Designing Systems for Molecular Query-Retrieval and Molecular Informatics
- Division of Information and Intelligent Systems
- Award Number: 0644418
- Principal Investigator: R. Singh (SFSU)
The ability to manage and efficaciously reason with molecular structural information has enormous impact both for bio-chemical research as well as for the discovery of new and more efficacious therapeutics. The advent of technologies like NMR, Crystallography, and Combinatorial Chemistry, allow us today to generate unprecedented amounts of information at the molecular structural level. However, the capacity to generate molecular structural data far exceeds our ability to effectively manage, query, and assimilate it at the state-of-the-art. From a computer science perspective, molecules are complex, multidimensional entities which present critical challenges for effective and efficient design of representation, retrieval, modeling, and interaction techniques. In this context, this research focuses on three challenges: (1) Designing techniques for representation and similarity-based matching of molecules, (2) Development of indexing strategies for molecular query-retrieval, and (3) Designing knowledge environments for discovery of therapeutics. The specific research innovations include design of standard coordinate systems to represent highly complex molecular surfaces, developing efficient information matching and retrieval techniques for comparing molecules, and design of integrated information management of molecular structures and biological properties including the development of user-data interaction techniques and algorithms for context supportive access to meta-knowledge. Broader Impact: Techniques and systems developed as part of this research will be made publicly available and allow fundamental advancements in management, exploration, analysis, and reasoning with molecular information. This has the potential to introduce ground breaking advancements in areas like drug/therapeutics discovery and thus is critical to the society at large. Furthermore, this research will establish "Molecular Query-Retrieval and Molecular Informatics" as an integral part of computer science research in information management, retrieval, analysis, and assimilation. This will allow computer scientists to participate and advance a critical and new interdisciplinary area. Finally, the education and outreach component will (a) develop models to enhance research experience and productivity of students, (b) providing exposure to computer science at the grassroots-level through novel interactions with students and teachers at K-12 levels, and (c) broaden participation by mentoring women and minority students.
- Tammy Chan
- Preeti Malik
- Emmanuel Yera
- Robert Bierman (Undergraduate)
- Connie Phong (Open University Program)
- Tobias Sayre
- Joanna Lipinski-Kruszka
- Tim Lee
- Ido Heskia
- Ben Dalziel
- D. Asarnow and R. Singh, "The Impact of Parameters and Structural Diversity in Maps of the Protein Universe," BMC Bioinformatics, 2013, To Appear.
- A. Peterman, M. J. Bennett, A. Frankel, and R. Singh, “Clustering PPI Networks of Mixed Host-Pathogen Data Using Biased Repeated Random Walks”, International Symposium on Bioinformatics Research and Application (ISBRA), 2013, (To Appear).
- R. Singh and W. Murad, "Protein disulfide topology determination through the fusion of mass spectrometric analysis and sequence-based prediction using Dempster-Shafer theory," BMC Bioinformatics, 14 (Suppl 2):S20, 2013.
- D. Asarnow and R. Singh, "Segmenting the Etiological Agent of Schistosomiasis for High-Content Screening," IEEE Transactions on Medical Imaging, 2013, To Appear, (Corresponding author R. Singh).
- H. Lee*, A. Moody-Davis, U. Saha, B. Suzuki, D. Asarnow, S. Chen, M. Arkin, C. Caffrey, and R. Singh*, "Quantification and Clustering of Phenotypic Screening Data Using Time Series Analysis for Chemotherapy of Schistosomiasis", BMC Genomics, 12 (Suppl 1):S4, 2012 (*H. Lee and R. Singh equal contributors. Corresponding author R. Singh).
- C. Marcellino, J. Gut, K. C. Lim, R. Singh, J. McKerrow, J. Sakanari, "WormAssay: A Novel Computer Application for Whole-Plate Screening of Macroscopic Parasites", PLoS Neglected Tropical Diseases, Accepted. To appear in 2012.
- R. Singh, W. Murad, and T. Lee, "Algorithmic Frameworks for Protein Disulfide-Connectivity Determination", in Algorithmic and AI Methods for Protein Bioinformatics, Yi Pan, J. Wang, and M. Li eds., Wiley 2012 (To Appear).
- R. Singh, "Quantitative High-Content Screening-Based Drug Discovery against Helmintic Diseases", in Target Validation, Drug and Vaccine Development for Helminth Diseases, C. Caffrey and P. Selzer eds., Wiley 2012 (To Appear).
- W. Murad, R. Singh, and T-Y. Yen, "An Efficient Algorithmic Approach for Mass Spectrometry-Based Disulfide Connectivity Determination in Proteins Using Multi-Ion Analysis", BMC Bioinformatics, 2011 (Corresponding author: R. Singh) (To Appear).
