ENCODE 2016: Agenda

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Wednesday, June 8th (Day 1)

8:00 – 10:00 a.m.     Registration | Breakfast | Information desk open   

10:00 - 10:30 a.m.    Introduction to ENCODE Data  (25 min. + 5 min. Q&A)

                                 "Welcome Overview of ENCODE data types"  

                                 Mike Pazin, NHGRI

10:30 - 11:15 a.m.    Keynote Lecture  - Nancy Cox  (40 min. + 5 min. Q&A)                           

11:15 - 12:30 p.m.    Scientific Session 1:  Common Disease

                                 "Genetic regulation of gene expression variation" 

                                               Barbara Stranger (Chicago) (20 minutes + 5 Q&A)

                                 "Regulation of bone and vitamin metabolism: Insights from ENCODE"

                                              J. Wesley Pike (Wisconsin)  (20 minutes + 5 Q&A)

                                 "Common disease burden in non-coding regions"

                                              Chris Cotsapas (Yale/Broad)  (20 minutes + 5 Q&A)                                    

12:30 - 1:30 p.m.      Lunch

1:30 – 2:15 p.m.       Workshop Session 1:  The ENCODE Encyclopedia    

                                               Zhiping Weng

2:15 - 3:15 p.m.       Workshop Session 2:  The ENCODE Data Coordination Center  

                                 Workshop 2.1: DCC tutorial Part I (portal, 1 hour)               

                                               Cricket Sloan

3:15 - 3:30 p.m.        Coffee Break

3:30 - 5:10 p.m.       Workshop Session 3:  Web-based Analysis Tools

                                 Workshop 2.2: ENCODE element browser and 3D browser (30 minutes)

                                              Feng Yue

                                 Workshop 2.3: RBP database         

                                             Brent Graveley and Eric VanNostrand (30 min)

                                 Workshop 2.4: RegulomeDB           

                                            Mike Snyder (20 minutes)

                                 Workshop 2.5: HaploReg

                                            Wouter Meuleman (10 minutes)

5:10 - 5:25 p.m.        Coffee Break

5:25 - 6:15 p.m.        Scientific Session 2:  Non-coding RNA

                                  "Comparative Analysis of Non-Coding Transcription using ENCODE and modENCODE data"

                                            Joel Rozowsky (Yale) (20 minutes + 5 Q&A)

                                  Human cellular identity considered in the context of organ of origin

                                            Tom Gingeras (CSHL) (20 minutes + 5 Q&A)

6:10 - 7:30 p.m.        Dinner

7:30 – 9:00 p.m.       Lightning Talks - Moderated by Feng Yue

                                 “Decoding Brain Epigenome Maps with Broad H3K4me3 Signals: Discovering Functional Epigenetic Patterns and                                    Their Dynamics in Gene Regulatory Networks” by Aslihan Dincer, Bin Zhang, Joel T. Dudley, Eric E. Schadt
                                  and Schahram Akbarian

                                  “The role of transcript-specific translation in human neuronal Differentiation” by Stephen Floor, John Blair, Dirk
                                  Hockemeyer, Helen Bateup and Jennifer Doudna

                                  “Crowdsourced analysis, curation, and visualization of ENCODE data with Quilt” by Aneesh Karve

                                  “Evaluation of U12-type non-canonical splicing events in human ENCODE RNA-Seq datasets and analysis of                                              biological functions for spliced sequences by Read-Spit-Fly algorithm” by Yongsheng Bai and Jeff Kinne

                                  “Spectacle: fast chromatin state annotation using spectral learning” by Kevin Chen

                                  “Integration of Genomic Big Data: Efficient Queries on ENCODE (Meta)data” by Stefano Perna, Abdulrahman                                              Kaitoua, Pietro Pinoli, Marco Masseroli and Stefano Ceri

                                  “Genome-wide association between transcription factor expression and chromatin accessibility reveals chromatin                                  state regulators” by David Lamparter,  Rico Rueedi, Daniel Marbach, Sven Bergmann and Zoltán Kutalik

