BEGIN:VCALENDAR
VERSION:2.0
PRODID:-//Institute for Quantitative and Computational Biosciences - ECPv6.15.20//NONSGML v1.0//EN
CALSCALE:GREGORIAN
METHOD:PUBLISH
X-ORIGINAL-URL:https://qcb.ucla.edu
X-WR-CALDESC:Events for Institute for Quantitative and Computational Biosciences
REFRESH-INTERVAL;VALUE=DURATION:PT1H
X-Robots-Tag:noindex
X-PUBLISHED-TTL:PT1H
BEGIN:VTIMEZONE
TZID:America/Los_Angeles
BEGIN:DAYLIGHT
TZOFFSETFROM:-0800
TZOFFSETTO:-0700
TZNAME:PDT
DTSTART:20210314T100000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0700
TZOFFSETTO:-0800
TZNAME:PST
DTSTART:20211107T090000
END:STANDARD
BEGIN:DAYLIGHT
TZOFFSETFROM:-0800
TZOFFSETTO:-0700
TZNAME:PDT
DTSTART:20220313T100000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0700
TZOFFSETTO:-0800
TZNAME:PST
DTSTART:20221106T090000
END:STANDARD
BEGIN:DAYLIGHT
TZOFFSETFROM:-0800
TZOFFSETTO:-0700
TZNAME:PDT
DTSTART:20230312T100000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0700
TZOFFSETTO:-0800
TZNAME:PST
DTSTART:20231105T090000
END:STANDARD
BEGIN:DAYLIGHT
TZOFFSETFROM:-0800
TZOFFSETTO:-0700
TZNAME:PDT
DTSTART:20240310T100000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0700
TZOFFSETTO:-0800
TZNAME:PST
DTSTART:20241103T090000
END:STANDARD
BEGIN:DAYLIGHT
TZOFFSETFROM:-0800
TZOFFSETTO:-0700
TZNAME:PDT
DTSTART:20250309T100000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0700
TZOFFSETTO:-0800
TZNAME:PST
DTSTART:20251102T090000
END:STANDARD
END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20240415T120000
DTEND;TZID=America/Los_Angeles:20240415T130000
DTSTAMP:20260412T104129
CREATED:20240407T153129Z
LAST-MODIFIED:20240407T153129Z
UID:26472-1713182400-1713186000@qcb.ucla.edu
SUMMARY:Frontiers in Computational Biosciences Seminar Series: Chongzhi Zang\, PhD\, Associate Professor\, University of Virginia
DESCRIPTION:TITLE: “Computational Methods for Trancriptional Regulation” \nHosted by Jingyi Jessica Li for Bioinformatics
URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-chongzhi-zang-phd-associate-professor-university-of-virginia/
LOCATION:Boyer 159
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2024/04/Chongzhi.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20240408T120000
DTEND;TZID=America/Los_Angeles:20240408T130000
DTSTAMP:20260412T104129
CREATED:20240407T152731Z
LAST-MODIFIED:20240407T152731Z
UID:26467-1712577600-1712581200@qcb.ucla.edu
SUMMARY:Frontiers in Computational Biosciences Seminar Series: Barbara Cheifet\, PhD\, Editor in Chief\, Nature Biotechnology
DESCRIPTION:TITLE: “Publishing for Impact” \nHosted by Jingyi Jessica Li for Bioinformatics
URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-barbara-cheifet-phd-editor-in-chief-nature-biotechnology/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2024/04/Barbara.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20240401T120000
DTEND;TZID=America/Los_Angeles:20240401T130000
DTSTAMP:20260412T104129
CREATED:20240401T144912Z
LAST-MODIFIED:20240401T145230Z
UID:26433-1711972800-1711976400@qcb.ucla.edu
SUMMARY:Frontiers in Computational Biosciences Seminar Series: Alexis Battle\, PhD\, Professor\, Biomedical Engineering\, Computer Science and Genetics Medicine Director\, Malone Center for Engineering in Healthcare\, Johns Hopkins University
DESCRIPTION:TITLE: “Multi-omic and temporal data for rare and common genetic variation”
URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-alexis-battle-phd-professor-biomedical-engineering-computer-science-and-genetics-medicine-director-malone-center-for-engineering-in-healthcar/
LOCATION:Boyer 159
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2024/04/ALEXIS.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230724T110000
DTEND;TZID=America/Los_Angeles:20230724T120000
DTSTAMP:20260412T104129
CREATED:20230719T153531Z
LAST-MODIFIED:20230719T153531Z
UID:24891-1690196400-1690200000@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Andras Gyorgy\, Assistant Professor of Electrical Engineering and Bioengineering - NYU Abu Dhabi
DESCRIPTION:TITLE: “Inducible plasmid copy number control and a blueprint for a synthetic genetic feedback optimizer” \nABSTRACT: The ability to control gene expression has been paradigm shifting for all areas of biological research\, especially for synthetic biology. This talk will focus on two recent advancements in gene expression control. First\, TULIP (TUnable Ligand Inducible Plasmid) is presented: a self-contained plasmid with inducible copy number control\, designed for portability across various Escherichia coli strains commonly used for cloning\, protein expression\, and metabolic engineering. As demonstrated through multiple application examples\, flexible plasmid copy number control via TULIP accelerates the design and optimization of gene circuits\, enables efficient probing of metabolic burden\, and facilitates the prototyping and recycling of modules in different genetic contexts. Second\, the blueprint of a genetic feedback module is presented to optimize a broadly defined performance metric by adjusting the production and decay rate of a set of regulator species. The optimizer can be implemented by combining available synthetic biology parts and components\, and it can be readily integrated with existing pathways and genetically encoded biosensors to ensure its successful deployment in a variety of settings when relying on mass action kinetics-based dynamics and parameter values typical in Escherichia coli.
