User profiles for Geoff Fudenberg
Geoffrey FudenbergUSC Verified email at usc.edu Cited by 19848 |
Predicting 3D genome folding from DNA sequence with Akita
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…
locus-specific contact patterns. Cohesin and CTCF (CCCTC-binding factor) are key regulators…
Emerging evidence of chromosome folding by loop extrusion
Chromosome organization poses a remarkable physical problem with many biological
consequences: How can molecular interactions between proteins at the nanometer scale …
consequences: How can molecular interactions between proteins at the nanometer scale …
[PDF][PDF] Formation of chromosomal domains by loop extrusion
Topologically associating domains (TADs) are fundamental structural and functional building
blocks of human interphase chromosomes, yet the mechanisms of TAD formation remain …
blocks of human interphase chromosomes, yet the mechanisms of TAD formation remain …
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Extracting biologically meaningful information from chromosomal interactions obtained with
genome-wide chromosome conformation capture (3C) analyses requires the elimination of …
genome-wide chromosome conformation capture (3C) analyses requires the elimination of …
High-order chromatin architecture determines the landscape of chromosomal alterations in cancer
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 …
better understanding of the mutational mechanisms of genomic alterations in cancer and the …
Two independent modes of chromatin organization revealed by cohesin removal
Imaging and chromosome conformation capture studies have revealed several layers of
chromosome organization, including segregation into megabase-sized active and inactive …
chromosome organization, including segregation into megabase-sized active and inactive …
Organization of the mitotic chromosome
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 …
century their internal organization remains largely unsolved. We applied chromosome …
Super-resolution imaging reveals distinct chromatin folding for different epigenetic states
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 …
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
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 …
Rather, Hi-C and imaging reveal a high degree of spatial organization on various length …
Heterochromatin drives compartmentalization of inverted and conventional nuclei
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, …
and inactive heterochromatic regions of the genome 1 , 2 . In conventional nuclei, …