BEGIN:VCALENDAR VERSION:2.0 PRODID:-//Institute for Quantitative and Computational Biosciences - ECPv6.17.1//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: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 BEGIN:DAYLIGHT TZOFFSETFROM:-0800 TZOFFSETTO:-0700 TZNAME:PDT DTSTART:20260308T100000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:-0700 TZOFFSETTO:-0800 TZNAME:PST DTSTART:20261101T090000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:-0800 TZOFFSETTO:-0700 TZNAME:PDT DTSTART:20270314T100000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:-0700 TZOFFSETTO:-0800 TZNAME:PST DTSTART:20271107T090000 END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20260724T160000 DTEND;TZID=America/Los_Angeles:20260724T170000 DTSTAMP:20260721T140507Z CREATED:20260721T140448Z LAST-MODIFIED:20260721T140507Z UID:29189-1784908800-1784912400@qcb.ucla.edu SUMMARY:Amy Goldberg\, Associate Professor\, Human Genetics\, UCLA DESCRIPTION:TITLE: “Evolutionary perspectives on malaria” \nPathogen genomics increasingly guides public health decisions\, yet organisms with complex life cycles can produce genealogies that violate assumptions of standard population genetic methods. Similarly\, despite decades of population-genetic methods to infer population or adaptive histories in humans\, allele frequencies are often modeled to be roughly constant on short timescales relevant for public health. Here I discuss computational methods to leverage the growing amounts of genomic data from both host and pathogen perspectives. In particular\, I consider genomic evolution on ecologically and epidemiologically relevant timescales\, with implications for public health and basic biology. URL:https://qcb.ucla.edu/event/amy-goldberg-associate-professor-human-genetics-ucla/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2026/07/PhotoHandler.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20260717T160000 DTEND;TZID=America/Los_Angeles:20260717T170000 DTSTAMP:20260713T164743Z CREATED:20260713T164743Z LAST-MODIFIED:20260713T164743Z UID:29179-1784304000-1784307600@qcb.ucla.edu SUMMARY:Neil Lin Assistant Professor\, Mechanical and Aerospace Engineering - UCL DESCRIPTION:“Unraveling Signaling Pathway Crosstalk Using LLMs” \nLiving cells do not process information through isolated\, linear pathways. Instead\, they rely on an intricate network of signaling crosstalk to make critical fate decisions. Deciphering this hidden cellular conversation remains one of the greatest challenges in targeted oncology and regenerative medicine. Yet traditional mechanistic models struggle to capture its complexity\, while the scale of modern single-cell datasets exceeds what can be analyzed manually. My lab asks a simple question: Can large language models\, designed to understand human language\, be repurposed to decode the language of cellular signaling? In this talk\, I will describe our efforts to develop LLMs as specialized\, locally deployed biological reasoning engines. By grounding these models in both the biomedical literature and high-dimensional single-cell data\, we show how they can identify key regulatory nodes where signaling pathways converge. Finally\, I will discuss how integrating biological knowledge with empirical data enables prediction of nonlinear cellular responses\, providing a scalable\, mechanistically informed framework for discovering novel therapeutic combinations. URL:https://qcb.ucla.edu/event/neil-lin-assistant-professor-mechanical-and-aerospace-engineering-ucl/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2026/07/neil_lin_headshot.jpg-copy.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20260710T160000 DTEND;TZID=America/Los_Angeles:20260710T170000 DTSTAMP:20260713T164528Z CREATED:20260713T164528Z LAST-MODIFIED:20260713T164528Z UID:29175-1783699200-1783702800@qcb.ucla.edu SUMMARY:Eric Deeds Professor\, Vice Chair\, Life Sciences Core - UCLA DESCRIPTION:“A lack of distinct cellular identities in scRNA-seq data: revisiting Waddington’s landscape” \nSingle-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\, organisms and technological measurement techniques 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. URL:https://qcb.ucla.edu/event/eric-deeds-professor-vice-chair-life-sciences-core-ucla/ LOCATION:Boyer Hall 159 CATEGORIES:Research Seminars,QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2026/07/eric-deeds.