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Items: 1 to 50 of 111

1.

yap1b, a divergent Yap/Taz family member, cooperates with yap1 in survival and morphogenesis via common transcriptional targets.

Vázquez-Marín J, Gutiérrez-Triana JA, Almuedo-Castillo M, Buono L, Gómez-Skarmeta JL, Mateo JL, Wittbrodt J, Martínez-Morales JR.

Development. 2019 Jun 21;146(13). pii: dev173286. doi: 10.1242/dev.173286.

PMID:
31142542
2.

Reprogramming Nuclear Architecture: Just a TAD.

Acemel RD, Gómez-Skarmeta JL.

Cell Stem Cell. 2019 May 2;24(5):679-681. doi: 10.1016/j.stem.2019.04.007.

PMID:
31051129
3.

Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians.

Madgwick A, Magri MS, Dantec C, Gailly D, Fiuza UM, Guignard L, Hettinger S, Gomez-Skarmeta JL, Lemaire P.

Dev Biol. 2019 Apr 15;448(2):71-87. doi: 10.1016/j.ydbio.2019.01.003. Epub 2019 Jan 17.

PMID:
30661644
4.

Amphioxus functional genomics and the origins of vertebrate gene regulation.

Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M.

Nature. 2018 Dec;564(7734):64-70. doi: 10.1038/s41586-018-0734-6. Epub 2018 Nov 21.

5.

Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum.

Ruiz JL, Tena JJ, Bancells C, Cortés A, Gómez-Skarmeta JL, Gómez-Díaz E.

Nucleic Acids Res. 2018 Oct 12;46(18):9414-9431. doi: 10.1093/nar/gky643.

6.

An evolutionary perspective of regulatory landscape dynamics in development and disease.

Franke M, Gómez-Skarmeta JL.

Curr Opin Cell Biol. 2018 Dec;55:24-29. doi: 10.1016/j.ceb.2018.06.009. Epub 2018 Jul 11. Review.

PMID:
30006052
7.

Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution.

Kittelmann S, Buffry AD, Franke FA, Almudi I, Yoth M, Sabaris G, Couso JP, Nunes MDS, Frankel N, Gómez-Skarmeta JL, Pueyo-Marques J, Arif S, McGregor AP.

PLoS Genet. 2018 May 3;14(5):e1007375. doi: 10.1371/journal.pgen.1007375. eCollection 2018 May.

8.

Evolutionary emergence of the rac3b/rfng/sgca regulatory cluster refined mechanisms for hindbrain boundaries formation.

Letelier J, Terriente J, Belzunce I, Voltes A, Undurraga CA, Polvillo R, Devos L, Tena JJ, Maeso I, Retaux S, Gomez-Skarmeta JL, Martínez-Morales JR, Pujades C.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):E3731-E3740. doi: 10.1073/pnas.1719885115. Epub 2018 Apr 2.

9.

A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins.

Letelier J, de la Calle-Mustienes E, Pieretti J, Naranjo S, Maeso I, Nakamura T, Pascual-Anaya J, Shubin NH, Schneider I, Martinez-Morales JR, Gómez-Skarmeta JL.

Nat Genet. 2018 Apr;50(4):504-509. doi: 10.1038/s41588-018-0080-5. Epub 2018 Mar 19.

10.

4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data.

Irastorza-Azcarate I, Acemel RD, Tena JJ, Maeso I, Gómez-Skarmeta JL, Devos DP.

PLoS Comput Biol. 2018 Mar 9;14(3):e1006030. doi: 10.1371/journal.pcbi.1006030. eCollection 2018 Mar.

11.

A common copy-number variant within SIRPB1 correlates with human Out-of-Africa migration after genetic drift correction.

Royo JL, Valls J, Acemel RD, Gómez-Marin C, Pascual-Pons M, Lupiañez A, Gomez-Skarmeta JL, Fibla J.

PLoS One. 2018 Mar 8;13(3):e0193614. doi: 10.1371/journal.pone.0193614. eCollection 2018.

12.

CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart.