- R. Singh, "Learning and Prediction of Complex Molecular Structure-Property Relationships: Issues and Strategies for Modeling Intestinal Absorption for Drug Discovery", in Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques, H. Lodhi and Y. Yamanishi eds., Idea House, 2010. Available online.
- J. Kim and R. Singh, "Residue Contexts: Non-Sequential Protein Structure Alignment Using Structural and Biochemical Features", International Symposium on Bioinformatics Research and Application (ISBRA), 2010, Lecture Notes in Bioinformatics, Springer, pp. 77-88.
- R. Singh, V. Popescu, L. Mennillo, B. Suzuki, and C. Caffrey, "Association Rule Discovery in Time-Series Phenomic Data", Bioimage Informatics, Carnegie-Mellon University, 2010 (peer-reviewed poster).
- W. Murad, R. Singh, and T-Y. Yen, "Polynomial Time Disulfide Bond Determination using Mass Spectrometry Data", IEEE Computational Structural Bioinformatics Workshop (CSBW), pp. 79-86, 2009.
- N. Postarnakevich and R. Singh, "Global-To-Local Representation and Visualization of Molecular Surfaces Using Deformable Models", ACM Symposium on Applied Computing (SAC), Bioinformatics Track, pp. 782-787, 2009.
- R. Singh, M. Pittas, I. Heskia, F. Xu, J. H. McKerrow, and C. Caffrey, "Automated Image-Based Phenotypic Screening for High-Throughput Drug Discovery", IEEE Symposium on Computer-Based Medical Systems (CBMS), pp. 1-8, 2009.
- R. Singh "A Review of Algorithmic Techniques for Disulfide-Bond Determination", Briefings in Functional Genomics and Proteomics, 2008, Vol. 7, pp. 157-172, 2008.
- R. Singh, M. Pittas, I. Heskia, F. Xu, J. H. McKerrow, and C. Caffrey, "Automated Image-Based Phenotypic Screening of Multi-Cellular Pathogens for High-Throughput Drug Discovery", Bioimage Informatics, Howard Hughes Medical Institute, Janelia Farm, 2009 (peer-reviewed poster).
- B. Dalziel, H. Yang, R. Singh, M. Gormley, and S. J. Fisher, "XMAS: An Experiential Approach for Visualization, Analysis, and Exploration of Time Series Microarray Data", International Conference on Bioinformatics Research and Development (BIRD), Communications in Computer and Information Science, Vol. 13, pp. 16-31, Springer Verlag, 2008.
- T. Lee and R. Singh,"Comparative Analysis of Disulfide Bond Determination Using Computational-Predictive Methods and Mass Spectrometry-Based Algorithmic Analysis", International Conference on Bioinformatics Research and Development (BIRD), Communications in Computer and Information Science, Vol. 13, pp. 140-153, Springer Verlag, 2008.
- T. Sayre and R. Singh, "Protein Structure Alignment and Comparison Using Residue Contexts", IEEE International Symposium on Bioinformatics and Life Science Modeling and Computing (BLSM), pp 796 – 801, 2008
- C. Phong and R. Singh, "Missing Value Estimation for Time Series Microarray Data Using Linear Dynamical Systems Modeling", IEEE International Symposium on Bioinformatics and Life Science Modeling and Computing (BLSM), pp. 814 – 819, 2008.
- R. Singh, "Surface Similarity-Based Molecular Query-Retrieval", BMC Cell-Biology, Vol. 8, Suppl.1 (S6): July, 2007.
- P. Malik, T. Chan, J. Vandergriff, J. Weisman, J. DeRisi, and R. Singh, "Information Management and Interaction in High-Throughput Screening for Drug Discovery", in Biological Database Modeling J. Chen and A. Sandhu eds., Artech House 2007.
- T. Lee, R. Singh, R. Yen, and B. Macher, "An Algorithmic Approach to Automated High-Throughput Identification of Disulfide Connectivity in Proteins Using Tandem Mass Spectrometry", Computational Systems Bioinformatics Conference (CSB), pp. 41 – 51, 2007.
- J. Lipinski-Kruzka and R. Singh, "Integrative Geometric-Hashing Approaches to Binding Site Modeling and Ligand-Protein Interaction Prediction", International Symposium on Visual Computing (ISVC), Lecture Notes in Computer Science, Vol. 4841, pp. 179-188, Springer Verlag, 2007.
- T. Lee, R. Singh, R. Yen, and B. Macher, "MS2DB: A Mass-Based Hashing Algorithm for the Identification of Disulfide Linkage Patterns in Protein Utilizing Mass Spectrometric Data", IEEE International Symposium on Computer-Based Medical Systems (CBMS), pp. 397 – 402, 2007.