 1-11, 2013. URL

Dickinson, Peter J. C., Povh, Janez. Moment approximations for set-semidefinite polynomials. Journal of optimization theory and applications 159 (1): 57-68, 2013. URL

Eichfelder, Gabriele, Povh, Janez. On the set-semidefinite representation of nonconvex quadratic programs over arbitrary feasible sets. Optimization letters 7 (6): 1373-1386, 2013. URL

Govorčin, Jelena, Gvozdenović, Nebojša, Povh, Janez. New heuristics for the vertex coloring problem based on semidefinite programming. Central European Journal of Operations Research 21 (1): S14-S25, 2013. URL

Govorčin, Jelena, Knor, Martin, Škrekovski, Riste. Line graph operation and small worlds. Information processing letters 113 (5-6): 196-200, 2013. URL

Grannell, M.J., Knor, Martin. Dihedral biembeddings and triangulations by complete and complete tripartite graphs. Graphs and combinatorics 29 (4): 921-932, 2013. URL

Hayes, Wayne, Sun, Kai, Pržulj, Nataša. Graphlet-based measures are suitable for biological network comparison. Bioinformatics 29 (4): 483-491, 2013. URL

Knor, Martin, Potočnik, Primož. A note on 2-subset-regular self-complementary 3-uniform hypergraphs. Ars combinatoria 111: 33-36, 2013. URL

Knor, Martin, Potočnik, Primož, Škrekovski, Riste. Wiener index of iterated line graphs of trees homeomorphic to H. Discrete Mathematics 313 (10): 1104-1111, 2013. URL

Knor, Martin, Potočnik, Primož, Škrekovski, Riste. Wiener index of iterated line graphs of trees homeomorphic to the claw K [sub] {1,3}. Ars mathematica contemporanea 6 (2): 211-219, 2013. URL

Knor, Martin, Škrekovski, Riste. Deterministic self-similar models of complex networks based on very symmetric graphs. Physica. A 392 (19): 4629-4637, 2013. URL

Levnajić, Zoran. Derivative-variable correlation reveals the structure of dynamical networks. The European physical journal. B, Condensed matter physics 7: 1-7 (art. no. 298), 2013. URL

Lužar, Borut, Škrekovski, Riste. Improved bound on facial parity edge coloring. Discrete Mathematics 313 (20): 2218-2222, 2013. URL

Mockovčiakova, Martina, Sotak, Roman. Arbitrarily large difference between d-strong chromatic index and its trivial lower bound. Discrete Mathematics 313 (19): 2000-2006, 2013. URL

Povh, Janez. Contribution of copositive formulations to the graph partitioning problem. Optimization 62 (1): 71-83, 2013. URL

Vukašinović, Vida, Gregor, Petr, Škrekovski, Riste. On the mutually independent Hamiltonian cycles in faulty hypercubes. Information sciences 236: 224-235, 2013. URL

Žitnik, Marinka, Janjić, Vuk, Larminie, Chris, Zupan, Blaž, Pržulj, Nataša. Discovering disease-disease associations by fusing systems-level molecular data. Scientific reports: 1-9, 2013. URL

## Conference contributions

Bučar, Jože, Povh, Janez. A KNN based algorithm for text categorization. 12th International Symposium on Operational Research in Slovenia (SOR '13) proceedings: 367-372, 2013.

Bučar, Jože, Povh, Janez. Sentiment analysis in web text : an overview. Recent advances in information science : proceedings of the 7th European Computing Conference (EEC '13): 154-159, 2013. URL

Bučar, Jože, Zidar, Dejan, Mertik, Matej. Case study web clipping : the preliminary work. Proceedings of the 5th International Conference on Information Technologies and Information Society (ITIS 2013): 36-39, 2013. URL

Bučar, Jože, Zidar, Dejan, Mertik, Matej. Web clipping case study : digital trace of SMEs : (preliminary work). Proceedings of the 4th RapidMiner community meeting and conference (RCOMM 2013): 219-224, 2013. URL

Cafuta, Kristijan, Klep, Igor, Povh, Janez. Constrained eigenvalue and trace-optimization of polynomials in noncommuting variables. System modelling and optimization: programme and abstracts: 80, 2013. URL

Cafuta, Kristijan, Klep, Igor, Povh, Janez. Optimizations of free polynomials. 12th International Symposium on Operational Research in Slovenia (SOR '13) proceedings: 33-38, 2013.

Damij, Nadja, Jelenc, Franc, Levnajić, Zoran. Simulation of clinical functioning processes as complex network. Recent advances in information science : proceedings of the 7th European Computing Conference (EEC '13): 424-429, 2013. URL

Dickinson, Peter J. C., Povh, Janez. Application of polynomial approximation hierarchy to quadratic assignment problem. 12th International Symposium on Operational Research in Slovenia (SOR '13) proceedings: 373-378, 2013.

Dobrovoljc, Andrej. Agent based vulnerability discovery model. 12th International Symposium on Operational Research in Slovenia (SOR '13) proceedings: 379-384, 2013.

Dobrovoljc, Andrej. An approach to identify organizational security vulnerabilities. Proceedings of the 5th International Conference on Information Technologies and Information Society (ITIS 2013): 54-58, 2013. URL

Govorčin, Jelena, Kastrin, Andrej, Lužar, Borut, Pinterič, Uroš, Povh, Janez, Pandiloska Jurak, Alenka. Network analysis of the competence centres in Slovenia. Proceedings of the 5th International Conference on Information Technologies and Information Society (ITIS 2013): 24-34, 2013. URL

Levnajić, Zoran. Looking for stable pluralism. Proceedings of the 5th International Conference on Information Technologies and Information Society (ITIS 2013): 23, 2013. URL

Levnajić, Zoran, Lužar, Borut, Povh, Janez, Perc, Matjaž. Interdisciplinarity of Slovenian research. Proceedings of the 5th International Conference on Information Technologies and Information Society (ITIS 2013): 15-20, 2013. URL

Lužar, Borut. On facial parity edge colorings. Seventh Czech-Slovak International Symposium on Graph Theory, Combinatorics, 2013.

Mertik, Matej. Selecting crossplatform for mobile application development : food market communities LOKeT. Proceedings of the 5th International Conference on Information Technologies and Information Society (ITIS 2013): 142-145, 2013. URL

Povh, Janez, Dickinson, Peter J. C. A new convex reformulation and approximation hierarchy for polynomial optimization. The fourth international conference on continuous optimization of the Mathematical Optimization Society: 88, 2013. URL

Ravnikar, Edo, Lužar, Borut, Ravnikar, Martin, Šoper, Roman. The Way to efficient management of complex engineering design. Proceedings of the 5th International Conference on Information Technologies and Information Society (ITIS 2013): 73-83, 2013. URL

Tome, Matjaž, Dobrovoljc, Andrej. Information solutions for diabetes patients and healthcare professionals. Proceedings of the 5th International Conference on Information Technologies and Information Society (ITIS 2013): 114-121, 2013. URL

Zelenika, Darko, Keguljevič, Simon, Dobrovoljc, Andrej, Povh, Janez, Ženko, Bernard, Tomas, Božo. Automatic invoice capture in small and medium-sized Slovenian enterprises : project overview. Proceedings of the 5th International Conference on Information Technologies and Information Society (ITIS 2013) 40-46, 2013. URL

Zelenika, Darko, Povh, Janez, Dobrovoljc, Andrej. Document categorization based on OCR technology : an overview. Recent advances in information science : proceedings of the 7th European Computing Conference (EEC '13): 409-414, 2013. URL

## 2012

Vesna Andova, Nathann Cohen and Riste Škrekovski. A note on Zagreb indices inequality for trees and unicyclic graphs. *Ars Mathematica Contemporanea* 5(1):73-76, 2012. BibTeX

@article{ISI:000305552500004, author = "Andova, Vesna and Cohen, Nathann and \v{S}krekovski, Riste", title = "{A note on Zagreb indices inequality for trees and unicyclic graphs}", journal = "{Ars Mathematica Contemporanea}", year = "{2012}", volume = "{5}", pages = "{73-76}", number = "{1}", issn = "{1855-3966}", times-cited = "{2}", unique-id = "{ISI:000305552500004}" }

Vesna Andova, Darko Dimitrov, Jiri Fink and Riste Škrekovski. Bounds on Gutman Index. *Match-Communications In Mathematical And In Computer Chemistry* 67(2):515-524, 2012. BibTeX

@article{ISI:000301817800018, author = "Andova, Vesna and Dimitrov, Darko and Fink, Jiri and \v{S}krekovski, Riste", title = "{Bounds on Gutman Index}", journal = "{Match-Communications In Mathematical And In Computer Chemistry}", year = "{2012}", volume = "{67}", pages = "{515-524}", number = "{2}", issn = "{0340-6253}", times-cited = "{1}", unique-id = "{ISI:000301817800018}" }

Vesna Andova, Tomislav Doslic, Matjaz Krnc, Borut Lužar and Riste Škrekovski. On the Diameter and Related Invariants of Fullerene Graphs. *Match-Communications In Mathematical And In Computer Chemistry* 68(1):109-130, 2012. BibTeX

@article{ISI:000307149200006, author = "Andova, Vesna and Doslic, Tomislav and Krnc, Matjaz and Lu\v{z}ar, Borut and \v{S}krekovski, Riste", title = "{On the Diameter and Related Invariants of Fullerene Graphs}", journal = "{Match-Communications In Mathematical And In Computer Chemistry}", year = "{2012}", volume = "{68}", pages = "{109-130}", number = "{1}", issn = "{0340-6253}", times-cited = "{0}", unique-id = "{ISI:000307149200006}" }

Kristijan Cafuta, Igor Klep and Janez Povh. Constrained polynomial optimization problems with noncommuting variables. *Siam Journal on Optimization* 22(2):363-383, 2012. BibTeX

@article{Cafuta2012, author = "Cafuta, Kristijan and Klep, Igor and Povh, Janez", title = "Constrained polynomial optimization problems with noncommuting variables", journal = "Siam Journal on Optimization", year = 2012, volume = 22, pages = "363-383", number = 2, doi = "10.1137/110830733", owner = "andrej", timestamp = "2012.09.03" }

Marek Cygan, Michal Pilipczuk and Riste Škrekovski. On the Inequality between Radius and Randic Index for Graphs. *Match-Communications In Mathematical And In Computer Chemistry* 67(2):451-466, 2012. BibTeX

@article{ISI:000301817800013, author = "Cygan, Marek and Pilipczuk, Michal and \v{S}krekovski, Riste", title = "{On the Inequality between Radius and Randic Index for Graphs}", journal = "{Match-Communications In Mathematical And In Computer Chemistry}", year = "{2012}", volume = "{67}", pages = "{451-466}", number = "{2}", issn = "{0340-6253}", times-cited = "{0}", unique-id = "{ISI:000301817800013}" }

Jiri Fink, Borut Lužar and Riste Škrekovski. Some remarks on inverse Wiener index problem. *Discrete Applied Mathematics* 160(12):1851-1858, August 2012. BibTeX

@article{ISI:000305260600019, author = "Fink, Jiri and Lu\v{z}ar, Borut and \v{S}krekovski, Riste", title = "Some remarks on inverse Wiener index problem", journal = "Discrete Applied Mathematics", year = "{2012}", volume = "{160}", pages = "{1851-1858}", number = "{12}", month = "{AUG}", doi = "{10.1016/j.dam.2012.02.028}", issn = "{0166-218X}", times-cited = "{0}", unique-id = "{ISI:000305260600019}" }

Petr Gregor, Riste Škrekovski and Vida Vukasinovic. QUEUE LAYOUTS OF HYPERCUBES. *SIAM Journal On Discrete Mathematics* 26(1):77-88, 2012. BibTeX

@article{ISI:000302182600008, author = "Gregor, Petr and \v{S}krekovski, Riste and Vukasinovic, Vida", title = "{QUEUE LAYOUTS OF HYPERCUBES}", journal = "{SIAM Journal On Discrete Mathematics}", year = "{2012}", volume = "{26}", pages = "{77-88}", number = "{1}", doi = "{10.1137/100813865}", issn = "{0895-4801}", times-cited = "{0}", unique-id = "{ISI:000302182600008}" }

David Hudak, Frantisek Kardos, Borut Lužar, Roman Sotak and Riste Škrekovski. Acyclic edge coloring of planar graphs with Delta colors. *Discrete Applied Mathematics* 160(9):1356-1368, June 2012. BibTeX

@article{ISI:000303286800007, author = "Hudak, David and Kardos, Frantisek and Lu\v{z}ar, Borut and Sotak, Roman and \v{S}krekovski, Riste", title = "Acyclic edge coloring of planar graphs with Delta colors", journal = "Discrete Applied Mathematics", year = "{2012}", volume = "{160}", pages = "{1356-1368}", number = "{9}", month = "{JUN}", doi = "{10.1016/j.dam.2012.01.017}", issn = "{0166-218X}", times-cited = "{0}", unique-id = "{ISI:000303286800007}" }

