Chan Zuckerberg Biohub Network’s Post

🔉CZ Biohub Chicago is thrilled to announce its first cohort of Investigators, 48 innovative scientists and engineers hailing from our three partner universities, Northwestern University, University of Illinois Urbana-Champaign, and University of Chicago. This funding will enable Investigators to perform high-risk, high-reward research on topics related to instrumented tissues, inflammation, and the functions of the immune system. Meet the inaugural class of #CZBiohubCHI Investigators! University of Illinois Urbana-Champaign Indrani Bagchi, Ph.D., Rohit Bhargava, Ph.D, Qian Chen, Ph.D., Martha Gillette, Ph.D., Bumsoo Han, Ph.D., Amy Wagoner Johnson, Ph.D., Auinash Kalsotra, Ph.D., Hyunjoon Kong, Ph.D., Catherine Murphy, Ph.D.,  M. Taher Saif, Ph.D., Mei Shen, Ph.D.,  Shannon Sirk, Ph.D.,  Bradley Sutton, Ph.D., Jonathan Sweedler, Ph.D.,  Yurii Vlasov, Ph.D., Ayelet Ziv-Gal, Ph.D.   Northwestern University Navdeep Chandel, Ph.D., Jaehyuk Choi, M.D., Ph.D., Lee Cooper, Ph.D., Igor Efimov, Ph.D., Horacio Espinosa, Ph.D., Dominic Fullenkamp, M.D., Ph.D., Yogesh Goyal, Ph.D., Neil Kelleher, Ph.D., John Kessler, M.D., Huiping Lee, M.D., Ph.D., Chad Mirkin, Ph.D., Elizabeth McNally, M.D, Ph.D., Chian-Yu Peng, Ph.D.,  Arthur Prindle, Ph.D.,  Ali Shilatifard, Ph.D.,  Lisa Volpatti, Ph.D. University of Chicago Luis Barreiro, Ph.D., Marcus Clark, M.D., Ph.D., Bryan Dickinson, Ph.D.,  Aaron Esser-Kahn, Ph.D., Margaret Gardel, Ph.D., Aly Khan, Ph.D., Yang Li, Ph.D., Peter Mauer, Ph.D., Alex Pearson, M.D., Ph.D., Samantha Riesenfeld, Ph.D., Benjamin Shogan, M.D., Allison Squires, Ph.D., Melody Swartz, Ph.D.,  Savas Tay, Ph.D., Vincenzo Vitelli, Ph.D., Sihong Wang, Ph.D.

For the first time, members of the CZ Biohub Network convened at Chan Zuckerberg Initiative's HQ Week, with #CZBiohubSF, #CZBiohubCHI, #CZBiohubNY all represented! It was great to meet and celebrate in person, and to share ideas about the bold, important science being done across our institutes!

Stay abreast of news and publications from across the CZ Biohub institutes, and subscribe to Nexus, the monthly newsletter of the CZ Biohub Network. Highlights from the latest issue: 📸 how #CZImagingInstitute scientists are accelerating contributions to the cryoET Data Portal 🧑💼 meet the new Computational Biology head @ #CZBiohubSF 💡 a “living bioelectronics” prototype from U. Chicago Read more ⤵️ https://lnkd.in/e6QK69pw

🔬Revolutionizing pathology with #AI: researchers have developed a “human-in-the-loop” framework called https://lnkd.in/eTNfcBeW to overcome limitations of off-the-shelf AI models for pathology. They found it to be better and faster than humans or AI working alone. Led by #CZBiohubSF Investigator James Zou and Zhi Huang of Stanford University School of Medicine, the study validated the model in two use cases: examining histology images for colorectal cancer and endometriosis. By allowing humans to give real-time feedback to the AI model, clinicians were able to double their sensitivity in identifying plasma cells in endometrial biopsies while having a tool adapted for their needs. Read the paper in Nature Biomedical Engineering ⤵️ https://lnkd.in/e39ePE55

🔊New in Nature Methods: label-free imaging of 3D dry mass and 3D orientation of biomolecules by measuring their permittivity tensor. This computational imaging module that can be added to any research 🔬! Read the paper, led by Shalin Mehta & the #CZBiohubSF Computational Microscopy team  ⤵️  https://lnkd.in/gAjB8pVH

Research would not be possible without Research Associates. We’re sad to say goodbye to these wonderful #CZBiohubSF RAs but excited to see them pursue their science dreams! Wishing you all the best (clockwise from top left): - Aditi Saxena, pursuing Ph.D. in Biological Sciences in Public Health (Immunology and Infectious Disease) at Harvard University - Hunter Woosley, pursuing Master’s/Ph.D. in Molecular Biology at Max Planck Institute for Multidisciplinary Sciences / University of Göttingen - Sarah Ancheta, pursuing Ph.D. in Biological and Medical Informatics at UCSF - Fitzgerald Small, pursuing Ph.D. in Biomedical Sciences at Albert Einstein College of Medicine - Josette Medicielo, pursuing M.D. at Medical College of Wisconsin #STEM #ScienceCareer

#CZBiohubSF is “computational biologists’ heaven,” says Yasin Şenbabaoğlu, Biohub SF’s new Director of Computational Biology. That’s because “Biohub researchers are generating unique, large datasets that aren’t being prioritized by industry or academia.” Şenbabaoğlu brings to his new role a wealth of experience in cancer immunology and genomics as well as the development of multimodal AI tools for biological discovery. Read about his journey and his vision for future projects: https://lnkd.in/ggjaWR-x #computationalbiology #datascience #genomics #cancer #AI

Omega, published today in Nature Methods, is a powerful new tool from Loïc Royer and colleagues at #CZBiohubSF. Omega allows users of the popular bioimaging software napari to do sophisticated imaging tasks without the need for complex commands or building code. Simply ask what you’d like napari to do, using natural language, and Omega takes over, issuing the proper napari commands in the background or creating code on the fly. Omega can even quickly create reusable widgets to make frequent tasks easier. Omega’s intelligent code editor enhances code management with automatic commenting, error detection, and correction features. Going beyond text, Omega can interpret visual data, integrating multiple data types to provide comprehensive image analysis. “The idea for Omega began with an invited perspective piece published in Nature Methods in 2023, in which I predicted that in the very near future bioimage analysis tasks will be solved through ‘conversations with the machine,’” said Royer. “Omega is a significant stride toward this vision.” Learn more: https://lnkd.in/gvkiUGn5

The #CZBiohubSF Rapid Response group just wrapped up a fun and rewarding two weeks at Meharry Medical College in Nashville, one of the oldest and largest historically black medical schools in the U.S. The group worked with Meharry students and faculty on genomic strategies for public health and clinical applications, including metagenomic sequencing (such as wet lab techniques and data analysis using CZ ID) and basic genomic epidemiology concepts. The Rapid Response group of the San Francisco Biohub has worked all over the world to improve infectious disease surveillance and response, especially in underserved areas. “Our partnership with Meharry Medical College is aligned with our mission of promoting increasing diversity of the STEM workforce and building equity in health, research, and medicine,” said Cristina Tato, senior director of the group. The team included instructors from University of California, San Francisco, California Department of Public Health, and Universidad Mayor de San Andrés in Bolivia. Shout out to Chan Zuckerberg Initiative for supporting student participation in the workshop. Learn more about the Rapid Response group: https://lnkd.in/gdnnyrKk #diversityinSTEM #STEMeducation #DiverseWorkforce #inclusion