STORIES REVEALED: REDISCOVERING US Carl R. Woese Institute for Genomic Biology 2020 Annual Report TABLE OF CONTENTS Director’s Message | 2 About the IGB | 6 Stories, Reflections and Awards from 2020 | 10 2020 Numbers, Publications, and Thanks | 102 About the Icons Abbreviations and Acronyms The success of the IGB depends on collaborations Research Themes and centers that transcend traditional disciplines and close ACPP partnerships between researchers and support Anticancer Discovery from Pets to People staff. Throughout this annual report, we use the icons below to indicate connections to the following BCXT research and impact areas. Biocomplexity BSD Biosystems Design CABBI Health Center for Advanced Bioenergy and Bioproducts Research that seeks to understand the Innovation origins and mechanisms of disease and CGD discovers new ways to promote wellness. Center for Genomic Diagnostics EIRH Environmental Impact on Reproductive Health Technology GSE Research that imagines, develops, and Genome Scale Engineering Center refines new tools that enable discovery GEGC and create solutions. Genomic Ecology of Global Change GNDP Gene Networks in Neural and Developmental Plasticity GSP Environment Genomic Security and Privacy Research that explores and protects ecosystems, especially those we rely on IGOH for food and fuel. Infection Genomics for One Health MME Microbiome Metabolic Engineering MMG Fundamental Research Mining Microbial Genomes “Blue Sky” research that creates the M-CELS knowledge base needed for future Multi-Cellular Engineered Living Systems progress. RBTE Regenerative Biology and Tissue Engineering Other abbreviations and acronyms Community Engagement Programs that promote open dialogue DOE between genomic research and society. Department of Energy IGB Carl R. Woese Institute for Genomic Biology NIH National Institutes of Health COVID-19 NSF Efforts that specifically dealt with National Science Foundation research and discovery related to COVID-19. USDA United States Department of Agriculture TAKE A DEEP BREATH. LET’S REFLECT ON OUR 2020. 2 2 AT THE BEGINNING OF 2020, NONE OF US HAD IMAGINED THAT THE WORLD WOULD BE OVERWHELMED BY A PANDEMIC. THINGS THAT WE TOOK FOR GRANTED: COMING INTO WORK, MEETING OUR FRIENDS AND FAMILY, ATTENDING CLASSES OR SOCIAL EVENTS, EVERYTHING CAME TO A GRINDING HALT. 3 DIRECTOR’S MESSAGE AND YET, AS MANY OTHERS HAVE, the community at the Carl R. Woese Institute for Genomic Biology remained resilient as we worked together to face this unique challenge. In this annual report you will read stories from different members of the IGB family. THEIR VOICES REMIND US THAT OUR FUNDAMENTAL QUALITIES OF PERSEVERANCE, TEAMWORK, SACRIFICE, AND EMPATHY REMAIN STRONG EVEN WHEN THE WORLD AROUND US LOOKS COMPLETELY DIFFERENT. OUR VOICES 20 Diana Ranoa 35 Jack Humphrey 53 Jing Dong 74 Shravan Dommaraju In early March, it became undeniably obvious that we needed to take several measures to curb the pandemic. Perhaps unsurprisingly, 94 members of the IGB approached the problem in different ways Ursula Ruiz Vera including volunteering their time, laboratory supplies, and equipment to help increase the COVID-19 testing; making 3D-printed cartridges that can carry out 30-minute COVID tests; building prototypes for AND 9 MORE emergency ventilators; and creating a web tool that can model the COVID-19 spike protein as it mutates, aiding the development of new drugs and vaccines. In addition to these important activities to help fight the pandemic, there were also other notable achievements. Two new IGB research themes—Environmental Impact on Reproductive Health and Multi- Cellular Engineered Living Systems—were established in the past year. We received new funding awards to develop faster COVID-19 4 IGB 2020 ANNUAL REPORT tests, study the prevention and treatment of breast cancer, and develop novel therapeutics for cancer and autoimmune disorders. Several faculty members were honored, including Lisa Ainsworth who was elected to the National Academy of Sciences and Alison Bell and Carl Bernacchi, who were elected to the American Association for the Advancement of Science, further emphasizing that we continued to maintain our pre-pandemic levels of success even in the dramatic environment of 2020. Personally, the pandemic forced me to adopt new routines to match my hybrid home/IGB office routine. Like many of the IGB faculty, I had to devise new ways to interact with my research group, a feat that was made possible because of their cooperation. Even establishing a new exercise routine was a challenge, as was convincing my Golden Retriever that I wasn’t at home exclusively to play with him…I’m not sure he ever got that message. Even though 2020 presented us with many new obstacles, we remained united and