Publications for Madhavi Ganapathiraju, PhD

2018

Roth A, Subramanian S, Ganapathiraju MK. Towards extracting supporting information about predicted protein-protein interactions. IEEE/ACM Trans Comput Biol Bioinform. 2018 Jul-Aug;15(4):1239-1246. doi: 10.1109/TCBB.2015.2505278. Epub 2015 Dec 7. PubMed PMID: 26672046.

Sundaravadivel P, Mohanty SP, Kougianos E, Yanambaka VP, Ganapathiraju MK. Smart-walk: An intelligent physiological monitoring system for smart families. 2018 IEEE International Conference on Consumer Electronics (ICCE). 2018 Jan 12-14, Las Vegas, NV. 1-4. doi: 10.1109/ICCE.2018.8326065.

Sundaravadivel P, Kesavan K, Kesavan L, Mohanty SP, Kougianos E, Ganapathiraju M. Smart-log: An automated, predictive nutrition monitoring system for infants through the IoT. 2018 IEEE International Conference on Consumer Electronics (ICCE). 2018 Jan 12-14, Las Vegas, NV. 1-4. doi: 10.1109/ICCE.2018.8326068.

2017

Chattopadhyay A, Ganapathiraju MK. Demonstration Study: A Protocol to Combine Online Tools and Databases for Identifying Potentially Repurposable Drugs. Data. 2017 May 24;2(2).

Liu X, Yagi H, Saeed S, Bais AS, Gabriel GC, Chen Z, Peterson KA, Li Y, Schwartz MC, Reynolds WT, Saydmohammed M, Gibbs B, Wu Y, Devine W, Chatterjee B, Klena NT, Kostka D, de Mesy Bentley KL, Ganapathiraju MK, Dexheimer P, Leatherbury L, Khalifa O, Bhagat A, Zahid M, Pu W, Watkins S, Grossfeld P, Murray SA, Porter GA Jr, Tsang M, Martin LJ, Benson DW, Aronow BJ, Lo CW. The complex genetics of hypoplastic left heart syndrome. Nat Genet. 2017 Jul;49(7):1152-1159. doi: 10.1038/ng.3870. Epub 2017 May 22. PubMed PMID: 28530678.

Malavia TA, Chaparala S, Wood J, Chowdari K, Prasad KM, McClain L, Jegga AG, Ganapathiraju MK, Nimgaonkar VL. Generating Testable Hypotheses for Schizophrenia and Rheumatoid Arthritis Pathogenesis by Integrating Epidemiological, Genomic and Protein Interaction Data. NPJ Schizophr. 2017 Feb 24;3:11. doi: 10.1038/s41537-017-0010-z. eCollection 2017. PubMed PMID: 28560257. PMCID: PMC5441529.

Subramanian S, Ganapathiraju MK. Antibody Exchange: Information extraction of biological antibody donation and a web-portal to find donors and seekers. Data (Basel). 2017 Dec;2(4). pii: 38. doi: 10.3390/data2040038. Epub 2017 Nov 21. PubMed PMID: 30498741. PMCID: PMC6258257. 

2016

Ganapathiraju MK, Thahir M, Handen A, Sarkar SN, Sweet RA, Nimgaonkar VL, Loscher CE, Bauer EM, Chaparala S: Schizophrenia interactome with 504 novel protein–protein interactions. NPJ Schizophr. 2016 Apr 27;2:16012. doi: 10.1038/npjschz.2016.12. eCollection 2016. PubMed PMID: 27336055. PMCID: PMC4898894.

Subramanian S, Chaparala S, Avali V, Ganapathiraju MK. A pilot study on the prevalence of DNA palindromes in breast cancer genomes. BMC Med Genomics. 2016 Dec;9(Suppl 3):73. doi: 10.1186/s12920-016-0232-3. PubMed PMID 28117658. PMCID: PMC5260791.

Embar V, Handen A, Ganapathiraju MK. Is the average shortest path length of gene set a reflection of their biological relatedness? J Bioinform Comput Biol. 2016 Dec;14(6):1660002. doi: 10.1142/S0129720016600027. PubMed PMID: 28073302. PMCID: PMC5726383.

