Spatially charting molecular cell types at single-cell resolution across the entire 3D volume of the brain is critical to illustrating the molecular basis of the tissue anatomy and functions. Yet, there is still a big gap between spatial cell atlas and tissue function. In this presentation, I will introduce a few experimental and computational advances in the mapping of RNA life cycle in our lab that further enable multi-modality deep profiling of cell types and states in situ, bridging single-cell molecular profiles with single-cell functional status in intact biological tissues and accelerating gene-to-function discoveries in development and diseases.

Celebrate the end of the year highlighting awards, honors and achievements by faculty and graduate students.

An awards ceremony will begin with a delicious selection of hors d'oeuvres, soda, beer and wine.

Csaba Forro, PhD and Daniel Wang, PhD, Group Leaders at Chan Zuckerberg Biohub Chicago

"Towards Mapping Inflammation in Real Time"  

"Spatiotemporal Molecular Profiling of Inflammation with Microengineered Devices"

Conference Website

The overarching goal of my laboratory is to understand the mechanisms by which master regulators of signal transduction cascades and gene transcription coordinate large-scale gene expression programs during development and human disease. We have made key discoveries defining fundamental molecular and network level changes underlying epilepsy using novel bioinformatic approaches to identify programmatic drivers of gene expression in disease. The tools we have developed are broadly applicable to understanding transcriptional dynamics across physiological and pathological contexts. These advances have enabled productive collaborations with colleagues in cancer biology, including work with the Miyamoto and Weaver laboratories to study tumor cell plasticity, mitotic checkpoint responses to therapy, and the tumor microenvironment. My long-standing interest in mathematics, combined with extensive experience in molecular and systems neuroscience, has positioned my laboratory to develop and apply innovative computational approaches to address complex biological questions that are otherwise intractable. A major focus of the lab is to define the metabolic, signaling, and epigenetic mechanisms that govern epilepsy and epileptogenesis. We aim to identify conserved master regulators of disease-associated transcriptional programs across multiple animal models and human epilepsy. To this end, I developed the algorithm MAGIC, which mines large-scale transcriptomic data to predict transcription factors and cofactors that drive disease-relevant gene expression changes. At the time of its development, existing approaches often performed poorly, with predictions approaching noise. Through extensive benchmarking, I demonstrated that MAGIC performs as well as, and often better than, existing methods (Roopra, 2020), representing a sustained, single-author effort over seven years. MAGIC subsequently enabled the identification of CP690550 (tofacitinib) as a potent disease-modifying therapy in mouse models of temporal lobe epilepsy (Hoffman et al., 2025).

Abstract:  How cells communicate — through synapses, contact-dependent signals, and secreted factors — shapes everything from neural circuit function to tumor progression. Yet the molecular logic of most cell-cell connections remains unmapped, in part because the tools to identify which cells talk to which, and what they say, have not existed. We have developed a suite of sequencing-based technologies to address this gap. Connectome-seq (Nature Methods, 2026) maps synaptic connectivity at single-cell resolution using split-fluorescent protein reconstitution across synaptic clefts combined with RNA barcoding, enabling simultaneous identification of connected pre- and postsynaptic neurons from complex tissue. Communicatome-seq extends this framework to map diverse heterotypic cell-cell contacts — including neuron-glia and neuron-cancer interactions — using modular contact sensors that reconstitute exclusively at physical interfaces. Complementing these connectivity maps, APEX2-based proximity labeling captures the proteome and transcriptome at synaptic microdomains, revealing the molecular machinery at specific connection sites. Together, these tools provide a path toward decoding the full communicatome of the brain and beyond.

Bio:  Boxuan Zhao is an Assistant Professor in the Department of Cell and Developmental Biology at the University of Illinois Urbana-Champaign, with affiliations in the Carl R. Woese Institute for Genomic Biology, the Neuroscience Program, and the Cancer Center at Illinois. His lab develops sequencing-based technologies to map cellular connectivity and communication, with applications spanning neural circuit wiring, tumor neuroscience, and epitranscriptomics. He trained with Liqun Luo and Alice Ting at Stanford for postdoc and Chuan He at the University of Chicago for PhD, and was named to the 2025 Clarivate Highly Cited Researchers list.

Scott Fraser, PhD
President, Dynamic Imaging, Head of Biohub, San Francisco

"Eavesdropping on Biology by Using New Instrumentation and AI to Foster Multiscale Imaging"

If you're graduating in the coming year and want a faculty job, you need to start preparing now. This summer is a crucial time to get organized and prepare application materials. Join us for this workshop to get tips on how to get ready for a faculty job search this fall. The workshop will address how the faculty job search process works, all of the application documents you will need to prepare, how to stay organized during the search, and more. We will also address how changing policy and economic landscapes might affect the 2026 academic job search.

No registration required. This workshop will take place on Zoom at https://go.grad.illinois.edu/eventspace

See the full listing of Graduate College workshops at go.grad.illinois.edu/workshops

*If you require any disability related accommodations to participate in this workshop more fully, please email gradsuccess@illinois.edu