January 31 – February 5, 2016

Rio Grande, Puerto Rico


Sunday, January 31                    


17:30   Dinner




Chairperson:   Dirk Schubeler, Friedrich Miescher Institute


Genetic effects on molecular phenotypes and disease biology

Emmanouil Dermitzakis


Shaping the blood: Lessons from Chromatin and single cell RNA dynamics

Ido Amit


Nucleotide characteristics, chromatin composition, and transcriptional relationships of RNA:DNA hybrids in the human genome

John Greally


Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM), a novel ligation-free approach

Ana Pombo, Robert A. Beagrie, Antonio Scialdone, Markus Schueler, Dorothee C.A. Kraemer, Mita Chotalia, Sheila Xie, Mariano Barbieri, Ines de Santiago, Liron-Mark Lavitas, Miguel R. Branco, James Fraser, Josee Dostie, Laurence Game, Niall Dillon, Paul Edwards and Mario Nicodemi


Regulatory roles of RNA repeats

Ezgi Hacisuleyman, Chinmay Shukula and John Rinn


Reading and writing DNA methylation

Dirk Schubeler


21:30   Social


Monday, February 1                    


7:30     Breakfast




Chairperson:   Kim McAllister, NIEHS


The 3D architecture of the breast cancer genome reveals oncogenic noncoding mutations regulating ESR1 expression

Swneke D. Bailey, Kinjal Desai, Parisa Mazrooei, Nicholas A. Sinnott-Armstrong, Mark Dowar, Xue Wu, Rossanna C. Pezo, Benjamin Haibe-Kains, Philippe L. Bedard, Trevor J. Pugh, Richard  C. Sallari and Mathieu Lupien


Mammalian SWI/SNF (BAF) complex structure and function in human cancer

Cigall Kadoch


Characterization of the Anti-Tumour Effects of EZH2 Inhibition in Atypical Teratoid Rhabdoid Tumours

Shengrui Feng, King Ching Ho, Rajat Singhania, Jonathon Torchia, Annie Huang and Daniel De Carvalho      


Cancer Mutations of mSWI/SNF Enhance Polycomb Activity at CpG- Island Promoters

Courtney Hodges, Benjamin Z. Stanton, Wai Lim Ku, Keji Zhao and Gerald R. Crabtree          


Integrated regulator genomics of renal cell carcinoma

Shreeram Akilesh, Kyle Siebenthall, Richard Sandstrom, Alex Reynolds,  Audra Johnson, Jemma Nelson and John Stamatoyannopoulos


Balancing Genomic Accessibility by BAF-Polycomb Opposition

Gerald Crabtree


TMPRSS2-ERG drives global mistargeting of mammalian SWI/SNF (BAF) complexes in prostate cancer

Gabriel Sandoval, John Pulice, Monica Schenone, David Takeda, Marius Pop, Gaylor Boulay, Miguel Rivera, Lucienne Ronco, William Hahn and Cigall Kadoch       


Genome-wide chromatin accessibility changes regulated by Nfib defines SCLC metastatic state and drives SCLC metastatic ability

Sarah Denny, Dian Yang, Monte Winslow, Julian Sage and William Greenleaf 


Profound TET loss-of-function results in genome instability and oncogenesis

Isaac López-Moyado, Ageliki Tsagaratou, Sini Rautio, Edah’ Gonz‡lez- Avalos, James Scott-Browne, David Adams, Harri LŠhdesmŠki and Anjana Rao     


A genome-epigenome perspective of clonal evolution in human tumors

Joseph Costello, Tali Mazor, Alex Pankov and Jun Song         



12:00   Lunch


13:30   WORKSHOP I – Accessing and Visualizing Epigenomic Data


Engaging epigenomics resources

Ting Wang, Washington University


Online resources of the Roadmap Epigenomics project

Wouter Meuleman, MIT


The WashU Epigenome Browser (Hands-on demo)

Renee Sears, Washington University


The Roadmap Epigenome Browser (Hands-on demo)

Nicole Rockweiler, Washington University





Chairperson:   Job Dekker, University of Massachusetts


Sex chromosomes: models for structure-function studies of Chromosomes

Job Dekker


Analyzing the dynamic landscape of 3D genome structures

Frank Alber


Gene expression changes in neuronal dierentiation captured by Hi-C Trees

Tiago Rito, Markus Schueler, Stuart Aitken, Andrea Maria Chiariello, James Fraser, Carmelo Ferrai, Mariano Barbieri, Kelly J. Morris, Masayoshi Itoh, Hideya Kawaji, Ines Jaeger, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, The FANTOM Consortium, Colin A. Semple, Josee Dostie, Mario Nicodemi and Ana Pombo           


