Journal

  1. Kalyani B. Karunakaran, N. Balakrishnan and Madhavi K. Ganapathiraju
    Novel Protein-Protein Interactions Highlighting the Crosstalk between Hypoplastic Left Heart Syndrome, Ciliopathies and Neurodevelopmental Delays (2022)

    Genes, 13 (4), 627, Apr 2022
  2. Karunakaran KB, Balakrishnan N, Ganapathiraju MK
    Interactome of SARS-CoV-2 modulated host proteins with computationally predicted PPIs: Insights from illustrative translational systems biology studies (2022)

    Frontiers in Systems Biology, Section on Integrated Systems Immunology, in Press, Feb 2022.
  3. Dunham B, Ganapathiraju MK
    Benchmark Evaluation of Protein–Protein Interaction Prediction Algorithms (2022)

    Molecules, 27 (41), Jan 2022.
  4. Becker-Krail DD, Parekh PK, Ketchesin KD, Yamaguchi S, Yoshino J, Hildebrand MA, Dunham B, Ganapathiraiu MK, Logan RW, McClung CA
    Circadian Transcription Factor NPAS2 and the NAD+‐Dependent Deacetylase SIRT1 Interact in the Mouse Nucleus Accumbens and Regulate Reward, (2022)

    European Journal of Neuroscience, 55( 3), 675– 693, 2022.
  5. Karunakaran KB, Yanamala N, Boyce G, Becich MJ, Ganapathiraju MK
    Malignant Pleural Mesothelioma Interactome with 364 Novel Protein-Protein Interactions (2021)

    Cancers, 13 (7), 1660 (2021).
  6. Madhavi K Ganapathiraju, Sandeep Subramanian, Srilakshmi Chaparala and Kalyani B Karunakaran
    A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes (2020)

    Human Genome Variation, 7, 40 (2020).
  7. Karunakaran, K.B., Chaparala, S., Lo, C.W. et al.
    Cilia interactome with predicted protein–protein interactions reveals connections to Alzheimer’s disease, aging and other neuropsychiatric processes (2020)

    Scientific Reports, 10, 15629 (2020).
  8. Karunakaran, KB, Chaparala S, and Ganapathiraju MK
    Potentially repurposable drugs for schizophrenia identified from its interactome (2019)

    Scientific Reports, 9 (1), 1-14, Sept 2019.
  9. Sundaravadivel, P, Kougianos E, Mohanty SP and Ganapathiraju MK
    Everything You Wanted to Know about Smart Health Care (2018)

    IEEE Consumer Electronics Magazine, 7(1), pp 18-28, Jan 2018.
  10. Roth A, Subramanian S, Ganapathiraju MK.
    Towards extracting supporting information about predicted protein-protein interactions (2018)

    IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15(4):1239-46, 2018.
  11. Subramanian S and Ganapathiraju MK
    Antibody Exchange: Information extraction of biological antibody donation and a web-portal to connect donors and seekers (2017)

    Data, 2(4), pp 38, Dec 2017.
  12. Liu X, Yagi H, …, Ganapathiraju MK, …, Lo CW
    The complex genetics of hypoplastic left heart syndrome (2017)

    Nature Genetics. 2017 Jul;49(7):1152-1159. doi: 10.1038/ng.3870 PMID: 28530678.
  13. Malavia TA, …, *Ganapathiraju MK, Nimgaonkar VL
    Generating testable hypotheses for schizophrenia and rheumatoid arthritis pathogenesis by integrating epidemiological, genomic and protein interaction data (2017)

    npj Schizophrenia, Feb 24;3:11. doi: 10.1038/s41537-017-0010-z. 2017. PMCID: PMC5441529.
  14. Chattopadhyay A, Ganapathiraju MK
    Demonstration Study: A Protocol to Combine Online Tools and Databases for Identifying Potentially Repurposable Drugs (2017)

    Data, May 24; 2(2). 2017
  15. Subramanian S, Chaparala S, Avali V, Ganapathiraju MK.
    A pilot study on the prevalence of DNA palindromes in breast cancer genomes (2016)

    BMC Medical Genomics. Vol: 9 Suppl: 3 Article No: 73. Dec 5 2016. PMCID: PMC5260791.
  16. Embar. V, Handen A, Ganapathiraju MK.
    Is the average shortest path length of gene set a reflection of their biological relatedness? (2016)

