Publications & Preprints

List of publications also available via Google Scholar.

Rini Shah , Maxime MC Tortora , Nessim Louafi , Hadi Rahmaninejad , Karissa L Hansen , Erika C Anderson , Kenya Bonitto , David Wen , Luca Giorgetti , Geoffrey Fudenberg , Elphège P Nora . Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption.  2026.
Paulina N Smaruj , David R Kelley , Geoffrey Fudenberg . Sequence design for three-dimensional genome folding using Akita Semifreddo.  2026.
Maxime MC Tortora , Geoffrey Fudenberg . The physical chemistry of interphase loop extrusion.  2026.
Jodi Lee , Jingshing Wu , Maureen Pittman , Zoe L Grant , Shuzhen Kuang , Daniel Quiat , Sarah U Morton , Geoff Fudenberg , Michela Traglia , Kelly A Hayes , Ritu Kumar , Benoit G Bruneau , Katherine S Pollard , Pediatric Cardiac Genomics Consortium . Structural variants in human congenital heart disease disrupt distal genomic regulatory contacts of developmental genes.  2026.
Yao Xiao , Erika C Anderson , Hadi Rahmaninejad , Elphege Nora , Geoffrey Fudenberg . The ChIP-FRiP pipeline quantifies co-binding and reveals how antibody background contributes to cohesin ChIP-seq patterns.  2026.
Erika C Anderson , Hadi Rahmaninejad , Abrar Aljahani , Emily M Arnold , Annie S Adachi , Rini Shah , Karissa L Hansen , Ivana Cavka , Alistair N Boettiger , Geoffrey Fudenberg , Elphège P Nora . The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control.  2026.
Timothy C Foldes , Karissa Hansen , Maxim Imakaev , Henrik Dahl Pinholt , Nezar Alexander Abdennur , Geoffrey C Fudenberg , Irie Carel , Tayma Handal , Fernanda Vargas-Romero , Elphege Nora , Leonid Mirny . Cohesin bridging as a physical principle of enhancer-promoter communication.  2026.
Valmik Ranparia , Geoffrey Fudenberg , Mark Chaisson . CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals.  2026.
Karissa L Hansen , Annie S Adachi , Luca Braccioli , Smit Kadvani , Ryan M Boileau , Moreno Martinovic , Bozhena Pokorny , Rini Shah , Erika C Anderson , Kaite Zhang , Irie Carel , Kenya Bonitto , Robert Blelloch , Geoffrey Fudenberg , Elzo de Wit , Elphège P Nora . Synergy between regulatory elements can render cohesin dispensable for distal enhancer function.  2025.
Tina Subic , Ali Tuğrul Balcı , Kristina Perevoshchikova , Diego Borges-Rivera , Jieni Hu , Geoffrey Fudenberg , Jacqueline Dresch , Maria Chikina . Mechanistic Genome Folding at Scale through the Differentiable Loop Extrusion Model.  2025.
Evonne McArthur , David C Rinker , Yang Cheng , Qixuan Wang , Juan Wang , Erin N Gilbertson , Geoff Fudenberg , Maureen Pittman , Kathleen Keough , Feng Yue , Katherine S Pollard , John A Capra . Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence.  2025.
Hadi Rahmaninejad , Yao Xiao , Maxime MC Tortora , Geoffrey Fudenberg . Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy.  2025.
Konrad Chudzik , Yuko Sato , Xingchi Yan , Simon Ullrich , Watanya Trakarnphornsombat , Lothar Schermelleh , Geoffrey Fudenberg , Hiroshi Kimura , Michael I Robson , Irina Solovei . Ab-trapping-a peripheral staining artifact in antibody-based microscopy and genomics.  2025.
Paulina N Smaruj , Yao Xiao , Geoffrey Fudenberg . Recipes and ingredients for deep learning models of 3D genome folding.  2025.
Geoffrey Fudenberg , Vijay Ramani . Relating DNA sequence, organization, and function.  2025.
Paulina N Smaruj , Fahad Kamulegeya , David R Kelley , Geoffrey Fudenberg . Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2.  2025.
Open2C , Nezar Abdennur , Geoffrey Fudenberg , Ilya M Flyamer , Aleksandra A Galitsyna , Anton Goloborodko , Maxim Imakaev , Sergey V Venev . Pairtools: from sequencing data to chromosome contacts.  2024.
