Sayan Ranu, and Ambuj Singh, Mining Statistically Significant Molecular Substructures for Efficient Molecular Classification, Journal of Chemical Information and Modeling, 2009.
Kathy Macropol, Tolga Can, and Ambuj Singh, RRW: repeated random walks on genome-scale protein networks for local cluster discovery, BMC Bioinformatics, 10:283, 2009.
Petko Bogdanov and Ambuj Singh, Molecular Function Prediction Using Neighborhood Features in IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2009.
Kyle Chipman and Ambuj Singh, Predicting genetic interactions with random walks on biological networks, BMC Bioinformatics, 10:17, 2009.
Sayan Ranu and Ambuj Singh, GraphSig: A Scalable Approach to Mining Significant Subgraphs in Large Graph Databases in 25th International Conference on Data Engineering (ICDE), 2009.
V. Ljosa and Ambuj Singh, Probabilistic Querying and Mining of Biological Images , Managing and Mining Uncertain Data,(Kluwer Academic), ed. C. Aggarwal.
K. Kvilekval and Ambuj Singh, BISQUE: A Scalable Biological Image Database and Analysis Framework , High-throughput image reconstruction and analysis: intelligent microscopy applications (Artech House), ed. R. Rao and G. Cecchi
A. LeBoeuf, S. Levy, M. Gaylord, A. Bhattacharya, Ambuj Singh, M. Jordan, L. Wilson, and S. Feinstein, FTDP-17 Mutations in tau Alter the Regulation of Microtubule Dynamics---an "Alternative Core" Model for Normal and Pathological Tau Action Journal of Biological Chemistry
Ahmet Bulut, Nick Koudas, Anand Meka, Ambuj K. Singh, Divesh Srivastava, Optimization Techniques for Reactive Network Monitoring in IEEE Transactions on Knowledge and Data Engineering.
Arnab Bhattacharya, Sasha Levy, Adria LeBoeuf, Michelle Gaylord, Leslie Wilson, Ambuj K Singh, Stuart C Feinstein, A general modeling and visualization tool for comparing different members of a group: application to studying tau-mediated regulation of microtubule dynamics in BMC Bioinformatics 2008, 9:339 (12 August 2008)
Huahai He and Ambuj K. Singh, "Graphs-at-a-time: Query Language and Access Methods for Graph Databases," in SIGMOD, June, 2008.
Brian E. Ruttenberg, Trairak Pisitkun, Mark A. Knepper, Jason D. Hoffert, "PhosphoScore: An Open-Source Phosphorylation Site Assignment Tool for MSn Data" in Journal of Proteome Research, 2008, DOI 10.1021/pr800169k
Nicholas Larusso, Brian Ruttenberg, Ambuj Singh and Todd Oakley "Type II Opsins: Evolutionary Origin by Internal Domain Duplication?" in Journal of Molecular Evolution, April, 2008. DOI 10.1007/s00239-008-9076-6
Vishwakarma Singh, Arnab Bhattacharya and Ambuj K. Singh, "Efficient Computation of Statistical Significance of Query Results in Databases," in SSDBM, July, 2008.
Vebjorn Ljosa and Ambuj K. Singh, "Top-k Spatial Joins of Probabilistic Objects," in Proceedings of the 24th International Conference on Data Engineering (ICDE), April, 2008.
Nicholas Larusso, Brian Ruttenberg, Ambuj Singh, "Probabilistic Analysis of Retinal Neuron Morphology," in Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining, 2008.
Sayan Ranu and Ambuj K. Singh, "Mining for Patterns on Theme Maps of Phenotyped Cells," in Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining, 2008.
Petko Bogdanov and Ambuj K. Singh, "Function Prediction Using Neighborhood Patterns," in BioKDD, August, 2008.
Vebjorn Ljosa and Ambuj K. Singh, "APLA: Indexing Arbitrary Probability Distributions," in Proceedings of the 23rd International Conference on Data Engineering (ICDE), April, 2007.
Arnab Bhattacharya, Anand Meka, Ambuj K. Singh, "MIST: Distributed Indexing and Querying in Sensor Networks using Statistical Models." in VLDB, 2007.
