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Madhavi Ganapathiraju

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Associate Professor at University of Pittsburgh

Department of Biomedical Informatics
Intelligent Systems Program
University of Pittsburgh Cancer Institute
Carnegie Mellon University's Language Technologies Institute

madhavi@pitt.edu
412-648-9552
The Offices at Baum
Department of Biomedical Informatics
5607 Baum Blvd, Pittsburgh, PA 15206

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  1. The complex genetics of hypoplastic left heart syndrome.
    TXiaoqin Liu, Hisato Yagi, Shazina Saeed, Abha S Bais, George C Gabriel, Zhaohan Chen, Kevin A Peterson, You Li, Molly C Schwartz, William T Reynolds, Manush Saydmohammed, Brian Gibbs, Yijen Wu, William Devine, Bishwanath Chatterjee, Nikolai T Klena, Dennis Kostka, Karen L de Mesy Bentley, Madhavi K Ganapathiraju, Phillip Dexheimer, Linda Leatherbury, Omar Khalifa, Anchit Bhagat, Maliha Zahid, William Pu, Simon Watkins, Paul Grossfeld, Stephen A Murray, George A Porter Jr, Michael Tsang, Lisa J Martin, D Woodrow Benson, Bruce J Aronow & Cecilia W Lo.
    Nature Genetics, Advance Online Publication (doi:10.1038/ng.3870), 2017.
  2. Generating testable hypotheses for schizophrenia and rheumatoid arthritis pathogenesis by integrating epidemiological, genomic and protein interaction data.
    Tulsi Malavia, Srilakshmi Chaparala, Joel Wood, Kodavali Chowdari, Konasale Prasad, Lora McClain, Anil Jegga, Madhavi K. Ganapathiraju and Vishwajit L. Nimgaonkar.
    NPJ Schizophrenia, 3, Article number: 11, 2017.
  3. DNA Palindromes in Cancer Genomes.
    Sandeep Subramanian, Srilakshmi Chaparala, Viji Avali and Madhavi Ganapathiraju.
    BMC Medical Genomics, in Press, 2016.
  4. Average shortest path distance of genes is not a reflection of their biological relatedness.
    Varsha Embar, Adam Handen and Madhavi Ganapathiraju.
    Journal of Computational Biology and Bioinformatics, Volume 14, Issue 06, 2016.
  5. Schizophrenia interactome with 504 novel protein-protein interactions.
    Madhavi Ganapathiraju, Mohamed Thahir, Adam Handen, Saumendra Sarkar, Robert Sweet, Vishwajit Nimgaonkar, Christine Loscher, Eileen Bauer, and Srilakshmi Chaparala.
    NPJ Schizophrenia, Vol 2, Article 16012, 2016.
    Nature post on Facebook.
  6. LENS: Lens for Enrichment and Network Studies of Human Proteins.
    Adam Handen and Madhavi Ganapathiraju
    BMC Medical Genomics, 8(Suppl 4):S2, 2015.
  7. Global genetic analysis in mice unveils central role for cilia in congenital heart disease.
    You Li, Nikolai T. Klena, George C. Gabriel, Xiaoqin Liu, Andrew J. Kim, Kristi Lemke, Yu Chen, Bishwanath Chatterjee, William Devine, Rama Rao Damerla, Chienfu Chang, Hisato Yagi, Jovenal T. San Agustin, Mohamed Thahir, Shane Anderton, Caroline Lawhead, Anita Vescovi, Herbert Pratt, Judy Morgan, Leslie Haynes, Cynthia L. Smith, Janan T. Eppig, Laura Reinholdt, Richard Francis, Linda Leatherbury, Madhavi K. Ganapathiraju, Kimimasa Tobita, Gregory J. Pazour & Cecilia W. Lo.
    Nature, 2015.
  8. Learning structure in gene expression data using deep architectures, with an application to gene clustering.
    Aman Gupta, Haohan Wang and Madhavi Ganapathiraju,
    IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2015.
  9. Towards extracting supporting information about predicted protein-protein interactions,
    Adam Roth and Madhavi Ganapathiraju
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015.
  10. Antiviral Activity of Human OASL Protein Is Mediated by Enhancing Signaling of the RIG-I RNA Sensor
    Zhu J, et al
    Immunity, Vol 40, Issue 6, 2014.
  11. Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions
    Usha Kuppuswamy, Seshan Ananthasubramanian1,Yanli Wang, Narayanaswamy Balakrishnan and Madhavi K Ganapathiraju
    Algorithms for Molecular Biology, Vol 9, Issue 10, 2014.
  12. Research prioritization through prediction of future impact on biomedical science: a position paper on inference analytics
    Madhavi Ganapathiraju and Naoki Orii
    GigaScience, Vol 2, Issue 11, 2013.
