Ming Ouyang

Associate Professor
Department of Computer Science
University of Massachusetts Boston
Email: ming dot ouyang at umb dot edu

Computer Science Undergraduate Programs

Computer Science is no more about computers
than astronomy is about telescopes.

Edsger Dijkstra (1930 -- 2002)

I am the UMB CS Undergraduate Program Director.

Office Hours


Recommended Reading


Everybody who is incapable of learning
has taken to teaching.
Oscar Wilde (1854 -- 1900)
The Decay of Lying , p.3

I am teaching:

I had taught:


Des chercheurs qui cherchent, on en trouve.
Des chercheurs qui trouvent, on en cherche.
Charles de Gaulle (1890 -- 1970)

I am interested in fast computation.  I work on parallelizing data analysis algorithms, statistical computation, and bioinformatics applications.

Google Scholar Citations: http://scholar.google.com/citations?hl=en&user=Xa_5OCoAAAAJ


  1. ompTri, triangle counting with a multi-core computer: https://github.com/mingouyang/ompTri
  2. bandDepth, parallel computation of band depth: https://github.com/mingouyang/bandDepth
  3. ompBFS, breadth-first search with a multi-core computer: https://github.com/mingouyang/ompBFS
  4. sort16, CUDA implementation of Van Voorhis's optimal sorting network for 16 numbers: https://github.com/mingouyang/sorting-16-numbers

Conference Papers

  1. Ouyang M, Xu H, Zhurkevich A.  Parallel computation of band depth.  Proceedings of the 21st IEEE International Conference on Computational Science and Engineering, 2018, 85-90.
  2. Donato E, Ouyang M, Peguero-Isalguez C.  Triangle counting with a multi-core computer.  Proceedings of IEEE High Performance Extreme Computing Conference (HPEC), 2018, 1-7.
  3. Belova M, Ouyang M. Breadth-first search with a multi-core computer. Proceedings of IEEE Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2017.
  4. Ouyang M. KNN in the Jaccard Space. Proceedings of IEEE High Performance Extreme Computing Conference (HPEC), 2016, 1-6.
  5. Kwon A, Ouyang M. Clustering of functional data by band depth. Proceedings the Bioinformatics Workshop of the Ninth EAI International Conference on Bio-inspired Information and Communications Technologies (BICT Bioinformatics), 2015.
  6. Kwon A, Ren D, Ouyang M, Garbett N. Robust functional profile identification for DSC thermograms. Proceedings the Bioinformatics Workshop of the Ninth EAI International Conference on Bio-inspired Information and Communications Technologies (BICT Bioinformatics), 2015.
  7. Ouyang M. Sorting sixteen numbers. Proceedings of IEEE High Performance Extreme Computing Conference (HPEC), 2015, 1-6.
  8. Maruseac M, Ghinita G, Ouyang M, Rughinis R. Hardware acceleration of private information retrieval protocols using GPUs. Proceedings of the 26th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP), 2015, 120-127.
  9. Maruseac M, Ghinita G, Ouyang M, Rughinis R. Towards efficient private spatial information retrieval using GPUs. Proceedings of the 22nd ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 2014, 405-408.
  10. Ali H, Ouyang M, Sheta W, Soliman A. Parallelizing the Berlekamp-Massey Algorithm. Proceedings of the Second International Conference on Computing, Measurement, Control and Sensor Network (CMCSN), 2014.
  11. Kim S, Ouyang M, Zhang X. Compute Spearman Correlation Coefficient with Matlab/CUDA. Proceedings of the 12th IEEE International Symposium on Signal Processing and Information Technology (ISSPIT), 2012, 55-60.
  12. Kim S, Ouyang M. Compute Distance Matrices with GPU. Proceedings of the Third Annual International Conference on Advances in Distributed and Parallel Computing (ADPC), 2012, 66-71.
  13. Mattingly WA, Chang D, Paris R. Smith N, Blevins H, Ouyang M. Robot design using Unity for computer games and robotic simulations. Proceedings of CGAMES USA, 2012, 56-59.
  14. Chang D, Kimmer C, Ouyang M. Accelerating the Nussinov RNA Folding Algorithm with CUDA/GPU. Proceedings of IEEE International Symposium on Signal Processing and Information Technology (ISSPIT), 2010, 120-125.
  15. Cheng A, Ouyang M. A simulation study on identifying aircraft touchdown point by using in-flight recorded data. Proceedings of the AIAA Guidance, Navigation, and Control Conference, 2010.
  16. Chang D, Ouyang M. Using CUDA in XNA games development. Proceedings of CGAMES USA, 2009, 96-99.
  17. Chang D, Kantardzic M, Ouyang M. Hierarchical clustering with CUDA/GPU. Proceedings of the ISCA 22nd International Conference on Parallel and Distributed Computing and Communication Systems (PDCCS), 2009, 7-12.
  18. Luken BP, Ouyang M, Desoky AH. AES and DES encryption with GPU. Proceedings of the ISCA 22nd International Conference on Parallel and Distributed Computing and Communication Systems (PDCCS), 2009, 67-70.
  19. Chang D, Desoky AH, Ouyang M, Rouchka EC. Compute pairwise Manhattan distance and Pearson correlation coefficient of data points with GPU. Proceedings of the 10th ACIS International Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (SNPD), 2009, 501-506.
  20. Chang D, Jones NA, Li D, Ouyang M, Ragade RK. Compute pairwise Euclidean distances of data points with GPUs. Proceedings of the IASTED International Symposium on Computational Biology and Bioinformatics (CBB) 2008, 278-283.
  21. Zhang P, Ouyang M, Welsh WJ. Modeling gene regulatory networks. Abstracts of papers of the American Chemical Society, 2005, 230:U1361-U1361.
  22. Pukazhenthi BS, Rockett JC, Ouyang M, Dix DJ, Howard J, Georgopoulos J, Welsh WJ, Wildt DE. Gene expression in the testes of normospermic versus teratospermic domestic cats using human cDNA microarray analyses. Biology of Reproduction, 2003, 191-192.
  23. Ouyang M, Case J, Burnside J. Divide and conquer machine learning for a genomics analogy problem, Lecture Notes in Artificial Intelligence, 2226:290-303, Springer-Verlag, 2001.
  24. Cheng A, Ouyang M. On algorithms for simplicial depth, Proceedings of the 13th Canadian Conference on Computational Geometry (CCCG), 2001, 53-56.

