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Researchers shrink camera to the size of a salt grain

Researchers at the University of Washington and Princeton University have created micro-sized cameras that produce the highest-quality images and widest field of view for full-color metasurface cameras to date, with great potential to spot problems in the human body and provide sensing capabilities for super-small robots.

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UW BIOFAB: A force for reproducible science

The UW’s Biofabrication Center, founded by UW ECE Professor and Chair Eric Klavins, partners with Agilent Technologies in pursuit of automated, reproducible research.

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UW BIOFAB: A force for reproducible science Banner

Professor Mo Li named 2021 Optica Fellow

UW ECE Professor Mo Li recently received the honor of being named an Optica Fellow for his leading contributions to the fields of optics and photonics.

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Professor Mo Li named 2021 Optica Fellow Banner

What causes a research paper to be highly cited?

What causes a research publication to become highly cited and stand the test of time? We asked UW ECE faculty to help shed some light on this intriguing question.

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Azadeh Yazdan receives $3.2M grant to investigate ways neurotechnology could induce targeted changes in the brain, leading to better treatments for stroke

UW ECE professor Azadeh Yazdan has received an NIH grant to experiment with using optogenetic stimulation, a cutting-edge neurotechnology, to induce targeted changes in the brain.

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Azadeh Yazdan receives $3.2M grant to investigate ways neurotechnology could induce targeted changes in the brain, leading to better treatments for stroke Banner

Small Business awards from DARPA and NASA fuel growth of UW spinout Tunoptix

Tunoptix, the Seattle-based optics startup co-founded by UW ECE Professors Karl Böhringer & Arka Majumdar, is developing next-gen meta-optics imaging systems.

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https://www.ece.uw.edu/spotlight/uw-biofab-a-force-for-reproducible-science/
https://www.ece.uw.edu/spotlight/mo-li-2021-optica-fellow/
https://www.ece.uw.edu/spotlight/highly-cited-papers/
https://www.ece.uw.edu/spotlight/azadeh-yazdan-neurotechnology-for-stroke/
https://www.ece.uw.edu/spotlight/small-business-awards-tunoptix/
https://www.ece.uw.edu/spotlight/eve-riskin-stars-2021/
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UW BIOFAB: A force for reproducible science

The UW’s Biofabrication Center, founded by UW ECE Professor and Chair Eric Klavins, partners with Agilent Technologies in pursuit of automated, reproducible research. [caption id="attachment_23658" align="aligncenter" width="907"]Undergraduate technicians perform common molecular biology tasks to enable the rapid design, construction and testing of genetically reprogrammed organisms for biotechnology applications and research. Dennis Wise / University of Washington Undergraduate technicians perform common molecular biology tasks to enable the rapid design, construction and testing of genetically reprogrammed organisms for biotechnology applications and research. Dennis Wise / University of Washington[/caption]   Article by Renske Dyedov, UW Institute for Nano-Engineered Systems (NanoES)

Key to advancing any new scientific discovery is the ability for researchers to independently repeat the experiments that led to it. In science today, particularly biology, the lack of reproducibility between experiments is a major problem that slows scientific progress, wastes resources and time, and erodes the public’s trust in scientific research.

[caption id="attachment_23672" align="alignright" width="232"]UW ECE Professor and Chair, Eric Klavins. Dennis Wise / University of Washington BIOFAB founder, and UW ECE Professor and Chair, Eric Klavins. Dennis Wise / University of Washington[/caption] At the University of Washington, researchers have access to the UW Biofabrication Center, or BIOFAB, a unique facility located in the Nanoengineering and Sciences building in which scientific protocols are encoded as computer programs, allowing undergraduate lab technicians to execute experiments according to detailed instructions. “The BIOFAB is unlike any other lab on campus,” says BIOFAB founder Eric Klavins, Professor and Chair of the UW Electrical & Computer Engineering Department (UW ECE). “In effect, we’ve been able to automate common protocols by using software to assist our student technicians. This ‘human-in-the-loop’ system goes a long way towards improving the replicability of biological research.” In an effort to expand the lab’s automation capabilities, the BIOFAB has partnered with Agilent Technologies Inc., a life sciences development and manufacturing company based in California’s Silicon Valley. Using state-of-the-art research equipment from Agilent, the BIOFAB will develop high-throughput workflows for common tasks of interest to members of the synthetic biology community.

Programming the biology lab

Computer programmers write code to tell a computer what to do and how to do it. For a given program, the same inputs consistently result in the same outputs. In contrast, two biology researchers can seemingly carry out the same experiment, but get different results. This is in part because instructions for how the experiment was conducted – whether documented in a lab notebook or published in a journal – are often vague or incomplete, leaving out details that the author may not have realized impacted the experimental outcome. [caption id="attachment_23657" align="alignleft" width="580"]Aquarium is a web-based software application that allows scientists to build executable protocols, design experimental workflows based on those protocols, manage the execution of protocols in the lab and automatically record the resulting data. Dennis Wise / University of Washington Aquarium is a web-based software application that allows scientists to build executable protocols, design experimental workflows based on those protocols, manage the execution of protocols in the lab and automatically record the resulting data. Dennis Wise / University of Washington[/caption] As a computer scientist turned synthetic biologist, Klavins realized what biologists needed was a more formal way – a programming language – to define how to conduct an experiment. This led to the development of Aquarium, a web-based software application that allows scientists to build executable protocols, design experimental workflows based on those protocols, manage the execution of protocols in the lab and automatically record the resulting data. “Aquarium provides the means to specify, as precisely as possible, how to obtain a result,” said Klavins. When it comes to engineering biology – reprogramming cells to produce chemicals or drugs, or perform complex functions like sensing toxic compounds in the environment – reproducibility is paramount. The BIOFAB uses Aquarium to standardize various scientific workflows, generating reliable and highly reproducible results. The BIOFAB is one of a growing number of labs known as biofoundries which are committed to efficiently engineering biological systems and workflows. BIOFAB operations are overseen by two lab managers, with a dozen or so undergraduate students executing jobs for BIOFAB clients. BIOFAB technicians perform common molecular biology tasks like DNA assembly and purification as a fee-for-service to the scientific community. Since its founding in 2014, the BIOFAB has run over 30,000 jobs for 300+ different clients at the UW and beyond. “The BIOFAB has been absolutely instrumental in establishing and executing robust Aquarium driven protocols for a major portion of our de novo design minibinder pipeline,” said Lance Stewart, Chief Strategy and Operations Officer at the UW’s Institute for Protein Design (IPD). IPD researchers use computers to design millions of minibinders – small, stable proteins that bind with high affinity to targets of interest – that must be produced and tested in the lab. IPD uses the BIOFAB to screen minibinder candidates for protein stability and protein:protein interactions, which involves constructing yeast libraries from chip synthesized oligonucleotide genes encoding minibinder designs and carrying out large scale fluorescence activated cell sorting and next generation DNA sequencing. “By handing off time-consuming wet lab work to our technicians, BIOFAB clients like IPD can focus more on the design and data analysis aspects of their experiments,” said Klavins.

Learning by doing

[caption id="attachment_23659" align="alignright" width="330"]BIOFAB technician Nicole Roullier. Dennis Wise / University of Washington BIOFAB technician Nicole Roullier. Dennis Wise / University of Washington[/caption] On any given day, the BIOFAB is buzzing with undergraduate technicians working together in harmony to complete an assortment of experiments for BIOFAB clients. Most technicians start working in the BIOFAB as freshman or sophomores, and for many, it’s their first real lab experience. Upon joining the lab, BIOFAB lab managers teach students basic lab skills, such as pipetting and sterile technique, and orient them to the lab. Armed with this foundational knowledge, BIOFAB technicians can begin executing a variety of different protocols by following the step-by-step instructions provided through Aquarium. Students become adept at performing complicated experimental workflows involving complex equipment through the process of doing them over and over again. “Aquarium allows us to effectively train many students simultaneously and get them working in the lab relatively quickly,” said Aza Allen, a lab manager at the BIOFAB. “Aquarium’s technician interface makes it easy to get undergraduate students, who do not necessarily know much about molecular biology when they start, to perform experiments reliably.” “I have learned so much beyond what could possibly be taught in a classroom setting,” said BIOFAB technician Nicole Roullier, a UW biochemistry senior. “Most undergraduates don’t have the opportunity to work with such sophisticated equipment and master advanced techniques like qPCR and next-generation sequencing (NGS). This hands-on training has built up my confidence in the lab in preparation for graduate school.”

A promising partnership

The BIOFAB provides critical automation and analytics infrastructure dedicated to enabling the rapid design, construction and testing of genetically reprogrammed organisms for biotechnology applications and research. Through its partnership with Agilent, the BIOFAB aims to offer new high-throughput capabilities that will further speed up and scale up synthetic biology research. “We’re thrilled to be partnering with Agilent,” said Klavins. “Their support will not only accelerate the development of innovative technologies, but will help us educate students using cutting-edge equipment, bolstering our ability to prepare students for success in their own future research and career.” “We think this is the start of an exciting collaboration,” said Kevin Meldrum, General Manager and Vice President of Genomics at Agilent. “We are pleased to be able to support researchers at the UW and the educational mission of the university through the BIOFAB. We see this as an investment in the future of our field.” [caption id="attachment_23660" align="alignleft" width="630"]Agilent’s state-of-the-art liquid-handling robot, the Bravo Automated Liquid Handling platform will help speed up and scale up synthetic biology research. Dennis Wise / University of Washington Agilent’s state-of-the-art liquid-handling robot, the Bravo Automated Liquid Handling platform will help speed up and scale up synthetic biology research. Dennis Wise / University of Washington[/caption] As a result of this partnership, the BIOFAB has acquired several valuable pieces of equipment, including Agilent’s state-of-the-art liquid-handling robot, the Bravo Automated Liquid Handling platform. While the Bravo can be used to automate sample preparation for a variety of different applications, the BIOFAB plans to initially use it to expedite its workflow for NGS. In addition to the Bravo, the BIOFAB has also acquired the AriaMx Real-Time PCR System, and the 5200 Fragment Analyzer System, a parallel capillary electrophoresis system. “Library preparation for high-throughput NGS is a tedious, labor-intensive process,” said Klavins. “Agilent’s Bravo will help make this workflow more efficient and reduce pipetting errors that make results less consistent, while also freeing up time for our technicians to work on less repetitive tasks. We know that there are certainly other workflows that would benefit from the use of Bravo, and we plan to engage BIOFAB users to identify which ones to pursue. We are thrilled to be able to bring this resource to the UW community, and are excited to see the compelling science that comes out as a result.” [post_title] => UW BIOFAB: A force for reproducible science [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => uw-biofab-a-force-for-reproducible-science [to_ping] => [pinged] => [post_modified] => 2021-11-24 10:21:02 [post_modified_gmt] => 2021-11-24 18:21:02 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23652 [menu_order] => 1 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [1] => WP_Post Object ( [ID] => 23624 [post_author] => 27 [post_date] => 2021-11-16 11:19:41 [post_date_gmt] => 2021-11-16 19:19:41 [post_content] => By Wayne Gillam | UW ECE News [caption id="attachment_23634" align="alignright" width="575"]Mo Li headshot UW ECE Professor Mo Li recently received the honor of being named an Optica Fellow for his leading contributions to the fields of optics and photonics. Li is also a professor in the UW Department of Physics and a member of the Institute for Nano-Engineered Systems at the UW. Photo by Ryan Hoover[/caption] On November 2, UW ECE Professor Mo Li received the honor of being named an Optica Fellow for his leading contributions to nanophotonics, optomechanics and integrated acousto-optics. Li’s pioneering research has been foundational to development of integrated nano-optomechanical systems, which enable novel ways of controlling light and interaction with materials using mechanical principles and light forces. His work developing integrated acousto-optics revealed and exploited the interaction between light and sound waves in nanophotonic systems, and he has also made important contributions to 2D material optoelectronics. Optica, formerly known as the Optical Society of America, or OSA, grants the honor of becoming an Optica Fellow to those who have achieved significant scientific accomplishment in the advancement of optics and photonics. The bylaws of this society allow only 10% of its membership to be designated as an Optica Fellow, and the number elected each year is limited to approximately 0.5% of the previous year’s membership total. Li joins his UW ECE colleague, Professor Lih Lin, who herself received the honor in 2019. “I am honored to be named as a Fellow of Optica, the society I have benefited tremendously from since I was a student,” Li said. Li, who is also a professor in the UW Department of Physics and a member of the Institute for Nano-Engineered Systems, has been making significant contributions to the fields of optics and photonics since he obtained his doctoral degree from Caltech in 2007. Since then, he has published more than 80 papers and been awarded six patents. He has been a member of Optica since 2007, and his distinctions include an Air Force Office of Scientific Research (AFOSR) Young Investigator Award; a National Science Foundation (NSF) CAREER award; and a McKnight Land-Grant Professorship and Borja Career Development Award from the University of Minnesota. Li’s postdoctoral work at Yale University from 2008 to 2010 helped to lay the foundation for the study of optical forces and optomechanical interactions in integrated photonics. In 2010, he began his independent research career as an assistant professor of electrical and computer engineering at the University of Minnesota, and in 2015, he was promoted to associate professor. While at the University of Minnesota, he continued his research in optomechanics and made leading contributions in many other areas of photonics, including 2D materials optoelectronics, mid-infrared photonics, optical spintronics and photonic sensors. Since joining the UW in 2018, Li has continued to branch out and build upon his previous work. In addition to leading the Laboratory of Photonic Devices at the UW, he is involved with cutting-edge quantum computing research and is a member of the steering committee for the Quantum X Initiative at the UW. His research collaborations at the University have included development of integrated photonic systems for powering quantum computing, creation of integrated photonics for optical computing and acceleration of artificial intelligence and machine learning. His research interests continue to span a wide range of technical areas related to optics and integrated photonics. “We are very fortunate to have Mo as a faculty member,” said UW ECE Professor and Chair Eric Klavins. “His contributions to the field of photonics have been groundbreaking, and what’s exciting is that he is still moving into new research areas. His work is foundational to UW ECE’s efforts developing quantum computing systems and our strong footprint in that area. I expect to see many more advancements result from his work, not only in optics and photonics, but also in areas these fields support such as quantum computing.” More information about Mo Li and his research can be found on his UW ECE bio page. [post_title] => Professor Mo Li named 2021 Optica Fellow [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => mo-li-2021-optica-fellow [to_ping] => [pinged] => [post_modified] => 2021-11-24 10:20:33 [post_modified_gmt] => 2021-11-24 18:20:33 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23624 [menu_order] => 2 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [2] => WP_Post Object ( [ID] => 23539 [post_author] => 27 [post_date] => 2021-11-05 10:10:09 [post_date_gmt] => 2021-11-05 17:10:09 [post_content] => By Wayne Gillam | UW ECE News [caption id="attachment_23542" align="alignright" width="625"]Headshots of 17 UW ECE faculty members What causes a research publication to become highly cited and stand the test of time? We asked these UW ECE faculty members — who have all written research publications that are frequently cited — to help shed some light on this intriguing question.[/caption] It’s widely known that the University of Washington Department of Electrical & Computer Engineering is located in Seattle, a major technology hub and home to companies such as Amazon, Microsoft and Boeing. This proximity to leading technology companies makes the research and learning environment at UW ECE exceptionally rich, collaborative and innovative. But what might be less known is that many faculty members in the Department are leading their respective fields both nationally and internationally. Many UW ECE faculty have had a major impact on electrical and computer engineering research over the years. These faculty members tend to be prolific authors of papers, books and other publications that are highly cited by researchers worldwide. A 2014 study showed that only 0.026% of research papers have over 1,000 citations, and according to Google Scholar, 17 UW ECE faculty members have had at least one publication, and sometimes many more, with over 1,000 citations. “Because many of our faculty are leading and at the cutting edge of their respective fields, their work often is heavily cited by their peers and those following in their footsteps,” said UW ECE Professor and Chair Eric Klavins. “I don’t think there is a magic formula for guaranteeing a research publication will become highly cited. But if there is one, our faculty seem to have cracked that code.” What sorts of variables lead to a research paper, book or article becoming highly cited? This is a question often asked by students, faculty and researchers. But it’s one that doesn’t appear to have a clear-cut answer. There are many factors that contribute to a research paper becoming well-known and frequently cited — for example, the impact of the research in academia and industry, the profile of the author, the topic the paper is addressing and the prominence of the journal or publication the paper is published in. However, even though it’s unlikely this question can ever be fully answered, useful insights can still be gained by asking faculty directly why specific work of theirs has been cited so frequently. To that end, the following is a listing of UW ECE faculty members who have authored frequently cited publications along with a link to one of their well-known papers, books or articles. Each work listed has over 1,000 citations, according to Google Scholar on October 15, 2021. Faculty were asked why they thought this particular paper or publication was so often cited, and their responses are below. As one might expect, there was no single, definitive answer to the question, “What caused your research publication to be highly cited?” However, examining feedback from UW ECE faculty revealed several common and general themes. Among the faculty surveyed, these three factors appeared to most often contribute to a research publication being highly cited:
  • Demonstrating first-of-its-kind and/or novel research results
  • Providing comprehensive guidance to a field or sector of a field with focus on real-world applications
  • Helping to lay groundwork for new or emerging theory and fields within engineering
Read on for specific answers from each UW ECE faculty member addressing what they think made their publication highly cited. The statements below are summaries of feedback received