Ganapathiraju MK, Karunakaran KB, Correa-Menendez J. Predicted protein interactions of IFITMs may shed light on mechanisms of Zika virus-induced microcephaly and host invasion. Version 2. F1000 Res. 2016 Aug 5 [revised 2017 Nov 21];5:1919. doi: 10.12688/f1000research9364.2. eCollection 2016. PubMed PMID: 2933329. PMCID: PMC5747333.

Ganapathiraju M, Chaparala S. Schizophrenia interactome: fully-labeled interactome network. NPJ Schizophr. 2016 Aug 24;2:16025. doi: 10.1038/npjschz.2016.25. PubMed PMID: 27602386. PMCID: PMC5007984.

2015

Li Y, Klena NT, Gabriel GC, Liu X, Kim AJ, Lemke K, Chen Y, Chatterjee B, Devine W, Damerla RR, Chang C, Yagi H, San Agustin JT, Thahir M, Anderton S, Lawhead C, Vescovi A, Pratt H, Morgan J, Haynes L, Smith CL, Eppig JT, Reinholdt L, Francis R, Leatherbury L, Ganapathiraju MK, Tobita K, Pazour GJ, Lo CW. Global genetic analysis in mice unveils central role for cilia in congenital heart disease. Nature. 2015 May 28;521(7553):520-4. doi: 10.1038/nature14269. Epub 2015 Mar 25.  PubMed PMID: 25807483. PMCID: PMC4617540.

Handen A, Ganapthiraju MK. LENS: web-based lens for enrichment and network studies of human proteins. BMC Med Genomics. 2015;8(Suppl 4):S2. doi:10.1186/1755-8794-8-S4-S2. Epub 2015 Dec 9. PubMed PMID: 26680011. PMCID: PMC4682415.

Gupta A, Wang H, Ganapathiraju M. Learning structure in gene expression data using deep architectures, with an application to gene clustering. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Washington, DC pp. 1328-1335. doi: 10.1109/BIBM.2015.7359871.

2014

Kuppuswamy U, Ananthasubramanian S, Wang Y, Balakrishnan N, Ganapathiraju MK. Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions. Algorithms Mol Biol. 2014 Apr 3;9(1):10. doi: 10.1186/1748-7188-9-10. PubMed PMID: 24708602. PMCID: PMC4124845.

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. Immunity. 2014 Jun 19; 40(6): 936–48. doi: 10.1016/j.immuni.2014.05.007. Epub 2014 Jun 12. PubMed PMID: 24931123. PMCID: PMC4101812.

2013

Ganapathiraju MK, Orii N. Research prioritization through prediction of future impact on biomedical science: a position paper on inference-analytics. Gigascience. 2013 Aug 30;2(1):11. doi: 10.1186/2047-217X-2-11. PubMed PMID: 24001106. PMCID: PMC3844564. 

Giorgio E, Rolyan H, Kropp L, Chakka AB, Yatsenko S, Gregorio ED, Lacerenza D, Vaula G, Talarico F, Mandich P, Toro C, Pierre EE, Labauge P, Capellari S, Cortelli P, Vairo FP, Miguel D, Stubbolo D, Marques LC, Gahl W, Boespflug-Tanguy O, Melberg A, Hassin-Baer S, Cohen OS, Pjontek R, Grau A, Klopstock T, Fogel B, Meijer I, Rouleau G, Bouchard JP, Ganapathiraju M, Vanderver A, Dahl N, Hobson G, Brusco A, Brussino A, Padiath QS. Analysis of LMNB1 Duplications in Autosomal Dominant Leukodystrophy Provides Insights into Duplication Mechanisms and Allele-Specific Expression. Hum Mutat. 2013 Aug;34(8):1160-71. doi: 10.1002/humu.22348. Epub 2013 May 28. Erratum in: Hum Mutat. 2014 Jan;35(1):149. PubMed PMID: 23649844. PMCID: PMC3714349.

Ananthasubramanian S, Carbonell JG, Ganapathiraju MK. Oracle Characterization for Active Learning for Protein-Protein Interaction Prediction. WCSB 2013; Finland. 2013.

2012

Ananthasubramanian S, Metri R, Khetan A, Gupta A, Handen A, Chandra N, Ganapathiraju M. Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction. Microb Inform Exp. 2012 Mar 21;2:4. doi: 10.1186/2042-5783-2-4. PubMed PMID: 22587966. PMCID: PMC3353838.

