Refereed Conference Proceedings Published

Agrawal, A., Perl, Y., Elhanan, G. (2013). Identifying Problematic Concepts in SNOMED CT using a Lexical Approach (vol. 192, pp. 773-777). Stud Health Technol Inform.: MEDINFO 2013.

Aksoy, C., Dimitriou, A., Theodoratos, D., Wu, X. (2013). In Weiyi Meng, Ling Feng, Stéphane Bressan, Werner Winiwarter, Wei Song (Eds.) (Ed.), XReason: A Semantic Approach that Reasons with Patterns to Answer XML Keyword Queries. (pp. 16 pages (299-314)). 18th International Conference on Database Systems for Advanced Applications (DASFAA), Proceedings Publisher: Springer.

Banerji, S., Sinha, A., Liu, C. (2012). Novel Color HWML Descriptors for Scene and Object Image Classification. Istanbul: the 3rd International Conference on Image Processing Theory, Tools & Applications.

Banerji, S., Sinha, A., Liu, C. (2012). Scene Image Classification: Some Novel Descriptors. Seoul: IEEE International Conference on Systems, Man, and Cybernetics.

Banerji, S., Sinha, A., Liu, C. (2013). A New Bag of Words LBP (BoWL) Descriptor for Scene Image Classification. York: 15th international conference on Computer Analysis of Images and Patterns.

Banerji, S., Sinha, A., Liu, C. (2013). HaarHOG: Improving the HOG Descriptor for Image Classification. Manchester: IEEE International Conference on Systems, Man, and Cybernetics.

Byron, K., Wang, J. T. L., Wen, D. (2012). Genome-wide Search for Coaxial Helical Stacking Motifs, Proceedings of the 12th IEEE International Conference on Bioinformatics and Bioengineering, Larnaca, Cyprus, November 2012, pp. 260-265.

Chen, B., Curtmola, R. (2012). POSTER: Robust Dynamic Remote Data Checking for Public Clouds (pp. 1043-1045). Proc. of the 19th ACM Conference on Computer and Communications Security (CCS ’12).

Chen, B., Curtmola, R. (2013). Towards Self-Repairing Replication-Based Storage Systems Using Untrusted Clouds (pp. 377-388). Proc. of the Third ACM Conference on Data and Application Security and Privacy. dl.acm.org/citation.cfm?doid=2435349.2435402

Daudelin, D., Geller, J., Perl, Y. (2012). Using Gamification and Crowdsourcing to Enhance Terminology Auditing (pp. 1714-1714). Chicago, IL: Proceedings of the American Medical Informatics Association (AMIA) Annual Meeting.

De, C., Shih, F. Y. (2012). Enhance hybrid texture synthesis. Las Vegas, Nevada: Proc. the 16th International Conference on Image Processing, Computer Vision, & Pattern Recognition.

Ding, X., Gibbons, P. B., Kozuch, M. A. (2013). A Hidden Cost of Virtualization when Scaling Multicore Applications (vol. 2013). USENIX. www.usenix.org/conference/hotcloud13/tech-schedule/workshop-program

Geller, J., Ochs, C., Perl, Y., Xu, J. (2012). New Abstraction Networks and a New Visualization Tool in Support of Auditing the SNOMED CT Content (pp. 237-246). Chicago, IL: Proceedings of the American Medical Informatics Association (AMIA) Annual Meeting.

He, Z., Halper, M. H., Perl, Y., Elhanan, G. (2012). Clinical clarity versus terminological order -- the readiness of SNOMED CT concept descriptors for primary care (pp. 1-6). Proceedings of the 2nd International Workshop on Managing Interoperability and Complexity in Health Systems (MIXHS'12).

He, Z., Ochs, C., Soldatova, L., Perl, Y., Arabandi, S., Geller, J. (2013). Auditing Redundant Import in Reuse of a Top Level Ontology for the Drug Discovery Investigations Ontology (pp. 46-49). Montreal, Quebec: Workshop on Vaccine and Drug Ontology Studies (VDOS 2013) collocated with Semantic Trilogy 2013.

