Selected Publications

(full list of publications available here: Google ScholarPubMed)


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:


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.
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


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

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


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

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


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


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

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.