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20241202T120000 DTEND;TZID=America/Los_Angeles:20241202T130000 DTSTAMP:20241002T181902Z CREATED:20241002T181856Z LAST-MODIFIED:20241002T181902Z UID:26980-1733140800-1733144400@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Stephen Montgomery\, PhD\, Stanford Medicine Endowed Professor of Pathology and Professor of Genetics\, Biomedical Data Science and Computer Science\, Stanford University DESCRIPTION:TITLE: TBD \nHosted by Brunilda Balliu for Genetics & Genomics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-stephen-montgomery-phd-stanford-medicine-endowed-professor-of-pathology-and-professor-of-genetics-biomedical-data-science-and-computer-science/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20241125T120000 DTEND;TZID=America/Los_Angeles:20241125T130000 DTSTAMP:20241002T181607Z CREATED:20241002T181607Z LAST-MODIFIED:20241002T181607Z UID:26976-1732536000-1732539600@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Andrea Ganna\, PhD\, Associate Professor at FIMM and HiLIFE; Research Associate\, Harvard Medical School and Massachusetts General Hospital DESCRIPTION:TITLE: TBD \nHosted by Sriram Sankararaman for Bioinformatics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-andrea-ganna-phd-associate-professor-at-fimm-and-hilife-research-associate-harvard-medical-school-and-massachusetts-general-hospital/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/10/Seminar-Series-Poster-–-Fall-2024-5.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20241118T120000 DTEND;TZID=America/Los_Angeles:20241118T130000 DTSTAMP:20241002T181338Z CREATED:20241002T181338Z LAST-MODIFIED:20241002T181338Z UID:26972-1731931200-1731934800@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Brenna M. Henn\, PdD\, Associate Professor\, Department of Anthropology; Co-Director\, Northern Cape Tuberculosis Project\, UC Davis DESCRIPTION:TITLE: TBD \nHosted by Noah Naitlen for Genetics & Genomics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-brenna-m-henn-pdd-associate-professor-department-of-anthropology-co-director-northern-cape-tuberculosis-project-uc-davis/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/10/Seminar-Series-Poster-–-Fall-2024-4.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20241104T120000 DTEND;TZID=America/Los_Angeles:20241104T130000 DTSTAMP:20241002T181018Z CREATED:20241002T181018Z LAST-MODIFIED:20241002T181018Z UID:26968-1730721600-1730725200@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Julia Salzman\, PhD\, Associate Professor\, Department of Biomedical Data Science and of Biochemistry\, Stanford University DESCRIPTION:TITLE: TBD \nHosted by Nandita Garud for Bioinformatics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-julia-salzman-phd-associate-professor-department-of-biomedical-data-science-and-of-biochemistry-stanford-university/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/10/Seminar-Series-Poster-–-Fall-2024-3.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20241028T120000 DTEND;TZID=America/Los_Angeles:20241028T130000 DTSTAMP:20241002T180736Z CREATED:20241002T180736Z LAST-MODIFIED:20241002T180736Z UID:26964-1730116800-1730120400@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Jayashree Kalpathy-Cramer\, PhD\, Professor\, Ophthalmology; Chief\, Division of Artificial Medical Intelligence\, Ophtalmology; Director\, Health Informatics\, CCTSI; University of Colorado - Anschutz Medical Center DESCRIPTION:TITLE: TBD \nHosted by William Hsu for Medical Informatics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-jayashree-kalpathy-cramer-phd-professor-ophthalmology-chief-division-of-artificial-medical-intelligence-ophtalmology-director-health-info/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/10/Seminar-Series-Poster-–-Fall-2024-2.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20241022T123000 DTEND;TZID=America/Los_Angeles:20241022T133000 DTSTAMP:20241011T162102Z CREATED:20241011T162102Z LAST-MODIFIED:20241011T162102Z UID:27013-1729600200-1729603800@qcb.ucla.edu SUMMARY:QCBio Research Seminar: Rizal Hariadi\, Associate Professor\, Department of Physics and Biodesign Institute\, Arizona State University DESCRIPTION:TITLE: Sensing and applying multi-axial tension to biomolecules using molecular devices built from DNA. \nABSTRACT: DNA nanotechnology enables the construction of molecular devices for diverse biomedical applications. By leveraging DNA’s exquisite positional control\, researchers can engineer sophisticated nanostructures that execute a range of tasks. In this talk\, I will present 2 DNA-based devices: an amphiphilic double-stranded DNA sensor for non-destructive detection of cytosolic