    Journal of Bioinformatics and Computational Biology 14:6, SI. Dec 2016. PMID: 28073302.
  17. Ganapathiraju MK, Mohamed TP, Handen A, S.N. Sarkar, R. A. Sweet, V. L. Nimgaonkar, C. E. Loscher, E. M. Bauer, and S. Chaparala.
    Schizophrenia interactome with 504 novel protein-protein interactions (2016)

    npj Schizophrenia. 2: p. 16012, February 2016. PMCID: PMC4898894.
  18. Ganapathiraju MK, Karunakaran KB, Correa-Menéndez J
    Predicted protein interactions of IFITMs may shed light on mechanisms of Zika virus-induced microcephaly and host invasion (2016)

    F1000Research. 2016;5.
  19. Handen A and Ganapathiraju MK.
    LENS: Web-based Lens for Enrichment and Network Studies of Human Proteins (2015)

    BMC Medical Genomics, Volume 8, Suppl 4, S2. PMCID: PMC4682415.
  20. Li Y, Klena N, Gabriel G, Liu X, Lemke K, Chen Y, Kim A, Chatterjee B, Damerla R, Chang C, Yagi H, Shan Y, Agustin JS, Mohamed TP, Anderton S, Lawhead C, Vescovi A, Weeks D, Pratt H, Morgan J, Haynes L, Smith C, Eppig J, Reinholdt L, Leatherbury L, Tobita K, Francis R, Ganapathiraju MK, Pazour G, Lo CW.
    Global genetic analysis in mice unveils central role for cilia in congenital heart disease (2015)

    Nature. 521(7553):520-4. PMCID: PMC4617540.
  21. Zhu J, Zhang Y, Ghosh A, Cuevas RA, Forero A, Dhar J, Ibsen MS, Schmid-Burgk JL, Schmidt T, Ganapathiraju MK, Fujita T, Hartmann R, Barik S, Hornung V, Coyne CB, Sarkar SN.
    Antiviral activity of human OASL protein is mediated by enhancing signaling of the RIG-I RNA sensor (2014)

    Immunity. 40 (6):936-48. PMCID: PMC4101812.
  22. Kuppuswamy U, Ananthasubramanian S, Yanli Wang, Balakrishnan N, Ganapathiraju MK.
    Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions (2014)

    Algorithms for Molecular Biology. 9 (1):10. PMID: 24708602, PMCID: PMC4124845.
  23. Ganapathiraju MK, Orii N.
    Research prioritization through prediction of future impact on biomedical science: a position paper on inference-analytics (2013)

    GigaScience. 2013 Aug 30; 2 (11). PMID: 24001106, PMCID: PMC3844564.
  24. Giorgio E, Rolyan H, …, Ganapathiraju MK, …, Padiath QS.
    Analysis of LMNB1 Duplications in Autosomal Dominant Leukodystrophy Provides Insights into Duplication Mechanisms and Allele-Specific Expression (2013)

    Human Mutation. 2013 May 3. PMID: 23649844, PMCID: PMC3714349.
  25. Ganapathiraju MK, Mitchell AD, Mohamed TP, Motwani K, Ananthasubramanian S.
    Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences (2012)

    Journal of Bioinformatics and Computational Biology. 10 (6):1250016.
  26. Mohamed TP, Sharma T, Ganapathiraju MK.
    An efficient heuristic method for active feature acquisition and its application to protein-protein interaction prediction (2012)

    BMC Proceedings. 6:S2. PMID: 23173746, PMCID: PMC3504800.
  27. Orii N, Ganapathiraju MK.
    Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function (2012)

    PloS One. 7 (11):e49029. PMID: 23209562, PMCID: PMC3509123.
  28. Ananthasubramanian S, Metri R, Khetan A, Gupta A, Handen A, Chandra N, Ganapathiraju MK.
    Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction (2012)

    Microbial Informatics and Experimentation. 2:4. PMID: 22587966, PMCID: PMC3353838.
  29. Osmanbeyoglu HU, Ganapathiraju MK.
    N-gram analysis of 970 microbial organisms reveals presence of biological language models (2011)

    BMC Bioinformatics. 12 (1):12. PMID: 21219653, PMCID: PMC3027111.
  30. Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK.
    Active machine learning for transmembrane helix prediction (2010)

    BMC Bioinformatics. 11:S58. PMID: 20122233, PMCID: PMC3009531.
  31. Mohamed TP, Carbonell JG, Ganapathiraju MK.
    Active learning for human protein-protein interaction prediction (2010)