Houle, M. E., Ma, X., Nett, M., Oria, V. (2012). Dimensional Testing for Multi-Step Similarity Search (pp. 299-308). Brussels, Belgium: IEEE International Conference on Data Mining. http://icdm2012.ua.ac.be/

Ji, X., Chun, S. A., Geller, J. (2013). In Robert De Virgilio, Fausto Giunchiglia, Letizia Tanca (Ed.), Social Infobuttons: Integrating Open Health Data with Social Data using Semantic Technology. New York, NY: Proceedings of the Fifth Workshop on Semantic Web Information Management (SWIM).

Li, X., Ng, S.-K., Wang, J. T. (2012). Proceedings of the 3rd Workshop on Biological Data Mining and its Applications in Healthcare. IEEE.

Liu, M. (2012). A Study of Transportability of an Existing Smoking Status Detection Module across Institutions (vol. 2012, pp. 577-586). American Medical Informatics Association Annual Symposium.

Mili, A., Abercrombie, R., Sheldon, F. (2013). Risk Assessment Methodology Based on the NISTIR 7628 Guideline (46th ed., pp. 8 pages). Washington DC: ACM/IEEE. www.hicss.hawaii.edu/

Mili, A., Jilani, L. L., Derbel, I. (2013). In Jose Cordeiro and David Marca and Marten van Sinderen (Ed.), ACME+ for Software Architecture Analysis (pp. 429-437). Reykjavik, Iceland: SciTePress. www.informatik.uni-trier.de/~ley/db/conf/icsoft/icsoft2013.html#DerbelJM13

Mili, A., Jilani, L. L., Derbel, I. (2013). In Leszek Maciaszek and Joaquim Felipe (Ed.), Architecture Level Prediction of Software Quality Attributes (pp. 15-24). Angers: SciTePress. www.informatik.uni-trier.de/~ley/db/conf/enase/enase2013.html#DerbelJM13

Mili, A., Rosner, N., Lopez Bombo, C. G., Aguirre, N., Jaoua, A., Frias, M. (2013). In Natarajan Shankar (Ed.), Parallel Bounded Verification of Alloy Models by Transcoping (pp. 15). Palo Alto, CA: SRI International. sites.google.com/site/vstte2013/home/program

Nakayama, M. K. (2012). Confidence Intervals for Quantiles When Applying Replicated Latin Hypercube Sampling and Sectioning (vol. 2012, pp. 8). Vista, CA: Autumn Simulation Conference, The Society for Modeling & Simulation International. scs.org/autumnsim#.UGnAE5jA8oM

Nakayama, M. K. (2012). In C. Laroque, J. Himmelspach, R. Pasupathy, O. Rose, and A. M. Uhrmacher (Ed.), Using Sectioning to Construct Confidence Intervals for Quantiles When Applying Importance Sampling (2012th ed., vol. 2012, pp. 12). Hanover, MD: Winter Simulation Conference. wintersim.org

Nakayama, M. K., 2012 Autumn Simulation Conference, "Confidence Intervals for Quantiles When Applying Replicated Latin Hypercube Sampling and Sectioning," The Society for Modeling & Simulation International, San Diego, CA. (October 28, 2012).

Ochs, C., Agrawal, A., Perl, Y., Halper, M. H., Tu, S., Carini, S., Sim, I., Noy, N., Musen, M., Geller, J. (2012). Deriving an Abstraction Network to Support Quality Assurance in OCRe (pp. 681-689). Chicago, IL: Proceedings of the American Medical Informatics Association (AMIA) Annual Meeting.

Ochs, C., He, Z., Perl, Y., Arabandi, S., Halper, M. H., Geller, J. (2013). Choosing the Granularity of Abstraction Networks for Orientation and Quality Assurance of the Sleep Domain Ontology (pp. 84-89). Montreal, Quebec: 4th International Conference on Biomedical Ontology ICBO 2013.

