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Items: 40

1.

Chromatin conformation analysis of primary patient tissue using a low input Hi-C method.

Díaz N, Kruse K, Erdmann T, Staiger AM, Ott G, Lenz G, Vaquerizas JM.

Nat Commun. 2018 Nov 29;9(1):4938. doi: 10.1038/s41467-018-06961-0.

2.
3.

The Birth of the 3D Genome during Early Embryonic Development.

Hug CB, Vaquerizas JM.

Trends Genet. 2018 Dec;34(12):903-914. doi: 10.1016/j.tig.2018.09.002. Epub 2018 Oct 3. Review.

4.

Xrp1 genetically interacts with the ALS-associated FUS orthologue caz and mediates its toxicity.

Mallik M, Catinozzi M, Hug CB, Zhang L, Wagner M, Bussmann J, Bittern J, Mersmann S, Klämbt C, Drexler HCA, Huynen MA, Vaquerizas JM, Storkebaum E.

J Cell Biol. 2018 Nov 5;217(11):3947-3964. doi: 10.1083/jcb.201802151. Epub 2018 Sep 12.

5.

A molecular roadmap for the emergence of early-embryonic-like cells in culture.

Rodriguez-Terrones D, Gaume X, Ishiuchi T, Weiss A, Kopp A, Kruse K, Penning A, Vaquerizas JM, Brino L, Torres-Padilla ME.

Nat Genet. 2018 Jan;50(1):106-119. doi: 10.1038/s41588-017-0016-5. Epub 2017 Dec 18.

6.

Transcriptional regulation of endothelial cell behavior during sprouting angiogenesis.

Jeong HW, Hernández-Rodríguez B, Kim J, Kim KP, Enriquez-Gasca R, Yoon J, Adams S, Schöler HR, Vaquerizas JM, Adams RH.

Nat Commun. 2017 Sep 28;8(1):726. doi: 10.1038/s41467-017-00738-7.

7.

Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription.

Hug CB, Grimaldi AG, Kruse K, Vaquerizas JM.

Cell. 2017 Apr 6;169(2):216-228.e19. doi: 10.1016/j.cell.2017.03.024.

8.

Cell-matrix signals specify bone endothelial cells during developmental osteogenesis.

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.

Nat Cell Biol. 2017 Mar;19(3):189-201. doi: 10.1038/ncb3476. Epub 2017 Feb 20.

9.

Developmental biology: Panoramic views of the early epigenome.

Vaquerizas JM, Torres-Padilla ME.

Nature. 2016 Sep 22;537(7621):494-496. doi: 10.1038/nature19468. Epub 2016 Sep 14. No abstract available.

PMID:
27626372
10.

Dual randomization of oligonucleotides to reduce the bias in ribosome-profiling libraries.

Lecanda A, Nilges BS, Sharma P, Nedialkova DD, Schwarz J, Vaquerizas JM, Leidel SA.

Methods. 2016 Sep 1;107:89-97. doi: 10.1016/j.ymeth.2016.07.011. Epub 2016 Jul 19.

11.

TADtool: visual parameter identification for TAD-calling algorithms.

Kruse K, Hug CB, Hernández-Rodríguez B, Vaquerizas JM.

Bioinformatics. 2016 Oct 15;32(20):3190-3192. Epub 2016 Jun 17.

12.

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly.

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

Nat Struct Mol Biol. 2015 Sep;22(9):662-71. doi: 10.1038/nsmb.3066. Epub 2015 Aug 3.

PMID:
26237512
13.

Response to Comments on "Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters".

Vaquerizas JM, Cavalli FM, Conrad T, Akhtar A, Luscombe NM.

Science. 2013 Apr 19;340(6130):273. doi: 10.1126/science.1232874.

14.

DNA-binding specificities of human transcription factors.

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.

Cell. 2013 Jan 17;152(1-2):327-39. doi: 10.1016/j.cell.2012.12.009.

15.

Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters.

Conrad T, Cavalli FM, Vaquerizas JM, Luscombe NM, Akhtar A.

Science. 2012 Aug 10;337(6095):742-6. doi: 10.1126/science.1221428. Epub 2012 Jul 19.

16.

The NSL complex regulates housekeeping genes in Drosophila.

Lam KC, Mühlpfordt F, Vaquerizas JM, Raja SJ, Holz H, Luscombe NM, Manke T, Akhtar A.

PLoS Genet. 2012;8(6):e1002736. doi: 10.1371/journal.pgen.1002736. Epub 2012 Jun 14.

17.

m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence.

Reimand J, Aun A, Vilo J, Vaquerizas JM, