Email: ryandward (at) gmail (dot) com
ORCID: https://orcid.org/0000-0001-9537-2461
Stack Overflow: ryandavidward
GitHub: ryandward
Google Scholar: Link
LinkedIn: Ryan Ward
PhD in Genetics
University of Wisconsin–Madison, 2024
Thesis: Genetic Determinants of Antibiotic Resistance and Susceptibility in Gram-negative Pathogens
BS in Genetics and Biotechnology
New Mexico State University, 2018
Master of Arts in Economics
New Mexico State University, 2010
Bachelor of Arts in Economics and Foreign Languages
New Mexico State University, 2007
Senior Scientist
Temporal Agriculture, 2025 – Present
Develops a new in-vivo plasmid editing platform for transient epigenetic modification in plants. Designs the vector systems that drive this process, including recombineering-compatible guide constructs and editing plasmids. The system is modular, does not require genomic integration, and is built to support rapid iteration in synthetic biology workflows.
These projects were developed independently or collaboratively in the open-source community. Most are unfunded, maintained voluntarily, and support scientific infrastructure or tooling used in experimental pipelines.
Developed a Python toolkit for building and analyzing genome-scale barcoded CRISPRi libraries. Includes modules for guide design, off-target filtering, and orientation-aware read parsing. Implements compressed read formats and sequence matching for high-throughput screens. GUI components support interactive design and targeting workflows.
Languages/Technologies: Python, Bowtie, Polars, SeqIO, JSON, Jupyter, PyQt, GitHub
Built a genome-wide CRISPRi library for E. coli and related enteric species, including Enterobacter cloacae and Klebsiella pneumoniae. Developed supporting bioinformatics infrastructure such as barcoder.distillreads and heuristicount, enabling orientation-aware, compressed read parsing. Led all aspects of repository architecture and pipeline reproducibility; supported with intellectual property filing.
Languages/Technologies: Python, R, Zstandard compression, GitHub Actions
Generated a genome-wide sgRNA reference library for CRISPRi-based knockdown across multiple Pseudomonas species, including P. aeruginosa PAO1, PA14, LESB58, and P. putida KT2440. Used strand-aware scripts to optimize guide selection by offset and direction, with outputs validated in BED format and visualized using NCBI genome tracks. Project supports Mobile-CRISPRi adaptation in diverse strains.
Languages/Technologies: Python, BEDtools, csvtotable, shell scripting, GitHub Pages
Built and continuously maintained a scalable, type-safe infrastructure for MMO-linked community operations for real-time scheduling, inventory, and user-role management. Integrated structured wiki-based inventories, searchable guild census data, and permission-aware slash commands. Architecture includes PostgreSQL-backed storage, Elasticsearch for full-text search, and MediaWiki for game-linked documentation.
Languages/Technologies: TypeScript, PostgreSQL, TypeORM, Discord.js, Elasticsearch, MediaWiki, Docker, GitHub Actions---
- Ward, R. D., Tran, J. S., Banta, A. B., et al. (2024). "Essential gene knockdowns reveal genetic vulnerabilities and antibiotic sensitivities in Acinetobacter baumannii." mBio. DOI: 10.1128/mbio.02051-23
- Ward, R. D., Stajich, J. E., Johansen, J. R., et al. (2021). "Metagenome sequencing to explore phylogenomics of terrestrial cyanobacteria." Microbiology Resource Announcements. DOI: 10.1128/MRA.00258-21
- Enright, A. L., Heelan, W., Ward, R. D., et al. (2024). "CRISPRi functional genomics in bacteria and its application to medical and industrial research." Microbiology and Molecular Biology Reviews. DOI: 10.1128/mmbr.00170-22
- Ward, R. D. et al. (2024). Pseudomonas aeruginosa essential gene perturbations that confer vulnerability to the mammalian host environment. bioRxiv. DOI: 10.1101/2024.11.05.622029
- Tran, J. S., Ward, R. D., Iruegas-López, R., Ebersberger, I., Peters, J. M. (2024). Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii. bioRxiv. DOI: 10.1101/2024.12.05.627103
- Yu, M. A., Banta, A. B., Ward, R. D., et al. (2023). Investigating Pseudomonas aeruginosa Gene Function During Pathogenesis Using Mobile-CRISPRi. Methods in Molecular Biology. DOI: 10.1007/978-1-0716-3473-8_2
- Enright, A. L., Banta, A. B., Ward, R. D., et al. (2023). "The genetics of aerotolerant growth in an alphaproteobacterium with a naturally reduced genome." mBio. DOI: 10.1128/mbio.01487-23
