Happening @ Michigan https://events.umich.edu/list/rss RSS Feed for Happening @ Michigan Events at the University of Michigan. RNA Collaborative Seminar (June 30, 2021 4:00pm) https://events.umich.edu/event/84166 84166-21620522@events.umich.edu Event Begins: Wednesday, June 30, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

REGISTRATION REQUIRED: https://umich.zoom.us/webinar/register/WN_6OEQ6sDAQ0-21GHm6d7VEQ

“Dynamic multivalent interactions drive mammalian RNA regulation”
Sethu Pitchiaya, Ph.D.
Dept of Urology

and

"Characterizing cellular RNA-protein interaction networks with chemical probes"
Chase Weidmann, Ph.D.
Dept of Biological Chemistry

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Lecture / Discussion Wed, 09 Jun 2021 15:28:29 -0400 2021-06-30T16:00:00-04:00 2021-06-30T17:00:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Sethu Pitchiaya & Chase Weidmann
Department of Computational Medicine & Bioinformatics || Weekly Seminar Series (September 8, 2021 4:00pm) https://events.umich.edu/event/86237 86237-21632210@events.umich.edu Event Begins: Wednesday, September 8, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Structural variants (SVs) are a source of pathogenic variants in a clinical referral population, however, they are often under-reported due to technical limitations of detection and difficulty with clinical interpretation. For example, mobile element insertions (MEIs) are estimated to lead to a positive finding in 1 out of 1000 rare genetic disease cases, yet the numbers are far lower in clinical diagnostic laboratories. Targeted NGS with short insert size libraries, unlike genome sequencing, will have very few discordant read pairs to indicate the presence of an SV. We, therefore, developed an SV detection tool called SCRAMble (Soft Clipped Read Alignment Mapper) to identify SV breakpoints in targeted NGS.

We applied SCRAMble to a prospective clinical referral cohort for exome sequencing to identify deletions and MEIs. We also applied SCRAMble to a hereditary cancer panel assay for the identification of a large inversion involving the MSH2 gene that causes Lynch syndrome. Adding breakpoint detection to clinical targeted sequencing identifies positive findings which were missed by prior testing and by other variant callers. Detecting breakpoints allows for more precise interpretation and for more targeted confirmation assays. By applying SV breakpoint detection, we are able to diagnose ~0.3% more cases. While this is a modest gain in diagnostic yield, for the patients and families involved, a positive diagnosis, even after prior testing, can have a meaningful impact on their lives.

Zoom link: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Livestream / Virtual Thu, 02 Sep 2021 14:28:18 -0400 2021-09-08T16:00:00-04:00 2021-09-08T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Rebecca Torene, Associate Director of Genomics Research | Data Science at GeneDx
RNA Innovation Seminar (September 13, 2021 4:00pm) https://events.umich.edu/event/86155 86155-21631746@events.umich.edu Event Begins: Monday, September 13, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

"Recent improvements in modeling and design of RNA-only structures"

ABSTRACT: The discovery and design of biologically important RNA molecules is outpacing three-structural characterization. I'll describe results from my and Wah Chiu's groups that demonstrate that cryo-electron microscopy can resolve maps of several kinds of RNA-only systems. These maps enable subnanometer-resolution 3D coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. If time allows, I'll describe work from the Eterna project to stabilize mRNA molecules to help accelerate worldwide COVID immunization.

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Lecture / Discussion Thu, 02 Sep 2021 12:54:16 -0400 2021-09-13T16:00:00-04:00 2021-09-13T17:00:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Rhiju Das, Stanford University
Department of Computational Medicine & Bioinformatics Weekly Seminar Series (September 15, 2021 4:00pm) https://events.umich.edu/event/86598 86598-21635116@events.umich.edu Event Begins: Wednesday, September 15, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Chromosomal instability (CIN) results in the accumulation of large-scale losses, gains, and rearrangements of DNA. The broad genomic complexity caused by CIN is a hallmark of cancer, however, there is no systematic framework to measure different types of CIN and their impact on clinical phenotypes. Here, we evaluate the extent, diversity and origin of chromosomal instability across 7,880 tumors representing 33 cancer types from the TCGA collection. We present a compendium of 17 copy number signatures characterizing specific types of CIN, with putative aetiologies supported by multiple independent data sources. The signatures predict drug response and identify new drug targets. Our framework refines the understanding of impaired homologous recombination, one of the most therapeutically targetable types of CIN. Our results illuminate a fundamental structure underlying genomic complexity and provide a resource to guide future CIN
research in human cancers.

Bio:

Florian Markowetz is a Senior Group Leader at the Cancer Research UK Cambridge Institute. He is a Royal Society Wolfson Research Merit Award holder and received a CRUK Future Leader in Cancer Research prize. He holds degrees in Mathematics (Dipl. math.) and Philosophy (M.A.) from the University of Heidelberg and a Dr. rer. nat. (PhD equivalent) in Computational Biology from Free University Berlin, for which he was awarded an Otto-Hahn Medal by the Max Planck Society. His group at the CRUK Cambridge Institute combines computational work on cancer evolution and image analysis of the tumor tissue with experimental work on understanding key cancer mechanisms like the estrogen receptor.

Zoom link: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Livestream / Virtual Thu, 09 Sep 2021 11:24:05 -0400 2021-09-15T16:00:00-04:00 2021-09-15T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Florian Markowetz (Senior Group Leader at the Cancer Research UK Cambridge Institute)
U-M Structure Seminar: "Structural basis for redox sensing by the cyanobacterial transcription regulator RexT" (September 17, 2021 10:00am) https://events.umich.edu/event/85431 85431-21626418@events.umich.edu Event Begins: Friday, September 17, 2021 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Bin Li, Ph.D.
Postdoctoral Research Fellow
University of Michigan, Bridwell-Rabb Lab

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Tue, 07 Sep 2021 14:09:31 -0400 2021-09-17T10:00:00-04:00 2021-09-17T11:00:00-04:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
Department of Computational Medicine & Bioinformatics Weekly Seminar (September 22, 2021 4:00pm) https://events.umich.edu/event/87282 87282-21640718@events.umich.edu Event Begins: Wednesday, September 22, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Histones are small proteins that package DNA into chromosomes, and a large number of studies have showed that several post-translational modification (PTM) sites on the histones are associated with both gene activation and silencing. Along with DNA and small non-coding RNA, histone PTMs make up epigenetic mechanisms that control gene expression patterns outside of DNA sequence mutations. Dysregulation of these chromatin networks underlie several human diseases such as cancer. Here I will give an update on technology advancements that have allowed for high-throughput quantitative analyses of histone PTMs and chromatin structure, and how we are applying these methods to understand epigenetic reprogramming found in malignant peripheral nerve sheath tumors (MPNSTs). MPNST is an aggressive sarcoma with recurrent loss of function alterations in polycomb-repressive complex 2 (PRC2), a histone-modifying complex involved in transcriptional silencing.

