Denis Duboule
Éditions Fayard

The complete list of publications can be found under:


Journal Articles

Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

H. Rekaik; L. Lopez-Delisle; A. Hintermann; B. Mascrez; C. Bochaton et al. 

Nature Genetics. 2023-06-15. DOI : 10.1038/s41588-023-01426-7.

Programming of Multicellular Patterning with Mechano-Chemically Microstructured Cell Niches

P. L. H. Newman; Q. Yip; P. Osteil; T. A. Anderson; J. Q. J. Sun et al. 

Advanced Science. 2023-03-30. DOI : 10.1002/advs.202204741.


Journal Articles

Context-dependent enhancer function revealed by targeted inter-TAD relocation

C. C. Bolt; L. Lopez-Delisle; A. Hintermann; B. Mascrez; A. Rauseo et al. 

Nature Communications. 2022-06-17. Vol. 13, num. 1, p. 3488. DOI : 10.1038/s41467-022-31241-3.

The (unusual) heuristic value of Hox gene clusters; a matter of time?

D. Duboule 

Developmental Biology. 2022-04-01. Vol. 484, p. 75-87. DOI : 10.1016/j.ydbio.2022.02.007.

Differential impact of TGF beta/SMAD signaling activity elicited by Activin A and Nodal on endoderm differentiation of epiblast stem cells

H. Knowles; N. Santucci; J. Studdert; H. N. Goh; K. Kaufman-Francis et al. 

Genesis. 2022-02-01.  p. e23466. DOI : 10.1002/dvg.23466.


Journal Articles

Transgenic Model Systems Have Revolutionized the Study of Disease

A. Mayran; C. C. Bolt 

Dna And Cell Biology. 2021-12-23. Vol. 41, num. 1, p. 49-52. DOI : 10.1089/dna.2021.0514.

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

A. R. Amandio; L. Beccari; L. Lopez-Delisle; B. Mascrez; J. Zakany et al. 

Genes & Development. 2021-11-01. Vol. 35, num. 21-22, p. 1490-1509. DOI : 10.1101/gad.348934.121.

Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations

C. C. Bolt; L. Lopez-Delisle; B. Mascrez; D. Duboule 

Nature Communications. 2021-08-18. Vol. 12, num. 1, p. 5013. DOI : 10.1038/s41467-021-25330-y.

Induction of a chromatin boundary in vivo upon insertion of a tad border

A. Willemin; L. Lopez-Delisle; C. C. Bolt; M-L. Gadolini; D. Duboule et al. 

Plos Genetics. 2021-07-01. Vol. 17, num. 7, p. e1009691. DOI : 10.1371/journal.pgen.1009691.

Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae

A. Allais-Bonnet; A. Hintermann; M-C. Deloche; R. Cornette; P. Bardou et al. 

Molecular Biology And Evolution. 2021-06-01. Vol. 38, num. 6, p. 2260-2272. DOI : 10.1093/molbev/msab021.


Journal Articles

Chromatin topology and the timing of enhancer function at the HoxD locus

E. Rodriguez-Carballo; L. Lopez-Delisle; A. Willemin; L. Beccari; S. Gitto et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2020-12-08. Vol. 117, num. 49, p. 31231-31241. DOI : 10.1073/pnas.2015083117.

pyGenomeTracks: reproducible plots for multivariate genomic datasets

L. Lopez-Delisle; L. Rabbani; J. Wolff; V. Bhardwaj; R. Backofen et al. 

Bioinformatics. 2020-08-03.  p. 1-2, btaa692. DOI : 10.1093/bioinformatics/btaa692.

A complex regulatory landscape involved in the development of mammalian external genitals

A. R. Amandio; L. Lopez-Delisle; C. C. Bolt; B. Mascrez; D. Duboule 

Elife. 2020-04-17. Vol. 9, p. e52962. DOI : 10.7554/eLife.52962.

Fryns type mesomelic dysplasia of the upper limbs caused by inverted duplications of the HOXD gene cluster

C. Le Caignec; O. Pichon; A. Briand; B. de Courtivron; C. Bonnard et al. 

European Journal Of Human Genetics. 2020-03-01. Vol. 28, num. 3, p. 324-332. DOI : 10.1038/s41431-019-0522-2.

Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs

F. Darbellay; A. Necsulea 

Molecular Biology And Evolution. 2020-01-01. Vol. 37, num. 1, p. 240-259. DOI : 10.1093/molbev/msz212.


Journal Articles

Commentary on paper by Leroy C. Stevens (1960)

D. Duboule 

Developmental Biology. 2019-10-01. Vol. 454, num. 1, p. 1-14. DOI : 10.1016/j.ydbio.2019.07.016.

Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes

E. Rodriguez-Carballo; L. Lopez-Delisle; N. Yakushiji-Kaminatsui; A. Ullate-Agote; D. Duboule 

BMC Biology. 2019-07-12. Vol. 17, p. 55. DOI : 10.1186/s12915-019-0677-x.

Constrained Transcriptional Polarity In The Organization Of Mammalian Hox Gene Clusters

F. Darbellay; C. Bochaton; L. Lopez-Delisle; B. Mascrez; P. Tschopp et al. 

bioRxiv. 2019-03-14. DOI : 10.1101/572875.

An extended regulatory landscape drives Tbx18 activity in a variety of prostate-associated cell lineages

S. Negi; C. C. Bolt; H. Zhang; L. Stubbs 

Developmental Biology. 2019-02-15. Vol. 446, num. 2, p. 180-192. DOI : 10.1016/j.ydbio.2018.11.023.

Tail Bud Progenitor Activity Relies on a Network Comprising Gdf11, Lin28, and Hox13 Genes

R. Aires; L. de Lemos; A. Novoa; A. D. Jurberg; B. Mascrez et al. 

Developmental Cell. 2019-02-11. Vol. 48, num. 3, p. 383-395.e8. DOI : 10.1016/j.devcel.2018.12.004.


Analysis of long-range gene regulation at the HoxD locus

A. R. De Carvalho Amândio Lhopitallier / D. Duboule (Dir.)  

Lausanne, EPFL, 2019. 


Journal Articles

Do RET somatic mutations play a role in Hirschsprung disease? Response

B. K. Kragesteen; D. Duboule; S. Mundlos; M. Spielmann 

Genetics In Medicine. 2018-11-01. Vol. 20, num. 11, p. 1481-1482. DOI : 10.1038/gim.2018.20.

Similarities and differences in the regulation of HoxD genes during chick and mouse limb development

N. Yakushiji-Kaminatsui; L. Lopez-Delisle; C. C. Bolt; G. Andrey; L. Beccari et al. 

Plos Biology. 2018-11-01. Vol. 16, num. 11, p. e3000004. DOI : 10.1371/journal.pbio.3000004.

Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids

L. Beccari; N. Moris; M. Girgin; D. A. Turner; P. Baillie-Johnson et al. 

Nature. 2018-10-11. Vol. 562, num. 7726, p. 272-276. DOI : 10.1038/s41586-018-0578-0.

Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

P. J. Fabre; M. Leleu; B. Mascrez; Q. Lo Giudice; J. Cobb et al. 

Bmc Biology. 2018-09-18. Vol. 16, p. 101. DOI : 10.1186/s12915-018-0570-z.

The ALK receptor in sympathetic neuron development and neuroblastoma

I. Janoueix-Lerosey; L. Lopez-Delisle; O. Delattre; H. Rohrer 

Cell and Tissue Research. 2018. Vol. 372, num. 2, p. 325-337. DOI : 10.1007/s00441-017-2784-8.

Noncoding copy-number variations are associated with congenital limb malformation

R. Flottmann; B. Kragesteen; S. Geuer; M. Socha; L. Allou et al. 

GENETICS IN MEDICINE. 2018. Vol. 20, num. 6, p. 599-607. DOI : 10.1038/gim.2017.154.


Coordinated Hoxd genes expression during embryogenesis is dependent on a strict disposition of genes and polarized regulators within the HoxD cluster

F. Darbellay / D. Duboule (Dir.)  

Lausanne, EPFL, 2018. 


Journal Articles

The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes.

E. Rodriguez-Carballo; L. Lopez-Delisle; Y. Zhan; P. J. Fabre; L. Beccari et al. 

Genes & Development. 2017. Vol. 31, num. 22, p. 2264-2281. DOI : 10.1101/gad.307769.117.

Control of growth and gut maturation by &ITHoxD&IT genes and the associated lncRNA &ITHaglr&IT

J. Zakany; F. Darbellay; B. Mascrez; A. Necsulea; D. Duboule 

Proceedings of the National Academy of Sciences of the United States of America. 2017. Vol. 114, num. 44, p. E9290-E9299. DOI : 10.1073/pnas.1712511114.

Large scale genomic reorganization of topological domains at the HoxD locus

P. J. Fabre; M. Leleu; B. H. Mormann; L. Lopez-Delisle; D. Noordermeer et al. 

Genome Biology. 2017. Vol. 18, num. 1, p. 149. DOI : 10.1186/s13059-017-1278-z.

Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells

A. R. Rodrigues; N. Yakushiji-Kaminatsui; Y. Atsuta; G. Andrey; P. Schorderet et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2017. Vol. 114, num. 12, p. 3139-3144. DOI : 10.1073/pnas.1620767114.