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-andras-gyorgy-assistant-professor-of-electrical-engineering-and-bioengineering-nyu-abu-dhabi/
LOCATION:Boyer Hall 130
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/07/Andras-Gyorgy-7.24.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230721T160000
DTEND;TZID=America/Los_Angeles:20230721T170000
DTSTAMP:20260412T104129
CREATED:20230719T152504Z
LAST-MODIFIED:20230719T152504Z
UID:24886-1689955200-1689958800@qcb.ucla.edu
SUMMARY:BIG Summer Research Seminar: Jimmy Hu\, Assistant Professor in the Division of Oral Biology & Medicine at the UCLA School of Dentistry
DESCRIPTION:TITLE: “Building a tooth from transcriptome to tissue morphogenesis” \nABSTRACT: During craniofacial development\, the oral epithelium begins as a morphologically homogeneous tissue that gives rise to locally complex structures\, including the teeth\, salivary glands\, and taste buds. How the epithelium is initially patterned and later shaped to generate diverse organ and cell types remains largely unknown. To elucidate the genetic programs that direct the formation of distinct oral epithelial populations\, we mapped the transcriptional landscape of embryonic day (E) 12 mouse mandibular epithelia at single cell resolution. Our analysis identified key transcription factors and gene regulatory networks that define different epithelial cell types. By examining the spatiotemporal patterning process along the oral-aboral axis\, our results inform a model where the dental field is progressively confined to its position by the formation of the aboral epithelium anteriorly and the non-dental oral epithelium posteriorly. As dental suprabasal cells are enriched with genes related to actomyosin-based motility\, we next studied mutant embryos lacking non-muscle myosin II to explore the roles of cellular forces during tooth morphogenesis. We found that myosin II is critical for maintaining cell-cell adhesion and for efficient cellular movement that drives dental epithelial invagination. Together\, our results describe the transcriptional regulation during oral epithelial patterning and unveil an actomyosin-based mechanism that promotes tooth invagination.
URL:https://qcb.ucla.edu/event/big-summer-research-seminar-jimmy-hu-assistant-professor-in-the-division-of-oral-biology-medicine-at-the-ucla-school-of-dentistry/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/07/Jimmy-Hu.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230714T160000
DTEND;TZID=America/Los_Angeles:20230714T170000
DTSTAMP:20260412T104129
CREATED:20230711T184053Z
LAST-MODIFIED:20230711T184148Z
UID:24861-1689350400-1689354000@qcb.ucla.edu
SUMMARY:BIG Summer Research Seminar: Xianghong Jasmine Zhou\, Professor\, Pathology and Laboratory Medicine at UCLA
DESCRIPTION:TITLE: “Liquid Biopsies for Precision Oncology.” \nABSTRACT: Liquid biopsies are new diagnostic approaches to profile molecular features of solid tumors by blood\, saliva\, urine\, and other body fluids. Such approaches offer non-invasive options in early cancer detection\, tumor sampling\, continuous monitoring\, and designing personalized therapeutic options. Therefore\, liquid biopsies have the potential to transform the field of clinical oncology. Recently\, cell-free DNA analysis from a simple blood draw received enormous attention for its promise in these applications. In this talk\, we will discuss several novel computational and experimental technologies on using cell-free DNA for the detection and monitoring of cancer and other diseases.