Zoom Link: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Livestream / Virtual Mon, 20 Sep 2021 15:27:41 -0400 2021-09-22T16:00:00-04:00 2021-09-22T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
U-M Structure Seminar: "Structure of a meiosis-specific complex central to BRCA2 localization at recombination sites (September 24, 2021 10:00am) https://events.umich.edu/event/85432 85432-21626419@events.umich.edu Event Begins: Friday, September 24, 2021 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Jayakrishnan Nandakumar, Ph.D.
University of Michigan
Associate Professor of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Tue, 07 Sep 2021 14:09:51 -0400 2021-09-24T10:00:00-04:00 2021-09-24T11:00:00-04:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
Picture a Scientist (September 24, 2021 12:00pm) https://events.umich.edu/event/86730 86730-21639091@events.umich.edu Event Begins: Friday, September 24, 2021 12:00pm
Location: Off Campus Location
Organized By: Biostatistics

Please join us virtually on Friday, September 24th to watch and discuss the film, Picture a Scientist! This groundbreaking documentary chronicles the lives of three women scientists, who share their own experiences with sexual harassment and discrimination in order to create a more equitable and welcoming field. Watch the movie any time through this link, or join us for an online watch party at 9:30am. Then tune in at noon, to listen to a student-moderated discussion by our distinguished panel members, Dr. Patricia Coleman-Burns, Heather Colohan, Dr. Reshma Jagsi and Dr. Anna Kirkland. This will be followed by breakout room discussions (same registration as for the panel discussion) at 1:05 pm for students, staff, faculty and mixed groups.
https://sph.umich.edu/biostat/biostat_dei/biostat_dei_events/index.html

PANEL DISCUSSION (12 - 1PM ET)

Patricia W. Coleman-Burns, PhD, MA, U-M University of Michigan assistant professor emerita of nursing and Black studies. In addition to co-chairing the UM Academic Women's Caucus and serving on the U-M Women of Color in the Academy Project Steering Committee, she has served on the board of Safehouse Center on domestic violence and sexual assault. Her research, including her GENESIS pipeline project and EPIC Feedback Model, focuses on Black racial identity, workforce diversity, and reducing health disparities.

Heather Colohan, LMSW, U-M Sexual Assault Prevention and Awareness Center (SAPAC) Educator and Program Manager for Community Outreach & Systems Advocacy. She provides support and educational workshops to students, staff and faculty affected by sexual assault. She also supervises Raise the Bar; a program that works with local bars and transportation services to provide tailored workshops on sexual assault and bystander intervention.

Reshma Jagsi, MD, DPhil, Michigan Medicine Deputy Chair of Radiation Oncology, Newman Family Professor of Radiation Oncology, Residency Program Director, and Director of the Center for Bioethics and Social Sciences. Her many contributions to the study of gender discrimination in medicine include JAMA articles Gender Differences in the Salaries of Physician Researchers, and Sexual Harassment and Discrimination Experiences of Academic Medical Faculty.

Anna Kirkland, PhD, JD, U-M LSA Arthur F. Thurnau Professor of Women’s Studies, Director, Women’s and Gender Studies and School of Public Health Professor in Health Management and Policy by courtesy appointment. Prof. Kirkland served as a committee member on the National Academies panel charged with studying sexual harassment in the STEM fields of academia, published in June 2018 as Sexual Harassment of Women: Climate, Culture, and Consequences in Academic Sciences, Engineering, and Medicine.

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Lecture / Discussion Fri, 17 Sep 2021 11:10:58 -0400 2021-09-24T12:00:00-04:00 2021-09-24T13:00:00-04:00 Off Campus Location Biostatistics Lecture / Discussion Picture a scientist
Department of Computational Medicine & Bioinformatics Weekly Seminar (September 29, 2021 4:00pm) https://events.umich.edu/event/87515 87515-21642906@events.umich.edu Event Begins: Wednesday, September 29, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Human complex traits result from genetic and environmental factors, and from their interactions. Many of these effects are mediated by changes in gene regulation. Indeed, most genetic variants associated with complex trait variation in humans are in regulatory regions. I will present some of our recent studies on gene-environment interactions in gene regulation, with a specific focus on cardiovascular health. I will present evidence that gene-environment interactions in molecular phenotypes are frequent, account for a substantial portion of complex trait variation and modify genetic risk for disease.

Research Focus:

My lab is interested in understanding the genetic and molecular basis of inter-individual and inter-population differences in complex phenotypes. We combine evolutionary and functional genomics approaches to study intermediate phenotypes (e.g.: transcription factor binding, gene expression, protein secretion, etc.) and how they are affected by gene-environment interactions. Our research is funded by the NIH.

Zoom link: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Livestream / Virtual Fri, 24 Sep 2021 14:01:53 -0400 2021-09-29T16:00:00-04:00 2021-09-29T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Francesca Luca, PhD (Wayne State University)
U-M Structure Seminar: "Discovery and structural characterization of a diastereoselective intramolecular Diels-Alderase." (October 1, 2021 10:00am) https://events.umich.edu/event/86435 86435-21634312@events.umich.edu Event Begins: Friday, October 1, 2021 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Sebastian Rivera
Graduate Student
University of Michigan, Sherman Lab

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Tue, 07 Sep 2021 14:16:37 -0400 2021-10-01T10:00:00-04:00 2021-10-01T11:00:00-04:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
RNA Innovation Seminar (October 4, 2021 4:00pm) https://events.umich.edu/event/86162 86162-21631753@events.umich.edu Event Begins: Monday, October 4, 2021 4:00pm
Location: 1027 E. Huron Building
Organized By: Center for RNA Biomedicine

"Fluorescent nucleoside analogues with new properties"

HYBRID EVENT
in-person: Forum Hall, Palmer Commons
Zoom: https://umich.zoom.us/webinar/register/WN__vvE2dtHQi-R3h05JUHBzQ

ABSTRACT
Fluorescent nucleoside analogues (FNAs) are powerful probes for studying the structure and dynamics of nucleic acids, which are vital to understanding RNA function, DNA damage repair, nucleic acid–protein interactions, regulatory mechanisms for gene expression, and other aspects of nucleic acid function. Existing FNAs are prone to quenching by base pairing and stacking, are clustered at the blue–green end of the visible spectrum, and have limited brightness as compared with conventional fluorophores. Studies of nucleic acid function would benefit greatly from overcoming these limitations. We have designed, synthesized, and studied a series of fluorescent pyrimidine analogues, aiming to address these limitations and develop a detailed understanding of the relationships between chemical structure and fluorescent responses to local environment in nucleic acids. Included in this series is a tricyclic cytidine analogue DEAtC that is nearly non-fluorescent as a nucleoside, but responds to matched base pairing and stacking with a fluorescence turn-on. A chlorinated tricyclic cytidine 8-Cl-tCO reports on local environment by changes in the vibrational fine structure of its emission spectra. To address the problem of limited brightness, we have design and synthesized a new NFA that we call ABN, which has a conjugated push–pull system similar to those found in bright fluorophores such as rhodamines. ABN is the brightest known FNA when present in duplex nucleic acids, and it is readily detected in single-molecule fluorescence measurements using both 1-photon and 2-photon excitation. Collectively, these FNAs offer new capabilities for biophysical studies on nucleic acids. Comparisons of their structure and properties help to reveal mechanisms for fluorescence changes in response to local environment in nucleic acids.

