I am a post-doc in the School of Computer Science at Carnegie Mellon University. I am interested in optimization, data mining, and network problems in computational biology.

Post-doc	Carnegie Mellon	2011-	[Advisor: Ziv Bar-Joseph]
PhD	Maryland	2010	[Advisor: Carl Kingsford]
MEng	Cornell	2006
BS	Cornell	2005
AA	Simon's Rock	2002

Contact: navlakha@cs.cmu.edu





Publications

• Algorithms in Nature: The Convergence of Systems Biology and Computational Thinking
  S. Navlakha and Z. Bar-Joseph. Nature/EMBO Molecular Systems Biology (MSB, 2011).
  [pdf]


• Link Prediction for Annotation Graphs using Graph Summarization
  A. Thor, P. Anderson, L. Raschid, S. Navlakha, B. Saha, S. Khuller, and X-N. Zhang. Proc. 10th Intl. Semantic Web Conference (ISWC, 2011).
  [pdf]


• Parsimonious Reconstruction of Network Evolution
  R. Patro, E. Sefer, J. Malin, G. Marçais, S. Navlakha, and C. Kingsford. Workshop on Algorithms in Bioinformatics (WABI, 2011).
  [pdf] [website]


• Network Archaeology: Uncovering Ancient Networks from Present-day Interactions
  S. Navlakha and C. Kingsford. PLoS Computational Biology, 2011.
  Presented at the 6th RECOMB Systems Biology Satellite Conference, 2010.
  [pdf] [website] [mit tech review] [engadget]


• Uncovering Many Views of Biological Networks Using Ensembles of Graph Partitions
  G. Duggal, S. Navlakha, M. Girvan, and C. Kingsford. Proc. 1st Intl. Workshop on Discovering, Summarizing, and Using Multiple Clusterings (KDD MultiClust, 2010).
  [pdf] [website]


• Alignment and Clustering of Phylogenetic Markers - Implications for Microbial Diversity Studies
  J.R. White, S. Navlakha, N. Nagarajan, M. Ghodsi, C. Kingsford, and M. Pop. BMC Bioinformatics, 2010.
  [pdf]


• The Power of Protein Interaction Networks for Assocating Genes with Diseases
  S. Navlakha and C. Kingsford. Bioinformatics, 2010.
  [pdf] [website] [faculty of 1000 review]


• Exploring Biological Network Dynamics with Ensembles of Graph Partitions
  S. Navlakha and C. Kingsford. Proc. 15th Intl. Pacific Symposium on Biocomputing
  (PSB, 2010).
  [pdf]


• Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information
  S. Navlakha, J. White, N. Nagarajan, M. Pop, and C. Kingsford. Proc. 13th Intl. Conf. on Research in Computational Molecular Biology (RECOMB, 2009).
  [pdf] [website]


• Revealing Biological Modules via Graph Summarization
  S. Navlakha, M.C. Schatz, and C. Kingsford. J. Comp. Biol., 2009.
  Presented at the 4th RECOMB Systems Biology Satellite Conference, 2008.
  [pdf pre-print] [video of talk]


• Graph Summarization with Bounded Error
  S. Navlakha, R. Rastogi, and N. Shrivastava. Proc. 33rd Intl. Conf. on Management of Data (SIGMOD, 2008).
  [pdf] [code]


• A Graph-based Approach to Vehicle Tracking in Traffic Camera Video Streams
  H. Haidarian-Shahri, G.M. Namata, S. Navlakha, A. Deshpande, and N. Roussopoulos. Proc. 4th Intl. Workshop on Data Management for Sensor Networks (VLDB DMSN, 2007).
  [pdf]