Skye Shepherd Selected for Young Innovator Award

July 20, 2022

Bioengineering graduate student Skye Shepherd was selected for the Young Innovator Award through the 2022 Young Innovator Program, offered and supported through the Catherine and Don Kleinmuntz Center for Genomics in Business and Society and Carl R. Woese Institute for Genomic Biology. The recognition also includes $20,000 to be used further develop Skye’s new idea for ultrasensitive detection of protein biomarkers.

Early respiratory virus detection research among Royal Society of Chemistry’s top citations

6/23/2022 10:06:55 AM Kim Gudeman, HMNTL

In 2019, researchers at the University of Illinois Urbana-Champaign were working on a rapid test that could detect horse respiratory viruses in less than 30 minutes using a nasal swab and a smartphone. When the COVID-19 outbreak began later that fall, the team was able to pivot quickly to include the SARS-CoV-2 virus among the pathogens that could be identified.

Covid virus
Covid virus

Their early study on COVID-19 was published in Lab on a Chip in April 2020, and in 2021 that paper was among the top 3% most cited Royal Society of Chemistry publications. It has been cited in many peer-reviewed journals, including ACS Nano and Scientific Reports.

“The timing was really good,” said Brian Cunningham, the Intel Alumni Endowed Chair in Electrical and Computer Engineering and one of the study’s authors. “We were already working on how to use mRNA to detect viruses quickly with an inexpensive device that everyone has (a smartphone), so we were able to transition to COVID-19 easily. Our paper may have been the first to show this capability.”

Brian Cunningham
Holonyak Lab faculty and study co-leader Brian Cunningham

Before the pandemic began, the team was already testing the diagnostic tool on horses located on UIUC’s Veterinary Medicine campus. Horses and other animals experience a viral transmission process similar to that of humans, and the interventions for suppressing disease spread – quarantining and distancing from others – are much the same. When the COVID-19 outbreak occurred, the scientists were able to parlay their work to include the SARS-CoV-2 strain.

Cunningham said the research’s magic sauce was in the detection process. Unlike polymerase chain reaction (PCR) tests, which are often considered the gold standard for virus detection, the UIUC test focused on nucleic acids. For that reason, the team was able to create a test that could work with samples at the same temperature for 30 minutes. PCR tests, on the other hand, must cycle among various temperatures – one reason why they require certain lab conditions and special equipment.

“Our test gives an answer really quickly,” Cunningham said. “And instead of having to use really expensive diagnostic tools in a laboratory, we were able to get similar results from a smartphone in the field.”

Rashid Bashir
Holonyak Lab faculty and study co-leader Rashid Bashir.

In addition to Cunningham, the authors include Grainger Engineering Dean Rashid Bashir, Animal Sciences Professor Matthew Wheeler, Bioengineering Research Scientist Anurup Ganguli, and graduate students Fu Sun (first author), Judy Nguyen, Ryan Brisbin, Krithika Shanmugam, and David L. Hirschberg. David M. Nash also contributed. The initial work was funded by the National Science Foundation.

Cunningham said that since the paper’s publication, his group has developed a second method for detecting COVID-19 and other viruses. While the original method broke the virus open to access its nucleic acid, the new process can detect the intact virus.

“The new test is better, faster, and more sensitive and can detect COVID-19 in five minutes at room temperature,” Cunningham said. “It’s a new technique, and we’re really excited about its possibilities.”

New Point of Care Diagnostic Instrument for Cancer Biomarkers

October 18, 2021
By: Ananya Sen

Current medical diagnostics involve sending samples to laboratory facilities, which can be difficult and expensive. Researchers at the University of Illinois Urbana-Champaign have designed a desk-sized instrument that can make the same measurements at the location where the samples are collected.

