Attend ECEE Seminar with guest Mirela Alistar, April 2
About:
Mirela Alistar is an assistant professor at the University of Colorado Boulder, with appointments in the ATLAS Institute and the Department of Computer Science, where she leads the Living Matter Lab. Her research sits at the intersection of design automation, cyber-physical systems and bioengineering, with a central goal of turning wet lab intent into executable, shareable protocols. She develops programmable microfluidic platforms for “personal laboratories” and open-source device extensions for biomedical workflows. In parallel, she builds computational tools for bacteriophage discovery and annotation. She received her doctoral degree from the Technical University of Denmark and completed postdoctoral work at the Hasso Plattner Institute.
Abstract:
Biology is still often executed as a manual craft: protocols are difficult to standardize, hard to reproduce across labs and slow to scale. This research treats biology as a computing and systems problem, building general frameworks and automated workflows for executable biology. It integrates two areas: programmable microfluidic biochips that run assays as cyber-physical programs and computational pipelines that prioritize and interpret biological candidates at the genomic scale.
On the systems side, this talk will describe how digital microfluidic, or DMF, platforms become practical when paired with design automation concepts, including microfluidic primitives, constraint-aware scheduling and routing and extensions that expand the assay space. It will highlight PhageBox, an open-source DMF extension designed to integrate on-chip capabilities beyond droplet actuation.
On the algorithmic side, the talk will demonstrate how phage discovery and analysis can be made scalable and resource-efficient. EnrichSeq automates discovery workflows, PhageScanner annotates metagenomic features and PhageFilter enables ultra-low-memory metagenomic filtering in field settings.
Overall, this work presents a suite of methods, algorithms and pipelines that transform wet lab protocols into executable, shareable and verifiable processes, with a focus on antibacterial strategies enabled by phages. The talk concludes with open problems at the intersection of computing and bioengineering, including compiling protocols under real-world variability, enabling closed-loop execution with runtime monitoring and recovery and supporting portable protocol deployment through standardized representations, automated calibration and verification of quantitative readouts across devices and labs.
ECEE seminar: From digital microfluidic biochips to scalable phage genomics
Thursday, April 2, 2026
1:30–2:30 p.m.
Goldwater Center (GWC) 487, Tempe campus [map]