biomarkers and a DNA origami platform for multi-axial mechanical manipulation of biomolecules. In the first part of my talk\, I will show synthetic transmembrane devices inspired by G protein-coupled receptors (GPCRs) that transduce signals across cell membranes. These amphiphilic DNA nanodevices detect specific intracellular oligonucleotides\, generating fluorescent signals without cell lysis and genetic engineering. In the second half of the talk\, I will present some recent results on a Holliday junction\, a model system in biophysics\, under multi-axial tension using the Multi-Axial Entropic Spring Tweezer along Rigid Origami (MAESTRO). This molecular tool\, which exploits the entropic elasticity of single-stranded DNA\, uncovers the non-ergodicity of Holliday junction dynamics. The talk concludes with a discussion on the potential applications of these devices\, including their use in high-throughput single-molecule biophysics of integrin signaling\, cryo-EM structural studies of integrins under tension\, and live-cell isolation targeting RNA markers. URL:https://qcb.ucla.edu/event/qcbio-research-seminar-rizal-hariadi-associate-professor-department-of-physics-and-biodesign-institute-arizona-state-university/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/10/Rizal_Hariadi.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20241021T120000 DTEND;TZID=America/Los_Angeles:20241021T130000 DTSTAMP:20241002T180358Z CREATED:20241002T180358Z LAST-MODIFIED:20241002T180358Z UID:26960-1729512000-1729515600@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Yin Yi\, PhD\, Assistant Professor\, UCLA DESCRIPTION:TITLE: TBD \nHosted by Kirk Lohmueller for Bioinformatics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-yin-yi-phd-assistant-professor-ucla/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/10/Seminar-Series-Poster-–-Fall-2024-1.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20241014T120000 DTEND;TZID=America/Los_Angeles:20241014T130000 DTSTAMP:20241002T170419Z CREATED:20241002T170419Z LAST-MODIFIED:20241002T170419Z UID:26952-1728907200-1728910800@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Ludmil Alexandrov\, Phd\, Professor\, Cellular and Molecular Medicine\, UC San Diego DESCRIPTION:TITLE: TBD \nHosted by Paul Spellman for Genetics & Genomics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-ludmil-alexandrov-phd-professor-cellular-and-molecular-medicine-uc-san-diego/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/10/Alexandrov.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20241007T120000 DTEND;TZID=America/Los_Angeles:20241007T130000 DTSTAMP:20241002T182126Z CREATED:20241002T165755Z LAST-MODIFIED:20241002T182126Z UID:26948-1728302400-1728306000@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Erik Andersen\, PhD\, Professor\, Johns Hopkins University DESCRIPTION:TITLE: “Mechanisms of differences in gene expression and organismal traits caused by structural variation (both real and imagined)” \nHosted by Leonid Kruglyak for Genetics & Genomics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-erik-andersen-phd-professor-johns-hopkins-university/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/10/andersen.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20240930T120000 DTEND;TZID=America/Los_Angeles:20240930T130000 DTSTAMP:20241002T170647Z CREATED:20241002T170647Z LAST-MODIFIED:20241002T170647Z UID:26956-1727697600-1727701200@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Armita Nourmohammad\, PhD\, Associate Professor\, University of Washington DESCRIPTION:TITLE: TBD \nHosted by Alexander Hoffmann for Bioinformatics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-armita-nourmohammad-phd-associate-professor-university-of-washington/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series,Research Seminars ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/10/Seminar-Series-Poster-–-Fall-2024.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20240605T113000 DTEND;TZID=America/Los_Angeles:20240605T120000 DTSTAMP:20240516T230852Z CREATED:20240503T141046Z LAST-MODIFIED:20240516T230852Z UID:26591-1717587000-1717588800@qcb.ucla.edu SUMMARY:Research-in-Progress (RIP) Seminar: Raag Agrawal (Boutros)\, Graduate Student in Genetics & Genomics\, UCLA/Caltech MSTP DESCRIPTION:TITLE: “Discovering biomarkers for predicting response to neo-adjuvant ADT and radionuclide treatment in high-risk prostate cancer” \nABSTRACT: Prostate cancer is the number one cause of cancer death in non-smoking American men. Next generation treatments for prostate cancer include androgen deprivation therapy (ADT) drugs such as Enzalutamide and radionuclide treatments like Lu-PSMA-617. While both of these treatment approaches are initially effective\, prostate cancer almost always recurs. We use multimodal genomic data to discover clinically useful prostate cancer subtypes to determine mechanisms of treatment resistance.  