For several years the Cunningham group has been developing microscopes that use photonic crystal biosensors—nanostructured glass surfaces that brightly reflect only one wavelength of light. “Although our original photonic crystal microscope is very versatile, it’s the size of a ping pong table,” said Brian Cunningham (CGD Director/MMG), the Intel Alumni Endowed Chair of Electrical and Computer Engineering. “We wanted to build a portable instrument that had the same detection capabilities. The new one we built can easily fit on a desk and costs around $7,000, compared to the non-portable microscope, which costs $200,000.”

The researchers had previously developed the larger photonic crystal microscope so that it could provide a strong contrast counting surface-attached gold nanoparticles, a feature that the portable version also shares. “The photonic crystals act like a mirror, but only for the color red. The gold nanoparticles are non-reflective and show up as dark spots,” Cunningham said. The microscopes can, therefore, be used to detect proteins or other biomarkers that are linked to the gold nanoparticles.

The portable versions use a red LED light, which gets reflected off the photonic crystal, and the image is captured by a webcam. “The system itself is quite easy to build and can be put together within a day,” said Nantao Li, a graduate student in the Cunningham lab and co-first author on the paper.

The portable microscope was used to detect specific microRNAs—small, single-stranded, non-coding RNAs—that are associated with prostrate cancer. Each gold nanoparticle was attached to a single-stranded piece of DNA, called the probe, which in turn was attached to pieces of single-stranded protector DNA. If the target miRNA sequence was present in the sample, it would displace the protector DNA, which would cause the nanoparticle to bind to the photonic crystal, according to Shreya Ghosh, a previous postdoctoral researcher in the Cunningham lab and the other co-first author of the paper.

Since almost every cancer has miRNAs associated with it, the microscope can, in theory, be used to detect different cancer types. “We are collaborating with researchers at the Mount Sinai Medical Center to diagnose lung cancer, and with Huntsman Cancer Institute to measure the effects of chemotherapy in prostate cancer,” Cunningham said. “We will also be working with Carle Hospital to detect miRNAs found in the blood of breast cancer patients.”

The researchers are working to lower the microscope cost even further. “We are trying to use smartphone cameras to capture the images. Our aim is to reduce the cost to less than $100,” Li said. They are also trying to build handheld versions of the microscope, which would consist of a box with an image sensor that can communicate wirelessly with a smartphone.

The Cunningham lab is currently seeking to establish a Center for Enhanced Biosensor Microscopy at the IGB, where they will be able to train researchers throughout the academic research community to use these instruments to detect any type of biomarker.

The study “A compact photonic resonator absorption microscope for point of care digital resolution nucleic acid molecular diagnostics” was published in Biomedical Optics Express. The work was funded by the National Institutes of Health, Jump ARCHES endowment through the Health Care Engineering Systems Center, Zhejiang University ZJU-UIUC Joint Research Center, Ronald H. Filler Scholarship for Cancer Scholars, and the Illinois Scholars in Undergraduate Research Scholarship.

Establishing the Center for Pathogen Diagnostics

9/30/2020, Kim Gudeman

With COVID-19 infecting more than 25.1 million worldwide to date, the pandemic has underscored the need for cost-effective, accurate, and quick diagnostics.

The University of Illinois, Urbana-Champaign and Zhejiang University are launching the Center for Pathogen Diagnostics (CPD) to create new detection systems that address limitations of current technologies, while leveraging the power of artificial intelligence and machine learning to analyze disease trends, analyze sensor data, and predict future outbreaks. The new devices – which will range from wearable sensors to mobile point-of-care devices to large laboratory instruments – will be able to detect pathogens that cause viral, bacterial, fungal, environmental, and food-borne illnesses.

“With COVID, we’re seeing the limitations of current best practices for virus detection,” said Brian Cunningham, the Intel Alumni Endowed Chair in the Department of Electrical and Computer Engineering at Illinois. “It takes too long to get results, and accuracy remains a concern. Instead of chemical testing, we’re interested in using new detection modalities, like detecting intact viruses, to create faster, more cost-effective diagnostics.”

