Geoffrey Fudenberg
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Explore the profile of Geoffrey Fudenberg including associated specialties, affiliations and a list of published articles.
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31
Citations
5009
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Recent Articles
21.
Schalbetter S, Goloborodko A, Fudenberg G, Belton J, Miles C, Yu M, et al.
Nat Cell Biol
. 2017 Aug;
19(9):1071-1080.
PMID: 28825700
Structural maintenance of chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply conserved SMC complexes, organize...
22.
Fudenberg G, Imakaev M
Nat Methods
. 2017 Jun;
14(7):673-678.
PMID: 28604723
Chromosome conformation capture (3C) and fluorescence in situ hybridization (FISH) are two widely used technologies that provide distinct readouts of 3D chromosome organization. While both technologies can assay locus-specific organization,...
23.
Hsieh T, Fudenberg G, Goloborodko A, Rando O
Nat Methods
. 2016 Nov;
13(12):1009-1011.
PMID: 27723753
We present Micro-C XL, an improved method for analysis of chromosome folding at mononucleosome resolution. Using long crosslinkers and isolation of insoluble chromatin, Micro-C XL increases signal-to-noise ratio. Micro-C XL...
24.
Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny L
Cell Rep
. 2016 May;
15(9):2038-49.
PMID: 27210764
Topologically associating domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes, yet the mechanisms of TAD formation remain unclear. Here, we propose that loop extrusion underlies...
25.
Khrameeva E, Fudenberg G, Gelfand M, Mirny L
J Bioinform Comput Biol
. 2016 Mar;
14(2):1641002.
PMID: 27021249
Three-dimensional (3D) organization of genomes affects critical cellular processes such as transcription, replication, and deoxyribo nucleic acid (DNA) repair. While previous studies have investigated the natural role, the 3D organization...
26.
Boettiger A, Bintu B, Moffitt J, Wang S, Beliveau B, Fudenberg G, et al.
Nature
. 2016 Jan;
529(7586):418-22.
PMID: 26760202
Metazoan genomes are spatially organized at multiple scales, from packaging of DNA around individual nucleosomes to segregation of whole chromosomes into distinct territories. At the intermediate scale of kilobases to...
27.
Kind J, Pagie L, de Vries S, Nahidiazar L, Dey S, Bienko M, et al.
Cell
. 2015 Sep;
163(1):134-47.
PMID: 26365489
Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large lamina-associated domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis...
28.
Imakaev M, Fudenberg G, Mirny L
FEBS Lett
. 2015 Sep;
589(20 Pt A):3031-6.
PMID: 26364723
Recently, Chromosome Conformation Capture (3C) based experiments have highlighted the importance of computational models for the study of chromosome organization. In this review, we propose that current computational models can...
29.
Doyle B, Fudenberg G, Imakaev M, Mirny L
PLoS Comput Biol
. 2014 Oct;
10(10):e1003867.
PMID: 25340767
The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters...
30.
Mizuguchi T, Fudenberg G, Mehta S, Belton J, Taneja N, Folco H, et al.
Nature
. 2014 Oct;
516(7531):432-435.
PMID: 25307058
Eukaryotic genomes are folded into three-dimensional structures, such as self-associating topological domains, the borders of which are enriched in cohesin and CCCTC-binding factor (CTCF) required for long-range interactions. How local...