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Contact name: Sharlene Denos
Contact email: denos@illinois.edu

Title: “Developing tools for single-molecule sequencing and imaging of RNA modifications.”

Mammalian cells expend large amounts of energy into generating >100 different enzyme-mediated RNA chemical modifications that can change the base-pairing, RNA secondary and tertiary structures, or recruitment of RNA binding proteins among many functions. Pseudouridine modified mRNAs are more resistant to RNAse-mediated degradation and have the potential to modulate immunogenicity and enhance translation in vivo. However, scientists have yet to understand the precise biological function of pseudouridine on mRNAs due to a lack of tools for their direct detection and quantification. 

Dr. Rouhanifard’s tea

m has recently developed an algorithm for identifying pseudouridylated sites directly on mammalian mRNA transcripts using nanopore sequencing. Dr. Rouhanifard’s team achieved this by exploiting systematic base-calling errors that occur at pseudouridylated sites as a function of deviations in the current signals for k-mers as well as long, synthetic mRNA controls bearing pseudouridines. The team created an important list of “ground truth”, pseudouridylated sites, and uncovered previously unreported, pseudouridylated sites. Using their algorithm, the team classifies types of pseudouridine hyper-modification that may occur on mRNAs: Type 1 is mRNA sites with high occupancy; Type 2 is mRNAs that may have >1 pseudouridine on a single read. Using their algorithm and pipeline, Dr. Rouhanifard’s team observed that; 1. Pseudouridine sites in the human transcriptome may be conserved or differentially expressed across cell types, and 2. Pseudouridine modifications are dynamically regulated in response to differentiation.

Contact name: Mollie Stevens
Contact email: mollie@illinois.edu
Contact phone: 217-244-2603

Join your colleagues this fall for informal conversation and coffee in the Beckman West Garden.

This Gather in the Garden Series will be from 10-10:30 a.m. every Tuesday.

Contact name: Jeanne N'Diaye
Contact email: jndiaye@illinois.edu

Two graduate students will present their research at the second Beckman Graduate Student Seminar of the fall semester: Saddam Hossain and Aravind Baby. Lunch will be provided to registered attendees. You may register here.

The event takes place Wednesday, October 4 at noon in 5602 Beckman Institute.

Contact name: Elena Romanova
Contact email: romanova@illinois.edu

Join us at noon on Wednesdays this fall for yoga with a view! All sessions are free and will be held in Beckman's fifth-floor tower room. All are welcome to bring their own mat! 

Contact name: Lexie Kesler
Contact email: lkesler@illinois.edu

Come find out more about the Beckman Institute for Advanced Science and Technology! Learn about the barrier-busting interdisciplinary research facility and community of innovation. Tours will be offered the first Thursday of the month from 10-10:30 a.m.

Contact name: Stacy Olson
Contact email: srolson@illinois.edu
Contact phone: 217-244-8373

Beckman-Brown Lecture on Interdisciplinary Science

Professor Emery N. Brown, M.D., Ph.D. is the Edward Hood Taplin Professor of Medical Engineering and Computational Neuroscience at MIT; the Warren M. Zapol Professor of Anesthesia at Harvard Medical School; and an anesthesiologist at Massachusetts General Hospital.

His talk is titled, "General Anesthesia, Neuromodulation and Altered States of Arousal."

The annual Beckman-Brown Lecture on Interdisciplinary Science honors Dr. Arnold O. Beckman, the founder of the Institute, and Dr. Theodore “Ted” Brown, the founding director. The series is funded by a gift from the Arnold and Mabel Beckman Foundation. Learn more.

Contact name: Mollie Stevens
Contact email: mollie@illinois.edu
Contact phone: 217-244-2603

Join your colleagues this fall for informal conversation and coffee in the Beckman West Garden.

This Gather in the Garden Series will be from 10-10:30 a.m. every Tuesday.

Contact name: Elena Romanova
Contact email: romanova@illinois.edu

Join us at noon on Wednesdays this fall for yoga with a view! All sessions are free and will be held in Beckman's fifth-floor tower room. All are welcome to bring their own mat! 

Contact name: Mollie Stevens
Contact email: mollie@illinois.edu
Contact phone: 217-333-3287

Fan Lam will present: "Multiscale, Multiparametric Biochemical Imaging of the Brain." Lam is an assistant professor in the Department of Bioengineering at UIUC, a full-time faculty member with the Beckman Institute and the director of the Master of Science in Biomedical Image Computing (MS-BIC) program.  

The seminar will be held at noon on Thursday, October 12 in Beckman Institute, room 1005. Lunch will be provided to registered attendees. You can register here.

Contact name: Mollie Stevens
Contact email: mollie@illinois.edu
Contact phone: 217-244-2603

Join your colleagues this fall for informal conversation and coffee in the Beckman West Garden.

This Gather in the Garden Series will be from 10-10:30 a.m. every Tuesday.

Contact name: Elena Romanova
Contact email: romanova@illinois.edu

Join us at noon on Wednesdays this fall for yoga with a view! All sessions are free and will be held in Beckman's fifth-floor tower room. All are welcome to bring their own mat! 

Contact name: Molly Stevens
Contact email: mollie@illinois.edu

Join members of the Beckman community for coffee and cookies in the Beckman Atrium. The Cookie Collab is scheduled for 3 p.m. on the third Thursday of each month. 

Contact name: Paritosh Gargya
Contact email: paritosh@illinois.edu

Title: “Computational understanding of biological patterns: 3D genome folding and landscape of stochastic cellular fate.”

Experimental measurements of chromosome conformation, epigenetic modifications, and stochastic cellular behavior present new opportunities for understanding fundamental biology. Dr. Liang will discuss how 3D polymer models using the CHROMATIX method and Hi-C chromosome conformation capture studies can identify a small set of non-random polymer interactions, which can drive chromatin folding. Large ensemble models of independently folded chromatin conformations can uncover hubs of many-body interactions, revealing novel mechanisms of promoter-enhancer interactions and gene regulation. Dr. Liang will then discuss the recent development of the ACME (accurate chemical master equation) method that can construct the exact time-evolving probabilistic landscapes of stochastic reaction networks by solving the underlying discrete chemical master equation. Examples of how these landscapes can be used to study cellular fate will be given. Finally, Dr. Liang will discuss how to meet the rising challenges of deciphering these newly computable high-dimensional probability landscapes and quantify their exact topological structures of peaks and cycles of various dimensions through persistent homology.

Contact name: Mollie Stevens
Contact email: mollie@illinois.edu
Contact phone: 217-244-2603

Join your colleagues this fall for informal conversation and coffee in the Beckman West Garden.

This Gather in the Garden Series will be from 10-10:30 a.m. every Tuesday.

Contact name: Elena Romanova
Contact email: romanova@illinois.edu

Join us at noon on Wednesdays this fall for yoga with a view! All sessions are free and will be held in Beckman's fifth-floor tower room. All are welcome to bring their own mat! 

Contact name: Mollie Stevens
Contact email: mollie@illinois.edu
Contact phone: 217-244-2603

Join your colleagues this fall for informal conversation and coffee in the Beckman West Garden.

This Gather in the Garden Series will be from 10-10:30 a.m. every Tuesday.