We further explore how these subtypes relate to the dearth of model systems in prostate cancer research – and whether we are ignoring clinically relevant genetic diversity in our drug development pipeline. URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-raag-agrawal-boutros-graduate-student-in-genetics-genomics-ucla-caltech-mstp/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/05/KGD3939.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20240605T110000 DTEND;TZID=America/Los_Angeles:20240605T113000 DTSTAMP:20240516T230749Z CREATED:20240503T141502Z LAST-MODIFIED:20240516T230749Z UID:26596-1717585200-1717587000@qcb.ucla.edu SUMMARY:Research-in-Progress (RIP) Seminar: Jonathan Mah (Garud-Lohmueller)\, Graduate Student in Bioinformatics Interdepartmental Program DESCRIPTION:TITLE: “Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history” \nABSTRACT: Despite the importance of gut commensal microbiota to human health\, there is little knowledge about their evolutionary histories\, including their demographic histories and distributions of fitness effects (DFE) of mutations. Here\, we infer the demographic histories and DFEs for amino-acid changing mutations of 27 of the most prevalent and abundant commensal gut microbial species in North Americans over timescales exceeding human generations. We find reductions in genetic variation in North American versus African rural microbiomes. Additionally\, some species in North American microbiomes display contractions in population size and others expansions\, potentially occurring at several key historical moments in human history. DFEs across species vary from highly to mildly deleterious\, with accessory genes experiencing more drift compared to core genes. Within genera\, DFEs tend to be more congruent\, reflective of underlying phylogenetic relationships. Together\, these findings suggest that gut microbes have distinct evolutionary histories\, possibly reflecting their unique roles. URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-jonathan-mah-garud-lohmueller-graduate-student-in-bioinformatics-interdepartmental-program/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/05/IMG_7439.jpeg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20240311T120000 DTEND;TZID=America/Los_Angeles:20240311T130000 DTSTAMP:20240109T214908Z CREATED:20240109T214908Z LAST-MODIFIED:20240109T214908Z UID:26273-1710158400-1710162000@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Alkes Price\, PhD\, Professor\, Harvard School of Public Health DESCRIPTION:TITLE: “Functional architectures of complex disease” \nHosted by Noah Zaitlen for Genetics & Genomics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-alkes-price-phd-professor-harvard-school-of-public-health/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/01/Seminar-Series-Poster-–-W2499-6.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20240304T120000 DTEND;TZID=America/Los_Angeles:20240304T130000 DTSTAMP:20240109T220014Z CREATED:20240109T214702Z LAST-MODIFIED:20240109T220014Z UID:26269-1709553600-1709557200@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Katherine L. Nathanson\, MD\, Deputy Director Penn Cancer Center\, University of Pennsylvania DESCRIPTION:TITLE: “The evolving landscape of hereditary breast cancer” \nHosted by Paul Spellman for Genetics & Genomics and UCLA JCCC URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-katherine-l-nathanson-md-deputy-director-penn-cancer-center-university-of-pennsylvania/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/01/Seminar-Series-Poster-–-W2499-5.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20240226T120000 DTEND;TZID=America/Los_Angeles:20240226T130000 DTSTAMP:20240109T202256Z CREATED:20240109T202256Z LAST-MODIFIED:20240109T202256Z UID:26256-1708948800-1708952400@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Chongyi Chen\, PhD\, Stadtman Investigator\, NCI DESCRIPTION:TITLE: “Quantitative mapping of DNA supercoiling tension throughout the human genome” \nHosted by Yi Yin for Genetics & Genomics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-chongyi-chen-phd-stadtman-investigator-nci/ LOCATION:Boyer 159 CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/01/Seminar-Series-Poster-–-W2499-2.