Publications

Selected Publications

(full list of publications available here: Google ScholarPubMed)

2020

 

Ing-Simmons E, Vaid R, Mannervik M & Vaquerizas JM. Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning.
bioRxiv, doi: https://doi.org/10.1101/2020.07.07.186791
bioRxiv

 

Burton A, Brochard V, Galan C, Ruiz-Morales ER, Rovira Q, Rodriguez-Terrones D, Kruse K, Le Gras S, Udayakumar VS, Chin HG, Eid A, Liu X, Wang C, Gao S, Pradhan S, Vaquerizas JM, Beaujean N, Jenuwein T & Torres-Padilla ME. Heterochromatin Establishment During Early Mammalian Development Is Regulated by Pericentromeric RNA and Characterized by Non-Repressive H3K9me3.
Nature Cell Biology, 22(7):767-778
Pubmed|Full text

 

Rhodes JDP*, Feldmann A*, Hernández-Rodríguez B*, Díaz N*, Brown JM, Fursova NA, Blackledge NP, Prathapan P, Dobrinic P, Huseyin M, Szczurek A, Kruse K, Nasmyth KA, Buckle VJ, Vaquerizas JM# & Klose RJ#. Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells.
Cell Reports, 30(3):820-835.e10
Pubmed|Full text

 

Kruse K, Hug CB, & Vaquerizas JM. FAN-C: A Feature-rich Framework for the Analysis and Visualisation of C data.
bioRxiv, doi: https://doi.org/10.1101/2020.02.03.932517
bioRxiv

2019

 

Ing-Simmons E & Vaquerizas JM. Visualising three-dimensional genome organisation in two dimensions.
Development,
Pubmed|Full text|Publisher

 

Kruse K, Díaz N, Enriquez-Gasca R, Gaume X, Torres-Padilla ME & Vaquerizas JM. Transposable elements drive reorganisation of 3D chromatin during early embryogenesis.
bioRxiv, doi: https://doi.org/10.1101/523712
bioRxiv

 

Luxán G, Stewen J, Díaz N, Kato K, Maney SK, Aravamudhan A, Berkenfeld F, Nagelmann N, Drexler HC, Zeuschner D, Faber C, Schillers H, Hermann S, Wiseman J, Vaquerizas JM, Pitulescu ME & Adams RH. Endothelial EphB4 maintains vascular integrity and transport function in adult heart.
eLife, 8. pii: e45863
Pubmed|Full text

2018

 

Díaz N*, Kruse K*, Erdmann T, Staiger AM, Ott G, Lenz G & Vaquerizas JM. Chromatin conformation analysis of primary patient tissue using a low input Hi-C method.
Nature Communications, 9: 4938
Pubmed|Full text|bioRxiv

 

Hug BC & Vaquerizas JM. The Birth of the 3D Genome during Early Embryonic Development.
Trends in Genetics, 34:903-914
PubMed|Full text

 

Hug BC & Vaquerizas JM. Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos.
JoVE, DOI: https://doi.org/10.3791/57001
PubMed|Full text

 

Rodriguez-Terrones D, Gaume X, Ishiuchi T, Weiss A, Kopp A, Kruse K, Penning A, Vaquerizas JM, Brino L & Torres-Padilla ME. A molecular roadmap for the emergence of early-embryonic-like cells in culture.
Nature Genetics, 50:106-119
PubMed|Publisher

2017

 

Hug CB, Grimaldi AG, Kruse KVaquerizas JM. Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription.
Cell, 169:216–228
PubMed|Full text|Preview|Research highlight

 

Jeong HW, Hernández-Rodríguez B, Kim J, Kim KP, Enriquez-Gasca R, Yoon J, Adams S, Schöler HR, Vaquerizas JM# & Adams RH#. Transcriptional regulation of endothelial cell behavior during sprouting angiogenesis.
Nature Communications, 8:726
PubMed|Publisher

 

Langen UH, Pitulescu ME, Kim JM, Enriquez-Gasca R, Sivaraj KK, Kusumbe AP, Singh A, Di Russo J, Bixel MG, Zhou B, Sorokin L, Vaquerizas JM & Adams RH. Cell–matrix signals specify bone endothelial cells during developmental osteogenesis.
Nature Cell Biology, 19:189-201
PubMed|Publisher

2016

 

Vaquerizas JM & Torres-Padilla ME. Developmental biology: Panoramic views of the early epigenome.
Nature, 537:494-496
PubMed|Publisher|Podcast

 

Kruse* K, Hug* CB, Hernández-Rodríguez BVaquerizas JM. TADtool: Visual Parameter Identification for TAD-calling Algorithms.
Bioinformatics, doi:10.1093/bioinformatics/btw368
PubMed|Publisher|Software

2015

 

Ishiuchi T, Enriquez-Gasca R, Mizutani E, Bošković A, Ziegler-Birling C, Rodriguez-Terrones D, Wakayama T, Vaquerizas JM & Torres-Padilla ME. Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly.
Nature Structural Molecular Biology, 22:662-671
PubMed|Publisher|News&Views|Media coverage|Media coverage

2012-2008

 

Lam KC*, Mühlpfordt F*, Vaquerizas JM*, Raja SJ, Holz H, Luscombe NM, Manke T & Akhtar A. 2012. The NSL Complex Regulates Housekeeping Genes in Drosophila.
PLoS Genetics, 8:e1002736
PubMed|Publisher

 

The ENCODE Project Consortium (including Vaquerizas JM). 2012. An Integrated Encyclopedia of DNA Elements in the Human Genome.
Nature, 489:57-74
PubMed|Publisher|Journal cover|Media coverage|Media coverage|Website

 

Vaquerizas JM*, Suyama R*, Kind J*, Miura K, Luscombe NM & Akhtar A. 2010. Nuclear pore proteins Nup153 and Megator define transcriptionally active regions in the Drosophila genome.
PLoS Genetics, 6:e1000846
PubMed|Publisher|Perspective|Epigenetics 2010

 

Vaquerizas JM, Kummerfeld SK, Teichmann SA & Luscombe NM. 2009. A census of human transcription factors: function, expression and evolution.
Nature Reviews Genetics, 10:252-63
PubMed|Publisher|Journal cover

 

Kind J*, Vaquerizas JM*, Gebhardt P, Gentzel M, Luscombe NM, Bertone P & Akhtar A. 2008. Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila.
Cell, 133:813-828
PubMed|Publisher|Perspective|NRG Research Highlight|Media coverage|Media coverage

#: co-corresponding authors; *: joint first authors

Click here for Juanma’s full list of publications.