Publications of the BioDM Group

Journal Publications

1. Comparative Experiments on Learning Information Extractors for Proteins and their Interactions
   Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Edward M. Marcotte, Raymond J. Mooney, Arun K. Ramani, Yuk W. Wong, 
   Journal Artificial Intelligence in Medicine (Special Issue on Summarization and Information Extraction from Medical Documents)    vol. 33, (2005), p. 139.
   [PS/GZ]


2. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
   Shailesh V. Date, Edward M. Marcotte, 
   Nature Biotechnology, 21, 9, 1055-1062    2003.
   [PDF]


3. Genome-Wide Analysis of the Biology of Stress Responses through Heat Shock Transcription Factor
   J. S. Hahn, Z. Hu, D. J. Thiele, V. R. Iyer, 
   Mol. Cell. Biol., vol. 24, (2004), p. 5249    2004
   [PDF]


4. Mapping DNA-Protein Interactions in Large Genomes by STAGE: Sequence Tag Analysis of Genomic Enrichment
   J. Kim, A. A. Bhinge, X. C. Morgan, V. R. Iyer, 
   Nature Methods, vol. , (2005), p. 47    2005
   [PDF]


5. Consolidating the Set of Known Human Protein-Protein Interactions in Preparation for Large-Scale Mapping of the Human Interactome
   Arun K. Ramani, Razvan Bunescu, Raymond J. Mooney, Edward M. Marcotte, 
   Genome Biology, vol. 6, (2005), p. r40    2005
   [PDF]


6. "Protein interaction networks from yeast to human Published
   P. Bork, L. J. Jensen, C. von Mering, Arun K. Ramani, I. Lee, Edward M. Marcotte, 
   Curr. Op. Struct. Biol., vol. 14, p. 292.    2004
   [PDF]


7. Development through the eyes of functional genomics . Published
   A. G Fraser, Edward M. Marcotte, 
   Curr. Op. Gen. Dev., vol. 14, p. 336    2004
   [PDF]


8. A probabilistic view of gene function
   A. G Fraser, Edward M. Marcotte, 
   Nature Genetics, vol. 36, p. 559    2004
   [PDF]


9. Protein function prediction using the Protein Link Explorer (PLEX)
   Shailesh V. Date, Edward M. Marcotte, 
   Bioinformatics    2005
   [PDF]


10. Global role of TATA-box binding protein recruitment to promoters in mediating gene expression profiles
    J. Kim, V. R. Iyer, 
    Mol. Cell. Biol, vol. 24, p. 8104    2004
    [PDF]


11. Exploring the posttranscriptional RNA world with DNA microarrays
    V. R. Iyer, 
    Trends Biotechnol., vol. 22, p. 498    2004
    [PDF]


12. Mapping DNA-Protein Interactions in Large Genomes by Sequence Tag Analysis of Genomic Enrichment
    J. Kim, A. A. Bhinge, X. C. Morgan, V. R. Iyer, 
    Nature Methods, vol. 2, p. 47    2005
    [PDF]


13. Systematic profiling of cellular phenotypes and gene function with whole-cell microarrays
    R. Narayanaswamy, W. Niu, A. Scouras, T. G. Hart, J. Davies, A. D. Ellington, 
    Proc. Natl. Acad. Sci., Submitted    2005
    [TODO]


14. Biosequence Use Cases in MoBIoS SQL
    Daniel P. Miranker, Willard J Briggs, Rui Mao, Shulin Ni, Weijia Xu, 
    Data Engineering Bulletin. p. 3.    2004
    [PDF]


15. An Assessment of a Metric Space Database Index to Support Sequence Homology
    Rui Mao, Weijia Xu, Neha Singh, Daniel P. Miranker, 
    International Journal on Artificial Intelligence Tools    2005
    [PDF]

Conference /Workshop Publications

1. Collective Information Extraction with Relational Markov Networks
   Razvan Bunescu, Raymond J. Mooney, 
   Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics, vol. p. 439.    July 2004.
   [PS/GZ]


2. A Probabilistic Framework for Semi-Supervised Clustering
   Sugato Basu, Mikhail Bilenko, Raymond J. Mooney, 
   Proceedings of the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, vol. p. 59.    2004
   [PDF]


3. Integrating Constraints and Metric Learning in Semi-Supervised Clustering
   Sugato Basu, Mikhail Bilenko, Raymond J. Mooney, 
   Proceedings of the 21st International Conference on Machine Learning    2004, p. 81
   [PDF]


4. Minimum Sum-Squared Residue Co-clustering of Gene Expression Data
   Hyuk Cho, Inderjit S. Dhillon, Yuqiang Guan, Suvrit Sra, 
   Proceedings of the Fourth SIAM International Conference on Data Mining    2004, p. 114
   [PDF]


5. A Generalized Maximum Entropy Approach to Bregman Co-Clustering and Matrix Approximations
   Arindam Banerjee, Inderjit S. Dhillon, Joydeep Ghosh, Srujuna Merugu, D. S. Modha, 
   Proceedings of The Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD-04)    2004, p. 509
   [PDF]


6. Using MoBIoS' Scalable Genome Joins to Find Conserved Primer Pair Candidates Between Two Genomes
   Weijia Xu, Willard J Briggs, Joanna Padolina, Wenguo Liu, C. Randall Linder, Daniel P. Miranker, 
   Proceedings of the International Conference on Intelligent Systems for Molecular Biology (ISMB-04) (also to appear as supplement to the Bioinformatics journal)    2004, p. 1214
   [PDF]