The team, which is comprised of researchers at Illinois and ZJU, represents five “pillars” of pathogen diagnostic technologies. First, researchers will study the interactions between pathogens and host cells at the molecular level, which will provide targets for new pathogen detection platforms.

Second, the team will develop sample pre-processing techniques that enable the breakdown of cells and extraction of DNA and RNA, so that viruses and bacteria can be identified. This step will help researchers create a device capable, for example, of differentiating COVID-19 (SARS-CoV-2) from influenza, which, while both viruses, have features that can be used to distinguish them from each other.

Researchers also will create biosensors that are more sensitive, which will lower false negatives and positives, and be able to detect different variations of SARS-CoV-2. One important direction is development of mobile smartphone-based platforms that allow test results to be obtained immediately after gathering a sample, and the fabrication of microfluidic devices that automate the pre-processing of test samples before the detection step.

Finally, the team will use AI and machine learning algorithms to analyze data that is produced by the sensors, and to monitor health trends for public health officials. For example, AI could be used to provide better modeling for disease transmission or to reduce the number of physical tests needed in a community by making inferences about infection rates from a small subset of the population.

Transitioning the technology to the marketplace will be an important component of the center as well, says Cunningham.

“The purpose of the center is to do innovative research that actively improves global public health,” he said. “Commercialization is one of the outcomes that we’re working towards.”

The Center for Pathogen Diagnostics will be located in the Holonyak Micro & Nanotechnology Laboratory. In addition to Cunningham, the Illinois research team includes: Yang Zhao, HMNTL Director Xiuling Li, and Lav Varshney, electrical and computer engineering; Yi Lu, chemistry; Steven Blanke, microbiology; and Xing Wang, Holonyak Micro & Nanotechnology Lab. The ZJU team includes Shaowei Fang, Qingjun Liu, Chun Zhou, Huan Hu, and Yu Lin.

The new five-year, $1.5 million center is not the first collaboration between the two universities. In 2016, The Zhejiang University-University of Illinois at Urbana-Champaign Institute (ZJUI) was launched on ZJU’s international campus in Haining, China, about 120 km southwest of Shanghai. ZJU-UIUC Institute faculty teach and research in broad program themes of engineering and system sciences; information and data sciences; and energy, environment, and infrastructure sciences. The Center is one of three research efforts that was just funded through the ZJUI initiative.

“The Center for Pathogen Diagnostics is another great example of the fruitful partnership that Illinois enjoys with ZJUI,” said Dean Rashid Bashir of The Grainger College of Engineering. “We look forward to working with ZJUI on solving urgent problems that are relevant to the entire global community.”

Portable Smartphone COVID Test

As COVID-19 continues to spread, bottlenecks in supplies and laboratory personnel have led to long waiting times for results in some areas. In a new study, University of Illinois, Urbana-Champaign researchers have demonstrated a prototype of a rapid COVID-19 molecular test and a simple-to-use, portable instrument for reading the results with a smartphone in 30 minutes, which could enable point-of-care diagnosis without needing to send samples to a lab.

The paper can be found on the Nanosensors Group “Publications” page, and at the Proceedings of the National Academy of Sciences website:

The press release to this news story can be found at:

Using Photonics to Generate “Hot Electrons” that Catalyze Chemical Transformations