Genomic characterization of the developing bat wing

Walter Eckalbar, Stephen Schlebusch, Mandy Mason, Zoe Gill, Betty Booker, Nadja Makki, Tara Friedrich, Katherine Pollard, Lucia Carbone, Jeff Wall, Nicola Illing and Nadav Ahituv


Chromatin interactions in single cells

Peter Fraser     


Genome-wide characterization of mammalian retrotransposon exaptation due to tissue-specific regulatory function

Aaron Hardin, Navneet Matharu and Nadav Ahituv


Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin

Jay Shendure, Matthew Snyder, Martin Kircher and Andrew Hill


Massively multiplexed single-cell Hi-C by combinatorial barcoding

Vijay Ramani, Xinxian Deng, Christine Disteche, Zhijun Duan and Jay Shendure


Enhancer States during Drosophila Development

Julia Zeitlinger  


18:05   Dinner –'Bievenidos a Puerto Rico'




Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

Joseph R. Ecker Salk Institute for Biological Studies and HHMI


20:30   Welcome Reception


Tuesday, February 2                   



7:30     Breakfast




Chairperson: Henk Stunnenberg, Radboud University, Netherlands


Genome-wide analysis of protein-DNA interactions

Arttu Jolma, Yimeng Yin, Bei Wei, Jian Yan, Teemu Kivioja, Syed Khund-Sayeed, Ekaterina Morgunova, Charles Vinson and Jussi Taipale


Blocks of tightly coupled DNA methylation in human stem cells and cancers.

Kun Zhang, Shicheng Guo, Dinh Diep and Nongluk Plongthongkum


Insights from methylome analysis

Stephan Beck


Nucleosome density ChIP-seq identifies distinct promoter associated chromatin modification signatures

Martin Hirst and Alireza Lorzadeh


Epigenomic establishment of macrophage tolerance and training

Henk Stunnenberg


Massively parallel reporter assays reveal glucocorticoid receptor interaction modules that direct gene expression responses to corticosteroids

Christopher Vockley, Anthony D'lppolito, Ian McDowell, William Majoros, Alexias Safi, Lingyun Song, Gregory Crawford and Timothy Reddy


Large-scale Inference of Activating and Repressive Nucleotides at High Resolution in Human Cell Types Using Tiling Reporter Assays

Jason Ernst, Tarjei Mikkelsen and Manolis Kellis


Synchronized mitochondrial and cytosolic translation programs

Stirling Churchman


Exploring the role of Tet1 in genomic imprinting

Jennifer Myers, Lara Abramowitz and Marisa Bartolomei


Towards Quantitative Epigenetics: Building the Foundation of Epigenomcis Roadmaps

Zhaoyu Li        


Single molecule characterization of histone marks co-occurrence reveals extensive dynamics of bivalent domains in mammalian development

Assaf Weiner, David Lara-Aristo, Vladik Krupalnik, Eyal David, Jacob Hanna and Ido Amit


Comprehensive mapping of chromatin dynamics during blood formation

David Lara Astiaso and Assaf Weiner



12:00   Lunch


13:30 WORKSHOP II – Analyzing DNA Methylation Data: A hands-on workshop

Fabian Müller, Max-Planck-Institut für Informa




Chairperson: Aleksander Milosavljevic, Baylor College of Medicine


From genomics to precision medicine: Uncovering and manipulating the genetic circuits underlying common disease

Manolis Kellis


Systematic identification of predictive casual GWAS SNPs within transcription factor binding sites that control chromatin landscape

Yunxian Liu and Michael Guertin


Sequence variation affecting transcription factor occupancy in highly diverged mouse strains

Matthew T Maurano, Jessica M Halow, Rachel Byron, Mark Groudine, M A Bender and John A



Systematic identification and characterization of regulatory variants in GWAS regions

Cong Guo, Christopher M. Vockley, Ian C. McDowell, William H. Majoros and Timothy E. Reddy


Allelic epigenomes shed light on the function of noncoding variants in the human genome