Huahai He and Ambuj K. Singh, "Efficient Algorithms for Mining Significant Substructures in Graphs with Quality Guarantees" in In Proceedings of the 2007 International Conference on Data Mining, 2007.
Petko Bogdanov, Swaroop Jagadish and Ambuj Singh, "Function Prediction Using Neighborhood Patterns," in Biotechechnology and Bioinformatics Symposium (BIOT), October, 2007.
Huahai He and Ambuj K. Singh, "GraphRank: Statistical Modeling and Mining of Significant Subgraphs in the Feature Space," in Proceedings of the 2006 IEEE International Conference on Data Mining (ICDM), December, 2006, doi:10.1109/ICDM.2006.79.
Manfred Auer, Hanchuan Peng and Ambuj Singh, "2006 International Workshop on Multiscale Biological Imaging, Data Mining and Informatics Research," in BMC Cell Biology, vol.8, supplement 1, 2006.
Vebjorn Ljosa and Ambuj K. Singh, "Probabilistic Segmentation and Analysis of Horizontal Cells," in Proceedings of the 2006 IEEE International Conference on Data Mining (ICDM), December, 2006, doi:10.1109/ICDM.2006.129.
Vebjorn Ljosa, and Ambuj K. Singh, "Probabilistic Segmentation of Horizontal Cells", Proceedings of the 2006 workshop on Multiscale Biological Imaging, Data Mining & Informatics, pages 39-40, September, 2006.
Arnab Bhattacharya, and Ambuj K. Singh, "Prediction of Growth Parameters of In Vitro Microtubules in Association with Different Isoforms of Tau", in Proceedings of the 2006 workshop on Multiscale Biological Imaging, Data Mining & Informatics, pages 53-54, September, 2006.
Chunghau Lee, Sigal Blay, Arne Ø. Mooers, Ambuj Singh, and Todd H. Oakley, "CoMET: A Mesquite package for comparing models of continuous character evolution on phylogenies", Evolutionary Bioinformatics Online.
Orhan Camoglu, Tolga Can, and Ambuj K. Singh, "Integrating Multi-Attribute Similarity Networks for Robust Representation of the Protein Space", Bioinformatics 22(13):1585-1592, 2006, doi:10.1093/bioinformatics/btl130.
Tamer Kahveci and Ambuj K. Singh, "Index Structures for Approximate Matching in Sequence Databases," In Handbook on Computational Biology, editor Srinivas Aluru, CRC Press. To appear.
Huahai He and Ambuj K. Singh, "Closure-tree: An Index Structure for Graph Queries,", In Proceedings of the 22nd International Conference on Data Engineering (ICDE), April, 2006, doi:10.1109/ICDE.2006.37.
Vebjorn Ljosa, Arnab Bhattacharya, and Ambuj K. Singh, "LB-Index: A Multi-Resolution Index Structure for Images," in Proceedings of the 22nd International Conference on Data Engineering (ICDE), April, 2006, doi:10.1109/ICDE.2006.85.
Anand Meka and Ambuj K. Singh, "Distributed Spatial Clustering in Sensor Networks," In Proceedings of the 10th International Conference on Extending Database Technology (EDBT), p. 980-1000, March, 2006, doi:10.1007/11687238_57.
Vebjorn Ljosa, Arnab Bhattacharya, and Ambuj K. Singh, "Indexing Spatially Sensitive Distance Measures Using Multi-Resolution Lower Bounds," In Proceedings of the 10th International Conference on Extending Database Technology (EDBT), p. 865-883, March, 2006, doi:10.1007/11687238_51.
Arnab Bhattacharya, Vebjorn Ljosa, Jia-Yu Pan, Mark R. Verardo, Hyungjeong Yang, Christos Faloutsos, and Ambuj K. Singh: "ViVo: Visual vocabulary construction for mining biomedical images," In Proceedings of the Fifth IEEE International Conference on Data Mining (ICDM), November, 2005. Received one of five "best student paper" awards.
Tolga Can, Orhan Camoglu, and Ambuj K. Singh, "Analysis of protein-protein interaction networks using random walks," In Proceedings of the 5th ACM SIGKDD Workshop on Data Mining in Bioinformatics, August, 2005.
