Refereed Journal Publications

(CoNe students' names are in bold, and undergraduates are underlined.)

24. Joseph Crawford and Tijana Milenkovic (2014), GREAT: GRaphlet Edge-based network AlignmenT, arXiv:1410.5103 [q-bio.MN], 2014. Also, under review.

23. Yihan Sun, Joseph Crawford, Jie Tang, and Tijana Milenkovic (2014), Simultaneous Optimization of Both Node and Edge Conservation in Network Alignment via WAVE, arXiv:1410.3301 [q-bio.MN], 2014. Also, under review.

22. Lei Meng, Yuriy Hulovatyy, Aaron Striegel, and Tijana Milenkovic (2014), On the Interplay Between Individuals' Evolving Interaction Patterns and Traits in Dynamic Multiplex Social Networks, under review, 2014.

21. Joseph Crawford, Yihan Sun, and Tijana Milenkovic (2014), Fair Evaluation of Global Network Aligners, arXiv:1407.4824 [q-bio.MN], 2014. Also, under review.

20. Yuriy Hulovatyy, Sidney D'Mello, Rafael A. Calvo, and Tijana Milenkovic (2014), Network Analysis Improves Interpretation of Affective Physiological Data, Journal of Complex Networks, DOI: 10.1093/comnet/cnu032. Also, in IEEE Proceedings of the 2nd International Workshop on Complex Networks and their Applications at the 9th International Conference on Signal-Image Technology and Internet-Based Systems (SITIS), Kyoto, Japan, December 2-5, 2013 (acceptance rate: 42%), DOI: 10.1109/SITIS.2013.82, pages: 470-477.

19. Fazle E. Faisal, Han Zhao, and Tijana Milenkovic (2014), Global Network Alignment In The Context Of Aging, IEEE/ACM Transactions on Computational Biology and Bioinformatics, PP(99):1, DOI: 10.1109/TCBB.2014.2326862. Also, in Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB), Washington DC, USA, September 22-25, 2013 (acceptance rate: 28%).

18. Vikram Saraph and Tijana Milenkovic (2014), MAGNA: Maximizing Accuracy in Global Network Alignment, Bioinformatics, 30(20): 2931-2940.

17. Fazle E. Faisal and Tijana Milenkovic (2014), Dynamic networks reveal key players in aging, Bioinformatics, 30(12): 1721-1729.

16. Andrew K. Rider, Tijana Milenkovic, Geoffrey H. Siwo, Richard S. Pinapati, Scott J. Emrich, Michael T. Ferdig, and Nitesh V. Chawla (2014), Networks' Characteristics Are Important For Systems Biology, Network Science, 2(02): 139-161.

15. Yuriy Hulovatyy, Ryan W. Solava, and Tijana Milenkovic (2014), Revealing missing parts of the interactome via link prediction, PLOS ONE, 9(3): e90073.

14. Ryan W. Solava, Ryan P. Michaels, and Tijana Milenkovic (2012), Graphlet-based edge clustering reveals pathogen-interacting proteins, Bioinformatics, 28(18): i480-i486. Also, in Proceedings of the 11th European Conference on Computational Biology (ECCB), Basel, Switzerland, September 9-12, 2012 (acceptance rate: 14%).

13. Tijana Milenkovic, Vesna Memisevic, Antoni Bonato, and Natasa Przulj (2011), Dominating biological networks, PLOS ONE, 6(8): e23016.

12. Arabidopsis Interactome Mapping Consortium (2011), Evidence for Network Evolution in an Arabidopsis Interactome Map, Science, 333(6042): 601-607.

11. Tijana Milenkovic, Weng L. Ng, Wayne Hayes, and Natasa Przulj (2010), Optimal Network Alignment with Graphlet Degree Vectors, Cancer Informatics, 9:121-137.

10. Hsiang Ho*, Tijana Milenkovic*, Vesna Memisevic, Jayavani Aruri, Natasa Przulj, and Anand K. Ganesan (2010), Protein Interaction Network Uncovers Melanogenesis Regulatory Network Components within Functional Genomics Datasets, BMC Systems Biology, 4:84.
*These authors contributed equally to this work

9. Robyn Kaake, Tijana Milenkovic, Natasa Przulj, Peter Kaiser, and Lan Huang (2010), Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy, Journal of Proteome Research, 9(4): 2016-2029.

8. Vesna Memisevic, Tijana Milenkovic, and Natasa Przulj (2010), Complementarity of network and sequence structure in homologous proteins, Journal of Integrative Bioinformatics, 7(3):135.

7. Vesna Memisevic, Tijana Milenkovic, and Natasa Przulj (2010), An integrative approach to modeling biological networks, Journal of Integrative Bioinformatics, 7(3):120.