    BMC Bioinformatics.11:S57. PMID: 20122232, PMCID: PMC3009530.
  32. Ganapathiraju MK, Balakrishnan N, Reddy R, Klein-Seetharaman J.
    Transmembrane helix prediction using amino acid property features and latent semantic analysis (2008)

    BMC Bioinformatics. 9:S4. PMID: 1831585, PMCID: PMC2259405.
  33. Ganapathiraju MK, Jursa CJ, Karimi HA, Klein-Seetharaman J.
    TMpro Web Server and Web Service: Transmembrane Helix Prediction Through Amino Acid Property Analysis (2007)

    Bioinformatics. 23 (20):2795-6. PMID: 17724062, PMCID: PMC3263380.
  34. Poddar A, Chandra N, Ganapathiraju MK, Sekar K, Klein-Seetharaman J, Reddy R, Balakrishnan N.
    Evolutionary insights from suffix array-based genome sequence analysis (2007)

    Journal of Biosciences. 32 (5):871-81. PMID: 17914229.
  35. Iannaccone A, Man D, …, Ganapathiraju MK, …, Klein-Seetharaman J.
    Retinitis pigmentosa associated with rhodopsin mutations: Correlation between phenotypic variability and molecular effects (2006)

    Vision Research. 46 (27):4556-67. PMID: 17014888.
  36. Balakrishnan N, Reddy R, Ganapathiraju MK, Ambati V.
    Digital Library of India: A testbed for Indian language research (2006)

    IEEE Technical Committee on Digital Libraries Bulletin. 3 (1).
  37. Tastan O, Yu E, Ganapathiraju MK, Aref A, Rader AJ, Klein-Seetharaman J.
    Comparison of Stability Predictions and Simulated Unfolding of Rhodopsin Structures (2006)

    Photochemistry and Photobiology. 83 (2):351-62. PMID: 17576347.
  38. Ganapathiraju MK, Manoharan V, Reddy R, Klein-Seetharaman J.
    Collaborative Discovery and Biological Language Modeling Interface (2006)

    Lecture Notes in Artificial Intelligence, LNCS/LNAI.3864:300-321.
  39. Ganapathiraju MK, Balakrishnan N, Reddy R, Klein-Seetharaman J.
    Computational Biology and Language (2005)

    Lecture Notes in Artificial Intelligence, LNCS/LNAI. 3345:25-47.
  40. Ganapathiraju MK, Balakrishnan M, Balakrishnan N, Reddy R.
    Om: One tool for many (Indian) languages (2005)

    Journal of Zhejiang University SCIENCE. 6 (11):1348-1353.
  41. Ganapathiraju M, Manoharan V, Klein-Seetharaman J.
    BLMT: statistical sequence analysis using N-grams (2004)

    Applied Bioinformatics. 3:193-200. PMID: 15693744.
  42. Ganapathiraju MK, Klein-Seetharaman J, Balakrishnan N, Reddy R.
    Characterization of Protein Secondary Structure using Latent Semantic Analysis (2004)

    IEEE Signal Processing Magazine. 21 (3):78-87.

Preprints

  1. Kalyani B. Karunakaran, N. Balakrishnan and Madhavi K. Ganapathiraju
    GPX4-associated Sedaghatian Type Spondylometaphyseal Dysplasia: A Protein Interactome Perspective (2022)

    Preprint available at bioRxiv
  2. Karunakaran, K.B., Ganapathiraju, M.K., Jain, S., Brahmachari, S., Balakrishnan, N.
    Drug Contraindications in Comorbid Diseases: a Protein Interactome Perspective (2022)

    Preprint available at bioRxiv
  3. Kalyani B. Karunakaran and Madhavi K. Ganapathiraju et al
    Malignant Peritoneal Mesothelioma Interactome with 417 Novel Protein-Protein Interactions (2021)

    Preprint available at Research Square
  4. Haohan Wang and Madhavi K. Ganapathiraju
    Evaluation of Protein-protein Interaction Predictors with Noisy Partially Labeled Data Sets (2015)

    Preprint available at arXiv.
  5. Haohan Wang and Madhavi K. Ganapathiraju
    Evaluating Protein-protein Interaction Predictors with a Novel 3-Dimensional Metric (2015)

    Preprint available at arXiv.
  6. Madhavi K Ganapathiraju
    Relevance of Cluster size in MMR based Summarizer: A Report (2002)

    Report available here.

