Institute for Quantitative Biomedicine (IQB)

IQB News and Announcement update

Join us for a special seminar January 9th 2025 with Wonpil Im

Since its original development in 2006, CHARMM-GUI (CHARMM-GUI) has proven to be an ideal web-based platform to interactively build complex molecular systems and prepare their simulation inputs with well-established and reproducible simulation protocols for state-of-the-art molecular simulations using widely used simulation packages with various force fields. The CHARMM-GUI development project has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of molecular simulation systems. Our philosophy in CHARMM-GUI development is less about providing the nuts and bolts of molecular modeling, but instead focused on helping users to achieve a task, such as building a membrane system or solvating a protein, by providing a streamlined interface. This design principle helps us to think of the workflow critically when designing the interface and new modules, which leads CHARMM-GUI to be accessible to users with little experience in modeling tools and remains useful to experts, especially for batch generation of systems. The CHARMM-GUI development project is still ongoing. CHARMM-GUI will continue to help expert and non-expert researchers from a broader range of the modeling and simulation community to build the complex molecular systems of their interest and prepare the input files for any general and advanced modeling and simulation through the large and unique scope of CHARMM-GUI functionality, allowing the research community to carry out innovative and novel molecular modeling and simulation research. In this talk, I will present the past, present, and future of the CHARMM-GUI development project, and some applications of specific modules will be also discussed.

Congratulations to Nora for the IQB Inclusive Leadership Award

Graduate student Nora Jaber has been selected for the 2025 IQB Inclusive Leadership Award in recognition of her outstanding achievements. Details

Congratulations to Dr. Judit Pénzes and Dr. Jason Kaelber

Congratulations to IQB faculty members Drs. Judit Pénzes and Jason Kaelber as well as their co-authors, Dr. Pénzes's husband Mr. Martin Holm and their collaborator Dr. Samantha Yost of REGENXBIO. An article they recently published in CellPress titled: Cryo-EM-based discovery of a pathogenic parvovirus causing epidemic mortality by black wasting disease in farmed beetles, was highlighted on science.org for the novel approach the authors used in order to identify an infectious organism, directly using high resolution Cryo-EM.
https://www.science.org/content/blog-post/cryo-em-rescue

Full Article:
https://www.cell.com/cell/fulltext/S0092-8674(24)00885-7

Congratulations to IQB Faculty Members Shishir Chundawat, Sagar Khare, and Debashish Bhattacharya!

We are pleased to announce the official launch of the 5-year Schmidt VIFF-funded Sargassum project. Led by José Avalos from Princeton University, along with Shishir Chundawat from Rutgers University and Loretta Roberson from the Marine Biological Laboratory, this initiative focuses on addressing environmental and economic challenges posed by excessive seaweed in coastal communities.

The project aims to utilize a carbon-neutral or negative refinery-style process to convert Sargassum seaweed into fuel, animal feed, and other valuable products. Shishir Chundawat, as the lead PI from Rutgers, alongside Dr. Debashish Bhattacharya and IQB's resident faculty, Dr. Sagar Khare, play crucial roles in this interdisciplinary effort.

José Avalos, lead investigator and associate professor of chemical and biological engineering at Princeton University, emphasized the project's potential impact: Much like how petroleum is refined into various fuels and petrochemicals, we aim to develop a biorefinery to transform Sargassum into sustainable products for everyday use. This initiative presents an opportunity to convert an environmental challenge into a lasting solution.

Funded as part of the Virtual Institute on Feedstocks of the Future initiative (VIFF), this project is one of five supported by Schmidt Sciences and the Foundation for Food & Agriculture Research, totaling up to $47.3 million over five years.

For further information, please visit Transforming troublesome seaweed into a feedstock of the future (Princeton) and Five Projects Receive Funding to Advance the Circular Bioeconomy with Biomass Feedstocks (Schmidt Sciences).

Congratulations to Dr. Sagar Khare Promoted to Full Professor

We are thrilled to announce a significant milestone in our community. Dr. Sagar Khare has been promoted to the position of Full Professor. This promotion reflects Dr. Khare's exceptional dedication, scholarly contributions, and leadership in our institution. Throughout his tenure, Dr. Khare has exemplified excellence in research, teaching, and service, enriching our academic environment. Please join us in congratulating Dr. Khare on this well-deserved achievement. His promotion not only underscores his expertise but also strengthens our commitment to academic excellence and innovation.

Notice of Award: $350,000 grant to upgrade RCNF instruments

We are thrilled to announce that Dr. Jason Kaelber has been awarded $350,000 from the NIH shared instrumentation program to acquire a K3 direct electron detector for the incoming Krios electron microscope. This camera will facilitate in situ structural biology and high-resolution protein structure determination for scientists using the Rutgers CryoEM & Nanoimaging Facility. The RCNF anticipates that the new instrumentation will be operational this fall.

Congratulations to Dr. Sagar Khare

We're excited to share that Professor Sagar Khare has been chosen for the prestigious Presidential Outstanding Faculty Scholar Award for 2023-2024. This honor recognizes his exceptional teaching and scholarly achievements at Rutgers University. As part of the award, Professor Khare will receive a $1000 grant from the Board of Trustees to support his academic endeavors. Please join us in congratulating Dr. Sagar Khare on this well-deserved recognition!

Congratulations to Dr. Sijian Wang

Please join us in congratulating Dr. Sijian Wang on his promotion from Associate Professor to Professor in the Department of Statistics. Sijian started his independent career at the University of Wisconsin, being promoted to Associate Professor in 2014 and joining Rutgers University as an Associate Professor in 2017. His research interests include: High-dimensional data analysis and big data analytics; Statistical learning and machine learning; Proteomics, bioinformatics, statistical genomics and precision medicine; Survival analysis and longitudinal data analysis; Statistical modeling and statistical practice. He is currently the Co-director for the Masters Program in Financial Statistics and Risk Management and the Masters Program in Data Science. We look forward to seeing Dr. Wang succeed in his new role.