Vinhthuy Phan

Peer-reviewed Publications

• Diem-Trang Pham, Vinhthuy Phan, "MetaBIDx: a new computational approach to bacteria identification in microbiomes ", Microbiome Research Reports 2024;3:25.
• Zaman, Alina, Amy Cook, Vinhthuy Phan, and Alistair Windsor. "A Practical Strategy for Training Graduate CS Teaching Assistants to Provide Effective Feedback." In Proceedings of the 2023 Conference on Innovation and Technology in Computer Science Education V. 1, pp. 285-291. 2023.
• Kritish Pahi and Vinhthuy Phan. 2023. A Cloud-Based Technology for Conducting In-class Exercises in Data Science and Machine Learning Courses. In Proceedings of the 54th ACM Technical Symposium on Computer Science Education V. 1 (SIGCSE 2023). Association for Computing Machinery, New York, NY, USA, 868–874.
• Phan, Vinhthuy, Laura Wright, and Bridgette Decent. "Optimizing Financial Aid Allocation to Improve Access and Affordability to Higher Education." Journal of Educational Data Mining 14.3 (2022): 26-51.
• Pham, Diem-Trang, & Phan, Vinhthuy (2022). Representing bacteria with unique genomic signatures. Frontiers in big data, 5, 1018356. https://doi.org/10.3389/fdata.2022.1018356
• Vinhthuy Phan, Laura Wright, and Bridgette Decent. 2022. "Addressing Competing Objectives in Allocating Funds to Scholarships and Need-based Financial Aid", Proceedings of the 15th International Conference on Educational Data Mining, International Educational Data Mining Society (EDM 2022), pp. 110--121. (Winner of the Best Paper Award)
• Amy Cook, Vinhthuy Phan, and Alistair Windsor. 2022. Improving TA Feedback on In-Class Coding Assignments for Introductory Computer Science. In Proceedings of the 27th ACM Conference on on Innovation and Technology in Computer Science Education Vol. 1 (ITiCSE '22). Association for Computing Machinery, New York, NY, USA, 421–427. https://doi.org/10.1145/3502718.3524746
• Eric Hicks, Amy Cook, Kriangsiri Malasri, Alina Zaman, and Vinhthuy Phan. 2022. Keep It Relevant! Using In-class Exercises to Predict Weekly Performance in CS1. In Proceedings of the 53rd ACM Technical Symposium on Computer Science Education - Volume 1 (SIGCSE 2022), Vol. 1. Association for Computing Machinery, New York, NY, USA, 154–160. https://doi.org/10.1145/3478431.3499357
• Amy Cook, Alina Zaman, Eric Hicks, Kriangsiri Malasri, and Vinhthuy Phan. 2022. Try That Again! How a Second Attempt on In-Class Coding Problems Benefits Students in CS1. In Proceedings of the 53rd ACM Technical Symposium on Computer Science Education - Volume 1 (SIGCSE 2022), Vol. 1. Association for Computing Machinery, New York, NY, USA, 509–515. https://doi.org/10.1145/3478431.3499362
• Quang Tran, Vinhthuy Phan. "Assembling Reads Improves Taxonomic Classification of Species". Genes 2020, 11, 946. (h5-index: 48)
• Quang Tran, Nam Sy Vo, Eric Hicks, Tin Nguyen and Vinhthuy Phan. "Analysis of Short-read Aligners using Sequence Complexity of Genomes". 2020. The 12th International Conference on Knowledge and Systems Engineering (KSE 2020), p312-p317.
• Eric Hicks, Quang Tran, Kriangsiri Malasri, Nam Sy Vo and Vinhthuy Phan. "Active Learning:The Almost Silver Bullet". 2020. The 12th International Conference on Knowledge and Systems Engineering (KSE 2020), p131-135.
• Vinhthuy Phan, Diem-Trang Pham, Caroline Melton, Adam Ramsey, Bernie Daigle Jr., and Jennifer Mandel, 2019, "icHET: Interactive Visualization of Cytoplasmic Heteroplasmy", Bioinformatics, 2019, 35(21):4411-4412. (h5-index: 110)
• Shanshan Gao, Quang Tran, and Vinhthuy Phan, 2019, "Understand Effective Coverage by Mapped Reads using Genome Repeat Complexity". In Proceedings of 11th International Conference on Bioinformatics and Computational Biology. Vol. 60, pages 65-73.