URL:https://qcb.ucla.edu/event/big-summer-research-seminar-xianghong-jasmine-zhou-professor-pathology-and-laboratory-medicine-at-ucla/
LOCATION:Boyer Hall 159
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/07/Jasmine_round-3.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230707T160000
DTEND;TZID=America/Los_Angeles:20230707T170000
DTSTAMP:20260412T104129
CREATED:20230627T234736Z
LAST-MODIFIED:20230627T234745Z
UID:24835-1688745600-1688749200@qcb.ucla.edu
SUMMARY:BIG Summer Research Seminar: Xia Yang\, Professor\, Integrative Biology and Physiology Molecular and Medical Pharmacology at UCLA
DESCRIPTION:TITLE: “Single Cell Multiomics Integration to Understand Complex Diseases.” \nABSTRACT: Recent advances in single cell multiomics technologies such as single cell RNA-seq\, single cell ATAC-seq\, and spatial transcriptomics have brought enormous opportunities that enable our understanding of the molecular underpinnings of pathophysiology at a single cell or cell type resolution. However\, integrative analysis across single cell multiomics domains has proven challenging.  I will introduce our recent efforts in single cell multiomics integration and gene regulatory network modeling\, present computational tools to carry out these analyses\, and showcase application examples in studies of various complex diseases. \n 
URL:https://qcb.ucla.edu/event/big-summer-research-seminar-xia-yang-professor-integrative-biology-and-physiology-molecular-and-medical-pharmacology-at-ucla/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/06/Xia-Yang-Ph.D..jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230630T160000
DTEND;TZID=America/Los_Angeles:20230630T170000
DTSTAMP:20260412T104129
CREATED:20230627T234352Z
LAST-MODIFIED:20230627T234352Z
UID:24831-1688140800-1688144400@qcb.ucla.edu
SUMMARY:BIG Summer Research Seminar: Eric Deeds\, Associate Professor\, Integrative Biology & Physiology - Vice Chair\, Life Sciences Core at UCLA
DESCRIPTION:TITLE: “A lack of distinct cellular identities in scRNA-seq data: revisiting Waddington’s landscape.” \nABSTRACT: Single-cell RNA sequencing is revolutionizing our understanding of development\, differentiation and disease. Analysis of this data is often challenging\, however\, and tasks like clustering cells to uncover distinct cellular identities sometimes yields results that fail to align with existing biological knowledge. We analyzed publicly available data where the cell identity for each cell is known a priori\, and found that cells of very different types and lineages do not occupy distinct regions of gene expression space. Rather\, cells from different lineages overlap extensively with one another\, significantly complicating attempts to recover distinct identities within the data. Indeed\, our analysis of available epigenetic data for a wide variety of tissues and organisms revealed these data are not consistent with the predictions of Waddington’s landscape\, suggesting a need to revisit our picture of gene expression changes during differentiation and development. \n 
URL:https://qcb.ucla.edu/event/big-summer-research-seminar-eric-deeds-associate-professor-integrative-biology-physiology-vice-chair-life-sciences-core-at-ucla/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/06/eric-deeds.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230623T163000
DTEND;TZID=America/Los_Angeles:20230623T170000
DTSTAMP:20260412T104129
CREATED:20230621T151413Z
LAST-MODIFIED:20230627T233954Z
UID:24821-1687537800-1687539600@qcb.ucla.edu
SUMMARY:BIG Summer Research Seminar: Brunilda Balliu\, Assistant Professor in the Departments of Pathology & Laboratory Medicine and Computational Medicine at UCLA
DESCRIPTION:TITLE: “FastGxC: a statistical framework for mapping context-specific regulatory variants using bulk and single-cell RNA-seq data.” \nABSTRACT: Recent studies suggest that context-specific eQTLs underlie genetic risk factors for complex diseases. However\, methods for identifying them are still nascent\, limiting their comprehensive characterization and downstream interpretation of disease-associated variants. In this talk\, I will introduce FastGxC\, a method to efficiently and powerfully map context-specific eQTLs by leveraging the correlation structure of bulk multi-tissue and single-cell RNA-seq studies. We applied FastGxC to simulated and real bulk and single-cell RNA-Seq data sets and show that FastGxC is orders of magnitude more powerful and computationally efficient than existing eQTL mapping approaches\, making previously yearlong computations possible in minutes. In addition\, FastGxC provides a three-fold increase in precision to identify relevant tissues and cell types for GWAS variants than standard eQTL mapping approaches. \n\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/06/Brunilda-Balliu-62323.mp4
URL:https://qcb.ucla.edu/event/big-summer-research-seminar-brunilda-balliu-assistant-professor-in-the-departments-of-pathology-laboratory-medicine-and-computational-medicine-at-ucla/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/06/Brunilda-Balliu-PhD-11r5x7.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230324T123000
DTEND;TZID=America/Los_Angeles:20230324T130000
DTSTAMP:20260412T104129
CREATED:20230319T153305Z
LAST-MODIFIED:20230327T174010Z
UID:24633-1679661000-1679662800@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Nicholas Wang (Boutros)\, Grad Student\, Bioinformatics
DESCRIPTION:TITLE: “Germline structural variants shape prostate cancer clinical and molecular evolution.” \nABSTRACT: Inherited genetic variation profoundly influences cancer risk and outcome. While the impact of germline single nucleotide polymorphisms has been well-studied in several cancer types\, the effects of germline structural variants (gSVs) on cancer biology and clinical outcomes is largely unknown. From our cohort of 300 men with localized\, intermediate risk prostate cancer\, we identified 6\,003 gSVs present in at least 3% of patients\, with 48 associated with recurrent somatic alterations or clinical outcome. Of these\, ~50% associated with expression of nearby genes or intersected with exons or regulatory regions. Using external cohorts\, we validated three gSVs that were strongly associated with poor clinical outcomes\, including an inversion at chr14q24.1 present in ~20% of patients. Notably\, a strong synergistic effect on outcome was observed in patients with somatic TP53 alterations or high genomic instability\, defining a new aggressive prostate cancer subtype with chr14INV as a novel\, recurrent biomarker. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/03/Nicholas-Wang-32423.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-nicholas-wang-boutros-grad-student-bioinformatics-p/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/03/Nicholas-Wang.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230324T120000
DTEND;TZID=America/Los_Angeles:20230324T123000
DTSTAMP:20260412T104129
CREATED:20230307T193641Z
LAST-MODIFIED:20230327T173940Z
UID:24514-1679659200-1679661000@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Dongyuan Song (Li JJ)\, Grad Student\, Bioinformatics IDP