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20240212T120000 DTEND;TZID=America/Los_Angeles:20240212T130000 DTSTAMP:20240109T220237Z CREATED:20240109T201544Z LAST-MODIFIED:20240109T220237Z UID:26248-1707739200-1707742800@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Nancy Zhang\, PhD\, Ge Li and Ning Zhao Professor\, University of Pennsylvania DESCRIPTION:TITLE: “Signal recovery in single cell data integration” \nHosted Jingyi Jessica Li for Bioinformatics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-nancy-zhang-phd-ge-li-and-ning-zhao-professor-university-of-pennsylvania/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/01/Seminar-Series-Poster-–-W2499.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20240205T120000 DTEND;TZID=America/Los_Angeles:20240205T130000 DTSTAMP:20240109T214410Z CREATED:20240109T214410Z LAST-MODIFIED:20240109T214410Z UID:26265-1707134400-1707138000@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Xuanyao Liu\, PhD\, Assistant Professor\, University of Chicago DESCRIPTION:TITLE: “Linking variants to function with powerful multivariate approaches” \nHosted by Brunilda Balliu for Bioinformatics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-xuanyao-liu-phd-assistant-professor-university-of-chicago/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/01/Seminar-Series-Poster-–-W2499-4.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20240129T000000 DTEND;TZID=America/Los_Angeles:20240129T130000 DTSTAMP:20240109T214106Z CREATED:20240109T214106Z LAST-MODIFIED:20240109T214106Z UID:26261-1706486400-1706533200@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Heidi Rehm\, PhD\, Co-Director\, Population and Medical Genetics\, Broad Institute; Chief Genomics Officer\, Mass General Hospital; Professor of Pathology\, Harvard Medical School DESCRIPTION:TITLE: “Advancing Genomic Medicine through Global Collaboration” \nHosted by Sulagna Saitta for Genetics & Genomics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-heidi-rehm-phd-co-director-population-and-medical-genetics-broad-institute-chief-genomics-officer-mass-general-hospital-professor-of-patho/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/01/Seminar-Series-Poster-–-W2499-3.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20240122T120000 DTEND;TZID=America/Los_Angeles:20240122T130000 DTSTAMP:20240109T201909Z CREATED:20240109T201909Z LAST-MODIFIED:20240109T201909Z UID:26252-1705924800-1705928400@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Katrina Claw\, PhD\, Assistant Professor\, University of Colorado – Anschutz Medical Campus DESCRIPTION:TITLE: “Pharmacogenomic variation in ancient humans and implications for human health” \nHosted by Jenny Papp for Genetics & Genomics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-katrina-claw-phd-assistant-professor-university-of-colorado-anschutz-medical-campus/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2024/01/Seminar-Series-Poster-–-W2499-1.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20240108T120000 DTEND;TZID=America/Los_Angeles:20240108T130000 DTSTAMP:20231224T111411Z CREATED:20231224T110456Z LAST-MODIFIED:20231224T111411Z UID:26229-1704715200-1704718800@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: William Speier\, PhD\, Associate Professor in the Department of Radiological Sciences DESCRIPTION:TITLE: “Multimodal deep learning models for thyroid cancer detection” \nHosted by William Hsu for Medical Informatics and UCLA JCCC. URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-monday-january-8-2024-william-speier-phd-associate-professor-in-the-department-of-radiological-sciences/ LOCATION:Boyer Hall 159 CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2023/12/WILLIAM-SPEIER.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20231207T120000 DTEND;TZID=America/Los_Angeles:20231207T143000 DTSTAMP:20231120T195105Z CREATED:20231120T165356Z LAST-MODIFIED:20231120T195105Z UID:26038-1701950400-1701959400@qcb.ucla.edu SUMMARY:Research-in-Progress (RIP) Seminar: MINI SYMPOSIUM - Emily Maciejewski (Ernst)\, Grad Student\, Computer Science - Chenlu Di (Lohmueller)\, Postdoc\, Ecology & Evolutionary Biology - Qingyang Wang (Li JJ)\, Grad Student\, Statistics - Alex Bermudez (Lin)\, Grad Student\, Bioengineering DESCRIPTION:12pm: Emily Maciejewski (Ernst)\, Grad Student\, Computer Science \nTITLE:  “Cross-species and tissue imputation of species-level DNA methylation samples” \nABSTRACT: DNA