Jesse R. Walsh
PHD CANDIDATE · BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
1322 Stafford Ave. Ames, IA 50010
 (507) 272-3514
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 jrwalsh@iastate.edu
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 https://github.com/jrwalsh
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 https://www.linkedin.com/in/jessewalsh
Education
Iowa State University
Ames, Iowa
PHD CANDIDATE IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
Aug. 2008 - Present
• Advisor: Julie A. Dickerson. Co-Advisor: Carolyn Lawrence-Dill
• Awarded IGERT Fellowship
• Anticipated Graduation: May 2016
Luther College
Decorah, Iowa
B.A. IN COMPUTER SCIENCE
Aug. 2003 - May 2006
• Awarded Regent Scholarship
• Graduated Cum Laude
Skills
Programming Java, R, MATLAB, Perl, C/C++, BASH Script
Software MySQL, Pathway Tools, Cytoscape, Blast, SOAPdenovo, Velvet, Abyss, Latex
Wet Lab PCR, Fatty Acid Extractions, GC-MS, Microbial Vector Transformations
Experience
Iowa State University
Ames, IA
GRADUATE RESEARCH ASSISTANT
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Aug. 2008 - Present
Electrical and Computer Engineering Department
Member of Center for Biorenewable Resources (CBiRC)
Journal Reviewer for Bioinformatics Jan. 2014
Rotating Research Assistant, Steve Whitham, Basil Nikolau, and Julie Dickerson 2008-2009
RTP Company
Winona, MN
DATA PROCESSING SOFTWARE ENGINEER
Aug. 2007 - Aug. 2008
• Develop custom applications
• Debug and troubleshoot existing programs
• Assist end-users with applications
Benchmark Electronics
Winona, MN
FACTORY ASSEMBLY LINE
Sept. 2006 - Aug. 2007
• Assembly of Home Medical Devices
• Contracted through Manpower Employment Agency
Mayo Clinic, Life Sciences Dept.
Rochester, MN
INTERNSHIP
June - Aug. 2005
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Designed and implemented 3 functional applications
Interacted with customers to define application requirement
Learned data warehousing concepts and worked on system/DB design
Developed an understanding of online systems processing
Delivered a summary presentation to the work group
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Selected Software Projects
CornCompare
Ames, IA
HTTPS://GITHUB.COM/JRWALSH/CORNCOMPARE (PRIVATE UNTIL PUBLICATION)
2015-2016
• Generates a report on the data content differences between CornCyc and MaizeCyc databases
• Automatically generates object matches between databases which use different identifiers
CycTools
Ames, IA
HTTPS://GITHUB.COM/JRWALSH/CYCTOOLS
2012-2014
• Graphical tool for managing and migrating functional annotations in BioCyc databases
• Flexible design allows users to modify functionality
PLEXdb redesign
Ames, IA
HTTP://JRWALSH.PUBLIC.IASTATE.EDU/PROJECT/PLEXDB/INDEX.HTML
Fall 2010
• In collaboration with John Van Hemert, updated PLEXdb schema to accomadate next-gen data
• Implemented and tested scripts to migrate data to new schema
Protein Secondary Structure Prediction
Ames, IA
HTTP://JRWALSH.PUBLIC.IASTATE.EDU/PROJECT/PSSP/INDEX.HTML
2008
• Implemented protein secondary structure prediction tool
• Featured sliding window for classification step
• Based on machine-learning tool SVMLight
Leadership
REU Mentor
Ames, IA
SPIRE-EIT REU 2010
June - Aug. 2010
• Mentor for 3 undergraduate students
• Research project
• Visualizing Data - http://www.vrac.iastate.edu/hci/reu/reu2010/
BCBGSO (formerly BCBLab)
Ames, IA
MEMBER
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2008-Present
Provides bioinformatics consulting services on campus
Makes available computer resources for use by ISU students
Actively participate in small projects sponsored by PI’s on campus
Took on a database design role in the CrystalBall project - machine-learning approaches to predicting protein crystalization conditions
for x-ray crystalography
Luther Computer Users Group (LCUG)
Decorah, IA
SECRETARY AND JOINT FOUNDER
2003-2006
• Promote and support computers and technology on campus
• Hosted fundraising events
• Sponsored and organized tour of IBM Rochester facilities and BlueGene Computer
Presentation
BCB Seminar Series
Ames, IA
PRESENTED “SYSTEMS BIOLOGY AND BIOMODELING OVERVIEW SEMINAR”
2012
• Introducing systems biology concepts to new BCB students and interested community members.
Publications
Journal Articles
Walsh, Jesse R., Taner Z. Sen, and Julie A. Dickerson (2014). “A computational platform to
maintain and migrate manual functional annotations for BioCyc databases”. In: BMC Systems
Biology 8.1, p. 115.