                                  “Identification of non-coding risk variants associated with complex diseases based on multi-omics profiles” by Li
                                   Chen, Peng Jin and Zhaohui Qin

                                  “Reconstruction and analysis of tissue-specific transcriptional regulatory networks with TRENA” by Seth Ament

                                  “GWAS of QT interval in Hispanics/Latinos generalizes 13 loci and identifies population-specific signals”
                                   by Raúl Méndez-Giráldez

                                  “ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data” by  Scott Lundberg, William                                    Tu, Brian Raught, Linda Penn, Michael Hoffman and Su-In Lee​

                                  “Comprehensive characterization of the genome sequences of K562 and HepG2” by Bo Zhou 


Thursday, June 9th (Day 2)

8:00 – 9:00 a.m.       Breakfast    

9:00 - 10:40 a.m.      Scientific Session 3: Cancer  

                                 "Regulatory variation in breast cancer"

                                           Mathieu Lupien (Toronto) (20 minutes + 5 Q&A)

                                 "Non-coding cancer drivers"

                                          Mike Snyder (Stanford)  (20 minutes + 5 Q&A)

                                 "Using ENCODE to interpret mutational patterns in cancer genomes"

                                     Shamil Sunyaev (Harvard)  (20 minutes + 5 Q&A)

                                  "Tools for analyzing cancer variation"

                                       Ekta Khurana (Cornell)  (20 minutes + 5 Q&A)     

10:40 - 11:00 a.m.    Coffee break

11:00 - 11:50 a.m.    Scientific Session 4: Functional validation of ENCODE element 

                                 "Comprehensive functional testing of ChIP-seq binding sites with ChIP-reporter assays"

                                         Tim Reddy (Duke)  (20 minutes + 5 Q&A)   

                                  "Using ENCODE to inform genome editing"

                                         Matthew L. Freedman (Dana-Faber/Harvard) (20 minutes + 5 Q&A)  

12:00 - 1:30 p.m.      Lunch   

1:30 - 3:30 p.m.        Workshop Session 4:  The ENCODE Uniform Pipeline Workshop  

                                  Workshop 4: DCC tutorial Part II (pipeline, 2 hours)            

                                            J. Seth Strattan and Ben Hitz (Stanford)

3:30 -3:50 p.m.         Coffee break

3:50 - 6:05 p.m.        Workshop Session 5: Advanced Analysis Tools

                                  Workshop 5.1          

                                          Jason Ernst (chromHMM, 30 minutes)

                                  Workshop 5.2          

                                          Max Libbrecht (Segway, 30 minutes)

                                  Workshop 5.3          

                                          Wouter Meuleman (epilogos, 15 minutes)

                                  Workshop 5.4

                                          Anshul Kundaje (Deep learning for genomics 50 minutes)

6:05 - 7:15 p.m.        Dinner

7:30 – 9:00 p.m.       Wine and Dessert Reception with Posters | DCC Live Help Desk   

 


Friday, June 10th (Day 3)

8:00 – 8:50 a.m.       Breakfast    

9:00 – 9:50 a.m.       Scientific Session 5:  RNA Binding Proteins

                                 "Comprehensive characterization of functional RNA element encoded in the human genome"

                                        Brent Graveley  (20 minutes + 5 Q&A)

                                 "Genetic variants and associated proteins in the regulation of pre-mRNA splicing"

                                         Grace Xiao  (20 minutes + 5 Q&A)

9:50 – 10:15 a.m.     Coffee break

10:15 - 11:30            Scientific Session 6:  3D genome organization

                                 "Organization and Regulation of Human Genome"

                                         Bing Ren (20 minutes + 5 Q&A)

                                 "Players and Models of Transcription Regulation in 3D genome​

                                         Yijun Ruan    (20 minutes + 5 Q&A)

                                 “Many transcription factors recognize DNA shape”

                                         Katie Pollard (20 minutes + 5 Q&A)

11:30 - 12:30 p.m.    Wrap up: Feedback from participants on ENCODE Resources and the Encyclopedia    

                                  ENCODE DCC and ENCODE PIs and/or NHGRI

12:30 p.m.                Adjourn