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Lecture / Discussion Fri, 10 Sep 2021 11:29:04 -0400 2021-10-04T16:00:00-04:00 2021-10-04T17:00:00-04:00 1027 E. Huron Building Center for RNA Biomedicine Lecture / Discussion Byron Purse, San Diego State University
Department of Computational Medicine & Bioinformatics Weekly Seminar (October 13, 2021 4:00pm) https://events.umich.edu/event/86441 86441-21634316@events.umich.edu Event Begins: Wednesday, October 13, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Understanding the genetic and molecular architecture of human disease is accelerated by robust model development and large-scale molecular profiling. I will present two studies leveraging big data analytics or automated machine learning to dissect human disease complexities: 1) Molecular and clinical signatures of SARS-CoV-2 infection in the US marines. This analysis revealed strong antiviral innate immunity set point in females contributing to sex differences in both molecular and clinical response to SARS-CoV-2 infection. A set of accurate biomarkers capable of detecting PCR false negative infections was implemented on small footprint devices. 2) Automated machine learning to interpret the effects of genetic variants. An automated framework, AMBER, was developed for efficiently searching neural network architectures to model genomic sequences. AMBER is useful in various biological applications, including fine mapping variants, partitioning genetic heritability, and in personalized medicine enabled by CRISPR/Cas9 genome editing. Together, these efforts demonstrate quantitative methods coupled with large-scale biomedical data as an effective avenue to decode human regulatory and disease biology.

Short Bio:

Frank Zhang is a Flatiron research fellow with Olga Troyanskaya at the Simons Foundation and Princeton University since 2019. Prior to that, he obtained his PhD at UCLA with Yi Xing. His research focuses on machine learning and statistical method developments for the prediction and interpretation of human molecular and genetic variations using biological big data. Recently, he works on adopting and developing cutting-edge neural architecture search methods to automate the design of deep neural networks in genomics. He is also interested in making deep learning in biomedicine more interpretable and equitable.

Zoom link: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Livestream / Virtual Tue, 07 Sep 2021 14:45:38 -0400 2021-10-13T16:00:00-04:00 2021-10-13T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
U-M Structure Seminar: "Watching enzymes at work: Structure and dynamics of cytochromes P450 using NMR" (October 15, 2021 10:00am) https://events.umich.edu/event/87284 87284-21640722@events.umich.edu Event Begins: Friday, October 15, 2021 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Thomas Pochapsky, Ph.D.
Professor of Chemistry and Biochemistry
Brandeis University

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Workshop / Seminar Mon, 20 Sep 2021 16:31:08 -0400 2021-10-15T10:00:00-04:00 2021-10-15T11:00:00-04:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
Grad School in the Biosciences (October 15, 2021 3:00pm) https://events.umich.edu/event/88102 88102-21650295@events.umich.edu Event Begins: Friday, October 15, 2021 3:00pm
Location: Off Campus Location
Organized By: Futures in Research, Science, Teaching - FIRST

A Zoom panel on applying and preparing for grad school, doing thesis research, and pursuing careers post-degree.

Professor, Postdoc, and Grad Student speakers from the Department of Molecular, Cellular, and Developmental Biology.

Zoom: https://umich.zoom.us/j/91884583350

Question Submission: https://forms.gle/KSiZLTCicKygKcWg9

FIRST Events: https://linktr.ee/FIRST_Org

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Workshop / Seminar Mon, 11 Oct 2021 14:43:59 -0400 2021-10-15T15:00:00-04:00 2021-10-15T15:00:00-04:00 Off Campus Location Futures in Research, Science, Teaching - FIRST Workshop / Seminar FIRST Logo
RNA Innovation Seminar: Tim Stasevich, Ph.D., Colorado State University (October 18, 2021 4:00pm) https://events.umich.edu/event/86166 86166-21631758@events.umich.edu Event Begins: Monday, October 18, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

KEYWORDS: translational regulation, gene expression, fluorescence microscopy, intrabodies, single-molecule imaging

ABSTRACT: My lab is creating technology to image mRNA translation in real time and with single-molecule precision in living cells. In this talk, I will introduce our technology and describe how it can be used to amplify fluorescence from newly synthesized proteins as they are being translated from single mRNAs. I will show how we quantify these signals to determine the size, shape, subcellular localization, and mobilities of mRNA translation sites, as well as their protein synthesis dynamics. I will then highlight a few recent applications of our technology, focusing mainly on a new biosensor we have developed to quantify how individual regulatory factors impact single mRNA translation dynamics. Using this biosensor, we provide evidence that human Argonaute2 (Ago2) shuts down translation by down regulating translation initiation on the minutes timescale and helping usher translationally silent mRNAs into P-bodies on the hours timescale. I will conclude by discussing new fluorescent intrabodies my lab is engineering to light up nascent and mature proteins in multiple colors. As these intrabodies can be encoded on plasmids, they can easily be adapted by other labs to image gene activity in diverse living systems.
Timothy J. Stasevich is an Associate Professor in the Department of Biochemistry and Molecular Biology at Colorado State University (CSU). His lab uses a combination of advanced fluorescence microscopy, genetic engineering, and computational modeling to study the dynamics of gene regulation in living mammalian cells. His lab helped pioneer the imaging of real-time single-mRNA translation dynamics in living cells1. Dr. Stasevich received his B.S. in Physics and Mathematics from the University of Michigan, Dearborn, and his Ph. D. in Physics from the University of Maryland, College Park. He transitioned into experimental biophysics as a post-doctoral research fellow in the laboratory of Dr. James G. McNally at the National Cancer Institute. During this time, he developed technology based on fluorescence microscopy to help establish gold-standard measurements of live-cell protein dynamics. Dr. Stasevich next moved to Osaka University, where he worked with Dr. Hiroshi Kimura as a Japan Society for the Promotion of Science Foreign Postdoctoral Research Fellow. While there, he helped create technology to image endogenous proteins and their post-translation modifications in vivo. This allowed him to image the live-cell dynamics of epigenetic histone modifications during gene activation for the first time2. Before joining the faculty at CSU, Dr. Stasevich spent a year as a Visiting Fellow at the HHMI Janelia Research Campus, where he applied superresolution fluorescence microscopy to improve the spatiotemporal resolution of endogenous protein imaging in live cells.
1. Morisaki, T. et al. Real-time quantification of single RNA translation dynamics in living cells. Science 352, 1425–1429 (2016).
2. Stasevich, T. J. et al. Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature 516, 272–275 (2014).

