Adam Handen, MS

Experience & Past Employment

Computational and Database Specialist

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. Manages patient registries for departmental biobanks.

Graduate Fellow

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

Instructs campers ages 8-18 in Python, Basic, Java, and web development. Created a web development curriculum for HTML5, CSS3, and JavaScript. Created a curriculum for Python. Co-authored current website (

Systems Administrator

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.

Student Researcher

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.


MS Biomedical Informatics - 2016

University of Pittsburgh - Pittsburgh PA

MS Bioinformatics - 2014

Rochester Institute of Technology - Rochester NY

BS Bioinformatics - 2014

Rochester Institute of Technology - Rochester NY


Stearman RS, Bui QM, Speyer G, Handen A, Cornelius AR, Graham BB, Kim S, Mickler EA, Tuder RM, Chan SY, Geraci MW. Systems Analysis of the Human Pulmonary Arterial Hypertension Lung Transcriptome. Am J Respir Cell Mol Biol. 2018 Dec 18. doi: 10.1165/rcmb.2018-0368OC. [Epub ahead of print] PubMed PMID: 30562042.

Bertero T, Handen AL, Chan SY. Factors Associated with Heritable Pulmonary Arterial Hypertension Exert Convergent Actions on the miR-130/301-Vascular Matrix Feedback Loop. Int J Mol Sci. 2018 Aug 4;19(8). pii: E2289. doi: 10.3390/ijms19082289. PubMed PMID: 30081553; PubMed Central PMCID: PMC6121519.

Smith B, Genuardi MV, Koczo A, Zou RH, Thoma FW, Handen A, Craig E, Hogan CM, Girard T, Althouse AD, Chan SY. Atrial arrhythmias are associated with increased mortality in pulmonary arterial hypertension. Pulm Circ. 2018 Jul-Sep;8(3):2045894018790316. doi: 10.1177/2045894018790316. Epub 2018 Jul 3. PubMed PMID: 29969045; PubMed Central PMCID: PMC6058427.

Lam HC, Liu HJ, Baglini CV, Filippakis H, Alesi N, Nijmeh J, Du H, Lope AL, Cottrill KA, Handen A, Asara JM, Kwiatkowski DJ, Ben-Sahra I, Oldham WM, Chan SY, Henske EP. Rapamycin-induced miR-21 promotes mitochondrial homeostasis and adaptation in mTORC1 activated cells. Oncotarget. 2017 Aug 4;8(39):64714-64727. doi: 10.18632/oncotarget.19947. eCollection 2017 Sep 12. PubMed PMID: 29029388; PubMed Central PMCID: PMC5630288.

Lam HC, Baglini CV, Lope AL, Parkhitko AA, Liu HJ, Alesi N, Malinowska IA, Ebrahimi-Fakhari D, Saffari A, Yu JJ, Pereira A, Khabibullin D, Ogorek B, Nijmeh J, Kavanagh T, Handen A, Chan SY, Asara JM, Oldham WM, Diaz-Meco MT, Moscat J, Sahin M, Priolo C, Henske EP. p62/SQSTM1 Cooperates with Hyperactive mTORC1 to Regulate Glutathione Production, Maintain Mitochondrial Integrity, and Promote Tumorigenesis. Cancer Res. 2017 Jun 15;77(12):3255-3267. doi: 10.1158/0008-5472.CAN-16-2458. Epub 2017 May 16. PubMed PMID: 28512249; PubMed Central PMCID: PMC5485875.

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

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.

Presentations and Conferences

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.

References available upon request