Publications for Madhavi Ganapathiraju, PhD

2017

Chattopadhyay A, Ganapathiraju MK. Demonstration Study: A Protocol to Combine Online Tools and Databases for Identifying Potentially Repurposable Drugs. Data 2017, 2, 15.

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. 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. Feb 24;3:11. doi: 10.1038/s41537-017-0010-z. eCollection 2017. PMID: 28560257. PMCID: PMC5441529.

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 Schizophrenia 2016, 2:16012. Link to Publication

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 Mar 25. doi: 10.1038/nature14269. [Epub ahead of print] PubMed PMID: 25807483.

Handen A, Ganapthiraju MK. LENS: web-based lens for enrichment and network studies of human proteins. BMC Medical Genomics. 2015;8(Suppl 4):S2. doi:10.1186/1755-8794-8-S4-S2.
 

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

2014

Jianzhong Zhu, Yugen Zhang, Arundhati Ghosh, Rolando A. Cuevas, Adriana Forero, Jayeeta Dhar, Mikkel Søes Ibsen, Jonathan Leo Schmid-Burgk, Tobias Schmidt, Madhavi K. Ganapathiraju, Takashi Fujita, Rune Hartmann, Sailen Barik, Veit Hornung, Carolyn B. Coyne, Saumendra N. Sarkar. Antiviral Activity of Human OASL Protein Is Mediated by Enhancing Signaling of the RIG-I RNA Sensor. Immunity. 2014 June 19; 40(6): 936–948.

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. PMID: 24708602

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. PMID: 24001106

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. Human mutation. 2013 May 3. PMID:23649844.

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

2012

Osmanbeyoglu HU, Ganapathiraju MK. N-gram analysis of 970 microbial organisms reveals presence of biological language models. BMC Bioinformatics. 2011; 12 (1):12. PMCID: PMC3027111. PMID: 21219653.

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 (in print).

Orii N, Ganapathiraju MK (2012) Wiki-Pi: a web resource to aid in the discovery of gene function via protein-protein interactions. PLoS ONE. 7(11): e49029. doi:10.1371/journal.pone.0049029

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

Thahir M, Sharma T, Ganapathiraju MK. An efficient heuristic method for active feature acquisition and its application to protein-protein interaction prediction. BMC Proceedings 2012, 6(Suppl 7):S2.

Orii N, Ganapathiraju MK (2012) 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.

Ganapathiraju MK, Mohamed T, Mitchell AD, Motwani K, Ananthasubramanian S. Suite of tools for statistical n-gram language modeling for pattern mining in whole genome sequences. Journal of Bioinformatics and Computational Biology. 2012; 10 (5). PMID: 22817111.

2011

Hatice Osmanbeyoglu and Madhavi Ganapathiraju, AMIA Translational Bioinformatics Summit, San Francisco, USA, March 7-9, 2011.

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.

2010

Mohamed TP, Carbonell JG, Ganapathiraju MK. Active learning for human protein-protein interaction prediction. BMC bioinformatics. 2010; 11:S57. PMCID: PMC3009530. PMID: 20122232.

Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK. Active machine learning for transmembrane helix prediction. BMC Bioinformatics. 2010; 11:S58. PMCID: PMC3009531. PMID: 20122233.

Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK. Active machine learning for transmembrane helix prediction. BMC Bioinformatics. 2010; 11:S58. PMCID: PMC3009531. PMID: 20122233.

2008

Madhavi Ganapathiraju, N. Balakrishnan, Raj Reddy and Judith Klein-Seetharaman, BMC Bioinformatics, vol 9, Suppl 1, 2008.

2007

Madhavi Ganapathiraju, Chritopher Jon Jursa, Hassan A. Karimi, and Judith Klein-Seetharaman, Bioinformatics, vol 23, issue 20, 2007.

A. Poddar, N. Chandra, Madhavi Ganapathiraju, K. Sekar, J. Klein-Seetharaman, R. Reddy and N. Balakrishnan, J. Biosciences, in print, 2007.

2006

"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.

"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.

"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.

"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.

"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.

"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.

2005

"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.

"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.

2004

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

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

"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.

"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.

"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.

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

2003

"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.

"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.

2002

"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.

"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.

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