Posts Tagged ‘hic’

HiGlass

Sunday, April 7th, 2019

https://higlass.io/

Untangling the Formation of DNA Loops – Scientific American

Wednesday, April 3rd, 2019

SCIENTIFIC AMERICAN MARCH 2019

Untangling the Formation of DNA Loops

New discoveries on ancient loops in DNA offer clues into gene regulation

By Erez Lieberman Aiden

https://www.scientificamerican.com/article/untangling-the-formation-of-dna-loops/

differential Hi-C analysis

Wednesday, July 11th, 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

Tuesday, October 31st, 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

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

Saturday, September 17th, 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

Thursday, July 28th, 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

Tuesday, December 16th, 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

Sunday, December 14th, 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

Saturday, July 19th, 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