Research Abstract:
The goal of translational research is to uncover perturbations in important pathways that lead to disease states so that therapeutic treatments may be designed. It is clear that most diseases are caused by a set of alterations at one or more levels of the genetic program. While there is a great need to integrate data derived from functional genomic experiments with that ascertained clinically from the evaluation and treatment of patients, there are no effective software, analytical, or visualization applications which can perform this overarching task. Thus, the long term goals of the Nagarajan lab are to conduct clinical and biomedical informatics research, to develop software applications which will simultaneously co-analyze and co-visualize a wide variety of functional genomics datasets, gene annotation, and clinicopathology data, and to utilize these heuristic algorithms in order to identify potential diagnostic markers and putative therapeutic targets required for effective clinical management of polyfactorial diseases. Therefore, the lab is involved in the following projects:
1) Developing gene relational network (GRN) construction tools that will predict GRNs using either a set of genes/proteins or primary profiling data sets (e.g. microarray expression profiling) and genome annotation information (e.g. pathway, protein-protein interaction, PubMed, and mRNA co-expression Gene Ontology databases).
2) Developing a comprehensive database of the electronic health record (EHR) at BJC HealthCare and Washington University in order to use the EHR for secondary research purposes.
3) Utilizing, extending, and developing novel natural language processing components to structure the EHR free text data and to identify semantic relationships between proteins using PubMed.
4) Leveraging bioinformatics and computational approaches to analyze (or co-analyze) microarray expression, copy number, and NextGen sequencing data sets.
Selected Publications:
Baloh RH, Strickland A, Ryu E, Le N, Fahrner T, Yang M, Nagarajan R, Milbrandt J. Congenital hypomyelinating neuropathy with lethal conduction failure in mice carrying the Egr2I268N mutation. J Neurosci 2009 Feb 25; 29(8):2312-21.
Gysbers M, Reichley R, Kilbridge PM, Noirot L, Nagarajan R, Dunagan WC, Bailey TC. Natural language processing to identify adverse drug events. AMIA Annul Symp Proc. 2008 Nov 6:961.
Deshmukh H, Yeh TH, Yu J, Sharma MK, Perry A, Leonard JR, Watson MA, Gutmann DH and Nagarajan R. High-resolution, dual-platform aCGH analysis reveals frequent HIPK2 amplification and increased expression in pilocytic astrocytomas. Oncogene 2008 Apr 14 (Epub ahead of print).
Chang LW, Payton JE, Yuan W, Ley TJ, Nagarajan R and Stormo GD. Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. Genome Biol 2008 9(2): p. R38.
Chang LW, Fontaine BR, Stormo GD, and Nagarajan R. PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. Nucleic Acids Res, 2007. 35: W238-244.
Last Updated: 09/03/2009 |