Vuk Janjic and Natasa Przulj. Biological function through network topology: a survey of the human diseasome.. *Brief Funct Genomics*, September 2012. URL BibTeX

@article{Janjic2012, author = "Vuk Janjic and Natasa Przulj", title = "Biological function through network topology: a survey of the human diseasome.", journal = "Brief Funct Genomics", year = 2012, month = "Sep", __markedentry = "[andrej:]", abstract = "Molecular network data are increasingly becoming available, necessitating the development of well performing computational tools for their analyses. Such tools enabled conceptually different approaches for exploring human diseases to be undertaken, in particular, those that study the relationship between a multitude of biomolecules within a cell. Hence, a new field of network biology has emerged as part of systems biology, aiming to untangle the complexity of cellular network organization. We survey current network analysis methods that aim to give insight into human disease.", doi = "10.1093/bfgp/els037", language = "eng", medline-pst = "aheadofprint", owner = "andrej", pii = "els037", pmid = 22962330, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1093/bfgp/els037" }

Vuk Janjić and Nataša Pržulj. The core diseasome.. *Mol Biosyst* 8(10):2614–2625, August 2012. URL BibTeX

@article{Janjic2012a, author = "Vuk Janjić and Nataša Pržulj", title = "The core diseasome.", journal = "Mol Biosyst", year = 2012, volume = 8, pages = "2614--2625", number = 10, month = "Aug", __markedentry = "[andrej:]", abstract = {Large amounts of protein-protein interaction (PPI) data are available. The human PPI network currently contains over 56 000 interactions between 11 100 proteins. It has been demonstrated that the structure of this network is not random and that the same wiring patterns in it underlie the same biological processes and diseases. In this paper, we ask if there exists a subnetwork of the human PPI network such that its topology is the key to disease formation and hence should be the primary object of therapeutic intervention. We demonstrate that such a subnetwork exists and can be obtained purely computationally. In particular, by successively pruning the entire human PPI network, we are left with a "core" subnetwork that is not only topologically and functionally homogeneous, but is also enriched in disease genes, drug targets, and it contains genes that are known to drive disease formation. We call this subnetwork the Core Diseasome. Furthermore, we show that the topology of the Core Diseasome is unique in the human PPI network suggesting that it may be the wiring of this network that governs the mutagenesis that leads to disease. Explaining the mechanisms behind this phenomenon and exploiting them remains a challenge.}, doi = "10.1039/c2mb25230a", institution = "Department of Computing, Imperial College London, London, SW7 2AZ, UK. This email address is being protected from spambots. You need JavaScript enabled to view it. .", language = "eng", medline-pst = "ppublish", owner = "andrej", pmid = 22820726, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1039/c2mb25230a" }

Andrew D King, Nataša Pržulj and Igor Jurisica. Protein complex prediction with RNSC.. *Methods Mol Biol* 804:297–312, 2012. URL BibTeX

@article{King2012, author = "Andrew D King and Nataša Pržulj and Igor Jurisica", title = "Protein complex prediction with RNSC.", journal = "Methods Mol Biol", year = 2012, volume = 804, pages = "297--312", __markedentry = "[andrej:]", abstract = "Graph theory analysis of biological networks, such as protein-protein interactions (PPIs), gene regulatory, metabolic, etc., has identified a strong relationship between topology of these networks and the underlying cellular function and biological processes (Sharan et al. Mol Syst Biol 3:88, 2007). We focus on PPI networks, in which nodes correspond to proteins and edges represent interactions among the proteins. The size of these networks is ever growing, and thus efficient identification of various network motifs and dense sub-networks has become necessary. Predicting highly connected sub-graphs in a PPI network is important to biologists as it may help to identify biologically meaningful protein complexes, and with further integrative analysis may lead to identifying dynamic assembly of individual subunits in these complexes. In this chapter, we describe one method for predicting protein complexes in two steps. The first step is to partition the nodes of a PPI network (i.e. proteins) into highly connected groups or clusters using the Restricted Neighbourhood Search Clustering algorithm. This provides a set of clusters that represent candidate complexes. The second step of the method is to filter the candidate complexes based on three criteria: minimum cluster size, minimum interaction density, and minimum functional homogeneity, which reflects the extent to which the proteins of the candidate cluster operate in the same functional group. Candidate complexes passing all three criteria are then put forward as predicted protein complexes. The effectiveness of this method is investigated in the previous studies (King et al. Bioinformatics 20:3013-3020, 2004; Brohee and van Helden BMC Bioinformatics 7:488, 2006; and Moschopoulos et al. BMC Bioinformatics 10(Suppl 6):S11, 2009).", doi = "10.1007/978-1-61779-361-5_16", institution = "Department of Industrial Engineering and Operations Research, Columbia University, New York, NY, USA.", keywords = "Algorithms; Animals; Caenorhabditis elegans; Cluster Analysis; Computational Biology, methods; Multiprotein Complexes, genetics; Protein Interaction Maps, genetics; Saccharomyces cerevisiae; Systems Biology, methods", language = "eng", medline-pst = "ppublish", owner = "andrej", pmid = 22144160, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1007/978-1-61779-361-5_16" }

M Knor, P Potocnik and R Škrekovski. On a conjecture about Wiener index in iterated line graphs of trees. *Discrete Mathematics* 312(6):1094-1105, 2012. BibTeX

@article{ISI:000300811200003, author = "Knor, M. and Potocnik, P. and \v{S}krekovski, R.", title = "{On a conjecture about Wiener index in iterated line graphs of trees}", journal = "{Discrete Mathematics}", year = "{2012}", volume = "{312}", pages = "{1094-1105}", number = "{6}", month = "{MAR 28}", doi = "{10.1016/j.disc.2011.11.023}", issn = "{0012-365X}", times-cited = "{0}", unique-id = "{ISI:000300811200003}" }

Martin Kochol and Riste Škrekovski. Brooks' Theorem for generalized dart graphs. *Information Processing Letters* 112(5):200-204, 2012. BibTeX

@article{ISI:000300467800009, author = "Kochol, Martin and \v{S}krekovski, Riste", title = "{Brooks' Theorem for generalized dart graphs}", journal = "{Information Processing Letters}", year = "{2012}", volume = "{112}", pages = "{200-204}", number = "{5}", month = "{FEB 28}", doi = "{10.1016/j.ipl.2011.11.010}", issn = "{0020-0190}", times-cited = "{0}", unique-id = "{ISI:000300467800009}" }

Vesna Memišević and Nataša Pržulj. C-GRAAL: common-neighbors-based global GRAph ALignment of biological networks.. *Integr Biol (Camb)* 4(7):734–743, July 2012. URL BibTeX

@article{Memisevic2012, author = "Vesna Memišević and Nataša Pržulj", title = "C-GRAAL: common-neighbors-based global GRAph ALignment of biological networks.", journal = "Integr Biol (Camb)", year = 2012, volume = 4, pages = "734--743", number = 7, month = "Jul", __markedentry = "[andrej:]", abstract = "Networks are an invaluable framework for modeling biological systems. Analyzing protein-protein interaction (PPI) networks can provide insight into underlying cellular processes. It is expected that comparison and alignment of biological networks will have a similar impact on our understanding of evolution, biological function, and disease as did sequence comparison and alignment. Here, we introduce a novel pairwise global alignment algorithm called Common-neighbors based GRAph ALigner (C-GRAAL) that uses heuristics for maximizing the number of aligned edges between two networks and is based solely on network topology. As such, it can be applied to any type of network, such as social, transportation, or electrical networks. We apply C-GRAAL to align PPI networks of eukaryotic and prokaryotic species, as well as inter-species PPI networks, and we demonstrate that the resulting alignments expose large connected and functionally topologically aligned regions. We use the resulting alignments to transfer biological knowledge across species, successfully validating many of the predictions. Moreover, we show that C-GRAAL can be used to align human-pathogen inter-species PPI networks and that it can identify patterns of pathogen interactions with host proteins solely from network topology.", doi = "10.1039/c2ib00140c", institution = "Department of Computer Science, University of California, Irvine, Irvine, CA 92697-3435, USA.", language = "eng", medline-pst = "ppublish", owner = "andrej", pmid = 22234340, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1039/c2ib00140c" }

Dutour M Sikiric, M Knor, P Potocnik, J Siran and R Škrekovski. Hyperbolic analogues of fullerenes on orientable surfaces. *Discrete Mathematics* 312(4):729-736, 2012. BibTeX

@article{ISI:000300481200003, author = "Sikiric, M. Dutour and Knor, M. and Potocnik, P. and Siran, J. and \v{S}krekovski, R.", title = "{Hyperbolic analogues of fullerenes on orientable surfaces}", journal = "{Discrete Mathematics}", year = "{2012}", volume = "{312}", pages = "{729-736}", number = "{4}", month = "{FEB 28}", doi = "{10.1016/j.disc.2011.11.009}", issn = "{0012-365X}", times-cited = "{0}", unique-id = "{ISI:000300481200003}" }

## 2011

Vesna Andova, Saso Bogoev, Darko Dimitrov, Marcin Pilipczuk and Riste Škrekovski. On the Zagreb index inequality of graphs with prescribed vertex degrees. *Discrete Applied Mathematics* 159(8):852-858, 2011. BibTeX

@article{ISI:000289539800020, author = "Andova, Vesna and Bogoev, Saso and Dimitrov, Darko and Pilipczuk, Marcin and \v{S}krekovski, Riste", title = "{On the Zagreb index inequality of graphs with prescribed vertex degrees}", journal = "{Discrete Applied Mathematics}", year = "{2011}", volume = "{159}", pages = "{852-858}", number = "{8}", month = "{APR 28}", doi = "{10.1016/j.dam.2011.01.002}", issn = "{0166-218X}", times-cited = "{3}", unique-id = "{ISI:000289539800020}" }

Vesna Andova, Nathann Cohen and Riste Škrekovski. Graph Classes (Dis)satisfying the Zagreb Indices Inequality. *Match-Communications In Mathematical And In Computer Chemistry* 65(3):647-658, 2011. BibTeX

@article{ISI:000290503400004, author = "Andova, Vesna and Cohen, Nathann and \v{S}krekovski, Riste", title = "{Graph Classes (Dis)satisfying the Zagreb Indices Inequality}", journal = "{Match-Communications In Mathematical And In Computer Chemistry}", year = "{2011}", volume = "{65}", pages = "{647-658}", number = "{3}", issn = "{0340-6253}", times-cited = "{6}", unique-id = "{ISI:000290503400004}" }

Arabidopsis Interactome Mapping Consortium. Evidence for network evolution in an Arabidopsis interactome map.. *Science* 333(6042):601–607, July 2011. URL BibTeX

@article{Consortium2011, author = "Arabidopsis Interactome Mapping Consortium", title = "Evidence for network evolution in an Arabidopsis interactome map.", journal = "Science", year = 2011, volume = 333, pages = "601--607", number = 6042, month = "Jul", __markedentry = "[andrej:]", abstract = "Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing about 6200 highly reliable interactions between about 2700 proteins. A global organization of plant biological processes emerges from community analyses of the resulting network, together with large numbers of novel hypothetical functional links between proteins and pathways. We observe a dynamic rewiring of interactions following gene duplication events, providing evidence for a model of evolution acting upon interactome networks. This and future plant interactome maps should facilitate systems approaches to better understand plant biology and improve crops.", doi = "10.1126/science.1203877", institution = "Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.", keywords = "14-3-3 Proteins, metabolism; Arabidopsis Proteins, genetics/metabolism; Arabidopsis, genetics/metabolism; Evolution, Molecular; Genes, Plant; Plant Growth Regulators, metabolism; Protein Interaction Mapping; Proteome; Signal Transduction; Transcription Factors, metabolism; Ubiquitination", language = "eng", medline-pst = "ppublish", owner = "andrej", pii = "333/6042/601", pmid = 21798944, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1126/science.1203877" }

Marek Cygan, Michal Pilipczuk and Riste Škrekovski. Relation Between Randic Index and Average Distance of Trees. *Match-Communications In Mathematical And In Computer Chemistry* 66(2):605-612, 2011. BibTeX

@article{ISI:000294591400006, author = "Cygan, Marek and Pilipczuk, Michal and \v{S}krekovski, Riste", title = "{Relation Between Randic Index and Average Distance of Trees}", journal = "{Match-Communications In Mathematical And In Computer Chemistry}", year = "{2011}", volume = "{66}", pages = "{605-612}", number = "{2}", issn = "{0340-6253}", times-cited = "{0}", unique-id = "{ISI:000294591400006}" }

Zdenek Dvorak, Bernard Lidicky and Riste Škrekovski. Randic index and the diameter of a graph. *European Journal Of Combinatorics* 32(3):434-442, April 2011. BibTeX