7. Model-Based Overlapping Clustering
   Arindam Banerjee, C. Krumpelman, Sugato Basu, Raymond J. Mooney, Joydeep Ghosh, 
   Proceedings of the Eleventh ACM SIGKDD International Conference on Knowledge Discovery and Data Mining    2005
   [PDF]


8. Semi-Supervised Graph-Based Clustering: A Kernel Approach
   SR, Sugato Basu, Inderjit S. Dhillon, Raymond J. Mooney, 
   Proceedings of the 22nd International Conference on Machine Learning    2005
   [PDF]


9. Subsequence Kernels for Relation Extraction
   Razvan Bunescu, Raymond J. Mooney, 
   Advances in Neural Information Processing Systems Conference    2005
   [PDF]


10. Robust One-Class Clustering Using Hybrid Global and Local Search
    Gunjan Gupta, Joydeep Ghosh, 
    Proceedings of the 22nd International Conference on Machine Learning    2005
    [PDF]


11. A Fast Kernel-based Multilevel Algorithm for Graph Clustering
    Inderjit S. Dhillon, Yuqiang Guan, SR, 
    Proceedings of the Eleventh ACM SIGKDD International Conference on Knowledge Discovery and Data Mining(KDD) vol. 11    2005
    [PDF]


12. Triangle Fixing Algorithms for the Metric Nearness Problem
    Inderjit S. Dhillon, Suvrit Sra, Joel A. Tropp, 
    Proceedings of the Neural Information Processing Systems Conference (NIPS), vol. 17, p. 361.    2004
    [PDF]


13. On Optimizing Distance-Based Similarity Search for Biological Databases
    Rui Mao, Weijia Xu, Smriti R. Ramakrishnan, Glen Nuckolls, Daniel P. Miranker, 
    Proc. of the Computational Systems Bioinformatics Conference    2005
    [PDF]


14. Case Study: Distance-Based Image Retrieval in the MoBIoS DBMS
    Rui Mao, Qasim Iqbal, Wenguo Liu, Daniel P. Miranker, 
    Proceedings of The 5th International Conference on Computer and Information Technology (CIT2005)    2005
    [PDF]


15. Clustering and Visualization of High-Dimensional Biological Datasets using a fast HMA Approximation
    Gunjan Gupta, A. Liu, Joydeep Ghosh, 
    Proc. ANNIE 2006, ASME    2006
    [PDF]


16. Hierarchical Density Shaving: A clustering and visualization framework for large biological datasets
    Gunjan Gupta, A. Liu, Joydeep Ghosh, 
    IEEE ICDM 2006 Workshop on Data Mining in Bioinformatics (DMB 2006)    2006
    [PDF]


17. Bregman Bubble Clustering: A Robust, Scalable Framework for Locating Multiple, Dense Regions in Data
    Gunjan Gupta, Joydeep Ghosh, 
    Proc. ICDM: The 2006 IEEE International Conference on Data Mining (ICDM2006)    2006
    [PDF]

Book(s) of other one-time publications(s)

1. Relational Markov Networks for Collective Information Extraction
   Razvan Bunescu, Raymond J. Mooney, 
   Workshop Proceedings Published, Banff Canada. Of Collection: T. Dietterich, L. Getoor, and K. Murphy, "Proceedings of the ICML-04 Workshop on Statistical Relational Learning and its Connections to Other Fields"    2004
   [TODO]


2. A Comparison of Inference Techniques for Semi-supervised Clustering with Hidden Markov Random Fields
   Sugato Basu, Mikhail Bilenko, 
   Workshop Proceedings Published, Banff Canada. Of Collection: T. Dietterich, L. Getoor, and K. Murphy, "Proceedings of the ICML-2004 Workshop on Statistical Relational Learning and its Connections to Other Fields"    2004
   [TODO]


3. Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions
   Arun K. Ramani, Edward M. Marcotte, Razvan Bunescu, Raymond J. Mooney, 
   Workshop Proceedings Published. Of Collection: "Proceedings of the ISMB BioLINK SIG: Linking Literature, Information and Knowledge for Biology"    2005
   [TODO]


4. Statistical Relational Learning for Natural-Language Information Extraction and Semantic Parsing
   Raymond J. Mooney, Razvan Bunescu, 
   Book Submitted. Of Collection: Lise Getoor and Ben Taskar, "Statistical Relational Learning"    2005
   [TODO]


5. Data Analysis with the Longhorn Array Database (LAD)
   P. J. Killion, V. R. Iyer, 
   Book Published, John Wiley & Sons. Of Collection: of Collection: Baxevanis A.D. & Davison D.B., "Unit 7.10 in Current Protocols in Bioinformatics"    2004
   [TODO]

Miscellaneous

1. Mining Knowledge from Text Using Information Extraction
   Raymond J. Mooney, Razvan Bunescu, 
   SIGKDD Explorations (special issue on Text Mining and Natural Language Processing)    2005
   [PDF]


2. Bregman Bubble Clustering: A Robust Framework for Mining Dense Clusters
   Gunjan Gupta, Joydeep Ghosh, 
   IDEAL-TR04    2006
   [PDF]


3. Automated Hierarchical Density Shaving and Gene DIVER
   Gunjan Gupta, A. Liu, Joydeep Ghosh, 
   IDEAL-TR05    2006
   [PDF]

Technical Reports