Biocomputing and Media Research Lab

Image: Figures pertaining to research

NSF CAREER:
Designing Systems for Molecular Query-Retrieval and Molecular Informatics

    Division of Information and Intelligent Systems
  • Award Number: 0644418
  • Principal Investigator: R. Singh (SFSU)

Abstract

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.


Research Foci


Students


Former 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

Publications

  • R. Eshleman and R. Singh, “Leveraging Graph Topology and Semantic Context for Pharmacovigilance through Twitter Streams”, BMC Bioinformatics, Vol. 17, (Suppl 13):335, 2016. (Corresponding author R. Singh)[PDF]
  • R. Singh, R. Beasley, T. Long and C. Caffrey, “Algorithmic Mapping and Characterization of the Drug-Induced Phenotypic Response Space of Parasites Causing Schistosomiasis”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, To Appear. (Corresponding author R. Singh) [PDF]
  • J. Dohrmann and R. Singh, “The SMAL web server: global multiple network alignment from pairwise alignments”, Bioinformatics, Accepted. (Corresponding author R. Singh)[PDF]
  • T. Long, R. J. Neitz, R. Beasley, C. Kalyanaraman, B. M. Suzuki, M. P. Jacobson, C. Dissous, J. H. McKerrow, D. H. Drewry, R. Singh, and C. R. Caffrey, “Structure-bioactivity relationship for benzimidazole thiophene inhibitors of polo-like-kinase 1 (PLK1), a potential drug target in Schistosoma mansoni”, PLoS Neglected Tropical Diseases, 10(1): e0004356, 2016. (Corresponding authors T. Long and C. R. Caffrey).[PDF]
  • R. Eshleman and R. Singh, "Progression Reconstruction from Unsynchronized Biological Data Using Cluster Spanning Trees", International Symposium on Bioinformatics Research and Application (ISBRA) 2016, Lecture Notes in Bioinformatics, Vol. 9683, pp. 136-147, Springer, 2016.[PDF]
  • J. Dohrmann, J. Puchin, and R. Singh, “Global Multiple Network Alignment by Combining Pairwise Network Alignments”, BMC Bioinformatics, Vol. 16, (Suppl 13):S11, 2015. (Corresponding author R. Singh) [PDF]
  • D. Asarnow*, L. R. Areola, B. Suzuki, C. Caffrey, and R. Singh*, “The QDREC Webserver: Determining Dose-Response Characteristics for Complex Macroparasites Using Phenotypic Drug Screening Data”, Bioinformatics, Vol. 31 (9), pp. 1515-1518, 2015 (*D. Asarnow and R. Singh equal contributors. Corresponding author R. Singh) [PDF]
  • T. Olson and R. Singh, “Computational Prediction of ATC Codes of Drug-Like Compounds Using Tiered Learning”, Proceeding of the Fifth IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2015 [PDF]
  • L. Rojo-Arreola, T. Long, D. Asarnow, B.M. Suzuki, R. Singh and C.R. Caffrey, "Chemical and genetic validation of the statin drug target for the potential treatment of the helminth disease, schistosomiasis," PLoS ONE, 9(1): e87594, 2014. (Corresponding author C.R. Caffrey). [PDF]
  • D. Asarnow and R. Singh, "Automatic Classification of Protein Structures Using Low-Dimensional Structure Space Mappings," BMC Bioinformatics, 15(Suppl 2):S1, 2014. (Corresponding author R. Singh). [PDF]
  • R. Singh, H. Yang, B. Dalziel, D. Asarnow, W. Murad, D. Foote, M. Gromley, J. Stillman, and S. Fisher, "Towards Human-Computer Synergistic Analysis of Large-Scale Biological Data", BMC Bioinformatics, 14(Suppl 14):S10, 2013. (Corresponding author R. Singh). [PDF]
  • W. Murad and R. Singh, "The MS2DB++ Webserver: Disulfide Bond Determination through Evidence Combination", IEEE Transactions on NanoBioscience, vol. 12, no. 4, pp. 340-342, 2013. (Corresponding author R. Singh). [PDF]
  • D. Asarnow and R. Singh, "The Impact of Parameters and Structural Diversity in Maps of the Protein Universe," BMC Proceedings, 7 (Suppl 7):S1, 2013. (Corresponding author R. Singh) [PDF]
  • R. Singh, H. Yang, B. Dalziel, D. Asarnow, W. Murad, D. Foote, M. Gromley, J. Stillman, and S. Fisher, "Towards Human-Computer Synergistic Analysis of Large-Scale Biological Data", BMC Bioinformatics, 14(Suppl 14):S10, 2013. (Corresponding author R. Singh). [PDF]
  • W. Murad and R. Singh, "The MS2DB++ Webserver: Disulfide Bond Determination through Evidence Combination", IEEE Transactions on NanoBioscience, vol. 12, no. 4, pp. 340-342, 2013. (Corresponding author R. Singh). [PDF]
  • D. Asarnow and R. Singh, "The Impact of Parameters and Structural Diversity in Maps of the Protein Universe," BMC Proceedings, 7 (Suppl 7):S1, 2013. (Corresponding author R. Singh) [PDF]
