University of Pittsburgh, Vascular Medicine Institute, 2016-present
Performs bioinformatics analyses and simulations to identify potential mechanisms of pulmonary hypertension and pulmonary arterial hypertension. Extracts and de-identifies UPMC patient records for use in retrospective cohort analyses.
University of Pittsburgh Department of Biomedical Informatics, 2013-2016
Performed research in biomedical informatics and maintained lab websites. Duties included performing data mining using Python, maintaining current websites and databases (Wiki-Pi), developing and implementing online bioinformatics tools and algorithms (LENS), and writing journal articles.
National Computer Camps, 2007-Present
Rochester Institute of Technology Department of Bioinformatics, 2009-2013
Maintained Linux based systems for the bioinformatics department. Duties included maintaining firewalls, setting up user accounts, maintaining websites and forums for faculty, installing new hardware, performing backups, writing documentation, and installing bioinformatics pipelines.
University of Pittsburgh Department of Biomedical Informatics, 2007-2012
Performed research in bioinformatics. Duties included implementing bioinformatics algorithms in Perl and Python and developing an in-house database using MySQL.
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/S0219720016600027. PubMed PMID: 28073302.
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. PubMed PMID: 27336055; PubMed Central PMCID: PMC4898894.
Uppal R, Mandava G, Romagnoli KM, King AJ, Draper AJ, Handen AL, Fisher AM, Becich MJ, Dutta-Moscato J. How can we improve Science, Technology, Engineering, and Math education to encourage careers in Biomedical and Pathology Informatics? J Pathol Inform. 2016 Jan 29;7:2. doi: 10.4103/2153-3539.175375. PubMed PMID: 26955500; PubMed Central PMCID: PMC4763503.
Handen A, Ganapathiraju 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; PubMed Central PMCID: PMC4682415.
Handen A. Determining a new alignment scoring matrix for disordered proteins. RIT Scholar Works. 2013. Thesis. Rochester Institute of Technology. Accessed from http://scholarworks.rit.edu/theses/21
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; PubMed Central PMCID: PMC3353838.
Handen A, Ganapathiraju MK. LENS: web-based lens for enrichment and network studies of human proteins. 2015. Poster. The International Conference on Bioinformatics.
Handen A, Ganapthiraju MK. Web-based Protein-Interaction Network Analysis Pipeline. 2014. Poster. AMIA Joint Summits on Translational Science.