@article{ISI:000287613300011, author = "Dvorak, Zdenek and Lidicky, Bernard and \v{S}krekovski, Riste", title = "{Randic index and the diameter of a graph}", journal = "{European Journal Of Combinatorics}", year = "{2011}", volume = "{32}", pages = "{434-442}", number = "{3}", month = "{APR}", doi = "{10.1016/j.ejc.2010.12.002}", issn = "{0195-6698}", times-cited = "{1}", unique-id = "{ISI:000287613300011}" }

Zdenek Dvorak, Bernard Lidicky and Riste Škrekovski. Graphs with two crossings are 5-choosable. *SIAM Journal On Discrete Mathematics* 25(4):1746-1753, 2011. BibTeX

@article{ISI:000298348400017, author = "Dvorak, Zdenek and Lidicky, Bernard and \v{S}krekovski, Riste", title = "{Graphs with two crossings are 5-choosable}", journal = "{SIAM Journal On Discrete Mathematics}", year = "{2011}", volume = "{25}", pages = "{1746-1753}", number = "{4}", doi = "{10.1137/11082703X}", issn = "{0895-4801}", times-cited = "{0}", unique-id = "{ISI:000298348400017}" }

Tomas Kaiser, Ondrej Rucky and Riste Škrekovski. GRAPHS WITH ODD CYCLE LENGTHS 5 AND 7 ARE 3-COLORABLE. *SIAM Journal On Discrete Mathematics* 25(3):1069-1088, 2011. BibTeX

@article{ISI:000295398200003, author = "Kaiser, Tomas and Rucky, Ondrej and \v{S}krekovski, Riste", title = "{GRAPHS WITH ODD CYCLE LENGTHS 5 AND 7 ARE 3-COLORABLE}", journal = "{SIAM Journal On Discrete Mathematics}", year = "{2011}", volume = "{25}", pages = "{1069-1088}", number = "{3}", doi = "{10.1137/090761860}", issn = "{0895-4801}", times-cited = "{0}", unique-id = "{ISI:000295398200003}" }

Tomas Kaiser, Matej Stehlik and Riste Škrekovski. On the 2-Resonance of fullerenes. *SIAM JOURNAL ON DISCRETE MATHEMATICS* 25(4):1737-1745, 2011. BibTeX

@article{ISI:000298348400016, author = "Kaiser, Tomas and Stehlik, Matej and \v{S}krekovski, Riste", title = "{On the 2-Resonance of fullerenes}", journal = "{SIAM JOURNAL ON DISCRETE MATHEMATICS}", year = "{2011}", volume = "{25}", pages = "{1737-1745}", number = "{4}", doi = "{10.1137/10078699X}", issn = "{0895-4801}", times-cited = "{0}", unique-id = "{ISI:000298348400016}" }

Oleksii Kuchaiev and Natasa Przulj. Integrative network alignment reveals large regions of global network similarity in yeast and human.. *Bioinformatics* 27(10):1390–1396, May 2011. URL BibTeX

@article{Kuchaiev2011, author = "Oleksii Kuchaiev and Natasa Przulj", title = "Integrative network alignment reveals large regions of global network similarity in yeast and human.", journal = "Bioinformatics", year = 2011, volume = 27, pages = "1390--1396", number = 10, month = "May", __markedentry = "[andrej:]", abstract = "High-throughput methods for detecting molecular interactions have produced large sets of biological network data with much more yet to come. Analogous to sequence alignment, efficient and reliable network alignment methods are expected to improve our understanding of biological systems. Unlike sequence alignment, network alignment is computationally intractable. Hence, devising efficient network alignment heuristics is currently a foremost challenge in computational biology.We introduce a novel network alignment algorithm, called Matching-based Integrative GRAph ALigner (MI-GRAAL), which can integrate any number and type of similarity measures between network nodes (e.g. proteins), including, but not limited to, any topological network similarity measure, sequence similarity, functional similarity and structural similarity. Hence, we resolve the ties in similarity measures and find a combination of similarity measures yielding the largest contiguous (i.e. connected) and biologically sound alignments. MI-GRAAL exposes the largest functional, connected regions of protein-protein interaction (PPI) network similarity to date: surprisingly, it reveals that 77.7\% of proteins in the baker's yeast high-confidence PPI network participate in such a subnetwork that is fully contained in the human high-confidence PPI network. This is the first demonstration that species as diverse as yeast and human contain so large, continuous regions of global network similarity. We apply MI-GRAAL's alignments to predict functions of un-annotated proteins in yeast, human and bacteria validating our predictions in the literature. Furthermore, using network alignment scores for PPI networks of different herpes viruses, we reconstruct their phylogenetic relationship. This is the first time that phylogeny is exactly reconstructed from purely topological alignments of PPI networks.Supplementary files and MI-GRAAL executables: http://bio-nets.doc.ic.ac.uk/MI-GRAAL/.", doi = "10.1093/bioinformatics/btr127", institution = "Department of Computer Science, University of California Irvine, Irvine, CA 92617, USA.", keywords = "Algorithms; Artificial Intelligence; Computational Biology, methods; Humans; Molecular Sequence Annotation; Proteins, chemistry/metabolism; Saccharomyces cerevisiae, genetics/metabolism; Sequence Alignment", language = "eng", medline-pst = "ppublish", owner = "andrej", pii = "btr127", pmid = 21414992, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1093/bioinformatics/btr127" }

Oleksii Kuchaiev, Aleksandar Stevanović, Wayne Hayes and Nataša Pržulj. GraphCrunch 2: Software tool for network modeling, alignment and clustering.. *BMC Bioinformatics* 12:24, 2011. URL BibTeX

@article{Kuchaiev2011a, author = "Oleksii Kuchaiev and Aleksandar Stevanović and Wayne Hayes and Nataša Pržulj", title = "GraphCrunch 2: Software tool for network modeling, alignment and clustering.", journal = "BMC Bioinformatics", year = 2011, volume = 12, pages = 24, __markedentry = "[andrej:]", abstract = {Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype.We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an algorithm for clustering nodes within a network based solely on their topological similarities. Using GraphCrunch 2, we demonstrate that eukaryotic and viral PPI networks may belong to different graph model families and show that topology-based clustering can reveal important functional similarities between proteins within yeast and human PPI networks.GraphCrunch 2 is a software tool that implements the latest research on biological network analysis. It parallelizes computationally intensive tasks to fully utilize the potential of modern multi-core CPUs. It is open-source and freely available for research use. It runs under the Windows and Linux platforms.}, doi = "10.1186/1471-2105-12-24", institution = "Department of Computer Science, University of California, Irvine, CA, USA.", keywords = "Algorithms; Cluster Analysis; Humans; Models, Biological; Protein Interaction Mapping, methods; Sequence Alignment; Software; Viral Proteins, metabolism", language = "eng", medline-pst = "epublish", owner = "andrej", pii = "1471-2105-12-24", pmid = 21244715, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1186/1471-2105-12-24" }

Zoran Levnajic. Emergent multistability and frustration in phase-repulsive networks of oscillators. *Physical Review E* 84(1, Part 2), 2011. BibTeX

@article{ISI:000293457800010, author = "Levnajic, Zoran", title = "{Emergent multistability and frustration in phase-repulsive networks of oscillators}", journal = "{Physical Review E}", year = "{2011}", volume = "{84}", number = "{1, Part 2}", month = "{JUL 29}", abstract = "{The collective dynamics of oscillator networks with phase-repulsive coupling is studied, considering various network sizes and topologies. The notion of link frustration is introduced to characterize and quantify the network dynamical states. In opposition to widely studied phase-attractive case, the properties of final dynamical states in our model critically depend on the network topology. In particular, each network's total frustration value is intimately related to its topology. Moreover, phase-repulsive networks in general display multiple final frustration states, whose statistical and stability properties are uniquely identifying them.}", article-number = "{016231}", doi = "{10.1103/PhysRevE.84.016231}", issn = "{1539-3755}", unique-id = "{ISI:000293457800010}" }

Zoran Levnajic and Arkady Pikovsky. Network Reconstruction from Random Phase Resetting. *Physical Review Letters* 107(3), 2011. BibTeX

@article{ISI:000292597400009, author = "Levnajic, Zoran and Pikovsky, Arkady", title = "{Network Reconstruction from Random Phase Resetting}", journal = "{Physical Review Letters}", year = "{2011}", volume = "{107}", number = "{3}", month = "{JUL 11}", abstract = "{We propose a novel method of reconstructing the topology and interaction functions for a general oscillator network. An ensemble of initial phases and the corresponding instantaneous frequencies is constructed by repeating random phase resets of the system dynamics. The desired details of network structure are then revealed by appropriately averaging over the ensemble. The method is applicable for a wide class of networks with arbitrary emergent dynamics, including full synchrony.}", article-number = "{034101}", doi = "{10.1103/PhysRevLett.107.034101}", issn = "{0031-9007}", unique-id = "{ISI:000292597400009}" }

Tijana Milenković, Vesna Memišević, Anthony Bonato and Nataša Pržulj. Dominating biological networks.. *PLoS One* 6(8):e23016, 2011. URL BibTeX

@article{Milenkovic2011, author = "Tijana Milenković and Vesna Memišević and Anthony Bonato and Nataša Pržulj", title = "Dominating biological networks.", journal = "PLoS One", year = 2011, volume = 6, pages = "e23016", number = 8, __markedentry = "[andrej:]", abstract = {Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI) networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A debate remains open about whether network properties of "biologically central (BC)" genes (i.e., their protein products), such as those involved in aging, cancer, infectious diseases, or signaling and drug-targeted pathways, exhibit some topological centrality compared to the rest of the proteins in the human PPI network.To help resolve this debate, we design new network-based approaches and apply them to get new insight into biological function and disease. We hypothesize that BC genes have a topologically central (TC) role in the human PPI network. We propose two different concepts of topological centrality. We design a new centrality measure to capture complex wirings of proteins in the network that identifies as TC those proteins that reside in dense extended network neighborhoods. Also, we use the notion of domination and find dominating sets (DSs) in the PPI network, i.e., sets of proteins such that every protein is either in the DS or is a neighbor of the DS. Clearly, a DS has a TC role, as it enables efficient communication between different network parts. We find statistically significant enrichment in BC genes of TC nodes and outperform the existing methods indicating that genes involved in key biological processes occupy topologically complex and dense regions of the network and correspond to its "spine" that connects all other network parts and can thus pass cellular signals efficiently throughout the network. To our knowledge, this is the first study that explores domination in the context of PPI networks.}, doi = "10.1371/journal.pone.0023016", institution = "Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana, United States of America.", keywords = "Aging, genetics; Algorithms; Humans; Pharmaceutical Preparations; Protein Binding; Protein Interaction Maps; Proteins, genetics/metabolism; Signal Transduction, genetics", language = "eng", medline-pst = "ppublish", owner = "andrej", pii = "PONE-D-11-03283", pmid = 21887225, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1371/journal.pone.0023016" }

Nataša Pržulj. Protein-protein interactions: making sense of networks via graph-theoretic modeling.. *Bioessays* 33(2):115–123, February 2011. URL BibTeX

@article{Przulj2011, author = "Nataša Pržulj", title = "Protein-protein interactions: making sense of networks via graph-theoretic modeling.", journal = "Bioessays", year = 2011, volume = 33, pages = "115--123", number = 2, month = "Feb", __markedentry = "[andrej:]", abstract = "The emerging area of network biology is seeking to provide insights into organizational principles of life. However, despite significant collaborative efforts, there is still typically a weak link between biological and computational scientists and a lack of understanding of the research issues across the disciplines. This results in the use of simple computational techniques of limited potential that are incapable of explaining these complex data. Hence, the danger is that the community might begin to view the topological properties of network data as mere statistics, rather than rich sources of biological information. A further danger is that such views might result in the imposition of scientific doctrines, such as scale-free-centric (on the modeling side) and genome-centric (on the biological side) opinions onto this area. Here, we take a graph-theoretic perspective on protein-protein interaction networks and present a high-level overview of the area, commenting on possible challenges ahead.", doi = "10.1002/bies.201000044", institution = "Department of Computing, Imperial College London, London, UK. This email address is being protected from spambots. You need JavaScript enabled to view it. ", keywords = "Algorithms; Animals; Computational Biology, methods; Computer Simulation; Genome; Humans; Models, Biological; Protein Binding; Protein Interaction Domains and Motifs; Proteins, metabolism; Research Design", language = "eng", medline-pst = "ppublish", owner = "andrej", pmid = 21188720, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1002/bies.201000044" }

## 2010

Kristijan Cafuta, Igor Klep and Janez Povh. A note on the nonexistence of sum of squares certificates for the Bessis-Moussa-Villani conjecture. *Journal Of Mathematical Physics* 51(8), August 2010. BibTeX