  • D. Asarnow and R. Singh, "Segmenting the Etiological Agent of Schistosomiasis for High-Content Screening," IEEE Transactions on Medical Imaging, vol. 32, no. 6, pp. 1007-10018, 2013. (Corresponding author R. Singh). [PDF]
  • 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. (Corresponding author R. Singh). [PDF]
  • W. Murad and R. Singh, "MS2DB+: A Software for Determination of Disulfide Bonds Using Multi-Ion Analysis", IEEE Transactions on NanoBioscience, vol. 12, no. 2, pp. 69-71, 2013. (Corresponding author R. Singh). [PDF]
  • R. Singh, Ya-Wen Hsu, and N. Moon, "Multiple-Perspective Interactive Search: A Paradigm for Exploratory Search and Information Retrieval on the Web", Journal of Multimedia Tools and Applications, Vol. 62 (2), pp. 507-543, 2013, (Corresponding author R. Singh). [PDF]
  • R. Singh, W. Murad, and T. Lee, "Algorithmic Frameworks for Protein Disulfide-Connectivity Determination", Chapter 9, Algorithmic and AI Methods for Protein Bioinformatics, Yi Pan, J. Wang, and M. Li eds., Wiley, pp. 171-204, 2013. [PDF]
  • 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. [PDF]
  • A. Shimoide, I. Kimball, A. Gutierrez, H. Lim, I. Yoon, J. T. Birmingham, R. Singh* and M. Fuse*, "Quantification and Analysis of Ecdysis in the Hornworm Manduca Sexta Using Machine Vision-based Tracking", Invertebrate Neuroscience, 2012, (*R. Singh, and M. Fuse Joint Corresponding Authors). [PDF]
  • 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). [PDF]
  • 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, Vol. 6(1):e1494, 2012 (Corresponding author C. Marcellino). [PDF]
  • R. Singh, "Quantitative High-Content Screening-Based Drug Discovery against Helminthic Diseases", in Parasitic Helminths: Targets, Screens, Drugs, and Vaccines, Ed. C. Caffrey, Wiley-Blackwell, pp. 159-179 2012. [PDF]
  • H. Lee and R. Singh, "Unsupervised Kernel Parameter Estimation by Constrained Non-Linear Optimization for Clustering Non-Linear Biological Data", IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 1-6, 2012. [PDF]
  • N. D. Martinez, P. Tonin, B. Bauer, R. C. Rael, R. Singh, S. Yoon, I. Yoon, and J. A. Dunne, "Sustaining Economic Exploitation of Complex Ecosystems in Computational Models of Coupled Human-Natural Networks", Proceedings of the Twenty-Sixth AAAI Conference on Artificial Intelligence (AAAI), pp. 326-334, 2012. [PDF]
  • H. Lee and R. Singh, "Symbolic Representation and Clustering of Bio-Medical Time-Series Data Using Non-Parametric Segmentation and Cluster Ensemble," IEEE International Symposium on Computer Based Medical Systems (CBMS), pp. 1-6, 2012. [PDF]
  • D. Asarnow and R. Singh, "Segmentation of Parasites for High-Content Screening using Phase Congruency and Grayscale Morphology", International Symposium on Visual Computing (ISVC), Lecture Notes in Computer Science, Vol. 7431, pp. 51-60, Springer, 2012. [PDF]
  • U. Saha and R. Singh, "Vision-Based Tracking of Complex Macroparasites for High-Content Phenotypic Drug Screening", International Symposium on Visual Computing (ISVC), Lecture Notes in Computer Science, Vol. 7432, pp. 104-114, Springer, 2012. [PDF]
  • 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, 12 (Suppl 1):S12, 2011 (Corresponding author: R. Singh). [PDF]
  • A. Moody-Davis, L. Mennillo and R. Singh, "Region Based Segmentation of Parasites for High-Throughput Screening," G. Bebis et al. (Eds.): International Symposium on Visiual Computing, Part I, LNCS 6938, pp. 44-54, 2011. [PDF]
  • A. Sasho, S. Zhu, and R. Singh, "Identification and Analysis of Cell Cycle Phase Genes by Clustering In Correspondence Subspaces", International Conference on Advances in Computing and Communications, 2011, Communications in Computer and Information Science, Volume 190, Part 4, 340-350. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • 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).
  • R. Singh, "A Review of Algorithmic Techniques for Disulfide-Bond Determination", Briefings in Functional Genomics and Proteomics, 2008, Vol. 7, pp. 157-172, 2008. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • R. Singh, "Surface Similarity-Based Molecular Query-Retrieval", BMC Cell-Biology, Vol. 8, Suppl.1 (S6): July, 2007. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • 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. [PDF]
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