- Johnson, R. A., Chan, A. N., Ward, R. D., et al. (2021). "Inhibition of Isoleucyl-tRNA Synthetase by the hybrid antibiotic thiomarinol." Journal of the American Chemical Society. DOI: 10.1021/jacs.1c02622
- Banta, A. B., Ward, R. D., Tran, J. S., et al. (2020). "Programmable Gene Knockdown in Diverse Bacteria Using Mobile-CRISPRi." Current Protocols in Microbiology. DOI: 10.1002/cpmc.130
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Systematic Dissection of Genetic Vulnerabilities in Acinetobacter baumannii
- Talk: Symposium on the Biology of Acinetobacter, Coimbra, Portugal
- Poster: EMBL Symposium: New Approaches and Concepts, Heidelberg, Germany
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Genetic Tradeoffs Underlying Synergistic Antibiotic Function in Acinetobacter baumannii
- Talk: UW-Madison Genetics Colloquium
- Poster: Genetics Retreat, K.B. Raper Symposium, Molecular Genetics of Bacteria and Phages, Perlman Symposium
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Stone Travel Award, 2023 ($1250)
- Supported conference attendance in Portugal and Germany
- Grad Student Executive Committee (2023–2024)
- Midwest Healthcare Case Competition (2022, Semi-finalist)
- Penn Healthcare Case Competition (2022)
- Genetics PhD Program Selections Committee (2021)
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Languages & Tools: R (tidyverse, Bioconductor, Shiny), Python (pandas, snakemake, numpy, matplotlib), TypeScript/JavaScript, Shell, Git, SQL
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Vector Engineering: Build and test modular tools for in-vivo plasmid engineering in E. coli, using scarless recombineering (λ-Red, Cas9) and simple ligation-based cloning. Focus on vector systems that don't require in vitro enzymes or genomic edits. Designed gRNA platforms and editing protocols for fast, clean plasmid manipulation.
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Bioinformatics: CRISPRi guide design, essential gene libraries, Tn-seq, genome assembly, metagenomics, sequence compression formats
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Statistical Approaches: GLMs, linear mixed models, Bayesian modeling, enrichment testing, multivariate methods
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Visualization & Interfaces: Interactive dashboards (Shiny, D3.js), static figures (ggplot2, seaborn), data storytelling and reproducible documentation
Worked on CRISPRi-based genetic screening in Acinetobacter baumannii and related species. Built vector systems and automated batch cloning for mutant libraries. Set up pipelines to analyze Tn-seq and chemical-genomics data, mostly in R and Python. Co-wrote papers, contributed to experimental planning, and made tools to keep figures and output reproducible.
- Built and cloned guide libraries for essential gene knockdowns.
- Wrote scripts to process sequencing and phenotype data.
- Helped with plots and documentation for publications and grants.
- Showed new lab members how to use our analysis tools.
Prepared environmental cyanobacterial isolates for sequencing as part of a JGI-funded desert phylogenomics effort. Performed DNA extraction, gel verification, and sample normalization for submission. Maintained annotated records for strain tracking and coordinated material transfer for community sequencing pipelines.
Ran methylation inhibition experiments in duckweed and Arabidopsis. Looked at phenotypes and matched them to genome-wide methylation patterns. Did a lot of data cleanup and simple stats in R.
Worked on genome assemblies for a legume and an insect species using short-read data. Used Linux-based tools and did comparisons to existing genomes. Most work done on HPC.
Helped with in vitro and in vivo validation of candidate cancer drug targets. Ran drug response assays and helped prep compounds for animal experiments. Did basic data logging and write-up support.
Senior Scientist
Leads development of high-throughput synthetic biology tools with an emphasis on automation, reproducibility, and toolchain scalability. Builds and maintains pipelines enabling programmable plant epigenetics.
Scribe & Translator
Supported clinical workflows through multilingual documentation.
Policy Analyst
Analyzed and reported on regional agricultural policy and international infrastructure projects.
Data Analyst
Developed custom infrastructure and conducted surveillance data analysis for the FDA’s food import risk profiling system.
Last modified: May 13, 2025