Publications

In preparation / under review ...

"Gene ontology enrichment"

"Open source toolkit for pattern mining in genome sequences"

 

Computational Biology

  1. "N-gram analysis of 970 microbial organisms reveals presence of biological language models",
    Ulku Osmanbeyoglu and Madhavi Ganapathiraju,
    BMC Bioinformatics, 12(12), 2011

  2. "Rapid Development of Viral-Human Interactome Prediction System for New Viruses",
    Ulku Osmanbeyoglu and Madhavi Ganapathiraju,
    AMIA Translational Bioinformatics Summit, March 7-9 2011, San Francisco, USA.

  3. "Active Learning for Human Protein-Protein Interaction Prediction",
    Thahir P. Mohamed, Jaime G. Carbonell and Madhavi Ganapathiraju,
    BMC Bioinformatics, vol 11, Suppl 1, 2010.

  4. "Active Machine Learning for Membrane Protein Structure Prediction",
    Hatice U. Osmanbeyogly, Jessica A. Wehner, Jaime G. Carbonell and Madhavi Ganapathiraju,
    BMC Bioinformatics, vol 11, Suppl 1, 2010.

  5. "TMpro: Transmembrane Helix Prediction Using Amino Acid Properties and Latent Semantic Analysis",
    Madhavi Ganapathiraju, N. Balakrishnan, Raj Reddy and Judith Klein-Seetharaman,
    BMC Bioinformatics, vol 9, Suppl 1, 2008.

  6. "TMpro: Webserver and Webservice for Transmembrane Helix Prediction Using Amino Acid Properties",
    Madhavi Ganapathiraju, Chritopher Jon Jursa, Hassan A. Karimi, and Judith Klein-Seetharaman,
    Bioinformatics, vol 23, issue 20, 2007.

  7. "Evolutionary insights from suffix array based genome sequence analysis",
    A. Poddar, N. Chandra, Madhavi Ganapathiraju, K. Sekar, J. Klein-Seetharaman, R. Reddy and N. Balakrishnan,
    J. Biosciences, in print, 2007.

  8. "Collaborative Discovery and Biological Language Modeling Interface",
    Madhavi Ganapathiraju, Vijayalaxmi Manoharan, Raj Reddy and Judith Klein-Seetharaman,
    Lecture Notes in Artificial Intelligence, LNCS/LNAI 3864, 2006.

  9. "Retinitis pigmentosa associated with rhodopsin mutations: Correlation between phenotypic variability and molecular effects",
    Iannaccone A, D. Man, N. Waseem, BJ. Jennings, Madhavi Ganapathiraju, K. Gallaher, E. Reese, SS. Bhattacharya, J. Klein-Seetharaman,
    Vision Research, vol 46, issue 27, pp 4556-67, 2006.

  10. "Comparison of stability predictions and simulated unfolding of rhodopsin structures",
    Oznur Tastan, Esther Yu, Madhavi Ganapathiraju, Anes Aref, AJ Rader and Judith Klein-Seetharaman,
    Photobiology and photochemistry, vol 63, issue 2, pp 351-363, 2006.

  11. "Computational Biology and Language",
    Madhavi Ganapathiraju, N. Balakrishnan, Raj Reddy and Judith Klein-Seetharaman,
    Lecture Notes in Artificial Intelligence, LNCS/LNAI 3345, 2004.

  12. "BLMT: Statistical sequence analysis using n-grams",
    Madhavi Ganapathiraju, Vijayalaxmi Manoharan and Judith Klein-Seetharaman,
    Applied Bioinformatics, vol. 3, issue 2, November 2004.

  13. "Characterization of Protein Secondary Structure using Latent Semantic Analysis",
    Madhavi Ganapathiraju, Judith Klein-Seetharaman, N. Balakrishnan and Raj Reddy,
    IEEE Signal Processing Magazine, vol. 21, issue 3, May 2004.

  14. "BLMT Web Server: Interactive Language Technologies for Analogous Biological Data",
    Vijayalaxmi Manoharan, Madhavi Ganapathiraju and Judith Klein-Seetharaman,
    Workshop on Ambient Intelligence and (Everyday) Life, Donostia, San-Sebastian, Spain, 2005.