Open2C , Nezar Abdennur , Sameer Abraham , Geoffrey Fudenberg , Ilya M Flyamer , Aleksandra A Galitsyna , Anton Goloborodko , Maxim Imakaev , Betul A Oksuz , Sergey V Venev , Yao Xiao . Cooltools: Enabling high-resolution Hi-C analysis in Python.  2024.
Open2C , Nezar Abdennur , Geoffrey Fudenberg , Ilya M Flyamer , Aleksandra A Galitsyna , Anton Goloborodko , Maxim Imakaev , Sergey Venev . Bioframe: operations on genomic intervals in Pandas dataframes.  2024.
Tsung-Yu Lu , Paulina N Smaruj , Geoffrey Fudenberg , Nicholas Mancuso , Mark JP Chaisson . The motif composition of variable number tandem repeats impacts gene expression.  2023.
Geoffrey Fudenberg , Elphège P Nora . Embryogenesis without CTCF in flies and vertebrates.  2021.
Xiaofan Jin , Geoff Fudenberg , Katherine S. Pollard . Genome-wide variability in recombination activity is associated with meiotic chromatin organization.  2021.
Geoff Fudenberg , David R. Kelley , Katherine S. Pollard . Predicting 3D genome folding from DNA sequence with Akita.  2020.
Elphège P. Nora , Laura Caccianini , Geoffrey Fudenberg , Kevin So , Vasumathi Kameswaran , Abigail Nagle , Alec Uebersohn , Bassam Hajj , Agnès Le Saux , Antoine Coulon , Leonid A. Mirny , Katherine S. Pollard , Maxime Dahan , Benoit G. Bruneau . Molecular basis of CTCF binding polarity in genome folding.  2020.
Jelena Erceg , Jumana AlHaj Abed , Anton Goloborodko , Bryan R. Lajoie , Geoffrey Fudenberg , Nezar Abdennur , Maxim Imakaev , Ruth B. McCole , Son C. Nguyen , Wren Saylor , Eric F. Joyce , T. Niroshini Senaratne , Mohammed A. Hannan , Guy Nir , Job Dekker , Leonid A. Mirny , C.-ting Wu . The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.  2019.
Stephanie A. Schalbetter , Geoffrey Fudenberg , Jonathan Baxter , Katherine S. Pollard , Matthew J. Neale . Principles of meiotic chromosome assembly revealed in S. cerevisiae.  2019.
Jumana AlHaj Abed , Jelena Erceg , Anton Goloborodko , Son C. Nguyen , Ruth B. McCole , Wren Saylor , Geoffrey Fudenberg , Bryan R. Lajoie , Job Dekker , Leonid A. Mirny , C.-ting Wu . Highly structured homolog pairing reflects functional organization of the Drosophila genome.  2019.
Martin Falk , Yana Feodorova , Natalia Naumova , Maxim Imakaev , Bryan R. Lajoie , Heinrich Leonhardt , Boris Joffe , Job Dekker , Geoffrey Fudenberg , Irina Solovei , Leonid A. Mirny . Heterochromatin drives compartmentalization of inverted and conventional nuclei.  2019.
Geoff Fudenberg , Katherine S. Pollard . Chromatin features constrain structural variation across evolutionary timescales.  2019.
Johannes Nuebler , Geoffrey Fudenberg , Maxim Imakaev , Nezar Abdennur , Leonid A. Mirny . Chromatin organization by an interplay of loop extrusion and compartmental segregation.  2018.
Wibke Schwarzer , Nezar Abdennur , Anton Goloborodko , Aleksandra Pekowska , Geoffrey Fudenberg , Yann Loe-Mie , Nuno A. Fonseca , Wolfgang Huber , Christian H Haering , Leonid Mirny , Francois Spitz . Two independent modes of chromatin organization revealed by cohesin removal.  2017.
Stephanie Andrea Schalbetter , Anton Goloborodko , Geoffrey Fudenberg , Jon-Matthew Belton , Catrina Miles , Miao Yu , Job Dekker , Leonid Mirny , Jonathan Baxter . SMC complexes differentially compact mitotic chromosomes according to genomic context.  2017.