Linda Shapiro

Linda Shapiro headshotRole at UW ECE: Professor Research focus: Data Science, Biosystems Publication: Book, Computer and robot vision, Addison-Wesley Longman, 1991 Number of citations: 6,791 Why was this book so highly cited? This two-volume set became the authoritative reference for a comprehensive introduction to computer vision. It provided a comprehensive background on theory and algorithms while also linking to real-world applications.  

Jeffrey Bilmes

Jeff Bilmes headshot Role at UW ECE: Professor Research focus: Machine learning, AI, Biosystems, Data Science Publication:A gentle tutorial of the EM algorithm and its application to parameter estimation for Gaussian mixture and hidden Markov models,” ICSI Journal, 1998 Number of citations: 3,559 Why was this paper so highly cited? The Expectation-Maximization (EM) algorithm is needed in very important machine learning scenarios where there are variables that interact with those in the dataset but were hidden or not observed. It is an effective and general approach, yet it was not widely understood before this paper. This was the first paper to fully develop the EM algorithm for maximum-likelihood estimation in a way that made it easy to understand by a broad sector of the machine learning community.  

Maryam Fazel

Maryam Fazel headshot Role at UW ECE: Moorthy Family Professor, Associate Chair for Research Research focus: Data Science, Robotics and Controls Publication:Guaranteed minimum-rank solutions of linear matrix equations via nuclear norm minimization,” SIAM Review, 2010 Number of citations: 3,502 Why was this paper so highly cited? This paper was the first to show how to estimate low-rank matrices perfectly from highly incomplete information. This surprising result ushered in the new research field of matrix completion and sensing, which found many applications, including in recommender systems, dynamical system identification and phase retrieval in imaging.  

Sumit Roy

Sumit Roy headshotRole at UW ECE: Professor Research focus: Computing and Networking Publication:Data mules: Modeling and analysis of a three-tier architecture for sparse sensor networks,” Ad Hoc Networks, 2003 Number of citations: 2,617 Why was this paper so highly cited? This was the first analytical model for the impact of mobile ubiquitous local area network extensions, or MULES, collecting data in what was then the very new and emerging field of sensor networking. MULES can pick up data from sensors when in close range, buffer it and pass data off to wired access points. Because of the close range, this approach allowed for large power savings at the sensors and therefore became an important part of modern sensor networking.  

Linda Bushnell

Linda Bushnell headshotRole at UW ECE: Research Professor Research focus: Robotics and Controls Publication:Stability analysis of networked control systems,” IEEE Transactions on Control Systems Technology, 2002 Number of citations: 2,481 Why was this paper so highly cited? The significance of this work is in the combining of communication constraints and control specifications, which had not been previously addressed, for the scheduling of real-time network traffic, such as those used in the controller area network (CAN) protocol in modern automobiles. This paper helped to pave the way for a significant body of work as demonstrated by the hundreds of papers, books and conference tracks that reference it.  

Scott Hauck

Scott Hauck headshotRole at UW ECE: Professor Research focus: VLSI and Digital Systems Publication:Reconfigurable computing: a survey of systems and software,” ACM Computing Surveys, 2002 Number of citations: 2,271 Why was this paper so highly cited? In the mid 1990's field-programmable gate array (FPGA)-based computation was in its infancy, with much promise and many approaches. Since then, it has become a major force in high-performance computing. This paper served as the introduction to this field for researchers, guiding many to this evolving field.  

Daniel Kirschen

Daniel Kirschen headshotRole at UW ECE: Donald W. and Ruth Mary Close Professor Research focus: Power and Energy Systems Publication: Book, Fundamentals of Power System Economics, John Wiley & Sons, 2004 Number of citations: 2,024 Why was this book so highly cited? This book became widely used because it looked at an important problem from two different perspectives: It rigorously explained the economics of electricity markets for electrical engineers, while also explaining the underlying engineering to economists. The second edition was published in 2018.  

Joshua Smith

Josh Smith headshotRole at UW ECE: Milton and Delia Zeutschel Professor in Entrepreneurial Excellence, PMP Coordinator Research focus: Biosystems, Photonics and Nano Devices, Power and Energy Systems Publication:Analysis, experimental results, and range adaptation of magnetically coupled resonators for wireless power transfer,” IEEE Transactions on Industrial Electronics, 2010 Number of citations: 1,873 Why was this paper so highly cited? This paper provides a new visualization of the state space of high Q-coupled resonator wireless power transfer systems. The visualization immediately suggests a simple control scheme that can keep the transferred power level constant despite disturbances. The paper showed experimentally that the control scheme actually worked — with the counter-intuitive net result of wireless power transfer that doesn't drop off with distance.  

Shwetak Patel

Shwetak Patel headshotRole at UW ECE: Washington Research Foundation Endowed Professor Research focus: Biosystems, Data Science, Computing and Networking Publication:Experimental security analysis of a modern automobile,” 2010 IEEE Symposium on Security and Privacy Number of citations: 1,863 Why was this paper so highly cited? This paper was the first to show an actual over-the-air attack of the embedded systems infrastructure in a modern automobile. The paper received a 2020 IEEE Test of Time award in addition to a number of other honors. The paper is highly cited because it contributed in large part to launching the auto security field. The U.S. Department of Transportation has adopted several guidelines from the paper, and this work is now integral in the automobile industry.  

Les Atlas

Les Atlas headshotRole at UW ECE: Professor Research focus: Biosystems, Data Science Publication:Improving generalization with active learning,” Machine Learning, 1994 Number of citations: 1,843 Why was this paper so highly cited? This paper was the start of a now-common approach, called active learning, within the field of machine learning. It combined a novel idea of how babies learn speech with the theory of machine learning, including neural nets. Active learning was shown to allow more efficient use of labeled training data. Because most machine learning problems have limited amounts of labeled training data, this approach offered a potentially more efficient and lower cost training approach, inspiring many subsequent papers.  

Mari Ostendorf

Mari Ostendorf headshotRole at UW ECE: System Design Methodologies Professor Research focus: Data Science Publication:ToBI: A standard for labeling English prosody,” Proceedings of the 2nd International Conference on Spoken Language Processing, 1992 Number of citations: 1,786 Why was this paper so highly cited? Prosody is the patterns of stress and intonation in a language. It is accepted to be central to our understanding of language. While much of language can be transcribed into words and represented as text, usual text transcriptions do not transcribe prosody. This paper offered an approach to transcribe prosody, which became a standard, greatly benefiting the field of natural language processing.  

Blake Hannaford

Blake Hannaford headshotRole at UW ECE: Professor Research focus: Robotics and Controls, Biosystems Publication:Measurement and modeling of McKibben pneumatic artificial muscles,” IEEE Transactions on Robotics and Automation, 1996 Number of citations: 1,741 Why was this paper so highly cited? A goal of robotics is to make mechanical actuators behave in a manner similar to human skeletal muscle. This paper recognized that while pioneers in artificial muscle research had inspired many and took advantage of artificial muscles’ compatibility with the human body, there was little or no engineering theory of how artificial muscles worked, and no formal comparison with human muscle. This paper provided the necessary new theory and experimental verification to lay the groundwork used by many researchers in both rehabilitation robotics and soft robotics, which have exploded in use in recent years.  

Henrique (Rico) Malvar

Rico Malvar headshotRole at UW ECE: Affiliate Professor Research focus: Data compression, signal processing, image compression, audio compression, multimedia signal enhancement, multimedia protection and forensics, human-computing interfaces, hardware devices and accessibility Publication: Book, Signal processing with lapped transforms, Artech, 1992 Number of citations: 1,458 Why was this book so highly cited? This book describes the basic theory and applications of lapped transforms in signal processing. These transforms are now commonly used in audio and image compression and enhancement, geophysics, digital communications, and other applications.  

Georg Seelig

Georg Seelig headshotRole at UW ECE: Professor Research focus: Biosystems Publication:Enzyme-free nucleic acid logic circuits,” Science, 2006 Number of citations: 1,384 Why was this paper so highly cited? In DNA computing, scientists and engineers try to identify a minimal set of rationally designed molecular building blocks that enable them to reconstruct the kind of molecular computation performed by cells and living organisms. The goal of this work was not to understand biology but to develop reliable engineering paradigms for molecular systems that were also transparent because they were man-made, rather than having evolved over millions of years. This paper introduced such a systematic approach based on DNA strand displacement. The approach has since been used widely and effectively, and it provides the foundation for today’s dynamic DNA nanotechnology.  

Michael Taylor

Michael Taylor headshotRole at UW ECE: Associate Professor Research focus: Computing and Networking Publication:The raw microprocessor: A computational fabric for software circuits and general-purpose programs,” IEEE Micro, 2002 Number of citations: 1,311 Why was this paper so highly cited? This paper presented the first physically scalable multicore microprocessor design and implementation, foreshadowing how many multicores are designed today. The challenge faced by very large-scale integration (VLSI) designers was: How can chip designers leverage growing quantities of chip resources even as wire delays become substantial? This paper provided the influential architecture that achieved the maximum amount of performance and energy efficiency in the face of wire delay.  

Mo Li

Mo Li headshotRole at UW ECE: Professor, Graduate Program Coordinator Research focus: Photonics and Nano Devices Publication:Ultra-sensitive NEMS-based cantilevers for sensing, scanned probe and very high-frequency applications,” Nature Nanotechnology, 2007 Number of citations: 1,189 Why was this paper so highly cited? Nanoscale mechanical sensors (dubbed NEMS) offer a greatly enhanced sensitivity that is unattainable with past microscale devices. This paper reported the first very-high-frequency, self-sensing nanocantilevers for chemical gas sensing and analysis in ambient conditions. By measuring its vibration frequency change, the nanocantilever can detect the mass of 30,000 water molecules (or 1 attogram (10-18 g).  

