Publication

Diem-Trang Pham, Shanshan Gao, Vinhthuy Phan, "An accurate and fast alignment-free method for profiling microbial communities", 2017, Journal of Bioinformatics and Computational Biology, Vol. 15, No. 3 1740001.

Quang Tran, Shanshan Gao and Vinhthuy Phan, "Analysis of optimal alignments unfolds aligners’ bias in existing variant profiles", BMC Bioinformatics 2016 17(Suppl 13):349.

Diem-Trang Pham, Shanshan Gao, Vinhthuy Phan, "An alignment-free method for profiling microbial communities", 2016, Proceedings of the 8th International Conference on Bioinformatics and Computational Biology, pages 109-114 (BiCOB 2016).

Quang Tran, Shanshan Gao, Vinhthuy Phan, "Repeat complexity of genomes as a means to predict the performance of short-read aligners", 2016, Proceedings of the 8th International Conference on Bioinformatics and Computational Biology, pages 135-142, (BiCOB 2016)

V. Phan, S. Gao, Q. Tran and N. Vo, ``How genome complexity can explain the hardness of aligning reads to genomes". BMC Bioinformatics 2015, 16(Suppl 17):S3.

N. Vo, V Phan, "Exploiting dependencies of pairwise comparison outcomes to predict patterns of gene response". BMC Bioinformatics 2014, 15(Suppl 11):S2 doi:10.1186/1471-2105-15-S11-S2.

N. Vo, Q. Tran, N. Niraula, V. Phan, "RandAL: a randomized approach to aligning DNA sequences to reference genomes", BMC Genomics 2014, 15(Suppl 5):S2 doi:10.1186/1471-2164-15-S5-S2.

Vinhthuy Phan, Shanshan Gao, Quang Tran and Nam Vo, "How genome complexity can explain the hardness of aligning reads to genomes". Proceedings of the 4th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2014.

N. Vo, Q. Tran, N. Niraula, V. Phan, "A Randomized Algorithm for Aligning DNA Sequences to Reference Genomes", The 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2013.

N. Vo, T. Sutter, V Phan, "mDAG: A web tool for analyzing, visualizing, and interpreting response patterns in gene expression data with multiple treatments", Advances in Bioscience and Biotechnology, 2013, 4(6): 706-709.

N. Vo, V. Phan, "Exploiting Dependencies of Patterns in Gene Expression Analysis Using Pairwise Comparisons", 2013, proceedings of the 9th International Symposium on Bioinformatics Research and Applications (ISBRA), 173-184.

V. Phan, N. Vo, T. Sutter, "Inferring Directed-graph Patterns of Gene Responses to Treatments", 2013, proceedings of the 5th International Conference on Bioinformatics and Computational Biology (BiCOB), 7-12.

C. Simmons, S. Shiva, V. Phan, V. Shandilya, 2012, “IRS: An Issue Resolution System for Cyber Attack Classification and Management”, proceedings of the 2012 International Conference on Security and Management, p53-59.

N. Vo and V. 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.

N. Vo, V. Phan, T. Sutter, 2012, “Predicting Possible Directed-graph Patterns of Gene Expressions in Studies Involving Multiple Treatments”, proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 579-581.

S. Roy, K. Heinrich, V. Phan, M.W. Berry, R. Homanyouni, 2011, "Latent Semantic Indexing of PubMed abstract for identification of transcription factor candidates from microarray derived gene sets", BMC Bioinformatics, 12(Suppl 10):S19

V. Phan, N. Vo, T.R. Sutter, 2011, "mDAG: a web-based tool for analyzing microarray data with multiple treatments", BMC Bioinformatics, 12(Suppl 7):A7.

M. Garzon, K. Bobba, A. Neel, V. Phan, 2010, "DNA-Based Indexing", International Journal of Nanotechnology and Molecular Computation, 2(3):25-45.

V. Phan, S. Saha, A. Pandey, T.Y. Wong. “Synthetic Gene Design with a Large Number of Hidden Stop Codons”, International Journal of Data Mining and Bioinformatics, Vol. 4, No. 4, p377-394, 2010.

V. Phan, A. Thomas, K. Malasri, C.H. Sutter, “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, 2010.

M. Garzon, K. Bobba, A. Neel, V. Phan, 2010, "DNA-Based Indexing", International Journal of Nanotechnology and Molecular Computation, 2(3):25-45.

M. Garzon, T.Y. Wong, V. Phan, 2009. “DNA Chips for Species identification and Biological Phylogenies”, 15th International Meeting on DNA Computing, Lecture Notes in Computer Science, DNA Computing and Molecular Programming, Vol. 5877, p55-66.

