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Jason Porta
Structural Biologist
Monroe
Summary
Dynamic CryoEM Specialist with a passion for computation, adept in Python and Bash scripting, streamlining data collection and enhancing productive output. Proven analytical thinker with an affinity to mentor students and postdocs. Known to have a love of data processing, management of big data and data cleaning reliability and adaptability, with swift capacity to learn and apply new skills, I am ready to tackle new challenges and advance research objectives with dedication and enthusiasm.
Overview
13
13
years of professional experience
1
1
Language
Work History
Cryo-EM Reconstruction Specialist
The Hormel Institute - University of Minnesota
05.2024 - 06.2025
- Computational reconstructions and image processing of cryo-electron microscopy (CryoEM) datasets (i.e., TRAIL-s:DR5:FC).
- Refined experimental design and streamlined data collection approaches significantly boost efficiency and reduce the costs of using the Krios microscope.
- Data sorting and cleaning with Python and Bash scripting freed up over 200 TB of disk space for the institute's HPC cluster.
- Created user documentation and protocols to assist researchers in daily lab and computational tasks (i.e., data cleaning, HPC job submission, and sample vitrification).
- Lead the adoption of new software tools (https://github.com/3dem/emhub), and wrote custom modules that streamlined workflows across multiple shared resource facilities.
Research Fellow
Life Sciences Institute - University of Michigan
01.2018 - 01.2024
- Structural determination of the Caveolin-1 8S complex by Cryo-EM single-particle analysis.
- Conducted single-particle cryo-electron microscopic studies (CryoEM) of riboswitch-bound RNA polymerases.
- Worked in a cross-functional group to create automated data processing pipelines for the lab and Cryo-EM facility using Python and Bash.
- Applied machine learning algorithms for automated particle picking (i.e., positive-unlabeled convolutional neural networks, deep learning neural networks, and generative adversarial networks).
- Mentored graduate students and postdocs on navigating the Linux OS, shell scripting, and troubleshooting.
- Trained new graduate students and postdocs in glow discharging, sample vitrification of sample grids, and single-particle Cryo-EM and cryo-electron tomography (Cryo-ET) data collection.
- Linux (RHEL) administration of workstations in our computational lab.
- Managed big data on our computing cluster and was responsible for finding storage solutions (i.e., created data management documentation, regular cron jobs, and cold storage servers).
- Created lab manuals and documentation regarding single-particle data collection, data management, and data processing for the Ohi Lab and LSI.
Postdoctoral Research Fellow
Purdue University
04.2012 - 04.2017
- Conducted single-particle cryo-electron microscopy (CryoEM) studies of the neutralizing effects of antibody-bound, lipid-enveloped alphaviruses.
- Experienced in working in a BSL-2/3 environment.
- Used freeze-plunging robots (Vitrobot/CP3) for vitrifying Cryo-EM sample grids.
- Screened samples for Cryo-EM data collection using a 200 kV Phillips CM200, Phillips CM300 (BSL-3), and 300 keV Titan Krios transmission electron microscopes.
- Carried out image processing, reconstruction, and refinement of lipid-enveloped viruses and their antibody Fab fragment-bound equivalents.
- Semi- and automated model building of coordinates into charge density maps.
- Trained new lab members in sample vitrification, collection, and image processing from CryoEM and CryoET data.
- TEM hardware alignment for the Rossmann Lab.
- Maintained and further developed in-house software for coordinate fitting into charge density maps (EMfit) and NCS averaging using GFORTRAN and C.
- Installed and configured automated data collection software (Leginon/Appion) for Purdue's first direct electron detector.
- Used high-performance computing (HPC) clusters for batch submission (PBS) of jobs for data processing.
- Pursued independent and complementary research interests.
- Leveraged interpersonal and communication skills to mentor PhD, graduate and undergraduate students.
- Authored professional scientific papers for publishing in peer-reviewed journals.
Education
Ph.D. - Structural Biology & Biophysics
University of Nebraska Medical Center
Omaha, NE 05.2001 -
Bachelor of Science - Chemistry
University of Toledo
Toledo, OH 05.2001 -
Skills
Analytical thinking
Troubleshooting techniques
ETL development
Advanced SQL queries
Data validation
Python
CryoEM grid vitrification
CryoEM data collection
Bash scripting
CryoEM data processing
Data cleaning and management
CryoEM single particle anaylsis
Cryo-electron tomography
Accomplishments
- Analytical chemistry award 2002 - University of Toledo Department of Chemistry.
- Henry R. Kreider Scholarship in chemistry 2002 - University of Toledo Department of Chemistry.
- Arthur H and Virginia Black scholarship in chemistry 2002 - University of Toledo Department of Chemistry.
- Ohio Space Grant Consortium scholarship 2002 - The effects of microgravity on protein crystallization.
- Best talk for a Biochemistry & molecular biology student award 2007 · Midwest Student Biomedical Research Forum.
- Travel award recipient 2008 - Gordon research conference: Diffraction methods in structural biology.
- Travel award recipient 2009 - American crystallographic association annual conference.
- Nebraska Space Grant Consortium 2009-2011 - Graduate fellowship recipient.
- Structural biology & biophysics fellowship program 2007-2010 - United States Department of Education.
- Travel award recipient 2010 - Gordon research conference: Diffraction methods in structural biology.
- Margaret C Etter student lecturer award for service crystallography 2010 - American crystallographic association annual conference.
- Travel award recipient, International Union of Crystallography (IUCr) 2011 - XXII Congress, Madrid, Spain.
- National Institutes of Health (NIH) and National Institutes of allergy and infectious diseases (NIAID) - F32 Ruth Kirchestein Postdoctoral fellowship 2012-2017.
Interests
Timeline
Cryo-EM Reconstruction Specialist
The Hormel Institute - University of Minnesota
05.2024 - 06.2025
Research Fellow
Life Sciences Institute - University of Michigan
01.2018 - 01.2024
Postdoctoral Research Fellow
Purdue University
04.2012 - 04.2017
Ph.D. - Structural Biology & Biophysics
University of Nebraska Medical Center
05.2001 -
Bachelor of Science - Chemistry
University of Toledo
05.2001 -
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