Conference

  1. Rachakonda L, Kothari A, Mohanty SP, Kougianos E, Ganapathiraju MK.
    Stress-Log: An IoT-based Smart System to Monitor Stress-Eating (2019)

    IEEE International Conference on Consumer Electronics (ICCE). 2019 Jan 11 (pp. 1-6). IEEE.
  2. Rachakonda L, Mohanty SP, Kougianos E, Karunakaran K, Ganapathiraju MK.
    Smart-Pillow: An IoT based Device for Stress Detection Considering Sleeping Habits (2018)

    IEEE International Symposium on Smart Electronic Systems Dec 17 (pp. 161-166).
  3. Sundaravadivel P, Mohanty SP, Kougianos E, Yanambaka P, Ganapathiraju MK.
    Smart-Walk: An Intelligent Physiological Monitoring System for Smart Families (2018)

    IEEE International Conference on Consumer Electronics (ICCE), Las Vegas NV, 2018
  4. Sundaravadivel P, Kesavan K, Kesavan L, Mohanty SP, Kougianos E, Ganapathiraju MK.
    SmartLog: An Automated, Predictive Nutrition Monitoring System for Infants Through IoT (2018)

    IEEE International Conference on Consumer Electronics (ICCE), Las Vegas NV, 2018
  5. Aman Gupta, Haohan Wang and Ganapathiraju MK
    Learning structure in gene expression data using deep architectures, with an application to gene clustering (2015)

    IEEE Workshop on Biomedical Visual Search and Deep Learning, 2015.
  6. Ananthasubramanian S, Carbonell JG, Ganapathiraju MK.
    Oracle Characterization for Active Learning for Protein-Protein Interaction Prediction (2011)

    WCSB 2013: 10th International Conference on Computational Biology proceedings; 2013.
  7. Ganapathiraju MK, Mohamed TP, Mitchell AD.
    Applying N-Gram Language Modeling for Pattern Mining in Whole Genome Sequences (2011)

    Languages in Biology and Medicine; Singapore.
  8. Osmanbeyloglu HU, Ganapathiraju MK.
    Rapid Deployment of Viral-Human Interactome Prediction for New Viruses. (2011)

    AMIA Translational Bioinformatics Summit; March, 7-11, 2011 San Francisco, CA, USA.
  9. Balajapally P, Pydimarri P, Ganapathiraju MK, Balakrishnan N, Reddy R.
    Multilingual Book Reader: Transliteration, Word-to-Word Translation and Full-text Translation (2006)

    VALA 2006: 13th Biennial Conference and Exhibition Conference of Victorian Association for Library Automation; Melbourne, Australia 2006.
  10. Ganapathiraju MK, Levin L.
    TelMore: Morphological Generator for Telugu Nouns and Verbs (2006)

    Proc. Second International Conference on Universal Digital Library. Alexandria, Egypt.
  11. Manoharan V, Ganapathiraju M, Klein-Seetharaman J.
    BLMT Web Server: Interactive Language Technologies for Analogous Biological Data (2005)

    Workshop on Ambient Intelligence and Everyday Life; San Sebastian, Spain.
  12. Balakrishnan N, Reddy R, Ganapathiraju MK, Gogineni H.
    Million Books to Web: Technological Challenges and Research Issues (2004)

    Proc. Tamil Internet Conference; Singapore 2004. p.227-242.
  13. Jayaraman A, Sangani S, Ganapathiraju M, Balakrishnan N.
    OmSE: Tamil Search Engine (2004)

    Proc. Tamil Internet conference; Singapore, p.23-29.
  14. Ganapathiraju MK, Weisser D, Reddy R, Klein-Seetharaman J.
    Yule value tables from Protein Datasets of different categories: emphasis on membrane proteins (2004)

    Proc.SCI2004; Orlando, Florida, USA.
  15. Sivaraman B, Ganapathiraju MK, Klein-Seetharaman J, Balakrishnan N, Reddy R.
    Extensions to Biological Language Modeling Toolkit (BLMT) (2003)

    Biological Language Conference; Pittsburgh, PA.
  16. Ganapathiraju MK, Balakrishnan N, Reddy R.
    Improving Recognition Accuracy on CVSD speech in mismatched conditions (2003)

    WSEAS Transactions on Computers. 2 (4).
  17. Ganapathiraju MK, Weisser D, Klein-Seetharaman J, Rosenfeld R, Carbonell JG, Reddy R.
    Comparative N-Gram Analysis of Whole-Genome Sequences (2002)

    HLT2001: Human Language Technologies Conference; San Diego, CA.