Andrew E. Bruno

Senior Programmer Analyst

Education

• B.S. Computer Science, University at Buffalo, June 2003
• M.S. Bioinformatics and Biostatistics, University at Buffalo, February 2013

Teaching

• BCH519 - Introduction to Bioinformatics and Computational Biology

Software

• MARCO - MAchine Recognition of Crystallization Outcomes
• Coldfront - HPC Resource Allocation System
• TREAT - Trypanosome RNA Editing Alignment Tool
• mokey - FreeIPA self-service account managment tool
• iquota - Linux CLI tools for Isilon OneFS SmartQuota reporting
• xtuition - An expert crystallization knowledge system
• Cockatoo - A similarity metric for macromolecular crystallization conditions
• FUSIM - a software tool for simulating fusion transcripts
• miRdSNP - a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes
• UBMoD - An open source data warehouse and web portal for mining statistical data from resource managers (TORQUE and OpenPBS) in high-performance computing environments.

Publications

1. Andrew E. Bruno, Patrick Charbonneau, Janet Newman, Edward H. Snell, David R. So, Vincent Vanhoucke, Christopher J. Watkins, Shawn Williams, Julie Wilson. Classification of crystallization outcomes using deep convolutional neural networks. PLoS ONE, 2018. doi:10.1371/journal.pone.0198883
2. Rachel M. Simpson, Andrew E. Bruno, Runpu Chen, Kaylen Lott, Brianna L. Tylec, Jonathan E. Bard, Yijun Sun, Michael J. Buck, Laurie K. Read. Trypanosome RNA Editing Mediator Complex proteins have distinct functions in gRNA utilization. Nucleic Acids Research, 2017. doi:10.1093/nar/gkx458
3. Andrew E. Bruno, Alexei S. Soares, Robin L. Owen and Edward H. Snell. The use of haptic interfaces and web services in crystallography: an application for a 'screen to beam' interface. Journal of Applied Crystallography, 2016. doi:10.1107/S160057671601431X
4. Rachel M. Simpson, Andrew E. Bruno, Jonathan E. Bard, Michael J. Buck and Laurie K. Read. High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing. RNA, 2016. doi:10.1261/rna.055160.115
5. Diana Fusco, Timothy J. Barnum, Andrew E. Bruno, Joseph R. Luft, Edward H. Snell, Sayan Mukherjee, Patrick Charbonneau. Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms. PLoS ONE, 9(7): e101123, 2014. doi:10.1371/journal.pone.0101123
6. Andrew E. Bruno, Amanda M. Ruby, Joseph R. Luft, Thomas D. Grant, Jayaraman Seetharaman, Gaetano T. Montelione, John F. Hunt, Edward H. Snell. Comparing Chemistry to Outcome: The Development of a Chemical Distance Metric, Coupled with Clustering and Hierarchal Visualization Applied to Macromolecular Crystallography. PLoS ONE, 9(6): e100782, 2014. doi:10.1371/journal.pone.0100782
7. Sreevidya Sadananda Sadasiva Rao, Lori A. Shepherd, Andrew E. Bruno, Song Liu, and Jeffrey C. Miecznikowski. Comparing Imputation Procedures for Affymetrix Gene Expression Datasets Using MAQC Datasets. Advances in Bioinformatics, vol. 2013, Article ID 790567, 2013. doi:10.1155/2013/790567
8. J.U. Patel, S.J. Guercio, A.E. Bruno, M.D. Jones, T.R. Furlani. Implementing green technologies and practices in a high performance computing center. 2013 International Green Computing Conference Proceedings, IGCC 2013, Arlington, VA USA. June 27-29 2013. doi:10.1109/IGCC.2013.6604474
9. Andrew E. Bruno, Jeffrey C. Miecznikowski, Maochun Qin, Jianmin Wang and Song Liu. FUSIM: a software tool for simulating fusion transcripts. BMC Bioinformatics, 14:13, 2013. doi:10.1186/1471-2105-14-13
10. Thomas R. Furlani, Matthew D. Jones, Steven M. Gallo, Andrew E. Bruno, Charng-Da Lu, Amin Ghadersohi, Ryan J. Gentner, Abani Patra, Robert L. DeLeon, Gregor von Laszewski, Fugang Wang, and Ann Zimmerman. Performance metrics and auditing framework using application kernels for high-performance computer systems. Concurrency and Computation: Practice and Experience , 2012. doi:10.1002/cpe.2871
11. Andrew E. Bruno, Li Li, James L. Kalabus, Yuzhuo Pan, Aiming Yu, Zihua Hu. miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes. BMC Genomics, 13(1):44, 2012. doi:10.1186/1471-2164-13-44
12. Zihua Hu and Andrew E. Bruno. The influence of 3'UTRs on MicroRNA Function Inferred from Human SNP Data. Comparative and Functional Genomics, 2011:910769, 2011. doi:10.1155/2011/910769
13. Thomas R. Furlani, Matthew D. Jones, Steven M. Gallo, Andrew E. Bruno, Charng-Da Lu, Amin Ghadersohi, Ryan J. Gentner, Abani K. Patra, Robert L. DeLeon, Gregor von Laszewski, Lizhe Wang, and Ann Zimmerman. Performance metrics and auditing framework for high performance computer systems. In Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery, TG '11, pages 16:1-16:1, New York, NY, USA, 2011. ACM. doi:10.1145/2016741.2016759
14. Daniel P. Gaile, Lori A. Shepherd, Andrew E. Bruno, Song Liu, Carl D. Morrison, Lara E. Sucheston, and Jeffrey C. Miecznikowski. iGenomicViewer: R package for visualisation of high dimension genomic data. International Journal of Bioinformatics Research and Applications, 6:584-593, 2010. doi:10.1504/IJBRA.2010.038739
15. J. A. Delmerico, N. A. Byrnes, A. E. Bruno, M. D. Jones, S. M. Gallo, and V. Chaudhary. Comparing the performance of clusters, Hadoop, and Active Disks on microarray correlation computations. In Proc. International High Performance Computing (HiPC) Conference, pages 378-387, 2009. doi:10.1109/HIPC.2009.5433190 (Acceptance rate: 18.8%, 49/261)

