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Publications:
Underlined authors are students.

Book Chapters:
  1. Saeed Salem. Mining frequent subgraph patterns for classifying biological data.
    In Xiao-Li Li, See Kiong Ng, and Jason T. L. Wang, editors, Biological Data Mining and its Applications in Healthcare, pages 147-167. World Scientific, 2014.
Journals:
  1. Abubakr O Al-Abbasi, Lutfi Samara, Saeed Salem, Ridha Hamila, Naofal Al-Dhahir.
    A Unified Framework for Differentiated Services in Intelligent Healthcare Systems.
    IEEE Transactions on Network Science and Engineering, 2021.
  2. Saeed Salem, Mohammed Alokshiya, Mohammad Al Hasan.
    RASMA: A Reverse Search Algorithm for Mining Frequent Subgraphs.
    BMC BioData Mining, 14(1), pp. 1-23, 2021.
  3. Sarim Zafar, Muhammad Usman Sarwar, Saeed Salem, Muhammad Zubair Malik.
    Language and Obfuscation Oblivious Source Code Authorship Attribution.
    IEEE Access 8, 197581-197596, 2020.
  4. Mohammed Alokshiya, Saeed Salem, Fidaa Abed.
    A Linear Delay Algorithm for Enumerating All Connected Induced Subgraphs.
    BMC Bioinformatics, 20(12), 319, 2019.
  5. Jeff Anderson, Maral Azizi , Saeed Salem, Hyunsook Do.
    On the Use of Usage Patterns from Telemetry Data for Test Case Prioritization.
    Information and Software Technology, 113, pp. 110-130, 2019.
  6. Saeed Salem. Template edge similarity graph clustering for mining multiple gene expression datasets.
    International Journal of Data Mining and Bioinformatics, 18(1), pp. 28-39, 2017.
  7. Aditya Goparaju, Tyler Brazier, Saeed Salem.
    Mining representative maximal dense cohesive subnetworks.
    Network Modeling Analysis in Health Informatics and Bioinformatics, 4(1), pp. 1-11, 2015.
  8. George D Yocum, Joseph P Rinehart, David P Horvath, William P Kemp, Jordi Bosch, Rami Alroobi, Saeed Salem.
    Key molecular processes of the diapause to post-diapause quiescence transitionin the alfalfa leafcutting bee megachile rotundata identified by comparative transcriptome analysis.
    Physiological Entomology, 40(2), pp. 103-112, 2015.
  9. Xiuzhen Huang, et. al.
    Big data-a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm.
    BioData Mining, 8(1):7, 2015.
  10. Saeed Salem, Cagri Ozcaglar.
    Hybrid coexpression link similarity graph clustering for mining biological modules from multiple gene expression datasets.
    BioData Mining, 7(1):16, 2014.
  11. Yang Mei, Minfei Su, Gaurav Soni, Saeed Salem, Christopher L. Colbert, Sangita C. Sinha.
    Intrinsically disordered regions in autophagy proteins.
    Proteins: Structure, Function, and Bioinformatics, 82(4), pp. 565-578, 2014.
  12. Rami Alroobi, Syed Ahmed, Saeed Salem.
    Mining maximal cohesive induced subnetworks and patterns by integrating i biological networks with multiple data sources.
    Interdisciplinary Sciences: Computational Life Sciences, 5(3), pp. 211-224, 2013.
  13. Saeed Salem, Rami Alroobi, Shadi Banitaan, Loqmane Seridi, Ibrahim Aljarah, James Brewer.
    Improving functional modules discovery by enriching interaction networks with gene profiles.
    Current Bioinformatics, 8(3), pp. 328-338, 2013.
  14. Xiuzhen Huang, et. al.
    No-boundary thinking in bioinformatics research.
    BioData Mining, 6(1):19, 2013.
  15. Vibin Ramakrishnan, Sai Praveen Srinivasan, Saeed Salem, Suzanne Matthews, Wilfredo Colon, Mohammed J. Zaki, Chris Bystroff.
    GeoFold: Topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability.
    Proteins: Structure, Function, and Bioinformatics, 80(3), pp. 920-934, 2012.
  16. Mohammad Al Hasan, Saeed Salem, Mohammed J. Zaki.
    SimClus: an effective algorithm for clustering with a lower bound on similarity.
    Knowledge and Information Systems Jouranl, 28(3), pp. 665-685, 2011.
  17. Saeed Salem, Mohammed J. Zaki, Chris Bystroff.
    FlexSnap: Flexible Non-sequential Protein Structural Alignment.
    Algorithms for Molecular Biology Journal, 5(12), 2010.