Geoffrey Fudenberg , Maxim Imakaev . FISH-ing for captured contacts: towards reconciling FISH and 3C.  2017.
Geoffrey Fudenberg , Nezar Abdennur , Maxim Imakaev , Anton Goloborodko , Leonid A. Mirny . Emerging Evidence of Chromosome Folding by Loop Extrusion.  2017.
Tsung-Han S. Hsieh , Geoffrey Fudenberg , Anton Goloborodko , Oliver J. Rando . Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome.  2016.
Geoffrey Fudenberg , Maxim Imakaev , Carolyn Lu , Anton Goloborodko , Nezar Abdennur , Leonid A. Mirny . Formation of Chromosomal Domains by Loop Extrusion.  2016.
Ekaterina E Khrameeva , Geoffrey Fudenberg , Mikhail S Gelfand , Leonid A Mirny . History of chromosome rearrangements reflects the spatial organization of yeast chromosomes.  2016.
Alistair N. Boettiger , Bogdan Bintu , Jeffrey R. Moffitt , Siyuan Wang , Brian J. Beliveau , Geoffrey Fudenberg , Maxim Imakaev , Leonid A. Mirny , Chao-ting Wu , Xiaowei Zhuang . Super-resolution imaging reveals distinct chromatin folding for different epigenetic states.  2016.
Maxim V. Imakaev , Geoffrey Fudenberg , Leonid A. Mirny . Modeling chromosomes: Beyond pretty pictures.  2015.
Jop Kind , Ludo Pagie , Sandra S. de Vries , Leila Nahidiazar , Siddharth S. Dey , Magda Bienko , Ye Zhan , Bryan Lajoie , Carolyn A. de Graaf , Mario Amendola , Geoffrey Fudenberg , Maxim Imakaev , Leonid A. Mirny , Kees Jalink , Job Dekker , Alexander van Oudenaarden , Bas van Steensel . Genome-wide maps of nuclear lamina interactions in single human cells.  2015.
Geoffrey Fudenberg . Three-Dimensional Chromosome Organization in Eukaryotes.  2015.
Takeshi Mizuguchi , Geoffrey Fudenberg , Sameet Mehta , Jon-Matthew Belton , Nitika Taneja , Hernan Diego Folco , Peter FitzGerald , Job Dekker , Leonid Mirny , Jemima Barrowman , Shiv I. S. Grewal . Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe.  2014.
Boryana Doyle , Geoffrey Fudenberg , Maxim Imakaev , Leonid A. Mirny . Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions.  2014.
Natalia Naumova , Maxim Imakaev , Geoffrey Fudenberg , Ye Zhan , Bryan R. Lajoie , Leonid A. Mirny , Job Dekker . Organization of the mitotic chromosome.  2013.
Geoff Fudenberg , Jon-Matthew Belton , Anton Goloborodko , Maxim Imakaev , Job Dekker , Leonid Mirny . Polymer models of yeast S. cerevisiae genome organization.  2013.
Maxim Imakaev , Geoffrey Fudenberg , Rachel Patton McCord , Natalia Naumova , Anton Goloborodko , Bryan R. Lajoie , Job Dekker , Leonid A. Mirny . Iterative correction of Hi-C data reveals hallmarks of chromosome organization.  2012.
Geoffrey Fudenberg , Leonid A. Mirny . Higher order chromatin structure: bridging physics and biology.  2012.
Geoff Fudenberg , Gad Getz , Matthew Meyerson , Leonid A. Mirny . High order chromatin architecture shapes the landscape of chromosomal alterations in cancer.  2011.
Geoffrey Fudenberg , Gad Getz , Matthew Meyerson , Leonid Mirny . High-order chromatin architecture determines the landscape of chromosomal alterations in cancer.  2011.
Geoffrey Fudenberg , Liam Paninski . Bayesian image recovery for dendritic structures under low signal-to-noise conditions.  2009.
Kirill I Bolotin , KJ Sikes , Zhifang Jiang , M Klima , G Fudenberg , James Hone , Phaly Kim , Horst L Stormer . Ultrahigh electron mobility in suspended graphene.  2008.
Horst Stormer , Kirill Bolotin , Martin Klima , Kenneth Sikes , Geoff Fudenberg , James Hone , Philip Kim . Fabrication of gated suspended graphene devices.  2008.