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Working Manuscripts
Walsh, Jesse R. and Julie A. Dickerson (2016). “Modeling Effect of Metabolic Constraints on
Transcription Factor Activity Levels”. In: Bioinformatics. In writing.
Walsh, Jesse R., Mary L. Schaeffer, Peifen Zhang, Seung Y. Rhee, Julie A. Dickerson, and Taner
Z. Sen (2016). “The Scope of Metabolic Pathway Resources Depends on Initial Enzymatic Function
Assignments and Level of Manual Curation: A Case for Maize”. In: Plant Physiology. To be submitted
spring 2016.
Conference Proceedings
Schaeffer, Mary, Taner Z. Sen, Jack Gardiner, Ethalinda Cannon, Scott M. Birkett, Jesse R.
Walsh, Lisa C. Harper, Julie Dickerson, and Carolyn J. Lawrence (2013). “Pathways at MaizeGDB:
Strategies for Curation and Data Sharing”. In: Plant and Animal Genome XXI.
Walsh, Jesse R. and Julie A. Dickerson (2013). “Semi-automated Constraint-based Metabolic
Model Generation”. In: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics. BCB’13. Washington DC, USA: ACM, 668:668–668:668.
Posters
Walsh, Jesse R., Erin E. Boggess, Yingxi Chen, Laura R. Jarboe, and Julie A. Dickerson (2015).
Bioinformatics for E. coli. CBiRC 7th Annual Site Visit. Poster.
Walsh, Jesse R. and Julie A. Dickerson (2015). Modeling Effect of Metabolic Constraints on
Transcription Factor Activity Levels. CBiRC 7th Annual Working Meeting. Poster.
Walsh, Jesse R., Erin E. Boggess, and Julie A. Dickerson (2014). Bioinformatics for E. coli.
CBiRC 6th Annual Site Visit. Poster.
Walsh, Jesse R. and Julie A. Dickerson (2014). Integrating Regulatory and Metabolic Networks in
E. coli. CBiRC 6th Annual Working Meeting. Poster.
Walsh, Jesse R., Yao Fu, Erin E. Boggess, Jackie Shanks, Laura R. Jarboe, and Julie A. Dickerson
(2013). Bioinformatics for E. coli. CBiRC 5th Annual Site Visit. Poster.
Walsh, Jesse R., Taner Z. Sen, and Julie A. Dickerson (2013). Integrated Methods for Draft
Metabolic Model Generation. CBiRC 5th Annual Working Meeting. Poster.
Walsh, Jesse R., Taner Z. Sen, Mary L. Schaeffer, Jack M. Gardiner, Lisa C. Harper, Ethalinda
Cannon, Carson Andorf, Darwin Campbell, Carolyn J. Lawrence, and Julie A. Dickerson (2013).
CycTools: Interface for Exploring and Updating BioCyc Databases. Maize Genetics Conference, St.
Charles, IL. Poster.
Boggess, Erin E., Yao Fu, Jesse R. Walsh, Liam Royce, Jackie Shanks, Laura R. Jarboe, and
Julie A. Dickerson (2012). Investigating the Effects of Octanoic Acid on E. coli. CBiRC 4th Annual
Site Visit. Poster.
Walsh, Jesse R., Julie A. Dickerson, Ting Wei Tee, Jong Moon Yoon, and Jackie Shanks (2012).
BioCycTools: A Tool for the Rapid Generation of Metabolic Models. CBiRC 4th Annual Working
Meeting. Poster.
Fu, Yao, Jesse R. Walsh, Erin E. Boggess, Yanfen Fu, Liam Royce, Laura R. Jarboe, Jackie
Shanks, and Julie A. Dickerson (2011). Bioinformatics for E. Coli. CBiRC 3th Annual Site Visit.
Poster.
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Walsh, Jesse R. and Julie A. Dickerson (2011). EcoCyc as a Platform for the Metabolic Engineering
of E. Coli. ACM-BCB Conference, Chicago, IL. Poster.
Walsh, Jesse R. (2010). Project 2E: E. coli Bioinformatics. CBiRC 2th Annual Site Visit. Poster.
Walsh, Jesse R. and Julie A. Dickerson (2010). Data Modeling of EcoCyc Pathways. CBiRC 2th
Annual Working Meeting. Poster.
Sethuraman, Arun, Sweta Vangaveti, Jesse R. Walsh, Scott Boyken, Erin Boggess, Yves Sucaet,
and Julie Hoy (2009). Prediction of Protein Crystallization using Recursive Partition Trees. NMBIS
Conference, Santa Fe, NM. Poster.
Walsh, Jesse R., John Van Hemert, and Julie A. Dickerson (2009). Integration of E. coli Metabolic
Data. CBiRC 1th Annual Working Meeting. Poster.
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