  13. Analysis of LMNB1 Duplications in Autosomal Dominant Leukodystrophy Provides Insights into Duplication Mechanisms and Allele-Specific Expression,
    Elisa Giorgio, Harshvardhan Rolyan, Laura Kropp, Anish Baswanth Chakka, Svetlana Yatsenko, Eleonora Di Gregorio, Daniela Lacerenza, Giovanna Vaula, Flavia Talarico, Paola Mandich, Camilo Toro, Eleonore Eymard Pierre, Pierre Labauge, Sabina Capellari, Pietro Cortelli, Filippo Pinto Vairo, Diego Miguel, Danielle Stubbolo, Lourenco Charles Marques, William Gahl, Odile BoespflugTanguy, Atle Melberg, Sharon HassinBaer, Oren S Cohen, Rastislav Pjontek, Armin Grau, Thomas Klopstock, , Brent Fogel, Inge Meijer, Guy Rouleau, JeanPierre L Bouchard, Madhavi Ganapathiraju, Adeline Vanderver, Niklas Dahl, Grace Hobson, , Alfredo Brusco, , Alessandro Brussino, Quasar Saleem Padiath,
    Human Mutation, 2013
  14. Oracle characterization for Active Learning for Protein-Protein Interaction Prediction,
    Seshan Ananthasubramanian, Jaime G. Carbonell and Madhavi Ganapathiraju,
    WCSB2013: 10th International Workshop on Computational and Systems Biology,Tampere, Finland, 2013.
  15. Wiki-Pi: A Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein Function,
    Naoki Orii and Madhavi Ganapathiraju,
    PLOS One, 7 (11), 2012.
  16. An efficient heuristic method for active feature acquisition and its application to protein-protein interaction prediction,
    Thahir Mohamed, Tarun Sharma and Madhavi Ganapathiraju,
    BMC Proceedings 2012, 6(Suppl 7):S2.
  17. Suite of tools for statistical n-gram language modeling for pattern mining in whole genome sequences’‘,
    Madhavi Ganapathiraju, Asia D. Mitchell, Mohamed Thahir, Kamiya Motwani, Seshan Ananthasubramanian,
    Journal of Bioinformatics and Computational Biology, Vol. 10, No. 6 (2012) 1250016 (22 pages).
  18. Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction,
    Seshan Ananthasubramanian, Rahul Metri, Ankur Khetan, Aman Gupta, Adam Handen, Nagasuma Chandra and Madhavi K Ganapathiraju,
    Microbial Informatics and Experimentation, 2012 2 (4).
  19. Applying N-Gram Language Modeling for Pattern Mining in Whole Genome Sequences,
    Madhavi Ganapathiraju, Mohamed Thahir, Asia D. Mitchell,
    LBM2011: Languages in Biology and Medicine, Singapore, 2011.
  20. N-gram analysis of 970 microbial organisms reveals presence of biological language models,
    Ulku Osmanbeyoglu and Madhavi Ganapathiraju,
    BMC Bioinformatics, 12(12), 2011.
  21. 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.
  22. Active Learning for Human Protein-Protein Interaction Prediction,
    Thahir P. Mohamed, Jaime G. Carbonell and Madhavi Ganapathiraju,
    BMC Bioinformatics, vol 11, Suppl 1, 2010.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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, pp. 300–321, 2006.
  28. 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.
  29. 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.
  30. Computational Biology and Language,
    Madhavi Ganapathiraju, N. Balakrishnan, Raj Reddy and Judith Klein-Seetharaman,
    Lecture Notes in Artificial Intelligence, LNCS/LNAI 3345, pp. 25-47, 2004.
  31. BLMT: Statistical sequence analysis using n-grams,
    Madhavi Ganapathiraju, Vijayalaxmi Manoharan and Judith Klein-Seetharaman,
    Applied Bioinformatics, vol. 3, issue 2, November 2004.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. TelMore: Morphological Generator for Telugu Nouns and Verbs SOURCECODE is on Github,
    Madhavi Ganapathiraju and Lori Levin,
    Proc. Second International Conference on Universal Digital Library, Vol Alexandria, Egypt, Nov 17-19, 2006
  42. 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.
  43. 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.
  44. OmSE: Tamil Search Engine,
    Anandh Jayaraman, Srinivas Sangani, Madhavi Ganapathiraju and N. Balakrishnan,
    Proc. Tamil Internet conference, pp 23-29, December 2004.
  45. Relevance of Cluster Size in MMR Summarization, Madhavi Ganapathiraju (Advisor: Jaime G. Carbonell), Report for 11-745, 2002.
  46. 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.
  47. 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

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