Research Support

• Regulation of RNA Editing in Trypanosoma Brucei
  • Understand the molecular mechanisms of RNA editing in kinetoplastid parasites, which cause African sleeping sickness, Chagas' disease, and leishmaniasis
  • 2R01AI061580-06A1      PI: Read, Laurie
  • National Institute of Allergy & Infectious Disease
  • 08/2012 - 07/2016
  • Role: Data Analyst/Programmer
• Western New York Stem Cell Culture and Analysis Center
  • Provide facilities that will make it faster and more efficient for researchers currently using stem cells to generate, culture, analyze and test these cells both in vitro and in therapeutic non human models.
  • C026714      PI: Gronostajski, Richard
  • New York State Department of Health
  • 11/2011 - 10/2015
  • Role: Data Manager
• Technology Audit and Insertion Service for TeraGrid
  • Development of an active set of tools and services to monitor the advanced TG:XD cyberinfrastructure and insure its ability to meet the research needs of the end user as well as an advanced web-based interface to present role-specific views of audit results.
  • OCI1025159      PI: Furlani, Thomas
  • National Science Foundation
  • 07/2010 - 06/2015
  • Role: System Administrator
• Development of An Expert Crystallization Knowledge System
  • Development of an expert crystallization knowledge system and web-based user interface to optimize conditions and factors that drive the crystallization of macromolecular samples.
  • 1R01GM088396      PI: Snell, Edward H
  • National Institutes of Health (subcontract from Hauptman Woodward Institute)
  • 01/2010 - 12/2014
  • Role: Programmer/Database Administrator