Howard Chizeck

Howard Chizeck headshotRole at UW ECE: Professor Emeritus Research focus: Robotics and Controls, Biosystems Publication:Controllability, stabilizability, and continuous-time Markovian jump linear quadratic control,” IEEE Transactions on Automatic Control, 1990 Number of citations: 1,108 Why was this paper so highly cited? This paper establishes necessary and sufficient conditions for optimal steady state quadratic control of continuous-time linear systems that possess randomly jumping parameters, which can be described by finite-state Markov processes. This seminal paper established a direction of theoretical development and has been applied to a wide variety of practical problems, including wireless communication and traffic control. [post_title] => What causes a research paper to be highly cited? [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => highly-cited-papers [to_ping] => [pinged] => [post_modified] => 2021-11-17 14:03:14 [post_modified_gmt] => 2021-11-17 22:03:14 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23539 [menu_order] => 3 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [3] => WP_Post Object ( [ID] => 23387 [post_author] => 27 [post_date] => 2021-10-18 17:18:47 [post_date_gmt] => 2021-10-19 00:18:47 [post_content] => By Wayne Gillam | UW ECE News [caption id="attachment_23390" align="alignright" width="525"]Azadeh Yazdan on the UW campus UW ECE Assistant Professor Azadeh Yazdan recently received a five-year grant from the National Institutes of Health to experiment with using optogenetic stimulation, a cutting-edge neurotechnology, to induce targeted changes in the brain. Her research could lead to better treatments for neurological disorders and diseases such as stroke. Photo by Ryan Hoover[/caption] Stroke is a killer, and for those who survive, it can have a devastating impact. According to the World Stroke Organization, the disease is a leading cause of death and disability globally, causing an estimated 5.5 million deaths and 116 million years of healthy life to be lost each year. It is also a very common experience. One in four adults over the age of 25 will have a stroke in their lifetime. So, why is this disease so deadly and debilitating? The answer to that question has to do in part with how stroke can cause the connections between neurons in the brain to deteriorate, break or disappear entirely, often resulting in death, loss of bodily functions and disability. Unfortunately, there is no cure for this disease. But what if scientists and engineers could use neurotechnology, which has shown promise in treating other neurological conditions such as those caused by spinal cord injury, to intervene? Could key neural connections be targeted and induced to heal and repair themselves after a stroke has occurred? UW ECE Assistant Professor Azadeh Yazdan is investigating possible answers to these questions. Yazdan, who is the Washington Foundation Innovation Assistant Professor of Neuroengineering in UW ECE and the UW Department of Bioengineering and a member of the Center for Neurotechnology, has several years of research experience studying possible ways to treat neurological disorders and diseases such as stroke. What happens in a lot of these disorders is that there is aberrant neural connectivity in one or more areas,” Yazdan said. “For example, if someone has a stroke, they are missing connections between brain areas, whereas if someone has a psychiatric disorder such as post-traumatic stress disorder, they might have connections in the brain that are not supposed to be there.” Yazdan’s research focuses on using neurotechnology to induce targeted changes in the brain, reorganizing neural pathways in ways that could address these connectivity issues, helping the brain to heal and recover after injury. She recently received a $3.2M, five-year grant from the National Institutes of Health to further advance her work in this area and to specifically study functional recovery following an ischemic lesion in the brain, a condition that is commonly known as a stroke. [caption id="attachment_23397" align="alignleft" width="600"]Amy Orsborn, Eberhard Fetz, Ricky Wang headshots Co-investigators on the NIH grant include, from left to right, UW professors Amy Orsborn, Eberhard Fetz and Ricky Wang.[/caption] “I’m excited to help people who are dealing with neurological disorders, and I think this research could be especially helpful in finding better treatments for stroke,” Yazdan said. “But also, what we learn will have applications beyond stroke. If we can show targeted reorganization in the brain, the knowledge could be used to better treat diseases that are similar to stroke such as traumatic brain injury or cerebral palsy, as well as psychiatric disorders such as depression.” Yazdan is now in the midst of assembling her research team for work supported by the new grant, and she is recruiting for a postdoctoral researcher and lab technician. Co-investigators on the NIH grant include Amy Orsborn, the Clare Boothe Luce Assistant Professor at UW ECE and the UW Department of Bioengineering, who specializes in therapeutic neural interfaces; Eberhard Fetz, a UW professor of physiology and biophysics, who was one of the early pioneers of brain-computer interface development; and Ricky Wang, a UW professor in bioengineering and ophthalmology. “I am looking forward to working with Dr. Yazdan on this exciting project,” Orsborn said. “The work will shed new light on how neurotechnology can be used to rewire brain networks, which will have wide-ranging therapeutic applications.”

Optogenetic stimulation of the brain

For her NIH-funded research, Yazdan will primarily be using optogenetics to stimulate neurons in the brain instead of electricity, which is currently the go-to form of brain stimulation for neural engineering. Optogenetics is a technology that uses light to activate and inhibit neurons, and although it has been around for several decades, it is a relative newcomer to neurotechnology. Optogenetics has the advantages of being more precise and controllable than electrical stimulation, and it will allow Yazdan and her team to tease apart complicated neural circuits in ways that will be useful for better understanding neural network connectivity. “With optogenetics, we have the capability of recording during the stimulation period to see how the neural network is evolving, and what neural changes can lead to functional changes and recovery through simultaneous behavioral measures,” Yazdan said. “Following a lesion in the brain, we can measure a behavioral deficit, and we can also measure neural and functional recovery as a result of our stimulation parameters.”   [caption id="attachment_23392" align="aligncenter" width="1200"]Photo illustration showing use of optogenetics in the brain This illustration shows targeted reorganization of the brain using optogenetics, a cutting-edge neurotechnology that uses light to activate and inhibit neurons in the brain. Far left: An area of the brain is targeted for modification. Center: The targeted area of the brain is illuminated to control the activity of underlying neural circuits using optogenetics. Far right: A demonstration of how connectivity between two neurons can change following optogenetic intervention. Note the subtle change in the connecting line between neurons. It brightens, showing that the neural connection has strengthened. Illustration provided by Azadeh Yazdan.[/caption]   Yazdan has been working for several years developing optogenetic tools capable of giving more precise and cell-type specific manipulations of the brain, as well as interfaces that can enable scientists and engineers to manipulate and record from large areas of the brain. Concurrent with her NIH-funded research, she is co-leading a multi-institutional effort to develop a ‘smart dura,’ a device that has the capability to perform optogenetic stimulation and also allows unprecedented large-scale access to the brain. The smart dura will enable Yazdan and her research team to record and manipulate neural network activity with unmatched, high resolution. “The brain network structure is actually a big mediator of the changes that we’re seeing. There are no two people who have the same stroke and the same damage,” Yazdan said. “So, in this grant, we’re also including the network structure information into the design of our stimulation protocols. For future stroke therapies, you can imagine that brain stimulation protocols could be customized to a patient’s stroke.”

What the future holds

By the end of the five-year NIH grant, the research team is aiming to establish a proof of concept that demonstrates the effectiveness of refined brain stimulation patterns for targeted neurorehabilitation and ‘rewiring’ of the brain. Their work will also help scientists and engineers better understand neural circuits and connectivity in the areas of the brain that are studied. Yazdan said that long-term goals for this line of research depend in part on what the team discovers over the next five years. But because her team is studying functional recovery following stroke, she is hoping that she can pair up with clinicians to apply some of their research findings in a clinical setting. She is also interested in expanding the focus of the research to encompass other neurological and psychological disorders. “A long-term goal that I have is to see how we can manipulate the brain and induce these targeted changes, which could be used for treating different neurological disorders, beyond stroke,” Yazdan said. “This grant will be a really good first step for that.” She also noted that because much is still unknown when it comes to neurological disorders and diseases such as stroke, it has historically been difficult for scientists and engineers to develop effective treatments. “We have about one billion people worldwide that suffer from some kind of neurological disorder. In this research, we will learn much that could help us improve current brain stimulation-based therapies,” Yazdan said. “This work could also open up a lot of opportunities for us to understand the brain and its response to stimulation. Basically, it will help us to better understand how to induce these targeted changes to the brain in ways that could potentially cure someone.” For more information about the research described in this article, contact Azadeh Yazdan. [post_title] => Azadeh Yazdan receives $3.2M grant to investigate ways neurotechnology could induce targeted changes in the brain, leading to better treatments for stroke [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => azadeh-yazdan-neurotechnology-for-stroke [to_ping] => [pinged] => [post_modified] => 2021-11-17 14:03:21 [post_modified_gmt] => 2021-11-17 22:03:21 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23387 [menu_order] => 4 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [4] => WP_Post Object ( [ID] => 23360 [post_author] => 26 [post_date] => 2021-10-14 13:51:49 [post_date_gmt] => 2021-10-14 20:51:49 [post_content] =>
Story by UW Institute for Nano-Engineered Systems (NanoES)
[caption id="attachment_2983" align="alignright" width="301"]Arka Majumdar (left) and Karl Böhringer (right) Arka Majumdar (left) and Karl Böhringer (right)[/caption] Tunoptix, a Seattle-based optics startup co-founded by Karl Böhringer and Arka Majumdar, professors in the University of Washington Department of Electrical & Computer Engineering (UW ECE), was awarded a $1,500,000 Small Business Technology Transfer (STTR) Phase II grant from the Defense Advanced Research Projects Agency (DARPA). This highly competitive award provides funding for Tunoptix to continue developing next-generation imaging systems for use on satellites or aircrafts where weight, size and power are critical. Lenses with large apertures, the opening through which light travels, are needed to capture images in low-light environments. The extremely large aperture lenses currently used by the defense and aerospace industries for surveillance and space exploration are generally very heavy and bulky. For example, the lens in the Hubble space telescope, which has an aperture of about 2 meters, is roughly 1,000 kilograms. Reducing the size, weight and power of such optical systems would significantly reduce their cost. Meta-optics – engineered surfaces consisting of an array of nanoscale structures that can focus light – are emerging as a promising alternative to traditional lenses. Although meta-optics are lightweight and exceptionally thin (< 1mm), they cannot generate high quality color images. There are some solutions for full-color imaging, but all of them are generally limited to small apertures, about 100 – 200 micrometers in diameter. Tunoptix is developing large aperture (~1cm-10cm) metalenses combined with advanced AI-based image reconstruction software to capture high quality full-color images.
Comparison between a conventional compound refractive imaging system and a Tunoptix current-generation computational imaging system. The conventional imaging system requires multiple optics to correct chromatic and geometric aberrations, resulting in a heavy and bulky package. The Tunoptix computational meta-optic is a single-element, flat solution with a drastically reduced package weight and size that encodes information from the scene. The computational imaging software is jointly designed with the meta-optic and recovers the high-quality image or desired information from the data in the intermediate image encoded by the meta-optic. Image courtesy of Tunoptix.

