Geoffrey Fudenberg

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Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption
Sequence design for three-dimensional genome folding using Akita Semifreddo
The physical chemistry of interphase loop extrusion
The ChIP-FRiP pipeline quantifies co-binding and reveals how antibody background contributes to cohesin ChIP-seq patterns
The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control
CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals
Synergy between regulatory elements can render cohesin dispensable for distal enhancer function
Mechanistic Genome Folding at Scale through the Differentiable Loop Extrusion Model
Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
Ab-trapping-a peripheral staining artifact in antibody-based microscopy and genomics
Recipes and ingredients for deep learning models of 3D genome folding
Relating DNA sequence, organization, and function
Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2
Pairtools: from sequencing data to chromosome contacts
Cooltools: Enabling high-resolution Hi-C analysis in Python
Bioframe: operations on genomic intervals in Pandas dataframes
The motif composition of variable number tandem repeats impacts gene expression
Embryogenesis without CTCF in flies and vertebrates
Molecular basis of CTCF binding polarity in genome folding
Highly structured homolog pairing reflects functional organization of the Drosophila genome
Principles of meiotic chromosome assembly revealed in S. cerevisiae
The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos
Heterochromatin drives compartmentalization of inverted and conventional nuclei
Chromatin organization by an interplay of loop extrusion and compartmental segregation
Two independent modes of chromatin organization revealed by cohesin removal
SMC complexes differentially compact mitotic chromosomes according to genomic context
FISH-ing for captured contacts: towards reconciling FISH and 3C
Emerging Evidence of Chromosome Folding by Loop Extrusion
Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome
Formation of Chromosomal Domains by Loop Extrusion
History of chromosome rearrangements reflects the spatial organization of yeast chromosomes
Super-resolution imaging reveals distinct chromatin folding for different epigenetic states
Modeling chromosomes: Beyond pretty pictures
Genome-wide maps of nuclear lamina interactions in single human cells
Three-Dimensional Chromosome Organization in Eukaryotes
Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe
Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions
Organization of the mitotic chromosome
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Higher order chromatin structure: bridging physics and biology
High-order chromatin architecture determines the landscape of chromosomal alterations in cancer
Bayesian image recovery for dendritic structures under low signal-to-noise conditions