  15. "Yule value tables from Protein Datasets of different categories: emphasis on membrane proteins" [Invited Talk],
    Madhavi Ganapathiraju, Deborah Weisser, Raj Reddy and Judith Klein-Seetharaman,
    Proc. SCI2004, Florida, USA, 2004.
  16. "Extensions to Biological Language Modeling Toolkit (BLMT)",
    Balakrishnan Sivaraman, Madhavi Ganapathiraju, Judith Klein-Seetharaman, N. Balakrishnan and Raj Reddy,
    BLC2003: Biological Language Conference, Pittsburgh USA, November 2003.
  17. "Comparative n-gram analysis of whole-genome sequences"
    Madhavi Ganapathiraju, Deborah Weisser, Judith Klein-Seetharaman, Roni Rosenfeld, Jaime Carbonell and Raj Reddy,
    HLT'02: Human Language Technologies Conference, San Diego, March, 2002.
  18. "Rare and frequent amino acid n-grams in whole-genome protein sequences",
    Madhavi Ganapathiraju, Judith Klein-Seetharaman, Roni Rosenfeld, Jaime Carbonell and Raj Reddy, 
    RECOMB'02: The Sixth Annual International Conference on Research in Computational Molecular Biology, Washington DC, USA, April, 2002.

Digital Library and Indian Language Processing

  1. "Digital Library of India: a testbed for Indian language research",
    N. Balakrishnan, Raj Reddy, Madhavi Ganapathiraju, Vamshi Ambati,
    IEEE Technical Committee on Digital Libraries (TCDL) Bulletin, vol 3, issue 1, 2006.

  2. "Om: One tool for many (Indian) languages",
    Ganapathiraju Madhavi, Balakrishnan Mini, Balakrishnan N., Reddy Raj,
    Journal of Zhejiang University SCIENCE, Vol 6A, No. 11, pp 1348-1353, Oct 2005.

  3. "Improving Recognition Accuracy on CVSD speech in mismatched conditions",
    Madhavi Ganapathiraju, N. Balakrishnan and Raj Reddy,
    WSEAS Transactions on Computers, Vol 2, Issue 4, October 2003.
  1. "TelMore: Morphological Generator for Telugu Nouns and Verbs",
    Madhavi Ganapathiraju and Lori Levin,
    Proc. Second International Conference on Universal Digital Library, Vol Alexandria, Egypt, Nov 17-19, 2006

  2. "Multilingual Book Reader: Transliteration, Word-to-Word Translation and Full-text Translation",
    Prashanth Balajapally, Phanindra Pydimarri, Madhavi Ganapathiraju, N. Balakrishnan, Raj Reddy,
    VALA 2006: 13th Biennial Conference and Exhibition Conference of Victorian Association for Library Automation, Melbourne, Australia, February 8-10, 2006.

  3. "Million Books to Web: Technological Challenges and Research Issues",
    N. Balakrishnan, Raj Reddy, Madhavi Ganapathiraju and Hemant Gogineni,
    Proc. Tamil Internet conference, pp 227-242, December 2004.

  4. "OmSE: Tamil Search Engine",
    Anandh Jayaraman, Srinivas Sangani, Madhavi Ganapathiraju and N. Balakrishnan,
    Proc. Tamil Internet conference, pp 23-29, December 2004.

Theses

  1. "Relevance of Cluster Size in MMR Summarization",
    Madhavi Ganapathiraju (Advisor: Jaime G. Carbonell),
    Report for 11-745, 2002.

  2. Ph.D. Thesis: "Application of Language Technologies to Computational Biology: Transmembrane Helix Prediction and Characterization",
    Madhavi Ganapathiraju. Thesis Supervisors: Raj Reddy and Judith Klein-Seetharaman,
    Language Technologies Institute, Carnegie Mellon University, Pittsburgh PA 15213 USA.

  3. M.Engg. "Thesis: Speech Recognition on MPEG/Audio"
    Madhavi Ganapathiraju. Advisors: Prof. N. Balakrishnan and Prof. P. S. Naidu,
    Department of Electrical and Communications Engineering, Indian Institute of Science, Bangalore, 560012, India