Publications

List of publications also available via Google Scholar.

Nezar Abdennur , Sameer Abraham , Geoff Fudenberg , Ilya M Flyamer , Aleksandra A Galitsyna , Anton Goloborodko , Maxim Imakaev , Betul A Oksuz , Sergey V Venev , others . Cooltools: enabling high-resolution Hi-C analysis in Python.  2022.
Open2C , Nezar Abdennur , Geoffrey Fudenberg , Ilya Flyamer , Aleksandra A. Galitsyna , Anton Goloborodko , Maxim Imakaev , Sergey V. Venev . Bioframe: Operations on Genomic Intervals in Pandas Dataframes.  2022.
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.
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.
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 textitS. 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.
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.