Selected publications

Click here for a full updated list of my publications in PubMed.


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


Ing-Simmons E & Vaquerizas JM. Visualising three-dimensional genome organisation in two dimensions.
Development, 146: dev177162
Pubmed|Full text|Publisher

Kruse KDíaz NEnriquez-Gasca R, Gaume X, Torres-Padilla ME & Vaquerizas JM. Transposable elements drive reorganisation of 3D chromatin during early embryogenesis.
bioRxiv, doi:

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


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 K & Vaquerizas JM. 2017. Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription. Cell, 169:216–228
PubMed | Publisher | Full text | Preview

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. 2017. Cell–matrix signals specify bone endothelial cells during developmental osteogenesis. Nature Cell Biology, doi:10.1038/ncb3476
PubMed | Publisher


Vaquerizas JM & Torres-Padilla ME. 2016. Developmental biology: Panoramic views of the early epigenome. Nature, 537:494-496
PubMed | Publisher | Podcast

Kruse K*Hug CB*Hernández-Rodríguez B & Vaquerizas JM. 2016. TADtool: Visual Parameter Identification for TAD-calling Algorithms. Bioinformatics, doi:10.1093/bioinformatics/btw368
PubMed | Publisher | Software

Lecanda A, Nilges BS, Sharma P, Nedialkova DD, Schwarz J, Vaquerizas JM & Leidel SA. 2016. Dual randomization of oligonucleotides to reduce the bias in ribosome-profiling libraries. Methods, pii: S1046-2023(16)30220-1
PubMed | Publisher


Ishiuchi T, Enriquez-Gasca R, Mizutani E, Bošković A, Ziegler-Birling C, Rodriguez-Terrones D, Wakayama T, Vaquerizas JM & Torres-Padilla ME. 2015. 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


Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T & Taipale J. 2013. DNA-binding specificities of human transcription factors. Cell 152:327-39
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

Conrad T*, Cavalli FM*, Vaquerizas JM, Luscombe NM & Akhtar A. 2012. Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters. Science, 337:742-6.
PubMed | Publisher

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


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

* indicates joint first authors

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