User profiles for Geoff Fudenberg

Geoffrey Fudenberg

USC
Verified email at usc.edu
Cited by 19848

Predicting 3D genome folding from DNA sequence with Akita

G Fudenberg, DR Kelley, KS Pollard - Nature methods, 2020 - nature.com
In interphase, the human genome sequence folds in three dimensions into a rich variety of
locus-specific contact patterns. Cohesin and CTCF (CCCTC-binding factor) are key regulators…

Emerging evidence of chromosome folding by loop extrusion

G Fudenberg, N Abdennur, M Imakaev… - Cold Spring Harbor …, 2017 - symposium.cshlp.org
Chromosome organization poses a remarkable physical problem with many biological
consequences: How can molecular interactions between proteins at the nanometer scale …

[PDF][PDF] Formation of chromosomal domains by loop extrusion

G Fudenberg, M Imakaev, C Lu, A Goloborodko… - Cell reports, 2016 - cell.com
Topologically associating domains (TADs) are fundamental structural and functional building
blocks of human interphase chromosomes, yet the mechanisms of TAD formation remain …

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

M Imakaev, G Fudenberg, RP McCord, N Naumova… - Nature …, 2012 - nature.com
Extracting biologically meaningful information from chromosomal interactions obtained with
genome-wide chromosome conformation capture (3C) analyses requires the elimination of …

High-order chromatin architecture determines the landscape of chromosomal alterations in cancer

G Fudenberg, G Getz, M Meyerson, L Mirny - Nature Precedings, 2011 - nature.com
The rapid growth of cancer genome structural information provides an opportunity for a
better understanding of the mutational mechanisms of genomic alterations in cancer and the …

Two independent modes of chromatin organization revealed by cohesin removal

…, A Goloborodko, A Pekowska, G Fudenberg… - Nature, 2017 - nature.com
Imaging and chromosome conformation capture studies have revealed several layers of
chromosome organization, including segregation into megabase-sized active and inactive …

Organization of the mitotic chromosome

N Naumova, M Imakaev, G Fudenberg, Y Zhan… - Science, 2013 - science.org
Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a
century their internal organization remains largely unsolved. We applied chromosome …

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

…, B Bintu, JR Moffitt, S Wang, BJ Beliveau, G Fudenberg… - Nature, 2016 - nature.com
Metazoan genomes are spatially organized at multiple scales, from packaging of DNA around
individual nucleosomes to segregation of whole chromosomes into distinct territories 1 , 2 …

[PDF][PDF] Chromatin organization by an interplay of loop extrusion and compartmental segregation

J Nuebler, G Fudenberg, M Imakaev, N Abdennur… - Biophysical …, 2018 - cell.com
Eukaryotic chromatin, is far from being simply a randomly arranged polymer in the cell nucleus.
Rather, Hi-C and imaging reveal a high degree of spatial organization on various length …

Heterochromatin drives compartmentalization of inverted and conventional nuclei

…, H Leonhardt, B Joffe, J Dekker, G Fudenberg… - Nature, 2019 - nature.com
The nucleus of mammalian cells displays a distinct spatial segregation of active euchromatic
and inactive heterochromatic regions of the genome 1 , 2 . In conventional nuclei, …