6. Oleksii Kuchaiev*, Tijana Milenkovic*, Vesna Memisevic, Wayne Hayes, and Natasa Przulj (2010), Topological network alignment uncovers biological function and phylogeny, Journal of the Royal Society Interface, 7(50): 1341-1354.
*These authors contributed equally to this work

5. Tijana Milenkovic, Vesna Memisevic, Anand K. Ganesan, and Natasa Przulj (2010), Systems-level Cancer Gene Identification from Protein Interaction Network Topology Applied to Melanogenesis-related Interaction Networks, Journal of the Royal Society Interface, 7(44): 423-437, 2010.

4. Tijana Milenkovic*, Ioannis Filippis*, Michael Lappe, and Natasa Przulj (2009), Optimized Null Model for Protein Structure Networks, PLOS ONE 4(6): e5967.
*These authors contributed equally to this work

3. Courtney Guerrero, Tijana Milenkovic, Natasa Przulj, J. J. Jones, Peter Kaiser, Lan Huang (2008) Characterization of the Yeast Proteasome Interaction Network by QTAX-Based Tag-Team Mass Spectrometry and Protein Interaction Network Analysis, PNAS 105(36): 13333-13338.

2. Tijana Milenkovic and Natasa Przulj (2008) Uncovering Biological Network Function via Graphlet Degree Signatures; Cancer Informatics 2008:6 257-273.

1. Tijana Milenkovic, Jason Lai, and Natasa Przulj (2008) GraphCrunch: a tool for large network analyses, BMC Bioinformatics 9:70. Highly accessed.

 

Refereed Full Conference Papers

(CoNe students' names are in bold, and undergraduates are underlined.)

7. Boyoung Yoo, Huili Chen, Fazle E. Faisal, and Tijana Milenkovic (2014), Improving identification of key players in aging via network de-noising, In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB), Newport Beach, CA, USA, September 20-23, 2014 (acceptance rate: 22%), pages 164-173.

6. Lei Meng, Tijana Milenkovic, and Aaron Striegel (2014), Systematic Dynamic and Heterogeneous Analysis of Rich Social Network Data, In Springer-Verlag (on the Studies in Computational Intelligence Series) Proceedings of the 5th Workshop on Complex Networks (CompleNet), Bologna, Italy, March 12-14, 2014 (acceptance rate: 25%).

5. Yuriy Hulovatyy, Sidney D'Mello, Rafael A. Calvo, and Tijana Milenkovic (2013), Network Analysis Improves Interpretation of Affective Physiological Data, In IEEE Proceedings of the 2nd International Workshop on Complex Networks and their Applications at the 9th International Conference on Signal-Image Technology and Internet-Based Systems (SITIS), Kyoto, Japan, December 2-5, 2013 (acceptance rate: 42%), DOI: 10.1109/SITIS.2013.82, pages: 470-477. Also, in Journal of Complex Networks, DOI: 10.1093/comnet/cnu032, 2014.

4. Tijana Milenkovic, Han Zhao, and Fazle E. Faisal (2013), Global Network Alignment In The Context Of Aging, In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB), Washington DC, USA, September 22-25, 2013 (acceptance rate: 28%). Also, in IEEE/ACM Transactions on Computational Biology and Bioinformatics, PP(99):1, DOI: 10.1109/TCBB.2014.2326862, 2014.

3. Ryan W. Solava, Ryan P. Michaels, and Tijana Milenkovic (2012), Graphlet-based edge clustering reveals pathogen-interacting proteins, Proceedings of the 11th European Conference on Computational Biology (ECCB), Basel, Switzerland, September 9-12, 2012 (acceptance rate: 14%). Also, in Bioinformatics, 28(18): i480-i486, 2014.

2. Vesna Memisevic, Tijana Milenkovic, and Natasa Przulj (2010), Complementarity of network and sequence structure in homologous proteins, Proceedings of the 6th International Symposium on Integrative Bioinformatics, 22-24 March 2010, Cambridge, United Kingdom.

1. Vesna Memisevic, Tijana Milenkovic, and Natasa Przulj (2010), An integrative approach to modeling biological networks, Proceedings of the 6th International Symposium on Integrative Bioinformatics, 22-24 March 2010, Cambridge, United Kingdom.

 

Refereed Book Chapters

2.Tijana Milenkovic and Natasa Przulj, Topological Characteristics of Molecular Networks, a chapter in Functional Coherence of Molecular Networks in Bioinformatics, edited by Mehmet Koyuturk, Shankar Subramaniam, and Ananthto Grama, Springer, 2012.

1. Natasa Przulj and Tijana Milenkovic, Computational Methods for Analyzing and Modeling Biological Networks, a chapter in Biological Data Mining, edited by Jake Chen and Stefano Lonardi, Chapman & Hall/CRC; 1 edition, September 1, 2009.