methylation data is highly informative to study a variety of aspects of mammalian biology. The availability of such data for many mammals at conserved sites was recently vastly enhanced by the development and large-scale application of the mammalian methylation array. For instance\, we consider here 13\,245 samples profiled on this array representing 348 species and 59 tissues from 746 species-tissue combinations. While having some coverage of many different species and tissue types\, this data only captures 3.6% of potential species-tissue combinations. We thus developed CMImpute (Cross-species Methylation Imputation) which uses a Conditional Variational Autoencoder to impute DNA methylation of non-profiled species-tissue combinations. In cross-validation\, we show that CMImpute yields high correlation with held-out observed values\, outperforming multiple baselines. We then train a model on all the data to impute 19\,786 new species-tissue combinations. We expect CMImpute and our imputed data resource will be useful for DNA methylation analyses across mammalian species. \n  \n12:30pm: Chenlu Di (Lohmueller)\, Postdoc\, Ecology & Evolutionary Biology \nTITLE: “Inference of fitness effects of mutations in noncoding regions of the human genome” \nABSTRACT: TBD \n  \n1:30pm: Qingyang Wang (Li JJ)\, Grad Student\, Statistics \nTITLE “Review of computational methods for estimating cell potency from single-cell RNA-seq data” \nABSTRACT: In single-cell RNA sequencing (scRNA-seq) data analysis\, a critical challenge is to infer hidden dynamic cellular processes from measured static cell snapshots. To tackle this challenge\, many computational methods have been developed from distinct perspectives. Besides the common perspectives of inferring trajectories (or pseudotime) and RNA velocity\, another important perspective is to estimate the differentiation potential of cells\, which is commonly referred to as “cell potency.” In this review\, we provide a comprehensive summary of 11 computational methods that estimate cell potency from scRNA-seq data under different assumptions\, some of which are even conceptually contradictory. We divide these methods into three categories: mean-based\, entropy-based\, and correlation-based methods\, depending on how a method summarizes gene expression levels of a cell or cell type into a potency measure. Our review focuses on the key similarities and differences of the methods within each category and between the categories\, providing a high-level intuition of each method. Moreover\, we use a unified set of mathematical notations to detail the 11 methods’ methodologies and summarize their usage complexities\, including the number of ad-hoc parameters\, the number of required inputs\, and the existence of discrepancies between the method description in publications and the method implementation in software packages. Realizing the conceptual contradictions of existing methods and the difficulty of fair benchmarking without single-cell-level ground truths\, we conclude that accurate estimation of cell potency from scRNA-seq data remains an open challenge. \n  \n2:00pm: Alex Bermudez (Lin)\, Grad Student\, Bioengineering \nTITLE: “TCell Morphology Impacts Chromatin States During Crowding” \nABSTRACT: Variability is an inherent characteristic of all biological systems\, exemplified by the diverse shapes\, sizes\, and gene expression profiles of cells comprising tissues. Despite its ubiquity\, our understanding of how such a phenotypic heterogeneity plays a role in regulating cell biology remains incomplete. In this talk\, I will discuss how cell shape heterogeneity arises and its impacts on chromatin organization of each cell during epithelial crowding\, a canonical process where cells proliferate until a densely packed monolayer forms. Our findings suggest that cell morphological heterogeneity is not mere noise\, but a crucial factor driving chromatin state and gene expression\, directing tissue development and remodeling. URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-mini-symposium-emily-maciejewski-ernst-grad-student-computer-science-chenlu-di-lohmueller-postdoc-ecology-evolutionary-biology-qingyang-wang-l/ LOCATION:Boyer Hall 130 CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=application/pdf:https://qcb.ucla.edu/wp-content/uploads/sites/14/2023/11/Mini-Symposium-12723-1.pdf END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20231204T120000 DTEND;TZID=America/Los_Angeles:20231204T130000 DTSTAMP:20231017T092236Z CREATED:20231017T092149Z LAST-MODIFIED:20231017T092236Z UID:25854-1701691200-1701694800@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Monday\, December 4\, 2023 Graciela Gonzalez-Hernandez\, PhD\, Vice Chair of Research and Education\, Department of Computational Biomedicine\, Cedars-Sinai Medical Center DESCRIPTION:TITLE: “ChatGPT for Clinical Informatics: what can LLMs do now for Health AI?” \nHosted by William Hsu for Medical Informatics \n  URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-monday-december-4-2023-graciela-gonzalez-hernandez-phd-vice-chair-of-research-and-education-department-of-computational-biomedicine-cedars/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2023/10/Picture6.