To Prospective Students

We are always looking for serious Ph.D. students. If you are a well-motivated and self-driven student interested in pursuing a Ph.D. degree on topics related to search data structures, computational biology, bioinformatics, biometrics, machine learning, digital health, or related areas, please send me an email with your CV.

To Current Students

If you need to meet me, please come in during my office hours. If you can’t meet by then, send me an email and we can arrange a different time.

Active / Completed Projects

NSF Sponsored Projects

• NSF NRT: Bridges in Digital Health
• RII Track 2 FEC: Multi-Scale Integrative Approach to Digital Health: Collaborative Research and Education in Smart Health in West Virginia and Arkansas
• DBI: Community Building for Long Non-Coding RNA, 2018 - 2022
• Social Media Based Analysis of Adverse Drug Events: User Modeling, Signal Reliability, and Signal Validation, 2018 - 2022
• BigData Spoke: Integrating Biological Big Data Research into Student Training and Education, 2018 - 2022
• BigData Spoke: Large-Scale Medical Informatics for Patient Care Coordination and Engagement, 2016 - 2020
• EAGER: The CRUFS Framework, 2015 - 2018
• EAGER: Computational Public Drug Surveillance, 2012 - 2015

The following NSF projects are collaborative projects with Professor Amar Mukherjee of University of Central Florida and Professor Tim Bell of University of Canterbury in New Zealand. Various students (both undergraduate and graduate students) were involved in the projects. The projects are listed below:

• ITR Collaborative: Compressed Search and Retrieval for Very Large Text and Image Repositories, 2003-2007. See abstract and reports
• International Collaboration in Research on Data Compression, 2004 - 2007. See abstract and reports
• Collaborative: Compressed Domain Search for Text and Images using Sorted Contexts, CISE, 2002-2005. See abstract and reports

Related major publications

• Don Adjeroh, Tim Bell, and Amar Mukherjee, The Burrows Wheeler Transform: Data Compression, Suffix Arrays, and Pattern Matching , Springer-Verlag, July 2008.
• Y. Zhang and D.A. Adjeroh, “PPAM: Prediction by partial approximate matching for lossless image compression” , IEEE Transactions on Image Processing, 17(6), pp. 924-935, June 2008.
• D. A. Adjeroh, U. Kandaswamy, and J. Vernon Odom, “Texton-based segmentation of retinal vessels”, Journal of Optical Society of America (JOSA-A), 24(5), May 2007.
• D. A. Adjeroh, Y. Zhang, and R. Parthe, “On denoising and compression of DNA microarray images”, Pattern Recognition, vol. 39, no. 12, (Special Issue on Bioinformatics), pp. 2478-2493. Dec. 2006.

See also the list of publications

Related Software

• BSMP: Simple BWT-based compression program (download)
• bwtsearch: Pattern matching on BWT text (requires BSMP) (download)
• RKNN: Random KNN Classification and Regression (link)
• PSA: Probabilistic suffix array: efficient modeling and prediction of protein families (download)
• fWK: Fast Weighted Kendall Correlation (download)
• K2 and K2*: Alignment-free Sequence Similarity Measurement (download)
• SSAW: Sequence Similarity Analysis using Stationary Discrete Wavelet Transform (download)

Related CourseWork

• EE 568 - Information Theory
• CS 791 - String Algorithms
• CS 558 - Multimedia Systems

Conference/Workshop Organization

• IEEE BIBM'20 LncRNA Workshop
• SBP-BRiMS
• NSF BBD SPOKE: Workshop on Plant Image Analysis, August 10, 2020

Other Projects and Sponsors

• DOE CAREER Award
• NASA-WV Space Consortium
• WV-EPSCOR RCG
• WV-EPSCOR RGI
• NSF-CITeR
• DOD-ONR
• DHS
• DOJ/NIJ
• NHPRC

Selected Publications

Book

• Don Adjeroh, Tim Bell, and Amar Mukherjee, The Burrows Wheeler Transform: Data Compression, Suffix Arrays and Pattern Matching , Springer, 2008.

