Welcome new tenure-track BioE faculty


Allen Xu and Laura Schmitt

Experiencing a period of rapid growth, the Bioengineering Department proudly announces the addition of five new faculty--Joseph Irudayaraj, Shuming Nie, Kris Kilian, Thom Gaj, and Shannon Sirk. Collectively, they will strengthen BioE's expertise in nanotechnology, genetic editing, cellular imaging, biomaterials, and protein engineering.

Joseph Irudayaraj

Jospeh Irudayaraj is a Founder Professor in Bioengineering.
Jospeh Irudayaraj is a Founder Professor in Bioengineering.

An expert in nanomaterials for biosensors and monitoring live cell dynamics, Joseph Irudayaraj is a prolific researcher in the biomedical imaging and nanosensor technology fields. His groundbreaking work in phenotyping cancer cells has been successfully commercialized into a globally marketed diagnostic tool by Cytoviva Inc., a leading provider of advanced optical microscopy and hyperspectral imaging technologies.

Irudayaraj spent more than a decade at Purdue University, where he made a significant breakthrough in utilizing gold nanorods and dark field plasmon imaging techniques, which made it possible to evaluate multiple different surface proteins and mRNA splicing at once in live cancer cells, with single cell resolution. This is not possible when using conventional or other advanced methods.

Utilizing the concepts of lateral flow technology, his team has also developed one of the most sensitive color-based point of care technologies for cervical cancer screening, which is currently being evaluated for venture capital funding.

Using single cell spectroscopy and super-resolution imaging techniques, Irudayaraj continued to explore the intracellular mechanisms associated with epigenetics (chemical modification of DNA), phosphorylation (implicated in cell signaling), and mRNA expression in live cells for toxicity (drug and contaminants) studies and in expounding on epigenetic mechanisms and signaling pathways.

At Illinois, Irudayaraj is focusing on live cell monitoring across different model organisms incorporating super-resolution lifetime imaging and spectroscopy. His research lab  is located in Carle Hospital’s Stephens Family Clinical Research Institute, which allows him to directly collaborate with physicians and researchers at the U of I Micro + Nanotechnology Lab (MNTL).

“My group will work closely with clinicians to fill the gap in the market,” said Irudayaraj, who is a Founder Professor in Bioengineering and holds appointments in the Carl Woese Institute for Genomic Biology and MNTL. “We will develop simple devices or biomaterials for point-of-care diagnostics.”

He added: “I look forward to partnering with the top-class faculty at Illinois in the field of biomedical sciences and human health and working closely with the faculty in bioengineering and materials.”

Irudayaraj earned his PhD from Purdue and was a faculty member at Purdue, Penn State, Utah State, and University of Saskatchewan. He is an AIMBE Fellow, a recipient of the Purdue College of Engineering Research Excellence Award and University Faculty scholar award.

Shuming Nie

A pioneer in advancing biomedical nanotechnology, Shuming Nie is joining the Illinois Bioengineering Department as the Grainger Distinguished Chair in Engineering on September 1. Nie comes to Illinois from Emory University and the Georgia Institute of Technology, where he had been the Wallace H. Coulter Distinguished Chair Professor in Biomedical Engineering for more than 10 years.

Shuming Nie is a Grainger Distinguished Chair in Engineering.
Shuming Nie is a Grainger Distinguished Chair in Engineering.

Nie’s academic work is primarily in the areas of nanomedicine, molecular engineering, and image-guided/minimally invasive/robotic surgery. His major academic achievements include the discovery of colloidal metal nanoparticles that are able to amplify the efficiencies of surface-enhanced Raman scattering (SERS) by 14-15 orders of magnitude, his pioneering work on water-soluble semiconductor quantum dots for biomedical applications, and his breakthrough work in developing multifunctional smart nanoparticles for targeted drug delivery and intraoperative cancer imaging.

Early in his career while at Indiana University, Nie published a groundbreaking paper in Science magazine describing the use of metallic nanoparticles and surface-enhanced Raman scattering to detect and characterize single molecules and nanoparticles at room temperature, a feat that was previously not possible. This monumental breakthrough allowed for the nanoscale analysis of complex mixtures and biological systems, which has a variety of potential applications, including bioimaging.

