Madhavi Ganapathiraju, PhD

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.

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.

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.

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.

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.

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