DESCRIPTION:TITLE: “ClusterDE: a post-clustering differentially expressed (DE) gene identification method robust to false-positive inflation caused by double-dipping” \nABSTRACT: In typical single-cell RNA-seq data analysis\, first\, a clustering algorithm is applied to cluster cells; then\, a statistical method is used to identify the differentially expressed (DE) genes between the cell clusters. However\, this common procedure uses the same data twice\,  an issue known as “double dipping”: the same gene expression data are used to define cell clusters and DE genes\, leading to false-positive DE genes even when the cell clusters are spurious. To overcome this challenge\, we propose ClusterDE\, a post-clustering DE method for controlling the false discovery rate (FDR) regardless of clustering quality. The core idea of ClusterDE is to generate in silico negative control data with only one cluster\, which can be used in contrast to real data for evaluating the whole clustering+DE procedure. Using comprehensive simulation and real data analysis\, we show that ClusterDE can not only has solid FDR control but also finds cell-type marker genes that are biologically meaningful. ClusterDE is fast\, transparent\, and adaptive to a wide range of clustering methods and statistical tests. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/03/Dongyuan-Song-32423.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-dongyuan-song-li-jj-grad-student-bioinformatics-idp/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/03/UCLA.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230317T123000
DTEND;TZID=America/Los_Angeles:20230317T130000
DTSTAMP:20260412T104129
CREATED:20230311T171133Z
LAST-MODIFIED:20230319T155440Z
UID:24581-1679056200-1679058000@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Helena Winata (Boutros)\, Grad Student\, Bioinformatics IDP
DESCRIPTION:TITLE: “Efficient\, Multi Sample Inference of Cancer Phylogeny.” \nABSTRACT: Cancer is characterized by the ongoing accumulation of somatic mutations that may lead to dysregulated cellular proliferation. The selection of advantageous mutations leads to clonal expansions of progressively more aberrant and fit cancer cells. Reconstructing the evolutionary history of a tumor allows us to understand key events in disease progression and mechanisms that lead to disease lethality.  Sequencing multiple tumor samples provide an opportunity to study tumor evolution in much greater detail and accuracy than was previously feasible through single-sample datasets. However\, current reconstruction methods utilize stochastic-search algorithms\, which iterates through a parameter space to jointly infer clone populations and their phylogeny. As tumor phylogenetic topology increases in complexity\, the parameter space grows exponentially\, and stochastic-search algorithms become computationally intractable. To circumvent current computational limitations\, we developed a heuristic-based algorithm for subclonal reconstruction that leverages fundamental principles of cancer biology to encode heuristics that reduce the solution space to biologically plausible phylogenies. Benchmarking on real and simulated datasets are ongoing\, and preliminary results indicate a ten-fold reduction in runtime. We have thus presented a novel method for rapid and optimized reconstruction of tumor evolutionary histories from multi-sample datasets.  \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/03/Helena-Winata-31723.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-helena-wimata-boutros-grad-student-bioinformatics-idp/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/03/QCbio_pic-copy.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230317T120000
DTEND;TZID=America/Los_Angeles:20230317T123000
DTSTAMP:20260412T104129
CREATED:20230314T170407Z
LAST-MODIFIED:20230319T154301Z
UID:24592-1679054400-1679056200@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Jessica Ding (Yang)\, Grad Student\, Molecular\, Cellular\, and Integrative Physiology
DESCRIPTION:TITLE: “Multi-tissue single-cell level understanding of Alzheimer’s disease points to the therapeutic potential of nutritional and metabolic modulation.” \nABSTRACT: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by extracellular amyloid plaque deposition and intracellular neurofibrillary tangles. The direct cause of abnormal protein accumulation and aggregation is largely unknown\, and no treatments exist to effectively delay or prevent development of AD. AD onset and progression is affected by many genetic and environmental factors\, and exploration of significant risk factors for AD may help elucidate its complexity. AD is often comorbid with metabolic syndrome\, which includes hypertension\, elevated blood glucose and triglycerides\, and abdominal obesity. We investigate the potential connection between AD and metabolic syndrome by testing the effect of high fructose consumption\, omega-3 fatty acid docosahexaenoic acid (DHA)\, and nicotinamide riboside (NR) on hippocampal and hypothalamic single cell transcriptomes of the 5XFAD mouse model of amyloid accumulation. We report that metabolically challenging 5XFAD mice with fructose promotes expression of certain proinflammatory genes that may further exacerbate neuronal loss. Supplementation of 5XFAD with DHA and NR was shown to downregulate microglial activation genes\, but DHA and NR on 5XFAD with fructose background also enhanced specific aspects of microglial function while downregulating fructose-induced exacerbation of proinflammatory genes\, which may indicate mechanisms to counteract further worsening of AD by fructose. Overlaying differentially expressed genes (DEGs) onto a microglial gene regulatory network showed fructose\, DHA\, and NR target shared and specific aspects of the disease subnetwork. We also observed that fructose led to a depletion of an intermediate activated microglial state which was enhanced by DHA and NR. Transcriptomic signatures derived from this study showed high enrichment of GWAS signals including cell-type specific nutrition DEGs\, regulatory network modules\, and microglia trajectory associated genes. Our study has demonstrated that metabolic modulation impacts AD transcriptomic signatures and has significant implications for the treatment of AD with DHA and NR or modulators that enhance associated mechanisms. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/03/Jessica-Ding-3.17.23.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-jessica-ding-yang-grad-student-molecular-cellular-and-integrative-physiology/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/03/Ding-Jessica.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230313T160000
DTEND;TZID=America/Los_Angeles:20230313T170000
DTSTAMP:20260412T104130
CREATED:20230103T165307Z
LAST-MODIFIED:20230103T165307Z
UID:23261-1678723200-1678726800@qcb.ucla.edu
SUMMARY:QCBio/Bioinformatics/Human Genetics seminar: Min Xu\, PhD\, Assistant Professor\, Computational Biology Department\, Co-Director\, MS in Computational Biology Program\, Carnegie Mellon University
DESCRIPTION:TITLE: “Automatic analysis of cryo-electron tomography using computer vision and machine learning.”
