ENCODE 2020: Research Applications and Users Meeting
Sept 30 - Oct 2, 2020
Virtual event
All times listed at EST.
Full playlist of talks and workshops
Wednesday, September 30 | |
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10:00 AM – 10:10 AM |
Opening remarks and housekeeping Roderic Guigó | Centre for Genomic Regulation (CRG) |
10:10 AM – 10:50 AM |
KEYNOTE LECTURE Aravinda Chakravarti | NYU Langone Health |
10:50 AM – 11:50 AM |
SESSION 1 Stephanie Morris | NIH/NHGRI “ENCODE: The Encyclopedia of DNA Elements”
Paul Flicek | European Bioinformatics Institute (EBI) "Comparative regulatory genomics approaches to understanding transcriptional regulation"
John Stamatoyannopoulos | University of Washington Genome Sciences "High-resolution maps of regulatory DNA: Key insights and forward perspective" |
11:50 AM – 12:10 PM | BREAK + Meet the speakers |
12:10 PM – 1:50 PM |
WORKSHOPS I
ENCODE Portal Navigation Using the GENCODE reference annotation of human and mouse genes and transcripts |
1:50 PM – 2:30 PM | BREAK |
2:30 PM – 3:00 PM |
Joel Rozowsky | Yale School of Medicine "The ENCODE EN-TEx Resource" Elise Flynn | Columbia University and New York Genome Center "Transcription factor regulation of genetic variant effects across tissues and individuals" Giacomo Cavalli | Institute of Human Genetics, CNRS / University of Montpellier "Heterogeneous single-cell organization of chromosomes into TADs and chromatin nanodomains" Pablo Villegas-Mirón | Institut de Biologia Evolutiva (UPF-CSIC) "Intronic enhancers regulate the expression of genes involved in tissue-specific functions and homeostasis" Grigory Ryabykh| Lomonosov Moscow State University "RNA-Chrom: database genome-wide RNA-chromatin interactions" |
3:00 PM - 4:00 PM |
SESSION 2 Alessandra Breschi | Tempus “A limited set of transcriptional programs define major cell types”
Wouter Meuleman | Altius Institute for Biomedical Sciences “Index and biological spectrum of human DNase I hypersensitive sites”
Jeff Vierstra | Altius Institute for Biomedical Sciences |
4:00 PM – 4:30 PM | BREAK + Meet the speakers |
Thursday, October 1 | ||
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10:00 AM – 10:40 AM |
KEYNOTE LECTURE Nicole Soranzo | Welcome Sanger Institute “Studying genetics in a whole biological system: large-scale genomic approaches to understand disease risk” |
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10:40 AM – 11:40 AM |
SESSION 3 — Technology Zhiping Weng | UMass Medical School “An atlas of polymerase III-transcribed Alu elements across human cell types and tissues”
Brenton Graveley | Department of Genetics and Genome Sciences, UConn Health “A large-scale binding and functional map of human RNA-binding proteins”
Young-Sook Kim | Duke University |
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11:40 AM – 12:00 PM |
BREAK + Meet the speakers |
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12:00 PM – 1:50 PM |
WORKSHOPS
Navigating the ENCODE Encyclopedia with SCREEN
Running ENCODE uniform processing pipelines on Google Cloud using Caper server Using the GENCODE reference annotation of human and mouse genes and transcripts |
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1:50 PM – 2:30 PM | BREAK + Meet the speakers | |
2:30 PM – 3:00 PM |
Saumya Agrawal | RIKEN Center for Integrative Medical Sciences "The biological role of long noncoding RNAs in human cells inferred from chromatin conformation data" Pavel Kuksa | Penn Neurodegeneration Genomics Center, University of Pennsylvania "FILER: Harmonized, scalable Functional Genomics Repository and API" Lance Hentges | University of Oxford "LanceOtron: a deep learning peak caller for genomic sequencing analysis" Christophe Tav | Centre de Recherche du CHU de Québec-Université Laval "Regionalized transcriptional response to glucocorticoid stimulation" Venkat Maladi | UT Southwestern Medical Center "TReNCo: Accurate topologically associating domain (TAD) aware regulatory network construction." |
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3:00 PM – 4:00 PM |
SESSION 4 Mike Snyder | Department of Genetics, Stanford University “Noncoding regions in cancer and silencers”
Mark Gerstein | Yale School of Medicine “Using ENCODE Data for Cancer Genomics”
Bing Ren | University of California, San Diego “An atlas of dynamic chromatin landscapes in mouse fetal development” |
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4:00 PM – 4:30 PM |
BREAK + Meet the speakers |
Friday, October 2 | |
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10:00 AM – 10:40 AM |
KEYNOTE LECTURE Piero Carninci | RIKEN Center for Integrative Medical Sciences “Decoding human genome: an international effort spanning two decades” |
10:40 AM – 11:40 AM |
SESSION 5 Ross Hardison | The Pennsylvania State University “A VISION for integration and application of ENCODE data in differentiating blood cells”
Manolis Kellis | MIT and Broad Institute
Annika Weimer | Project Manager, ENCODE production center, Snyder lab, Stanford, CA |
11:40 AM – 12:00 PM |
BREAK + Meet the speakers |
12:00 PM – 1:50 PM |
WORKSHOPS
An interactive introduction to Factorbook Ledidi: Designing genome edits that induce functional activity
Running ENCODE uniform processing pipelines on Google Cloud using Caper server Using the GENCODE reference annotation of human and mouse genes and transcripts |
1:50 PM - 2:30 PM |
BREAK |
2:30 PM – 3:10 PM |
SESSION 6 Joe Ecker | HHMI-Salk Institute for Biological Studies “Spatiotemporal DNA methylome dynamics of the developing mouse fetus and beyond”
Ali Mortazavi | UCI School of Biological Sciences |
3:10 PM – 3:20 PM | Final remarks |
3:20 PM – 3:50 PM | BREAK + Meet the speakers |