Ochs, C., Perl, Y., Geller, J. (2013). BLUSNO: A System for Orientation, Visualization, and Quality Assurance of SNOMED CT Using Abstraction Networks (pp. 127-128). Montreal, Quebec: 4th International Conference on Biomedical Ontology ICBO 2013.

Sinha, A., Banerji, S., Liu, C. (2012). Gabor-Based Novel Local, Shape and Color Features for Image Classification. Doha: the 19th International Conference on Neural Information Processing.

Sinha, A., Banerji, S., Liu, C. (2012). Novel Color Gabor-LBP-PHOG (GLP) Descriptors for Object and Scene Image Classification. Mumbai: The Eighth Indian Conference on Vision, Graphics and Image Processing.

Sinha, A., Banerji, S., Liu, C. (2012). Novel Color, Shape and Texture-based Scene Image Descriptors. Cluj-Napoca: IEEE International Conference on Intelligent Computer Communication and Processing.

Sinha, A., Banerji, S., Liu, C. (2012). Novel Gabor-PHOG Features for Object and Scene Image Classification. Hiroshima: Structural, Syntactic, and Statistical Pattern Recognition, Lecture Notes in Computer Science.

Talasila, M., Curtmola, R., Borcea, C. M. (2013). Improving Location Reliability in Crowd Sensed Data with Minimal Efforts (pp. 1-8). Proc. of the Sixth Joint IFIP/IEEE Wireless and Mobile Networking Conference. www.wmnc2013.org/

Tian, J., Zhang, W., Wang, G. (2012). Duty-cycle Scheduling for Intruder Detection in Wireless Sensor Networks. The 24th IASTED International Conference on Parallel and Distributed Computing and Systems (PDCS).

Yi Yu, Roger Zimmermann, Ye Wang, Vincent Oria: Recognition and Summarization of Chord Progressions and Their Application to Music Information Retrieval. In proceedings of IEEE International Symposium on Multimedia, ISM 2012: 9-16.

Zhong, L., Wang, J. T. L., Wen, D., Shapiro, B. A. (2012). Pre-miRNA Classification via Combinatorial Feature Mining and Boosting, Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, Philadelphia, Pennsylvania, October 2012, pp. 369-372.

Refereed Journal Articles Published

Aziz, A., Haque, M. E., Borcea, C. M., Hassan, Y. K., Yamada, S. (2013). Managing Disconnected Mobile Nodes in a Delay Tolerant Network with HALF Routing Protocol. IEICE Transactions on Communications, E96-B(7), 15. search.ieice.org/bin/summary.php?id=e96-b_7_1691&category=B&year=2013&lang=E&abst=

Agrawal, A., He, Z., Perl, Y., Wei, D., Halper, M. H., Elhanan, G., Chen, Y. (2013). The readiness of SNOMED problem list concepts for meaningful use of electronic health records. Artificial Intelligence in Medicine, 58(2), 73-80.

Aird, K. M., Zhang, G., Li, H., Tu, Z., Bilter, B. G., Garipov, A., Wu, H., Wei, Z., Wagner, S. N., Herlyn, M., Zhang, R. (2013). Suppression of Nucleotide Metabolism Underlies the Establishment and Maintenance of Oncogene-Induced Senescence. Cell reports, 3(4), 1252–1265.

Banerji, S., Sinha, A., Liu, C. (2013). New Image Descriptors based on Color, Texture, Shape, and Wavelets for Object and Scene Image Classification. Neurocomputing, 117, 173-185.

Bao, M., Cervantes-Cervantes, M., Zhong, L., Wang, J. T. (2012). Searching for Non-coding RNAs in Genomic Sequences Using ncRNAscout. Genomics, Proteomics & Bioinformatics, 10, 114-121.

Bitler, B. G., Fink, F. S., Wei, Z., Peterson, J. R., Zhang, R. (2013). A High-Content Screening Assay for Small-Molecule Modulators of Oncogene-Induced Senescence. Journal of biomolecular screening, 18(9), 1054-61.

Briskorn, D., Leung, J. Y. (2013). Minimizing Maximum Lateness of Jobs in Inventory Constrai Scheduling. Journal of the Operational Research Society, 1-14.