@article{ISI:000281905000050, author = "Cafuta, Kristijan and Klep, Igor and Povh, Janez", title = "{A note on the nonexistence of sum of squares certificates for the Bessis-Moussa-Villani conjecture}", journal = "{Journal Of Mathematical Physics}", year = "{2010}", volume = "{51}", number = "{8}", month = "{AUG}", doi = "{10.1063/1.3462915}" }

Nathann Cohen, Darko Dimitrov, Roi Krakovski, Riste Škrekovski and Vida Vukasinovic. On Wiener Index of Graphs and Their Line Graphs. *Match-Communications In Mathematical And In Computer Chemistry* 64(3):683-698, 2010. BibTeX

@article{ISI:000284555400010, author = "Cohen, Nathann and Dimitrov, Darko and Krakovski, Roi and \v{S}krekovski, Riste and Vukasinovic, Vida", title = "{On Wiener Index of Graphs and Their Line Graphs}", journal = "{Match-Communications In Mathematical And In Computer Chemistry}", year = "{2010}", volume = "{64}", pages = "{683-698}", number = "{3}", issn = "{0340-6253}", times-cited = "{6}", unique-id = "{ISI:000284555400010}" }

Zdenek Dvorak, Daniel Kral and Riste Škrekovski. Non-Rainbow Colorings of 3-, 4-and 5-Connected Plane Graphs. *Journal Of Graph Theory* 63(2):129-145, February 2010. BibTeX

@article{ISI:000273584500004, author = "Dvorak, Zdenek and Kral, Daniel and \v{S}krekovski, Riste", title = "{Non-Rainbow Colorings of 3-, 4-and 5-Connected Plane Graphs}", journal = "{Journal Of Graph Theory}", year = "{2010}", volume = "{63}", pages = "{129-145}", number = "{2}", month = "{FEB}", doi = "{10.1002/jgt.20414}", issn = "{0364-9024}", times-cited = "{1}", unique-id = "{ISI:000273584500004}" }

Zdenek Dvorak, Bernard Lidicky and Riste Škrekovski. 3-CHOOSABILITY OF TRIANGLE-FREE PLANAR GRAPHS WITH CONSTRAINTS ON 4-CYCLES. *Siam Journal On Discrete Mathematics* 24(3):934-945, 2010. BibTeX

@article{ISI:000282291600015, author = "Dvorak, Zdenek and Lidicky, Bernard and \v{S}krekovski, Riste", title = "{3-CHOOSABILITY OF TRIANGLE-FREE PLANAR GRAPHS WITH CONSTRAINTS ON 4-CYCLES}", journal = "{Siam Journal On Discrete Mathematics}", year = "{2010}", volume = "{24}", pages = "{934-945}", number = "{3}", doi = "{10.1137/080743020}", issn = "{0895-4801}", times-cited = "{2}", unique-id = "{ISI:000282291600015}" }

Louis Esperet, Daniel Kral, Petr Skoda and Riste Škrekovski. An improved linear bound on the number of perfect matchings in cubic graphs. *European Journal Of Combinatorics* 31(5):1316-1334, July 2010. BibTeX

@article{ISI:000278729800011, author = "Esperet, Louis and Kral, Daniel and Skoda, Petr and \v{S}krekovski, Riste", title = "{An improved linear bound on the number of perfect matchings in cubic graphs}", journal = "{European Journal Of Combinatorics}", year = "{2010}", volume = "{31}", pages = "{1316-1334}", number = "{5}", month = "{JUL}", doi = "{10.1016/j.ejc.2009.11.008}", issn = "{0195-6698}", times-cited = "{2}", unique-id = "{ISI:000278729800011}" }

Petr Gregor and Riste Škrekovski. On generalized middle-level problem. *Information Sciences* 180(12):2448-2457, 2010. BibTeX

@article{ISI:000277471400008, author = "Gregor, Petr and \v{S}krekovski, Riste", title = "{On generalized middle-level problem}", journal = "{Information Sciences}", year = "{2010}", volume = "{180}", pages = "{2448-2457}", number = "{12}", month = "{JUN 15}", doi = "{10.1016/j.ins.2010.02.009}", issn = "{0020-0255}", times-cited = "{0}", unique-id = "{ISI:000277471400008}" }

Frederic Havet, Daniel Kral, Jean-Sebastien Sereni and Riste Škrekovski. Facial colorings using Hall's Theorem. *European Journal Of Combinatorics* 31(3):1001-1019, April 2010. BibTeX

@article{ISI:000275701300027, author = "Havet, Frederic and Kral, Daniel and Sereni, Jean-Sebastien and \v{S}krekovski, Riste", title = "{Facial colorings using Hall's Theorem}", journal = "{European Journal Of Combinatorics}", year = "{2010}", volume = "{31}", pages = "{1001-1019}", number = "{3}", month = "{APR}", doi = "{10.1016/j.ejc.2009.10.003}", issn = "{0195-6698}", times-cited = "{1}", unique-id = "{ISI:000275701300027}" }

Hsiang Ho, Tijana Milenković, Vesna Memisević, Jayavani Aruri, Natasa Przulj and Anand K Ganesan. Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets.. *BMC Syst Biol* 4:84, 2010. URL BibTeX

@article{Ho2010, author = "Hsiang Ho and Tijana Milenković and Vesna Memisević and Jayavani Aruri and Natasa Przulj and Anand K Ganesan", title = "Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets.", journal = "BMC Syst Biol", year = 2010, volume = 4, pages = 84, __markedentry = "[andrej:]", abstract = {RNA-mediated interference (RNAi)-based functional genomics is a systems-level approach to identify novel genes that control biological phenotypes. Existing computational approaches can identify individual genes from RNAi datasets that regulate a given biological process. However, currently available methods cannot identify which RNAi screen "hits" are novel components of well-characterized biological pathways known to regulate the interrogated phenotype. In this study, we describe a method to identify genes from RNAi datasets that are novel components of known biological pathways. We experimentally validate our approach in the context of a recently completed RNAi screen to identify novel regulators of melanogenesis.In this study, we utilize a PPI network topology-based approach to identify targets within our RNAi dataset that may be components of known melanogenesis regulatory pathways. Our computational approach identifies a set of screen targets that cluster topologically in a human PPI network with the known pigment regulator Endothelin receptor type B (EDNRB). Validation studies reveal that these genes impact pigment production and EDNRB signaling in pigmented melanoma cells (MNT-1) and normal melanocytes.We present an approach that identifies novel components of well-characterized biological pathways from functional genomics datasets that could not have been identified by existing statistical and computational approaches.}, doi = "10.1186/1752-0509-4-84", institution = "Department of Biological Chemistry, University of California, Irvine, 92697-1700, USA.", keywords = "Computational Biology, methods; Gene Regulatory Networks, genetics; Genomics, methods; Humans; Melanins, biosynthesis/genetics; Melanocytes, metabolism; Models, Biological; Protein Interaction Mapping, methods; RNA Interference; Receptor, Endothelin B, metabolism; Signal Transduction, genetics", language = "eng", medline-pst = "epublish", owner = "andrej", pii = "1752-0509-4-84", pmid = 20550706, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1186/1752-0509-4-84" }

Robyn M Kaake, Tijana Milenković, Natasa Przulj, Peter Kaiser and Lan Huang. Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy.. *J Proteome Res* 9(4):2016–2029, April 2010. URL BibTeX

@article{Kaake2010, author = "Robyn M Kaake and Tijana Milenković and Natasa Przulj and Peter Kaiser and Lan Huang", title = "Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy.", journal = "J Proteome Res", year = 2010, volume = 9, pages = "2016--2029", number = 4, month = "Apr", __markedentry = "[andrej:]", abstract = "Ubiquitin-proteasome dependent protein degradation plays a fundamental role in the regulation of the eukaryotic cell cycle. Cell cycle transitions between different phases are tightly regulated to prevent uncontrolled cell proliferation, which is characteristic of cancer cells. To understand cell cycle phase specific regulation of the 26S proteasome and reveal the molecular mechanisms underlying the ubiquitin-proteasome degradation pathway during cell cycle progression, we have carried out comprehensive characterization of cell cycle phase specific proteasome interacting proteins (PIPs) by QTAX analysis of synchronized yeast cells. Our efforts have generated specific proteasome interaction networks for the G1, S, and M phases of the cell cycle and identified a total of 677 PIPs, 266 of which were not previously identified from unsynchronized cells. On the basis of the dynamic changes of their SILAC ratios across the three cell cycle phases, we have employed a profile vector-based clustering approach and identified 20 functionally significant groups of PIPs, 3 of which are enriched with cell cycle related functions. This work presents the first step toward understanding how dynamic proteasome interactions are involved in various cellular pathways during the cell cycle.", doi = "10.1021/pr1000175", institution = "Cell Biology, University of California, Irvine, California 92697-4560, USA.", keywords = "Cell Cycle Proteins, chemistry/classification/metabolism; Flow Cytometry; Formaldehyde; Fungal Proteins, chemistry/classification/metabolism; Immunoprecipitation; Isotope Labeling; Proteasome Endopeptidase Complex, chemistry/classification/metabolism; Protein Interaction Mapping, methods; Reproducibility of Results; Tandem Mass Spectrometry, methods; Yeasts, metabolism", language = "eng", medline-pst = "ppublish", owner = "andrej", pmid = 20170199, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1021/pr1000175" }

Frantisek Kardos, Matjaz Krnc, Borut Lužar and Riste Škrekovski. Cyclic 7-edge-cuts in fullerene graphs. *Journal Of Mathematical Chemistry* 47(2):771-789, February 2010. BibTeX

@article{ISI:000273480100012, author = "Kardos, Frantisek and Krnc, Matjaz and Lu\v{z}ar, Borut and \v{S}krekovski, Riste", title = "{Cyclic 7-edge-cuts in fullerene graphs}", journal = "{Journal Of Mathematical Chemistry}", year = "{2010}", volume = "{47}", pages = "{771-789}", number = "{2}", month = "{FEB}", doi = "{10.1007/s10910-009-9599-0}", issn = "{0259-9791}", times-cited = "{1}", unique-id = "{ISI:000273480100012}" }

Igor Klep and Janez Povh. Semidefinite programming and sums of hermitian squares of noncommutative polynomials. *Journal Of Pure And Applied Algebra* 214(6):740-749, June 2010. BibTeX

@article{ISI:000274928100003, author = "Klep, Igor and Povh, Janez", title = "{Semidefinite programming and sums of hermitian squares of noncommutative polynomials}", journal = "{Journal Of Pure And Applied Algebra}", year = "{2010}", volume = "{214}", pages = "{740-749}", number = "{6}", month = "{JUN}", doi = "{10.1016/j.jpaa.2009.07.003}" }

Lukasz Kowalik, Borut Lužar and Riste Škrekovski. An improved bound on the largest induced forests for triangle-free planar graphs. *Discrete Mathematics And Theoretical Computer Science* 12(1):29-42, 2010. BibTeX

@article{ISI:000275225700003, author = "Kowalik, Lukasz and Lu\v{z}ar, Borut and \v{S}krekovski, Riste", title = "{An improved bound on the largest induced forests for triangle-free planar graphs}", journal = "{Discrete Mathematics And Theoretical Computer Science}", year = "{2010}", volume = "{12}", pages = "{29-42}", number = "{1}", issn = "{1365-8050}", times-cited = "{0}", unique-id = "{ISI:000275225700003}" }

Oleksii Kuchaiev, Tijana Milenkovic, Vesna Memisevic, Wayne Hayes and Natasa Przulj. Topological network alignment uncovers biological function and phylogeny.. *J R Soc Interface* 7(50):1341–1354, September 2010. URL BibTeX

@article{Kuchaiev2010, author = "Oleksii Kuchaiev and Tijana Milenkovic and Vesna Memisevic and Wayne Hayes and Natasa Przulj", title = "Topological network alignment uncovers biological function and phylogeny.", journal = "J R Soc Interface", year = 2010, volume = 7, pages = "1341--1354", number = 50, month = "Sep", __markedentry = "[andrej:]", abstract = "Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology and disease. Comparison and alignment of biological networks will probably have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. We demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from our alignments. Topology-based alignments have the potential to provide a completely new, independent source of phylogenetic information. Our alignment of the protein-protein interaction networks of two very different species-yeast and human-indicate that even distant species share a surprising amount of network topology, suggesting broad similarities in internal cellular wiring across all life on Earth.", doi = "10.1098/rsif.2010.0063", institution = "Department of Computer Science, University of California, Irvine, CA 92697-3435, USA.", keywords = "Algorithms; Computational Biology; Humans; Models, Biological; Phylogeny; Proteins, chemistry/genetics/metabolism; Saccharomyces cerevisiae Proteins, chemistry/genetics/metabolism; Saccharomyces cerevisiae, genetics/metabolism", language = "eng", medline-pst = "ppublish", owner = "andrej", pii = "rsif.2010.0063", pmid = 20236959, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1098/rsif.2010.0063" }