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20231201T133000 DTEND;TZID=America/Los_Angeles:20231201T140000 DTSTAMP:20231201T221917Z CREATED:20231018T093230Z LAST-MODIFIED:20231201T221917Z UID:25893-1701437400-1701439200@qcb.ucla.edu SUMMARY:Research-in-Progress (RIP) Seminar: Samir Akre (Bui)\, Graduate Student in Medical Informatics DESCRIPTION:TITLE: “Detection of Symptoms of Depression Using Data From the iPhone and Apple Watch.” \nABSTRACT: Digital health data from consumer wearable devices and smartphones have the potential to improve our understanding of mental illness. However\, in conditions like depression\, there is not yet a consistent uniform measurement tool whose result can be reliably used as a gold standard measure of depression severity. This work seeks to specify what symptoms and dimensions of depression can be detected using vitals\, activity\, and sleep monitored by consumer wearable devices. Machine learning models are fit to digital health data and used to detect responses to individual questions from self-reports as well as summary scores. Data is analyzed from an ongoing study with data from the Apple Watch\, iPhone\, and validated self-reports. The digital health data investigated was found to detect depression severity and specific symptoms like poor appetite\, aspects of anhedonia\, and sleep timings (ROC AUC 0.63 to 0.72). \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/10/Samir-Akre.mp4 URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-samir-akre-bui-graduate-student-in-medical-informatics/ LOCATION:ZOOM\, CA\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2023/10/Akre-Samir-AMIA2022_crop.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20231201T130000 DTEND;TZID=America/Los_Angeles:20231201T133000 DTSTAMP:20231201T222154Z CREATED:20231030T181641Z LAST-MODIFIED:20231201T222154Z UID:25976-1701435600-1701437400@qcb.ucla.edu SUMMARY:Research-in-Progress (RIP) Seminar: Kaija Gahm (Pinter-Wollman)\, Graduate Student in Ecology & Evolutionary Biology DESCRIPTION:TITLE: “An updated movement path randomization method to distinguish social and spatial drivers of animal interactions.” \nABSTRACT: Studying the spatial-social interface requires tools that distinguish between social and spatial drivers of interactions. Testing hypotheses regarding the factors determining animal interactions often involves comparing observed interactions with reference or ’null’ models. One approach to constructing reference models that account for spatial drivers of social interactions is randomizing animal movement paths to decouple their spatial and social phenotypes while maintaining environmental effects on movements. Here we propose a new randomization approach. Using agent-based simulations\, we explore the utility of the new approach for different types of animal movements and compare its performance to existing approaches. We show that our method provides reference models that are more similar to the original tracking data\, while still distinguishing between social and spatial drivers. Furthermore\, the new approach results in fewer false-positives than other approaches\, especially when animals do not return to the same place each night but change movement foci\, either locally or directionally. Finally\, we show that interactions among GPStracked griffon vultures (Gyps fulvus) emerge from social attraction rather than from their movement patterns alone. We conclude by highlighting the biological situations in which the new method might be most suitable for testing hypotheses about the underlying causes of social interactions. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/10/Kaija-Gahm.mp4 URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-kaija-gahm-pinter-wollman-graduate-student-in-ecology-evolutionary-biology/ LOCATION:ZOOM\, CA\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2023/10/Kaija_Headshot_Final-3.