3D Genome Organization in Gene Regulation

Tuesday May 16

3:00pm – 3:45pm:

Sunduz Keles – “Statistical methods for profiling long range chromatin interactions from repetitive regions of the genome”

3:45pm – 4:00pm:

Rohan Paul, Jianlin Shao, Ferhat Ay – “Predicting topological domains from ChIP-seq data using pairwise feature extraction”

4:00pm – 4:15pm:

Jacob Schreiber, Maxwell Libbrecht, Jeffrey Bilmes and William Noble – “Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architecture”

4:15pm – 4:30pm:

Shilu Zhang, Deborah Chasman, Sara Knaack and Sushmita Roy – “In silico prediction of high-resolution Hi-C interaction matrices”

Wednesday, May 17

9:00am – 9:45am:

Sheng Zhong – “Systematic mapping of genomic-interaction loci for hundreds of non-coding RNAs.”

9:45am – 10:00am:

Michael Sauria, Teresa Luperchio, Karen Reddy and James Taylor – “Chromosome Conformation in Context”

10:00am – 10:30am:

Sushmita Roy – “Computational methods to study dynamics of long-range gene regulation”

10:30am – 11:00am: COFFEE BREAK

11:00am – 11:45am:

Michael Hoffman – “Novel inferences from Hi-C data with protein-coding gene data”

11:45am – 12:00pm:

Feng Yue, Yan Zhang, Lin An, Ming Hu and Jijun Tang – “HiCPlus: a deep convolutional neural network for Hi-C interaction matrix enhancement”

12:00pm – 3:15pm: LUNCH and MAIN CONFERENCE BREAK

3:15pm – 3:45pm:

Ferhat Ay – “In sickness and in health: Gene regulation via 3D chromatin organization”

3:45pm – 4:00pm:

Abhijit Chakraborty and Ferhat Ay – “A versatile pipeline to simulate Hi-C data with genomic rearrangements (AVeSim)”

4:00pm – 4:15pm:

Kimberly MacKay, Christopher Eskiw and Anthony Kusalik – “A Logical Approach to Modelling the Three-Dimensional Genome”

4:15pm – 4:35pm: COFFEE BREAK

4:35pm – 4:50pm:

Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Ross Hardison, William Noble, Feng Yue and Qunhua Li – “HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient”

4:50pm – 5:05pm:

Tim Kunz and Shaun Mahony – “Visualizing and exploring chromatin interactions using the self-organizing map”

5:05pm – 5:20pm:

Bohdan Khomtchouk, Derek Van Booven and Claes Wahlestedt – “geneXtendeR: R/Bioconductor package for functional annotation of histone modification ChIP-seq data in a 3D genome world”

5:20pm – 5:25pm: Closing Remarks