worked together to find solutions. IN ADDITION TO CHALLENGING OUR SCIENTIFIC PRACTICES, THE PAST YEAR HAS REQUIRED US TO CHANNEL OUR HUMANITY AND REACH OUT TO ONE ANOTHER. With the vaccine rollout, it is likely that our struggles with the pandemic will abate over the next year. However, I hope that when we look back on our efforts and recall what was done well and what could have been done better, we will use the lessons we learned from each other to make our community stronger. Don Ort ACTING DIRECTOR CARL R. WOESE INSTITUTE FOR GENOMIC BIOLOGY 5 DIRECTOR’S MESSAGE 6 IGB 2020 ANNUAL REPORT WE ARE PERSISTENT DRIVEN DELIBERATE COMMITTED SUPPORTIVE EMPATHETIC RESILIENT INTENTIONAL CREATIVE STRONG RESOURCEFUL. WE ARE THE IGB COMMUNITY. ABOUT IGB The Carl R. Woese Institute for Genomic Biology (IGB) was founded in 2007 with the intention of facilitating genomic research across the campus. IGB members are drawn from many schools and departments, including biology, chemistry, physics, engineering, sociology, and business. What unites them is a shared vision of what a genomics-based approach can achieve: a healthier global population, increased food and fuel security, a toolbox of genomic technologies to meet future societal challenges, and a deep knowledge of the diversity of life on our planet. OUR MISSION To advance life science research at the University of Illinois Urbana-Champaign and to stimulate bio-economic development in the state of Illinois. 7 ABOUT THE IGB IGB STRATEGIC PARTNERSHIPS, RESEARCH THEMES, AND CENTERS IGB’s research is organized into research themes, each of which comprises multiple laboratory groups brought together by shared scientific approaches and goals. Our research themes are connected through their overlap within three broad areas of fundamental and applied research: health challenges and solutions, genomic technologies, and environmental resources and conservation. Our scientists participate in a variety of strategic partnerships with academic, governmental and industry partners. STRATEGIC HPCBio PARTNERSHIPS High Performance Biological Computing (HPCBio) was created to address the need for a structure that could supply infrastructure, user support and training, and R&D capability in computational genomics to the Illinois research community. HPCBio provides a single, straightforward point of access, open to researchers from all campus units, helping them to find solutions to their biomedical data management and analysis problems. KnowEnG: NIH Center of Excellence in Big Data Computing KnowEnG is a National Institutes of Health-funded initiative that brings together researchers from the University of Illinois and Mayo Clinic to create a Center of Excellence in Big Data Computing. It is part of the Big Data to Knowledge (BD2K) Initiative that NIH launched in 2012 to tap the wealth of information contained in biomedical Big Data. KnowEnG is one of 11 Centers of Excellence in Big Data Computing funded by NIH in 2014. Microbial Systems Initiative The goal of the Microbial Systems Initiative (MSI) is to sustain a vibrant microbial sciences research and training enterprise at the University of Illinois Urbana-Champaign. Illinois microbial systems research addresses critical problems in health, agriculture, energy, and many other sectors. The MSI carries out ongoing activities to build collaboration across disciplines, provide world class training opportunities, and build environments of inclusive excellence. Personalized Nutrition Initiative The Personalized Nutrition Initiative is a campus-wide initiative under the leadership of the Office of the Vice Chancellor for Research and Innovation, in partnership with the IGB and the College of Agricultural, Consumer and Environmental Sciences, to facilitate transdisciplinary collaborative efforts across campus to answer fundamental questions regarding how nutrition modulates health and disease across the lifespan and to translate that information to clinical care and the public. 8 IGB 2020 ANNUAL REPORT RESEARCH Anticancer Discovery from Gene Networks in Neural and THEMES AND Pets to People (ACPP) Developmental Plasticity CENTERS Develops cancer treatments (GNDP) in pet animals that translate Examines the effects of to human disease coordinated gene activity on biological diversity Biocomplexity (BCXT) Explores the origin of life Genomic Security and Privacy and the behavior of (GSP) biological systems Considers the implications of genomic applications Biosystems Design (BSD) on an individual’s security Applies engineering and privacy principles to real and artificial biological systems Infection Genomics for One Health (IGOH) Center for Advanced Examines how microbes Bioenergy and Bioproducts in human-inhabited Innovation (CABBI) environments influence