Q.T. Tran, X. Lijing, V. Phan, S. Goodwin, M. Rahman, V. Jin, C.H. Sutter, B. Roebuck, T. Kensler, E.O. George, T.R. Sutter, 2009. "Chemical genomics of cancer chemopreventive dithiolethiones", Carcinogenesis, 30(3):480-486.

V. Phan, E.O. George, Q.T. Tran, S. Goodwin, S. Boddreddigari, T.R. Sutter, 2009. “Analyzing Microarray Data with Transitive Directed Acyclic Graphs”, Journal of Bioinformatics and Computational Biology, 7(1):135-156.

V. Phan, M Garzon. "On Codeword Design in Metric DNA Spaces", Journal of Natural Computing, 8(3):571-588, 2009.

M. Garzon, V. Phan, A. Neel, 2009. “Optimal DNA Codes for Computing and Self-Assembly”, Int. Journal of Nanotechnology and Molecular Computation, 1(1):1-17.

V. Phan, N. Furlotte, 2008. “Motif Tool Manager: a web-based framework for motif discovery”, Bioinformatics 24(24):2930-2931.

V. Phan, K Malasri, 2008. "BioTDMS: a General-purpose System for Integrative Management of Bioinformatics Tools and Data", Int. Journal of Computational Biology and Drug Design, (1):2 174-184.

V. Phan, S. Saha, A. Pandey, T.Y. Wong, 2008. “Synthetic Gene Design with a Large Number of Hidden Stop Codons”, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), p141-146.

V. Phan, E.O. George, Q.T. Tran, T. Sutter, 2008. “Toward a Combinatorial Approach to the Sample Size Problem in Multiple-treatment Microarray Studies”, 2008 Int. Conference on Bioinformatics & Computational Biology (BIOCOMP 2008), p175-181.

V. Phan, A. Thomas, 2007. “Stability of RNA Structural Motifs and Its Influence on Editing Efficiency by ADARS”, Int. Conference on Bioinformatics & Computational Biology (BIOCOMP 2007), p679-685. pdf

V. Phan, A. Thomas, 2007. “How to Build a System that Manages Bioinformatics Content”, Proceedings of the 2007 International Conference on Enterprise Information Systems and Web Technologies, p266-272. pdf

K. Bobba, A. Neal, M. Garzon, V. Phan, 2006. “Reason and Talking DNA: Can DNA understand English? Can we tell?”, 12th International Meeting on DNA Computing, Springer-Verlag Lecture Notes in Computer Science, 4287:337-349.

M. Garzon, V. Phan, S. Roy, A. Neal, 2006. “In Search of Optimal Codes for DNA Computing”, 12th International Meeting on DNA Computing, Springer-Verlag Lecture Notes in Computer Science, 4287:143-156.

M. Garzon, V. Phan, K. Bobba, R. Kontham, 2006. "Sensitivity and Capacity of Microarray Encodings", Eleventh International Meeting on DNA Computing, Lecture Notes in Computer Science, 3892:81-95, Springer-Verlag.

V. Phan, 2006. “A Method for Constructing Large DNA Codesets” in “Advanced Computational Methods for Biocomputing and Bioimaging”, edited by T. Pham, H. Yan and D. Crane, Nova Science Publishers, New York. pdf

V. Phan, M. Garzon, 2005. "Information Encoding using DNA", Tenth International Meeting on DNA Computing, Lecture Notes in Computer Science, 3384:281-292, Springer-Verlag. pdf

V. Phan, S. Skiena, 2005. “An Improved Time-sensitive Metaheuristic Framework for Combinatorial Optimization”, III Workshop on Efficient and Experimental Algorithms, Lecture Notes in Computer Science, 3059:432-445, Springer-Verlag. pdf

V. Phan, P. Sumazin, S. Skiena, 2003. “A Model for Analyzing Black-box Optimization”, Workshop on Algorithms and Data Structures, Lecture Notes in Computer Science, 2748:424-438, Springer-Verlag. pdf

V. Phan, M. Mukherjee, 2002. "Improved Line-End Fore-Shortening and Corner-Rounding Control in Optical Proximity Correction using Radius of Curvature Method", Proc. SPIE, Optical Microlithography XV 4691:1082-1090. pdf

V. Phan, P. Sumazin, S. Skiena, 2002. “A Time-sensitive System for Black-box Optimization”, Algorithm Engineering and Experiments, Lecture Notes in Computer Science, 2409:16-28, Springer-Verlag. pdf

V. Phan, S. Skiena, 2001. "Dealing with Errors in Interactive Sequencing by Hybridization", Bioinformatics, (17):10 862-70. pdf

V. Phan, S. Skiena, 2002. “Coloring Graphs with a General Heuristic Engine”, Computational Symposium on Graph Coloring and its Generalization, pages 92-99, Ithaca, New York. pdf