URL:https://qcb.ucla.edu/event/qcbio-bioinformatics-human-genetics-seminar-min-xu-phd-assistant-professor-computational-biology-department-co-director-ms-in-computational-biology-program-carnegie-mellon-university/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/01/MIN.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230310T123000
DTEND;TZID=America/Los_Angeles:20230310T130000
DTSTAMP:20260412T104130
CREATED:20230304T013953Z
LAST-MODIFIED:20230310T223250Z
UID:24493-1678451400-1678453200@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Brandon Tsai (Boutros)\, Grad Student\, Human Genetics
DESCRIPTION:TITLE: “Exercise and tumor genomic landscapes in 2\,702 patients with cancer” \nABSTRACT: Approximately two-thirds of cancer diagnoses globally are attributed to modifiable lifestyle factors such as smoking\, diet and inactivity. Conversely\, regular exercise is linked to decreased risk of multiple cancers. However\, the underlying molecular mechanisms are not fully elucidated. Specifically\, how exercise impacts tumor genomic landscapes has not been considered. To address this gap\, we integrated clinical annotation of exercise exposure with tumor mutational profiling of 2\,702 patients with cancer. Exercise exposure was evaluated by validated questionnaire and tumor genomic profiling of ≥ 505 commonly mutated cancer genes was performed using the Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actional Cancer Targets (MSK-IMPACT) assay. Among the most represented cancer types were breast (n = 629)\, lung (n = 525)\, endometrial (n = 260)\, colorectal (n = 213) and prostate (n = 177). We found that exercise influences the genomic landscapes of tumors in a cancer-type specific manner. For instance\, breast and lung cancers from exercising patients had lower tumor mutation burden (TMB) compared with non-exercisers. A pan-cancer analysis revealed a higher risk ratio among exercisers for mutations in ERBB2 and lower risk ratio for mutations in PIK3CA and CDKN2A. Overall\, this study shows that exercise regulates tumor genomic landscapes in a cancer-site specific manner. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/03/Brandon-Tsai-31023.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-brandon-tsai-boutros-grad-student-human-genetics/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/03/KGD_8087.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230310T120000
DTEND;TZID=America/Los_Angeles:20230310T123000
DTSTAMP:20260412T104130
CREATED:20230304T013617Z
LAST-MODIFIED:20230310T233042Z
UID:24486-1678449600-1678451400@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Daniel Ha (Yang)\, Postdoc\, Dept. Integrative Biology and Physiology
DESCRIPTION:TITLE: ““Cross-tissue multiomics studies reveal gutbrain interactions mediating the effect of Akkermansia muciniphila in counteracting fructose-induced obesity” \nABSTRACT: The gut bacterium Akkermansia muciniphila (A. muciniphila) has been implicated in anti-obesity effects\, but a systems level understanding of the molecular mechanisms is lacking. We carried out multiomics studies to investigate the molecular cascades mediating the anti-obesity effect of A. muciniphila in a fructoseinduced obesity mouse model. We found that A. muciniphila colonization triggered significant shifts in gut microbiota composition\, gut and plasma metabolites\, and gene expression in hypothalamic neurons. Multiomics integration and network analysis prioritized the metabolite oleoylethanolamide (OEA) in the gut and circulation as a regulator of gut-brain interactions that underlie the A. muciniphila antiobesity effect. Oral administration of OEA counteracted the fructose-induced obesity through the regulation of hypothalamic anorexigenic neuropeptides such as oxytocin and arginine vasopressin. Our multiomics investigation and experimental validation elucidates the molecular regulators and pathways involved in the communication between A. muciniphila in the gut and hypothalamic neurons that counter fructose-induced obesity. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/03/Daniel-Ha-3.10.23.mp4\n 
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-daniel-ha-yang-postdoc-dept-integrative-biology-and-physiology/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/03/headshot_photo-1-180x180-DanHa-copy.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230306T160000
DTEND;TZID=America/Los_Angeles:20230306T170000
DTSTAMP:20260412T104130
CREATED:20230103T165103Z
LAST-MODIFIED:20230103T165103Z
UID:23257-1678118400-1678122000@qcb.ucla.edu
SUMMARY:QCBio/Bioinformatics/Human Genetics seminar: Zoltán Kutalik\, PhD\, Associate Professor\, University of Lausanne
DESCRIPTION:TITLE: “Pushing the boundaries of causal inference.”