While at Emory and Georgia Tech, Nie developed innovative applications of nanoparticles in cancer treatment, including in-vivo imaging of tumors, targeted drug delivery, and diagnostic tools. He created quantum dots that bound to antibodies and could target proteins on the surface of cancer cells—effectively highlighting tumors that are often difficult to visualize.

He has also developed an even more effective imaging scheme that uses gold nanoparticles to highlight tumors. This work led to a commercial image-guided surgical system that allows surgeons to better visualize tumors in real time during a procedure, making it possible to excise tumors that were previously inoperable due to location or obscurity.

More recently, Nie has explored the use of bioconjugated nanoparticles for therapeutic drug delivery, making it possible to deliver the drugs directly to the tumors with minimal damage to non-cancerous cells. This type of therapeutics could result in more effective cancer treatment with far fewer side effects.

Nie has collaborated with thoracic surgeons at the University of Pennsylvania, neurosurgeons at Mount Sinai in New York, and GI surgeons at Emory to develop clinically applicable nanoparticles and spectroscopic instrumentation for intraoperative cancer detection and image-guided surgery. During the last 5 years, his collaborative teams have been engaged in seven clinical trials for image-guided cancer surgery, enrolling more than 300 cancer patients at multiple hospital sites. 

According to Google Scholar, Nie’s work has been cited over 58,000 times, while two of his breakthrough papers published in Science have each been cited over 8,000 times.

Nie was attracted to Illinois because of the campus’ deep scholarship,  the amazing opportunities in interdisciplinary research, and the country’s first engineering-based college of medicine.

“At this stage of my career, I am most excited to explore new areas that could make a real impact, such as cell-based immunotherapy for cancer, wearable electro-optic devices for molecular and cellular monitoring, and artificial intelligence for extracting useful information from massive spectroscopic data,” said Nie, who has trained more than 30 doctoral students and postdoctoral fellows who are making an impact at top academic institutions and biotech companies. “Moving to a new institution means new people, new facilities, new ideas, and new possibilities.”

A Fellow of both the AAAS and IAMBE, Nie has received the MilliPub Club Award, Merck Award, Nature Publishing’s Achievement Award in Nanomedicine, and the UK’s Rank Prize in Opto-electronics. He earned his PhD from Northwestern University.

In addition to his faculty position with Bioengineering, Nie will hold joint appointments in the Electrical & Computer Engineering Department and the Micro + Nanotechnology Lab. 

Kristopher Kilian

Kristopher Kilian’s research group explores how both natural and synthetic materials influence the signaling that controls cell fate and function. They specialize in designing and developing models of tissue to more accurately explore cell signaling and tissue assembly across numerous physiological and pathological conditions including development and cancer. An Illinois Materials Science and Engineering faculty member since 2011, Kilian formally joined the Bioengineering faculty this past year.

Recently, his group developed a chemical array to culture metastatic cancer cells, which typically lose their stem cell characteristics when they are removed from the body during a biopsy. Kilian’s array will enable researchers to test different drug treatments on the stem-like cells—an important development since these cells often respond differently to drugs used to target the main tumor.

A recipient of a 2015 National Science Foundation CAREER award for young faculty, Kilian has previously used engineered tissue environments in various patterns and shapes to study skin cancer. Working with researchers in Veterinary Medicine, Kilian’s team discovered that the curve along the edge of a tumor may play an important role in activating a few cancer cells to break away and spread to other parts of the body.

“My training has spanned biotechnology, materials chemistry, and cell biology,” said Kilian. “In recent years it became clear that at the core we are bioengineers. Joining the department was like coming home.”

Among the courses Kilian teaches are Advanced Bioinstrumentation (BIOE 507), Design and Use of Biomaterials (MSE 470), and Phases and Phase Relations (MSE 201).

Kilian earned his doctorate from the University of New South Wales, and he investigated new methods for directing stem cell differentiation as a National Institutes of Health (NIH) post-doctoral fellow at the University of Chicago.  In 2008, he received the NIH Ruth L. Kirchstein National Research Service Award.  

