• The similarity-aware relational intersect database operator 

      Al Marri, Wadha J.; Malluhi, Qutaibah; Ouzzani, Mourad; Tang, Mingjie; Aref, Walid G. ( Springer International Publishing , 2014 , Conference Paper)
      Identifying similarities in large datasets is an essential operation in many applications such as bioinformatics, pattern recognition, and data integration. To make the underlying database system similarity-aware, the core ...
    • Using the Sadakane compressed suffix tree to solve the all-pairs suffix-prefix problem 

      Rachid, Maan Haj; Malluhi, Qutaibah; Abouelhoda, Mohamed ( Hindawi , 2014 , Article)
      The all-pairs suffix-prefix matching problem is a basic problem in string processing. It has an application in the de novo genome assembly task, which is one of the major bioinformatics problems. Due to the large size of ...
    • A Practical and Scalable Tool to Find Overlaps between Sequences 

      Rachid, Maan Haj; Malluhi, Qutaibah ( Hindawi , 2015 , Article)
      The evolution of the next generation sequencing technology increases the demand for efficient solutions, in terms of space and time, for several bioinformatics problems. This paper presents a practical and easy-to-implement ...
    • Assessing the effects of data selection and representation on the development of reliable E. coli sigma 70 promoter region predictors 

      Abbas, Mostafa M.; Mohie-Eldin, Mostafa M.; El-Manzalawy, Yasser ( Public Library of Science , 2015 , Article)
      As the number of sequenced bacterial genomes increases, the need for rapid and reliable tools for the annotation of functional elements (e.g., transcriptional regulatory elements) becomes more desirable. Promoters are the ...
    • Similarity Group-by Operators for Multi-Dimensional Relational Data 

      Tang, Mingjie; Tahboub, Ruby Y.; Aref, Walid G.; Atallah, Mikhail J.; Malluhi, Qutaibah M.; ... more authors ( IEEE Computer Society , 2016 , Conference Paper)
      The SQL group-by operator plays an important role in summarizing and aggregating large datasets in a data analytics stack. While the standard group-by operator, which is based on equality, is useful in several applications, ...
    • A scalable solution for finding overlaps between sequences using map-reduce 

      Haj Rachid, Maan; Malluhi, Qutaibah M. ( The International Society for Computers and Their Applications (ISCA) , 2016 , Conference Paper)
      The overlap stage of a string graph-based assembler is considered one of the most time- and space-consuming stages in any de novo overlap-based assembler. This is due to the huge output of the next-generation sequencing ...
    • Skyline Discovery and Composition of Multi-Cloud Mashup Services 

      Zhang, Fan; Hwang, Kai; Khan, Samee U.; Malluhi, Qutaibah M. ( Institute of Electrical and Electronics Engineers , 2016 , Article)
      A cloud mashup is composed of multiple services with shared datasets and integrated functionalities. For example, the elastic compute cloud (EC2) provided by Amazon Web Service (AWS), the authentication and authorization ...
    • Privacy preserving computation in cloud using noise-free fully homomorphic encryption (FHE) schemes 

      Wang, Yongge; Malluhi, Qutaibah M. ( Springer Verlag , 2016 , Conference Paper)
      With the wide adoption of cloud computing paradigm, it is important to develop appropriate techniques to protect client data privacy in the cloud. Encryption is one of the major techniques that could be used to achieve ...
    • FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues 

      EL-Manzalawy, Yasser; Abbas, Mostafa; Malluhi, Qutaibah; Honavar, Vasant ( Public Library of Science (PLoS) , 2016 , Article)
      A wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses are mediated by RNA-protein interactions. However, experimental determination ...
    • Using Sparse Matrices to Prevent Information Leakage in Cloud Computing 

      Khan K.; Shaheen M.; Wang Y. ( Institute of Electrical and Electronics Engineers Inc. , 2018 , Conference Paper)
      Cloud computing represents the promise of outsourcing of scientific computing such as matrix multiplication. However, this can introduce new vulnerabilities such as information leakage. Cloud server intentionally or ...