ENCODE 2020: Research Applications and Users Meeting

Name: ENCODE 2020: Research Applications and Users Meeting
Start: Wed, 09/30/2020 - 10:00 EST
End: Wed, 10/02/2019 - 15:50 EST
Location: National Institute of Health

Event Details

On Sept. 30 - Oct. 2, 2020, the National Human Genome Research Institute (NHGRI) sponsored the ENCODE 2020: Research Applications and Users Meeting. The goal of the meeting was to help researchers leverage ENCODE’s 15,000+ freely available genomic datasets to accelerate their own research.

The virtual meeting featured:

Hands-on workshops on learning to navigate, analyze, and integrate ENCODE data
Leading-edge research applications from distinguished invited speakers
Tutorials on data processing pipelines and analysis tools that facilitate working with ENCODE data
Short talks selected from abstracts

Sep 30, 2020, 10:00 AM to

Oct 2, 2019, 3:50 PM

Virtual

Agenda

Wednesday, September 30
10:00 a.m. – 10:10 a.m.	Opening remarks and housekeeping Roderic Guigó \| Centre for Genomic Regulation (CRG)
10:10 a.m. – 10:50 a.m.	KEYNOTE LECTURE Aravinda Chakravarti \| NYU Langone Health " Sequence-based studies of regulatory control"
10:50 a.m. – 11:50 a.m.	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 Sta.m.atoyannopoulos \| University of Washington Genome Sciences " High-resolution maps of regulatory DNA: Key insights and forward perspective"
11:50 a.m. – 12:10 p.m.	BREAK + Meet the speakers
12:10 p.m. – 1:50 p.m.	WORKSHOPS I ENCODE Portal Navigation Using the GENCODE reference annotation of human and mouse genes and transcripts Juicebox — visualizing the genome in 3D
1:50 p.m. – 2:30 p.m.	BREAK
2:30 p.m. – 3:00 p.m.	FLASH TALKS 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 p.m. - 4:00 p.m.	SESSION 2 Alessandra Breschi \| Tempus “A limited set of transcriptional progra.m.s 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 “Footprinting the human genome”
4:00 p.m. – 4:30 p.m.	BREAK + Meet the speakers

Thursday, October 1
10:00 a.m. – 10:40 a.m.	KEYNOTE LECTURE Nicole Soranzo \| Welcome Sanger Institute “Studying genetics in a whole biological system: large-scale genomic approaches to understand disease risk”
10:40 a.m. – 11:40 a.m.	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 “Detecting regulatory elements in STARR-seq”
11:40 a.m. – 12:00 p.m.	BREAK + Meet the speakers
12:00 p.m. – 1:50 p.m.	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 Juicebox — visualizing the genome in 3D
1:50 p.m. – 2:30 p.m.	BREAK + Meet the speakers
2:30 p.m. – 3:00 p.m.	FLASH TALKS 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."
3:00 p.m. – 4:00 p.m.	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 develop.m.ent”
4:00 p.m. – 4:30 p.m.	BREAK + Meet the speakers

Friday, October 2
10:00 a.m. – 10:40 a.m.	KEYNOTE LECTURE Piero Carninci \| RIKEN Center for Integrative Medical Sciences “Decoding human genome: an international effort spanning two decades”
10:40 a.m. – 11:40 a.m.	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 “Integrative analysis of 10,000 epigenomic maps across 800 biosamples for regulatory genomics and disease dissection” Annika Weimer \| Project Manager, ENCODE production center, Snyder lab, Stanford, CA “Mapping regulatory regions of the human genome”
11:40 a.m. – 12:00 p.m.	BREAK + Meet the speakers
12:00 p.m. – 1:50 p.m.	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 p.m. - 2:30 p.m.	BREAK
2:30 p.m. – 3:10 p.m.	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 “The long and short transcriptomes of ENCODE 3 and 4”
3:10 p.m. – 3:20 p.m.	Final remarks
3:20 p.m. – 3:50 p.m.	BREAK + Meet the speakers

Last updated: December 18, 2020