Byron, K., Laing, C., Wen, D., Wang, J. T. (2013). A Computational Approach to Finding RNA Tertiary Motifs in Genomic Sequences: A Case Study. Recent Patents on DNA & Gene Sequences, 7, 115-122.

Calvin, J. M. (2012). An adaptive univariate global optimization algorithm and its convergence rate under the Wiener measure. Informatica, 22(4), 489-505.

Cardinale, C. J., Wei, Z., Panossian, S., Wang, F., Kim, C. E., Mentch, F. D., Chiavacci, R. M., Kachelries, K. E., Pandey, R., Grant, S. F., Baldassano, R. N., Hakonarson, H. (2013). Targeted resequencing identifies defective variants of decoy receptor 3 in pediatric-onset inflammatory bowel disease. Genes and immunity, 14, 447–452.

Cardone, G., Foschini, L., Borcea, C. M., Bellavista, P., Corradi, A., Talasila, M., Curtmola, R. (2013). Fostering ParticipAction in Smart Cities: a Geo-Social CrowdSensing Platform. IEEE Communications Magazine, 51(6), 8. www.comsoc.org/commag

Cheng, K., McHugh, J., Deek, F. P. (2013). On the Use of Paired Comparisons to Construct Group Preference Scales for Decision Making. Journal of Group Decision and Negotiation, 22(3), 519-540.

Dong, J., Curtmola, R., Nita-Rotaru, C., Yau, D. (2012). Pollution Attacks and Defenses in Wireless Inter-flow Network Coding Systems. Transactions on Dependable and Secure Computing / IEEE Computer Society, 9(5), 15 pages. www.computer.org/portal/web/tdsc

Duan, L., Liu, M. (2013). Adverse Drug Effect Detection. IEEE Journal of Biomedical and Health Informatics, 17(2), 305-311.

Geller, J., He, Z., Perl, Y., Morrey, P., Xu, J. (2013). Rule-based support system for multiple UMLS semantic type assignments. Journal of Biomedical Informatics, 46(1), 97-110.

Gerbessiotis, A. (2012). An improved reliability bound of a probabilistic parallel integer sorting algorithm. Elsevier, 112(34), 976-979. http://www.sciencedirect.com/science/article/pii/S0020019012002608

Gu, H., Elhanan, G., Perl, Y., Hripcsak, G., Cimino, J. J., Xu, J., Chen, Y., Geller, J., Morrey, P. (2012). A study of terminology auditors' performance for UMLS semantic type assignments. Journal of Biomedical Informatics, 45(6), 1042-1048.

Gu, J., Liu, C. (2013). Feature Local Binary Patterns with Application to Eye Detection. Neurocomputing, 113, 138-152.

Hu, H., Nau, M., Ehrenberg, P., Chenine, A., Daye, Z., Wei, Z., Michael, N., Vahey, M., Kim, J., Marovich, M., Ratto-Kim, S. (2012). Distinct gene expression profiles associated with the susceptibility of pathogen-specific CD4+ T cells to HIV-1 infection. Retrovirology, 9(s2), O46.

Hu, H., Nau, M., Ehrenberg, P., Chenine, A., Macedo, C., Zhou, Y., Daye, Z., Wei, Z., Vahey, M., Michael, N., Kim, J., Marovich, M., Ratto-Kim, S. (2013). Distinct gene-expression profiles associated with the susceptibility of pathogen-specific CD4 T cells to HIV-1 infection. Blood, 121(7), 1136-1144.

Hua, L., Wang, J. T., Ji, X., Malhotra, A., Khaladkar, M., Shapiro, B. A., Zhang, K. (2012). A Method for Discovering Common Patterns from Two RNA Secondary Structures and Its Application to Structural Repeat Detection. Journal of Bioinformatics and Computational Biology, 10, 1-15.