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Lecture / Discussion Thu, 30 Sep 2021 10:17:54 -0400 2021-10-18T16:00:00-04:00 2021-10-18T17:00:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Tim Stasevich, Colorado State University
Department of Computational Medicine & Bioinformatics Weekly Seminar (October 20, 2021 4:00pm) https://events.umich.edu/event/88315 88315-21652404@events.umich.edu Event Begins: Wednesday, October 20, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

The Ye lab is focused on harnessing the power of single cell and computational genomics to understand how immune cells sense and respond to their environment. Utilizing new experimental methods we have developed to enable multiplexed single-cell sequencing, I will describe results from sequencing 1.2M cells from ~250 samples to understand the cellular and molecular bases of systemic lupus erythmatosus and COVID-19. I will also describe how population scale single cell sequencing can enable dissection of the genetic architecture of gene expression and annotation of disease associated variants. Finally, I’ll touch on novel experimental workflows to further increase the throughput of single-cell genomics and for encoding orthogonal information into single-cell sequencing assays.

Research Overview:

The Ye lab is interested in how the interaction between genetics and environment affect human variation at the level of molecular phenotypes. To study these interactions, the lab couples high-throughput sequencing approaches that measure cellular response under environmental challenges with population genetics where such measurements are collected and analyzed across large patient cohorts. The lab develops novel experimental approaches that enable the large-scale collection of functional genomic data *en masse* and computational approaches that translate the data into novel biological insights. This approach is used to initially study primary human immune cells in both healthy and diseased patients to understand host pathogen interactions and its role in autoimmunity.

Zoom link: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Livestream / Virtual Fri, 15 Oct 2021 14:50:45 -0400 2021-10-20T16:00:00-04:00 2021-10-20T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
U-M Structure Seminar: “The Structural Basis for Control of Methylation Extent in Polyketide Synthase Metal-dependent C-methyltransferases” (October 22, 2021 10:00am) https://events.umich.edu/event/85433 85433-21626420@events.umich.edu Event Begins: Friday, October 22, 2021 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Yongtong Lao
Graduate Student
Janet Smith Lab
University of Michigan

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Mon, 20 Sep 2021 16:31:40 -0400 2021-10-22T10:00:00-04:00 2021-10-22T11:00:00-04:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
Department of Computational Medicine & Bioinformatics Weekly Seminar (October 27, 2021 4:00pm) https://events.umich.edu/event/88276 88276-21652019@events.umich.edu Event Begins: Wednesday, October 27, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:
Molecular classification has transformed the diagnosis and treatment of diffuse gliomas, creating targets for precision therapies. However, timely and efficient access to molecular diagnostic methods remains difficult, causing a significant barrier to deliver molecularly-targeted therapies. We aim to develop an innovative point-of-care diagnostic screening method that provides rapid and accurate molecular classification of diffuse gliomas through artificial intelligence and optical imaging in order to improve the comprehensive care of brain tumor patients.

Bio:
Dr. Todd Hollon is a neurosurgeon and research scientist who specializes in brain tumors. He is an Assistant Professor of Neurosurgery. He completed his postdoctoral training in the UM Translational Molecular Imaging Laboratory under the supervision of Drs. Daniel Orringer and Honglak Lee. His postdoctoral work focused on the application of deep neural networks to advanced imaging methods to improve the speed and accuracy of intraoperative brain tumor diagnosis. He hopes to be part of the next generation of young scientists that uses computation and machine learning to make scientific breakthroughs.

Host: Josh Welch, PhD

https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

In-Person: Forum Hall, Palmer Commons

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Livestream / Virtual Thu, 14 Oct 2021 14:26:31 -0400 2021-10-27T16:00:00-04:00 2021-10-27T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
Writing Graduate School Application Statements (October 29, 2021 3:00pm) https://events.umich.edu/event/88774 88774-21657750@events.umich.edu Event Begins: Friday, October 29, 2021 3:00pm
Location: Off Campus Location
Organized By: Futures in Research, Science, Teaching - FIRST

What to include/avoid and how to frame your story while writing academic and personal statements for research-based grad programs.

Seminar/Discussion

Zoom Link: https://umich.zoom.us/j/95163992475

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Workshop / Seminar Fri, 29 Oct 2021 12:12:00 -0400 2021-10-29T15:00:00-04:00 2021-10-29T16:00:00-04:00 Off Campus Location Futures in Research, Science, Teaching - FIRST Workshop / Seminar FIRST Logo
Department of Computational Medicine & Bioinformatics Weekly Seminar (November 3, 2021 4:00pm) https://events.umich.edu/event/88449 88449-21654119@events.umich.edu Event Begins: Wednesday, November 3, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract
My research group works in the area of mathematical oncology, where we use mathematical models to decipher the complex networks of reactions inside of cancer cells and interactions between cells. Immune cells use hundreds of biochemical reactions to respond to their environment, become activated, and kill cancer cells. Understanding the complexity of these reaction networks requires computational tools and mathematical models. We combine detailed, mechanistic modeling with machine learning to study these networks, better understand cancer and immune cells, and predict ways to control tumor growth. In this talk, I will present our recent work aimed at predicting the dynamics of immune cell behaviors across three scales: intracellular signaling pathways in CAR T cells, the collective behavior of a heterogeneous population of immune cells, and tumor-immune interactions at the tissue scale. Our models generate novel mechanistic insight into immune cell activation and predict the effects of immunotherapeutic strategies.


Biography
Stacey D. Finley is the Gordon S. Marshall Early Career Chair and Associate Professor of Biomedical Engineering at the University of Southern California. Dr. Finley received her B.S. in Chemical Engineering from Florida A & M University and obtained her Ph.D. in Chemical Engineering from Northwestern University. She completed postdoctoral training at Johns Hopkins University in the Department of Biomedical Engineering. Dr. Finley joined the faculty at USC in 2013, and she leads the Computational Systems Biology Laboratory. Dr. Finley has joint appointments in the Departments of Chemical Engineering and Materials Science and Quantitative and Computational Biology, and she is a member of the USC Norris Comprehensive Cancer Center. Dr. Finley is also the Founding Director of the Center for Computational Modeling of Cancer at USC. Her research is supported by grants from NSF, NIH, and the American Cancer Society.

