Posts Tagged ‘hic’

differential Hi-C analysis

July 10, 2018

https://genome.cshlp.org/content/28/3/412.long

It is kind of a similar idea about finding the differential chromatin interactions

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. – PubMed – NCBI

October 30, 2017

Comparative…3D chromosomal architecture identifies a novel fetal Hb reg. element http://GenesDev.cshlp.org/content/31/16/1704.abstract #Pseudogene shifts v. promotor

DNA’s secret weapon against knots and tangles

May 7, 2017

DNA’s secret weapon against knots & tangles http://www.Nature.com/news/dna-s-secret-weapon-against-knots-and-tangles-1.21838 Quick overview of recent models of loop extrusion w/ cohesin & CTCF

whole genome assembly from Hi-C data

April 2, 2017

De novo assembly of the A aegypti genome using #HiC, by @erezaterez et al http://science.ScienceMag.org/content/early/2017/03/22/science.aal3327.full Works on human too, w. promise for #SVs

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

Olga Dudchenko1,2,3,4,
Sanjit S. Batra1,2,3,*,
Arina D. Omer1,2,3,*,
Sarah K. Nyquist1,3,
Marie Hoeger1,3,
Neva C. Durand1,2,3,
Muhammad S. Shamim1,2,3,
Ido Machol1,2,3,
Eric S. Lander5,6,7,
Aviva Presser Aiden1,2,8,9,
Erez Lieberman Aiden1,2,3,4,5,†

Science 23 Mar 2017:
eaal3327
DOI: 10.1126/science.aal3327

on whole genome assembly from Hi-C reads. There is also some info on chromosomal rearrangement from Hi-C.

PETModule: a motif module based approach for enhancer target gene prediction : Scientific Reports

September 17, 2016

PETModule…enhancer-target-gene prediction
http://www.nature.com/articles/srep30043 Compares activity
correlations against a Hi-C/ChIA-PET gold std.

Spatial confinement is a major determinant of the folding landscape of human chromosomes

July 28, 2016

Gamze Gursoy, Yun Xu, Amy Kenter and Jie Liang. “Spatial confinement is a major determinant of folding landscape of human genome”, Nucleic Acids Research, 2014, 42 (13), 8223-8230

Confinement is a major determinant of the #folding…of chromosomes http://NAR.oxfordjournals.org/content/42/13/8223.full Simulations of self-avoiding chain growth

http://nar.oxfordjournals.org/content/42/13/8223.full

hi-C for 9 cell types

December 16, 2014

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of #Chromatin Looping
http://www.cell.com/cell/abstract/S0092-8674(14)01497-4 HiC data for 9 celltypes

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Suhas S.P. Rao
,Miriam H. Huntley
Neva C. Durand
Elena K. Stamenova
Ivan D. Bochkov
James T. Robinson
Adrian L. Sanborn
Ido Machol
Arina D. Omer
Eric S. Lander
Erez Lieberman Aiden

DOI: http://dx.doi.org/10.1016/j.cell.2014.11.021

http://www.cell.com/cell/abstract/S0092-8674(14)01497-4

hi-C for 9 cell types

December 14, 2014

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Suhas S.P. Rao
,Miriam H. Huntley
Neva C. Durand
Elena K. Stamenova
Ivan D. Bochkov
James T. Robinson
Adrian L. Sanborn
Ido Machol
Arina D. Omer
Eric S. Lander
Erez Lieberman Aiden

DOI: http://dx.doi.org/10.1016/j.cell.2014.11.021

http://www.cell.com/cell/abstract/S0092-8674(14)01497-4

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data

July 19, 2014

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data
http://nar.oxfordjournals.org/content/early/2014/01/24/nar.gkt1411.full