Jiang, S., Ding, X., Yu, Y., Davis, K. (2013). A Prefetching Scheme Exploiting both Data Layout and Access History on the Disk. ACM Transactions on Storage (TOS), 9(3), 10:1--10:23. dl.acm.org/citation.cfm?id=2508010

Jilani, L. L., Mraihi, O., Louhichi, A., Ghardallou, W., Bsaïes, K., Mili, A. (2013). Invariant functions and invariant relations: An alternative to invariant assertions. J. Symb. Comput. 48: 1-36.

Jostins, J., Ripke, S. K., Duerr, R. H., McGovern, D. P., Hui, K. Y., Lee, J. C., Schumm, P., Sharma, Y., Anderson, C. A., Essers, J., Mitrovic, M., Ning, K., Cleynen, I., Theatre, E., Spain, S. L., Raychaudhuri, S., Goyette, P., Wei, Z. (2012). Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature, 491(7422), 119-124.

Kurose, H., Yamada, S., Borcea, C. M. (2013). TCR: Tag Caching Router Architecture with Folksonomies for CGM Contents. IEICE Transactions on Communications, J96-B(2), 12. search.ieice.org/bin/summary.php?id=j96-b_2_71&category=B&year=2013&lang=E&abst=j

Laing, C., Wen, D., Wang, J. T., Schlick, T. (2012). Predicting Coaxial Helical Stacking in RNA Junctions. Nucleic Acids Research, 40, 487-498.

Lee, K., Leung, J. Y., Pinedo, M. (2013). Makespan Minimization in Online Scheduling with Machine Eligibility. Annals of Operations Research, 204, 189-222.

Leung, J. Y., Chen, Z.-L. (2013). Integrated Production and Distribution with Fixed Delivery Departure Dates. Operations Research Letters, 41, 290-283.

Li, J., Glessner, J. T., Zhang, H., Hou, C., Wei, Z., Bradfield, J. P., Mentch, F. D., Guo, Y., Kim, C., Xia, Q., Chiavacci, R. M., Thomas, K. A., Qiu, H., Grant, S. F., Furth, S. L., Hakonarson, H., Sleiman, P. M. (2013). GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children. Human molecular genetics, 22(7), 1457-1464.

Li, X. H., Zhao, Y. Q., Liao, M., Shih, F. Y., Shi, Y.-Q. (2012). Detection of tampered region for JPEG images by using mode based first digit features. EURASIP Journal on Advances in Signal Processing, 190, 22. asp.eurasipjournals.com/content/2012/1/190

Li, X. H., Zhao, Y. Q., Liao, M., Shih, F. Y., Shi, Y.-Q. (2012). Passive detection of copy-paste forgery between JPEG images. Journal of Central South University of Technology, 19, 13.

Liu, C. (2013). Effective Use of Color Information for Large Scale Face Verification. Neurocomputing, 101, 43-51.

Liu, M. (2012). Extracting Epidemiologic Exposure and Outcome Terms from Literature using Machine Learning Approaches. International Journal of Data Mining and Bioinformatics, 6(4), 447-459.

Liu, M. (2012). Software Project Risk Analysis using Bayesian Networks with Causality Constraints. Decision Support Systems.

Liu, M. (2013). Comparative Analysis of Pharmacovigilance Methods in Detection of Adverse Drug Reactions from Electronic Medical Records. Journal of the American Medical Informatics Association, 20(3), 420-426.

Lynch, G., Shih, F. Y., Liao, H.-Y. (2013). An efficient expanding block algorithm for image copy-move forgery detection. Information Sciences, 239(8), 253-265.

Mili, A. (2012). Invariant Relations, Invariant Functions and Loop Functions. Springer, 8(3), 195-212. http://link.springer.com/journal/11334

Mili, A., Aissa, A. B., Abercrombie, R., Sheldon, F. (2012). Defining and Computing a Value Based Cybersecurity Measure. Springer, 10(4), 443-453. www.springer.com/business+%26+management/business+information+systems/journal/10257

O'Rawe, J., Jiang, T., Sun, G., Wu, Y., Wang, W., Bodily, P., Tian, L., Hakonarson, H., Johnson, W. E., Wei, Z., Wang, K., Lyon, G. (2013). Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Medicine, 5(3), Article 28.

