Events
Past Event
Seminar: The Physical Encoding of Transcriptional Memories
Center for Physical Genomics and Engineering (CPGE)
12:00 PM
Details
Abstract
Remarkably, the human genome encodes the complexity of hundreds of cell types for more than a century from transient embryonic signals. Proper organ function then relies on millions of diverse cells responding coherently to shared stimuli. Coordinating complex behavior across many cell states requires a robust mechanism. At the nanoscale, the human genome physically assembles into several thousand mass-fractal packing domains. Unlike TADs, packing domains represent nanoscale, continuous chromatin density distributions that physically couple high-density heterochromatin cores with transcriptionally active surfaces. In this talk, Dr. Almassalha describes how transcription guides the formation of packing domains by creating geometric specificity for chromatin remodeling enzymes based on their sizes. In turn, transcriptional reactions benefit from optimized physiochemical conditions at the domain surface that can be maintained for decades by the geometric specificity of the remodeling enzymes. In effect, our genome is a self-assembling geometric computational system that physically encodes transcriptional memories as packing domains in a manner reminiscent of reinforcement learning in neural networks. Dr. Almassalha will then discuss how this system is relevant to human health by examining domain formation in muscle development and aging.
About Luay Almassalha, MD, PhD
Luay Almassalha, MD, PhD is a sixth-year fellow in the Department of Gastroenterology and Hepatology at the Northwestern Feinberg School of Medicine and a 2024 Starzl Research Scholar recipient. He is working toward his goal of becoming an independent physician-scientist running a lab at the intersection of mathematics, chromatin biology, and nanoscopic imaging to address gaps in the knowledge of disease of the gastrointestinal tract. After receiving his MD and PhD training, through the Northwestern University Medical-Scientist Training Program under the mentorship of Dr. Vadim Backman and Dr. Igal Szleifer, he completed clinical training in Internal Medicine and is currently completing his training in Gastroenterology and Hepatology. Motivated by his clinical experience with patients impacted by immune disorders and cancers throughout the gastrointestinal tract, he investigates how the physical folding of the genome intersects with human disease. His goal is to apply the understanding of physical and chemical properties of the genome to these disorders to develop new treatments as well as prognostic and diagnostic tools.
Time
Friday, January 17, 2025 at 12:00 PM - 1:00 PM
Contact
Calendar
Center for Physical Genomics and Engineering (CPGE)
BME Seminar Series: Zotero Workshop
McCormick - Biomedical Engineering Department (BME)
4:00 PM
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Tech L361, Technological Institute
Details
In this session, BME grad students will receive a brief introduction to general library services and literature searching. After that, they will be introduced to Zotero, a reference management tool. Zotero can help researchers collect, organize, annotate, share, and cite research. Using a citation management tool saves researchers hours of time and lots of frustration.
**Participants are encouraged to bring a laptop so they can start using Zotero during the session.
Becca Greenstein (Associate Librarian)
rgreenst@northwestern.edu
Time
Thursday, January 23, 2025 at 4:00 PM - 5:00 PM
Location
Tech L361, Technological Institute Map
Contact
Calendar
McCormick - Biomedical Engineering Department (BME)
BME Seminar Series: Dr. Huiliang (Evan) Wang
McCormick - Biomedical Engineering Department (BME)
4:00 PM
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Tech L361, Technological Institute
Details
Coming Soon!
Time
Thursday, January 30, 2025 at 4:00 PM - 5:00 PM
Location
Tech L361, Technological Institute Map
Contact
Calendar
McCormick - Biomedical Engineering Department (BME)
The Monthly Seminar on Physical Genomics: Mechanisms of Chromosome Folding - Job Dekker, PhD
Center for Physical Genomics and Engineering (CPGE)
12:00 PM
Details
Abstract
Chromosomes are intricately folded to facilitate accurate gene expression, DNA replication, and chromosome compaction and segregation as cells divide. I will first briefly introduce the current understanding of how mammalian chromosomes fold, focusing on the two known mechanisms that are currently widely studied: spatial segregation of eu- and heterochromatin through biophysical phase separation, and chromatin loop formation through loop extrusion by molecular motors such as cohesin and condensin complexes. I will then focus on how activity and interplay among multiple loop extruding complexes fold chromosomes, using mitotic chromosome formation as example. Next, I will address the question how cell type-specific interphase chromosome folding is inherited through mitosis. I will present evidence that interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm.
About Job Dekker
Job Dekker received his undergraduate and graduate training at Utrecht University in The Netherlands. As a post-doctoral fellow in the laboratory of Nancy Kleckner at Harvard University, he developed chromosome conformation capture methodology. He is currently an Investigator of the Howard Hughes Medical Institute and Professor in the Department of Systems Biology at the University of Massachusetts Chan Medical School. His laboratory studies how genomes are folded in three dimensions. His work has led to insights into the formation of chromatin loops involved in long-range gene regulation, the organization of the interphase nucleus, the structure of metaphase chromosomes, and general folding principles of genomes. His group pioneered the use of genome folding data for genome assembly. His lab explores chromosome folding mechanisms in organisms with unusual genome organizations, such as dinoflagellates.
Sponsored by the Center for Physical Genomics and Engineering, the Cancer and Physical Sciences Program at the Robert H. Lurie Comprehensive Cancer Center, and NIH Grants T32GM142604 and U54CA268084
Time
Friday, January 31, 2025 at 12:00 PM - 1:00 PM
Contact
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Center for Physical Genomics and Engineering (CPGE)
BME Seminar Series: Dr. Anders Sejr Hansen
McCormick - Biomedical Engineering Department (BME)
4:00 PM
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Tech L361, Technological Institute
Details
Coming Soon!
Time
Thursday, March 6, 2025 at 4:00 PM - 5:00 PM
Location
Tech L361, Technological Institute Map
Contact
Calendar
McCormick - Biomedical Engineering Department (BME)
BME Seminar Series: Dr. Chi Zhang
McCormick - Biomedical Engineering Department (BME)
4:00 PM
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Tech L361, Technological Institute
Details
Coming Soon!
Time
Thursday, April 3, 2025 at 4:00 PM - 5:00 PM
Location
Tech L361, Technological Institute Map
Contact
Calendar
McCormick - Biomedical Engineering Department (BME)
BME Seminar Series: Dr. Ross Ethier
McCormick - Biomedical Engineering Department (BME)
4:00 PM
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Tech L361, Technological Institute
Details
Coming Soon!
Time
Thursday, April 17, 2025 at 4:00 PM - 5:00 PM
Location
Tech L361, Technological Institute Map
Contact
Calendar
McCormick - Biomedical Engineering Department (BME)
BME Seminar Series: Dr. Robert Rose
McCormick - Biomedical Engineering Department (BME)
4:00 PM
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Tech L361, Technological Institute
Details
Coming Soon!
Time
Thursday, May 1, 2025 at 4:00 PM - 5:00 PM
Location
Tech L361, Technological Institute Map
Contact
Calendar
McCormick - Biomedical Engineering Department (BME)
BME Seminar Series: Dr. Ji-Xin Cheng
McCormick - Biomedical Engineering Department (BME)
4:00 PM
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Tech L361, Technological Institute
Details
Coming Soon!
Time
Thursday, May 15, 2025 at 4:00 PM - 5:00 PM
Location
Tech L361, Technological Institute Map
Contact
Calendar
McCormick - Biomedical Engineering Department (BME)