Eric Klavins

About

Eric Klavins is the Professor and Chair of the Electrical & Computer Engineering Department at the University of Washington in Seattle. He received a B.M. in Music in 1992 and a B.S. in computer science in 1996 from San Francisco State University. He received M.S. and Ph.D. degrees in computer science and engineering in 1999 and 2001 from the University of Michigan, Ann Arbor. From 2001 to 2003 he was a postdoctoral scholar in the Control and Dynamical Systems Department at the California Institute of Technology where he worked with Richard Murray. In 2003 Eric was hired in Electrical Engineering at the University of Washington in Seattle; he received tenure in 2009. He holds adjunct appointments in Computer Science and Engineering and in Bioengineering. Until approximately 2008, Klavins’ research was primarily in computer science and control systems, focusing on stochastic processes, robotics and self-assembly. At about this time, he learned the basics of genetic engineering. In the n

Research topics

• Computer Science
• Computational biology
• Biology
• Artificial Intelligence
• Operating system
• Data science
• Software engineering
• Database
• Biochemistry
• Genetics

Selected publications

• Perturbing the energy landscape for improved packing during computational protein design

  Proteins Structure Function and Bioinformatics · 2020 · 193 citations

  The FastDesign protocol in the molecular modeling program Rosetta iterates between sequence optimization and structure refinement to stabilize de novo designed protein structures and complexes. FastDesign has been used previously to design novel protein folds and assemblies with important applications in research and medicine. To promote sampling of alternative conformations and sequences, FastDesign includes stages where the energy landscape is smoothened by reducing repulsive forces. Here, we…

  PublisherOA PDFDOI

• Automated design of thousands of nonrepetitive parts for engineering stable genetic systems

  Nature Biotechnology · 2020 · 137 citations

  PublisherOA PDFDOI

• Synthetic hormone-responsive transcription factors can monitor and re-program plant development

  eLife · 2018-05-01 · 125 citations

  articleOpen access

  Developmental programs sculpt plant morphology to meet environmental challenges, and these same programs have been manipulated to increase agricultural productivity (Doebley et al., 1997; Khush, 2001). Hormones coordinate these programs, creating chemical circuitry (Vanstraelen and Benková, 2012) that has been represented in mathematical models (Refahi et al., 2016; Prusinkiewicz et al., 2009); however, model-guided engineering of plant morphology has been limited by a lack of tools (Parry et al…

  PublisherDOI

• Aquarium: open-source laboratory software for design, execution and data management

  Synthetic Biology · 2021 · 42 citations

  Senior authorCorresponding

  Automation has been shown to improve the replicability and scalability of biomedical and bioindustrial research. Although the work performed in many labs is repetitive and can be standardized, few academic labs can afford the time and money required to automate their workflows with robotics. We propose that human-in-the-loop automation can fill this critical gap. To this end, we present Aquarium, an open-source, web-based software application that integrates experimental design, inventory manage…

  PublisherOA PDFDOI

• OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories

  EBioMedicine · 2019-11-22 · 35 citations

  articleOpen access

  BACKGROUND: HIV drug resistance (HIVDR) testing can assist clinicians in selecting treatments. However, high complexity and cost of genotyping assays limit routine testing in settings where HIVDR prevalence has reached high levels. METHODS: The oligonucleotide ligation assay (OLA)-Simple kit was developed for detection of HIVDR against first-line non-nucleoside/nucleoside reverse transcriptase inhibitors and validated on 672 codons (168 specimens) from subtypes A, B, C, D, and AE. The kit uses d…

  PublisherDOI

Recent grants

• Collaborative Research: Molecular Programming Architectures, Abstractions, Algorithms, and Applications

  NSF · $2.1M · 2013–2018

• RoL: FELS: EAGER: Exploring the adaptive possibilities of 'redundancy' in a plant defense hormone signaling pathway

  NSF · $300k · 2018–2021

• Estimation & Observation of Stochastic Biochemical Networks

  NSF · $335k · 2010–2013

Frequent coauthors

• Jennifer L. Nemhauser

  University of Washington

  15 shared

• David Baker

  University of Washington

  14 shared

• Nils Napp

  Cornell University

  13 shared

• Alberto Carignano

  University of Washington

  10 shared

• David Thorsley

  Samsung (United States)

  10 shared

• John-Michael McNew

  9 shared

• Arjun Khakhar

  Colorado State University

  9 shared

• Joshua D. Bishop

  University of Washington

  9 shared

Education

• PhD, EECS

  University of Michigan

  2001

Awards & honors

• 8 faculty named 2017 Amazon Catalyst Fellows
• Klavins and Javidi latest CAREER recipients
• Klavins and Seelig Win NSF Award for Molecular Programming
• Eric Klavins Wins Faculty Innovator Award
• Two EE Faculty Receive CoMotion Innovation Fund Awards

Similar researchers at University of Washington

• James Davenporth-41
• Daniela Rosnerh-35
• Daniela Huppenkothenh-33