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Scientific Publications

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/ Nature

An integrated view of the structure and function of the human 4D nucleome

  • Job Dekker
  • Betul Akgol Oksuz
  • Yang Zhang
  • Ye Wang
  • Miriam K. Minsk
  • Shuzhen Kuang
  • Liyan Yang
  • Johan H. Gibcus
  • Nils Krietenstein
  • Oliver J. Rando
  • Jie Xu
  • Derek H. Janssens
  • Steven Henikoff
  • Alexander Kukalev
  • Andréa Willemin
  • Warren Winick-Ng
  • Rieke Kempfer
  • Ana Pombo
  • Miao Yu
  • Pradeep Kumar
  • Liguo Zhang
  • Andrew S. Belmont
  • Takayo Sasaki
  • Tom van Schaik
  • Laura Brueckner
  • Daan Peric-Hupkes
  • Bas van Steensel
  • Ping Wang
  • Haoxi Chai
  • Minji Kim
  • Yijun Ruan
  • Ran Zhang
  • Sofia A. Quinodoz
  • Prashant Bhat
  • Mitchell Guttman
  • Wenxin Zhao
  • Shu Chien
  • Yuan Liu
  • Sergey V. Venev
  • Dariusz Plewczynski
  • Ibai Irastorza Azcarate
  • Dominik Szabó
  • Christoph J. Thieme
  • Teresa Szczepińska
  • Mateusz Chiliński
  • Kaustav Sengupta
  • Mattia Conte
  • Andrea Esposito
  • Alex Abraham
  • Ruochi Zhang
  • Yuchuan Wang
  • Xingzhao Wen
  • Qiuyang Wu
  • Yang Yang
  • Jie Liu
  • Lorenzo Boninsegna
  • Asli Yildirim
  • Yuxiang Zhan
  • Andrea Maria Chiariello
  • Simona Bianco
  • Lindsay Lee
  • Ming Hu
  • Yun Li
  • R. Jordan Barnett
  • Ashley L. Cook
  • Daniel J. Emerson
  • Claire Marchal
  • Peiyao Zhao
  • Peter J. Park
  • Burak H. Alver
  • Andrew J. Schroeder
  • Rahi Navelkar
  • Clara Bakker
  • William Ronchetti
  • Shannon Ehmsen
  • Alexander D. Veit
  • Nils Gehlenborg
  • Ting Wang
  • Daofeng Li
  • Xiaotao Wang
  • Mario Nicodemi
  • Bing Ren
  • Sheng Zhong
  • Jennifer E. Phillips-Cremins
  • David M. Gilbert
  • Katherine S. Pollard
  • Frank Alber
  • Jian Ma
  • William S. Noble
  • Feng Yue
/ bioRxiv

Specialised super-enhancer networks in stem cells and neurons

  • Izabela Harabula
  • Liam Speakman
  • Francesco Musella
  • Luca Forillo
  • Luna Zea-Redondo
  • Alexander Kukalev
  • Robert A. Beagrie
  • Kelly J. Morris
  • Lucas Fernandes
  • Ibai Irastorza-Azcarate
  • Ana M. Fernandes
  • Silvia Carvalho
  • Dominik Szabó
  • Carmelo Ferrai
  • Mario Nicodemi
  • Lonnie Welch
  • Ana Pombo
/ Proceedings of the National Academy of Sciences of the United States of America

Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues

  • Johannes Stein
  • Maria Ericsson
  • Michel Nofal
  • Lorenzo Magni
  • Sarah Aufmkolk
  • Ryan B. McMillan
  • Laura Breimann
  • Conor P. Herlihy
  • S. Dean Lee
  • Andréa Willemin
  • Jens Wohlmann
  • Laura Arguedas-Jimenez
  • Peng Yin
  • Ana Pombo
  • George M. Church
  • Chao-Ting Wu
/ Molecular Systems Biology

Extensive folding variability between homologous chromosomes in mammalian cells

  • I. Irastorza-Azcarate
  • A. Kukalev
  • R. Kempfer
  • C.J. Thieme
  • G. Mastrobuoni
  • J. Markowski
  • G. Loof
  • T.M. Sparks
  • E. Brookes
  • K.N. Natarajan
  • S. Sauer
  • A.G. Fisher
  • M. Nicodemi
  • B. Ren
  • R.F. Schwarz
  • S. Kempa
  • A. Pombo
/ bioRxiv

Oncogene silencing via ecDNA micronucleation

  • L. Brückner
  • R. Xu
  • J. Tang
  • A. Herrmann
  • I.T.L. Wong
  • S. Zhang
  • F. Tu
  • M. Pilon
  • A. Kukalev
  • K. Pardon
  • O. Sidorova
  • J. Atta
  • Q. Yu
  • D. Pradella
  • M. Ilić
  • M. Novais-Cruz
  • S. Kaltenbach
  • D. Treue
  • M. Giurgiu
  • S. Herzog
  • A.S. Hollinger
  • M. Fernandez
  • F. Becker
  • V.R. Louma
  • R. Schmargon
  • J. Dörr
  • D. Gamlin
  • A. Lehmann
  • D. Gürgen
  • M. Richter
  • F. Dubois
  • F. Simeoni
  • B.R. Pennycook
  • A. Hamilton
  • R.K. Lindemann
  • M. Fischer
  • V. Bafna
  • G. Wahl
  • R.P. Koche
  • H.Y. Chang
  • S. Papathanasiou
  • R. Medema
  • B. Spanjaard
  • A. Ventura
  • A. Pombo
  • W. Huang
  • B. Werner
  • P.S. Mischel
  • A.G. Henssen
/ bioRxiv

A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons

  • D. Szabó
  • V. Franke
  • S. Bianco
  • M.Y. Batiuk
  • E.J. Paul
  • A. Kukalev
  • U.G. Pfisterer
  • I. Irastorza-Azcarate
  • A.M. Chiariello
  • S. Demharter
  • L. Zea-Redondo
  • J.P. Lopez-Atalaya
  • M. Nicodemi
  • A. Akalin
  • K. Khodosevich
  • M.A. Ungless
  • W. Winick-Ng
  • A. Pombo
/ Biology Open

SRRM2 splicing factor modulates cell fate in early development

  • S. Carvalho
  • L. Zea-Redondo
  • T.C.C. Tang
  • P. Stachel-Braum
  • D. Miller
  • P. Caldas
  • A. Kukalev
  • S. Diecke
  • S. Grosswendt
  • A.R. Grosso
  • A. Pombo
/ Molecular Cell

Epigenetic regulatory layers in the 3D nucleus

  • A. Willemin
  • D. Szabo
  • A. Pombo
/ Nature Methods

Genome architecture mapping detects transcriptionally active, multiway chromatin contacts

  • C.J. Thieme
  • A. Pombo
/ Nature Methods

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C

  • R.A. Beagrie
  • C.J. Thieme
  • C. Annunziatella
  • C. Baugher
  • Y. Zhang
  • M. Schueler
  • A. Kukalev
  • R. Kempfer
  • A.M. Chiariello
  • S. Bianco
  • Y. Li
  • T. Davis
  • A. Scialdone
  • L.R. Welch
  • M. Nicodemi
  • A. Pombo