Orii N, Ganapathiraju MK. Wiki-Pi: a web server of annotated human protein-protein interactions to aid in discovery of protein function. PLoS ONE. 7(11): e49029. doi:10.1371/journal.pone.0049029. Epub 2012 Nov 28. PubMed PMID: 23209562. PMCID: PMC3509123.

Thahir M, Sharma T, Ganapathiraju MK. Active feature acquisition for protein-protein interaction prediction. BMC Bioinformatics. 2012; 6:S2.

Thahir M, Sharma T, Ganapathiraju MK. An efficient heuristic method for active feature acquisition and its application to protein-protein interaction prediction. BMC Proc. 2012 Nov 13;6 Suppl 7:S2. doi: 10.1186/1753-6561-6-S7-S2. Epub 2012 Nov 13. PubMed PMID: 23173746. PMCID: PMC3504800.

Orii N, Ganapathiraju MK. Wiki-Pi: A Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein Function. PLoS ONE. 2012 Nov 28;7(11): e49029. doi: 10.1371/journal.pone.0049029. Epub 2012 Nov 28. PubMed PMID: 23209562. PMCID: PMC3509123.

Ganapathiraju MK, Mitchell AD, Thahir M, Motwani K, Ananthasubramanian S. Suite of tools for statistical n-gram language modeling for pattern mining in whole genome sequences. J Bioinform Comput Biol. 2012 Dec;10(6):1250016. doi: 10.1142/S0219720012500163. Epub 2012 Jul 22. PubMed PMID: 22817111.

2011

Osmanbeyoglu H, Ganapathiraju M. Rapid Deployment of Viral-Human Interactome Prediction for New Viruses. AMIA Translational Bioinformatics Summit, San Francisco, USA, March 7-9, 2011.

Ganapathiraju M, Thahir M, Mitchell AD. Applying N-Gram Language Modeling for Pattern Mining in Whole Genome Sequences. LBM2011: Languages in Biology and Medicine, Singapore, 2011.

2010

Mohamed TP, Carbonell JG, Ganapathiraju MK. Active learning for human protein-protein interaction prediction. BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S57. doi: 10.1186/1471-2105-1-S1-S57. PubMed PMID: 20122232. PMCID: PMC3009530.

Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK. Active machine learning for transmembrane helix prediction. BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S58. doi: 10.1186/1471-2105-11-S1-S58. PubMed PMID: 20122233. PMCID: PMC3009531.

2008

Ganapathiraju M, Balakrishnan N, Reddy R, Klein-Seetharaman J. Transmembrane helix prediction using amino acid properties and latent semantic analysis. BMC Bioinformatics. 2008;9 Suppl 1:S4. doi: 10.1186/1471-2105-9-S1-S4. PubMed PMID: 18315857. PMCID: PMC2259405.

2007

Poddar A, Chandra N, Ganapathiraju M, Sekar K, Klein-Seetharaman J, Reddy R, Balakrishnan N. Evolutionary insights from suffix array-based genome sequence analysis. J. Biosci. 2007 Aug;32(5):871-81. PubMed PMID: 17914229.

Tastan O, Yu E, Ganapathiraju M, Aref A, Rader AJ, Klein-Seetharaman J. Comparison of stability predictions and simulated unfolding of rhodopsin structures. Photochem Photobiol. 2007 Mar-Apr;83(2):351-62. doi: 10.1562/2006-06-20-RA-942. PubMed PMID: 17576347.

Ganapathiraju M, Jursa CJ, Karimi HA, Klein-Seetharaman J. TMpro web server and web service: transmembrane helix production through amino acid property analysis. Bioinformatics. 2007 Oct 15;23(20):2795-6. Epub 2007 Aug 27. doi: 10.1093/bioinformatics/btm398. PubMed PMID: 17724062. PMCID: PMC3263380.

2006

Ganapathiraju M, Manoharan V, Reddy R, Judith Klein-Seetharaman J. Collaborative Discovery and Biological Language Modeling Interface. Lecture Notes in Artificial Intelligence, LNCS/LNAI. 2006. 3864.