Vitor Onuchic, Ivenise Carrero, Eugene Lurie, Piotr Pawliczek, Ronak Patel, Timur Galeev, Joel Rozowsky, Robert Altshuler, Zhuoyi Huang, Zhizhuo Zhang, Alan Harris, Fuli Yu, Mark Gerstein, Manolis Kellis and Aleksandar Milosavljevic


Epigenomic deconvolution of tumor tissue biology

Aleksandar Milosavljevic


Impact of transposable elements on transcription regulation in human

Guillaume Bourque



18:15               Dinner - Seafood by the Sea





Chairperson: Lisa Chadwick, NIEHS and 4D Nucleome Program


Many promoters of lncRNAs and mRNAs act as enhancers in local gene regulatory networks

Jesse Engreitz, Jenna Haines, Glen Munson, Patrick McDonel, Mitchell Guttman and Eric Lander


Differential enhancer transcription defines a gene regulatory network

Rangarajan Nadadur, Jenna Bekeny and Ivan Moskowitz


How a lncRNA shapes chromatin structure to control gene expression

Mitchell Guttman


Genome-wide views into the mechanisms of transcription regulation triggered by the stress response

John Lis, Charles Danko, Fabiana Duarte, Michael Guertin and Dig Bijay Mahat


Comprehensive RNA Polymerase II Interactomes Reveal the Distinct and Varied Roles for Each Phospho-CTD Residue

Kevin Harlen, Kristine Trotta, Erin Smith, Mohammad Mosaheb, Stephen Fuchs and Stirling Churchman


Integration of regulatory information at promoters through combinatorial control of the transcriptional cycle

Clarissa Scholes, Angela H. Depace and Alvaro Sanchez



21:30   Social / Poster Session I


Wednesday, February 3


7:30 Breakfast




Chairperson: Frederick Tyson, NIEHS


Cumulative impact of large chromosomal duplications and polychlorinated biphenyl exposure on DNA methylation, chromatin, and expression of synaptic genes

Keith Dunaway, Saharul Islam, Roy Chu, Rochelle Coulson, Dag Yasui, Diane Schroeder, Isaac Pessah, Paul Lott, Makiko Meguro-Horike, Shin-Ichi Horike, Ian Korf, Jesse Lopez and Janine Lasalle


Epigenomics and prenatal exposure to environmental pollutants: New Data from CHAMACOS Birth Cohort Study

Nina Holland, Paul Yousefi, Karen Huen, Daneida Lizarraga, Gwen Tindula, Kim Harley and Brenda Eskenazi


Regulatory landscape remodeling by endocrine disruptors

Kyle Siebenthall, Richard Sandstrom, Jessica Halow, Kristen Lee, R. Scott Hansen, Peter Sabo, Rajinder Kaul and John Stamatoyannopoulos


Epigenetic variation in the brain: neurodevelopment and neuropsychiatric disease

Jonathan Mill


Non-Genomic Signaling to MLL Developmentally Reprograms Histone Methylation and Susceptibility to Prostate Carcinogenesis

Quan Wang, Lindsey Treviño, Mario Medvedovic, Shuk-Mei Ho, Charles Foulds, Bert O'Malley and Cheryl Walker


Schizophrenia-associated epigenetic variation in the brain

Joana Viana, Eilis Hannon, Ruth Pidsley, Emma Dempster, Helen Spiers,Ruby Macdonald, Claire Troakes, Safa Al-Saraj, Naguib Mechawar, Gustavo Turecki, Leonard Schalkwyk, Nicholas Bray and Jonhattan Mill


Increased DNA Methylation Variability in Type 1 Diabetes Across Three Immune Effector Cell Types

Dirk Paul and Stephan Beck


Lactose intolerance is directed by DNA haplotype-dependent epigenetic aging

Viviane Labrie, Orion J Buske,Edward Oh, Richie Jeremian, Carolyn Ptak, Giedrius Gasiunas, Almantas Maleckas, Ruta Petereit, Aida Zvirbliene, Kestutis Adamonis, Edita Kriukienė, Karolis Koncevicius, Juozas Gordevičius, Akhil Nair, Aiping Zhang, Sasha Ebrahimi, Gabriel Oh, Virginijus Siksnys, Limas Kupcinskas, Michael Brudno, Art Petronis


