Refereed Journals

• Temate-Tiagueu Y, Al Seesi S, Mathew M, Mandric I, Rodriguez A, Bean K, Cheng Q, Glebova O, Mandoiu I, Lopanik NB, Zelikovsky A. (2016). Inferring metabolic pathway activity levels from RNA-Seq data. BMC genomics, 17(5), 542.
• 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) [Free Full Text]
• 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) [PUBMED]
  
• Q. Cheng, P. Berman, R. Harrison, A. Zelikovsky. (2013) Efficient Alignments of Metabolic Networks with Bounded Treewidth. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics.Page 413-429.  [Publisher site]
• 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.   [Publisher site]
• 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) Protein Bioinformatics.Page 413-429.  [Publisher site]

• Q. Cheng (2009) Network Alignments and their Applications. PhD Dissertation  

book chapters

1. Q. Cheng, A. Zelikovsky, Network Mapping of Metabolic Pathways, Analysis of Complex Networks: From Biology to Linguistics, Wiley-VCH , ISBN 978-3-527-32345-6, pp 271-293, 2009

2. Q. Cheng, Y. Zhang, X. Hu, N. Hundewale, A. Zelikovsky, Routing Using Messengers in Sparse and Disconnected Mobile Sensor Networks, Advances in Web Intelligence and Data Mining, Volume 23, Springer Berlin, pp 31-40, 2006  

Refereed Conferences and Workshops

1. Cheng, Q., Lopez, F. A., Duran, C., Camarillo, C., Oprea, T. I., & Schurer, S. (2017, November). The ontology reference model for visual selectivity analysis in drug-target interactions. In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 2091-2097). IEEE.
2. Cheng, Q., Ursu, O., Oprea, T. I., & Schurer, S. (2017, November). Learning reference-enriched approach towards large scale active ontology alignment and integration. In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 1658-1663). IEEE. 
3. 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.   [Publisher site]
4. 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. [Publisher site]
5. 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 (BioDM) , 687-694.  [Publisher site]
   
6. 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 (BioDM), 679-686.   [Publisher site]
7. Q. Cheng, J. Wei, A. Zelikovsky and M. Ogihara. (2010) WS-GraphMatching: A Web Service Tool for Graph Matching. Proceedings of 19th ACM Conference on Information and Knowledge Management (CIKM), Demo, 1949-1950 .   [Publisher site]
   
8. 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), pp 147-152. [Free Full Text]  
   
9. Q. Cheng, D. Kaur, R. Harrison, and A. Zelikovsky. (2007) Mapping and Filling Metabolic Pathways. RECOMB Satellite Conference on Systems Biology.  [Free Full Text]
   
10. 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).  [Publisher site]
11. 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).  [Publisher site]
12. 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).  [Publisher site]
13. 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.   [Publisher site]

Posters, Tech Reports and Others

1. Q. Cheng and Saurabh Sinha. (2013) Mining ChIP Data for Evidence of Underlying Mechanisms. 54th Annual Drosophila Conference (Poster).
   
2. Q. Cheng and Saurabh Sinha.  (2012) Computational Identification of Diverse Mechanisms underlying Transcription Factor_DNA Occupancy. Institute of Genomic Biology (IGB) of University of Illinois at Urbana-Champaign(UIUC)(Oral presentation)

3. Q. Cheng, P. Berman, and A. Zelikovsky. "Alignments Of Metabolic Networks With Bounded Treewidth ".International Symposium on Bioinformatics Research and Applications(ISBRA'10), 2010.(Short abstract)(Oral presentation)

4. Q. Cheng, R. Harrison, and A. Zelikovsky. "MetNetAligner: a web service tool for metabolic network alignments ".International Symposium on Bioinformatics Research and Applications(ISBRA'09), 2009.

5. Q. Cheng, R. Harrison, and A. Zelikovsky. "Graph comparison : homo-home morphism mapping in Metabolic Pathways".International Symposium on Bioinformatics Research and Applications(ISBRA'08), 2008. (pdf)

6. Q. Cheng, D. Kaur, R. Harrison, and A. Zelikovsky, "Studies in mining conserved subgraph among metabolic pathways", The SIAM international Conference on Data Mining (SDM 2008) (pdf) (ppt)

7. Q. Cheng, D. Kaur, R. Harrison, and A. Zelikovsky, "Mapping and Filling Metabolic Pathways ", 2007 Georgia Tech-ONRL International Conference on Bioinformatics (BINF 2007). (pdf)

8. Q. Cheng, A. Zelikovsky. "Optimal Mapping of Multi Source Trees into DAG in Biological Network".International Symposium on Bioinformatics Research and Applications(ISBRA'07), 2007. (pdf)

9. Q. Cheng, A. Zelikovsky. "Pair wise Alignment of Pathways". 2nd Annual Computational and Systems Biology Symposium , (CSBS 2007). (pdf)

10. X. Hu, D. H. Edwards and Q. Cheng. "A Simulation Environment for Neural/Behavioral Models of Behavioral Choice". The Second SECABC Fall Workshop ON Biocomputing, 2005. (pdf)