Qiong Cheng, PhD


QiongResearch Analyst

Dr. Qiong Cheng joined the University of Miami’s Center for Computational Science in February 2014. Dr. Cheng graduated from Georgia State University in December 2009 with a PhD in Computer Science. Upon graduating, She spent a little over a year training in CCS and then began work as a researcher with the Department of Computer Science at the University of Illinois in Urbana-Champaign.

Dr. Cheng’s research papers cover diverse fields such as modeling and simulation, parallel and distributed computing, and bioinformatics. Her interdisciplinary projects were published in PLOS Genetics, Bioinformatics, and Genome Research with a broad range of topics such as modeling and analysis of gene regulatory mechanisms, metabolic network analysis and comparison, conflict-sensitive dynamics prediction of phospherylation networks and protein-protein interaction networks. One of her first-author papers has been voted in “top 10 papers in regulatory genomics for 2012-13“. She was also awarded  the GSU Molecular Basis of Disease Fellowship in 2007, 2008, and 2009.

Her primary research interest lie in the application of machine learning, data mining, graph algorithms, and parallel and distributed computing in designing and analysis of algorithms for solving the problems in molecular biology and disease studies.


  1. Q. Cheng, M. Kazemian, H. Pham, C. Blatti, S. E. Celniker, S. A. Wolfe, M. H. Brodsky, S. Sinha. (2013) Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PLoS Genet 9(8): e1003571. doi:10.1371/journal.pgen.1003571 (Impact Factor: 8.69) (voted in “top 10 papers in regulatory genomics for 2012-13” at http://www.iscb.org/recomb-regsysgen2013-program/recomb-regsysgen2013-top10-paper-awards)
  2. M. S. Enuameh, Y. Asriyan, A. Richards, R. G. Christensen,V. L. Hall, M. Kazemian, C. Zhu, H. Pham, Q. Cheng, C. Blatti, J. A. Brasefield, M. D. Basciotta, J. Ou, J. C. McNulty, L. J. Zhu, S. E. Celniker, S. Sinha, G. D. Stormo, M. H. Brodsky, S. A. Wolfe. (2013) Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res. 2013 Jun;23(6):928-40. doi: 10.1101/gr.151472.112. Epub 2013 Mar 7. (Impact Factor: 13.608)
  3. Q. Cheng, P. Berman, R. Harrison, and A. Zelikovsky. (2013) Efficient Alignments of Metabolic Networks with Bounded Treewidth. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics. Wiley Book Series on Bioinformatics, 2013, pp. 413-430.
  4. Q. Cheng and A. Zelikovsky. (2011) Combinatorial Optimization Algorithms for Network Alignments and Their Applications. International Journal of Knowledge Discovery in Bioinformatics (IJKDB), 2(1), 1-23. 
  5. Q. Cheng, M. Ogihara, and V. Gupta. (2011) Learning Condition-Dependent Dynamical PPI Networks from Conflict- Sensitive Phosphorylation Dynamics. Proceedings of IEEE International conference on Bioinformatics and Biomedicine (BIBM), 309-312.
  6. Q. Cheng, M. Ogihara, and V. Gupta. (2011) Inferring Conflict-Sensitive Phosphorylation Dynamics. Proceedings of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), 430-434.
  7. Q. Cheng, P. Berman, R. Harrison, I. Mandoiu, and Alex Zelikovsky. (2010) Efficient Alignments of Metabolic Networks with Bounded Treewidth.  ICDM 2010 workshop on Biological Data Mining and its Applications in Healthcare (ICDMW), 687-694.
  8. Q. Cheng, J. Wei, A. Zelikovsky and M. Oghara. (2010) Fixed-Parameter Tractable Combinatorial Algorithms for Metabolic Networks Alignments. ICDM 2010 workshop on Biological Data Mining and its Applications in Healthcare (ICDMW), 679-686.  
  9. Q. Cheng, M. Ogihara, J. Wei, and A. Zelikovsky. (2010) WS-GraphMatching: A Web Service Tool for Graph Matching. Proceedings of 19th ACM Conference on Information and Knowledge Management (CIKM), Demo, 1949-1950.
  10. Q. Cheng, R. Harrison, and A. Zelikovsky. (2009) MetNetAligner: a web service tool for metabolic network alignments. Bioinformatics (2009) 25 (15): 1989-1990. (Impact factor: 5.468)
  11. Q. Cheng (2009) Network Alignments and their Applications. PhD Dissertation
  12. Q. Cheng, A. Zelikovsky. (2009) Network Mapping of Metabolic Pathways. Analysis of Complex Networks: From Biology to Linguistics, Wiley-VCH, ISBN 978-3-527-32345-6, 271-293.
  13. Q. Cheng, P. Berman, R. Harrison and A. Zelikovsky. (2008) Fast Alignments of Metabolic Networks. Proceedings of IEEE International conference on Bioinformatics and Biomedicine (BIBM), 147-152. 
  14. Q. Cheng, D. Kaur, R. Harrison, and A. Zelikovsky. (2007) Mapping and Filling Metabolic Pathways. RECOMB Satellite Conference on Systems Biology.
  15. Q. Cheng, R. Harrison, and A. Zelikovsky. (2007) Homomorphisms of Multisource Trees into Networks with Applications to Metabolic Pathways. Proceedings of IEEE 7-th International Symposium on BioInformatics and BioEngineering (BIBE), 350-357
  16. H. Botadra, Q. Cheng, S. K. Prasad, E. Aubanel and V. Bhavsar. (2007) iC2mpi : A Platform for Parallel Execution of Graph-Structured Iterative Computations. Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC) in conjunction with 21th International Parallel and Distributed Processing Symposium (IPDPS), 1-8.
  17. Q. Cheng, Y. Zhang, X. Hu, N. Hundewale, A. Zelikovsky. (2006) Routing Using Messengers in Sparse and Disconnected Mobile Sensor Networks. Proceedings of Atlantic Web Intelligence Conference (AWIC), 31-40
  18. N. Hundewale, Q. Cheng, X. Hu, A. Bourgeois and A. Zelikovsky. (2006) Autonomous Messenger Based Routing in Disjoint Clusters of Mobile Sensor Networks.  Proceedings of Spring Simulation Multiconference (SpringSim) pp. 57-64.

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