Journal Papers

  1. Schifano J, Cruz J, Vvedenskaya IO, Edifor R, Ouyang M, Husson RN, Nichels B, Woychik NA. tRNA is a new target for cleavage by a MazF toxin. Nucleic Acids Research, 2016, 44(3):1256-1270.
  2. Ali H, Ouyang M, Soliman A, Sheta W. Parallelizing the Berlekamp-Massey Algorithm. International Journal of Computer Science and Information Security, 2015, 13(11):42-46.
  3. Kwon A, Ouyang M, Cheng A. Resampling based classification using depth for functional curves. Communications in Statistics - Simulation and Computation, DOI: 10.1080/03610918.2014.944652, 2014.
  4. Kim S, Ouyang M, Jeong J, Shen C, Zhang X. A new method of peak detection for analysis of comprehensive two-dimensional gas chromatography mass spectrometry data. Annals of Applied Statistics, 2014, 8(2):1209-1231. [Abstract]
  5. States JC, Ouyang M, Helm CW. Systems approach to identify environmental exposures contributing to organ-specific carcinogenesis. Cancer Epidemiology, 2014, 38(3):321-327. [Abstract]
  6. Schifano J, Vvedenskaya IO, Knoblauch JG, Ouyang M, Nickels B, Woychik NA. An RNA-seq uncovers dual 23S and 16S rRNA targets of mycobacterial toxin MazF-mt3. Nature Communications, 2014, 5:3538. [Abstract]
  7. Schifano JM, Edifor R, Sharp JD, Ouyang M, Konkimalla A, Husson RN, Woychik NA. Mycobacterial toxin MazF-mt6 inhibits translation through cleavage of 23S rRNA at the ribosomal A site. PNAS, 2013, 110(21):8501-8506. [Full text]
  8. Hsu CH, Lin CY, Ouyang M, Guo YK. Biocloud: cloud computing for biological, genomics, and drug design. BioMed Research International, 2013, article ID 909470. [Full text]
  9. Rothenbacher F, Suzuki M, Hurley J, Montville T, Kirn T, Ouyang M, Woychik NA. Clostridium difficile MazF toxin exhibits selective, not global, mRNA cleavage. Journal of Bacteriology, 2012 194(13):3464-74. [Abstract]
  10. States JC, Ouyang M, Helm CW. Systems approach to identifying potential environmental exposures playing a role in ovarian crcinogenesis. Cancer Research, 2011 71(8 Supplement): 1326. [Abstract]
  11. Hurley JM, Cruz JW, Ouyang M, Woychik NA. Bacterial toxin RelE mediates frequent codon-independent mRNA cleavage from the 5' end of coding regions in vivo. Journal of Biological Chemistry, 2011 286(17):14770-14778. [Abstract]
  12. Baik S, Inoue K, Ouyang M, Inouye M. Significant bias against the ACA triplet in the mRNA sequence of Escherichia coli K-12. Journal of Bacteriology, 2009 191(19):6157-6166. [Abstract]
  13. Delker DA, Geter DR, Roop BC, Ward WO, Ahlborn GJ, Allen JW, Nelson GM, Ouyang M, Welsh W, Chen Y, O'Brien T, Kitchin KT. Oncogene expression profiles in K6/0DC mouse skin and papillomas following a chronic exposure to monomethylarsonous acid. Journal of Biochemical and Molecular Toxicology, 2009 23(6):406-18. [Abstract]
  14. Zhu L, Inoue K, Yoshizumi S, Kobayashi H, Zhang Y, Ouyang M, Kato F, Sugai M, Inouye M. Staphylococcus aureus MazF specifically cleaves a pentad sequence, UACAU, which is unusually abundant in the mRNA for pathogenic adhesive factor SraP. Journal of Bacteriology 2009 191(10):3248-55. [Abstract]
  15. Waidner L, Morgan R, Anderson A, Bernberg E, Kamboj S, Garcia M, Riblet S, Ouyang M, Isaacs G, Markis M, Meyers B, Green P, Burnside J. MicroRNAs of Gallid and Meleagrid Herpesviruses show generally conserved genomic locations and are virus-specific. Virology 2009 388(1):128-36. [Science Direct]