Zoran Levnajic and Igor Mezic. Ergodic theory and visualization. I. Mesochronic plots for visualization of ergodic partition and invariant sets. *Chaos* 20(3), September 2010. BibTeX

@article{ISI:000282438500014, author = "Levnajic, Zoran and Mezic, Igor", title = "{Ergodic theory and visualization. I. Mesochronic plots for visualization of ergodic partition and invariant sets}", journal = "{Chaos}", year = "{2010}", volume = "{20}", number = "{3}", month = "{SEP}", abstract = "{We present a computational study of a visualization method for invariant sets based on ergodic partition theory, first proposed by Mezicacute (Ph.D. thesis, Caltech, 1994) and Mezicacute and Wiggins {[}Chaos 9, 213 (1999)]. The algorithms for computation of the time averages of observables on phase space are developed and used to provide an approximation of the ergodic partition of the phase space. We term the graphical representation of this approximation-based on time averages of observables-a mesochronic plot (from Greek: meso-mean, chronos-time). The method is useful for identifying low-dimensional projections (e.g., two-dimensional slices) of invariant structures in phase spaces of dimensionality bigger than two. We also introduce the concept of the ergodic quotient space, obtained by assigning a point to every ergodic set, and provide an embedding method whose graphical representation we call the mesochronic scatter plot. We use the Chirikov standard map as a well-known and dynamically rich example in order to illustrate the implementation of our methods. In addition, we expose applications to other higher dimensional maps such as the Froeacuteschle map for which we utilize our methods to analyze merging of resonances and, the three-dimensional extended standard map for which we study the conjecture on its ergodicity {[}I. Mezicacute, Physica D 154, 51 (2001)]. We extend the study in our next paper {[}Z. Levnajicacute and I. Mezicacute, e-print arXiv:0808.2182] by investigating the visualization of periodic sets using harmonic time averages. Both of these methods are related to eigenspace structure of the Koopman operator {[}I. Mezicacute and A. Banaszuk, Physica D 197, 101 (2004)]. (c) 2010 American Institute of Physics. {[}doi: 10.1063/1.3458896]}", article-number = "{033114}", doi = "{10.1063/1.3458896}", issn = "{1054-1500}", unique-id = "{ISI:000282438500014}" }

Zoran Levnajic and Arkady Pikovsky. Phase resetting of collective rhythm in ensembles of oscillators. *Physical Review E* 82(5, Part 2), 2010. BibTeX

@article{ISI:000283777700003, author = "Levnajic, Zoran and Pikovsky, Arkady", title = "{Phase resetting of collective rhythm in ensembles of oscillators}", journal = "{Physical Review E}", year = "{2010}", volume = "{82}", number = "{5, Part 2}", month = "{NOV 3}", abstract = "{Phase resetting curves characterize the way a system with a collective periodic behavior responds to perturbations. We consider globally coupled ensembles of Sakaguchi-Kuramoto oscillators, and use the Ott-Antonsen theory of ensemble evolution to derive the analytical phase resetting equations. We show the final phase reset value to be composed of two parts: an immediate phase reset directly caused by the perturbation and the dynamical phase reset resulting from the relaxation of the perturbed system back to its dynamical equilibrium. Analytical, semianalytical and numerical approximations of the final phase resetting curve are constructed. We support our findings with extensive numerical evidence involving identical and nonidentical oscillators. The validity of our theory is discussed in the context of large ensembles approximating the thermodynamic limit.}", article-number = "{056202}", doi = "{10.1103/PhysRevE.82.056202}", issn = "{1539-3755}", unique-id = "{ISI:000283777700003}" }

Zoran Levnajic and Tomaz Prosen. Chaotic dephasing in a double-slit scattering experiment. *Chaos* 20(4), December 2010. BibTeX

@article{ISI:000285768500027, author = "Levnajic, Zoran and Prosen, Tomaz", title = "{Chaotic dephasing in a double-slit scattering experiment}", journal = "{Chaos}", year = "{2010}", volume = "{20}", number = "{4}", month = "{DEC}", abstract = "{We design a computational experiment in which a quantum particle tunnels into a billiard of variable shape and scatters out of it through a double-slit opening on the billiard's base. The interference patterns produced by the scattered probability currents for a range of energies are investigated in relation to the billiard's geometry which is connected to its classical integrability. Four billiards with hierarchical integrability levels are considered: integrable, pseudointegrable, weak-mixing, and strongly chaotic. In agreement with the earlier result by Casati and Prosen {[}Phys. Rev. A 72, 032111 (2005)], we find the billiard's integrability to have a crucial influence on the properties of the interference patterns. In the integrable case, most experiment outcomes are found to be consistent with the constructive interference occurring in the usual double-slit experiment. In contrast to this, nonintegrable billiards typically display asymmetric interference patterns of smaller visibility characterized by weakly correlated wave function values at the two slits. Our findings indicate an intrinsic connection between the classical integrability and the quantum dephasing, which is responsible for the destruction of interference. (C) 2010 American Institute of Physics. {[}doi:10.1063/1.3509768]}", article-number = "{043118}", doi = "{10.1063/1.3509768}", issn = "{1054-1500}", unique-id = "{ISI:000285768500027}" }

Zoran Levnajic and Bosiljka Tadic. Stability and chaos in coupled two-dimensional maps on gene regulatory network of bacterium E-coli. *Chaos* 20(3), September 2010. BibTeX

@article{ISI:000282438500015, author = "Levnajic, Zoran and Tadic, Bosiljka", title = "{Stability and chaos in coupled two-dimensional maps on gene regulatory network of bacterium E-coli}", journal = "{Chaos}", year = "{2010}", volume = "{20}", number = "{3}", month = "{SEP}", abstract = "{The collective dynamics of coupled two-dimensional chaotic maps on complex networks is known to exhibit a rich variety of emergent properties which crucially depend on the underlying network topology. We investigate the collective motion of Chirikov standard maps interacting with time delay through directed links of gene regulatory network of bacterium Escherichia coli. Departures from strongly chaotic behavior of the isolated maps are studied in relation to different coupling forms and strengths. At smaller coupling intensities the network induces stable and coherent emergent dynamics. The unstable behavior appearing with increase of coupling strength remains confined within a connected subnetwork. For the appropriate coupling, network exhibits statistically robust self-organized dynamics in a weakly chaotic regime. (c) 2010 American Institute of Physics. {[}doi: 10.1063/1.3474906]}", article-number = "{033115}", doi = "{10.1063/1.3474906}", issn = "{1054-1500}", unique-id = "{ISI:000282438500015}" }

Vesna Memisevic, Tijana Milenkovic and Natasa Przulj. An integrative approach to modeling biological networks.. *J Integr Bioinform* 7(3), 2010. URL BibTeX

@article{Memisevic2010, author = "Vesna Memisevic and Tijana Milenkovic and Natasa Przulj", title = "An integrative approach to modeling biological networks.", journal = "J Integr Bioinform", year = 2010, volume = 7, number = 3, __markedentry = "[andrej:]", abstract = {Networks are used to model real-world phenomena in various domains, including systems biology. Since proteins carry out biological processes by interacting with other proteins, it is expected that cellular functions are reflected in the structure of protein-protein interaction (PPI) networks. Similarly, the topology of residue interaction graphs (RIGs) that model proteins' 3-dimensional structure might provide insights into protein folding, stability, and function. An important step towards understanding these networks is finding an adequate network model, since models can be exploited algorithmically as well as used for predicting missing data. Evaluating the fit of a model network to the data is a formidable challenge, since network comparisons are computationally infeasible and thus have to rely on heuristics, or "network properties." We show that it is difficult to assess the reliability of the fit of a model using any network property alone. Thus, we present an integrative approach that feeds a variety of network properties into five machine learning classifiers to predict the best-fitting network model for PPI networks and RIGs. We confirm that geometric random graphs (GEO) are the best-fitting model for RIGs. Since GEO networks model spatial relationships between objects and are thus expected to replicate well the underlying structure of spatially packed residues in a protein, the good fit of GEO to RIGs validates our approach. Additionally, we apply our approach to PPI networks and confirm that the structure of merged data sets containing both binary and co-complex data that are of high coverage and confidence is also consistent with the structure of GEO, while the structure of less complete and lower confidence data is not. Since PPI data are noisy, we test the robustness of the five classifiers to noise and show that their robustness levels differ. We demonstrate that none of the classifiers predicts noisy scale-free (SF) networks as GEO, whereas noisy GEOs can be classified as SF. Thus, it is unlikely that our approach would predict a real-world network as GEO if it had a noisy SF structure. However, it could classify the data as SF if it had a noisy GEO structure. Therefore, the structure of the PPI networks is the most consistent with the structure of a noisy GEO.}, doi = "10.2390/biecoll-jib-2010-120", institution = "Department of Computer Science, University of California, Irvine, CA 92697-3435, USA.", keywords = "Models, Biological; Protein Binding; Protein Interaction Mapping, methods; Reproducibility of Results; Saccharomyces cerevisiae Proteins, metabolism; Saccharomyces cerevisiae, metabolism", language = "eng", medline-pst = "epublish", owner = "andrej", pii = 456, pmid = 20375453, timestamp = "2012.09.29", url = "http://dx.doi.org/10.2390/biecoll-jib-2010-120" }

Vesna Memisevic, Tijana Milenkovic and Natasa Przulj. Complementarity of network and sequence information in homologous proteins.. *J Integr Bioinform* 7(3), 2010. URL BibTeX

@article{Memisevic2010a, author = "Vesna Memisevic and Tijana Milenkovic and Natasa Przulj", title = "Complementarity of network and sequence information in homologous proteins.", journal = "J Integr Bioinform", year = 2010, volume = 7, number = 3, __markedentry = "[andrej:]", abstract = "Traditional approaches for homology detection rely on finding sufficient similarities between protein sequences. Motivated by studies demonstrating that from non-sequence based sources of biological information, such as the secondary or tertiary molecular structure, we can extract certain types of biological knowledge when sequence-based approaches fail, we hypothesize that protein-protein interaction (PPI) network topology and protein sequence might give insights into different slices of biological information. Since proteins aggregate to perform a function instead of acting in isolation, analyzing complex wirings around a protein in a PPI network could give deeper insights into the protein's role in the inner working of the cell than analyzing sequences of individual genes. Hence, we believe that one could lose much information by focusing on sequence information alone. We examine whether the information about homologous proteins captured by PPI network topology differs and to what extent from the information captured by their sequences. We measure how similar the topology around homologous proteins in a PPI network is and show that such proteins have statistically significantly higher network similarity than nonhomologous proteins. We compare these network similarity trends of homologous proteins with the trends in their sequence identity and find that network similarities uncover almost as much homology as sequence identities. Although none of the two methods, network topology and sequence identity, seems to capture homology information in its entirety, we demonstrate that the two might give insights into somewhat different types of biological information, as the overlap of the homology information that they uncover is relatively low. Therefore, we conclude that similarities of proteins' topological neighborhoods in a PPI network could be used as a complementary method to sequence-based approaches for identifying homologs, as well as for analyzing evolutionary distance and functional divergence of homologous proteins.", doi = "10.2390/biecoll-jib-2010-135", institution = "Department of Computer Science, University of California, Irvine, CA 92697-3435, USA.", keywords = "Amino Acid Sequence; Protein Binding; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins, chemistry/metabolism; Sequence Analysis, Protein; Sequence Homology, Amino Acid", language = "eng", medline-pst = "epublish", owner = "andrej", pii = 466, pmid = 20375452, timestamp = "2012.09.29", url = "http://dx.doi.org/10.2390/biecoll-jib-2010-135" }

Tijana Milenkovic, Vesna Memisevic, Anand K Ganesan and Natasa Przulj. Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data.. *J R Soc Interface* 7(44):423–437, March 2010. URL BibTeX

@article{Milenkovic2010a, author = "Tijana Milenkovic and Vesna Memisevic and Anand K Ganesan and Natasa Przulj", title = "Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data.", journal = "J R Soc Interface", year = 2010, volume = 7, pages = "423--437", number = 44, month = "Mar", __markedentry = "[andrej:]", abstract = "Many real-world phenomena have been described in terms of large networks. Networks have been invaluable models for the understanding of biological systems. Since proteins carry out most biological processes, we focus on analysing protein-protein interaction (PPI) networks. Proteins interact to perform a function. Thus, PPI networks reflect the interconnected nature of biological processes and analysing their structural properties could provide insights into biological function and disease. We have already demonstrated, by using a sensitive graph theoretic method for comparing topologies of node neighbourhoods called 'graphlet degree signatures', that proteins with similar surroundings in PPI networks tend to perform the same functions. Here, we explore whether the involvement of genes in cancer suggests the similarity of their topological 'signatures' as well. By applying a series of clustering methods to proteins' topological signature similarities, we demonstrate that the obtained clusters are significantly enriched with cancer genes. We apply this methodology to identify novel cancer gene candidates, validating 80 per cent of our predictions in the literature. We also validate predictions biologically by identifying cancer-related negative regulators of melanogenesis identified in our siRNA screen. This is encouraging, since we have done this solely from PPI network topology. We provide clear evidence that PPI network structure around cancer genes is different from the structure around non-cancer genes. Understanding the underlying principles of this phenomenon is an open question, with a potential for increasing our understanding of complex diseases.", doi = "10.1098/rsif.2009.0192", institution = "Department of Computer Science, University of California, Irvine, CA 92697-3435, USA.", keywords = "Cluster Analysis; Genes, Neoplasm; Genomics, methods; Humans; Melanins, metabolism; Models, Genetic; Neoplasms, genetics; Protein Interaction Mapping", language = "eng", medline-pst = "ppublish", owner = "andrej", pii = "rsif.2009.0192", pmid = 19625303, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1098/rsif.2009.0192" }