Gomez-Velazquez M, Badia-Careaga C, Lechuga-Vieco AV, Nieto-Arellano R, Tena JJ, Rollan I, Alvarez A, Torroja C, Caceres EF, Roy AR, Galjart N, Delgado-Olguin P, Sanchez-Cabo F, Enriquez JA, Gomez-Skarmeta JL, Manzanares M.

PLoS Genet. 2017 Aug 28;13(8):e1006985. doi: 10.1371/journal.pgen.1006985. eCollection 2017 Aug.

13.

Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements.

Vicente-García C, Villarejo-Balcells B, Irastorza-Azcárate I, Naranjo S, Acemel RD, Tena JJ, Rigby PWJ, Devos DP, Gómez-Skarmeta JL, Carvajal JJ.

Genome Biol. 2017 Jun 14;18(1):106. doi: 10.1186/s13059-017-1225-z.

14.

Topologically associated domains: a successful scaffold for the evolution of gene regulation in animals.

Acemel RD, Maeso I, Gómez-Skarmeta JL.

Wiley Interdiscip Rev Dev Biol. 2017 May;6(3). doi: 10.1002/wdev.265. Epub 2017 Mar 2. Review.

PMID:
28251841
15.

Cis-regulatory landscapes in development and evolution.

Maeso I, Acemel RD, Gómez-Skarmeta JL.

Curr Opin Genet Dev. 2017 Apr;43:17-22. doi: 10.1016/j.gde.2016.10.004. Epub 2016 Nov 11. Review.

PMID:
27842294
16.

Editorial.

Nóbrega MA, Gómez-Skarmeta JL.

Semin Cell Dev Biol. 2016 Sep;57:1. doi: 10.1016/j.semcdb.2016.07.023. No abstract available.

PMID:
27499506
17.

Assay for transposase-accessible chromatin and circularized chromosome conformation capture, two methods to explore the regulatory landscapes of genes in zebrafish.

Fernández-Miñán A, Bessa J, Tena JJ, Gómez-Skarmeta JL.

Methods Cell Biol. 2016;135:413-30. doi: 10.1016/bs.mcb.2016.02.008. Epub 2016 Mar 15.

PMID:
27443938
18.

The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity.

Sebé-Pedrós A, Ballaré C, Parra-Acero H, Chiva C, Tena JJ, Sabidó E, Gómez-Skarmeta JL, Di Croce L, Ruiz-Trillo I.

Cell. 2016 May 19;165(5):1224-1237. doi: 10.1016/j.cell.2016.03.034. Epub 2016 Apr 21.

19.

Active DNA demethylation at enhancers during the vertebrate phylotypic period.

Bogdanović O, Smits AH, de la Calle Mustienes E, Tena JJ, Ford E, Williams R, Senanayake U, Schultz MD, Hontelez S, van Kruijsbergen I, Rayon T, Gnerlich F, Carell T, Veenstra GJ, Manzanares M, Sauka-Spengler T, Ecker JR, Vermeulen M, Gómez-Skarmeta JL, Lister R.

Nat Genet. 2016 Apr;48(4):417-26. doi: 10.1038/ng.3522. Epub 2016 Feb 29.

20.

A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation.

Acemel RD, Tena JJ, Irastorza-Azcarate I, Marlétaz F, Gómez-Marín C, de la Calle-Mustienes E, Bertrand S, Diaz SG, Aldea D, Aury JM, Mangenot S, Holland PW, Devos DP, Maeso I, Escrivá H, Gómez-Skarmeta JL.

Nat Genet. 2016 Mar;48(3):336-41. doi: 10.1038/ng.3497. Epub 2016 Feb 1.

PMID:
26829752
21.

Genome-wide epigenetic cross-talk between DNA methylation and H3K27me3 in zebrafish embryos.

de la Calle Mustienes E, Gómez-Skarmeta JL, Bogdanović O.

Genom Data. 2015 Jul 22;6:7-9. doi: 10.1016/j.gdata.2015.07.020. eCollection 2015 Dec.

22.

Profiling of conserved non-coding elements upstream of SHOX and functional characterisation of the SHOX cis-regulatory landscape.

Verdin H, Fernández-Miñán A, Benito-Sanz S, Janssens S, Callewaert B, De Waele K, De Schepper J, François I, Menten B, Heath KE, Gómez-Skarmeta JL, De Baere E.