  16. H Cheng, M Niikura, T Kim, W Mao, KS MacLea, H Hunt, J Dodgson, J Burnside, R Morgan, M Ouyang, S Lamont, J Dekkers, J Fulton, M Soller, W Muir. Using integrative genomics to elucidate genetic resistance to Marek's disease in chickens. Developmental Biology 2008, 132:365-372.
  17. Zhu L, Phadtare S, Nariya H, Ouyang M, Husson RN, Inouye M. The mRNA interferases, MazF-mt3 and MazF-mt7 from Mycobacterium tuberculosis target unique pentad sequences in single-stranded RNA. Molecular Microbiology 2008, 69(3):559-69. [Abstract]
  18. Burnside J, Ouyang M, Anderson A, Bernberg E, Lu C, Meyers BC, Green PJ, Markis M, Isaacs GK, Huang E, Morgan R. Deep Sequencing of Chicken microRNAs. BMC Genomics 2008, 9:185. [Full article, highly accessed]
  19. Burd RS, Ouyang M, Madigan D. Bayesian logistic injury severity score: A method for predicting mortality using ICD-9 codes. Academic Emergency Medicine 2008, 15(5):466-475. [Abstract]
  20. Ouyang M, Garnett AT, Han TM, Lee A, Deng Y, Lee N, Liu HY, Amacher SL, Farber SA, Ho SY. A web based resource characterizing the zebrafish developmental profile of over 16,000 transcripts. Gene Expression Patterns 2008, 8:171-180. [Science Direct]
  21. Ahlborn GJ, Nelson GM, Ward WO, Knapp G, Allen JW, Ouyang M, Roop BC, Chen Y, O'Brien T, Kitchin KT, Delker DA. Dose response evaluation of gene expression profiles in the skin of K6/ODC mice exposed to sodium arsenite. Toxicology and Applied Pharmacology 2008, 227:400-416. [Science Direct]
  22. Liu A, Han R, Li J, Sun D, Ouyang M, Plummer M, Casaccia-Bonnefil P. The glial or neuronal fate choice of oligodendrocyte progenitors is modulated by their ability to acquire an epigenetic memory. Journal of Neuroscience 2007, 27(27):7339-43. [Abstract]
  23. Jörnsten R, Ouyang M, Wang HY. A meta-data based method for DNA microarray imputation. BMC Bioinformatics 2007, 8:109. [Full text]
  24. Jörnsten R, Wang HY, Welsh WJ, Ouyang M. DNA microarray data imputation and significance analysis of differential expression. Bioinformatics 2005, 21(22):4155-61. [Abstract]
  25. Duttagupta R, Tian B, Wilusz CJ, Khounh DT, Soteropoulos P, Ouyang M, Dougherty JP, Peltz SW. Global analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability. Molecular and Cellular Biology 2005, 25:5499-513. [Abstract]
  26. Glatt C, Ouyang M, Welsh WJ, Green J, O’Connor J, Frame S, Everds N, Poindexter G, Snajdr S, Delker D. Molecular characterization of thyroid toxicity: anchoring gene expression profiles to biochemical and pathological endpoints. Environmental Health Perspectives 2005, 113(10):1354-61. [Full article]
  27. Ouyang M, Welsh WJ, Georgopoulos P. Gaussian mixture clustering and imputation of microarray data. Bioinformatics 2004, 20(6):917-23. [Abstract]
  28. Roy A, Georgopoulos PG, Ouyang M, Freeman N, Lioy PJ. Environmental, dietary, demographic, and activity variables associated with biomarkers of exposure for benzene and lead. Journal of Exposure Analysis and Environmental Epidemiology 2003, 13(6):417-26. [Abstract]
  29. Ouyang M, Case J, Tirunagaru V, Burnside J. Five hundred sixty-five triples of chicken, human, and mouse candidate orthologs. Journal of Molecular Evolution 2003, 57(3):271-81. [Abstract]
  30. Ouyang M. How good are branching rules in DPLL?, Discrete Applied Mathematics 1998, 89:281-286.