Selected honors. 2016 NSF Faculty Early CAREER Award; 2016 Young Innovator by the Cellular and Molecular Bioengineering journal; Leah Edelstein-Keshet Prize from the Society of Mathematical Biology; Junior Research Award from the USC Viterbi School of Engineering; the Hanna Reisler Mentorship Award; 2018 AACR NextGen Star; 2018 Orange County Engineering Council Outstanding Young Engineer; Elected Fellow of the American Institute for Medical and Biological Engineering (2021)

Hosted by: Alan Boyle, PhD

https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Livestream / Virtual Wed, 20 Oct 2021 09:54:50 -0400 2021-11-03T16:00:00-04:00 2021-11-03T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Stacey D. Finley, Ph.D. (USC)
RNA Innovation Seminar (November 8, 2021 4:00pm) https://events.umich.edu/event/86167 86167-21631759@events.umich.edu Event Begins: Monday, November 8, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

"Harnessing diverse compact CRISPR-Cas3 for long-range genome engineering"
Zhonggang Hou, Ph.D.
Research Investigator
Biological Chemistry

and

"Microscopic Examination of Spatial Transcriptome through Seq-Scope"
Jun Hee Lee, PhD
Associate Professor
Molecular & Integrative Physiology

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Lecture / Discussion Mon, 25 Oct 2021 13:33:17 -0400 2021-11-08T16:00:00-05:00 2021-11-08T20:00:00-05:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Zhonggang Hou, Biological Chemistry & Jun Hee Lee, Molecular & Integrative Physiology
Department of Computational Medicine & Bioinformatics Weekly Seminar (November 10, 2021 4:00pm) https://events.umich.edu/event/88540 88540-21654960@events.umich.edu Event Begins: Wednesday, November 10, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Subspace classifiers have been around for a long time, beginning with feature selection, which in essence was a subspace selection technique. This talk will discuss the kind of subspace classifiers that Bledsoe and Browning presented in their 1959 paper and from which there have been a variety of extensions which we will discuss.

The Bledsoe and Browning subspace classifier quantizes measurement space. Each quantized observation tuple corresponds to a cell in measurement space. A collection of subspaces are selected at random. In the original form the subspaces were mutually exclusive. For each class, each cell of a subspace contained a number dependent on the number of observations of the training data that fell into that cell. For each class those numbers were combined in ways not dissimilar to random forests. For a given observation tuple, the class with the highest vote count was selected as the assigned class.

We will discuss a variety of principled extensions of the technique and make some comparisons with Neural Networks.

Research Interests:

High-dimensional space clustering, pattern recognition, knowledge discovery and artificial intelligence

Professor Haralick began his work as one of the principal investigators of the NASA ERTS satellite data doing remote sensing image analysis.

He has made a series of contributions in the field of computer vision. In the high-level vision area, he has worked on inferring 3D geometry from one or more perspective projection views.] He has also identified a variety of vision problems which are special cases of the consistent labeling problem. His papers on consistent labeling, arrangements, relation homomorphism, matching, and tree search translate some specific computer vision problems to the more general combinatorial consistent labeling problem and then discuss the theory of the look-ahead operators that speed up the tree search. The most basic of these is called Forward Checking. This gives a framework for the control structure required in high-level vision problems. He has also extended the forward-checking tree search technique to propositional logic.

Zoom: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Livestream / Virtual Fri, 22 Oct 2021 09:28:27 -0400 2021-11-10T16:00:00-05:00 2021-11-10T17:00:00-05:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Robert M. Haralick, PhD (City University of New York)
Presenting Your Research & Project Design (November 12, 2021 3:00pm) https://events.umich.edu/event/89144 89144-21660677@events.umich.edu Event Begins: Friday, November 12, 2021 3:00pm
Location: Off Campus Location
Organized By: Futures in Research, Science, Teaching - FIRST

A Zoom seminar on presenting to academic audiences, including basics of project design. Useful for those considering careers in science and/or preparing for grad school interviews that require a presentation.

Zoom link: https://umich.zoom.us/j/95315038837

FIRST linktree: https://linktr.ee/FIRST_Org

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Workshop / Seminar Wed, 10 Nov 2021 13:18:06 -0500 2021-11-12T15:00:00-05:00 2021-11-12T16:00:00-05:00 Off Campus Location Futures in Research, Science, Teaching - FIRST Workshop / Seminar FIRST Logo. The letters of "FIRST" are made up of chromosomes tethered to spindles during mitosis.
DCMB / CCMB Weekly Seminar Series (November 17, 2021 4:00pm) https://events.umich.edu/event/89137 89137-21660643@events.umich.edu Event Begins: Wednesday, November 17, 2021 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Talk title: Clinical Trajectory analysis to determine risk-factors of Copd: A COPDGene Study

Abstract:

Background

Chronic obstructive pulmonary disease (COPD) presents significant clinical heterogeneity and a wide variety of progression trajectories [1]. Clinical trajectory analysis (ClinTrajAn) is a powerful tool based on elastic principal graphs for the calculation of trajectories from large cross-sectional clinical data sets [2].

Aims and objectives

Our objective was to determine potential risk-factors by evaluate progression trajectories in COPD using ClinTrajAn on the COPDGene Phase I (baseline visit) dataset.

Methods

7883 participants, current and former smokers with GOLD 0 thru 4 COPD, from Phase I of the COPDGene study, were utilized for this work. 55 features were obtained for each subject, including demographics, spirometry, smoking history and computed tomography (CT), which included Parametric Response Mapping (PRM). Developed by our group, PRM is capable of simultaneously measuring small airways disease and emphysema which are the main contributors of airflow limitations in COPD. The resulting data matrix was analyzed with ClinTrajAn.

Results

A principal tree, with 13 branch segments and 8 termini, was generated (Figure 1). There was a clearly recognized trajectory from healthier subjects through decreasing lung function and increasing age (Figure 1 A), increasing in GOLD (Figure 1 B), to an emphysema high terminus (Figure 1 C). Notably this method illustrated numerous branching points along this trajectory.

Conclusions

In this study we used ClinTrajAn to obtain a map of disease progression trajectories in COPD including clinically recognized pathogenesis. Our next steps will be to further validate this approach using longitudinal data from the COPDGene follow-up visits.

References

1. Han MK, Agusti A, Calverley PM, Celli BR, Criner G, Curtis JL, Fabbri LM, Goldin JG, Jones PW, MacNee W, Make BJ. Chronic obstructive pulmonary disease phenotypes: the future of COPD. American journal of respiratory and critical care medicine. 2010 Sep 1;182(5):598-604.

