Selected Publications

(Full list of publications: Google ScholarPubMed)



Chang NC*, Rovira Q*, Wells J*, Feschotte C# & Vaquerizas JM#. Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
Genome Research, 32(7):1408-1423
Pubmed|Journal OA|bioRxiv


Ing-Simmons E, Rigau M, & Vaquerizas JM. Emerging mechanisms and dynamics of three-dimensional genome organisation at zygotic genome activation
Current Opinion Cell Biology, 74:37-46
Pubmed|Journal OA



Ing-Simmons E, Vaid R, Bing XY, Levine M, Mannervik M & Vaquerizas JM. Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning
Nature Genetics, 53(4):487-499
Pubmed|Journal OA|Journal cover|News & Views


Chanoumidou K, Hernández-Rodríguez B, Windener F, Thomas C, Stehling M, Mozafari S, Albrecht S, Ottoboni L, Antel J, Kim KP, Velychko S, Cui QL, Xu YKT, Martino G, Winkler J, Schöler HR, Baron-Van Evercooren A, Boespflug-Tanguy O, Vaquerizas JM, Ehrlich M & Kuhlmann T. One-step Reprogramming of Human Fibroblasts into Oligodendrocyte-like Cells by SOX10, OLIG2, and NKX6.2
Stem Cell Reports, 16(4):771-783
Pubmed|Journal OA



Kruse K, Hug CB & Vaquerizas JM. FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
Genome Biology, 21(1):303. doi: 10.1186/s13059-020-02215-9
Pubmed|Journal full text|Software


Galan S*, Machnik N*, Kruse K, Díaz N, Marti-Renom MA & Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction
Nature Genetics, 52(11):1247-1255
Pubmed|Journal|Full text


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


Takayama N, Murison A, Takayanagi SI, Arlidge C, Zhou S, Garcia-Prat L, Chan-Seng-Yue M, Zandi S, Gan OI, Boutzen H, Kaufmann KB, Trotman-Grant A, Schoof E, Kron K, Díaz N, Lee JJY, Medina T, De Carvalho DD, Taylor MD, Vaquerizas JM, Xie SZ, Dick JE, Lupien M. The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization.
Cell Stem Cell, S1934-5909(20)30539-7 doi: 10.1016/j.stem.2020.11.001


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:



Ing-Simmons E & Vaquerizas JM. Visualising three-dimensional genome organisation in two dimensions.
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:


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 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.