Tijana Milenković, Weng Leong Ng, Wayne Hayes and Natasa Przulj. Optimal network alignment with graphlet degree vectors.. *Cancer Inform* 9:121–137, 2010. BibTeX

@article{Milenkovic2010, author = "Tijana Milenković and Weng Leong Ng and Wayne Hayes and Natasa Przulj", title = "Optimal network alignment with graphlet degree vectors.", journal = "Cancer Inform", year = 2010, volume = 9, pages = "121--137", __markedentry = "[andrej:]", abstract = "Important biological information is encoded in the topology of biological networks. Comparative analyses of biological networks are proving to be valuable, as they can lead to transfer of knowledge between species and give deeper insights into biological function, disease, and evolution. We introduce a new method that uses the Hungarian algorithm to produce optimal global alignment between two networks using any cost function. We design a cost function based solely on network topology and use it in our network alignment. Our method can be applied to any two networks, not just biological ones, since it is based only on network topology. We use our new method to align protein-protein interaction networks of two eukaryotic species and demonstrate that our alignment exposes large and topologically complex regions of network similarity. At the same time, our alignment is biologically valid, since many of the aligned protein pairs perform the same biological function. From the alignment, we predict function of yet unannotated proteins, many of which we validate in the literature. Also, we apply our method to find topological similarities between metabolic networks of different species and build phylogenetic trees based on our network alignment score. The phylogenetic trees obtained in this way bear a striking resemblance to the ones obtained by sequence alignments. Our method detects topologically similar regions in large networks that are statistically significant. It does this independent of protein sequence or any other information external to network topology.", institution = "Department of Computing, Imperial College London SW7 2AZ, UK.", language = "eng", medline-pst = "epublish", owner = "andrej", pmid = 20628593, timestamp = "2012.09.29" }

Jozef Miskuf, Riste Škrekovski and Martin Tancer. Backbone colorings of graphs with bounded degree. *Discrete Applied Mathematics* 158(5):534-542, 2010. BibTeX

@article{ISI:000275582100016, author = "Miskuf, Jozef and \v{S}krekovski, Riste and Tancer, Martin", title = "{Backbone colorings of graphs with bounded degree}", journal = "{Discrete Applied Mathematics}", year = "{2010}", volume = "{158}", pages = "{534-542}", number = "{5}", month = "{MAR 6}", doi = "{10.1016/j.dam.2009.11.015}", issn = "{0166-218X}", times-cited = "{1}", unique-id = "{ISI:000275582100016}" }

Janez Povh. Semidefinite approximations for quadratic programs over orthogonal matrices. *Journal Of Global Optimization* 48(3):447-463, November 2010. BibTeX

@article{ISI:000282595400004, author = "Povh, Janez", title = "{Semidefinite approximations for quadratic programs over orthogonal matrices}", journal = "{Journal Of Global Optimization}", year = "{2010}", volume = "{48}", pages = "{447-463}", number = "{3}", month = "{NOV}" }

Natasa Przulj, Oleksii Kuchaiev, Aleksandar Stevanović and Wayne Hayes. Geometric evolutionary dynamics of protein interaction networks.. *Pac Symp Biocomput*, pages 178–189, 2010. BibTeX

@article{Przulj2010, author = "Natasa Przulj and Oleksii Kuchaiev and Aleksandar Stevanović and Wayne Hayes", title = "Geometric evolutionary dynamics of protein interaction networks.", journal = "Pac Symp Biocomput", year = 2010, pages = "178--189", __markedentry = "[andrej:]", abstract = "Understanding the evolution and structure of protein-protein interaction (PPI) networks is a central problem of systems biology. Since most processes in the cell are carried out by groups of proteins acting together, a theoretical model of how PPI networks develop based on duplications and mutations is an essential ingredient for understanding the complex wiring of the cell. Many different network models have been proposed, from those that follow power-law degree distributions and those that model complementarity of protein binding domains, to those that have geometric properties. Here, we introduce a new model for PPI network (and thus gene) evolution that produces well-fitting network models for currently available PPI networks. The model integrates geometric network properties with evolutionary dynamics of PPI network evolution.", institution = "Department of Computer Science, University of California, Irvine, CA, 92697-3425, USA. This email address is being protected from spambots. You need JavaScript enabled to view it. .", language = "eng", medline-pst = "ppublish", owner = "andrej", pii = "9789814295291_0020", pmid = 19908370, timestamp = "2012.09.29" }

## 2009

Darko Dimitrov, Tomas Dvorak, Petr Gregor and Riste Škrekovski. Gray Codes Avoiding Matchings. *Discrete Mathematics And Theoretical Computer Science* 11(2):123-147, 2009. BibTeX

@article{ISI:000272533400001, author = "Dimitrov, Darko and Dvorak, Tomas and Gregor, Petr and \v{S}krekovski, Riste", title = "{Gray Codes Avoiding Matchings}", journal = "{Discrete Mathematics And Theoretical Computer Science}", year = "{2009}", volume = "{11}", pages = "{123-147}", number = "{2}", issn = "{1365-8050}", times-cited = "{0}", unique-id = "{ISI:000272533400001}" }

Zdenek Dvorak and Riste Škrekovski. k-chromatic number of graphs on surfaces. *SIAM Journal On Discrete Mathematics* 23(1):477-486, 2009. BibTeX

@article{ISI:000208043700017, author = "Dvorak, Zdenek and \v{S}krekovski, Riste", title = "{k-chromatic number of graphs on surfaces}", journal = "{SIAM Journal On Discrete Mathematics}", year = "{2009}", volume = "{23}", pages = "{477-486}", number = "{1}", doi = "{10.1137/070688262}", issn = "{0895-4801}", times-cited = "{0}", unique-id = "{ISI:000208043700017}" }

Zdenek Dvorak, Daniel Kral, Pavel Nejedly and Riste Škrekovski. Distance constrained labelings of planar graphs with no short cycles. *Discrete Applied Mathematics* 157(12):2634-2645, 2009. 2nd Workshop on Graph Classes, Optimization and Width Parameters, Prague, CZECH REPUBLIC, OCT, 2005. BibTeX

@article{ISI:000267627800007, author = "Dvorak, Zdenek and Kral, Daniel and Nejedly, Pavel and \v{S}krekovski, Riste", title = "{Distance constrained labelings of planar graphs with no short cycles}", journal = "{Discrete Applied Mathematics}", year = "{2009}", volume = "{157}", pages = "{2634-2645}", number = "{12}", month = "{JUN 28}", note = "{2nd Workshop on Graph Classes, Optimization and Width Parameters, Prague, CZECH REPUBLIC, OCT, 2005}", doi = "{10.1016/j.dam.2008.08.013}", issn = "{0166-218X}", times-cited = "{1}", unique-id = "{ISI:000267627800007}" }

Zdenek Dvorak, Bernard Lidicky and Riste Škrekovski. Planar graphs without 3-, 7-, and 8-cycles are 3-choosable. *Discrete Mathematics* 309(20):5899-5904, 2009. BibTeX

@article{ISI:000271256900001, author = "Dvorak, Zdenek and Lidicky, Bernard and \v{S}krekovski, Riste", title = "{Planar graphs without 3-, 7-, and 8-cycles are 3-choosable}", journal = "{Discrete Mathematics}", year = "{2009}", volume = "{309}", pages = "{5899-5904}", number = "{20}", month = "{OCT 28}", doi = "{10.1016/j.disc.2009.04.010}", issn = "{0012-365X}", times-cited = "{0}", unique-id = "{ISI:000271256900001}" }

Petr Gregor and Riste Škrekovski. Long cycles in hypercubes with distant faulty vertices. *Discrete Mathematics And Theoretical Computer Science* 11(1):185-198, 2009. BibTeX

@article{ISI:000265108100001, author = "Gregor, Petr and \v{S}krekovski, Riste", title = "{Long cycles in hypercubes with distant faulty vertices}", journal = "{Discrete Mathematics And Theoretical Computer Science}", year = "{2009}", volume = "{11}", pages = "{185-198}", number = "{1}", issn = "{1365-8050}", times-cited = "{1}", unique-id = "{ISI:000265108100001}" }

Daniel Kral, Ondrej Pangrac, Jean-Sebastien Sereni and Riste Škrekovski. Long cycles in fullerene graphs. *Journal Of Mathematical Chemistry* 45(4):1021-1031, April 2009. BibTeX

@article{ISI:000264527700013, author = "Kral, Daniel and Pangrac, Ondrej and Sereni, Jean-Sebastien and \v{S}krekovski, Riste", title = "{Long cycles in fullerene graphs}", journal = "{Journal Of Mathematical Chemistry}", year = "{2009}", volume = "{45}", pages = "{1021-1031}", number = "{4}", month = "{APR}", doi = "{10.1007/s10910-008-9390-7}", issn = "{0259-9791}", times-cited = "{0}", unique-id = "{ISI:000264527700013}" }

Oleksii Kuchaiev and Natasa Przulj. Learning the structure of protein-protein interaction networks.. *Pac Symp Biocomput*, pages 39–50, 2009. BibTeX

@article{Kuchaiev2009b, author = "Oleksii Kuchaiev and Natasa Przulj", title = "Learning the structure of protein-protein interaction networks.", journal = "Pac Symp Biocomput", year = 2009, pages = "39--50", __markedentry = "[andrej:]", abstract = "Modeling and analyzing protein-protein interaction (PPI) networks is an important problem in systems biology. Many random graph models were proposed to capture specific network properties or mimic the way real PPI networks might have evolved. In this paper we introduce a new generative model for PPI networks which is based on geometric random graphs and uses the whole connectivity information of the real PPI networks to learn their structure. Using only the high confidence part of yeast S. cerevisiae PPI network for training our new model, we successfully reproduce structural properties of other lower-confidence yeast, as well as of human PPI networks coming from different data sources. Thus, our new approach allows us to utilize high quality parts of currently available PPI data to create accurate models for PPI networks of different species.", institution = "Department of Computer Science, University of California, Irvine, CA 92697-3425, USA. This email address is being protected from spambots. You need JavaScript enabled to view it. ", keywords = "Algorithms; Artificial Intelligence; Biometry; Databases, Protein; Models, Biological; Protein Interaction Mapping, statistics /&/ numerical data; Saccharomyces cerevisiae Proteins, metabolism; Saccharomyces cerevisiae, metabolism; Systems Biology", language = "eng", medline-pst = "ppublish", owner = "andrej", pmid = 19209694, timestamp = "2012.09.29" }

Oleksii Kuchaiev, Marija Rasajski, Desmond J Higham and Natasa Przulj. Geometric de-noising of protein-protein interaction networks.. *PLoS Comput Biol* 5(8):e1000454, August 2009. URL BibTeX

@article{Kuchaiev2009a, author = "Oleksii Kuchaiev and Marija Rasajski and Desmond J Higham and Natasa Przulj", title = "Geometric de-noising of protein-protein interaction networks.", journal = "PLoS Comput Biol", year = 2009, volume = 5, pages = "e1000454", number = 8, month = "Aug", __markedentry = "[andrej:]", abstract = "Understanding complex networks of protein-protein interactions (PPIs) is one of the foremost challenges of the post-genomic era. Due to the recent advances in experimental bio-technology, including yeast-2-hybrid (Y2H), tandem affinity purification (TAP) and other high-throughput methods for protein-protein interaction (PPI) detection, huge amounts of PPI network data are becoming available. Of major concern, however, are the levels of noise and incompleteness. For example, for Y2H screens, it is thought that the false positive rate could be as high as 64\%, and the false negative rate may range from 43\% to 71\%. TAP experiments are believed to have comparable levels of noise.We present a novel technique to assess the confidence levels of interactions in PPI networks obtained from experimental studies. We use it for predicting new interactions and thus for guiding future biological experiments. This technique is the first to utilize currently the best fitting network model for PPI networks, geometric graphs. Our approach achieves specificity of 85\% and sensitivity of 90\%. We use it to assign confidence scores to physical protein-protein interactions in the human PPI network downloaded from BioGRID. Using our approach, we predict 251 interactions in the human PPI network, a statistically significant fraction of which correspond to protein pairs sharing common GO terms. Moreover, we validate a statistically significant portion of our predicted interactions in the HPRD database and the newer release of BioGRID. The data and Matlab code implementing the methods are freely available from the web site: http://www.kuchaev.com/Denoising.", doi = "10.1371/journal.pcbi.1000454", institution = "Department of Computer Science, University of California, Irvine, California, USA.", keywords = "Algorithms; Computational Biology, methods; Databases, Protein; Humans; Models, Biological; Protein Interaction Mapping, methods; Proteins, chemistry/metabolism; ROC Curve; Reproducibility of Results; Sensitivity and Specificity; Signal Transduction", language = "eng", medline-pst = "ppublish", owner = "andrej", pmid = 19662157, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1371/journal.pcbi.1000454" }

