Publications

Refereed Journals & book chapters

• Temate-Tiagueu Y, Al Seesi S, Mathew M, Mandric I, Rodriguez A, Bean K, Cheng Q, Glebova O, Măndoiu 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 on 2016: 8.69) [Free Full Text]  (nominated as “Top ten paper award in the field of Regulatory and Systems Genomics, 2012-13”)

• 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 on 2016: 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 on 2016: 5.468)   [Free Full Text]

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

• 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, pp 271-293.

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

• Wei, Ellen, Bulusu, Harshini, Tang, Wenwu, and Cheng, Qiong. 2025. "Measuring Effects of Caffeine and Melatonin on Learning Trends of Danio rerio Juveniles Using Smart Sensing" The Journal of Emerging Investigators . (submitted)

Refereed Conferences and Workshops

• IEEE TLT 2025 (submitted)

• Which Method Excels in Anomaly Detection on Small, Isolated Labeled Data: LLMs, Federated Learning, ML, or Ensembles?  ICDM 2025 (triple-blinded review) (submitted)

• Explainable Skill Acquisition over Time via GraphRAG-Augmented Mastery Features, Fuzzy Clustering, and Hybrid Deep Models. ICDM 2025 (triple-blinded review) (submitted)

• Meta-analysis of the Effectiveness of Adaptive Scaffolding in Adaptive Pre-learning Flipped Classes. SIGCSE 2026 (triple-blinded review) (submitted)

• Zane Hutchens, Qiong Cheng. 2025. RAG-LLM Ensembled Framework for Automated Domain-Specific Concept Graph Extraction. FIE 2025

• Samhith Dara, Qiong Cheng. 2025. Evaluating Handwritten and Multimodal, Free-Style Responses in Algorithms and Data Structures: a RAG-LLM-Based Feedback Framework. FIE 2025

• Qiong Cheng, Harini Ramaprasad, Edward Fleming, Sharad Swaminathan, and Rahul Das “Comparison of the Effectiveness of Company-sponsored versus Student-selected Project-based Learning in Online Database Classes” In 2024 IEEE Frontiers in Education Conference (FIE)

• Qiong Cheng.  Online Prediction to Facilitate a Flipped and Adaptive Classroom. 2023 IEEE Frontiers in Education Conference (FIE)    

  • Area of focus:  Educational Data Analysis and Prediction.

• Qiong Cheng. Towards Connected Modern Teaching Machine: An Agile Adaptive Learning App to Customize Learning Materials and Assessments on the Fly. 2023 ACM technical symposium on Computer science education (SIGCSE).  (Demo paper) 

• Qiong Cheng.  "Identifying Temporal Biomarkers of Disease Development through a Thermodynamics-enriched Ensemble Framework," in 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Las Vegas, NV, USA, 2022 pp. 726-729.

• Q Cheng, M Garikipati, S Meenakshisundaram. Predicting at-risk Students to Facilitate Scaffolding Instructions. 2021 IEEE Frontiers in Education Conference (FIE)    

  • • Area of focus:  Educational Data Analysis and Prediction.

• Q Cheng, D Benton, A Quinn. Building a Motivating and Autonomy Environment to Support Adaptive Learning.  2021 IEEE Frontiers in Education Conference (FIE)    

  • • Area of focus:  Practice of Adaptive Learning.

• Q. Cheng, "Enrich a data structures course with parallelism", 2020 IEEE Frontiers in Education Conference (FIE)    

  • • Area of focus:  Parallel and Distribution Computing Education.

• Q. Cheng,  F. Lopez and A. Hadjixenofontos, "Integrating Introductory Data Science into Computer and Information Literacy through Collaborative Project-based Learning," 2019 IEEE Frontiers in Education Conference (FIE)    

  • • Area of focus:  Scientific methods in education.

• Q. Cheng, "Enhancing Essential Data Skills for College-wide Students," SIGCSE '19 Proceedings of the 50th ACM Technical Symposium on Computer Science Education. Minneapolis, MN, USA — February 27 - March 02, 2019. 1262-1262 (Poster)

• Q. Cheng, S. Mehta and S. Schürer, "A Gene Family-led Meta-Analysis of Drug-Target Interactions," 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 1618-1623. doi: 10.1109/BIBM.2018.8621087

  • • Area of focus: Data curation, ontology in applications, applications of graph theory

• 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.

• 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. 

• 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.   

• 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. 

• 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. 

• 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. 

• 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 .   

• 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. 

• Q. Cheng, D. Kaur, R. Harrison, and A. Zelikovsky. (2007) Mapping and Filling Metabolic Pathways. RECOMB Satellite Conference on Systems Biology.  [Free Full Text]

• 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]

• 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]

• 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]

• 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

• Q. Cheng and Saurabh Sinha. (2013) Mining ChIP Data for Evidence of Underlying Mechanisms. 54th Annual Drosophila Conference (Poster).

• 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)

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

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

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

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

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

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

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

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