URL:https://qcb.ucla.edu/event/qcbio-bioinformatics-human-genetics-seminar-zoltan-kutalik-phd-associate-professor-university-of-lausanne/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/01/ZOLTAN.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230306T140000
DTEND;TZID=America/Los_Angeles:20230306T150000
DTSTAMP:20260412T104130
CREATED:20230305T183912Z
LAST-MODIFIED:20230305T183912Z
UID:24502-1678111200-1678114800@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Gregoire Altan-Bonnet\, Principal Investigator – Immunodynamics group Laboratory of Integrative Cancer Immunology NCI\, NIH\, Bethesda MD
DESCRIPTION:TITLE: “Stochasticity in cancer immunotherapies: identifying the T cell subset that sparks tumor eradication” \nABSTRACT: We use an ex vivo model of tumor eradication to dissect the fundamental variability of clinical outcomes in cancer immunotherapies. We demonstrate that there exists an inherent stochastic variability in immune responses\, based on the low abundance of hyper-responsive naïve T cells (so-called Spark T cells) and feedback regulations amongst leukocytes. We introduce a methodology (combining hierarchical clustering of single-cell measurements and statistical matching with functional outcomes) to identify Spark T cells. We then carry out functional tests to model the mechanics of Spark T cells igniting global immune responses and tumor rejection.
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-gregoire-altan-bonnet-principal-investigator-immunodynamics-group-laboratory-of-integrative-cancer-immunology-nci-nih-bethesda-md/
LOCATION:Boyer 159
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/02/Altan-Bonnet.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230303T160000
DTEND;TZID=America/Los_Angeles:20230303T170000
DTSTAMP:20260412T104130
CREATED:20230217T151413Z
LAST-MODIFIED:20230217T151518Z
UID:24018-1677859200-1677862800@qcb.ucla.edu
SUMMARY:QCBio/Center for Biological Physics: Gregoire Altan-Bonnet\, Principal Investigator – Immunodynamics group Laboratory of Integrative Cancer Immunology NCI\, NIH\, Bethesda MD
DESCRIPTION:TITLE: “Stochasticity in cancer immunotherapies: identifying the T cell subset that sparks tumor eradication” \nABSTRACT: We use an ex vivo model of tumor eradication to dissect the fundamental variability of clinical outcomes in cancer immunotherapies. We demonstrate that there exists an inherent stochastic variability in immune responses\, based on the low abundance of hyper-responsive naïve T cells (so-called Spark T cells) and feedback regulations amongst leukocytes. We introduce a methodology (combining hierarchical clustering of single-cell measurements and statistical matching with functional outcomes)  to identify Spark T cells. We then carry out functional tests to model the mechanics of Spark T cells igniting global immune responses and tumor rejection.
URL:https://qcb.ucla.edu/event/qcbio-the-center-for-biological-physics-gregoire-altan-bonnet-principal-investigator-immunodynamics-group-laboratory-of-integrative-cancer-immunology-nci-nih-bethesda-md/
LOCATION:Boyer Hall 130
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/02/Altan-Bonnet.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230227T160000
DTEND;TZID=America/Los_Angeles:20230227T170000
DTSTAMP:20260412T104130
CREATED:20230103T164929Z
LAST-MODIFIED:20230124T190737Z
UID:23253-1677513600-1677517200@qcb.ucla.edu
SUMMARY:QCBio/Bioinformatics/Human Genetics seminar: Molly Przeworski\, PhD\, Professor\, Biological Sciences\, Systems Biology\, Columbia University
DESCRIPTION:TITLE: “Why do human germline mutation rates depend on sex and age.”
URL:https://qcb.ucla.edu/event/qcbio-bioinformatics-human-genetics-seminar-molly-przeworski-phd-professor-biological-sciences-systems-biology-columbia-university/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/01/MOLLY.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230213T160000
DTEND;TZID=America/Los_Angeles:20230213T170000
DTSTAMP:20260412T104130
CREATED:20230103T164743Z
LAST-MODIFIED:20230103T165457Z
UID:23249-1676304000-1676307600@qcb.ucla.edu
SUMMARY:QCBio/Bioinformatics/Human Genetics seminar: Jonathan Sebat\, PhD\, Chief\, Beyster Center for Molecular Genomics of Neuropsychiatric Diseases\, Professor of Psychiatry and Cellular and Molecular Medicine\, UC San Diego
DESCRIPTION:TITLE: “TBA”
URL:https://qcb.ucla.edu/event/qcbio-bioinformatics-human-genetics-seminar-jonathan-sebat-phd-chief-beyster-center-for-molecular-genomics-of-neuropsychiatric-diseases-professor-of-psychiatry-and-cellular-and-molecular-medicine/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/01/SEBAT.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230206T160000
DTEND;TZID=America/Los_Angeles:20230206T170000
DTSTAMP:20260412T104130
CREATED:20230103T164543Z
LAST-MODIFIED:20230103T164543Z
UID:23245-1675699200-1675702800@qcb.ucla.edu
SUMMARY:QCBio/Bioinformatics/Human Genetics seminar: Haiyuan Yu\, PhD\, Professor\, Biological Statistics and Computational Biology\, Cornell University
DESCRIPTION:TITLE: “New perspectives to dissect global dynamics of protein interactome and gene regulation in disease.”