Researchers in Prof. Brian Cunningham’s Nanosensors Group at the University of Illinois, in collaboration with Prof. Singamaneni’s research group at Washington University, described a new approach for efficiently catalyzing chemical reactions using light, in the journal ACS Photonics.   The researchers harnessed a new approach for amplifying electromagnetic fields in nanometer-scale volumes by coupling the energy from a laser into a nanostructured photonic crystal surface.  The electromagnetic fields in the photonic crystal resonate with the laser’s wavelength, and when a metal nanoparticle is placed onto the photonic crystal, the electrons in the metal resonate as well.    A portion of the resonating electrons become more reactive than ordinary electrons, and are able to transfer to nearby chemical molecules, and thus catalyze specific chemical reactions.  The reactive electrons are often referred to as being “hot,” even though they are not hot in the temperature sense. The research shows that, by coupling  laser light to a photonic crystal, chemical reactions are driven forward with greater efficiency, allowing less energy to perform a process than possible without the photonic crystal.  Because the approach uses low illumination power that can be distributed over large surface areas, we envision the potential for optically driven chemical reactors.  The reactors would be only several micrometers in height, with transparent windows, an inlet for precursors, an outlet for products, and nanoparticle-coated photonic crystals comprising the upper and lower surfaces.

ECE graduate student Qinglan Huang and IGB Fellow Taylor Canady led the research, which was performed in the Holonyak Micro and Nanotechnology Laboratory.  The paper, entitled “Enhanced Plasmonic Photocatalysis through Synergistic Plasmonic–Photonic Hybridization“, by  Q. Huang, T.D. Canady, G. Gupta, N. Li, S. Singamaneni and B.T. Cunningham, can be found at:  ACS Photonics (2020).

Check out the final paper here: FINAL published ACS2020.

Digital Diagnostics Review Paper in Lab on a Chip

The Nanosensors Group from the University of Illinois at Urbana-Champaign published a Critical Review for the journal Lab on a Chip, entitled “Digital Resolution Biomolecular Sensing for Diagnostics and Life Science Research.”  The co-authors of the paper are Qinglan Huang, Nantao Li, Hanyuan Zhang, Congyu Che, Fu Sun, Yanyu Zhang, Taylor Canady,  and Brian Cunningham.  The paper reviews an important and very challenging frontier of the field of biosensing, where novel technologies are demonstrating the ability to digitally count molecules with single-unit precision. Through the use of enzymatic chemical reactions, nanoparticle tags, ultra-sensitive transducers, multiplexing detection instruments, and novel biochemistry, the reviewed technologies are finding applications in life science research, drug discovery, and diagnostics.

The paper can be found on the Nanosensors Group “Publications” page, and at the Lab on a Chip web site:!divAbstract



Inexpensive, portable detector identifies pathogens in minutes

Editor’s notes:

To reach Brian Cunningham, call 217- 265-6291; email

The paper “Smartphone-based multiplex 30-minute nucleic acid test of live virus from nasal swab extract” is available online and from the U. of I. News Bureau. DOI: 10.1039/D0LC00304B

Interview on WILL about COVID Diagnostics


A team of University of Illinois researchers is working on a smartphone application that would detect the novel coronavirus within 30 minutes, without the need for a diagnostic lab.

Illinois Newsroom’s Brian Moline spoke with Brian Cunningham. He’s a professor of electrical and computer engineering, and a professor at Nick Holonyak Jr., Micro and Nanotechnology Lab on the Urbana campus.

He said that’s just one of several diagnostic technologies that his research team is working on in collaboration with others.

“One test we’re developing is based on detecting the nucleic acid sequence, part of the genome of the virus,” Cunningham said. “In that test, you take the virus, break it apart by putting it into a chemical that breaks the virus membrane and releases the RNA material. And then, in that test, you take that genomic sequence, you have a special molecule that recognizes it, and then turns each individual piece of the genome into thousands and then millions of individual copies that fluoresce. That test is performed inside a small, plastic cartridge that has an output that is readable by a phone.”

Cunningham said there are both advantages and disadvantages in working with smartphones.

“Of course, now, everybody has one,” he said. “It’s a powerful device that you can use in many ways, but you can also use it in measuring biological diagnostic tests. The downside is that it’s not approved by regulatory agencies to use a mobile device like that, for doing a test, and you have to show very rigorously that a phone-based system can give results that are equivalent to laboratory tests using clinical samples.”