• Nam Vo and Vinhthuy Phan, 2018, ”Leveraging known genomic variants to improve detection of variants, especially close-by Indels”. Bioinformatics, (34):17 2918-2926. (h5-index: 110)
• Vinhthuy Phan and Eric Hicks, 2018, "Code4Brownies: An Active Learning Solution for Teaching Programming and Problem Solving in the Classroom". In Proceedings of 23rd Annual ACM Conference on Innovation and Technology in Computer Science Education (ITiCSE18), pages 153-158. (h5-index: 20)
• Quang Tran, Diem-Trang Pham and Vinhthuy Phan, 2017, "Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities", BMC Bioinformatics, 18(Suppl 14):499. (h5-index: 61)
• Diem-Trang Pham, Shanshan Gao, Vinhthuy Phan, 2017, "An accurate and fast alignment-free method for profiling microbial communities", Journal of Bioinformatics and Computational Biology, Vol. 15, No. 3 1740001. DOI: http://dx.doi.org/10.1142/S0219720017400017 (h5-index: 16)
• Quang Tran, Shanshan Gao and Vinhthuy Phan, 2016, "Analysis of optimal alignments unfolds aligners' bias in existing variant profiles", BMC Bioinformatics, 17(Suppl 13):349. (h5-index: 61)
• Quang Tran, Shanshan Gao, Vinhthuy Phan, 2016, "Repeat complexity of genomes as a means to predict the performance of short-read aligners", Proceedings of the 8th International Conference on Bioin- formatics and Computational Biology (BiCOB 2016), pages 135-142.
• Vinhthuy Phan, Shanshan Gao, Quang Tran and Nam Sy Vo, 2015, "How genome complexity can explain the hardness of aligning reads to genomes". BMC Bioinformatics, 16(Suppl 17):S3. (h5-index: 61)
• Nam Sy Vo, Quang Tran, Nobal Niraula, Vinhthuy Phan, 2014, "RandAL: a randomized approach to aligning DNA sequences to reference genomes", BMC Genomics, 15(Suppl 5):S2 doi:10.1186/1471-2164- 15-S5-S2. (h5-index: 80)
• Nam Sy Vo, Vinhthuy Phan, 2014, "Exploiting dependencies of pairwise comparison outcomes to predict patterns of gene response". BMC Bioinformatics, 15(Suppl 11):S2 doi:10.1186/1471-2105-15-S11- S2. (h5-index: 61)
• Nam Sy Vo, Thomas Sutter, Vinhthuy Phan, 2013, "mDAG: A web tool for analyzing, visualizing, and interpreting response patterns in gene expression data with multiple treatments", Advances in Bioscience and Biotechnology, 4(6): 706-709. (h5-index: 17)
• Vinhthuy Phan, Nam Sy Vo, Thomas Sutter, 2013, "Inferring Directed-graph Patterns of Gene Re- sponses to Treatments", Proceedings of the 5th International Conference on Bioinformatics and Computational Biology, 7-12.
• Nam S. Vo, Vinhthuy Phan and Thomas Sutter, 2012, "Predicting Possible Directed-graph Patterns of Gene Expressions in Studies Involving Multiple Treatments, Proceedings of the ACM Conference on Bioin- formatics, Computational Biology and Biomedicine, 579-581.
• Nam S. Vo and Vinhthuy Phan, 2012, "Pattern Analysis: a Web-based Tool for Analyzing Response Patterns in Low-replication, Many-treatment Gene Expression Data". Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 539-541.
• Sujoy Roy, Kevin Heinrich, Vinhthuy Phan, Michael Berry, Ramin Homanyouni, 2011, "Latent Seman- tic Indexing of PubMed abstract for identification of transcription factor candidates from microarray derived gene sets", BMC Bioinformatics, 12(Suppl 10):S19 (h5-index: 61)
• Vinhthuy Phan, Nam Sy Vo, Thomas Sutter, 2011, "mDAG: a web-based tool for analyzing microarray data with multiple treatments", BMC Bioinformatics, 12(Suppl 7):A7. (h5-index: 61)
• Max Garzon, K. Bobba, Andrew Neel, Vinhthuy Phan, 2010, "DNA-Based Indexing", International Jour- nal of Nanotechnology and Molecular Computation, 2(3):25-45.
• VinhthuyPhan, AllenThomas, Kriangsiri Malasri, CarieSutter, 2010, "Stability of RNA Structural Motifs and Its Influence on Editing Efficiency by Adenosine Deaminases", International Journal of Bioinformatics Research and Application, Vol. 6, No. 1, p21-36. (h5-index: 9)
• Vinhthuy Phan, Sudip Saha, A. Pandey, Tit-Yee Wong. 2010, "Synthetic Gene Design with a Large Number of Hidden Stop Codons", International Journal of Data Mining and Bioinformatics, Vol. 4, No. 4, p377-394. (h5-index: 12)
• Vinhthuy Phan, Max Garzon. "On Codeword Design in Metric DNA Spaces", 2009, Journal of Natural Computing, 8(3):571-588.