2. Golovenkin SE, Bac J, Chervov A, Mirkes EM, Orlova YV, Barillot E, Gorban AN, Zinovyev A. Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data. GigaScience. 2020 Nov;9(11):giaa128.

Zoom link: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Lecture / Discussion Wed, 10 Nov 2021 09:47:40 -0500 2021-11-17T16:00:00-05:00 2021-11-17T17:00:00-05:00 Palmer Commons DCMB Seminar Series Lecture / Discussion
U-M Structure Seminar: "Strategies to minimize beam-induced motion in Cryo-EM data collection" (November 19, 2021 10:00am) https://events.umich.edu/event/86436 86436-21634313@events.umich.edu Event Begins: Friday, November 19, 2021 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Min Su, Ph.D.
Cryo-EM Resource Director
University of Michigan

Laura Koepping
Cryo-EM Research Specialist
University of Michigan

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Tue, 02 Nov 2021 16:06:42 -0400 2021-11-19T10:00:00-05:00 2021-11-19T11:00:00-05:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
Department of Computational Medicine & Bioinformatics Weekly Seminar (December 1, 2021 4:00pm) https://events.umich.edu/event/88514 88514-21654664@events.umich.edu Event Begins: Wednesday, December 1, 2021 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract:

Epigenetic control of gene expression is highly cell-type- and context-specific. Yet, despite its complexity, gene regulatory logic can be broken down into modular components consisting of a transcription factor (TF) activating or repressing the expression of a target gene through its binding to a cis-regulatory region. Recent advances in joint profiling of transcription and chromatin accessibility with single-cell resolution offer unprecedented opportunities to interrogate such regulatory logic. Here, we propose a nonparametric approach, TRIPOD, to detect and characterize three-way relationships between a TF, its target gene, and the accessibility of the TF’s binding site, using single-cell RNA and ATAC multiomic data. We apply TRIPOD to interrogate cell-type-specific regulatory logic in peripheral blood mononuclear cells and contrast our results to detections from enhancer databases, cis-eQTL studies, ChIP-seq experiments, and TF knockdown/knockout studies. We then apply TRIPOD to mouse embryonic brain data during neurogenesis and gliogenesis and identified known and novel putative regulatory relationships, validated by ChIP-seq and PLAC-seq. Finally, we demonstrate TRIPOD on SHARE-seq data of differentiating mouse hair follicle cells and identify lineage-specific regulation supported by histone marks for gene activation and super-enhancer annotations.

Hosted by: Joshua Welch, PhD

Speaker will be in-person and the seminar will be live-streamed via Zoom.

Zoom: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Lecture / Discussion Thu, 21 Oct 2021 14:55:35 -0400 2021-12-01T16:00:00-05:00 2021-12-01T17:00:00-05:00 Palmer Commons DCMB Seminar Series Lecture / Discussion Yuchao Jiang (Assistant Professor in the Departments of Biostatistics and Genetics at UNC)
U-M Structure Seminar: "Structural studies of JuvEV modular polyketide synthase" (December 3, 2021 10:00am) https://events.umich.edu/event/86440 86440-21634315@events.umich.edu Event Begins: Friday, December 3, 2021 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Sean Newmister, Ph.D.
Research Investigator
University of Michigan, Sherman Lab

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Fri, 19 Nov 2021 11:43:36 -0500 2021-12-03T10:00:00-05:00 2021-12-03T11:00:00-05:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
U-M Structure Seminar: "The Structural and Functional Diversity of Microbial Encapsulin Nanocompartments" (December 17, 2021 10:00am) https://events.umich.edu/event/86442 86442-21634317@events.umich.edu Event Begins: Friday, December 17, 2021 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Michael Andreas, Ph.D.
Postdoctoral Research Fellow
University of Michigan, Giessen Lab

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Wed, 01 Dec 2021 11:14:17 -0500 2021-12-17T10:00:00-05:00 2021-12-17T11:00:00-05:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
Cryo-ET Pipeline for Imaging Small Proteins in Large Biological Structures (January 13, 2022 9:30am) https://events.umich.edu/event/90501 90501-21671200@events.umich.edu Event Begins: Thursday, January 13, 2022 9:30am
Location: Taubman Biomedical Science Research Building
Organized By: U-M Structural Biology

Correlative Light, and Electron Microscopy (CLEM) Faculty Candidate Seminar

Shiwei Zhu, Ph.D.
Research Specialist- MacMicking Lab, HHMI-Immunology & Microbial Pathogenesis, Yale Systems Biology Institute, Yale University

Hosted by: Cell and Developmental Biology & The Life Sciences Institute

Hybrid Zoom Meeting link: https://umich.zoom.us/j/99429897480 for those that are unable to attend

The venue is accessible via elevator and ramp and if you require any accommodations to fully participate in this activity, please inform:
Lori Mirabitur - Phone: (734) 615-7509 - Email: longeway@umich.edu

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Lecture / Discussion Thu, 06 Jan 2022 12:23:25 -0500 2022-01-13T09:30:00-05:00 2022-01-13T10:30:00-05:00 Taubman Biomedical Science Research Building U-M Structural Biology Lecture / Discussion flier
Grad School Interviews Office Hour (January 21, 2022 10:00am) https://events.umich.edu/event/91167 91167-21677027@events.umich.edu Event Begins: Friday, January 21, 2022 10:00am
Location: Off Campus Location
Organized By: Futures in Research, Science, Teaching - FIRST

If you would like to ask current biology grad students about what interviewing at different grad programs is like, or practice interviewing yourself, please stop by.

Zoom link: https://umich.zoom.us/j/99108550897

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Workshop / Seminar Tue, 18 Jan 2022 11:11:32 -0500 2022-01-21T10:00:00-05:00 2022-01-21T11:00:00-05:00 Off Campus Location Futures in Research, Science, Teaching - FIRST Workshop / Seminar FIRST Logo with the name made out of chromosomes separating during mitosis.
U-M Structure Seminar: "Structural and dynamics investigation of NPSL2 by NMR" (January 21, 2022 10:00am) https://events.umich.edu/event/85434 85434-21626421@events.umich.edu Event Begins: Friday, January 21, 2022 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Yaping Liu, Ph.D.
Postdoctoral Research Fellow
University of Michigan, Sarah Keane Lab

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Mon, 03 Jan 2022 13:13:44 -0500 2022-01-21T10:00:00-05:00 2022-01-21T11:00:00-05:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
Bridging structural biology and virology: imaging processes in the native cellular context at molecular resolution (January 24, 2022 11:30am) https://events.umich.edu/event/90559 90559-21671685@events.umich.edu Event Begins: Monday, January 24, 2022 11:30am
Location: Taubman Biomedical Science Research Building
Organized By: U-M Structural Biology