Sci Rep. 2015 Dec 3;5:17667. doi: 10.1038/srep17667.

23.

Meis1 coordinates a network of genes implicated in eye development and microphthalmia.

Marcos S, González-Lázaro M, Beccari L, Carramolino L, Martin-Bermejo MJ, Amarie O, Mateos-San Martín D, Torroja C, Bogdanović O, Doohan R, Puk O, Hrabě de Angelis M, Graw J, Gomez-Skarmeta JL, Casares F, Torres M, Bovolenta P.

Development. 2015 Sep 1;142(17):3009-20. doi: 10.1242/dev.122176. Epub 2015 Aug 7.

24.

MIR retrotransposon sequences provide insulators to the human genome.

Wang J, Vicente-García C, Seruggia D, Moltó E, Fernandez-Miñán A, Neto A, Lee E, Gómez-Skarmeta JL, Montoliu L, Lunyak VV, Jordan IK.

Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):E4428-37. doi: 10.1073/pnas.1507253112. Epub 2015 Jul 27.

25.

A novel chromatin insulator regulates the chicken folate receptor gene from the influence of nearby constitutive heterochromatin and the β-globin locus.

González-Buendía E, Escamilla-Del-Arenal M, Pérez-Molina R, Tena JJ, Guerrero G, Suaste-Olmos F, Ayala-Ortega E, Gómez-Skarmeta JL, Recillas-Targa F.

Biochim Biophys Acta. 2015 Aug;1849(8):955-65. doi: 10.1016/j.bbagrm.2015.05.011. Epub 2015 Jun 14.

PMID:
26079690
26.

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders.

Gómez-Marín C, Tena JJ, Acemel RD, López-Mayorga M, Naranjo S, de la Calle-Mustienes E, Maeso I, Beccari L, Aneas I, Vielmas E, Bovolenta P, Nobrega MA, Carvajal J, Gómez-Skarmeta JL.

Proc Natl Acad Sci U S A. 2015 Jun 16;112(24):7542-7. doi: 10.1073/pnas.1505463112. Epub 2015 Jun 1.

27.

Analysis of opo cis-regulatory landscape uncovers Vsx2 requirement in early eye morphogenesis.

Gago-Rodrigues I, Fernández-Miñán A, Letelier J, Naranjo S, Tena JJ, Gómez-Skarmeta JL, Martinez-Morales JR.

Nat Commun. 2015 May 12;6:7054. doi: 10.1038/ncomms8054.

28.

TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors.

Cebola I, Rodríguez-Seguí SA, Cho CH, Bessa J, Rovira M, Luengo M, Chhatriwala M, Berry A, Ponsa-Cobas J, Maestro MA, Jennings RE, Pasquali L, Morán I, Castro N, Hanley NA, Gomez-Skarmeta JL, Vallier L, Ferrer J.

Nat Cell Biol. 2015 May;17(5):615-626. doi: 10.1038/ncb3160. Epub 2015 Apr 27.

29.

Long-range regulatory interactions at the 4q25 atrial fibrillation risk locus involve PITX2c and ENPEP.

Aguirre LA, Alonso ME, Badía-Careaga C, Rollán I, Arias C, Fernández-Miñán A, López-Jiménez E, Aránega A, Gómez-Skarmeta JL, Franco D, Manzanares M.

BMC Biol. 2015 Apr 17;13:26. doi: 10.1186/s12915-015-0138-0.

30.

Matricellular protein SPARC/osteonectin expression is regulated by DNA methylation in its core promoter region.

Torres-Núñez E, Cal L, Suárez-Bregua P, Gómez-Marin C, Moran P, Gómez-Skarmeta JL, Rotllant J.

Dev Dyn. 2015 May;244(5):693-702. doi: 10.1002/dvdy.24267. Epub 2015 Mar 31.

31.

Deep conservation of wrist and digit enhancers in fish.

Gehrke AR, Schneider I, de la Calle-Mustienes E, Tena JJ, Gomez-Marin C, Chandran M, Nakamura T, Braasch I, Postlethwait JH, Gómez-Skarmeta JL, Shubin NH.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):803-8. doi: 10.1073/pnas.1420208112. Epub 2014 Dec 22.