Tunoptix was previously awarded a $223k DARPA STTR Phase I grant to establish the feasibility of scaling their metasurface designs up to 10 centimeters. This STTR Phase II award will allow the company to begin fabricating its large aperture metasurface designs at the UW Washington Nanofabrication Facility (WNF), an open-access user facility that provides academic researchers and industry professionals access to nanofabrication tools and expertise.
[caption id="attachment_2981" align="alignnone" width="183"]Felix Heide Felix Heide[/caption]
A portion of the Phase II work will be carried out by the laboratory of Felix Heide, a computer science professor at Princeton University. Heide’s computational imaging lab will evaluate the imaging capability of Tunoptix’s metasurfaces and help optimize the algorithms used for image reconstruction. While the focus of Tunoptix’s work for DARPA has been imaging in the visible light range, their approach can work for any wavelength. Tunoptix recently received a NASA Small Business Innovation Research (SBIR) Phase I award to develop a compact hyperspectral imaging (HSI) system using their meta-optics technology. Compact HSI systems will be especially useful in carrying out satellite-based and rover-based imaging of planetary surfaces, airborne remote sensing of coastal and oceanic regions, and inspection of mission-critical satellite systems in space. “We are focused on revolutionizing the way optical systems are conceptualized, designed and manufactured,” said Majumdar. “Using well-established, high precision, low-cost semiconductor manufacturing techniques we are creating new, simple optical elements that will be critical for the evolution of optical design in the digital age. Moreover, by incorporating computational algorithms on the backend, we can improve image quality leaps and bounds over what was achievable using just meta-optics.” For those interested in advancing this technology, Tunoptix is hiring several positions including an optical test engineersoftware developer and AI consultant. [post_title] => Small Business awards from DARPA and NASA fuel growth of UW spinout Tunoptix [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => small-business-awards-tunoptix [to_ping] => [pinged] => [post_modified] => 2021-11-17 14:03:29 [post_modified_gmt] => 2021-11-17 22:03:29 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23360 [menu_order] => 5 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [5] => WP_Post Object ( [ID] => 23192 [post_author] => 27 [post_date] => 2021-10-04 14:21:09 [post_date_gmt] => 2021-10-04 21:21:09 [post_content] => by Wayne Gillam | UW ECE News [caption id="attachment_23200" align="alignright" width="550"]Eve Riskin headshot Professor Eve Riskin is returning to UW ECE after 15 years as an associate dean in the UW College of Engineering. And as co-founder and faculty director of STARS, she has plans to share this successful program model with colleges and universities across the country. STARS helps to make higher education more accessible and provides support for students from low-income, first-generation and underserved backgrounds. Photo by Ryan Hoover[/caption] After 15 years as an associate dean for the UW College of Engineering and one year on sabbatical, professor Eve Riskin has returned to the UW Department of Electrical & Computer Engineering this fall as the Department’s newly-appointed undergraduate program coordinator. In this role, Riskin will work closely with the UW ECE associate chair for education and student advising team to manage undergraduate policies, issues and admissions. “I’m really happy to be back at UW ECE,” Riskin said. “I’m so thrilled with the welcome the Department is giving me as I return. I hope to apply some of what I learned as an associate dean to UW ECE.” Riskin started her career at UW ECE in 1990. In addition to receiving several honors and awards over the years as an educator and for her research, she is well-known for her persistent and impactful work in diversity, equity and inclusion at the University. Riskin has received numerous awards related to expanding diversity and access to education, such as an ECEDHA Diversity Award, a Hewlett-Packard Harriett B. Rigas Award and a UW David B. Thorud Leadership Award. In 2020, her efforts were recognized with one of the nation’s highest honors, a Presidential Award for Excellence in Science, Mathematics and Engineering Mentoring. “When he was chair of UW ECE, Radha Poovendran nominated me for the ECEDHA and PAESMEM awards, and this was so kind of him,” Riskin said. “Eve is very inspiring. She has dedicated her career to increasing access to engineering for underrepresented students,” said UW ECE Professor and Chair Eric Klavins. “We are so excited to welcome her back to UW ECE and incredibly lucky to have her in the role of undergraduate program coordinator, where her expertise with diversity, equity and inclusion will have such a positive impact on our students.” Now, fresh from her sabbatical, Riskin shows no signs of slowing down. In addition to her duties as an instructor and her new role at UW ECE as undergraduate program coordinator, Riskin is continuing as faculty director of two successful programs she co-founded at the UW — UW ADVANCE, which is dedicated to the advancement of female faculty in STEM fields, and the Washington State Academic RedShirt program, which is known as STARS. According to Riskin, the STARS program holds a special place in her heart because of its powerful impact on students who come from low-income and underserved backgrounds. “Eve’s leadership has profoundly advanced our College’s mission to recruit and retain people from underrepresented or disadvantaged groups,” said professor Sam Burden, UW ECE’s Associate Chair for Diversity, Equity and Inclusion. “I was thrilled when she recruited me to pitch in on STARS, which is an outstanding program that has enabled unprecedented access to engineering education for women, underrepresented minorities and first-generation college students. We are extremely fortunate to have Eve back full-time in our Department, and I am eager to leverage her expertise to make UW ECE more diverse, equitable and inclusive for all.”

What is the STARS program?

[caption id="attachment_23202" align="alignright" width="450"]Sonya Cunningham and Eve Riskin at a social gathering Riskin (right) will be working closely with Sonya Cunningham (left), executive director of the STARS program at the UW, to spread the STARS program model nationwide.[/caption] The STARS program draws its inspiration from the concept of a “redshirt” year in college athletics, giving students an extra year of preparation to succeed in school. The program supports engineering and computer science students from low-income, first-generation and underserved backgrounds in navigating the transition to college-level courses, and it is welcoming its ninth cohort this fall. This two-year program includes a specialized curriculum designed to build learning skills and strengthen academic preparation for core math and science prerequisites. Riskin was the principal investigator for two National Science Foundation grants that helped to launch STARS at the UW and provide substantial support for the program over the last eight years. Now, with the support of colleagues and a third NSF grant, she is laying the groundwork for an upcoming conference to be held in June 2022 on the UW campus, which will share details about how the program works with representatives from colleges and universities across the nation. “We’re going to share the STARS program model and have people look under the hood,” Riskin said. “We’ll examine curricula, we’ll talk about fundraising, and we’ll have a panel with STARS students — testimonials, so they can hear about the impact on students. We’ll share documents, processes, curriculum, policies, everything we created for STARS, so we can help other institutions across the country get started with their own, similar programs.” [caption id="attachment_23281" align="alignleft" width="400"]Lindi Mujugira headshot 2 STARS’ new director, Lindi Rubadiri-Mujugira, will be responsible for much of the staff oversight and hands-on work needed to keep the program running smoothly while Riskin and Cunningham focus on fundraising and sharing the STARS program model. Photo by David Tsay[/caption] Riskin will be working closely with Sonya Cunningham, executive director of the STARS program at the UW, to spread the STARS program model nationwide. The two have formed a strong and effective partnership over the years, and according to Riskin, Cunningham has played a key role in the program’s ongoing success. “STARS wouldn’t be half the program without her,” Riskin said. “Sonya is one of the very best student services professionals in the country. She just has a knack for knowing what a student needs, figuring out what obstacle is holding that student back and helping them get around it. There are many students out there who have college degrees and are now working engineers that would not have succeeded without her. And they tell her that, so that’s really meaningful.” Almost 300 students have participated in the STARS program to date. STARS has also brought on a new director, Lindi Rubadiri-Mujugira, who will be responsible for much of the staff oversight and hands-on work needed to keep the program running smoothly while Riskin and Cunningham are focused on fundraising and disseminating the program model, especially through the June 2022 national conference.

The impact of STARS

Like Riskin, Cunningham is enthusiastic about the impact of the program. “What is most exciting to me about STARS is that it has immeasurable far-reaching implications individually, locally, nationally and globally,” Cunningham said. “There is the obvious possibility to end the intergenerational cycle of poverty for individuals, and beyond this, the program places very diverse students squarely at the decision-making table. This will improve not just the problem-solving process but also the kinds of problems that are chosen to be solved.” Over the first eight cohorts, 79% of STARS students remain enrolled in engineering or computer science, or have graduated. This very high rate of success means better jobs and brighter futures for students. Further evidence of STARS’ impact on students can be found within the program participants’ own words. Mathew Garcia headshot

Mathew Garcia, year two at UW ECE

“The STARS program supported me during the difficult transition from high school to university, and it also prepared me for an exciting future in engineering. I not only built lifelong friendships with the other members of my cohort, but I also made important connections with the incredibly caring staff that inspired me to continue studying STEM during tough times. Through these connections and skills gained during my time at STARS, I gained an amazing internship at Boeing that will be instrumental as I continue to grow as an engineer in the years to come.”       Grace Kariuki headshot

Grace Kariuki, 2021 UW ECE graduate, Research Software Engineer at IBM Research

“I would have never imagined from that first day of transition week how much the STARS program would completely change my life. The incredible staff supported me throughout the entire five years and helped me find lots of opportunities to build my experience. As a graduate, I will soon begin my journey as an engineer at my dream job in my dream city. Through STARS, I also found lifelong friends whom I consider my family. I will forever be grateful to STARS.”         Diallo Wilson headshot

Diallo Wilson, graduating Fall 2021 from UW ECE

“STARS has been my main support network throughout my collegiate career. The tough love early, the cohort model and the excellent faculty taught me that I am someone with my own unique value and set of skills. Rather than being disappointed in what I do not have or understand, STARS taught me to think more about what I do have and that hard work and sacrifice will always be necessary to accomplish my goals.”         Doama Verdizcp headshot

Diana Verduzco, year four at UW ECE

“Being a part of the STARS program provided many opportunities to become a successful student and accomplish my goals. I had the privilege to be a part of a community and was constantly given support by faculty and staff as well as my lifelong friends I met through STARS. Their encouragement and guidance have genuinely gotten me this far. Through this program, I have also had opportunities to intern for companies, gain hands-on experience, communicate with people in industry and get a head start on what the real world looks like. I’m so grateful for this program because I wouldn’t be where I am today without it!”    

A bright future for STARS

[caption id="attachment_23252" align="alignright" width="450"]Eve Riskin and Sonya Cunningham with the first STARS cohort Riskin (far right) and Cunningham (second from right) with the first graduating class from STARS. Over the first eight cohorts, 79% of STARS students remain enrolled in engineering or computer science, or have graduated. This very high rate of success means better jobs and brighter futures for students.[/caption] Alongside her new role as UW ECE undergraduate program coordinator and planning for the June 2022 national STARS conference, Riskin will be fund-raising and working continuously behind the scenes to ensure that STARS remains successful and sustainable over the long term. She remains firmly committed to the vision she has had for the program since its inception, and she is optimistic about the future. “This is about institutional transformation,” Riskin said. “If you want people to succeed, instead of focusing so much on trying to fix the student, you should fix your system. We’re fixing our system to better fit students who didn’t come from privileged backgrounds. We’re finding that STARS students are capable of succeeding and doing many wonderful things in the world. And in fact, many already are.” For more information about the STARS program, visit the program website or contact Eve Riskin, Sonya Cunningham or Lindi Rubadiri-Mujugira. [post_title] => Eve Riskin returns to UW ECE with plans to share the STARS program nationwide [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => eve-riskin-stars-2021 [to_ping] => [pinged] => [post_modified] => 2021-11-17 14:03:38 [post_modified_gmt] => 2021-11-17 22:03:38 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23192 [menu_order] => 6 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) ) [_numposts:protected] => 6 [_rendered:protected] => 1 [_classes:protected] => Array ( [0] => view-block [1] => block--spotlight-robust-news ) [_finalHTML:protected] =>
https://www.ece.uw.edu/spotlight/uw-biofab-a-force-for-reproducible-science/
https://www.ece.uw.edu/spotlight/mo-li-2021-optica-fellow/
https://www.ece.uw.edu/spotlight/highly-cited-papers/
https://www.ece.uw.edu/spotlight/azadeh-yazdan-neurotechnology-for-stroke/
https://www.ece.uw.edu/spotlight/small-business-awards-tunoptix/
https://www.ece.uw.edu/spotlight/eve-riskin-stars-2021/
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UW BIOFAB: A force for reproducible science

The UW’s Biofabrication Center, founded by UW ECE Professor and Chair Eric Klavins, partners with Agilent Technologies in pursuit of automated, reproducible research. [caption id="attachment_23658" align="aligncenter" width="907"]Undergraduate technicians perform common molecular biology tasks to enable the rapid design, construction and testing of genetically reprogrammed organisms for biotechnology applications and research. Dennis Wise / University of Washington Undergraduate technicians perform common molecular biology tasks to enable the rapid design, construction and testing of genetically reprogrammed organisms for biotechnology applications and research. Dennis Wise / University of Washington[/caption]   Article by Renske Dyedov, UW Institute for Nano-Engineered Systems (NanoES)

Key to advancing any new scientific discovery is the ability for researchers to independently repeat the experiments that led to it. In science today, particularly biology, the lack of reproducibility between experiments is a major problem that slows scientific progress, wastes resources and time, and erodes the public’s trust in scientific research.

[caption id="attachment_23672" align="alignright" width="232"]UW ECE Professor and Chair, Eric Klavins. Dennis Wise / University of Washington BIOFAB founder, and UW ECE Professor and Chair, Eric Klavins. Dennis Wise / University of Washington[/caption] At the University of Washington, researchers have access to the UW Biofabrication Center, or BIOFAB, a unique facility located in the Nanoengineering and Sciences building in which scientific protocols are encoded as computer programs, allowing undergraduate lab technicians to execute experiments according to detailed instructions. “The BIOFAB is unlike any other lab on campus,” says BIOFAB founder Eric Klavins, Professor and Chair of the UW Electrical & Computer Engineering Department (UW ECE). “In effect, we’ve been able to automate common protocols by using software to assist our student technicians. This ‘human-in-the-loop’ system goes a long way towards improving the replicability of biological research.” In an effort to expand the lab’s automation capabilities, the BIOFAB has partnered with Agilent Technologies Inc., a life sciences development and manufacturing company based in California’s Silicon Valley. Using state-of-the-art research equipment from Agilent, the BIOFAB will develop high-throughput workflows for common tasks of interest to members of the synthetic biology community.

Programming the biology lab

Computer programmers write code to tell a computer what to do and how to do it. For a given program, the same inputs consistently result in the same outputs. In contrast, two biology researchers can seemingly carry out the same experiment, but get different results. This is in part because instructions for how the experiment was conducted – whether documented in a lab notebook or published in a journal – are often vague or incomplete, leaving out details that the author may not have realized impacted the experimental outcome. [caption id="attachment_23657" align="alignleft" width="580"]Aquarium is a web-based software application that allows scientists to build executable protocols, design experimental workflows based on those protocols, manage the execution of protocols in the lab and automatically record the resulting data. Dennis Wise / University of Washington Aquarium is a web-based software application that allows scientists to build executable protocols, design experimental workflows based on those protocols, manage the execution of protocols in the lab and automatically record the resulting data. Dennis Wise / University of Washington[/caption] As a computer scientist turned synthetic biologist, Klavins realized what biologists needed was a more formal way – a programming language – to define how to conduct an experiment. This led to the development of Aquarium, a web-based software application that allows scientists to build executable protocols, design experimental workflows based on those protocols, manage the execution of protocols in the lab and automatically record the resulting data. “Aquarium provides the means to specify, as precisely as possible, how to obtain a result,” said Klavins. When it comes to engineering biology – reprogramming cells to produce chemicals or drugs, or perform complex functions like sensing toxic compounds in the environment – reproducibility is paramount. The BIOFAB uses Aquarium to standardize various scientific workflows, generating reliable and highly reproducible results. The BIOFAB is one of a growing number of labs known as biofoundries which are committed to efficiently engineering biological systems and workflows. BIOFAB operations are overseen by two lab managers, with a dozen or so undergraduate students executing jobs for BIOFAB clients. BIOFAB technicians perform common molecular biology tasks like DNA assembly and purification as a fee-for-service to the scientific community. Since its founding in 2014, the BIOFAB has run over 30,000 jobs for 300+ different clients at the UW and beyond. “The BIOFAB has been absolutely instrumental in establishing and executing robust Aquarium driven protocols for a major portion of our de novo design minibinder pipeline,” said Lance Stewart, Chief Strategy and Operations Officer at the UW’s Institute for Protein Design (IPD). IPD researchers use computers to design millions of minibinders – small, stable proteins that bind with high affinity to targets of interest – that must be produced and tested in the lab. IPD uses the BIOFAB to screen minibinder candidates for protein stability and protein:protein interactions, which involves constructing yeast libraries from chip synthesized oligonucleotide genes encoding minibinder designs and carrying out large scale fluorescence activated cell sorting and next generation DNA sequencing. “By handing off time-consuming wet lab work to our technicians, BIOFAB clients like IPD can focus more on the design and data analysis aspects of their experiments,” said Klavins.