URL:https://qcb.ucla.edu/event/qcbio-bioinformatics-human-genetics-seminar-haiyuan-yu-phd-professor-biological-statistics-and-computational-biology-cornell-university/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/01/HAIYUAN.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230130T160000
DTEND;TZID=America/Los_Angeles:20230130T170000
DTSTAMP:20260412T104130
CREATED:20230103T164305Z
LAST-MODIFIED:20230103T164305Z
UID:23241-1675094400-1675098000@qcb.ucla.edu
SUMMARY:QCBio/Bioinformatics/Human Genetics seminar: Soojin Yi\, PhD\, Professor\, Ecology\, Evolution\, and Marine Biology\, UC Santa Barbara
DESCRIPTION:TITLE: “DNA Methylation in Brain Evolution and Neuropsychiatric Disorders.”
URL:https://qcb.ucla.edu/event/qcbio-bioinformatics-human-genetics-seminar-soojin-yi-phd-professor-ecology-evolution-and-marine-biology-uc-santa-barbara/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/01/SOOJIN.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230123T160000
DTEND;TZID=America/Los_Angeles:20230123T170000
DTSTAMP:20260412T104130
CREATED:20230103T164043Z
LAST-MODIFIED:20230103T164043Z
UID:23234-1674489600-1674493200@qcb.ucla.edu
SUMMARY:QCBio/Bioinformatics/Human Genetics seminar: Pleuni Pennings\, PhD\, Associate Professor\, Biology\, San Francisco State University
DESCRIPTION:TITLE: “Part 1: “How important is evolution vs transmission of drug resistance”. \nPart 2: “Computing skills for every biology student.”
URL:https://qcb.ucla.edu/event/qcbio-bioinformatics-human-genetics-seminar-pleuni-pennings-phd-associate-professor-biology-san-francisco-state-university/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/01/Pleuni.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230113T140000
DTEND;TZID=America/Los_Angeles:20230113T150000
DTSTAMP:20260412T104130
CREATED:20221220T011503Z
LAST-MODIFIED:20230103T165800Z
UID:23065-1673618400-1673622000@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Friedrich Simmel\, Department of Bioscience\, School of Natural Sciences\, TU Munich\, Germany
DESCRIPTION:TITLE: “Electric actuation of DNA-based molecular machines.” \nABSTRACT: A wide range of machine-like molecular assemblies have been generated over the past years. Most of them have been driven (or controlled) by DNA hybridization\, utilization of buffer changes\, or using chemical modifications such as photoswitches. A more recently explored strategy is the use of electrical fields for the manipulation of DNA devices\, which enables fast and computer-controlled actuation. In the talk\, several examples of such DNA origami-based „nanorobotic“ systems will be discussed\, including a DNA „robot arm“\, molecular springs\, an origami based Brownian ratchet with rotary movement\, and others. On a slightly different topic\, also a novel strategy to control microswimmers using AC electrical fields will be presented.
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-friedrich-simmel-department-of-bioscience-school-of-natural-sciences-tu-munich-germany/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2022/12/Fritzphoto_small.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230109T160000
DTEND;TZID=America/Los_Angeles:20230109T170000
DTSTAMP:20260412T104130
CREATED:20230103T163728Z
LAST-MODIFIED:20230103T165741Z
UID:23228-1673280000-1673283600@qcb.ucla.edu
SUMMARY:QCBio/Bioinformatics/Human Genetics seminar: Shamil Sunyaev\, PhD\, Professor\, Biomedical Informatics\, Harvard Medical School
DESCRIPTION:TITLE: “Statistics\, Biology and Applications of Human Mutation.”
URL:https://qcb.ucla.edu/event/qcbio-bioinformatics-human-genetics-seminar-shamil-sunyaev-phd-professor-biomedical-informatics-harvard-medical-school/
LOCATION:Boyer 159
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/01/shamil.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20221215T133000
DTEND;TZID=America/Los_Angeles:20221215T140000
DTSTAMP:20260412T104130
CREATED:20221125T154144Z
LAST-MODIFIED:20221215T225950Z
UID:22826-1671111000-1671112800@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Zhiqian Zhai (Li JJ)\, Graduate Student in Statistics
DESCRIPTION:TITLE: “Supervised capacity preserving mapping: a clustering guided visualization method for scRNA-seq data.” \nABSTRACT: Recently\, various computational methods have been developed to analyze the scRNAseq data\, such as clustering and visualization. However\, current visualization methods\, including t-SNE and UMAP\, are challenged by the limited accuracy of rendering the geometric relationship of populations with distinct functional states. Most visualization methods are unsupervised\, leaving out information from the clustering results or given labels. This leads to the inaccurate depiction of the distances between the bona fide functional states. In particular\, UMAP and t-SNE are not optimal to preserve the global geometric structure. They may result in a contradiction that clusters with near distance in the embedded dimensions are in fact further away in the original dimensions. Besides\, UMAP and t-SNE cannot track the variance of clusters. Through the embedding of t-SNE and UMAP\, the variance of a cluster is not only associated with the true variance but also is proportional to the sample size. Here\, we present supCPM\, a robust supervised visualization method\, which separates different clusters\, preserves the global structure and tracks the cluster variance. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2022/11/Zhiqian-Zhai-edited.mp4\n 
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-zhiqian-zhai-li-jj-graduate-student-in-statistics/
LOCATION:Boyer Hall 159
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2022/11/Zhiqian-Zhai-picture.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20221215T130000
DTEND;TZID=America/Los_Angeles:20221215T133000
DTSTAMP:20260412T104130
CREATED:20221128T171205Z
LAST-MODIFIED:20221215T225915Z
UID:22840-1671109200-1671111000@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Roni Haas (Boutros)\, Postdoc in Human Genetics