Journal Papers

• R. Beal and D. Adjeroh. “Variations of the parameterized longest previous factor”, Journal of Discrete Algorithms, in press.
• R. Beal and D. Adjeroh. “p-Suffix sorting as arithmetic coding”, Journal of Discrete Algorithms , in press.
• R. Beal and D. Adjeroh. “Parameterized longest previous factor”, Theoretical Computer Science , 437: 21-34, 2012.
• J. Lin, D. Adjeroh and B-H Jiang. “The Probabilistic Suffix Array: Efficient modeling and prediction of protein families”, Bioinformatics, 28 (10): 1314-1323, 2012.
• U. Kandaswamy, D. Adjeroh, S. Schuckers, and A. Hanbury, “Robust color texture under illumination variations”, IEEE Transactions on SMC-B , 42 (1), 58-68, 2012.
• J. Lin, and D. Adjeroh, “All-against-all circular pattern matching”, The Computer Journal , 2011.
• Z. Abu Deeb, D.A. Adjeroh, and B-H Jiang, “Protein surface characterization using an invariant descriptor”, International Journal of Biomedical Imaging, (Special Issue on Mathematical Methods for Images and Surfaces), 2011; 2011:918978.
• L. Shengqiao, D. Adjeroh, and E J. Harner, “Random KNN feature selection – A fast and stable alternative to random forests”, BMC-Bioinformatics, 12:450, 2011.
• S.D. Sawant and D. Adjeroh. “Balanced multiple description coding for 3D DCT video”, IEEE Transactions on Broadcasting , 57 (4), 765-766, Dec. 2011.
• U. Kandaswamy, S. Schuckers, and D. Adjeroh. “Comparison of texture analysis schemes under non-ideal conditions”, IEEE Transactions on Image Processing, 20 (8), 2260-2274, 2011.
• D. Adjeroh and F. Nan. “Suffix sorting via Shannon-Fano-Elias codes”, Algorithms, (Special Issue on Data Compression), 3(2), 145-167, 2010.
• J. Lin, Y. Jiang, Y. and D. Adjeroh. “The virtual suffix tree”, International Journal of Foundations of Computer Science, 20(6), 1109-1133, 2009.
• D. Adjeroh, M-C Lee, N. Banda and U. Kandaswamy, “Adaptive edge-oriented shot boundary detection”, EURASIP J. Image & Video Processing, vol. 2009, 2009: ID 859371, 13 pages
• D. A. Adjeroh and S. Sawant, “Error-resilient transmission of 3D DCT coded video”, IEEE Transactions on Broadcasting, 5(2), 178-189, June 2009.
• M.H. Yaghmaee and D. Adjeroh, “Priority-based rate control for service differentiation and congestion control in wireless multimedia sensor networks”, Computer Networks, 53 (11), 1798-1811, 2009
• Y. Jiang, B. Cukic, D. Adjeroh, H. D. Skinner, J. Lin, Q. J. Shen, and B-H Jiang, “An algorithm for identifying novel targets of transcription factor families: Application to Hypoxia-inducible Factor 1 targets”, Cancer Bioinformatics, 7, 75-89, 2009.
• M.C. Lee, R.K.W. Chan, and D. A. Adjeroh, “Fast Three-Dimensional Discrete Cosine Transform”, SIAM Journal on Scientific Computing, 30(6), 3087-3107, 2008.
• Y. Zhang and D.A. Adjeroh, “Prediction by partial approximate matching for lossless image compression”, IEEE Transactions on Image Processing, 17(6), 924-935, June 2008.
• Y. Zhang, X. Zhou, J. Lu, J. Lichtman, D. Adjeroh, and STC Wong, “3-D axon structure extraction and analysis in confocal fluorescence microscopy images”, Neural Computation, 20(8), 1899-1927, 2008.
• D. A. Adjeroh and U. Kandaswamy, “Game-theoretic analysis of network community structure”, International Journal of Computational Intelligence Research , 3(4), Dec. 2007.
• D. A. Adjeroh, U. Kandaswamy, and J. Vernon Odom, “Texton-based segmentation of retinal vessels”, Journal of Optical Society of America (JOSA-A), 24(5), May 2007.
• Yong Zhang*, X. Zhou, A. Degterev, M. Lipinski, D. A. Adjeroh, J. Yuan, and S.T.C. Wong, “Automated neurite extraction using dynamic programming for high-throughput screening of neuron-based assay”, Neuroimage, 35(4), 1502-1515, May 2007.
• Yong Zhang*, X. Zhou, Bernardo L. Sabatini, D. A. Adjeroh, and S.T.C. Wong, “Dendrite spine detection using curvilinear structure detector and LDA classifier”, Neuroimage, 36(2), 346-360, Jun 2007.
• D. A. Adjeroh, Y. Zhang, and R. Parthe, “On denoising and compression of DNA microarray images”, Pattern Recognition, vol. 39, no. 12, (Special Issue on Bioinformatics), pp. 2478-2493. Dec. 2006.
• U. Kandaswamy, D.A. Adjeroh and MC Lee, “Efficient texture analysis of SAR imagery”, IEEE Transactions on Geosciences and Remote Sensing, 43(9), 2075- 2083, September 2005.
• A. Firth, T.C. Bell, A. Mukherjee and D.A. Adjeroh, “A comparison of BWT approaches to string pattern matching”, Software-Practice and Experience, 35: 1217-1258, May 2005.
• D.A. Adjeroh, and Lee, M.C., “Scene-adaptive transform domain video partitioning”, IEEE Transactions on Multimedia, 6 (1), 58-69, February 2004.
• Adjeroh, D.A. and Lee, M.C., “On Ratio-Based Color Indexing”, IEEE Transactions on Image Processing, 10, 1, January 2001, pp. 36-48.
• Adjeroh, D.A. and Lee, M.C., “An Occupancy Model for Image Retrieval and Similarity Evaluation”, IEEE Transactions on Image Processing, 9, 1, January 2000, pp. 120-131.
• Adjeroh, D. A., Lee, M.C., and King, I., “A Distance Measure for Video Sequences”, Computer Vision and Image Understanding, 75, ¹⁄₂, 25-45, July/August, 1999, Academic Press Publishers, Boston.
• Adjeroh D. A. and Nwosu, K. C., “Multimedia Database Management - Requirements and Issues”, IEEE Multimedia, Special Issue on Multimedia Database Systems, June-Sept., 24-33, 1997.
• Adjeroh, D. A. and Lee, M.C., “Robust and Efficient Transform Domain Video Sequence Analysis: An Approach from the Generalized Color Ratio Model”, Journal of Visual Communication and Image Representation, 8, 2, 182-207, 1997.
• Lee, M.C., Chan, R.K.W. and Adjeroh, D. A. “Quantization of 3D-DCT Coefficients and Scan Order for Video Compression”, Journal of Visual Communication and Image Representation, 8, 4, 405-422, 1997