Oleksii Kuchaiev, Po T Wang, Zoran Nenadic and Natasa Przulj. Structure of brain functional networks.. *Conf Proc IEEE Eng Med Biol Soc* 2009:4166–4170, 2009. URL BibTeX

@article{Kuchaiev2009, author = "Oleksii Kuchaiev and Po T Wang and Zoran Nenadic and Natasa Przulj", title = "Structure of brain functional networks.", journal = "Conf Proc IEEE Eng Med Biol Soc", year = 2009, volume = 2009, pages = "4166--4170", __markedentry = "[andrej:]", abstract = {Brain is a complex network optimized both for segregated and distributed information processing. To perform cognitive tasks, different areas of the brain must "cooperate," thereby forming complex networks of interactions also known as brain functional networks. Previous studies have shown that these networks exhibit "small-world" characteristics. Small-world topology, however, is a general property of all brain functional networks and does not capture structural changes in these networks in response to different stimuli or cognitive tasks. Here we show how novel graph theoretic techniques can be utilized for precise analysis of brain functional networks. These techniques allow us to detect structural changes in brain functional networks in response to different stimuli or cognitive tasks. For certain types of cognitive tasks we have found that these networks exhibit geometric structure in addition to the small-world topology. The method has been applied to the electrocorticographic signals of six epileptic patients.}, doi = "10.1109/IEMBS.2009.5333938", institution = "Computer Science Department, University of California, Irvine, CA, USA. This email address is being protected from spambots. You need JavaScript enabled to view it. ", keywords = "Algorithms; Brain Mapping, methods; Brain, pathology/physiology; Cognition; Computer Simulation; Computers; Electroencephalography, methods; Epilepsy, diagnosis/pathology; Humans; Models, Neurological; Models, Statistical; Nerve Net; Neural Pathways, physiology; Signal Processing, Computer-Assisted; Software", language = "eng", medline-pst = "ppublish", owner = "andrej", pmid = 19964621, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1109/IEMBS.2009.5333938" }

Borut Lužar, Riste Škrekovski and Martin Tancer. Injective colorings of planar graphs with few colors. *Discrete Mathematics* 309(18):5636-5649, 2009. BibTeX

@article{ISI:000271375600015, author = "Lu\v{z}ar, Borut and \v{S}krekovski, Riste and Tancer, Martin", title = "{Injective colorings of planar graphs with few colors}", journal = "{Discrete Mathematics}", year = "{2009}", volume = "{309}", pages = "{5636-5649}", number = "{18}", month = "{SEP 28}", doi = "{10.1016/j.disc.2008.04.005}", issn = "{0012-365X}", times-cited = "{5}", unique-id = "{ISI:000271375600015}" }

Jerome Malick, Janez Povh, Franz Rendl and Angelika Wiegele. Regularization methods for semidefinite programming. *SIAM Journal On Optimization* 20(1):336-356, 2009. BibTeX

@article{ISI:000266055700014, author = "Malick, Jerome and Povh, Janez and Rendl, Franz and Wiegele, Angelika", title = "{Regularization methods for semidefinite programming}", journal = "{SIAM Journal On Optimization}", year = "{2009}", volume = "{20}", pages = "{336-356}", number = "{1}", doi = "{10.1137/070704575}" }

Tijana Milenković, Ioannis Filippis, Michael Lappe and Natasa Przulj. Optimized null model for protein structure networks.. *PLoS One* 4(6):e5967, 2009. URL BibTeX

@article{Milenkovic2009, author = "Tijana Milenković and Ioannis Filippis and Michael Lappe and Natasa Przulj", title = "Optimized null model for protein structure networks.", journal = "PLoS One", year = 2009, volume = 4, pages = "e5967", number = 6, __markedentry = "[andrej:]", abstract = "Much attention has recently been given to the statistical significance of topological features observed in biological networks. Here, we consider residue interaction graphs (RIGs) as network representations of protein structures with residues as nodes and inter-residue interactions as edges. Degree-preserving randomized models have been widely used for this purpose in biomolecular networks. However, such a single summary statistic of a network may not be detailed enough to capture the complex topological characteristics of protein structures and their network counterparts. Here, we investigate a variety of topological properties of RIGs to find a well fitting network null model for them. The RIGs are derived from a structurally diverse protein data set at various distance cut-offs and for different groups of interacting atoms. We compare the network structure of RIGs to several random graph models. We show that 3-dimensional geometric random graphs, that model spatial relationships between objects, provide the best fit to RIGs. We investigate the relationship between the strength of the fit and various protein structural features. We show that the fit depends on protein size, structural class, and thermostability, but not on quaternary structure. We apply our model to the identification of significantly over-represented structural building blocks, i.e., network motifs, in protein structure networks. As expected, choosing geometric graphs as a null model results in the most specific identification of motifs. Our geometric random graph model may facilitate further graph-based studies of protein conformation space and have important implications for protein structure comparison and prediction. The choice of a well-fitting null model is crucial for finding structural motifs that play an important role in protein folding, stability and function. To our knowledge, this is the first study that addresses the challenge of finding an optimized null model for RIGs, by comparing various RIG definitions against a series of network models.", doi = "10.1371/journal.pone.0005967", institution = "Department of Computer Science, University of California Irvine, Irvine, CA, USA.", keywords = "Algorithms; Amino Acid Motifs; Animals; Cluster Analysis; Computational Biology, methods; Computer Simulation; Databases, Protein; Humans; Models, Theoretical; Protein Folding; Proteins, chemistry; Proteome; Proteomics, methods", language = "eng", medline-pst = "epublish", owner = "andrej", pmid = 19557139, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1371/journal.pone.0005967" }

Jozef Miskuf, Riste Škrekovski and Martin Tancer. Backbone colorings and generalized Mycielski graphs. *Siam Journal On Discrete Mathematics* 23(2):1063-1070, 2009. BibTeX

@article{ISI:000267744700033, author = "Miskuf, Jozef and \v{S}krekovski, Riste and Tancer, Martin", title = "{Backbone colorings and generalized Mycielski graphs}", journal = "{Siam Journal On Discrete Mathematics}", year = "{2009}", volume = "{23}", pages = "{1063-1070}", number = "{2}", doi = "{10.1137/080717596}", issn = "{0895-4801}", times-cited = "{1}", unique-id = "{ISI:000267744700033}" }

Reza Naserasr, Yared Nigussie and Riste Škrekovski. Homomorphisms of triangle-free graphs without a K-5-minor. *Discrete Mathematics* 309(18, SI):5789-5798, 2009. BibTeX

@article{ISI:000271375600033, author = "Naserasr, Reza and Nigussie, Yared and \v{S}krekovski, Riste", title = "{Homomorphisms of triangle-free graphs without a K-5-minor}", journal = "{Discrete Mathematics}", year = "{2009}", volume = "{309}", pages = "{5789-5798}", number = "{18, SI}", month = "{SEP 28}", doi = "{10.1016/j.disc.2009.04.032}", issn = "{0012-365X}", times-cited = "{0}", unique-id = "{ISI:000271375600033}" }

Janez Povh and Franz Rendl. Copositive and semidefinite relaxations of the quadratic assignment problem. *Discrete Optimization* 6(3):231-241, August 2009. BibTeX

@article{ISI:000267412700002, author = "Povh, Janez and Rendl, Franz", title = "{Copositive and semidefinite relaxations of the quadratic assignment problem}", journal = "{Discrete Optimization}", year = "{2009}", volume = "{6}", pages = "{231-241}", number = "{3}", month = "{AUG}", doi = "{10.1016/j.disopt.2009.01.002}" }

## 2008

Zdenek Dvorak, Riste Škrekovski and Martin Tancer. List-coloring squares of sparse subcubic graphs. *SIAM Journal On Discrete Mathematics* 22(1):139-159, 2008. BibTeX

@article{ISI:000254460900009, author = "Dvorak, Zdenek and \v{S}krekovski, Riste and Tancer, Martin", title = "{List-coloring squares of sparse subcubic graphs}", journal = "{SIAM Journal On Discrete Mathematics}", year = "{2008}", volume = "{22}", pages = "{139-159}", number = "{1}", doi = "{10.1137/050634049}", issn = "{0895-4801}", times-cited = "{5}", unique-id = "{ISI:000254460900009}" }

Z Dvorak, R Škrekovski and T Valla. Planar graphs of odd-girth at least 9 are homomorphic to the Petersen graph. *SIAM Journal On Discrete Mathematics* 22(2):568-591, 2008. BibTeX

@article{ISI:000256452900010, author = "Dvorak, Z. and \v{S}krekovski, R. and Valla, T.", title = "{Planar graphs of odd-girth at least 9 are homomorphic to the Petersen graph}", journal = "{SIAM Journal On Discrete Mathematics}", year = "{2008}", volume = "{22}", pages = "{568-591}", number = "{2}", doi = "{10.1137/060650507}", issn = "{0895-4801}", times-cited = "{1}", unique-id = "{ISI:000256452900010}" }

Zdenek Dvorak, Daniel Kral, Pavel Nejedly and Riste Škrekovski. Coloring squares of planar graphs with girth six. *European Journal Of Combinatorics* 29(4):838-849, May 2008. BibTeX

@article{ISI:000255363800004, author = "Dvorak, Zdenek and Kral, Daniel and Nejedly, Pavel and \v{S}krekovski, Riste", title = "{Coloring squares of planar graphs with girth six}", journal = "{European Journal Of Combinatorics}", year = "{2008}", volume = "{29}", pages = "{838-849}", number = "{4}", month = "{MAY}", doi = "{10.1016/j.ejc.2007.11.005}", issn = "{0195-6698}", times-cited = "{13}", unique-id = "{ISI:000255363800004}" }

Cortnie Guerrero, Tijana Milenkovic, Natasa Przulj, Peter Kaiser and Lan Huang. Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis.. *Proc Natl Acad Sci U S A* 105(36):13333–13338, September 2008. URL BibTeX

@article{Guerrero2008, author = "Cortnie Guerrero and Tijana Milenkovic and Natasa Przulj and Peter Kaiser and Lan Huang", title = "Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis.", journal = "Proc Natl Acad Sci U S A", year = 2008, volume = 105, pages = "13333--13338", number = 36, month = "Sep", __markedentry = "[andrej:]", abstract = "Quantitative analysis of tandem-affinity purified cross-linked (x) protein complexes (QTAX) is a powerful technique for the identification of protein interactions, including weak and/or transient components. Here, we apply a QTAX-based tag-team mass spectrometry strategy coupled with protein network analysis to acquire a comprehensive and detailed assessment of the protein interaction network of the yeast 26S proteasome. We have determined that the proteasome network is composed of at least 471 proteins, significantly more than the total number of proteins identified by previous reports using proteasome subunits as baits. Validation of the selected proteasome-interacting proteins by reverse copurification and immunoblotting experiments with and without cross-linking, further demonstrates the power of the QTAX strategy for capturing protein interactions of all natures. In addition, >80\% of the identified interactions have been confirmed by existing data using protein network analysis. Moreover, evidence obtained through network analysis links the proteasome to protein complexes associated with diverse cellular functions. This work presents the most complete analysis of the proteasome interaction network to date, providing an inclusive set of physical interaction data consistent with physiological roles for the proteasome that have been suggested primarily through genetic analyses. Moreover, the methodology described here is a general proteomic tool for the comprehensive study of protein interaction networks.", doi = "10.1073/pnas.0801870105", institution = "Departments of Physiology and Biophysics and Developmental and Cell Biology, University of California, Irvine, CA 92697, USA.", keywords = "Mass Spectrometry; Proteasome Endopeptidase Complex, metabolism; Protein Binding; Protein Interaction Mapping; Proteins, chemistry/isolation /&/ purification/metabolism; Saccharomyces cerevisiae, metabolism", language = "eng", medline-pst = "ppublish", owner = "andrej", pii = 0801870105, pmid = 18757749, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1073/pnas.0801870105" }

Frederic Havet, Jean-Sebastien Sereni and Riste Škrekovski. 3-facial coloring of plane graphs. *SIAM Journal On Discrete Mathematics* 22(1):231-247, 2008. BibTeX