Iannaccone A, Man D, Waseem N, Jennings BJ, Ganapathiraju M, Gallaher K, Reese E, Bhattacharya SS, Klein-Seetharaman J. Retinitis pigmentosa associated with rhodopsin mutations: Correlation between phenotypic variability and molecular effects. Vision Res. 2006 Dec;46(27):4556-67. Epub 2006 Oct 2. doi: 10.1016/j.visres.2006.08.018. PubMed PMID: 17014888.

Balakrishnan N, Reddy R, Ganapathiraju M, Ambati V. Digital Library of India: a testbed for Indian language research. IEEE Technical Committee on Digital Libraries (TCDL) Bulletin. 2006;3(1).

Ganapathiraju M, Levin L.TelMore: Morphological Generator for Telugu Nouns and Verbs. Proc. Second International Conference on Universal Digital Library, Vol Alexandria, Egypt, Nov 17-19, 2006.

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

2005

Manoharan V, Ganapathariju M, Klein-Seetharaman J. BLMT Web Server: Interactive Language Technologies for Analogous Biological Data. Workshop on Ambient Intelligence and (Everyday) Life, Donostia, San-Sebastian, Spain, 2005.

Ganapathiraju M, Balakrishnan M, Balakrishnan N, Reddy R. Om: One tool for many (Indian) languages. Journal of Zhejiang University SCIENCE. 2005 Oct;6A(11):1348-1353.

2004

Ganapathiraju M,  Balakrishnan N, Reddy R, Klein-Seetharaman J. Computational Biology and Language. Lecture Notes in Artificial Intelligence, LNCS/LNAI. 2004. 3345.

Ganapathiraju M, Manoharan V, Klein-Seetharaman J. BLMT: Statistical sequence analysis using n-grams. J Appl Bioinformatics. 2004;3(2-3):193-200. doi: 10.2165/00822942-200403020-00013. PubMed PMID: 15693744.

Ganapathiraju M, Klein-Seetharaman J, Balakrishnan N, Reddy R. Characterization of Protein Secondary Structure using Latent Semantic Analysis. IEEE Signal Processing Magazine. 2004 May;21(3):78-87. doi: 10.1109/MSP.2004.1296545. 

Ganapathiraju M, Weisser D, Reddy R, Klein-Seetharaman J. Yule value tables from Protein Datasets of different categories: emphasis on membrane proteins. Proc. SCI2004, Florida, USA, 2004.

Balakrishnan N, Reddy R, Ganapathiraju M, Gogineni H. Million Books to Web: Technological Challenges and Research Issues. Proc. Tamil Internet conference, pp 227-242, December 2004.

Jayaraman A, Sangani S, Ganapathiraju M, Balakrishnan N. OmSE: Tamil Search Engine. Proc. Tamil Internet conference, pp 23-29, December 2004.

2003

Sivaraman B, Ganapathiraju M, Klein-Seetharaman J, Balakrishnan N, Reddy R. Extensions to Biological Language Modeling Toolkit (BLMT). BLC2003: Biological Language Conference, Pittsburgh USA, November 2003.

Ganapathiraju M, Balakrishnan N, Reddy R. Improving Recognition Accuracy on CVSD speech in mismatched conditions. WSEAS Transactions on Computers, Vol 2, Issue 4, October 2003.

2002

Ganapathiraju M, Weisser D, Klein-Seetharaman J, Rosenfeld R, Carbonell J, Reddy R. Comparative n-gram analysis of whole-genome sequences.  HLT'02: Human Language Technologies Conference, San Diego, March, 2002.

Ganapathiraju M, Klein-Seetharaman J, Rosenfeld R, Carbonell J, Reddy R. Rare and frequent amino acid n-grams in whole-genome protein sequences. RECOMB'02: The Sixth Annual International Conference on Research in Computational Molecular Biology, Washington DC, USA, April, 2002.

Sundaravadivel P, Kougianos E, Mohanty SP, Ganapathiraju MK. Everything You Wanted to Know about Smart Health Care: Evaluating the Different Technologies and Components of the Internet of Things for Better Health. IEEE Consumer Electronics Mag. 2018 Jan;7(1):18-28. doi: 10.1109/MCE.2017.2755378.

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