Ambuj K. Singh, Arnab Bhattacharya, and Vebjorn Ljosa, "Current challenges in bioimage database design," Proceedings of the International Workshop on Bioimage Data Mining and Informatics, IEEE Computational Systems Bioinformatics Conference (CSB), p. 375--379, August, 2005, doi:10.1109/CSBW.2005.47. Invited talk and abstract.
Orhan Camoglu, Tolga Can, Ambuj K. Singh and Y. F. Wang, "Decision Tree Based Information Integration for Automated Protein Classification," Journal of Bioinformatics and Computational Biology, 3(3):717-742, June, 2005, doi:10.1142/S0219720005001259.
Ying Feng, Divyakant Agrawal, Amr E. Abaddi and Ambuj K. Singh, "Scalable and Progressive Ranking for Preference Queries," In Proceedings of the 14th ACM Conference on Information and Knowledge Management (CIKM), November, 2005.
Anand Meka and Ambuj K. Singh, "DIST: A Distributed Spatio-temporal Index Structure for Sensor Networks," In Proceedings of the 14th ACM Conference on Information and Knowledge Management (CIKM), November, 2005.
Ahmet Bulut and Ambuj K. Singh, "A Unified Framework for Monitoring Data Streams in Real Time," In Proceedings of 21st International Conference on Data Engineering, p. 44-55, April, 2005, doi:10.1109/ICDE.2005.13.
Ahmet Bulut, Roman Vitenberg, and Ambuj K. Singh, "Distributed Data Streams Indexing using Content-based Routing Paradigm," In Proceedings of 19th International Parallel and Distributed Processing Symposium, April, 2005, doi:10.1109/IPDPS.2005.170.
Ahmet Bulut, Ambuj K. Singh, P. Shin, H. Jasso, T. Fountain, L. Yan, and A. Elgamal, "Real-time Nondestructive Structural Health Monitoring using Support Vector Machines and Wavelets," In Advanced Sensor Technologies for Nondestructive Evaluation and Structural Health Monitoring (NDE05), March, 2005.
Ambuj K. Singh, "Scalable Index Structures for Biological Data", in Jason Tsong-Li Wang, Mohammed Javeed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Data Mining in Bioinformatics, p. 275-296, Springer, 2005, ISBN 1-85233-671-4.
Kristian Kvilekval and Ambuj K. Singh, "SPREE: Object Prefetching for Mobile Computers", in Proceedings of the International Symposium on Distributed Objects and Applications (DOA), October, 2004, doi:10.1007/b102176.
Tolga Can, Orhan Camoglu, Ambuj K. Singh, and Y.-F. Wang, "Automated Protein Classification Using Consensus Decision", in Proceedings of the Third International IEEE Computer Society Computational Systems Bioinformatics Conference (CSB), p. 224-235, August, 2004.
Roman Vitenberg, Kristian Kvilekval and Ambuj K. Singh, "Increasing Concurrency in Databases using Program Analysis," In Proceedings of the 18th European Conference on Object-Oriented Programming (ECOOP), June, 2004, doi:10.1007/b98195.
Chao-I Chen, Xiaofang Lei, Vebjorn Ljosa, Thomas A. McCloskey, Chiou-Wei Tsai, S. Rao Jammalamadaka, Joel H. Rothman, and Ambuj K. Singh, "A Bayesian approach toward analyzing the network of genes involved in C. elegans programmed cell death," West Coast Worm Meeting, 2004 (poster and talk).
Tamer Kahveci, Vebjorn Ljosa, and Ambuj K. Singh, "Speeding up whole-genome alignment by indexing frequency vectors," Bioinformatics, 20(13):2122-2134, 2004, doi:10.1093/bioinformatics/bth212.
Arnab Bhattacharya, Tamer Kahveci, and Ambuj K. Singh, Motif Finding and Multiple Alignment through Vector-Space Embeddings of Protein Sequences, in Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB), March, 2004 (poster paper).
Orhan Camoglu, Tamer Kahveci, Ambuj K. Singh, "Index-based Similarity Search for Protein Structure Databases," Journal of Bioinformatics and Computational Biology, 2(1):99-126, March, 2004, doi:10.1142/S0219720004000491.
Arnab Bhattacharya, Tolga Can, Tamer Kahveci, Ambuj K. Singh, and Y.-F. Wang, "ProGreSS: Simultaneous Searching of Protein Databases by Sequence and Structure," in Proceedings of the 9th Pacific Symposium on Biocomputing (PSB), p. 264-275, January, 2004.