• Nhu-Quynh Tran, L. Xu, Vinhthuy Phan, S. Goodwin, M. Rahman, V. Jin, C.H. Sutter, B. Roebuck, T. Kensler, E.O. George, Thomas Sutter, 2009, "Chemical Genomics of Cancer Chemopreventive Dithiolethiones", Carcinogenesis, 30(3):480-486. (h5-index: 64)
• Max Garzon, Tit-Yee Wong, Vinhthuy Phan, 2009. "DNA Chips for Species identification and Biological Phylogenies", 15th International Conference on DNA Computing and Molecular Programming, Vol. 5877, p55-66.
• VinhthuyPhan, NickFurlotte, 2008, "MotifToolManager: a web-based framework for motif discovery", Bioinformatics, 24(24):2930-2931. (h5-index: 110)
• Vinhthuy Phan, E.O. George, Nhu-Quynh Tran, S. Goodwin, S. Boddreddigari, Thomas Sutter, 2009, "Analyzing Microarray Data with Transitive Directed Acyclic Graphs", Journal of Bioinformatics and Computational Biology, 7(1):135-156. (h5-index: 16)
• Vinhthuy Phan and Max H. Garzon. 2009. "On codeword design in metric DNA spaces". Journal of Natural Computing, Vol. 8, No. 3, 571-588. DOI=http://dx.doi.org/10.1007/s11047-008-9088-6
• Max Garzon, Vinhthuy Phan, Andrew Neel, 2009, "Optimal DNA Codes for Computing and Self- Assembly", International Journal of Nanotechnology and Molecular Computation, (1):1 1-17.
• Vinhthuy Phan, E.O. George, Nhu-Quynh Tran, Thomas Sutter, 2008, "Toward a Combinatorial Approach to the Sample Size Problem in Multiple-treatment Microarray Studies", Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, p175-181.
• Vinhthuy Phan, Kriangsiri Malasri, 2008, "BioTDMS: a General-purpose System for Integrative Man- agement of Bioinformatics Tools and Data", International Journal of Computational Biology and Drug De- sign, (1):2 174-184. (h5-index: 9)
• Kiran Bobba, Andrew Neal, Max Garzon, Vinhthuy Phan, 2006, "Reason and Talking DNA: Can DNA understand English? Can we tell?", The 12th International Meeting on DNA Computing, Lecture Notes in Computer Science, 4287:337-349, Springer-Verlag.
• Max Garzon, Vinhthuy Phan, Sujoy Roy, Andrew Neal, 2006, "In Search of Optimal Codes for DNA Computing", 12th International Meeting on DNA Computing, Lecture Notes in Computer Science, 4287:143-156.
• Max Garzon, Vinhthuy Phan, Kiran Bobba, R. Kontham, 2005, "Sensitivity and Capacity of Microarray Encodings", 11th International Meeting on DNA Computing, Lecture Notes in Computer Science, 3892:81-95.
• VinhthuyPhan, MaxGarzon, 2005, "The Capacity of DNA for Information Encoding", 10th International Meeting on DNA Computing, Lecture Notes in Computer Science, 3384:281-292.
• Vinhthuy Phan, S. Skiena, 2005, "An Improved Time-sensitive Metaheuristic Framework for Combinatorial Optimization", 3rd Workshop on Efficient and Experimental Algorithms, Lecture Notes in Computer Science, 3059:432-445.
• Vinhthuy Phan, Pavel Sumazin, Steve Skiena, 2003, "A Model for Analyzing Black-box Optimization", Workshop on Algorithms and Data Structures, Lecture Notes in Computer Science, 2748:424-438.
• Vinhthuy Phan, Pavel Sumazin, S. Skiena, 2002, "A Time-sensitive System for Black-box Optimization", Algorithm Engineering and Experiments, Lecture Notes in Computer Science, 2409:16-28.
• Vinhthuy Phan, Steve Skiena, 2002, "Coloring Graphs with a General Heuristic Engine", Computational Symposium on Graph Coloring and its Generalization, pages 92-99.
• VinhthuyPhan, MaharahMukherjee, 2002, "Improved Line End Fore-Shortening and Corner-Rounding Control in Optical Proximity Correction using Radius of Curvature Method", Proceedingds of SPIE, Optical Microlithography XV, 4691:1082- 1090.
• Vinhthuy Phan, Steve Skiena, 2001, "Dealing with Errors in Interactive Sequencing by Hybridization", Bioinformatics, (17):10 862-70. (h5-index: 110)