Correlative Light and Electron Microscopy (CLEM) Faculty Candidate Seminar

Luiza Mendonca, Ph.D.
Research Fellow, Wellcome Centre for Human
Genetics, Division of Structural Biology
(STRUBI), University of Oxford

Hosted By:
Department of Cell and Developmental Biology
Life Science Institute
Biosciences Initiative

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Lecture / Discussion Thu, 06 Jan 2022 12:20:14 -0500 2022-01-24T11:30:00-05:00 2022-01-24T12:30:00-05:00 Taubman Biomedical Science Research Building U-M Structural Biology Lecture / Discussion Luiza
RNA Faculty Candidate Seminar (January 31, 2022 4:00pm) https://events.umich.edu/event/89608 89608-21664520@events.umich.edu Event Begins: Monday, January 31, 2022 4:00pm
Location: Taubman Biomedical Science Research Building
Organized By: Center for RNA Biomedicine

In-person/Hybrid seminar co-hosted by the Center for RNA Biomedicine, the Department of Biological Chemistry and the Department of Biophysics

Talk title: “The scanning mechanism of mRNA translation initiation in humans”

Keywords: mRNA, translation, ribosome, helicase

Abstract: Decoding the genetic information into protein is fundamental for all kingdoms of life. It requires precise mechanisms to transcribe the DNA into mRNA, which then can be translated by the ribosome to produce proteins. Translation initiation of eukaryotic mRNAs is a dynamic process regulated by over a dozen protein eukaryotic initiation factors (eIFs). This process starts with the binding of eukaryotic initiation factors eIF1, eIF1A, eIF3, eIF5, and a ternary complex of eIF2–GTP–tRNAiMet (TC) to the 40S small ribosomal subunit, forming the 43S preinitiation complex (43S PIC). Once assembled, the 43S PIC is recruited to the 5′ untranslated region (UTR) of mRNA by the multifactor cap-binding complex eIF4F, forming the 48S initiation complex (48S). The 48S then scans along the 5′ UTR mRNA to locate a start codon. The eIF4F binding site in the 48S and how mRNA is inserted into the mRNA channel in the 40S small ribosomal subunit remained unknown. To gain insights into the molecular mechanism underlining the assembly of the 48S, we used cryo-electron microscopy to determine the structure of a reconstituted human 48S. The structure sheds light on the early events of translation initiation complex assembly, including how eIF4F interacts with the 43S during the scanning process.

If you are having trouble registering, please contact Martina Jerant at mjerant@umich.edu

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Lecture / Discussion Tue, 04 Jan 2022 11:24:42 -0500 2022-01-31T16:00:00-05:00 2022-01-31T17:00:00-05:00 Taubman Biomedical Science Research Building Center for RNA Biomedicine Lecture / Discussion Jailson (Jay) Brito Querido, MRC Laboratory of Molecular Biology
U-M Structure Seminar: “The GRAFFENDOR (Graphene-based Affinity grid for the Endogenous Proteins) Grid" (February 18, 2022 10:00am) https://events.umich.edu/event/85437 85437-21626424@events.umich.edu Event Begins: Friday, February 18, 2022 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Uhn-Soo Cho, Ph.D.
Associate Professor of Biological Chemistry, Medical School
University of Michigan

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Mon, 24 Jan 2022 08:22:17 -0500 2022-02-18T10:00:00-05:00 2022-02-18T11:00:00-05:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
Weekly Seminar for DCMB / CCMB (February 23, 2022 4:00pm) https://events.umich.edu/event/92060 92060-21686457@events.umich.edu Event Begins: Wednesday, February 23, 2022 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

In the Peixoto lab we use genomic approaches to understand gene expression and its epigenetic regulation in response to learning and sleep deprivation, and its alteration in autism spectrum disorders. This requires combining behavioral paradigms in mice, molecular biology and the analysis of high-throughput data in the brain in vivo. It also requires using the right data analysis tools to be able to capture the effect of learning or sleep in the context of an ever-active brain. In this talk we will discuss the effects of learning on chromatin accessibility and the effects of sleep loss in gene expression, with an emphasis on how data analysis influences our ability to detect novel and reproducible biology.

Short bio:

Lucia Peixoto received her bachelor’s degree in Biochemistry from the Universidad de la Republica in her native Uruguay in 2002. She subsequently earned her Ph.D. at The University of Pennsylvania under the mentorship of Dr. David S. Roos, using genomic and computational biology approaches to understand host-pathogen interactions. She completed her postdoctoral training in Neuroscience with Dr. Ted Abel at The University of Pennsylvania in 2015. During her fellowship, she was also a trainee at the Training Program in Neurodevelopmental disabilities at the Children’s Hospital of Philadelphia. As a trainee at CHOP, she completed a clinical internship at the Center for Autism Research under the supervision of Dr. Robert Schultz. She became an Assistant Professor at Washington State University in 2015 and has since been recognized with a K01 Early Career Faculty award from NIH/NINDS and a pilot award from the Simons Foundation Autism Research Initiative. She is also a member of the board of directors of the International Society of computational biology (ISCB) and cochair the Equity, Diversity and Inclusion committee of ISCB. Her lab uses behavior, electrophysiology, molecular biology and genomic approaches to understand how sleep and learning modulate transcription and how this may be altered in Autism Spectrum Disorders.

Zoom livestream link: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Workshop / Seminar Mon, 07 Feb 2022 14:54:44 -0500 2022-02-23T16:00:00-05:00 2022-02-23T17:00:00-05:00 Off Campus Location DCMB Seminar Series Workshop / Seminar
U-M Structure Seminar: "Machine learning in cryo-EM" (February 25, 2022 10:00am) https://events.umich.edu/event/85438 85438-21626425@events.umich.edu Event Begins: Friday, February 25, 2022 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Yilai Li, Ph.D.
Postdoctoral Research Fellow
University of Michigan, Cianfrocco Lab

This seminar is only open to UM researchers.

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Workshop / Seminar Wed, 02 Feb 2022 10:48:48 -0500 2022-02-25T10:00:00-05:00 2022-02-25T11:00:00-05:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
U-M Structure Seminar: "Defining Human Cytochrome P450 8B1 Structure and Function: Supporting Drug Design for Nonalcoholic Fatty Liver Disease and Diabetes" (March 4, 2022 10:00am) https://events.umich.edu/event/85439 85439-21626426@events.umich.edu Event Begins: Friday, March 4, 2022 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Jinghan Liu
Graduate Student
University of Michigan, Emily Scott Lab

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Thu, 10 Feb 2022 12:49:21 -0500 2022-03-04T10:00:00-05:00 2022-03-04T11:00:00-05:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
Data Science in Health Disparities Research Symposium (March 11, 2022 9:00am) https://events.umich.edu/event/91976 91976-21684826@events.umich.edu Event Begins: Friday, March 11, 2022 9:00am
Location: Palmer Commons
Organized By: DCMB Seminar Series

Additional speakers on the topics of:

How data science can be used to understand racial health disparities

How data science with biased data exacerbates health disparities

Lunch and discussion sessions following the talks.

