Posts Tagged ‘hic’
HiGlass
April 6, 2019Untangling the Formation of DNA Loops – Scientific American
April 3, 2019SCIENTIFIC 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
July 10, 2018https://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, 2017Comparative…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, 2017DNA’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, 2017De 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, 2016PETModule…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, 2016Gamze 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
hi-C for 9 cell types
December 16, 2014A 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, 2014A 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
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