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20231129T133000 DTEND;TZID=America/Los_Angeles:20231129T140000 DTSTAMP:20231130T154218Z CREATED:20231116T191717Z LAST-MODIFIED:20231130T154218Z UID:26027-1701264600-1701266400@qcb.ucla.edu SUMMARY:Research-in-Progress (RIP) Seminar: Christy Lee (Li JJ)\, Graduate Student in Statistics and Data Science DESCRIPTION:TITLE: “scDEED: a statistical method for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters.” \nABSTRACT: Two-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-distributed stochastic neighbor embedding(t-SNE) and uniform manifold approximation and projection (UMAP) are commonly used for visualizing cell clusters; however\, it is well known that t-SNE and UMAP’s 2D embedding might not reliably inform the similarities among cell clusters. Motivated by this challenge\, we present a statistical method\, scDEED\, for detecting dubious cell embeddings output by any 2D-embedding method. By calculating a reliability score for every cell embedding\, scDEED identifies the cell embeddings with low reliability scores as dubious and those with high reliability scores as trustworthy. Moreover\, by minimizing the number of dubious cell embeddings\, scDEED provides intuitive guidance for optimizing the hyperparameters of an embedding method.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/11/Christy-Lee.mp4 URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-christy-lee-li-jj-graduate-student-in-statistics-and-data-science/ LOCATION:ZOOM\, CA\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2023/11/Christy_Lee_profile.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20231129T130000 DTEND;TZID=America/Los_Angeles:20231129T133000 DTSTAMP:20231130T153643Z CREATED:20231113T160845Z LAST-MODIFIED:20231130T153643Z UID:26015-1701262800-1701264600@qcb.ucla.edu SUMMARY:Research-in-Progress (RIP) Seminar: Matthew Soldano (Pellegrini)\, Staff Research Associate\, Institute for Genomics and Proteomics at DGSOM DESCRIPTION:TITLE: “A Non-Invasive Epigenetic Measure of Inflammation.” \nABSTRACT: Existing epigenetic phenotype tests often lack mechanistic explanations of the observed correlations between specific methylation sites and phenotypes. This raises the crucial question: are these correlations primarily a result of marginal correlations\, or do they stem from plausible biological mechanisms? To delve deeper into this question\, we conducted a Targeted Epigenome Association Study focusing on CpG sites associated with aging\, metabolism\, and obesity. Our study leveraged a clinical investigation on fitness\, encompassing comprehensive measurements of phenotypes\, traditional biomarkers linked to metabolism\, obesity\, and fitness\, as well as extensive profiling of hundreds of metabolites and proteins. Additionally\, we had access to buccal swabs for targeted bisulfite sequencing. Our analysis discovered eight CpG sites exhibiting robust associations with the complement system\, alongside indicators of adiposity and epithelial cell ratio found in the buccal swab samples. These sites reside within the region of the peptidoglycan recognition 1 gene promoter\, a protein that senses inflammatory processes. This discovery sheds light on the intricate interplay between epigenetic markers with oral and systemic inflammation pathways.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/11/Matthew-Soldano.mp4 URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-matthew-soldano-pellegrini-graduate-student-institute-for-genomics-and-proteomics-at-dgsom/ LOCATION:ZOOM\, CA\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/jpeg:https://qcb.ucla.edu/wp-content/uploads/sites/14/2023/11/Matthew-Soldano.jpeg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20231127T120000 DTEND;TZID=America/Los_Angeles:20231127T130000 DTSTAMP:20231017T091350Z CREATED:20231017T091350Z LAST-MODIFIED:20231017T091350Z UID:25845-1701086400-1701090000@qcb.ucla.edu SUMMARY:Frontiers in Computational Biosciences Seminar Series: Qunhua Li\, PhD\, Associate Professor\, Department of Statistics\, The Pennsylvania State University DESCRIPTION:TITLE: “TBD” \nHosted by Jingyi Jessica Li for Bioinformatics URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-qunhua-li-phd-associate-professor-department-of-statistics-the-pennsylvania-state-university/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:QCBio Seminar Series ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2023/10/Picture5.png END:VEVENT END:VCALENDAR