Learning by doing

[caption id="attachment_23659" align="alignright" width="330"]BIOFAB technician Nicole Roullier. Dennis Wise / University of Washington BIOFAB technician Nicole Roullier. Dennis Wise / University of Washington[/caption] On any given day, the BIOFAB is buzzing with undergraduate technicians working together in harmony to complete an assortment of experiments for BIOFAB clients. Most technicians start working in the BIOFAB as freshman or sophomores, and for many, it’s their first real lab experience. Upon joining the lab, BIOFAB lab managers teach students basic lab skills, such as pipetting and sterile technique, and orient them to the lab. Armed with this foundational knowledge, BIOFAB technicians can begin executing a variety of different protocols by following the step-by-step instructions provided through Aquarium. Students become adept at performing complicated experimental workflows involving complex equipment through the process of doing them over and over again. “Aquarium allows us to effectively train many students simultaneously and get them working in the lab relatively quickly,” said Aza Allen, a lab manager at the BIOFAB. “Aquarium’s technician interface makes it easy to get undergraduate students, who do not necessarily know much about molecular biology when they start, to perform experiments reliably.” “I have learned so much beyond what could possibly be taught in a classroom setting,” said BIOFAB technician Nicole Roullier, a UW biochemistry senior. “Most undergraduates don’t have the opportunity to work with such sophisticated equipment and master advanced techniques like qPCR and next-generation sequencing (NGS). This hands-on training has built up my confidence in the lab in preparation for graduate school.”

A promising partnership

The BIOFAB provides critical automation and analytics infrastructure dedicated to enabling the rapid design, construction and testing of genetically reprogrammed organisms for biotechnology applications and research. Through its partnership with Agilent, the BIOFAB aims to offer new high-throughput capabilities that will further speed up and scale up synthetic biology research. “We’re thrilled to be partnering with Agilent,” said Klavins. “Their support will not only accelerate the development of innovative technologies, but will help us educate students using cutting-edge equipment, bolstering our ability to prepare students for success in their own future research and career.” “We think this is the start of an exciting collaboration,” said Kevin Meldrum, General Manager and Vice President of Genomics at Agilent. “We are pleased to be able to support researchers at the UW and the educational mission of the university through the BIOFAB. We see this as an investment in the future of our field.” [caption id="attachment_23660" align="alignleft" width="630"]Agilent’s state-of-the-art liquid-handling robot, the Bravo Automated Liquid Handling platform will help speed up and scale up synthetic biology research. Dennis Wise / University of Washington Agilent’s state-of-the-art liquid-handling robot, the Bravo Automated Liquid Handling platform will help speed up and scale up synthetic biology research. Dennis Wise / University of Washington[/caption] As a result of this partnership, the BIOFAB has acquired several valuable pieces of equipment, including Agilent’s state-of-the-art liquid-handling robot, the Bravo Automated Liquid Handling platform. While the Bravo can be used to automate sample preparation for a variety of different applications, the BIOFAB plans to initially use it to expedite its workflow for NGS. In addition to the Bravo, the BIOFAB has also acquired the AriaMx Real-Time PCR System, and the 5200 Fragment Analyzer System, a parallel capillary electrophoresis system. “Library preparation for high-throughput NGS is a tedious, labor-intensive process,” said Klavins. “Agilent’s Bravo will help make this workflow more efficient and reduce pipetting errors that make results less consistent, while also freeing up time for our technicians to work on less repetitive tasks. We know that there are certainly other workflows that would benefit from the use of Bravo, and we plan to engage BIOFAB users to identify which ones to pursue. We are thrilled to be able to bring this resource to the UW community, and are excited to see the compelling science that comes out as a result.” [post_title] => UW BIOFAB: A force for reproducible science [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => uw-biofab-a-force-for-reproducible-science [to_ping] => [pinged] => [post_modified] => 2021-11-24 10:21:02 [post_modified_gmt] => 2021-11-24 18:21:02 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23652 [menu_order] => 1 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [1] => WP_Post Object ( [ID] => 23624 [post_author] => 27 [post_date] => 2021-11-16 11:19:41 [post_date_gmt] => 2021-11-16 19:19:41 [post_content] => By Wayne Gillam | UW ECE News [caption id="attachment_23634" align="alignright" width="575"]Mo Li headshot UW ECE Professor Mo Li recently received the honor of being named an Optica Fellow for his leading contributions to the fields of optics and photonics. Li is also a professor in the UW Department of Physics and a member of the Institute for Nano-Engineered Systems at the UW. Photo by Ryan Hoover[/caption] On November 2, UW ECE Professor Mo Li received the honor of being named an Optica Fellow for his leading contributions to nanophotonics, optomechanics and integrated acousto-optics. Li’s pioneering research has been foundational to development of integrated nano-optomechanical systems, which enable novel ways of controlling light and interaction with materials using mechanical principles and light forces. His work developing integrated acousto-optics revealed and exploited the interaction between light and sound waves in nanophotonic systems, and he has also made important contributions to 2D material optoelectronics. Optica, formerly known as the Optical Society of America, or OSA, grants the honor of becoming an Optica Fellow to those who have achieved significant scientific accomplishment in the advancement of optics and photonics. The bylaws of this society allow only 10% of its membership to be designated as an Optica Fellow, and the number elected each year is limited to approximately 0.5% of the previous year’s membership total. Li joins his UW ECE colleague, Professor Lih Lin, who herself received the honor in 2019. “I am honored to be named as a Fellow of Optica, the society I have benefited tremendously from since I was a student,” Li said. Li, who is also a professor in the UW Department of Physics and a member of the Institute for Nano-Engineered Systems, has been making significant contributions to the fields of optics and photonics since he obtained his doctoral degree from Caltech in 2007. Since then, he has published more than 80 papers and been awarded six patents. He has been a member of Optica since 2007, and his distinctions include an Air Force Office of Scientific Research (AFOSR) Young Investigator Award; a National Science Foundation (NSF) CAREER award; and a McKnight Land-Grant Professorship and Borja Career Development Award from the University of Minnesota. Li’s postdoctoral work at Yale University from 2008 to 2010 helped to lay the foundation for the study of optical forces and optomechanical interactions in integrated photonics. In 2010, he began his independent research career as an assistant professor of electrical and computer engineering at the University of Minnesota, and in 2015, he was promoted to associate professor. While at the University of Minnesota, he continued his research in optomechanics and made leading contributions in many other areas of photonics, including 2D materials optoelectronics, mid-infrared photonics, optical spintronics and photonic sensors. Since joining the UW in 2018, Li has continued to branch out and build upon his previous work. In addition to leading the Laboratory of Photonic Devices at the UW, he is involved with cutting-edge quantum computing research and is a member of the steering committee for the Quantum X Initiative at the UW. His research collaborations at the University have included development of integrated photonic systems for powering quantum computing, creation of integrated photonics for optical computing and acceleration of artificial intelligence and machine learning. His research interests continue to span a wide range of technical areas related to optics and integrated photonics. “We are very fortunate to have Mo as a faculty member,” said UW ECE Professor and Chair Eric Klavins. “His contributions to the field of photonics have been groundbreaking, and what’s exciting is that he is still moving into new research areas. His work is foundational to UW ECE’s efforts developing quantum computing systems and our strong footprint in that area. I expect to see many more advancements result from his work, not only in optics and photonics, but also in areas these fields support such as quantum computing.” More information about Mo Li and his research can be found on his UW ECE bio page. [post_title] => Professor Mo Li named 2021 Optica Fellow [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => mo-li-2021-optica-fellow [to_ping] => [pinged] => [post_modified] => 2021-11-24 10:20:33 [post_modified_gmt] => 2021-11-24 18:20:33 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23624 [menu_order] => 2 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [2] => WP_Post Object ( [ID] => 23539 [post_author] => 27 [post_date] => 2021-11-05 10:10:09 [post_date_gmt] => 2021-11-05 17:10:09 [post_content] => By Wayne Gillam | UW ECE News [caption id="attachment_23542" align="alignright" width="625"]Headshots of 17 UW ECE faculty members What causes a research publication to become highly cited and stand the test of time? We asked these UW ECE faculty members — who have all written research publications that are frequently cited — to help shed some light on this intriguing question.[/caption] It’s widely known that the University of Washington Department of Electrical & Computer Engineering is located in Seattle, a major technology hub and home to companies such as Amazon, Microsoft and Boeing. This proximity to leading technology companies makes the research and learning environment at UW ECE exceptionally rich, collaborative and innovative. But what might be less known is that many faculty members in the Department are leading their respective fields both nationally and internationally. Many UW ECE faculty have had a major impact on electrical and computer engineering research over the years. These faculty members tend to be prolific authors of papers, books and other publications that are highly cited by researchers worldwide. A 2014 study showed that only 0.026% of research papers have over 1,000 citations, and according to Google Scholar, 17 UW ECE faculty members have had at least one publication, and sometimes many more, with over 1,000 citations. “Because many of our faculty are leading and at the cutting edge of their respective fields, their work often is heavily cited by their peers and those following in their footsteps,” said UW ECE Professor and Chair Eric Klavins. “I don’t think there is a magic formula for guaranteeing a research publication will become highly cited. But if there is one, our faculty seem to have cracked that code.” What sorts of variables lead to a research paper, book or article becoming highly cited? This is a question often asked by students, faculty and researchers. But it’s one that doesn’t appear to have a clear-cut answer. There are many factors that contribute to a research paper becoming well-known and frequently cited — for example, the impact of the research in academia and industry, the profile of the author, the topic the paper is addressing and the prominence of the journal or publication the paper is published in. However, even though it’s unlikely this question can ever be fully answered, useful insights can still be gained by asking faculty directly why specific work of theirs has been cited so frequently. To that end, the following is a listing of UW ECE faculty members who have authored frequently cited publications along with a link to one of their well-known papers, books or articles. Each work listed has over 1,000 citations, according to Google Scholar on October 15, 2021. Faculty were asked why they thought this particular paper or publication was so often cited, and their responses are below. As one might expect, there was no single, definitive answer to the question, “What caused your research publication to be highly cited?” However, examining feedback from UW ECE faculty revealed several common and general themes. Among the faculty surveyed, these three factors appeared to most often contribute to a research publication being highly cited:
  • Demonstrating first-of-its-kind and/or novel research results
  • Providing comprehensive guidance to a field or sector of a field with focus on real-world applications
  • Helping to lay groundwork for new or emerging theory and fields within engineering
Read on for specific answers from each UW ECE faculty member addressing what they think made their publication highly cited. The statements below are summaries of feedback received

Linda Shapiro

Linda Shapiro headshotRole at UW ECE: Professor Research focus: Data Science, Biosystems Publication: Book, Computer and robot vision, Addison-Wesley Longman, 1991 Number of citations: 6,791 Why was this book so highly cited? This two-volume set became the authoritative reference for a comprehensive introduction to computer vision. It provided a comprehensive background on theory and algorithms while also linking to real-world applications.  

Jeffrey Bilmes

Jeff Bilmes headshot Role at UW ECE: Professor Research focus: Machine learning, AI, Biosystems, Data Science Publication:A gentle tutorial of the EM algorithm and its application to parameter estimation for Gaussian mixture and hidden Markov models,” ICSI Journal, 1998 Number of citations: 3,559 Why was this paper so highly cited? The Expectation-Maximization (EM) algorithm is needed in very important machine learning scenarios where there are variables that interact with those in the dataset but were hidden or not observed. It is an effective and general approach, yet it was not widely understood before this paper. This was the first paper to fully develop the EM algorithm for maximum-likelihood estimation in a way that made it easy to understand by a broad sector of the machine learning community.  

Maryam Fazel

Maryam Fazel headshot Role at UW ECE: Moorthy Family Professor, Associate Chair for Research Research focus: Data Science, Robotics and Controls Publication:Guaranteed minimum-rank solutions of linear matrix equations via nuclear norm minimization,” SIAM Review, 2010 Number of citations: 3,502 Why was this paper so highly cited? This paper was the first to show how to estimate low-rank matrices perfectly from highly incomplete information. This surprising result ushered in the new research field of matrix completion and sensing, which found many applications, including in recommender systems, dynamical system identification and phase retrieval in imaging.  