Cunningham said his group has completed successful testing of the smartphone application using respiratory viruses from horses. He has submitted the research to the journal Lab on a Chip to be considered for fast-track publication. You can read that submission below.

Cunningham said they have also submitted applications for emergency funding to the National Science Foundation and the National Institutes of Health.

In addition to the smartphone application, Cunningham said his research team is also working on a biosensor method of testing that detects and counts the intact coronavirus from nasal swab extract. He said they are also working on another test that would detect if a person has antibodies that could give them immunity to COVID-19.

Announcing the Center for Genomic Diagnostics

January 29, 2020
By: Claudia Lutz

A new research center at the University of Illinois directed by Donald Biggar Willett Professor in Engineering Brian Cunningham aims to revolutionize diagnostics and personalized medicine, developing technologies that are at once more accurate, more affordable, and more practical for routine care.

The Carl R. Woese Institute for Genomic Biology (IGB) and the Grainger College of Engineering are working together to support the launch the new Center for Genomic Diagnostics (CGD), which will be housed within the IGB. The CGD will also take advantage of specialized laboratory space and equipment in Illinois’ Holonyak Micro and Nanotechnology Lab.

The vision for the new center begins with molecules called biomarkers that are naturally produced as part of a healthy biological state or disease process. If such a molecule is produced in detectably larger or smaller quantities in certain conditions, it can serve as the basis for a reliable test for that condition. For example, the hormone human chorionic gonadotropin, which is detected in urine by home tests during early pregnancy, is a biomarker. Other biomarkers signal the presence of diseases, including some types of cancer.

“Our goal for the center is first to use genomics and bioinformatics to identify novel biomarkers,” Cunningham said. “As we seek to validate how biomarker presence and concentration changes with a specific health condition, we’re also interested in developing novel biochemistry methods for selectively detecting those molecules with methods that are simple, yet extremely sensitive.”

The concept for the center emerged from Cunningham’s research theme at the IGB, Omics Nanotechnology for Cancer Precision Medicine, which was established in 2016. The theme brings together computational, biochemical, biomedical, and engineering approaches to biomarker discovery and innovations in the realm of biomarker detection. In its conversion from a theme to a center, members are broadening their focus on cancer to include a wide variety of diseases and conditions.

“There are biomarkers for diseases other than cancer, as well as biomarkers that provide information on a person’s nutrition, environment, microbiome, and metabolism,” Cunningham said. “There are genomic biomarkers for infection and immunity, for inflammation and sepsis, and surprisingly even for environmental exposure, psychological stress, and anxiety . . . So that’s how we’re turning from a cancer group into a genomic diagnostic center, so we can consider things more broadly.”

The center already works closely with the Cancer Center at Illinois. With its expanded scope, the CGD is also growing its relationships with Illinois’ Health Care Engineering Systems Center, as well as the Mayo Clinic and Illinois Alliance.

“Our diagnostic [capability] is one of the things that allows medicine to be personalized,” Cunningham said. “So if you can have a test for a biomarker that tells the clinician something about a particular patient, they have a specific gene is being expressed, or they have a protein molecule that is present in high levels, the information can indicate that the patient is more likely to have successful treatment with a particular drug.”

The faculty and research staff that will join the center from the original IGB research theme and from around campus represent a diversity of backgrounds and expertise.

“Our team includes faculty with backgrounds that span bioinformatics, biochemistry, chemistry, biology, and nutrition, along with engineers like myself whose specialty is detection instrumentation and biosensors.” Cunningham said; the center also involves clinicians from Mayo Clinic, Carle, OSF Hospital, Stanford, and Huntsman Cancer Institute “who could give us guidance about what kind of information would better guide their treatment decisions.  Our clinical partners also inform us about the shortcomings of currently available technologies—and help us target our work to where it can have the greatest clinical impact.”

The center was initiated in January 2020, and is planning a symposium to showcase its research goals later this spring.