Thomas Gaj

Thomas Gaj is developing strategies to treat neurodegenerative diseases like amyotrophic lateral sclerosis (ALS) through targeted gene correction, while also working to improve the safety of genome editing. He will join the Illinois Bioengineering faculty in January 2018 as an assistant professor.

Thom Gaj joins the Illinois BioE faculty in January 2018.
Thom Gaj joins the Illinois BioE faculty in January 2018.

Although there is no cure for ALS, scientists have discovered a number of mutations that cause the disease, including those in the superoxide dismutase 1 (SOD1) gene, which are responsible for nearly 25% of inherited ALS cases and represent one of the most common genetic causes for the disease. While a post-doctoral fellow at the University of California, Berkeley, Gaj was recently part of a research team that harnessed the power of a widely-used gene editing technique to treat ALS.

Specifically, Gaj combined a class of clinically promising viral gene delivery vehicles called AAV with CRISPR-Cas9 nucleases to inactivate a mutated copy of the SOD1 gene in the spinal cord of an animal model of ALS.

“One of the things we’re excited about going forward is designing new gene-editing strategies that are capable of targeting other common disease-causing mutations and then correcting these mutations within the cells affected by disease,” said Gaj. “It’s ambitious, but we have exciting data that speaks to the feasibility of this approach.”

Gaj earned his PhD in chemistry from the Scripps Research Institute, where he discovered that many commonly used gene editing enzymes can be delivered directly into cells as purified proteins instead of DNA. This approach improved the safety of gene editing, leading to fewer unwanted mutations and is now a widely used by the genome editing community.

According to Gaj, he decided to join the Illinois Bioengineering faculty in part because of the College of Engineering’s overall strengths and the new engineering-based Carle Illinois College of Medicine.

“We take an engineering approach to gene therapy,” said Gaj. “We want to develop new technologies that can address very specific therapeutic problems. Everyone in Bioengineering is working toward engineering new medical solutions, so this is an exciting place to be.”

Gaj also anticipates working with other Illinois researchers on developing new modes for delivering gene editing tools into cells, including non-viral technologies that could potentially prove safer and less immunogenic than viral methods.

In addition to launching his Illinois research, Gaj looks forward to designing and developing a new graduate-level course focused on highlighting the therapeutic and translational potential of cell engineering strategies.

Shannon Sirk

With expertise in protein engineering, antibodies, and genome editing, Shannon Sirk aims to harness the natural power of microbes to develop biological therapeutics that can effectively treat cancer and other diseases. She will join the Illinois Bioengineering faculty as an assistant professor in January 2018.

Shannon Sirk will join the Illinois BioE faculty in January 2018.
Shannon Sirk will join the Illinois BioE faculty in January 2018.

For the past three years, Sirk has been working as a post-doctoral scholar in the Chemical Engineering department at Stanford University, where she is investigating the gut microbiota and its role in processing the cancer-fighting chemicals found in cruciferous vegetables such as broccoli and kale.

 “The gut microbiota is a very complex system,” Sirk said about the tens of trillions of micro-organisms living in every human’s intestine. “Until we really understand what the players are doing and how the microbes interact with what you feed them, we cannot possibly hope to engineer therapeutic solutions for human health or even try to predict what will happen when we perturb the system.”

Using bioinformatics, genetic engineering, and biochemical characterization, Sirk and her colleagues have identified a key metabolic pathway responsible for enzymatically activating a class of dietary chemicals that exhibit cancer-preventing characteristics. Their work has revealed functional details of the complicated yet critical interactions between gut microbes, food, and health outcomes.

According to Sirk, she chose to join the Illinois Bioengineering faculty because of the people, facilities, and great engineering college. “The people work hard but they are also happy,” said Sirk, who will be an affiliate of the Carl Woese Institute for Genomic Biology in addition to her Bioengineering position. “That’s the type of team I want to be a part of—it really appealed to me, along with the opportunities for collaboration, the amazing facilities and resources, and the dedicated and enthusiastic student body.”

Sirk earned her PhD in Molecular and Medical Pharmacology in 2009 from UCLA and then spent four years as a post-doctoral researcher at the Scripps Research Institute. There, she conducted protein engineering studies and was part of a team that developed methods to safely disrupt specific genes within cells, prior to the widespread adoption of the CRISPR gene modification technique.