Sumit Roy

Sumit Roy headshotRole at UW ECE: Professor Research focus: Computing and Networking Publication:Data mules: Modeling and analysis of a three-tier architecture for sparse sensor networks,” Ad Hoc Networks, 2003 Number of citations: 2,617 Why was this paper so highly cited? This was the first analytical model for the impact of mobile ubiquitous local area network extensions, or MULES, collecting data in what was then the very new and emerging field of sensor networking. MULES can pick up data from sensors when in close range, buffer it and pass data off to wired access points. Because of the close range, this approach allowed for large power savings at the sensors and therefore became an important part of modern sensor networking.  

Linda Bushnell

Linda Bushnell headshotRole at UW ECE: Research Professor Research focus: Robotics and Controls Publication:Stability analysis of networked control systems,” IEEE Transactions on Control Systems Technology, 2002 Number of citations: 2,481 Why was this paper so highly cited? The significance of this work is in the combining of communication constraints and control specifications, which had not been previously addressed, for the scheduling of real-time network traffic, such as those used in the controller area network (CAN) protocol in modern automobiles. This paper helped to pave the way for a significant body of work as demonstrated by the hundreds of papers, books and conference tracks that reference it.  

Scott Hauck

Scott Hauck headshotRole at UW ECE: Professor Research focus: VLSI and Digital Systems Publication:Reconfigurable computing: a survey of systems and software,” ACM Computing Surveys, 2002 Number of citations: 2,271 Why was this paper so highly cited? In the mid 1990's field-programmable gate array (FPGA)-based computation was in its infancy, with much promise and many approaches. Since then, it has become a major force in high-performance computing. This paper served as the introduction to this field for researchers, guiding many to this evolving field.  

Daniel Kirschen

Daniel Kirschen headshotRole at UW ECE: Donald W. and Ruth Mary Close Professor Research focus: Power and Energy Systems Publication: Book, Fundamentals of Power System Economics, John Wiley & Sons, 2004 Number of citations: 2,024 Why was this book so highly cited? This book became widely used because it looked at an important problem from two different perspectives: It rigorously explained the economics of electricity markets for electrical engineers, while also explaining the underlying engineering to economists. The second edition was published in 2018.  

Joshua Smith

Josh Smith headshotRole at UW ECE: Milton and Delia Zeutschel Professor in Entrepreneurial Excellence, PMP Coordinator Research focus: Biosystems, Photonics and Nano Devices, Power and Energy Systems Publication:Analysis, experimental results, and range adaptation of magnetically coupled resonators for wireless power transfer,” IEEE Transactions on Industrial Electronics, 2010 Number of citations: 1,873 Why was this paper so highly cited? This paper provides a new visualization of the state space of high Q-coupled resonator wireless power transfer systems. The visualization immediately suggests a simple control scheme that can keep the transferred power level constant despite disturbances. The paper showed experimentally that the control scheme actually worked — with the counter-intuitive net result of wireless power transfer that doesn't drop off with distance.  

Shwetak Patel

Shwetak Patel headshotRole at UW ECE: Washington Research Foundation Endowed Professor Research focus: Biosystems, Data Science, Computing and Networking Publication:Experimental security analysis of a modern automobile,” 2010 IEEE Symposium on Security and Privacy Number of citations: 1,863 Why was this paper so highly cited? This paper was the first to show an actual over-the-air attack of the embedded systems infrastructure in a modern automobile. The paper received a 2020 IEEE Test of Time award in addition to a number of other honors. The paper is highly cited because it contributed in large part to launching the auto security field. The U.S. Department of Transportation has adopted several guidelines from the paper, and this work is now integral in the automobile industry.  

Les Atlas

Les Atlas headshotRole at UW ECE: Professor Research focus: Biosystems, Data Science Publication:Improving generalization with active learning,” Machine Learning, 1994 Number of citations: 1,843 Why was this paper so highly cited? This paper was the start of a now-common approach, called active learning, within the field of machine learning. It combined a novel idea of how babies learn speech with the theory of machine learning, including neural nets. Active learning was shown to allow more efficient use of labeled training data. Because most machine learning problems have limited amounts of labeled training data, this approach offered a potentially more efficient and lower cost training approach, inspiring many subsequent papers.  

Mari Ostendorf

Mari Ostendorf headshotRole at UW ECE: System Design Methodologies Professor Research focus: Data Science Publication:ToBI: A standard for labeling English prosody,” Proceedings of the 2nd International Conference on Spoken Language Processing, 1992 Number of citations: 1,786 Why was this paper so highly cited? Prosody is the patterns of stress and intonation in a language. It is accepted to be central to our understanding of language. While much of language can be transcribed into words and represented as text, usual text transcriptions do not transcribe prosody. This paper offered an approach to transcribe prosody, which became a standard, greatly benefiting the field of natural language processing.  

Blake Hannaford

Blake Hannaford headshotRole at UW ECE: Professor Research focus: Robotics and Controls, Biosystems Publication:Measurement and modeling of McKibben pneumatic artificial muscles,” IEEE Transactions on Robotics and Automation, 1996 Number of citations: 1,741 Why was this paper so highly cited? A goal of robotics is to make mechanical actuators behave in a manner similar to human skeletal muscle. This paper recognized that while pioneers in artificial muscle research had inspired many and took advantage of artificial muscles’ compatibility with the human body, there was little or no engineering theory of how artificial muscles worked, and no formal comparison with human muscle. This paper provided the necessary new theory and experimental verification to lay the groundwork used by many researchers in both rehabilitation robotics and soft robotics, which have exploded in use in recent years.  

Henrique (Rico) Malvar

Rico Malvar headshotRole at UW ECE: Affiliate Professor Research focus: Data compression, signal processing, image compression, audio compression, multimedia signal enhancement, multimedia protection and forensics, human-computing interfaces, hardware devices and accessibility Publication: Book, Signal processing with lapped transforms, Artech, 1992 Number of citations: 1,458 Why was this book so highly cited? This book describes the basic theory and applications of lapped transforms in signal processing. These transforms are now commonly used in audio and image compression and enhancement, geophysics, digital communications, and other applications.  

Georg Seelig

Georg Seelig headshotRole at UW ECE: Professor Research focus: Biosystems Publication:Enzyme-free nucleic acid logic circuits,” Science, 2006 Number of citations: 1,384 Why was this paper so highly cited? In DNA computing, scientists and engineers try to identify a minimal set of rationally designed molecular building blocks that enable them to reconstruct the kind of molecular computation performed by cells and living organisms. The goal of this work was not to understand biology but to develop reliable engineering paradigms for molecular systems that were also transparent because they were man-made, rather than having evolved over millions of years. This paper introduced such a systematic approach based on DNA strand displacement. The approach has since been used widely and effectively, and it provides the foundation for today’s dynamic DNA nanotechnology.  

Michael Taylor

Michael Taylor headshotRole at UW ECE: Associate Professor Research focus: Computing and Networking Publication:The raw microprocessor: A computational fabric for software circuits and general-purpose programs,” IEEE Micro, 2002 Number of citations: 1,311 Why was this paper so highly cited? This paper presented the first physically scalable multicore microprocessor design and implementation, foreshadowing how many multicores are designed today. The challenge faced by very large-scale integration (VLSI) designers was: How can chip designers leverage growing quantities of chip resources even as wire delays become substantial? This paper provided the influential architecture that achieved the maximum amount of performance and energy efficiency in the face of wire delay.  

Mo Li

Mo Li headshotRole at UW ECE: Professor, Graduate Program Coordinator Research focus: Photonics and Nano Devices Publication:Ultra-sensitive NEMS-based cantilevers for sensing, scanned probe and very high-frequency applications,” Nature Nanotechnology, 2007 Number of citations: 1,189 Why was this paper so highly cited? Nanoscale mechanical sensors (dubbed NEMS) offer a greatly enhanced sensitivity that is unattainable with past microscale devices. This paper reported the first very-high-frequency, self-sensing nanocantilevers for chemical gas sensing and analysis in ambient conditions. By measuring its vibration frequency change, the nanocantilever can detect the mass of 30,000 water molecules (or 1 attogram (10-18 g).  

Howard Chizeck

Howard Chizeck headshotRole at UW ECE: Professor Emeritus Research focus: Robotics and Controls, Biosystems Publication:Controllability, stabilizability, and continuous-time Markovian jump linear quadratic control,” IEEE Transactions on Automatic Control, 1990 Number of citations: 1,108 Why was this paper so highly cited? This paper establishes necessary and sufficient conditions for optimal steady state quadratic control of continuous-time linear systems that possess randomly jumping parameters, which can be described by finite-state Markov processes. This seminal paper established a direction of theoretical development and has been applied to a wide variety of practical problems, including wireless communication and traffic control. [post_title] => What causes a research paper to be highly cited? [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => highly-cited-papers [to_ping] => [pinged] => [post_modified] => 2021-11-17 14:03:14 [post_modified_gmt] => 2021-11-17 22:03:14 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23539 [menu_order] => 3 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [3] => WP_Post Object ( [ID] => 23387 [post_author] => 27 [post_date] => 2021-10-18 17:18:47 [post_date_gmt] => 2021-10-19 00:18:47 [post_content] => By Wayne Gillam | UW ECE News [caption id="attachment_23390" align="alignright" width="525"]Azadeh Yazdan on the UW campus UW ECE Assistant Professor Azadeh Yazdan recently received a five-year grant from the National Institutes of Health to experiment with using optogenetic stimulation, a cutting-edge neurotechnology, to induce targeted changes in the brain. Her research could lead to better treatments for neurological disorders and diseases such as stroke. Photo by Ryan Hoover[/caption] Stroke is a killer, and for those who survive, it can have a devastating impact. According to the World Stroke Organization, the disease is a leading cause of death and disability globally, causing an estimated 5.5 million deaths and 116 million years of healthy life to be lost each year. It is also a very common experience. One in four adults over the age of 25 will have a stroke in their lifetime. So, why is this disease so deadly and debilitating? The answer to that question has to do in part with how stroke can cause the connections between neurons in the brain to deteriorate, break or disappear entirely, often resulting in death, loss of bodily functions and disability. Unfortunately, there is no cure for this disease. But what if scientists and engineers could use neurotechnology, which has shown promise in treating other neurological conditions such as those caused by spinal cord injury, to intervene? Could key neural connections be targeted and induced to heal and repair themselves after a stroke has occurred? UW ECE Assistant Professor Azadeh Yazdan is investigating possible answers to these questions. Yazdan, who is the Washington Foundation Innovation Assistant Professor of Neuroengineering in UW ECE and the UW Department of Bioengineering and a member of the Center for Neurotechnology, has several years of research experience studying possible ways to treat neurological disorders and diseases such as stroke. What happens in a lot of these disorders is that there is aberrant neural connectivity in one or more areas,” Yazdan said. “For example, if someone has a stroke, they are missing connections between brain areas, whereas if someone has a psychiatric disorder such as post-traumatic stress disorder, they might have connections in the brain that are not supposed to be there.” Yazdan’s research focuses on using neurotechnology to induce targeted changes in the brain, reorganizing neural pathways in ways that could address these connectivity issues, helping the brain to heal and recover after injury. She recently received a $3.2M, five-year grant from the National Institutes of Health to further advance her work in this area and to specifically study functional recovery following an ischemic lesion in the brain, a condition that is commonly known as a stroke. [caption id="attachment_23397" align="alignleft" width="600"]Amy Orsborn, Eberhard Fetz, Ricky Wang headshots Co-investigators on the NIH grant include, from left to right, UW professors Amy Orsborn, Eberhard Fetz and Ricky Wang.[/caption] “I’m excited to help people who are dealing with neurological disorders, and I think this research could be especially helpful in finding better treatments for stroke,” Yazdan said. “But also, what we learn will have applications beyond stroke. If we can show targeted reorganization in the brain, the knowledge could be used to better treat diseases that are similar to stroke such as traumatic brain injury or cerebral palsy, as well as psychiatric disorders such as depression.” Yazdan is now in the midst of assembling her research team for work supported by the new grant, and she is recruiting for a postdoctoral researcher and lab technician. Co-investigators on the NIH grant include Amy Orsborn, the Clare Boothe Luce Assistant Professor at UW ECE and the UW Department of Bioengineering, who specializes in therapeutic neural interfaces; Eberhard Fetz, a UW professor of physiology and biophysics, who was one of the early pioneers of brain-computer interface development; and Ricky Wang, a UW professor in bioengineering and ophthalmology. “I am looking forward to working with Dr. Yazdan on this exciting project,” Orsborn said. “The work will shed new light on how neurotechnology can be used to rewire brain networks, which will have wide-ranging therapeutic applications.”

