William Scott Raymond
williamscottraymond@gmail.com

Education
Colorado State University
Bachelor of Science - Chemical and Biological Engineering
Bachelor of Science - Biomedical Engineering
Bachelor of Science - Chemical and Biological Engineering
Bachelor of Science - Biomedical Engineering
GPA 3.35
Fall 2012 - Spr 2017
Colorado State University
Doctorate of Philosophy - Bioengineering
Dissertation: Stochastic modeling to explore the Central Dogma of molecular biology and to design more informative single-molecule live-cell fluorescence microscopy experiments.
Doctorate of Philosophy - Bioengineering
Dissertation: Stochastic modeling to explore the Central Dogma of molecular biology and to design more informative single-molecule live-cell fluorescence microscopy experiments.
Fall 2018 - Spr 2024
Work Experience
Research Assistant - Colorado State University
- Developed Python packages aimed at providing our research to the public
Sept 2017 - Aug 2018
Undergraduate Research Assistant - Colorado State University
- Completed an honors thesis focusing on a Python GUI for solving bursting gene models
Summer 2017
Publications
"Methods in Quantitative Biology – from Analysis of Single-Cell Microscopy Images to Inference of Predictive Models for Stochastic Gene Expression"
Contributing Author
Contributing Author
UNDER REVIEW
January 2025
PLOS One
April 2025
Frontiers in Cell and Developmental Biology
May 2023
Bio-protocol
August 2022
Nature Communications
May 2021
PLOS Computational Biology
October 2019
Physical Biology
May 2018
Teaching experience
Course Instructor - Colorado State University
BIOM 421 - Transport Phenomena
BIOM 421 - Transport Phenomena
- Taught senior undergraduate engineering students principles in transport phenomena including topics such as pharmacokinetics, fluid dynamics, mass transport, and FEM / FVM analyses.
- Created an engaging and vibrant learning environment by providing real world examples of where taught principles are applied.
Jan 2023 - May 2023
Learning Assistant - UQ-Bio summer school
- Taught and assisted various levels of student from undergraduate to first year PhD students at the undergraduate quantitiative biology summer school across a myriad of topics: ODE modeling, Machine learning, Python coding, MCMC, stochastic simulation, and finite state projection.
- Generated lecture materials used for teaching students on topics for learning Python, TASEP modelling, and introduction to machine learning. Provided these materials as open source Colab notebooks.
- Designed each year's T-shirts!
Summer 2021, 2022, 2023, & 2024
Graduate Teaching Assistant - Colorado State University
BIOM 421 - Transport phenomena
BIOM 421 - Transport phenomena
- Assited in grading and running office hours.
- Directly supported students' learning by helping with question and answer sessions.
Fall 2020, Fall 2021
Accepted Talks
UQ-Bio 2023 Guest Lecturer - Fort Collins, Colorado
- Gave a 15 minute talk on my dissertation project combining mechanistic mRNA models to extend the color pallette of NCT experiments.
- Presented a poster on my publication "Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments"
June 2023
UQ-Bio 2023 Guest Lecturer - Fort Collins, Colorado
- Gave a 15 minute talk on my dissertation project combining mechanistic mRNA models to extend the color pallette of NCT experiments.
- Presented a poster on my publication "Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments"
June 2023
APS March Meeting - Las Vegas, Nevada
- Talk title: "Combining mechanistic and statistical models to enable Nascent Chain Tracking for multiple mRNAs using a single color"
March 2023
Q-bio Conference - Rutgers University
- Talk title: "Stochastic Simulation Identification Toolkit"
Summer 2017
Conference Attendences
qCMB Symposium - Fort Collins, Colorado
Attendee and poster presenter
Attendee and poster presenter
- Presented a poster on my publication "Identification of Potential Riboswitch Elements in Homo Sapiens 5'UTR Sequences using Positive-Unlabeled Machine Learning."
June 2024
Rocky Mountain RNA Symposium - Aurora, Colorado
Attendee and poster presenter
Attendee and poster presenter
- Presented a poster on my preprint "Identification of Potential Riboswitch Elements in Homo Sapiens 5'UTR Sequences using Positive-Unlabeled Machine Learning."
April 2024
qCMB Symposium - Fort Collins, Colorado
Attendee and poster presenter
Attendee and poster presenter
- Gave a 2.5 minute lightning talk advertising my poster.
- Presented a poster on my publication "Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments"
June 2023
Outreach
Guest Judge CSU Gradshow - Colorado State University
Fall 2024
Engineering Mentor - Colorado State University
- Helped incoming freshmen engineers adjust to their new college environment and classes.
- Mentored freshmen with their courswork and provided office hours.
- Volunteered for Engineering E-days and assisted prospective freshmen interested in engineering
Fall & Spring 2014