Michael Alonge
Software Engineer | Computational Biologist | Team LeadSoftware engineer and computational biologist with 10+ years of experience designing and leading scalable genomics analysis. Ph.D. in Computer Science from Johns Hopkins with a strong publication record in top journals including Cell, Science, and Nature. Skilled in cloud-native architecture, data engineering, and bioinformatics, with a proven ability to bridge genomics and software engineering to build reliable, production-ready systems for biotech.
Professional Experience
Lead Software Engineer, Computational Biology
Ohalo Genetics Remote- Lead design and development of Ohalo’s genomics data platform for breeding and gene editing programs
- Manage and mentor a cross-functional team of software engineers and bioinformaticians
- Set strategic direction for genomics and bioinformatics in support of IP and product development
Lead Computational Biologist
Ohalo Genetics Remote- Led bioinformatics strategy and analysis for Ohalo’s Boosted Breeding™ foundational patents
- Developed Ohalo’s first scalable genotyping pipeline, supporting breeding and gene editing initiatives
- Directed genomics analysis for all programs, including Ohalo’s ‘FruitionOne’ Almond program
Ph.D. Student, Computer Science
Johns Hopkins University Baltimore, MD- Published multiple first-author papers in journals including Cell and Science
- Invited speaker at a Galaxy webinar and the Boyce Thompson Institute for Plant Research
Research Associate I and II: Computational Biology
Driscoll's Watsonville, CA- Generated reference genome assemblies to enable downstream genomics analyses
- Designed and executed computational pipelines supporting strawberry and raspberry breeding programs
- Collaborated with molecular biologists and breeders to integrate genomics into crop improvement
Selected Projects
Integrating a print-friendly and web-friendly resume into an Astro website
I built a modern resume system that combines Astro's static site generation with the JSON Resume standard and print-optimized CSS to create both an SEO-friendly web presence and recruiter-ready PDF downloads.
Education
Ph.D. in Computer Science
Johns Hopkins UniversityBachelor of Science in Biomolecular Engineering
University of California, Santa CruzSelected Publications
The complete sequence of a human genome
ScienceAs a member of the Telomere-to-Telomere Consortium, I helped polish the initial CHM13 draft assembly to correct small and structural misassemblies. For example, I finished the telomere on the p-arm of chromosome 18. — https://doi.org/10.1126/science.abj6987
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Nature MethodsA companion paper to the CHM13 assembly paper, my colleagues and I describe our methods for polishing the initial draft assembly. — https://doi.org/10.1038/s41592-022-01440-3
Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
Genome BiologyI introduced RagTag, a general-purpose genome assembly scaffolding and improvement tool. — https://doi.org/10.1186/s13059-022-02823-7
The genetic and epigenetic landscape of the Arabidopsis centromeres
ScienceI led the assembly of all five Columbia Arabidopsis thaliana centromeres—the first time this had ever been accomplished for a plant species, to our knowledge. — https://doi.org/10.1126/science.abi7489
Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
CellI led an effort to catalog and characterize structural variation in 100 tomato varieties using Oxford Nanopore sequencing. I led an analysis that found that breeding introgressions from wild material substantially altered the genome structure of modern varieties. — https://doi.org/10.1016/j.cell.2020.05.021
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
Nature BiotechnologyI helped benchmark the accuracy of structural variant calls generated from PacBio HiFi sequencing. — https://doi.org/10.1038/s41587-019-0217-9