Conference/Workshop Publications

• Sushil K. Jain* and D.A. Adjeroh, “Edge-Based Prediction for Lossless Compression of Hyperspectral Images”, Proceedings, IEEE Data Compression Conference, Snowbird, UT, March 2007, pp. 153-162.
• D.A Adjeroh., U. Kandaswamy*, N. Zhang, A. Mukherjee, M. T. Brown, and T.C. Bell, “BWT-based efficient shape matching”, Proc., ACM SAC 2007, South Korea, 2007.
• F. Nan* and D. A. Adjeroh “An algorithm for suffix sorting and its applications”, Proc. IEEE Conference on Computational Systems Bioinformatics, Stanford, CA, August, 2006.
• D. A. Adjeroh, “Optimal coding rate selection for UEP of 3D video using RCPC codes”, Proc., IEEE Data Compression Conference, Snowbird, UT, March 2006.
• D. A. Adjeroh and F. Nan*, “On compressibility of protein sequences”, IEEE Data Compression Conference, Snowbird, UT, March 2006.
• A. Hanbury, U. Kandaswamy*, and D. A. Adjeroh, “Illumination-invariant morphological texture classification”, Proc. International Symposium on Mathematical Morphology, Paris France, Springer-Verlag, April 2005, pp. 337- 386.
• F. Nan* and D. Adjeroh, “On complexity measures for biological sequences”, Proc. IEEE Conference on Computational Systems Bioinformatics, Stanford University, CA, Aug. 2004, pp. 522- 526.
• N. Zhang, A. Mukherjee, D.A. Adjeroh, and T.C. Bell, “Approximate pattern matching using the Burrows-Wheeler Transform”, Proceedings, IEEE Data Compression Conference, March 2003.
• D.A Adjeroh., Y. Zhang*, A. Mukherjee, M. Powell, and T.C. Bell, “DNA sequence compression using the Burrows-Wheeler transform”, Proceedings, IEEE Bioinformatics Conference, Stanford University, CA, August 14-16, 2002, pp. 303 - 313.
• D.A. Adjeroh, A. Mukherjee, T.C. Bell, M. Powell, and N. Zhang, “Pattern matching in BWT-transformed text”, Proc., IEEE Data Compression Conference, Snowbird, Utah, April 2-4, 2002, pp 445,
• T. Bell, M. Powell, A. Mukherjee and D.A. Adjeroh, “Searching BWT compressed text with the Boyer-Moore algorithm and binary search”, Proc. IEEE Data Compression Conference, Snowbird, Utah, April 2-4, 2002, pp. 112 - 121.
• Adjeroh, D.A and Brown, M. T., “A Three-Component Method for Shape-Based Image Retrieval” Proceedings, Advanced Concepts for Intelligent Vision Systems (ACIVS’2001), Baden-Baden Germany, Jul. 30 - Aug. 3, 2001.
• Adjeroh, D. A., King, I., and Lee, M.C., “Video Sequence Similarity Matching”, Proceedings, IAPR International Workshop on Multimedia Information Analysis & Retrieval, Hong Kong, August 13-14, 1998.
• Adjeroh, D. A. and Lee, M.C., “Adaptive Transform Domain Video Scene Analysis”, Proceedings, IEEE International Conference on Multimedia Computing & Systems, Ontario Canada, June 3-6, 1997.
• Orji, C. U., Naphtali R., Adjeroh, D.A., and Nwosu, K. C., “Dynamic Reallocation of Multimedia Data Objects”, Proc., Pacific Workshop on Distributed Multimedia Systems, Hong Kong, pp. 163-170, 1996.

Book Chapters

• Bourlai T., Kalka N., Cao D., Decann B., Jafri Z., Nicolo F., Whitelam C., Zuo J., Adjeroh D., Cukic B., Dawson J., Hornak L., Ross A. and Schmid N.A., “Ascertaining human identity in night environments”, in Distributed Video Sensor Networks, Bhanu, B.; Ravishankar, C.V.; Roy-Chowdhury, A.K.; Aghajan, H.; Terzopoulos, D. (Eds.), Springer 2011.
• Adjeroh, D.A. and Lee, M.C., “Synchronization and User Interaction in Distributed Multimedia Presentation Systems”, in Nwosu, K.C, Thuraisingham, B. and Bera, P.B., (eds.) Multimedia Database\ Systems: Design and Implementation Strategies, Kluwa Academic Publishers, 1996.