Saeed Salem's Publications

Publications:

Journals:

Vibin Ramakrishnan, Sai Praveen Srinivasan, Saeed Salem, Suzanne Matthews, Wilfredo Colon, Mohammed J. Zaki, and Chris Bystroff. GeoFold: Topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability. Proteins: Structure, Function, and Bioinformatics, xx(x), DOI: 10.1002/prot.23249, 2011. (to appear)
Mohammad Al Hasan,Saeed Salem, and 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.
Saeed Salem, Mohammed J. Zaki, and Chris Bystroff. FlexSnap: Flexible Non-sequential Protein Structural Alignment. Algorithms for Molecular Biology Journal, 5(12), 2010.
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, and Vineet Gupta. Proteomic and Phospho-proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling. PLoS ONE , 4(10), 2009.
Saeed Salem, Mohammed J. Zaki, and Chris Bystroff. SNAP: Iterative Non-Sequential Protein Structural Alignment. Journal of Bioinformatics and Computational Biology, 7(3), pp. 571-596, 2009.
Mohammad Al Hasan, Vineet Chaoji, Saeed Salem, and Mohammed J. Zaki. Robust Partitional Clustering by Outlier and Density Insensitive Seeding. Pattern Recognition Letter, 30(11), pp. 994-1002, 2009.
Vineet Chaoji, Mohammad Al Hasan, Saeed Salem, and Mohammed J. Zaki. SPARCL: Efficient and Effective ShaPe-baseD Clustering. Knowledge and Information Systems Jouranl, 21(2), pp. 201-229, 2009.
Vineet Chaoji, Mohammad Al Hasan, Saeed Salem, Jeremy Besson, and 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.
Vineet Chaoji, Mohammad Al Hasan, Saeed Salem, and 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:

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.
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.
Jianfei Wu, Loai Al Nimer, 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.
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.
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.
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.
Mohammad Al Hasan, Saeed Salem, Benjarath Pupacdi, and 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)
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.
Vineet Chaoji, Mohammad Al Hasan, Saeed Salem, and 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.
Mohammad Al Hasan, Vineet Chaoji, Saeed Salem, Jeremy Besson, and 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.
Mohammad Al Hasan, Vineet Chaoji, Saeed Salem, and 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.
Mohammad Al Hasan, Vineet Chaoji, Saeed Salem, Nagender Parimi, and Mohammed J. Zaki. DMTL: A Generic Data Mining Template Library. LCSD 2005, Workshop of OOPSLA. San Diego, CA, October 2005.
Mohammed J. Zaki, Nagender Parimi, Nilanjana De, Feng Gao, Benjarath Phoophakdee, Joe Urban, Vineet Chaoji, Mohammad Al Hasan, and Saeed Salem. Towards Generic Pattern Mining. In Proceedings of the Third International Conference on Formal Concept Analysis. Lens, France, February 2005.

Abstracts:

Vibin Ramakrishnan, Saeed Salem, Sai Praveen Srinivasan, Suzanne Matthews, Mohammed J. Zaki, Wilfredo Colon, and 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.
Vibin Ramakrishnan, Saeed Salem, Mohammed J. Zaki, and 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.

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