Pellegrino, R., Sunaga, D. Y., Guindalini, C., Martins, R. C. S., Mazzotti, D. R., Wei, Z., Daye, Z. John, Andersen, M. L., Tufik, S. (2012). Whole-blood genome-wide gene expression profile in males after prolonged wakefulness and sleep recovery. Physiological Genomics, 44(21), 1003-1012.

Spirollari, J., Wang, S. X., Wang, J. T. (2012). Using Folding Ensemble and Stem Probability Maximization Methods to Predict RNA H-Type Pseudoknots. Tsinghua Science and Technology, 17, 691-700.

Wang, W., Hu, W., Hou, F., Hu, P., Wei, Z. (2012). SNVerGUI: a desktop tool for variant analysis of next-generation sequencing data. Journal of Medical Genetics, 49(12), 753-755.

Wei, Z., Wang, W., Bradfield, J. P., Li, J., Cardinale, C., Frackelton, E., Kim, C., Mentch, F. D., Van Steen, K., Visscher, P. M., Baldassano, R. N., Hakonarson, H. (2013). Large Sample Size, Wide Variant Spectrum, and Advanced Machine-Learning Technique Boost Risk Prediction for Inflammatory Bowel Disease. The American Journal of Human Genetics, 92(6), 1008–1012.

Wu, X., Souldatos, S., Theodoratos, D., Dalamagas, T., Vassiliou, Y., Sellis, T. (2012). Processing and Evaluating Partial Tree Pattern Queries on XML data. IEEE Transactions on Data and Knowledge Engineering, IEEE Computer Society Publications, 24(12), 16 pages (2244-2259). http://www.computer.org/portal/web/tkde/home

Wu, X., Theodoratos, D. (2013). A Survey on XML Streaming Evaluation Techniques. Very Large Databases Journal (VLDBJ), Publisher: Springer, 26 pages (177 - 202). http://www.vldb.org/vldb_journal/

Younis, I., Dittmar, K., Wang, W., Foley, S. W., Berg, M. G., Hu, K. Y., Wei, Z., Wan, L., Dreyfuss, G. (2013). Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA. eLife, 2, e00780.

Zhang, X., Shasha, D., Song, Y., Wang, J. T. (2012). Fast Elastic Peak Detection for Mass Spectrometry Data Mining. IEEE Transactions on Knowledge and Data Engineering, 24, 634-648.

Zhao, Y. Q., Liao, M., Shih, F. Y., Shi, Y.-Q. (2012). Tampered region detection of inpainting JPEG images. Optik- International Journal for Light and Electron Optics, 6.

Zhong, L., Wang, J. T., Wen, D., Aris, V., Soteropoulos, P., Shapiro, B. A. (2013). Effective Classification of MicroRNA Precursors Using Feature Mining and AdaBoost Algorithms. OMICS: A Journal of Integrative Biology, 17, 486-493.

Refereed Book Chapters Published

Gu, J., Liu, C. (2012). In K. Saeed and T. Nagashima (Ed.), Local Texture Descriptors for Biometric Detection: New Local Quaternary Pattern Descriptors and Case Study on Eye Detection (pp. 129-151). Springer: Biometrics and Kansei Engineering.

Wei, Z., Minturn, J., Rappaport, E., Brodeur, G., Li, H. (2013). Network-Based Analysis of Multivariate Gene Expression Data (pp. 121-139). Statistical Methods for Microarray Data Analysis/Springer.

Wei, Z., Baldassano, S., Hakonarson, H. (2012). In Petar Mamula, Jonathan E. Markowitz, Robert N. Baldassano (Ed.), Genetics of Inflammatory Bowel Diseases (pp. 3-12). Pediatric Inflammatory Bowel Disease/Springer.

Preface Published

Li, X., Ng, S.-K., Wang, J. T. (2012). Preface to the IEEE ICDM 3rd Workshop on Biological Data Mining and its Applications in Healthcare (pp. i-iii). IEEE.