DESCRIPTION:TITLE: “Proteogenomic characterization of the molecular determinants of prostate cancer radioresistance.” \nABSTRACT: Prostate Cancer (PC)\, the second most common cause of cancer death in men\, is frequently treated using radiotherapy with curative intent. Despite its effectiveness\, radiotherapy often results in aggressive PC relapse characterized by radioresistance. The diversity in therapeutic response to radiotherapy\, and the molecular processes underlining radioresistance are not fully understood. Here we integrated genomic\, transcriptomic\, and proteomic investigations to comprehensively characterize the molecular determinants of PC radioresistance. To model radioresistance\, we have created Conventional-Fractionation (CF) and Hypo-Fractionated (HF) isogenic radioresistant cells that represent different therapeutic regimens: the traditional CF radiotherapy with daily small radiation doses over weeks\, and the relatively new HF radiotherapy with high radiation doses across several single treatments. We discovered that CF radioresistant cells gained twice the number of somatic single-nucleotide variants than HF. Nevertheless\, the gained mutations\, irrespective of the treatment schedule\, converged on mutational signatures associated with mismatch DNA repair. CF radioresistant cells demonstrated strong and exclusive dysregulation of driver and hallmark-cancer genes in RNA abundance profiles. The differences in protein abundance display cell-fraction-dependent clusters\, foremost of which are elevated levels of DNA repair proteins in CF radioresistant cell nuclei. Collectively\, we observed a far more aggressive phenotype in CF radioresistant cells compared to HF. The clinical relevance of our top potential therapeutic targets was assessed using a cohort of 380 PC patients. Our study provides a platform for the development of therapies for radio-recurrent PC. Ongoing proteogenomic integration will help understand the relationships amongst radioresistance-associated changes at the DNA\, RNA\, and protein levels. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2022/11/Roni-Haas.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-roni-haas-boutros-postdoc-in-human-genetics/
LOCATION:Boyer Hall 159
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2022/11/RoniHaas1-scaled.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20221207T120000
DTEND;TZID=America/Los_Angeles:20221207T123000
DTSTAMP:20260412T104130
CREATED:20221108T003622Z
LAST-MODIFIED:20221207T211458Z
UID:22610-1670414400-1670416200@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Guanao Yan (Li JJ)\, Graduate Student in Statistics
DESCRIPTION:TITLE: “scReadSim: a single-cell RNA-seq and ATAC-seq read simulator.” \nABSTRACT: Rapid advances of single-cell RNA-seq and ATAC-seq technologies have propelled the development of many computational tools\, benchmarking of which demands realistic simulators. However\, few simulators can generate sequencing reads\, and none of the existing read simulators aim to mimic real cells\, hindering the benchmarking of low-level computational tools that process reads. To fill this gap\, we propose scReadSim\, a single-cell RNA-seq and ATAC-seq read simulator that generates synthetic cells which mimic real cells. Trained on real data\, scReadSim can generate synthetic data in FASTQ and BAM formats. By deploying scReadSim on sci-ATAC-seq and 10x Multiome (ATAC+RNA) data\, we show that the scReadSim synthetic data resemble real data at both read and count levels. Moreover\, as a flexible simulator\, scReadSim enables users to arbitrarily specify open chromatin regions for the synthetic scATAC-seq reads\, and is also capable of allowing varying the cell number and sequencing depths for the synthetic data. To illustrate the versatile usage of scReadSim\, we include two exemplar benchmark studies to show that scReadSim provides unique molecular identifier (UMI) counts for benchmarking scRNA-seq deduplication tools and can accommodate user-specified open chromatin regions (“ground truths”) to generate single-cell ATAC-seq data. Our benchmark applications of scReadSim show that cellranger is a preferred scRNA-seq deduplication tool\, and MACS3 achieves top performance in scATAC-seq peak calling. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2022/11/video1156562562.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-guanao-yan-li-jj-graduate-student-in-statistics/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2022/11/Guanao.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20221207T110000
DTEND;TZID=America/Los_Angeles:20221207T113000
DTSTAMP:20260412T104130
CREATED:20221109T215644Z
LAST-MODIFIED:20221202T183112Z
UID:22650-1670410800-1670412600@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Mark Xiang (Hoffmann)\, Graduate Student in Bioinformatics
DESCRIPTION:TITLE: “Heterogeneity in cell states: Is it important whether cell states are heritable or change rapidly?” \nABSTRACT: Cells of the same cell type show molecular and phenotypic heterogeneity. Is the particular cell state of a given cell heritable from one generation to the next?  Previous work in liver cancer cells indicates that the molecular network that controls cell death may change within hours\, but the data from B-cells shows that their cell state is durable and heritable.  In this project\, I address this question by formulating a model of B-cell-mediated antibody responses.  This model recapitulates the Darwinian selection process to produce high affinity antibodies against an antigen. I then test how heterogeneity in the cell states affects the antibody repertoire\, and then what the effect of heritability of those cell states might be. The preliminary results from model simulation will be presented and discussed.
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-mark-xiang-hoffmann-graduate-student-in-bioinformatics/
LOCATION:Boyer Hall 159
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2022/11/Mark_Xiang_Profile_Photo-1.png
END:VEVENT
END:VCALENDAR