{"669993":{"#nid":"669993","#data":{"type":"event","title":"Center for Integrative Genomics Advanced Research Seminar (CIGars)","body":[{"value":"\u003Cp\u003EThe Center of Integrative Genomics (CIG) welcomes our invited speaker,\u0026nbsp;\u003Ca href=\u0022http:\/\/jsb.ucla.edu\/about-jingyi-jessica-li\u0022 id=\u0022OWA3756c2df-f9f1-0724-b327-19ae998c1322\u0022 rel=\u0022noreferrer noopener\u0022 target=\u0022_blank\u0022 title=\u0022http:\/\/jsb.ucla.edu\/about-jingyi-jessica-li\u0022\u003EJingyi Jessica Li\u003C\/a\u003E\u003Ca href=\u0022http:\/\/jsb.ucla.edu\/about-jingyi-jessica-li\u0022\u003E, Ph.D.\u003C\/a\u003E, Professor in the Department of Statistics, Department of Human Genetics, and Department of Biomathematics at the University of California, Los Angeles for a special Advanced Research Seminar:\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003E\u201c\u003Cem\u003EClusterDE: a Post-clustering Differential Expression (DE) Method Robust to False-positive Inflation Caused by Double Dipping\u003C\/em\u003E\u201d\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003E\u003Ca href=\u0022http:\/\/jsb.ucla.edu\/about-jingyi-jessica-li\u0022\u003EJingyi Jessica Li, Ph.D.\u003C\/a\u003E\u003C\/strong\u003E\u003Cbr \/\u003E\r\nProfessor, Department of Statistics\u0026nbsp;\u003Cbr \/\u003E\r\nDepartment of Human Genetics\u003Cbr \/\u003E\r\nDepartment of Biomathematics\u0026nbsp;\u003Cbr \/\u003E\r\nUniversity of California, Los Angeles\u003C\/p\u003E\r\n\r\n\u003Cp\u003EIn typical single-cell RNA-seq (scRNA-seq) data analysis, a clustering algorithm is applied to find putative cell types as clusters, and then a statistical differential expression (DE) test is employed to identify the differentially expressed (DE) genes between the cell clusters. However, this common procedure uses the same data twice, an issue known as \u201cdouble dipping\u201d: the same data is used twice to define cell clusters as potential cell types and DE genes as potential cell-type marker genes, leading to false-positive cell-type marker 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) of identified DE genes regardless of clustering quality, which can work as an add-on to popular pipelines such as Seurat. The core idea of ClusterDE is to generate real-data-based synthetic null data containing only one cluster, in contrast to the real data, for evaluating the whole procedure of clustering followed by a DE test. Using comprehensive simulation and real data analysis, we show that ClusterDE has not only solid FDR control but also the ability to identify cell-type marker genes as top DE genes and distinguish them from housekeeping genes. ClusterDE is fast, transparent, and adaptive to various clustering algorithms and DE tests. Besides scRNA-seq data, ClusterDE generally applies to post-clustering DE analysis, including single-cell multi-omics data analysis.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EJingyi Jessica Li\u003C\/strong\u003E, Professor of Statistics and Data Science (also affiliated with Biostatistics, Computational Medicine, and Human Genetics), leads a research group titled the Junction of Statistics and Biology at UCLA. With a Ph.D. from UC Berkeley and B.S. from Tsinghua University, Li focuses on developing interpretable statistical methods for biomedical data. Her research delves into quantifying the central dogma, extracting hidden information from transcriptomics data, and ensuring statistical rigor in data analysis by employing synthetic negative controls. Recipient of multiple awards including the NSF CAREER Award, Sloan Research Fellowship, ISCB Overton Prize, and COPSS Emerging Leaders Award, her contributions have gained recognition in the fields of computational biology and statistics.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cbr \/\u003E\r\nEnjoy free lunch\u0026nbsp;and hear about a wide range of work happening in the local bioscience community!\u003C\/p\u003E\r\n","summary":"","format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003E\u201c\u003Cem\u003EClusterDE: a Post-clustering Differential Expression (DE) Method Robust to False-positive Inflation Caused by Double Dipping\u003C\/em\u003E\u201d - Jingyi Jessica Li, Ph.D., UCLA\u003C\/p\u003E\r\n","format":"limited_html"}],"field_summary_sentence":[{"value":"\u201cClusterDE: a Post-clustering Differential Expression (DE) Method Robust to False-positive Inflation Caused by Double Dipping\u201d -\u00a0Jingyi Jessica Li, Ph.D., UCLA"}],"uid":"35486","created_gmt":"2023-09-28 13:04:09","changed_gmt":"2023-09-28 13:05:08","author":"Christina Wessels","boilerplate_text":"","field_publication":"","field_article_url":"","field_event_time":{"event_time_start":"2023-10-20T12:00:00-04:00","event_time_end":"2023-10-20T13:00:00-04:00","event_time_end_last":"2023-10-20T13:00:00-04:00","gmt_time_start":"2023-10-20 16:00:00","gmt_time_end":"2023-10-20 17:00:00","gmt_time_end_last":"2023-10-20 17:00:00","rrule":null,"timezone":"America\/New_York"},"location":"Engineered Biosystems Building (EBB), CHOA Seminar Room, 950 Atlantic Drive NW, Atlanta, GA ","extras":[],"groups":[{"id":"1292","name":"Parker H. Petit Institute for Bioengineering and Bioscience (IBB)"}],"categories":[],"keywords":[{"id":"187423","name":"go-bio"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[{"id":"1795","name":"Seminar\/Lecture\/Colloquium"}],"invited_audience":[{"id":"78761","name":"Faculty\/Staff"},{"id":"177814","name":"Postdoc"},{"id":"78771","name":"Public"},{"id":"174045","name":"Graduate students"},{"id":"78751","name":"Undergraduate students"}],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003E\u003Ca href=\u0022mailto:sboettle3@gatech.edu\u0022 id=\u0022OWAe72787e1-2f7b-385d-ab30-f7816ae604aa\u0022 title=\u0022mailto:sboettle3@gatech.edu\u0022\u003EStefanie Boettle\u003C\/a\u003E\u0026nbsp;\u2013 event inquiries\u0026nbsp;\u003C\/p\u003E\r\n","format":"limited_html"}],"email":[],"slides":[],"orientation":[],"userdata":""}}}