32.

The conserved barH-like homeobox-2 gene barhl2 acts downstream of orthodentricle-2 and together with iroquois-3 in establishment of the caudal forebrain signaling center induced by Sonic Hedgehog.

Juraver-Geslin HA, Gómez-Skarmeta JL, Durand BC.

Dev Biol. 2014 Dec 1;396(1):107-20. doi: 10.1016/j.ydbio.2014.09.027. Epub 2014 Oct 2.

33.

A polymorphic enhancer near GREM1 influences bowel cancer risk through differential CDX2 and TCF7L2 binding.

Lewis A, Freeman-Mills L, de la Calle-Mustienes E, Giráldez-Pérez RM, Davis H, Jaeger E, Becker M, Hubner NC, Nguyen LN, Zeron-Medina J, Bond G, Stunnenberg HG, Carvajal JJ, Gomez-Skarmeta JL, Leedham S, Tomlinson I.

Cell Rep. 2014 Aug 21;8(4):983-90. doi: 10.1016/j.celrep.2014.07.020. Epub 2014 Aug 14.

34.

sox21a directs lateral line patterning by modulating FGF signaling.

Ariza-Cosano A, Bensimon-Brito A, Gómez-Skarmeta JL, Bessa J.

Dev Neurobiol. 2015 Jan;75(1):80-92. doi: 10.1002/dneu.22211. Epub 2014 Jul 18.

35.

SIRPB1 copy-number polymorphism as candidate quantitative trait locus for impulsive-disinhibited personality.

Laplana M, Royo JL, García LF, Aluja A, Gomez-Skarmeta JL, Fibla J.

Genes Brain Behav. 2014 Sep;13(7):653-62. doi: 10.1111/gbb.12154. Epub 2014 Jul 23.

36.

Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period.

Tena JJ, González-Aguilera C, Fernández-Miñán A, Vázquez-Marín J, Parra-Acero H, Cross JW, Rigby PW, Carvajal JJ, Wittbrodt J, Gómez-Skarmeta JL, Martínez-Morales JR.

Genome Res. 2014 Jul;24(7):1075-85. doi: 10.1101/gr.163915.113. Epub 2014 Apr 7.

37.

New frontiers in the evolution of fin development.

Freitas R, Gómez-Skarmeta JL, Rodrigues PN.

J Exp Zool B Mol Dev Evol. 2014 Nov;322(7):540-52. doi: 10.1002/jez.b.22563. Epub 2014 Feb 12. Review.

PMID:
24677573
38.

Obesity-associated variants within FTO form long-range functional connections with IRX3.

Smemo S, Tena JJ, Kim KH, Gamazon ER, Sakabe NJ, Gómez-Marín C, Aneas I, Credidio FL, Sobreira DR, Wasserman NF, Lee JH, Puviindran V, Tam D, Shen M, Son JE, Vakili NA, Sung HK, Naranjo S, Acemel RD, Manzanares M, Nagy A, Cox NJ, Hui CC, Gomez-Skarmeta JL, Nóbrega MA.

Nature. 2014 Mar 20;507(7492):371-5. doi: 10.1038/nature13138. Epub 2014 Mar 12.

39.

Restless legs syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon.

Spieler D, Kaffe M, Knauf F, Bessa J, Tena JJ, Giesert F, Schormair B, Tilch E, Lee H, Horsch M, Czamara D, Karbalai N, von Toerne C, Waldenberger M, Gieger C, Lichtner P, Claussnitzer M, Naumann R, Müller-Myhsok B, Torres M, Garrett L, Rozman J, Klingenspor M, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Beckers J, Hölter SM, Meitinger T, Hauck SM, Laumen H, Wurst W, Casares F, Gómez-Skarmeta JL, Winkelmann J.

Genome Res. 2014 Apr;24(4):592-603. doi: 10.1101/gr.166751.113. Epub 2014 Mar 18.

40.

A mobile insulator system to detect and disrupt cis-regulatory landscapes in vertebrates.

Bessa J, Luengo M, Rivero-Gil S, Ariza-Cosano A, Maia AH, Ruiz-Ruano FJ, Caballero P, Naranjo S, Carvajal JJ, Gómez-Skarmeta JL.

Genome Res. 2014 Mar;24(3):487-95. doi: 10.1101/gr.165654.113. Epub 2013 Nov 25.

41.

Deep conservation of cis-regulatory elements in metazoans.

Maeso I, Irimia M, Tena JJ, Casares F, Gómez-Skarmeta JL.

Philos Trans R Soc Lond B Biol Sci. 2013 Nov 11;368(1632):20130020. doi: 10.1098/rstb.2013.0020. Print 2013 Dec 19. Review.

42.

Several cis-regulatory elements control mRNA stability, translation efficiency, and expression pattern of Prrxl1 (paired related homeobox protein-like 1).

Regadas I, Matos MR, Monteiro FA, Gómez-Skarmeta JL, Lima D, Bessa J, Casares F, Reguenga C.

J Biol Chem. 2013 Dec 20;288(51):36285-301. doi: 10.1074/jbc.M113.491993. Epub 2013 Nov 8.

43.

Embryonic DNA methylation: insights from the genomics era.

Bogdanović O, Gómez-Skarmeta JL.

Brief Funct Genomics. 2014 Mar;13(2):121-30. doi: 10.1093/bfgp/elt039. Epub 2013 Sep 23. Review.

PMID:
24064195
44.

Early evolution of the T-box transcription factor family.

Sebé-Pedrós A, Ariza-Cosano A, Weirauch MT, Leininger S, Yang A, Torruella G, Adamski M, Adamska M, Hughes TR, Gómez-Skarmeta JL, Ruiz-Trillo I.

Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16050-5. doi: 10.1073/pnas.1309748110. Epub 2013 Sep 16.

45.

Heartbeat-driven pericardiac fluid forces contribute to epicardium morphogenesis.

Peralta M, Steed E, Harlepp S, González-Rosa JM, Monduc F, Ariza-Cosano A, Cortés A, Rayón T, Gómez-Skarmeta JL, Zapata A, Vermot J, Mercader N.

Curr Biol. 2013 Sep 23;23(18):1726-35. doi: 10.1016/j.cub.2013.07.005. Epub 2013 Aug 15.

46.

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild.

Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Raineri E, Estellé J, Fernandez-Callejo M, Valles M, Ritscher L, Schöneberg T, de la Calle-Mustienes E, Casillas S, Rubio-Acero R, Melé M, Engelken J, Caceres M, Gomez-Skarmeta JL, Gut M, Bertranpetit J, Gut IG, Abello T, Eichler EE, Mingarro I, Lalueza-Fox C, Navarro A, Marques-Bonet T.

BMC Genomics. 2013 May 31;14:363. doi: 10.1186/1471-2164-14-363.

47.

The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos.

Bogdanović O, Fernández-Miñán A, Tena JJ, de la Calle-Mustienes E, Gómez-Skarmeta JL.

Methods. 2013 Aug 15;62(3):207-15. doi: 10.1016/j.ymeth.2013.04.011. Epub 2013 Apr 23.

PMID:
23624103
48.

Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression.

Ariza-Cosano A, Visel A, Pennacchio LA, Fraser HB, Gómez-Skarmeta JL, Irimia M, Bessa J.

BMC Genomics. 2012 Dec 19;13:713. doi: 10.1186/1471-2164-13-713.

49.

Hoxd13 contribution to the evolution of vertebrate appendages.

Freitas R, Gómez-Marín C, Wilson JM, Casares F, Gómez-Skarmeta JL.

Dev Cell. 2012 Dec 11;23(6):1219-29. doi: 10.1016/j.devcel.2012.10.015.

50.

Suppression of Bmp4 signaling by the zinc-finger repressors Osr1 and Osr2 is required for Wnt/β-catenin-mediated lung specification in Xenopus.

Rankin SA, Gallas AL, Neto A, Gómez-Skarmeta JL, Zorn AM.

Development. 2012 Aug;139(16):3010-20. doi: 10.1242/dev.078220. Epub 2012 Jul 12.

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