Optogenetic stimulation of the brain

For her NIH-funded research, Yazdan will primarily be using optogenetics to stimulate neurons in the brain instead of electricity, which is currently the go-to form of brain stimulation for neural engineering. Optogenetics is a technology that uses light to activate and inhibit neurons, and although it has been around for several decades, it is a relative newcomer to neurotechnology. Optogenetics has the advantages of being more precise and controllable than electrical stimulation, and it will allow Yazdan and her team to tease apart complicated neural circuits in ways that will be useful for better understanding neural network connectivity. “With optogenetics, we have the capability of recording during the stimulation period to see how the neural network is evolving, and what neural changes can lead to functional changes and recovery through simultaneous behavioral measures,” Yazdan said. “Following a lesion in the brain, we can measure a behavioral deficit, and we can also measure neural and functional recovery as a result of our stimulation parameters.”   [caption id="attachment_23392" align="aligncenter" width="1200"]Photo illustration showing use of optogenetics in the brain This illustration shows targeted reorganization of the brain using optogenetics, a cutting-edge neurotechnology that uses light to activate and inhibit neurons in the brain. Far left: An area of the brain is targeted for modification. Center: The targeted area of the brain is illuminated to control the activity of underlying neural circuits using optogenetics. Far right: A demonstration of how connectivity between two neurons can change following optogenetic intervention. Note the subtle change in the connecting line between neurons. It brightens, showing that the neural connection has strengthened. Illustration provided by Azadeh Yazdan.[/caption]   Yazdan has been working for several years developing optogenetic tools capable of giving more precise and cell-type specific manipulations of the brain, as well as interfaces that can enable scientists and engineers to manipulate and record from large areas of the brain. Concurrent with her NIH-funded research, she is co-leading a multi-institutional effort to develop a ‘smart dura,’ a device that has the capability to perform optogenetic stimulation and also allows unprecedented large-scale access to the brain. The smart dura will enable Yazdan and her research team to record and manipulate neural network activity with unmatched, high resolution. “The brain network structure is actually a big mediator of the changes that we’re seeing. There are no two people who have the same stroke and the same damage,” Yazdan said. “So, in this grant, we’re also including the network structure information into the design of our stimulation protocols. For future stroke therapies, you can imagine that brain stimulation protocols could be customized to a patient’s stroke.”

What the future holds

By the end of the five-year NIH grant, the research team is aiming to establish a proof of concept that demonstrates the effectiveness of refined brain stimulation patterns for targeted neurorehabilitation and ‘rewiring’ of the brain. Their work will also help scientists and engineers better understand neural circuits and connectivity in the areas of the brain that are studied. Yazdan said that long-term goals for this line of research depend in part on what the team discovers over the next five years. But because her team is studying functional recovery following stroke, she is hoping that she can pair up with clinicians to apply some of their research findings in a clinical setting. She is also interested in expanding the focus of the research to encompass other neurological and psychological disorders. “A long-term goal that I have is to see how we can manipulate the brain and induce these targeted changes, which could be used for treating different neurological disorders, beyond stroke,” Yazdan said. “This grant will be a really good first step for that.” She also noted that because much is still unknown when it comes to neurological disorders and diseases such as stroke, it has historically been difficult for scientists and engineers to develop effective treatments. “We have about one billion people worldwide that suffer from some kind of neurological disorder. In this research, we will learn much that could help us improve current brain stimulation-based therapies,” Yazdan said. “This work could also open up a lot of opportunities for us to understand the brain and its response to stimulation. Basically, it will help us to better understand how to induce these targeted changes to the brain in ways that could potentially cure someone.” For more information about the research described in this article, contact Azadeh Yazdan. [post_title] => Azadeh Yazdan receives $3.2M grant to investigate ways neurotechnology could induce targeted changes in the brain, leading to better treatments for stroke [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => azadeh-yazdan-neurotechnology-for-stroke [to_ping] => [pinged] => [post_modified] => 2021-11-17 14:03:21 [post_modified_gmt] => 2021-11-17 22:03:21 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23387 [menu_order] => 4 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [4] => WP_Post Object ( [ID] => 23360 [post_author] => 26 [post_date] => 2021-10-14 13:51:49 [post_date_gmt] => 2021-10-14 20:51:49 [post_content] =>
Story by UW Institute for Nano-Engineered Systems (NanoES)
[caption id="attachment_2983" align="alignright" width="301"]Arka Majumdar (left) and Karl Böhringer (right) Arka Majumdar (left) and Karl Böhringer (right)[/caption] Tunoptix, a Seattle-based optics startup co-founded by Karl Böhringer and Arka Majumdar, professors in the University of Washington Department of Electrical & Computer Engineering (UW ECE), was awarded a $1,500,000 Small Business Technology Transfer (STTR) Phase II grant from the Defense Advanced Research Projects Agency (DARPA). This highly competitive award provides funding for Tunoptix to continue developing next-generation imaging systems for use on satellites or aircrafts where weight, size and power are critical. Lenses with large apertures, the opening through which light travels, are needed to capture images in low-light environments. The extremely large aperture lenses currently used by the defense and aerospace industries for surveillance and space exploration are generally very heavy and bulky. For example, the lens in the Hubble space telescope, which has an aperture of about 2 meters, is roughly 1,000 kilograms. Reducing the size, weight and power of such optical systems would significantly reduce their cost. Meta-optics – engineered surfaces consisting of an array of nanoscale structures that can focus light – are emerging as a promising alternative to traditional lenses. Although meta-optics are lightweight and exceptionally thin (< 1mm), they cannot generate high quality color images. There are some solutions for full-color imaging, but all of them are generally limited to small apertures, about 100 – 200 micrometers in diameter. Tunoptix is developing large aperture (~1cm-10cm) metalenses combined with advanced AI-based image reconstruction software to capture high quality full-color images.
Comparison between a conventional compound refractive imaging system and a Tunoptix current-generation computational imaging system. The conventional imaging system requires multiple optics to correct chromatic and geometric aberrations, resulting in a heavy and bulky package. The Tunoptix computational meta-optic is a single-element, flat solution with a drastically reduced package weight and size that encodes information from the scene. The computational imaging software is jointly designed with the meta-optic and recovers the high-quality image or desired information from the data in the intermediate image encoded by the meta-optic. Image courtesy of Tunoptix.

Tunoptix was previously awarded a $223k DARPA STTR Phase I grant to establish the feasibility of scaling their metasurface designs up to 10 centimeters. This STTR Phase II award will allow the company to begin fabricating its large aperture metasurface designs at the UW Washington Nanofabrication Facility (WNF), an open-access user facility that provides academic researchers and industry professionals access to nanofabrication tools and expertise.
[caption id="attachment_2981" align="alignnone" width="183"]Felix Heide Felix Heide[/caption]
A portion of the Phase II work will be carried out by the laboratory of Felix Heide, a computer science professor at Princeton University. Heide’s computational imaging lab will evaluate the imaging capability of Tunoptix’s metasurfaces and help optimize the algorithms used for image reconstruction. While the focus of Tunoptix’s work for DARPA has been imaging in the visible light range, their approach can work for any wavelength. Tunoptix recently received a NASA Small Business Innovation Research (SBIR) Phase I award to develop a compact hyperspectral imaging (HSI) system using their meta-optics technology. Compact HSI systems will be especially useful in carrying out satellite-based and rover-based imaging of planetary surfaces, airborne remote sensing of coastal and oceanic regions, and inspection of mission-critical satellite systems in space. “We are focused on revolutionizing the way optical systems are conceptualized, designed and manufactured,” said Majumdar. “Using well-established, high precision, low-cost semiconductor manufacturing techniques we are creating new, simple optical elements that will be critical for the evolution of optical design in the digital age. Moreover, by incorporating computational algorithms on the backend, we can improve image quality leaps and bounds over what was achievable using just meta-optics.” For those interested in advancing this technology, Tunoptix is hiring several positions including an optical test engineersoftware developer and AI consultant. [post_title] => Small Business awards from DARPA and NASA fuel growth of UW spinout Tunoptix [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => small-business-awards-tunoptix [to_ping] => [pinged] => [post_modified] => 2021-11-17 14:03:29 [post_modified_gmt] => 2021-11-17 22:03:29 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23360 [menu_order] => 5 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [5] => WP_Post Object ( [ID] => 23192 [post_author] => 27 [post_date] => 2021-10-04 14:21:09 [post_date_gmt] => 2021-10-04 21:21:09 [post_content] => by Wayne Gillam | UW ECE News [caption id="attachment_23200" align="alignright" width="550"]Eve Riskin headshot Professor Eve Riskin is returning to UW ECE after 15 years as an associate dean in the UW College of Engineering. And as co-founder and faculty director of STARS, she has plans to share this successful program model with colleges and universities across the country. STARS helps to make higher education more accessible and provides support for students from low-income, first-generation and underserved backgrounds. Photo by Ryan Hoover[/caption] After 15 years as an associate dean for the UW College of Engineering and one year on sabbatical, professor Eve Riskin has returned to the UW Department of Electrical & Computer Engineering this fall as the Department’s newly-appointed undergraduate program coordinator. In this role, Riskin will work closely with the UW ECE associate chair for education and student advising team to manage undergraduate policies, issues and admissions. “I’m really happy to be back at UW ECE,” Riskin said. “I’m so thrilled with the welcome the Department is giving me as I return. I hope to apply some of what I learned as an associate dean to UW ECE.” Riskin started her career at UW ECE in 1990. In addition to receiving several honors and awards over the years as an educator and for her research, she is well-known for her persistent and impactful work in diversity, equity and inclusion at the University. Riskin has received numerous awards related to expanding diversity and access to education, such as an ECEDHA Diversity Award, a Hewlett-Packard Harriett B. Rigas Award and a UW David B. Thorud Leadership Award. In 2020, her efforts were recognized with one of the nation’s highest honors, a Presidential Award for Excellence in Science, Mathematics and Engineering Mentoring. “When he was chair of UW ECE, Radha Poovendran nominated me for the ECEDHA and PAESMEM awards, and this was so kind of him,” Riskin said. “Eve is very inspiring. She has dedicated her career to increasing access to engineering for underrepresented students,” said UW ECE Professor and Chair Eric Klavins. “We are so excited to welcome her back to UW ECE and incredibly lucky to have her in the role of undergraduate program coordinator, where her expertise with diversity, equity and inclusion will have such a positive impact on our students.” Now, fresh from her sabbatical, Riskin shows no signs of slowing down. In addition to her duties as an instructor and her new role at UW ECE as undergraduate program coordinator, Riskin is continuing as faculty director of two successful programs she co-founded at the UW — UW ADVANCE, which is dedicated to the advancement of female faculty in STEM fields, and the Washington State Academic RedShirt program, which is known as STARS. According to Riskin, the STARS program holds a special place in her heart because of its powerful impact on students who come from low-income and underserved backgrounds. “Eve’s leadership has profoundly advanced our College’s mission to recruit and retain people from underrepresented or disadvantaged groups,” said professor Sam Burden, UW ECE’s Associate Chair for Diversity, Equity and Inclusion. “I was thrilled when she recruited me to pitch in on STARS, which is an outstanding program that has enabled unprecedented access to engineering education for women, underrepresented minorities and first-generation college students. We are extremely fortunate to have Eve back full-time in our Department, and I am eager to leverage her expertise to make UW ECE more diverse, equitable and inclusive for all.”

What is the STARS program?

[caption id="attachment_23202" align="alignright" width="450"]Sonya Cunningham and Eve Riskin at a social gathering Riskin (right) will be working closely with Sonya Cunningham (left), executive director of the STARS program at the UW, to spread the STARS program model nationwide.[/caption] The STARS program draws its inspiration from the concept of a “redshirt” year in college athletics, giving students an extra year of preparation to succeed in school. The program supports engineering and computer science students from low-income, first-generation and underserved backgrounds in navigating the transition to college-level courses, and it is welcoming its ninth cohort this fall. This two-year program includes a specialized curriculum designed to build learning skills and strengthen academic preparation for core math and science prerequisites. Riskin was the principal investigator for two National Science Foundation grants that helped to launch STARS at the UW and provide substantial support for the program over the last eight years. Now, with the support of colleagues and a third NSF grant, she is laying the groundwork for an upcoming conference to be held in June 2022 on the UW campus, which will share details about how the program works with representatives from colleges and universities across the nation. “We’re going to share the STARS program model and have people look under the hood,” Riskin said. “We’ll examine curricula, we’ll talk about fundraising, and we’ll have a panel with STARS students — testimonials, so they can hear about the impact on students. We’ll share documents, processes, curriculum, policies, everything we created for STARS, so we can help other institutions across the country get started with their own, similar programs.” [caption id="attachment_23281" align="alignleft" width="400"]Lindi Mujugira headshot 2 STARS’ new director, Lindi Rubadiri-Mujugira, will be responsible for much of the staff oversight and hands-on work needed to keep the program running smoothly while Riskin and Cunningham focus on fundraising and sharing the STARS program model. Photo by David Tsay[/caption] Riskin will be working closely with Sonya Cunningham, executive director of the STARS program at the UW, to spread the STARS program model nationwide. The two have formed a strong and effective partnership over the years, and according to Riskin, Cunningham has played a key role in the program’s ongoing success. “STARS wouldn’t be half the program without her,” Riskin said. “Sonya is one of the very best student services professionals in the country. She just has a knack for knowing what a student needs, figuring out what obstacle is holding that student back and helping them get around it. There are many students out there who have college degrees and are now working engineers that would not have succeeded without her. And they tell her that, so that’s really meaningful.” Almost 300 students have participated in the STARS program to date. STARS has also brought on a new director, Lindi Rubadiri-Mujugira, who will be responsible for much of the staff oversight and hands-on work needed to keep the program running smoothly while Riskin and Cunningham are focused on fundraising and disseminating the program model, especially through the June 2022 national conference.

The impact of STARS

Like Riskin, Cunningham is enthusiastic about the impact of the program. “What is most exciting to me about STARS is that it has immeasurable far-reaching implications individually, locally, nationally and globally,” Cunningham said. “There is the obvious possibility to end the intergenerational cycle of poverty for individuals, and beyond this, the program places very diverse students squarely at the decision-making table. This will improve not just the problem-solving process but also the kinds of problems that are chosen to be solved.” Over the first eight cohorts, 79% of STARS students remain enrolled in engineering or computer science, or have graduated. This very high rate of success means better jobs and brighter futures for students. Further evidence of STARS’ impact on students can be found within the program participants’ own words. Mathew Garcia headshot

Mathew Garcia, year two at UW ECE

“The STARS program supported me during the difficult transition from high school to university, and it also prepared me for an exciting future in engineering. I not only built lifelong friendships with the other members of my cohort, but I also made important connections with the incredibly caring staff that inspired me to continue studying STEM during tough times. Through these connections and skills gained during my time at STARS, I gained an amazing internship at Boeing that will be instrumental as I continue to grow as an engineer in the years to come.”       Grace Kariuki headshot

Grace Kariuki, 2021 UW ECE graduate, Research Software Engineer at IBM Research

“I would have never imagined from that first day of transition week how much the STARS program would completely change my life. The incredible staff supported me throughout the entire five years and helped me find lots of opportunities to build my experience. As a graduate, I will soon begin my journey as an engineer at my dream job in my dream city. Through STARS, I also found lifelong friends whom I consider my family. I will forever be grateful to STARS.”         Diallo Wilson headshot

Diallo Wilson, graduating Fall 2021 from UW ECE

“STARS has been my main support network throughout my collegiate career. The tough love early, the cohort model and the excellent faculty taught me that I am someone with my own unique value and set of skills. Rather than being disappointed in what I do not have or understand, STARS taught me to think more about what I do have and that hard work and sacrifice will always be necessary to accomplish my goals.”         Doama Verdizcp headshot

Diana Verduzco, year four at UW ECE

“Being a part of the STARS program provided many opportunities to become a successful student and accomplish my goals. I had the privilege to be a part of a community and was constantly given support by faculty and staff as well as my lifelong friends I met through STARS. Their encouragement and guidance have genuinely gotten me this far. Through this program, I have also had opportunities to intern for companies, gain hands-on experience, communicate with people in industry and get a head start on what the real world looks like. I’m so grateful for this program because I wouldn’t be where I am today without it!”    

A bright future for STARS

[caption id="attachment_23252" align="alignright" width="450"]Eve Riskin and Sonya Cunningham with the first STARS cohort Riskin (far right) and Cunningham (second from right) with the first graduating class from STARS. Over the first eight cohorts, 79% of STARS students remain enrolled in engineering or computer science, or have graduated. This very high rate of success means better jobs and brighter futures for students.[/caption] Alongside her new role as UW ECE undergraduate program coordinator and planning for the June 2022 national STARS conference, Riskin will be fund-raising and working continuously behind the scenes to ensure that STARS remains successful and sustainable over the long term. She remains firmly committed to the vision she has had for the program since its inception, and she is optimistic about the future. “This is about institutional transformation,” Riskin said. “If you want people to succeed, instead of focusing so much on trying to fix the student, you should fix your system. We’re fixing our system to better fit students who didn’t come from privileged backgrounds. We’re finding that STARS students are capable of succeeding and doing many wonderful things in the world. And in fact, many already are.” For more information about the STARS program, visit the program website or contact Eve Riskin, Sonya Cunningham or Lindi Rubadiri-Mujugira. [post_title] => Eve Riskin returns to UW ECE with plans to share the STARS program nationwide [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => eve-riskin-stars-2021 [to_ping] => [pinged] => [post_modified] => 2021-11-17 14:03:38 [post_modified_gmt] => 2021-11-17 22:03:38 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23192 [menu_order] => 6 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) ) [post_count] => 6 [current_post] => -1 [in_the_loop] => [post] => WP_Post Object ( [ID] => 23652 [post_author] => 26 [post_date] => 2021-11-24 10:21:02 [post_date_gmt] => 2021-11-24 18:21:02 [post_content] =>

UW BIOFAB: A force for reproducible science

The UW’s Biofabrication Center, founded by UW ECE Professor and Chair Eric Klavins, partners with Agilent Technologies in pursuit of automated, reproducible research. [caption id="attachment_23658" align="aligncenter" width="907"]Undergraduate technicians perform common molecular biology tasks to enable the rapid design, construction and testing of genetically reprogrammed organisms for biotechnology applications and research. Dennis Wise / University of Washington Undergraduate technicians perform common molecular biology tasks to enable the rapid design, construction and testing of genetically reprogrammed organisms for biotechnology applications and research. Dennis Wise / University of Washington[/caption]   Article by Renske Dyedov, UW Institute for Nano-Engineered Systems (NanoES)

Key to advancing any new scientific discovery is the ability for researchers to independently repeat the experiments that led to it. In science today, particularly biology, the lack of reproducibility between experiments is a major problem that slows scientific progress, wastes resources and time, and erodes the public’s trust in scientific research.

[caption id="attachment_23672" align="alignright" width="232"]UW ECE Professor and Chair, Eric Klavins. Dennis Wise / University of Washington BIOFAB founder, and UW ECE Professor and Chair, Eric Klavins. Dennis Wise / University of Washington[/caption] At the University of Washington, researchers have access to the UW Biofabrication Center, or BIOFAB, a unique facility located in the Nanoengineering and Sciences building in which scientific protocols are encoded as computer programs, allowing undergraduate lab technicians to execute experiments according to detailed instructions. “The BIOFAB is unlike any other lab on campus,” says BIOFAB founder Eric Klavins, Professor and Chair of the UW Electrical & Computer Engineering Department (UW ECE). “In effect, we’ve been able to automate common protocols by using software to assist our student technicians. This ‘human-in-the-loop’ system goes a long way towards improving the replicability of biological research.” In an effort to expand the lab’s automation capabilities, the BIOFAB has partnered with Agilent Technologies Inc., a life sciences development and manufacturing company based in California’s Silicon Valley. Using state-of-the-art research equipment from Agilent, the BIOFAB will develop high-throughput workflows for common tasks of interest to members of the synthetic biology community.

Programming the biology lab

Computer programmers write code to tell a computer what to do and how to do it. For a given program, the same inputs consistently result in the same outputs. In contrast, two biology researchers can seemingly carry out the same experiment, but get different results. This is in part because instructions for how the experiment was conducted – whether documented in a lab notebook or published in a journal – are often vague or incomplete, leaving out details that the author may not have realized impacted the experimental outcome. [caption id="attachment_23657" align="alignleft" width="580"]Aquarium is a web-based software application that allows scientists to build executable protocols, design experimental workflows based on those protocols, manage the execution of protocols in the lab and automatically record the resulting data. Dennis Wise / University of Washington Aquarium is a web-based software application that allows scientists to build executable protocols, design experimental workflows based on those protocols, manage the execution of protocols in the lab and automatically record the resulting data. Dennis Wise / University of Washington[/caption] As a computer scientist turned synthetic biologist, Klavins realized what biologists needed was a more formal way – a programming language – to define how to conduct an experiment. This led to the development of Aquarium, a web-based software application that allows scientists to build executable protocols, design experimental workflows based on those protocols, manage the execution of protocols in the lab and automatically record the resulting data. “Aquarium provides the means to specify, as precisely as possible, how to obtain a result,” said Klavins. When it comes to engineering biology – reprogramming cells to produce chemicals or drugs, or perform complex functions like sensing toxic compounds in the environment – reproducibility is paramount. The BIOFAB uses Aquarium to standardize various scientific workflows, generating reliable and highly reproducible results. The BIOFAB is one of a growing number of labs known as biofoundries which are committed to efficiently engineering biological systems and workflows. BIOFAB operations are overseen by two lab managers, with a dozen or so undergraduate students executing jobs for BIOFAB clients. BIOFAB technicians perform common molecular biology tasks like DNA assembly and purification as a fee-for-service to the scientific community. Since its founding in 2014, the BIOFAB has run over 30,000 jobs for 300+ different clients at the UW and beyond. “The BIOFAB has been absolutely instrumental in establishing and executing robust Aquarium driven protocols for a major portion of our de novo design minibinder pipeline,” said Lance Stewart, Chief Strategy and Operations Officer at the UW’s Institute for Protein Design (IPD). IPD researchers use computers to design millions of minibinders – small, stable proteins that bind with high affinity to targets of interest – that must be produced and tested in the lab. IPD uses the BIOFAB to screen minibinder candidates for protein stability and protein:protein interactions, which involves constructing yeast libraries from chip synthesized oligonucleotide genes encoding minibinder designs and carrying out large scale fluorescence activated cell sorting and next generation DNA sequencing. “By handing off time-consuming wet lab work to our technicians, BIOFAB clients like IPD can focus more on the design and data analysis aspects of their experiments,” said Klavins.

Learning by doing

[caption id="attachment_23659" align="alignright" width="330"]BIOFAB technician Nicole Roullier. Dennis Wise / University of Washington BIOFAB technician Nicole Roullier. Dennis Wise / University of Washington[/caption] On any given day, the BIOFAB is buzzing with undergraduate technicians working together in harmony to complete an assortment of experiments for BIOFAB clients. Most technicians start working in the BIOFAB as freshman or sophomores, and for many, it’s their first real lab experience. Upon joining the lab, BIOFAB lab managers teach students basic lab skills, such as pipetting and sterile technique, and orient them to the lab. Armed with this foundational knowledge, BIOFAB technicians can begin executing a variety of different protocols by following the step-by-step instructions provided through Aquarium. Students become adept at performing complicated experimental workflows involving complex equipment through the process of doing them over and over again. “Aquarium allows us to effectively train many students simultaneously and get them working in the lab relatively quickly,” said Aza Allen, a lab manager at the BIOFAB. “Aquarium’s technician interface makes it easy to get undergraduate students, who do not necessarily know much about molecular biology when they start, to perform experiments reliably.” “I have learned so much beyond what could possibly be taught in a classroom setting,” said BIOFAB technician Nicole Roullier, a UW biochemistry senior. “Most undergraduates don’t have the opportunity to work with such sophisticated equipment and master advanced techniques like qPCR and next-generation sequencing (NGS). This hands-on training has built up my confidence in the lab in preparation for graduate school.”

A promising partnership

The BIOFAB provides critical automation and analytics infrastructure dedicated to enabling the rapid design, construction and testing of genetically reprogrammed organisms for biotechnology applications and research. Through its partnership with Agilent, the BIOFAB aims to offer new high-throughput capabilities that will further speed up and scale up synthetic biology research. “We’re thrilled to be partnering with Agilent,” said Klavins. “Their support will not only accelerate the development of innovative technologies, but will help us educate students using cutting-edge equipment, bolstering our ability to prepare students for success in their own future research and career.” “We think this is the start of an exciting collaboration,” said Kevin Meldrum, General Manager and Vice President of Genomics at Agilent. “We are pleased to be able to support researchers at the UW and the educational mission of the university through the BIOFAB. We see this as an investment in the future of our field.” [caption id="attachment_23660" align="alignleft" width="630"]Agilent’s state-of-the-art liquid-handling robot, the Bravo Automated Liquid Handling platform will help speed up and scale up synthetic biology research. Dennis Wise / University of Washington Agilent’s state-of-the-art liquid-handling robot, the Bravo Automated Liquid Handling platform will help speed up and scale up synthetic biology research. Dennis Wise / University of Washington[/caption] As a result of this partnership, the BIOFAB has acquired several valuable pieces of equipment, including Agilent’s state-of-the-art liquid-handling robot, the Bravo Automated Liquid Handling platform. While the Bravo can be used to automate sample preparation for a variety of different applications, the BIOFAB plans to initially use it to expedite its workflow for NGS. In addition to the Bravo, the BIOFAB has also acquired the AriaMx Real-Time PCR System, and the 5200 Fragment Analyzer System, a parallel capillary electrophoresis system. “Library preparation for high-throughput NGS is a tedious, labor-intensive process,” said Klavins. “Agilent’s Bravo will help make this workflow more efficient and reduce pipetting errors that make results less consistent, while also freeing up time for our technicians to work on less repetitive tasks. We know that there are certainly other workflows that would benefit from the use of Bravo, and we plan to engage BIOFAB users to identify which ones to pursue. We are thrilled to be able to bring this resource to the UW community, and are excited to see the compelling science that comes out as a result.” [post_title] => UW BIOFAB: A force for reproducible science [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => uw-biofab-a-force-for-reproducible-science [to_ping] => [pinged] => [post_modified] => 2021-11-24 10:21:02 [post_modified_gmt] => 2021-11-24 18:21:02 [post_content_filtered] => [post_parent] => 0 [guid] => https://www.ece.uw.edu/?post_type=spotlight&p=23652 [menu_order] => 1 [post_type] => spotlight [post_mime_type] => [comment_count] => 0 [filter] => raw ) [comment_count] => 0 [current_comment] => -1 [found_posts] => 780 [max_num_pages] => 130 [max_num_comment_pages] => 0 [is_single] => [is_preview] => [is_page] => [is_archive] => 1 [is_date] => [is_year] => [is_month] => [is_day] => [is_time] => [is_author] => [is_category] => [is_tag] => [is_tax] => [is_search] => [is_feed] => [is_comment_feed] => [is_trackback] => [is_home] => [is_404] => [is_embed] => [is_paged] => [is_admin] => [is_attachment] => [is_singular] => [is_robots] => [is_posts_page] => [is_post_type_archive] => 1 [query_vars_hash:WP_Query:private] => c64914061c8ecf9b16abe746203f6ad7 [query_vars_changed:WP_Query:private] => 1 [thumbnails_cached] => [stopwords:WP_Query:private] => [compat_fields:WP_Query:private] => Array ( [0] => query_vars_hash [1] => query_vars_changed ) [compat_methods:WP_Query:private] => Array ( [0] => init_query_flags [1] => parse_tax_query ) ) )
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