Importance of single cell resolution in tissue based epigenomic research

Tan A. Ince, Sandro Santagata, E. Andres Houseman and J. Chuck Harrell


Metabolic and Gene Regulatory Networks

Marian Walhout


12:00   Lunch


13:00 WORKSHOP III – Integrative Tools and Resources


ChromHMM: Chromatin state discovery and characterization

Jason Ernst, UCLA


The ENCODE encyclopedia and variant annotation using RegulomeDB and HaploReg

Jill Moore, University of Massachusetts Medical School


Juicebox: Visualization software for Hi-C data

Erez Lieberman-Aiden, Baylor College of Medicine





Chairperson: Marisa Bartolomei, University of Pennsylvania


Factors involved in maintaining the organization of the human inactive chromosome

Brian Chadwick, Emily Darrow, Andrew Seberg and Zhuo Sun


Allele-specific FISH reveals epigenetic mosaicism in an imprinting mutant

Paul Ginard, Jennifer Kalish, Connie Jiang, Arjun Raj and Marisa Bartolomei


The Xist lncRNA recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing

Chun-Kan Chen, Mario Blanco, Constanza Jackson, Erik Aznauryan, Christine Surka, Amy Chow and Mitchell Guttman


Unusual maintenance of X-chromosome Inactivation predisposes female lymphocytes for increased expression from the inactive X

Montserrat Anguera


The mammalian sperm epigenome

Oliver Rando


Relationship between Xi compaction and gene silencing

Zhuo Sun and Brian Chadwick


Diploid maps of chromatin interactions reveal allele-specific looping and the unique structural conformation of the inactive X chromosome

Miriam Huntley, Suhas Rao, Neva Durand, Elena Stamenova, Ivan Bochkov, James Robinson, Adrian Sanborn, Ido Machol, Arina Omer, Eric Lander and Erez Lieberman Aiden


Nucleoporin-mediated regulation of a genomic imprinted domain

Mellissa Mann, Saqib Sachani, Liyue Zhang, Carlee White and Lauren Landschoot


Deciphering mechanisms of monoallelic olfactory receptor expression

Stavros Lomvardas and Kevin Monahan



17:50   Dinner - 'Taste of Caribbean Islands'




Chairperson: Steven Jones, Canada's Michael Smith Genome Sciences Centre


Deep learning frameworks for regulatory genomics and epigenomics

Chuan Sheng Foo, Nicholas Sinnott-Armstrong, Avanti Shrikumar, Yonatan Israeli, William Greenleaf and Anshul Kundaje


Not Just a Black Box: Interpretable Deep Learning for Genomics and Epigenomics

Avanti Shrikumar and Anshul Kundaje


epilogos: A statistical approach for mining multi-tissue chromatin state annotations

Wouter Meuleman and Manolis Kellis


Global models of transcriptional regulation in 127 human cell types

Brian Cleary, Aviv Regev and Eric Lander


Modular Combinatorial Binding among Human Trans-acting Factors Reveals Direct and Indirect Factor Binding

Yuchun Guo and David Gifford


Integrating regulatory information away from equilibrium

Angela DePace, Clarissa Scholes, Javier Estrada, Felix Wong, Alvaro Sanchez and Jeremy Gunawardena


Deciphering the Role of Various Mechanisms in Transcription Factor-DNA Binding on a Protein Family-Specific Basis

Beibei Xin, Satyanarayan Rao, Tsu-Pei Chiu, Lin Yang and Remo Rohs


Principles of epigenome conservation

Ting Wang



21:30   Social / Poster Session II


Thursday, February 4


7:30     Breakfast




Chairperson: John Satterlee, NIDA and 4D Nucleome Program


The Human Genome's 3D Code

Erez Lieberman-Aiden  


Analysis of RNA binding specificities of proteins using RHT-SELEX

Estefania Mondragon, Arttu Jolma, Jussi Taipale and Louis J. Maher


Leveraging spectral encoding for high-dimensional biological multiplexing

H. Q. Nguyen, B. C. Baxter, C. A. Diaz-Botia, K. Brower, J. L. DeRisi, K.S. Thorn and P.M. Fordyce


A Novel Tool to Comprehensively Map Organization of RNA and DNA in Higher-Order Nuclear Structures

Sofia Quinodoz, Noah Ollikainen, Alexander Shishkin, Pamela Russell, Mason Lai, Amy Chow and Mitchell Guttman


Single-cell chromatin accessibility reveals principles of regulatory variation

Jason Buenrostro, Beijing Wu, Ulrike Litzenburger, Dave Ruff, Michael Gonzales, Michael Snyder, Chang Howard, Ravi Majeti, Ryan Corces and William Greenleaf