@article{ISI:000254460900014, author = "Havet, Frederic and Sereni, Jean-Sebastien and \v{S}krekovski, Riste", title = "{3-facial coloring of plane graphs}", journal = "{SIAM Journal On Discrete Mathematics}", year = "{2008}", volume = "{22}", pages = "{231-247}", number = "{1}", doi = "{10.1137/060664124}", issn = "{0895-4801}", times-cited = "{3}", unique-id = "{ISI:000254460900014}" }

Desmond J Higham, Marija Rasajski and Natasa Przulj. Fitting a geometric graph to a protein-protein interaction network.. *Bioinformatics* 24(8):1093–1099, April 2008. URL BibTeX

@article{Higham2008, author = "Desmond J Higham and Marija Rasajski and Natasa Przulj", title = "Fitting a geometric graph to a protein-protein interaction network.", journal = "Bioinformatics", year = 2008, volume = 24, pages = "1093--1099", number = 8, month = "Apr", __markedentry = "[andrej:]", abstract = "Finding a good network null model for protein-protein interaction (PPI) networks is a fundamental issue. Such a model would provide insights into the interplay between network structure and biological function as well as into evolution. Also, network (graph) models are used to guide biological experiments and discover new biological features. It has been proposed that geometric random graphs are a good model for PPI networks. In a geometric random graph, nodes correspond to uniformly randomly distributed points in a metric space and edges (links) exist between pairs of nodes for which the corresponding points in the metric space are close enough according to some distance norm. Computational experiments have revealed close matches between key topological properties of PPI networks and geometric random graph models. In this work, we push the comparison further by exploiting the fact that the geometric property can be tested for directly. To this end, we develop an algorithm that takes PPI interaction data and embeds proteins into a low-dimensional Euclidean space, under the premise that connectivity information corresponds to Euclidean proximity, as in geometric-random graphs. We judge the sensitivity and specificity of the fit by computing the area under the Receiver Operator Characteristic (ROC) curve. The network embedding algorithm is based on multi-dimensional scaling, with the square root of the path length in a network playing the role of the Euclidean distance in the Euclidean space. The algorithm exploits sparsity for computational efficiency, and requires only a few sparse matrix multiplications, giving a complexity of O(N(2)) where N is the number of proteins.The algorithm has been verified in the sense that it successfully rediscovers the geometric structure in artificially constructed geometric networks, even when noise is added by re-wiring some links. Applying the algorithm to 19 publicly available PPI networks of various organisms indicated that: (a) geometric effects are present and (b) two-dimensional Euclidean space is generally as effective as higher dimensional Euclidean space for explaining the connectivity. Testing on a high-confidence yeast data set produced a very strong indication of geometric structure (area under the ROC curve of 0.89), with this network being essentially indistinguishable from a noisy geometric network. Overall, the results add support to the hypothesis that PPI networks have a geometric structure.MATLAB code implementing the algorithm is available upon request.", doi = "10.1093/bioinformatics/btn079", institution = "Department of Mathematics, University of Strathclyde, Glasgow G1 1XH, UK.", keywords = "Algorithms; Computer Simulation; Gene Expression Profiling, methods; Models, Biological; Models, Statistical; Multigene Family, physiology; Protein Interaction Mapping, methods; Proteome, metabolism; Signal Transduction, physiology; Software", language = "eng", medline-pst = "ppublish", owner = "andrej", pii = "btn079", pmid = 18344248, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1093/bioinformatics/btn079" }

Tomas Kaiser and Riste Škrekovski. Cycles intersecting edge-cuts of prescribed sizes. *SIAM Journal On Discrete Mathematics* 22(3):861-874, 2008. BibTeX

@article{ISI:000258895500003, author = "Kaiser, Tomas and \v{S}krekovski, Riste", title = "{Cycles intersecting edge-cuts of prescribed sizes}", journal = "{SIAM Journal On Discrete Mathematics}", year = "{2008}", volume = "{22}", pages = "{861-874}", number = "{3}", doi = "{10.1137/070683635}", issn = "{0895-4801}", times-cited = "{6}", unique-id = "{ISI:000258895500003}" }

Frantisek Kardos and Riste Škrekovski. Cyclic edge-cuts in fullerene graphs. *Journal Of Mathematical Chemistry* 44(1):121-132, July 2008. BibTeX

@article{ISI:000255629500008, author = "Kardos, Frantisek and \v{S}krekovski, Riste", title = "{Cyclic edge-cuts in fullerene graphs}", journal = "{Journal Of Mathematical Chemistry}", year = "{2008}", volume = "{44}", pages = "{121-132}", number = "{1}", month = "{JUL}", doi = "{10.1007/s10910-007-9296-9}", issn = "{0259-9791}", times-cited = "{7}", unique-id = "{ISI:000255629500008}" }

Lukasz Kowalik, Jean-Sebastien Sereni and Riste Škrekovski. TOTAL-COLORING OF PLANE GRAPHS WITH MAXIMUM DEGREE NINE. *SIAM Journal On Discrete Mathematics* 22(4):1462-1479, 2008. BibTeX

@article{ISI:000260848300013, author = "Kowalik, Lukasz and Sereni, Jean-Sebastien and \v{S}krekovski, Riste", title = "{TOTAL-COLORING OF PLANE GRAPHS WITH MAXIMUM DEGREE NINE}", journal = "{SIAM Journal On Discrete Mathematics}", year = "{2008}", volume = "{22}", pages = "{1462-1479}", number = "{4}", doi = "{10.1137/070688389}", issn = "{0895-4801}", times-cited = "{14}", unique-id = "{ISI:000260848300013}" }

Zoran Levnajic and Bosiljka Tadic. Self-organization in trees and motifs of two-dimensional chaotic maps with time delay. *Journal Of Statistical Mechanics-Theory And Experiment*, March 2008. BibTeX

@article{ISI:000254787000019, author = "Levnajic, Zoran and Tadic, Bosiljka", title = "{Self-organization in trees and motifs of two-dimensional chaotic maps with time delay}", journal = "{Journal Of Statistical Mechanics-Theory And Experiment}", year = "{2008}", month = "{MAR}", abstract = "{We study two-dimensional chaotic standard maps coupled along the edges of scale-free trees and tree-like subgraphs (4-star) with a non-symplectic coupling and time delay between the nodes. Apart from the chaotic and regular 2-periodic motion, the coupled map system exhibits a variety of dynamical effects in a wide range of coupling strengths. This includes dynamical localization, emergent periodicity and the appearance of strange non-chaotic attractors. Near the strange attractors we find long-range correlations in the intervals of return times to specified parts of the phase space. We substantiate the analysis with the finite-time Lyapunov stability. We also give some quantitative evidence of how the small-scale dynamics at 4-star motifs participates in the genesis of the collective behavior at the whole network.}", article-number = "{P03003}", doi = "{10.1088/1742-5468/2008/03/P03003}", issn = "{1742-5468}", unique-id = "{ISI:000254787000019}" }

Tijana Milenković, Jason Lai and Natasa Przulj. GraphCrunch: a tool for large network analyses.. *BMC Bioinformatics* 9:70, 2008. URL BibTeX

@article{Milenkovic2008, author = "Tijana Milenković and Jason Lai and Natasa Przulj", title = "GraphCrunch: a tool for large network analyses.", journal = "BMC Bioinformatics", year = 2008, volume = 9, pages = 70, __markedentry = "[andrej:]", abstract = {The recent explosion in biological and other real-world network data has created the need for improved tools for large network analyses. In addition to well established global network properties, several new mathematical techniques for analyzing local structural properties of large networks have been developed. Small over-represented subgraphs, called network motifs, have been introduced to identify simple building blocks of complex networks. Small induced subgraphs, called graphlets, have been used to develop "network signatures" that summarize network topologies. Based on these network signatures, two new highly sensitive measures of network local structural similarities were designed: the relative graphlet frequency distance (RGF-distance) and the graphlet degree distribution agreement (GDD-agreement). Finding adequate null-models for biological networks is important in many research domains. Network properties are used to assess the fit of network models to the data. Various network models have been proposed. To date, there does not exist a software tool that measures the above mentioned local network properties. Moreover, none of the existing tools compare real-world networks against a series of network models with respect to these local as well as a multitude of global network properties.Thus, we introduce GraphCrunch, a software tool that finds well-fitting network models by comparing large real-world networks against random graph models according to various network structural similarity measures. It has unique capabilities of finding computationally expensive RGF-distance and GDD-agreement measures. In addition, it computes several standard global network measures and thus supports the largest variety of network measures thus far. Also, it is the first software tool that compares real-world networks against a series of network models and that has built-in parallel computing capabilities allowing for a user specified list of machines on which to perform compute intensive searches for local network properties. Furthermore, GraphCrunch is easily extendible to include additional network measures and models.GraphCrunch is a software tool that implements the latest research on biological network models and properties: it compares real-world networks against a series of random graph models with respect to a multitude of local and global network properties. We present GraphCrunch as a comprehensive, parallelizable, and easily extendible software tool for analyzing and modeling large biological networks. The software is open-source and freely available at http://www.ics.uci.edu/~bio-nets/graphcrunch/. It runs under Linux, MacOS, and Windows Cygwin. In addition, it has an easy to use on-line web user interface that is available from the above web page.}, doi = "10.1186/1471-2105-9-70", institution = "Department of Computer Science, University of California, Irvine, CA 92697-3435, USA. This email address is being protected from spambots. You need JavaScript enabled to view it. ", keywords = "Algorithms; Computer Graphics; Computer Simulation; Models, Biological; Proteome, metabolism; Signal Transduction, physiology; Software; User-Computer Interface", language = "eng", medline-pst = "epublish", owner = "andrej", pii = "1471-2105-9-70", pmid = 18230190, timestamp = "2012.09.29", url = "http://dx.doi.org/10.1186/1471-2105-9-70" }

Tijana Milenković and Natasa Przulj. Uncovering biological network function via graphlet degree signatures.. *Cancer Inform* 6:257–273, 2008. BibTeX

@article{Milenkovic2008a, author = "Tijana Milenković and Natasa Przulj", title = "Uncovering biological network function via graphlet degree signatures.", journal = "Cancer Inform", year = 2008, volume = 6, pages = "257--273", __markedentry = "[andrej:]", abstract = "Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods for determining protein function have shifted their focus from targeting specific proteins based solely on sequence homology to analyses of the entire proteome based on protein-protein interaction (PPI) networks. Since proteins interact to perform a certain function, analyzing structural properties of PPI networks may provide useful clues about the biological function of individual proteins, protein complexes they participate in, and even larger subcellular machines.We design a sensitive graph theoretic method for comparing local structures of node neighborhoods that demonstrates that in PPI networks, biological function of a node and its local network structure are closely related. The method summarizes a protein's local topology in a PPI network into the vector of graphlet degrees called the signature of the protein and computes the signature similarities between all protein pairs. We group topologically similar proteins under this measure in a PPI network and show that these protein groups belong to the same protein complexes, perform the same biological functions, are localized in the same subcellular compartments, and have the same tissue expressions. Moreover, we apply our technique on a proteome-scale network data and infer biological function of yet unclassified proteins demonstrating that our method can provide valuable guidelines for future experimental research such as disease protein prediction.Data is available upon request.", institution = "Department of Computer Science, University of California, Irvine, CA 92697-3435, USA.", language = "eng", medline-pst = "ppublish", owner = "andrej", pmid = 19259413, timestamp = "2012.09.29" }

Bosiuka Tadic and Zoran Levnajic. Robust dynamical effects in traffic and chaotic maps on trees. *Pramana-Journal Of Physics* 70(6):1099-1108, June 2008. 2nd Conference and Workshop on Perspectives in Nonlinear Dyanmics, Trieste, ITALY, JUL 16-27, 2007. BibTeX

@article{ISI:000257111700014, author = "Tadic, Bosiuka and Levnajic, Zoran", title = "{Robust dynamical effects in traffic and chaotic maps on trees}", journal = "{Pramana-Journal Of Physics}", year = "{2008}", volume = "{70}", pages = "{1099-1108}", number = "{6}", month = "{JUN}", note = "{2nd Conference and Workshop on Perspectives in Nonlinear Dyanmics, Trieste, ITALY, JUL 16-27, 2007}", abstract = "{In the dynamic processes on networks collective effects emerge due to the couplings between nodes, where the network structure may play an important role. Interaction along many network links in the nonlinear dynamics may lead to a kind of chaotic collective behavior. Here we study two types of well-defined diffusive dynamics on scale-free trees: traffic of packets as navigated random walks, and chaotic standard maps coupled along the network links. We show that in both cases robust collective dynamic effects appear, which can be measured statistically and related to non-ergodicity of the dynamics on the network. Specifically, we find universal features in the fluctuations of time series and appropriately defined return-time statistics.}", doi = "{10.1007/s12043-008-0114-0}", issn = "{0304-4289}", unique-id = "{ISI:000257111700014}" }