Iowa State University Ames, IA 2008-Present
M.S., Human Computer Interaction, Bioinformatics and Computational Biology
Iowa State University Ames, IA 2002- May 2008
B.S., Management Information Systems, International Business, Computer Science and Philosophy
Instituto Filippi- Paderno del Grappa, Italy May 2007 - July 2007
International University
Research Experience
Veterinary Medical Research Institute Ames,IA August 2006 - Present
Bioinformatics and Computational Biology / Medical Bacteriology
NSF funded project to build the first E. colidatabase for visualizing plasmid maps, performing cross-database searches for genes and proteins, performing alignments between plasmids, and performing BLAST searches of sequences with an easy to use Perl/CGI/Java/MySql driven interface.
Phylogenetics and molecular phylogeny to create relational trees for scientific papers - also creating in house tree reading and modification program. Use of Manatee with MySql for manual annotation.
PCR (Polymerase chain reaction) Analysis; Virulence Testing of bacteria in the C. elegans model, Variety of bench work/Lab work.
Veterinary Diagnostic Lab Ames, IA April 2005 - September 2005
Software developer
Using mainly Java, JSP and Struts creating web-based applications for VDL.
The main project used multiple existing classes to create an interoffice (VDL) posting system used to coordinate tasks and manage requests among the community of users with ability of scope and security.
Work experience
College of Veterinary Medicine Ames,IA May 2004 - August 2006
Computer Service Technician
Network Administrator and end-user support, set up many workstations and servers (Various Microsoft/Linux servers, SQL, implemented Ghost images [in Labs] etc.) along with hardware troubleshooting and repair of numerous varieties (all platforms of computers, printers, medical diagnostic equipment, etc.)
Internship experience
The Toro Company Minneapolis,MN May 2006 - August 2006
SystemMonitoring Analyst Intern
Project Manager of the Intern group as Technical and Design lead. Created an internal website for IT and other departments through Confluence Wiki and Portal technologies to deliver dynamic content.
Network Modeling through SNMP and network protocol analyzers. Using Aprisma Spectrum, wrote scripts in Perl and threw alarms when a warning through SNMP triggered with root cause analysis.
REFERRED PUBLICATIONS/ACCEPTED/IN PREP MANUSCRIPTS
Johnson, T.J., Wannemeuhler, Y.M., Baldwin, L., Mangiamele, P., Kariyawasam, S., and Nolan. L.K. 2008. Can Multilocus Sequence Typing and Virulence Genotyping be Used to Predict Virulence in Extraintestinal Pathogenic Escherichiacoli? In preparation
Johnson, T.J., Wannemuehler, Y., Johnson, S.J., Doetkott, C., Cloud, S., DebRoy, C., Barnes, H.J., Mangiamele, P., and Nolan, L.K. 2008. Predictors of Avian Pathogenic Escherichiacoli (APEC) Virulence and their Use in Discriminating APEC from Avian Fecal Commensal Escherichiacoli Isolates. In preparation
PRESENTATIONS AT SCIENTIFIC MEETINGS
Mangiamele, P., Johnson, T.J., Wannemuehler, Y.M., and Nolan, L.K.
Creation of an Escherichia coli Plasmid Genome Database. Proceedings of the AVMA-AAAP Annual Meeting, WashingtonDC, July 2007 (Travel Award) Paul Mangiamele, Timothy J. Johnson, and Lisa K. Nolan E. coli Plasmid Genome Database: A Tool to Study the Plasmids of Avian Pathogenic E. coli and Related Bacteria. Proceedings of the AVMA-AAAP Annual Meeting, WashingtonDC, accepted for July 2008 (Travel Award) Luke G. Baldwin, Timothy J. Johnson, Yvonne Wannemuehler, Paul Mangiamele, Subhashinie Kariyawasam, and Lisa K. Nolan Virulence of Avian and Human Extraintestinal Pathogenic Escherichiacoli Assigned to Different Sequence Types. Proceedings of the AVMA-AAAP Annual Meeting, WashingtonDC, accepted for July 2008 Johnson, T.J., Kariyawasam, S., Wannemuehler, Y., Mangiamele, P., Johnson, S.J., Doetkott, C., Skyberg, J.A., Lynne, A.M., and Nolan, L.K. Analysis of the Complete Genome of an Avian Pathogenic Escherichiacoli Isolate. Proceedings of the AVMA-AAAP Annual Meeting, Washington DC, July 2007
MEMBERSHIP IN PROFESSIONAL SOCIETIES
American Veterinary Medical Association/American Association of Avian Pathologists
RESEARCH INTERESTS
To create new knowledge by leveraging experience in computer systems in biological research
Simplifying the human computer interface needed to utilize computational tools, making accessible a range of complex data
Computational approaches towards understanding the virulence mechanisms of microbial pathogens of agricultural and human health importance
Research Skills
Taking benchwork knowledge and experience in microbiology and creating information systems to enable further research
Use of SAS and statistical knowledge coupled with higher level programming
Elective/influential coursework
Human Computer Interaction 350 - Human Factors in Technology - Understanding human behavior and cognition at the human computer interface level. Particularity, it examines the emergent interactive technologies, human computer interaction, user centered design, usability analysis, and usability testing.
Human Computer Interaction655 - Organizational and Social Implications of Human Computer Interaction - Examining opportunities and implications of information technologies and human computer interaction on social and organizational systems as well as the scientific philosophy that grounds our understanding of these systems, developing an understanding of how our ontological assumptions driven our work and our evaluations of its outcomes.
Computer Science 575 Computational Perception - covered statistical and algorithmic methods for sensing, recognizing, and interpreting the activities of people by a computer. Focus on machine perception techniques that facilitate and augment human-computer interaction. The main goal of the class is computational perception on both theoretical and practical levels.
Computer Science544 Bioinformatics and Computational Biology - an overview of bioinformatics with a significant problem-solving component, including hands-on practice using computational tools to solve a variety of biological problems. Topics include: database searching, sequence alignment, gene prediction, RNA and protein structure prediction, construction of phylogenetic trees, comparative and functional genomics.
Computer Skills and Qualifications
Programming in C++, Java, C#, Spring, hibernate, PL/SQL, JSP, Perl, Velocity, SAS, Python, MatLab, PHP 5 and COBOL
Use of Matlab and OpenCV for image processing and computational vision
Proficiency in MS Visual Studio Devel, Word, Excel, Access, Photoshop/GIMP and Illustrator
Competency writing HTML with JavaScript and Perl to create interfaces and designing content
Excellent knowledge of Windows NT and Unix networking and security
PC and mainframe/server hardware installation, configuration, troubleshooting and repair
Significant Experience with NT/2000/XP/Vista, Linux (Gentoo, Debian, Redhat, Ubuntu), and Mac OS X/OS9
Volunteer Webmaster/Web Developer for Worldly Goods and IowaState Physics department
