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Items: 31

1.

Lineage specific transcription factors and epigenetic regulators mediate TGFβ-dependent enhancer activation.

Fueyo R, Iacobucci S, Pappa S, Estarás C, Lois S, Vicioso-Mantis M, Navarro C, Cruz-Molina S, Reyes JC, Rada-Iglesias Á, de la Cruz X, Martínez-Balbás MA.

Nucleic Acids Res. 2018 Feb 9. doi: 10.1093/nar/gky093. [Epub ahead of print]

PMID:
29438503
2.

Is H3K4me1 at enhancers correlative or causative?

Rada-Iglesias A.

Nat Genet. 2018 Jan;50(1):4-5. doi: 10.1038/s41588-017-0018-3. No abstract available.

PMID:
29273804
3.

Ready, Set…Poised!: Polycomb target genes are bound by poised RNA polymerase II throughout differentiation.

Rada-Iglesias A.

Mol Syst Biol. 2017 Oct 23;13(10):950. doi: 10.15252/msb.20177968. No abstract available.

4.

Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples.

Rehimi R, Bartusel M, Solinas F, Altmüller J, Rada-Iglesias A.

J Vis Exp. 2017 Aug 29;(126). doi: 10.3791/56186.

PMID:
28872116
5.

PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation.

Cruz-Molina S, Respuela P, Tebartz C, Kolovos P, Nikolic M, Fueyo R, van Ijcken WFJ, Grosveld F, Frommolt P, Bazzi H, Rada-Iglesias A.

Cell Stem Cell. 2017 May 4;20(5):689-705.e9. doi: 10.1016/j.stem.2017.02.004. Epub 2017 Mar 9.

PMID:
28285903
6.

Imputation of orofacial clefting data identifies novel risk loci and sheds light on the genetic background of cleft lip ± cleft palate and cleft palate only.

Ludwig KU, Böhmer AC, Bowes J, Nikolic M, Ishorst N, Wyatt N, Hammond NL, Gölz L, Thieme F, Barth S, Schuenke H, Klamt J, Spielmann M, Aldhorae K, Rojas-Martinez A, Nöthen MM, Rada-Iglesias A, Dixon MJ, Knapp M, Mangold E.

Hum Mol Genet. 2017 Feb 15;26(4):829-842. doi: 10.1093/hmg/ddx012.

7.

GARLIC: a bioinformatic toolkit for aetiologically connecting diseases and cell type-specific regulatory maps.

Nikolic M, Papantonis A, Rada-Iglesias A.

Hum Mol Genet. 2017 Feb 15;26(4):742-752. doi: 10.1093/hmg/ddw423.

8.

Epigenomics-Based Identification of Major Cell Identity Regulators within Heterogeneous Cell Populations.

Rehimi R, Nikolic M, Cruz-Molina S, Tebartz C, Frommolt P, Mahabir E, Clément-Ziza M, Rada-Iglesias A.

Cell Rep. 2016 Dec 13;17(11):3062-3076. doi: 10.1016/j.celrep.2016.11.046.

9.

Foxd3 Promotes Exit from Naive Pluripotency through Enhancer Decommissioning and Inhibits Germline Specification.

Respuela P, Nikolić M, Tan M, Frommolt P, Zhao Y, Wysocka J, Rada-Iglesias A.

Cell Stem Cell. 2016 Jan 7;18(1):118-33. doi: 10.1016/j.stem.2015.09.010.

10.

Genetic variation within transcriptional regulatory elements and its implications for human disease.

Rada-Iglesias A.

Biol Chem. 2014 Dec;395(12):1453-60. doi: 10.1515/hsz-2014-0109. Review.

PMID:
25205712
11.

Human genetic variation within neural crest enhancers: molecular and phenotypic implications.

Rada-Iglesias A, Prescott SL, Wysocka J.

Philos Trans R Soc Lond B Biol Sci. 2013 May 6;368(1620):20120360. doi: 10.1098/rstb.2012.0360. Print 2013. Review.

12.

Pioneering barren land: mitotic bookmarking by transcription factors.

Rada-Iglesias A.

Dev Cell. 2013 Feb 25;24(4):342-4. doi: 10.1016/j.devcel.2013.02.005.

13.

Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest.

Rada-Iglesias A, Bajpai R, Prescott S, Brugmann SA, Swigut T, Wysocka J.

Cell Stem Cell. 2012 Nov 2;11(5):633-48. doi: 10.1016/j.stem.2012.07.006. Epub 2012 Sep 13.

14.

The homeodomain-leucine zipper (HD-Zip) class I transcription factors ATHB7 and ATHB12 modulate abscisic acid signalling by regulating protein phosphatase 2C and abscisic acid receptor gene activities.