  18. Amir H. Qureshi, Vineet Chaoji, Dony Maiguel, Hafeez Faridi, Constantinos Barth, Erliang Zheng, Saeed M. Salem, Mudita Singhal, David Sarracino, Bryan Krastins, Mitsunori Ogihara, Mohammed J. Zaki, Vineet Gupta.
    Proteomic and Phospho-proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling.
    PLoS ONE , 4(10), 2009.
  19. Saeed Salem, Mohammed J. Zaki, Chris Bystroff.
    SNAP: Iterative Non-Sequential Protein Structural Alignment.
    Journal of Bioinformatics and Computational Biology, 7(3), pp. 571-596, 2009.
  20. Mohammad Al Hasan, Vineet Chaoji, Saeed Salem, Mohammed J. Zaki.
    Robust Partitional Clustering by Outlier and Density Insensitive Seeding.
    Pattern Recognition Letter, 30(11), pp. 994-1002, 2009.
  21. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem, Mohammed J. Zaki.
    SPARCL: Efficient and Effective ShaPe-baseD Clustering.
    Knowledge and Information Systems Jouranl, 21(2), pp. 201-229, 2009.
  22. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem, Jeremy Besson, Mohammed J. Zaki.
    ORIGAMI: A Novel and Efficient Approach for Mining Representative Orthogonal Graph Patterns.
    Journal of Statistical Analysis and Data Mining, 1(2), pp. 67-84, 2008.
  23. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem, Mohammed J. Zaki.
    An Integrated, Generic Approach to Pattern Mining: Data Mining Template Library.
    Journal of Data Mining and Knowledge Discovery, 17(3), pp. 457-495, 2008.
Conferences and Workshops:
  1. Alex Davila Frias, Saeed Salem , Om Yadav.
    Deep Neural Networks (DNNs) for all-terminal network reliability estimation.
    In Proceedings of the 2021 Annual Reliability and Maintainability Symposium. Orlando, FL, January 25-28, 2021.
    [SRE Stan Oftshun Award for the best student paper by an SRE member]
  2. Riyad Hakim, Saeed Salem .
    Efficiently mining rich subgraphs from vertex-attributed graphs.
    In Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB 2020), Virtual Event, USA, September 21-24, 2020.
  3. San Ha Seo, Saeed Salem .
    Mining representative approximate frequent coexpression subnetworks.
    In Proceedings of the second International Workshop on High Performance Computing, Big Data Analytics and Integration for Multi-Omics Biomedical Data (HPC-BOD 2020) (co-located with ACM BCB), Virtual Event, September 21-24, 2020.
  4. San Ha Seo, Saeed Salem .
    Post-Processing Summarization for Mining Frequent Dense Subnetworks.
    In Proceedings of the second workshop on Machine Learning Models for Multi-omics Data Integration (MODI 2020) (co-located with ACM BCB), Virtual Event, September 21-24, 2020.
  5. San Ha Seo, Saeed Salem .
    Mining approximate frequent dense modules from multiple gene expression datasets.
    In Proceedings of the 12th International Conference on Bioinformatics and Computational Biology (BICOB 2020), EPiC Series in Computing, 70, Virtual Event, March 2020.
  6. Mohammed Alokshiya, Saeed Salem , Fidaa Abed.
    A Linear Delay Linear Space Algorithm for Enumeration of All Connected Induced Subgraphs.
    In Proceedings of the fifth International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2018) (co-located with ACM BCB), Abstract, August 2018.
  7. Bassam Qormosh, Eihab El Radie, Saeed Salem.
    Classifying Gene Coexpression Networks Using State Subnetworks.
    In Proceedings of the 10th International Workshop on Biological Network Analysis and Integrative Graph-Based Approaches (IWBNA) (co-located with IEEE BIBM), pages 1731-1735, November 2017.
  8. Eihab El Radie, Saeed Salem.
    Mining Quasi Frequent Coexpression Subnetworks.
    In Proceedings of the 10th International Workshop on Biological Network Analysis and Integrative Graph-Based Approaches (IWBNA) (co-located with IEEE BIBM), pages 1736-1740, November 2017.
  9. Eihab El Radie, Saeed Salem.
    Parallel Algorithm for Mining Maximal Frequent Subgraphs.
    In Proceedings of the 8th International Workshop on High Performance Bioinformatics and Biomedicine (HiBB) (co-located with IEEE BIBM), pages 1965-1971, November 2017.
  10. Aditya Goparaju, Saeed Salem.
    A Parallel Algorithm for Mining Maximal Cohesive Subgraphs.
    In Proceedings of the 9th International Conference on Bioinformatics and Computational Biology (BICOB), March 2017.
  11. Jeff Anderson, Hyunsook Do, Saeed Salem.
    Customized Regression Testing Using Telemetry Usage Patterns.
    In Proceedings of the 32nd IEEE International Conference on Software Maintenance and Evolution (ICSME), pages 572-581, October 2016.
  12. Aditya Goparaju, Saeed Salem.
    A Multithreaded Algorithm for Mining Maximal Cohesive Dense Modules from Interaction Networks with Gene Profiles.
    In Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB), pages 671-678, October 2016.
  13. Jeff Anderson, Hyunsook Do, Saeed Salem.
    Experience report: Mining test results for reasons other than functional correctness.
    In Proceedings of the 2015 IEEE 26th International Symposium on Software Reliability Engineering (ISSRE), pages 405-415, November 2015.
  14. Aditya Goparaju, Bassam Qormosh, Saeed Salem.
    Mining maximal subnetworks from interaction network with node attributes.
    In Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pages 1630-1635, November 2015.
  15. Jeff Anderson, Hyunsook Do, Saeed Salem.
    Striving for failure: An industrial case study about test failure prediction.
    In Proceedings of the 2015 IEEE/ACM 37th IEEE International Conference on Software Engineering(ICSE), volume 2 of ICSE 2015, pages 49-58, May 2015.
  16. Rami Alroobi, Saeed Salem.
    Discovering Dysregulated Phenotype-Related Gene Patterns.
    In Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), pages 524-532, Newport Beach, CA, USA, September 2014.
  17. Jeff Anderson, Saeed Salem, Hyunsook Do.
    Improving the Effectiveness of Test Suite Through Mining Historical Data.
    In Proceedings of the 11th Working Conference on Mining Software Repositories (MSR'14; co-located with ICSE2014), pages 142-151, India, May 2014.
  18. Saeed Salem, Cagri Ozcaglar.
    MFMS: Maximal frequent module set mining from multiple human gene expression data sets.
    In Proceedings of the 12th International Workshop on Data Mining in Bioinformatics, (BIOKDD'13; in conjunction with ACM KDD.13), pages 51-57, Chicago, IL, USA, August 2013.
  19. Saeed Salem, Rami Alroobi, Syed Ahmed, Mohammad Hossain.
    Discovering maximal cohesive subgraphs and patterns from attributed biological networks.
    In Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (IWBNA'12; in conjunction with IEEE-BIBM'12), pages 203-210, Philadelphia, PA, USA, October 2012.
  20. Saeed Salem, Shadi Banitaan, Ibrahim Aljarah, Rami Alroobi.
    Mining maximal-homogeneous subnetworks using protein interaction networks and gene profiles.
    In Proceedings of the ISCA 4th International Conference on Bioinformatics and Computational Biology (BICoB-2012), Las Vegas, Nevada, USA, March 2012.
  21. Saeed Salem, Shadi Banitaan, Ibrahim Aljarah, James E. Brewer, Rami Alroobi.
    Discovering Communities in Social Networks Using Topology and Attributes.
    In Proceedings of the 10th International Conference on Machine Learning and Applications and Workshops (ICMLA), Honolulu, Hawaii, December 2011.
  22. Charith D. Chitraranjan, Loai Alnemer, Omar Al-Azzam, Saeed Salem, Anne M. Denton, Muhammad J. Iqbal, Shahryar F. Kianian.
    Frequent Substring-Based Sequence Classification with an Ensemble of Support Vector Machines Trained Using Reduced Amino Acid Alphabets.
    In Proceedings of the 10th International Conference on Machine Learning and Applications and Workshops (ICMLA), Special Session on Machine Learning in Bioinformatics and Computational Biology. Honolulu, Hawaii, December 2011.
  23. Ibrahim Aljarah, Shadi Banitaan, Sameer Abufardeh, Wei Jin, Saeed Salem.
    Selecting discriminating terms for bug assignment: a formal analysis.
    In Proceedings of the 7th International Conference on Predictive Models in Software Engineering (PROMISE 2011). Banff, Alberta, Canada, September 2011.
  24. Saeed Salem, Rami Alroobi, Shadi Banitaan, Loqmane Seridi, James Brewer, Ibrahim Aljarah.
    CLARM: An Integrative Approach for Functional Modules Discovery.
    In Proceeding of the 3rd International Workshop on Bio-molecular Network Analysis (IWBNA) (in conjuction with ACM-BCB 2011). Chicago, USA, August 2011.
  25. Jianfei Wu, Loai Al Nemer, Omar Al Azzam, Charith Chitraranjan, Saeed Salem, Anne M. Denton.
    Sequential Data Clustering.
    In Proceedings of the Ninth International Conference on Machine Learning and Applications (ICMLA), Challenge Poster. Washington, DC, December 2010.
  26. Shadi Banitaan, Saeed Salem, Wei Jin, Ibrahim Aljarah.
    A formal study of classification techniques on Entity Discovery and their application to Opinion Mining.
    In Proceedings of the 2nd International Workshop on Search and Mining User-generated Contents (with ACM CIKM). Toronto, Canada, October 2010.
  27. Saeed Salem, Khedidja Seridi, Loqmane Seridi, Jianfei Wu, Mohammed J. Zaki.
    VOKNN: Voting-based Nearest Neighbor Approach for Scalable SVM Training.
    In Proceedings of the 2nd Workshop on Large-scale Data Mining: Theory and Applications (with ACM SIGKDD). Washington, DC, July 2010.
  28. Saeed Salem, Mohammed J. Zaki, Chris Bystroff.
    FlexSnap: Flexible Non-Sequential Protein Structural Alignment.
    In Proceedings of the 9th International Workshop on Algorithms in Bioinformatics (WABI). Philadelphia, PA, September 2009.
  29. Mohammad Al Hasan, Saeed Salem, Benjarath Pupacdi, Mohammed J. Zaki.
    Clustering with lower bound on Similarity.
    In Proceedings of the 13th Pacific-Asia Conference on Knowledge Discovery and Data Mining. Bangkok, Thailand, April 2009. (Best Paper Award)
  30. Saeed Salem, Mohammed J. Zaki.
    Iterative Non-Sequential Protein Structural Alignment.
    In Proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB). Stanford, CA, August 2008.
  31. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem, Mohammed J. Zaki.
    SPARCL: Efficient and Effective ShaPe-baseD Clustering.
    In Proceedings of the 8th IEEE International Conference on Data Mining. Pisa, Italy, December 2008.
  32. Mohammad Al Hasan, Vineet Chaoji, Saeed Salem, Jeremy Besson, Mohammed J. Zaki.
    ORIGAMI: Mining Representative Orthogonal Graph Patterns.
    In Proceedings of the 7th IEEE International Conference on Data Mining. Omaha, NE, USA, October 2007.
  33. Mohammad Al Hasan, Vineet Chaoji, Saeed Salem, Mohammed J. Zaki.
    Link Prediction using Supervised Learning.
    In Proceedings of the 4th Workshop of Link analysis, Counterterrorism and Security (with SIAM). Bethesda, MD, USA, April 2006.
  34. Mohammad Al Hasan, Vineet Chaoji, Saeed Salem, Nagender Parimi, Mohammed J. Zaki.
    DMTL: A Generic Data Mining Template Library.
    LCSD 2005, Workshop of OOPSLA. San Diego, CA, October 2005.
  35. Mohammed Javeed Zaki, Nilanjana De, Feng Gao, Nagender Parimi, Benjarath Phoophakdee, Joe Urban, Vineet Chaoji, Mohammad Al Hasan, Saeed Salem.
    Towards Generic Pattern Mining.
    In Proceedings of the First Conference on Pattern Recognition and Machine Intelligence, PReMI 2005, Kolkata, India, December 2005
  36. Mohammed J. Zaki, Nagender Parimi, Nilanjana De, Feng Gao, Benjarath Phoophakdee, Joe Urban, Vineet Chaoji, Mohammad Al Hasan, Saeed Salem.
    Towards Generic Pattern Mining.
    In Proceedings of the 3rd International Conference on Formal Concept Analysis, ICFCA 2005. Lens, France, February 2005.
Abstracts:
  1. Vibin Ramakrishnan, Saeed Salem, Sai Praveen Srinivasan, Suzanne Matthews, Mohammed J. Zaki, Wilfredo Colon, Chris Bystroff.
    GeoFold: A mechanistic model to study the effect of topology on protein unfolding pathways and kinetics.
    In Proceedings of 3Dsig: Structural Bioinformatics and Computational Biophysics Satellite Meeting, an ISMB satellite meeting, abstract. Toronto, Canada, 2008.
  2. Vibin Ramakrishnan, Saeed Salem, Mohammed J. Zaki, Chris Bystroff.
    Simulation of Protein folding Pathways and Folding kinetics Using Statistical Mechanical Model.
    In Proceedings of the 5th International Conference on Bioinformatics (InCoB), abstract. New Delhi, India, December 2006.