Journal Articles

A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus

L. Beccari; N. Yakushiji-Kaminatsui; J. M. Woltering; A. Necsulea; N. Lonfat et al. 

Genes & Development. 2016-05-19. Vol. 30, num. 10, p. 1172-1186. DOI : 10.1101/gad.281055.116.

Hotair Is Dispensible for Mouse Development

A. R. Amandio; A. Necsulea; E. Joye; B. Mascrez; D. Duboule 

Plos Genetics. 2016. Vol. 12, num. 12, p. e1006232. DOI : 10.1371/journal.pgen.1006232.

Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape

R. Schep; A. Necsulea; E. Rodriguez-Carballo; I. Guerreiro; G. Andrey et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2016. Vol. 113, num. 48, p. E7720-E7729. DOI : 10.1073/pnas.1617141113.

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan

I. Guerreiro; S. Gitto; A. Novoa; J. Codourey; H. Thi Hanh Nguyen et al. 

Elife. 2016. Vol. 5, p. e16087. DOI : 10.7554/eLife.16087.


Journal Articles

Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency

O. Joshi; S-Y. Wang; T. Kuznetsova; Y. Atlasi; T. Peng et al. 

Cell Stem Cell. 2015. Vol. 17, num. 6, p. 748-757. DOI : 10.1016/j.stem.2015.11.010.

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states

P. J. Fabre; A. Benke; E. Joye; T. H. Nguyen Huynh; S. Manley et al. 

Proceedings of the National Academy of Sciences of the United States of America. 2015. Vol. 112, num. 45, p. 13964-13969. DOI : 10.1073/pnas.1517972112.

Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model

J. M. Woltering; D. Duboule 

Mechanisms Of Development. 2015. Vol. 138, p. 64-72. DOI : 10.1016/j.mod.2015.07.006.

Structure, function and evolution of topologically associating domains (TADs) at HOX loci

N. Lonfat; D. Duboule 

FEBS letters. 2015. Vol. 589, num. 20 Pt A, p. 2869-2876. DOI : 10.1016/j.febslet.2015.04.024.

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome

R. A. W. Wiberg; D. L. Halligan; R. W. Ness; A. Necsulea; H. Kaessmann et al. 

Genome Biology And Evolution. 2015. Vol. 7, num. 8, p. 2432-2444. DOI : 10.1093/gbe/evv155.

Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain

M. Vieux-Rochas; P. J. Fabre; M. Leleu; D. Duboule; D. Noordermeer 

Proceedings of the National Academy of Sciences of the United States of America. 2015. Vol. 112, num. 15, p. 4672-7. DOI : 10.1073/pnas.1504783112.


Journal Articles

Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci

N. Lonfat; T. Montavon; F. Darbellay; S. Gitto; D. Duboule 

Science. 2014. Vol. 346, num. 6212, p. 1004-1006. DOI : 10.1126/science.1257493.

Considerations when investigating IncRNA function in vivo

A. R. Bassett; A. Akhtar; D. P. Barlow; A. P. Bird; N. Brockdorff et al. 

Elife. 2014. Vol. 3, p. e03058. DOI : 10.7554/eLife.03058.

Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs

J. Lopez-Rios; A. Duchesne; D. Speziale; G. Andrey; K. A. Peterson et al. 

NATURE. 2014. Vol. 511, num. 7507, p. 46-U553. DOI : 10.1038/nature13289.

Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

D. Noordermeer; M. Leleu; P. Schorderet; E. Joye; F. Chabaud et al. 

eLife. 2014. Vol. 3, p. e02557. DOI : 10.7554/eLife.02557.

Evolving Hox Activity Profiles Govern Diversity in Locomotor Systems

H. Jung; E. Mazzoni; N. Soshnikova; O. Hanley; B. Venkatesh et al. 

Developmental Cell. 2014. Vol. 29, num. 2, p. 171-187. DOI : 10.1016/j.devcel.2014.03.008.

SnapShot: Hox Gene Regulation

G. Andrey; D. Duboule 

Cell. 2014. Vol. 156, num. 4. DOI : 10.1016/j.cell.2014.01.060.

The evolution of lncRNA repertoires and expression patterns in tetrapods

A. Necsulea; M. Soumillon; M. Warnefors; A. Liechti; T. Daish et al. 

Nature. 2014. Vol. 505, num. 7485, p. 635-640. DOI : 10.1038/nature12943.

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

F. P. A. David; J. Delafontaine; S. Carat; F. J. Ross; G. Lefebvre et al. 

PLoS ONE. 2014. Vol. 9, num. 1, p. e85879. DOI : 10.1371/journal.pone.0085879.