Single-cell transcriptional profiling of the mouse dentate gyrus

Hannah Hochgerner, Amit Zeisel, Peter Lönnerberg and Sten Linnarsson


Elucidating Chromatin Architecture by Combinatorial Co-ImmunePrecipitation (co-ChIP)

Ronen Sadeh, Roee Launer-Wachs, Hava Wandel, Ayelet Rahat and Nir Friedman


Epigenetic priming of enhancers predicts developmental competence during endodermal lineage differentiation

Feng Yue, Allen Wang, Yan Li, Maike Sander and Bing Ren


Molecular anatomy of the brain by single-cell RNA-seq

Sten Linnarsson



12:00   Lunch

Excursions (El Yunque, Rain Forest and Old San Juan)





Chairperson: John Rinn, Harvard University


Repeat Browser: a resource to wrangle sequencing data in a TEcentric manner

Deepak Purushotham, Daofeng Li and Ting Wang


Targets for Developmental Reprogramming in the Liver

Lindsey Treviño, Cristian Coarfa, Quan Wang, Charles Foulds, Bert O'Malley and Cheryl Walker


Mapping epigenomic pathways of resilience acquired in early life

Annie Ciernia, Dag Yasui, Akanksha Singh, Jessica Cope, Tallie Baram, Keith Dunaway and Janine Lasalle


Aberrant DNA hypomethylation following loss or amplification of mutant IDH1 in glioma

Tali Mazor, Llewellyn E. Jalbert, Aleksandr Pankov, Josie Hayes, Sarah J. Nelson, Andrew W. Bollen, Susan Chang, Arie Perry, Adam B. Olshen, Henrik Bengtsson, Joanna J. Phillips and Joseph Costello


The impact of metabolic adaptations on epigenetic profiles in taxane resistance in triple-negative breast cancer

Genevieve Deblois, Yunchi Kao, Alexandra Fedor, Benjamin Haibe-Kains and Mathieu Lupien


A comprehensive map and comparative analysis of cis-regulatory elements in the zebrafish genome

Hongbo Yang, Tingting Liu, Yanli Wang, Glenn Gerhard and Feng Yue


The roles of tRNA modifications in translation in Saccharomyces cerevisiae

Hsin-Jung Chou, Elisa Donnard and Oliver Rando


Epigenome changes of osteoblasts during zebrafish fin regeneration

Hyung Joo Lee, Stephen Johnson and Ting Wang


Limited sets of transcription factors are strongly active in specific cell types

Bei Wei, Inderpreet Sur, Arttu Jolma and Jussi Taipale



19:10   Dinner – Pig Roast


20:30   Beach Party



Friday, February 5


7:30     Breakfast




Chairperson: John Stamatoyannopulos, University of Washington


Epigenome Editing with CRISPR/Cas9 Technologies for Programming Cell Phenotype and Functional Epigenomics

Charles Gersbach, Pablo Perez-Pinera, Lauren Polstein, Ami Kabadi, Isaac Hilton, Pratiksha Thakore, Joshua Black, Tyler Klann, Gregory Crawford and Timothy Reddy


Epigenome Editing with CRISPR/Cas9 for Annotating Regulatory Element Function

Tyler Klann, Pratiksha Thakore, Isaac Hilton, Gregory Crawford, Timothy Reddy and Charles Gersbach


Conditional "Carpet Bombing" CRISPR/Cas9-based genome engineering in zebrafish

Hyo Sik Jang, Stephen L. Johnson and Ting Wang


Cas9-mediated in situ saturating mutagenesis for enhancer functional dissection

Daniel Bauer


Finding chromatin marks that matter using a CRISPR-based epigenetic screening method

Anna Köferle, Stefan H. Stricker, James Barrett, Catherine King and Stephan Beck


Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

Adrian Sanborn, Suhas Rao, Su-Chen Huang, Neva Durand, Miriam Huntley, Andrew Jewett, Ivan Bochkov, Dharmaraj Chinnappan, Ashok Cutkosky, Jian Li, Kristopher Geeting, Andreas Gnirke, Alexandre Melnikov, Doung McKenna, Elena Stamenova, Eric Lander and Erez Lieberman Aiden


CRISPR/Cas9 for complex transcription regulation and disease modeling

Stanley Qi


11:30   Lunch