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Software
Check out GraphCrunch, our new network analysis
and modeling software, published
in BMC Bioinformatics (highly accessed).
Publications
Oleksii Kuchaiev‡,
Tijana Milenkovic‡,
Vesna Memisevic, Wayne Hayes, Natasa Przulj (2008), Topological network alignment uncovers biological function and
phylogeny, arXiv:0810.3280v1
[q-bio.MN], under review.
‡These authors
contributed equally to this work
C. Guerrero, T.
Milenkovic, N. Przulj, J. J.
Jones, P. Kaiser, L. 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.
Tijana Milenkovic and Natasa Przulj (2008) Uncovering Biological Network Function via
Graphlet Degree Signatures; Cancer Informatics
2008:6 257–273.
Tijana Milenkovic, Jason Lai, and Natasa Przulj (2008) GraphCrunch:
a tool for large network analyses, BMC Bioinformatics
9:70. Highly accessed.
Tijana Milenkovic‡,
Ioannis Filippis‡, Michael Lappe, and Natasa Przulj, Optimized Null Model for Protein Structure
Networks, under revision.
‡These authors
contributed equally to this work
Refereed Book Chapters
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, CRC
Press, forthcoming.
Contributed
talks
Tijana Milenkovic and Natasa Przulj, “Uncovering Biological Network
Function via Graphlet Degree Signatures”, 12th
Serbian Mathematical Congress, Novi Sad, Serbia, August 28 – September 2,
2008.
Tijana Milenkovic and Natasa Przulj, “From
network structure to biological function in protein-protein interaction
networks”, BioPathways meeting at ISMB’08,
Tijana
Milenkovic and Natasa Przulj, “Uncovering Biological Network Function via
Graphlet Degree Signatures”, BioPathways
'07 pre-conference of
Tutorials
Natasa Przulj and Tijana Milenkovic, “Biological Networks: Analyses, Models, Functions, and Disease”, the 9th International Conference on Systems Biology, ICSB'08, Gothenburg , Sweden
Theses
Tijana Milenkovic, Interplay of topology and biology in protein-protein interaction networks, MS thesis, Information and Computer Science, University of
California, Irvine, June 2008.
Refereed Posters
T.
Milenkovic, I. Filippis, M. Lappe,
and N. Przulj, “Optimized null model
for protein structure networks”, a poster at the 7th European
Conference on Computational Biology, ECCB’08, Cagliary, Italy.
Tijana
Milenkovic and Natasa Przulj, “Uncovering Biological Network Function via
Graphlet Degree Signatures”, a poster at the 7th European Conference
on Computational Biology, ECCB’08, Cagliary, Italy.
Tijana
Milenkovic, Jason Lai, and Natasa
Przulj, “GraphCrunch: A Tool for
Large Network Analyses”, a poster at the 7th European Conference on
Computational Biology, ECCB’08, Cagliary, Italy.
Tijana
Milenkovic and Natasa Przulj, “Uncovering disease genes and function via
graphlet degree signatures”, a poster at the 9th
International Conference on Systems Biology, ICSB'08,
T.
Milenkovic, I. Filippis, M. Lappe,
and N. Przulj, “Optimized null
model for protein structure networks”, a poster at the 9th
International Conference on Systems Biology, ICSB'08, Gothenburg, Sweden.
Tijana
Milenkovic, Jason Lai, and Natasa
Przulj, “GraphCrunch: A tool for
large network analyses”, a poster at the 9th International
Conference on Systems Biology, ICSB'08, Gothenburg, Sweden.
T.
Milenkovic, I. Filippis, M. Lappe,
and N. Przulj, “Optimized Null
Model for Residue Interaction Graphs”, a poster at the 16th
Annual International Conference on Intelligent Systems for Molecular Biology,
ISMB’08, Toronto, Canada.
Tijana
Milenkovic and Natasa Przulj, “Uncovering Biological Network Function via
Graphlet Degree Signatures”, a poster at the 16th Annual
International Conference on Intelligent Systems for Molecular Biology,
ISMB’08, Toronto, Canada.
Cortnie Guerrero, Tijana
Milenkovic, Jeffrey J. Jones, Natasa Przulj, Peter Kaiser, and Lan Huang,
“Characterizing the 26S Proteasome Network in Yeast using a
Quantitative In-Vivo Crosslinking Strategy and PPI Network Analysis”,
56th ASMS Conference on Mass Spectrometry, Denver,
Colorado, 2008.
T.
Milenkovic and Natasa Przulj, “Protein Signatures: Interplay of Topology
and Biology”, a poster at the RECOMB
Satellite Conference on Systems Biology 2007, University of California, San
Diego, November 30 – December 1, 2007.
T.
Milenkovic, J. Lai, and N. Przulj,
“GraphCrunch: A Tool for Large
Network Analyses”, a poster at the RECOMB Satellite Conference on Systems Biology 2007, University of California,
San Diego, November 30 – December 1, 2007.
T.
Milenkovic, I. Filippis, M. Lappe,
and N. Przulj, “Optimized Null
Model for Residue Interaction Graphs”, a poster at the RECOMB Satellite Conference on Systems
Biology 2007, University of California, San Diego, November 30 –
December 1, 2007.
T.
Milenkovic, J. Lai, and N. Przulj,
“GraphCrunch: A Tool for Large
Network Analyses”, a poster at the Eight International Conference
T. Milenkovic, I. Filippis, M. Lappe, and N. Przulj, “Optimized Null Model for Residue
Interaction Graphs”, a poster at the Eight International
T.
Milenkovic, J. Lai, and N. Przulj,
“GraphCrunch: A Tool for Large
Network Analyses”, a poster at the 15th Annual International
Teaching
Assistant/Reader Positions
CS 132: Computer Networks
(Fall 2008)
CS 146: Programming in
Multitasking Operating Systems (Spring 2008)
CS 115: Computer
Simulation (Spring 2008)
CS 171: Introduction
to Artificial Intelligence (Winter 2008)
CS 133: Advanced
Computer Networks (Spring 2007)
CS 122A: Introduction
to Data Management (Winter 2007)