Geoffrey Fudenberg
Overview
Explore the profile of Geoffrey Fudenberg including associated specialties, affiliations and a list of published articles.
Author names and details appear as published. Due to indexing inconsistencies, multiple individuals may share a name, and a single author may have variations. MedLuna displays this data as publicly available, without modification or verification
Snapshot
Snapshot
Articles
31
Citations
5009
Followers
0
Related Specialties
Related Specialties
Top 10 Co-Authors
Top 10 Co-Authors
Published In
Published In
Affiliations
Affiliations
Soon will be listed here.
Recent Articles
1.
Fudenberg G, Ramani V
Science
. 2025 Feb;
387(6734):580.
PMID: 39913601
Cross-species mosaic genomes provide insight into synthetic chromosome design.
2.
Smaruj P, Kamulegeya F, Kelley D, Fudenberg G
PLoS Comput Biol
. 2025 Feb;
21(2):e1012824.
PMID: 39903776
Interphase mammalian genomes are folded in 3D with complex locus-specific patterns that impact gene regulation. CTCF (CCCTC-binding factor) is a key architectural protein that binds specific DNA sites, halts cohesin-mediated...
3.
Smaruj P, Xiao Y, Fudenberg G
Curr Opin Genet Dev
. 2025 Jan;
91:102308.
PMID: 39862604
Three-dimensional genome folding plays roles in gene regulation and disease. In this review, we compare and contrast recent deep learning models for predicting genome contact maps. We survey preprocessing, architecture,...
4.
Rahmaninejad H, Xiao Y, Tortora M, Fudenberg G
bioRxiv
. 2024 Oct;
PMID: 39416077
In mammalian interphase cells, genomes are folded by cohesin loop extrusion limited by directional CTCF barriers. This interplay leads to the enrichment of cohesin at barriers, isolation between neighboring topologically...
5.
Tortora M, Fudenberg G
bioRxiv
. 2024 Sep;
PMID: 39229088
Loop extrusion constitutes a universal mechanism of genome organization, whereby structural maintenance of chromosomes (SMC) protein complexes load onto the chromatin fiber and generate DNA loops of increasingly-larger sizes until...
6.
Abdennur N, Fudenberg G, Flyamer I, Galitsyna A, Goloborodko A, Imakaev M, et al.
PLoS Comput Biol
. 2024 May;
20(5):e1012164.
PMID: 38809952
The field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive and heterogeneous 3C+ data require...
7.
Abdennur N, Abraham S, Fudenberg G, Flyamer I, Galitsyna A, Goloborodko A, et al.
PLoS Comput Biol
. 2024 May;
20(5):e1012067.
PMID: 38709825
Chromosome conformation capture (3C) technologies reveal the incredible complexity of genome organization. Maps of increasing size, depth, and resolution are now used to probe genome architecture across cell states, types,...
8.
Abdennur N, Fudenberg G, Flyamer I, Galitsyna A, Goloborodko A, Imakaev M, et al.
Bioinformatics
. 2024 Feb;
40(2).
PMID: 38402507
Motivation: Genomic intervals are one of the most prevalent data structures in computational genome biology, and used to represent features ranging from genes, to DNA binding sites, to disease variants....
9.
Lu T, Smaruj P, Fudenberg G, Mancuso N, Chaisson M
Genome Res
. 2023 Apr;
33(4):511-524.
PMID: 37037626
Understanding the impact of DNA variation on human traits is a fundamental question in human genetics. Variable number tandem repeats (VNTRs) make up ∼3% of the human genome but are...
10.
Abdennur N, Fudenberg G, Flyamer I, Galitsyna A, Goloborodko A, Imakaev M, et al.
bioRxiv
. 2023 Feb;
PMID: 36824968
The field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive and heterogeneous 3C+ data require...