3D Genomics: Computational approaches for analyzing the role of 3D chromatin organization in gene regulation

Intelligent Systems for Molecular Biology (ISMB), 2018

July 7, 2018 -- Chicago, IL

Session Topics:


Long-range gene regulatory interactions are defined as interactions between a region of regulatory DNA sequence and a target gene that can be hundreds of kilobases away. Such interactions are emerging as important determinants of cell type specific expression and the effect of regulatory sequence variants on complex phenotypes including those associated with diseases. The field of regulatory genomics has recently witnessed significantly increased interest in the three-dimensional structure of DNA in the nucleus, catalyzed by the availability of chromosome conformation capture (3C) data sets that characterize the 3D organization of chromatin at a genome-wide scale. This organization, also referred to as the 3D nucleome, is not only important for packing the genome into the nucleus, but it also has significant impact on how the genome functions. With the emergence of these new data types, there is an increasingly growing demand for computational tools that can systematically analyze these data. These tools range from data processing issues (e.g. mapping and normalization) to data analysis issues, such as predicting chromosomal organizational units (e.g. TADs), identifying significant interactions between regulatory elements (e.g. enhancer-promoter), examining the interplay of transcription factors, architectural proteins and chromatin states in establishing these interactions, and examining how these interactions are impacted by sequence variants.

Call for contributed talks

We are inviting you to submit abstracts for short talks (15 mins) for our 3DGenome session. Please use this link and select the 3DGenome Special session to submit abstracts by April 27th. Looking forward to hearing about your latest work in 3D/4D Nucleome and relevant topics.

Invited Speakers

Name Title Affiliation
William Noble Prof. of Genome Sciences & Computer Science University of Washington (Keynote)
Mathieu Blanchette Prof. of Computer Science McGill University
Jian Ma Associate Prof. of Computational Biology and Machine Learning Carnegie Mellon University
Feng Yue Assistant Prof. Biochemistry and Molecular Biology Penn State
Geoffrey Fudenberg Postdoctoral Scholar UC San Francisco
Ferhat Ay Assistant Prof. of Computational Biology La Jolla Institute & UC San Diego (Organizer)
Sushmita Roy Assistant Prof. of Biostatistics and Medical Informatics University of Wisconsin - Madison (Organizer)


10:15 am - 10:20 am Session Overview and Introductions
10:20 am - 11:00 am Impact of structural variants on 3D genome structure in cancer cells
Feng Yue
11:00 am - 11:10 am Identification of locus-specific changes in chromosome conformation between cell types reveals enrichment of enhancers
Lila Rieber and Shaun Mahony
11:10 am - 11:20 am Identification of differential TADs across conditions and cell lines
Tao Yang, Belinda Giardine, Ross Hardison, and Qunhua Li
11:20 am - 11:30 am Unlocking the TAD: Chromatin folding with CHROMATIX
Alan Perez-Rathke and Jie Liang
11:30 am - 11:40 am SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS
Serhan Yılmaz, Oznur Tastan, and A. Ercument Cicek
11:40 am - 11:50 am A graph-regularized non-negative matrix factorization method to discover organizational units of chromosomes
Da-Inn Lee and Sushmita Roy
11:50 am - 12:00 pm TreeHiC: Hierarchical testing for differential chromatin interaction analysis
Duy Nguyen, Ye Zheng, and Sunduz Keles
12:00 pm - 12:40 pm Continuous-trait probabilistic model for comparing nuclear genome organization of multiple species
Jian Ma
2:00 pm - 2:40 pm High-resolution analysis of chromatin conformation capture data
Mathieu Blanchette
2:40 pm - 2:45 pm FIND: difFerential chromatin INteractions Detection using a spatial Poisson process
Mohamed Nadhir Djekidel, Yang Chen, and Michael Q Zhang
2:45 pm - 2:50 pm Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin
Asa Thibodeau, Eladio Marquez, Dong-Guk Shin, Martha Paola Vera-Licona, and Duygu Ucar
2:50 pm - 2:55 pm HiCAGE: an R package for large-scale annotation and visualization of 3C-based genomic data
Michael Workman, Tiago Silva, Simon Coetzee, and Dennis Hazelett
2:55 pm - 3:00 pm CompartmentExplorer: an accurate method for genomic compartments prediction from 3D genome data
Haitham Ashoor, Jiahui Wang, Xiaowen Chen, and Sheng Li
3:00 pm - 3:10 pm FitHiChIP: Statistical analysis of high-resolution HiChIP and PLAC-seq data
Sourya Bhattacharyya, Pandurangan Vijayanand, and Ferhat Ay
3:10 pm - 3:20 pm Conserved CTCF binding sites act as allosteric hotspots: A computational knock-out study using nC-SAC model
Gamze Gursoy, Arianna Girardi, and Jie Liang
3:20 pm - 4:00 pm Modeling and predicting the 3D genome
William Noble
4:40 pm - 5:20 pm Connections between the structure and function of 3D genome folding
Geoffrey Fudenberg
5:20 pm - 5:30 pm Nuclear topology modulates the mutational landscapes of cancer genomes
Kyle Smith, Lin Liu, Franziska Michor, Shridar Ganesan, and Subhajyoti De
5:30 pm - 5:40 pm Computational Detecting Cancer-associated Disorders of Chromatin Interactions from ChIA-PET data
Yong Chen, Kelly Daescu, and Michael Zhang
5:40 pm - 5:45 pm In silico modelling of longevity in Drosophila – a network approach
Bethany Hall, Nadia Chuzhanova, Jonathan Crofts, and Yvonne Barnett
5:45 pm - 5:50 pm Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings
Natalie Sauerwald, She Zhang, Carl Kingsford, and Ivet Bahar
5:50 pm - 5:55 pm mHi-C: robust leveraging of multi-mapping reads in Hi-C analysis
Ye Zheng, Ferhat Ay, and Sunduz Keles
5:55 pm - 6:00 pm In silico prediction of high resolution chromosomal contact counts in multiple cell lines
Shilu Zhang, Brittany Baur, Deborah Chasman, Sara Knaack, and Sushmita Roy


Please direct questions to Ferhat Ay (ferhatay@lji.org).