Tamer Kahveci and Ambuj K. Singh, "Optimizing Similarity Search for Arbitrary Length Time Series Queries," IEEE Transactions on Knowledge and Data Engineering, 16(4):418-433, doi:10.1109/TKDE.2004.1269667.
Ambuj K. Singh and B.S. Manjunath and Robert F. Murphy, "A Distributed Database for Biomolecular Images,", SIGMOD Record, 33(2):65-71, June, 2004, doi:10.1145/1024694.1024705.
Tamer Kahveci and Ambuj K. Singh, "Progressive Searching of Biological Sequences,", IEEE Data Engineering Bulletin, 27(3):32-39, September, 2004.
Ahmet Bulut and Ambuj K. Singh. "Stardust: Data Stream Indexing for Sensor Networks," in Proceedings of the 1st international conference on Embedded networked sensor systems (SENSYS), November 2003. (Demo paper)
Maureen Heymans, Ambuj K. Singh: "Deriving phylogenetic trees from the similarity analysis of metabolic pathways," Bioinformatics 19(S1):138-146, 2003.
Maureen Heymans, Ambuj K. Singh: "Deriving phylogenetic trees from the similarity analysis of metabolic pathways," In Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology (ISMB), July, 2003.
Ahmet Bulut, Roman Vitenberg, Fatih Emekçi, and Ambuj K. Singh, "An Adaptive and Scalable Middleware for Distributed Indexing of Data Streams," in Proceedings of the First International Workshop on Databases, Information Systems, and Peer-to-Peer Computing (DBISP2P), p. 123-137, September, 2003, doi:10.1007/b95270
Orhan Camoglu, Tamer Kahveci, and Ambuj K. Singh, "Towards Index-based Similarity Search for Protein Structure Databases," In Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference (CSB), p. 148-158, 2003, doi:10.1109/CSB.2003.1227314
Tamer Kahveci and Ambuj K. Singh, "Genome on Demand: Interactive Substring Searching," In Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference (CSB), p. 551-552, doi:10.1109/CSB.2003.1227405 (poster paper).
Orhan Camoglu, Tamer Kahveci and Ambuj K. Singh, "PSI: Indexing Protein Structures for Fast Similarity Search," Bioinformatics 19(S1):i81-i83, 2003.
Orhan Camoglu, Tamer Kahveci and Ambuj K. Singh, "PSI: Indexing Protein Structures for Fast Similarity Search," In Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology (ISMB), July, 2003.
Ahmet Bulut and Ambuj K. Singh, "SWAT: Hierarchical Stream Summarization in Large Networks," In Proceedings of the 19th International Conference on Data Engineering (ICDE), 2003, doi:10.1109/ICDE.2003.1260801
Tamer Kahveci, Christian A. Lang, and Ambuj K. Singh, "Joining Massive High-Dimensional Databases," In Proceedings of the 19th International Conference on Data Engineering (ICDE), 2003, doi:10.1109/ICDE.2003.1260798.
Tamer Kahveci and Ambuj K. Singh, "Fast Alignment of Large Genome Databases: A Demonstration," In Proceedings of the 19th International Conference on Data Engineering (ICDE), 2003, doi:10.1109/ICDE.2003.1260862 (demo paper).
Christian A. Lang and Ambuj K. Singh, "Faster Similarity Search for Multimedia Data via Query Transformations," Intl. Journal of Image and Graphics 3(1):3-29, January, 2003, doi:10.1142/S0219467803000890.
Tamer Kahveci and Ambuj K. Singh, "MAP: Searching Large Genome Databases," In Proceedings of the 8th Pacific Symposium on Biocomputing (PSB), p. 303-314, January, 2004.
R. Lencevicius and Urs Hoelzle and Ambuj K. Singh, "Dynamic Query-Based Debugging of Object-oriented Programs," Automated Software Engineering, 10(1):39-74, January, 2003, doi:10.1023/A:1021816917888.
Ambuj K. Singh, "Querying and Mining Biological Databases," OMICS A Journal of Integrative Biology, 7(1):7-8, doi:10.1089/153623103322006472.