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Workshop / Seminar Mon, 07 Feb 2022 10:37:38 -0500 2022-03-11T09:00:00-05:00 2022-03-11T15:00:00-05:00 Palmer Commons DCMB Seminar Series Workshop / Seminar
U-M Structure Seminar: "High throughput screening of small molecule binding partners for the FMN riboswitch by a multidisciplinary approach" (March 18, 2022 10:00am) https://events.umich.edu/event/85436 85436-21626423@events.umich.edu Event Begins: Friday, March 18, 2022 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Elizabeth Tidwell
Graduate Student
University of Michigan, Koutmos Lab

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Thu, 03 Mar 2022 11:40:42 -0500 2022-03-18T10:00:00-04:00 2022-03-18T11:00:00-04:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure
UM Structure Seminar: "Structures in situ: Discovering a new lattice inside alpha-carboxysomes" (March 25, 2022 12:00pm) https://events.umich.edu/event/89500 89500-21663332@events.umich.edu Event Begins: Friday, March 25, 2022 12:00pm
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Lauren Ann Metskas, Ph.D.
Assistant Professor
Purdue University

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Lecture / Discussion Mon, 28 Feb 2022 08:56:39 -0500 2022-03-25T12:00:00-04:00 2022-03-25T13:00:00-04:00 Life Sciences Institute U-M Structural Biology Lecture / Discussion U-M Structure
DCMB / CCMB Weekly Seminar presents Rehan Akbani, PhD (Associate Professor, University of Texas, MD Anderson Cancer Center) (March 30, 2022 4:00pm) https://events.umich.edu/event/93933 93933-21711327@events.umich.edu Event Begins: Wednesday, March 30, 2022 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

The TP53 tumor suppressor gene is frequently mutated in human cancers. We illustrate the “omics” landscape of the TP53 pathway across five data platforms in 10,225 patient samples from 33 cancers reported by The Cancer Genome Atlas (TCGA). More than 91% of TP53-mutant cancers exhibit second allele loss by mutation, chromosomal deletion, or copy-neutral loss of heterozygosity. TP53 mutations are associated with enhanced chromosomal instability, including increased amplification of oncogenes and deep deletion of tumor suppressor genes. Tumors with TP53 mutations differ from their non-mutated counterparts in RNA, miRNA, and protein expression patterns, with mutant TP53 tumors displaying enhanced expression of cell cycle progression genes and proteins. A mutant TP53 RNA expression signature shows significant correlation with reduced survival in 11 cancer types. Pathway activity scores were computed for all the samples using mRNA expression levels of ten TP53 pathway member genes. Gynecologic cancers show high activity of the pathway. The pathway is correlated with immune infiltration and EMT, and anti-correlated with RTK and RAS/MAPK pathways. In particular, a strong correlation with immune infiltration is observed in breast cancer. ATAC-seq data also show high chromatin accessibility of the pathway genes in breast cancer. Thus, the TP53 pathway has profound effects on tumor cell genomic structure, expression, and clinical outlook depending on tumor type.

Short Bio
Dr. Rehan Akbani is an Associate Professor at the University of Texas MD Anderson Cancer Center in Houston, Texas, in the Department of Bioinformatics and Computational Biology. He has worked at MD Anderson since 2009. He has played many leadership roles in major enterprises, including as PI on TCGA’s MD Anderson Genome Data Analysis Center (GDAC) grant. Within the TCGA consortium, he led four of TCGA’s analysis working groups and he’s been a co-author on each one of TCGA’s 33 marker papers and 27 pan-cancer papers since 2009. His primary contributions have been leading the analysis of proteomics data, and batch effects and quality control of omics data. He won the AACR “Team Science Award” in 2020 for his work in TCGA. He was conferred the “Highly Cited Researchers 2019” award by Web of Science for co-authoring the most highly cited papers in the past decade. He has over 87,700 citations and an h-index of 78 on Google Scholar. In 2014, he won the “Test of Time” award from the European Conference on Machine Learning (ECML) for publishing the most highly cited paper in ECML a decade ago. Currently, Dr. Akbani is the Co-Director of MD Anderson’s proteomics core and Co-Director of the metabolomics core, where he’s led the development of software pipelines for normalizing raw data and generating customer reports semi-automatically. He’s also contributed proteomics data analysis for projects including the Cancer Cell Line Encyclopedia (CCLE) and the MD Anderson Cell Line Project (MCLP).

Host: Veera Baladandayuthapani, Ph.D.
https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Lecture / Discussion Thu, 24 Mar 2022 12:32:18 -0400 2022-03-30T16:00:00-04:00 2022-03-30T17:00:00-04:00 Off Campus Location DCMB Seminar Series Lecture / Discussion Rehan Akbani, PhD (Associate Professor, University of TX MD Anderson Cancer Center)
U-M Structure Seminar: "Size doesn't matter: de novo generation of llama-derived nanobodies for biological research" (April 15, 2022 10:00am) https://events.umich.edu/event/90345 90345-21670437@events.umich.edu Event Begins: Friday, April 15, 2022 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Matthias Truttman, Ph.D.
Assistant Professor, Department of Molecular & Integrative Physiology
University of Michigan

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Livestream / Virtual Wed, 23 Mar 2022 10:41:54 -0400 2022-04-15T10:00:00-04:00 2022-04-15T11:00:00-04:00 Life Sciences Institute U-M Structural Biology Livestream / Virtual structure
U-M Structure Seminar: "Structural and kinetic characterization of a minimal archaeal RNase P" (April 29, 2022 10:00am) https://events.umich.edu/event/85441 85441-21626428@events.umich.edu Event Begins: Friday, April 29, 2022 10:00am
Location: Life Sciences Institute
Organized By: U-M Structural Biology

Catherine Wilhelm
Graduate Student
University of Michigan, Koutmos Lab

Hybrid: LSI Library and Zoom - https://umich.zoom.us/j/97763780708 (Password: structure)

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Workshop / Seminar Mon, 11 Apr 2022 14:00:58 -0400 2022-04-29T10:00:00-04:00 2022-04-29T11:00:00-04:00 Life Sciences Institute U-M Structural Biology Workshop / Seminar U-M Structure