Valdés AE, Overnäs E, Johansson H, Rada-Iglesias A, Engström P.

Plant Mol Biol. 2012 Nov;80(4-5):405-18. doi: 10.1007/s11103-012-9956-4. Epub 2012 Sep 12.

PMID:
22968620
15.
16.

Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates.

Ma Z, Swigut T, Valouev A, Rada-Iglesias A, Wysocka J.

Nat Struct Mol Biol. 2011 Feb;18(2):120-7. doi: 10.1038/nsmb.2000. Epub 2010 Dec 23.

PMID:
21183938
17.

A unique chromatin signature uncovers early developmental enhancers in humans.

Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J.

Nature. 2011 Feb 10;470(7333):279-83. doi: 10.1038/nature09692. Epub 2010 Dec 15.

18.

Integrative epigenomic and genomic analysis of malignant pheochromocytoma.

Sandgren J, Andersson R, Rada-Iglesias A, Enroth S, Akerstrom G, Dumanski JP, Komorowski J, Westin G, Wadelius C.

Exp Mol Med. 2010 Jul 31;42(7):484-502.

19.

CHD7 cooperates with PBAF to control multipotent neural crest formation.

Bajpai R, Chen DA, Rada-Iglesias A, Zhang J, Xiong Y, Helms J, Chang CP, Zhao Y, Swigut T, Wysocka J.

Nature. 2010 Feb 18;463(7283):958-62. doi: 10.1038/nature08733. Epub 2010 Feb 3.

20.

Nucleosomes are well positioned in exons and carry characteristic histone modifications.

Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J.

Genome Res. 2009 Oct;19(10):1732-41. doi: 10.1101/gr.092353.109. Epub 2009 Aug 17.

21.

Two polypyrimidine tracts in the nitric oxide synthase 2 gene: similar regulatory sequences with different properties.

Motallebipour M, Rada-Iglesias A, Westin G, Wadelius C.

Mol Biol Rep. 2010 Apr;37(4):2021-30. doi: 10.1007/s11033-009-9653-9. Epub 2009 Aug 8.

PMID:
19669598
22.

Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP.

Ameur A, Rada-Iglesias A, Komorowski J, Wadelius C.

Nucleic Acids Res. 2009 Jul;37(12):e85. doi: 10.1093/nar/gkp381. Epub 2009 May 18.

23.

Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation.

Rada-Iglesias A, Enroth S, Andersson R, Wanders A, Påhlman L, Komorowski J, Wadelius C.

Epigenetics. 2009 Feb 16;4(2):107-13. Epub 2009 Mar 1.

PMID:
19276669
24.

Histone acetylation and methylation at sites initiating divergent polycistronic transcription in Trypanosoma cruzi.

Respuela P, Ferella M, Rada-Iglesias A, Aslund L.

J Biol Chem. 2008 Jun 6;283(23):15884-92. doi: 10.1074/jbc.M802081200. Epub 2008 Apr 9.

25.

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders.

Rada-Iglesias A, Ameur A, Kapranov P, Enroth S, Komorowski J, Gingeras TR, Wadelius C.

Genome Res. 2008 Mar;18(3):380-92. doi: 10.1101/gr.6880908. Epub 2008 Jan 29.

26.

Monte Carlo feature selection for supervised classification.

Draminski M, Rada-Iglesias A, Enroth S, Wadelius C, Koronacki J, Komorowski J.

Bioinformatics. 2008 Jan 1;24(1):110-7. Epub 2007 Nov 28.

PMID:
18048398
27.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

28.

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes.

Rada-Iglesias A, Enroth S, Ameur A, Koch CM, Clelland GK, Respuela-Alonso P, Wilcox S, Dovey OM, Ellis PD, Langford CF, Dunham I, Komorowski J, Wadelius C.

Genome Res. 2007 Jun;17(6):708-19.

29.

In vitro analysis of DNA-protein interactions by proximity ligation.

Gustafsdottir SM, Schlingemann J, Rada-Iglesias A, Schallmeiner E, Kamali-Moghaddam M, Wadelius C, Landegren U.

Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3067-72. Epub 2007 Feb 20.

30.
31.

Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays.

Rada-Iglesias A, Wallerman O, Koch C, Ameur A, Enroth S, Clelland G, Wester K, Wilcox S, Dovey OM, Ellis PD, Wraight VL, James K, Andrews R, Langford C, Dhami P, Carter N, Vetrie D, Pontén F, Komorowski J, Dunham I, Wadelius C.

Hum Mol Genet. 2005 Nov 15;14(22):3435-47. Epub 2005 Oct 12.

PMID:
16221759

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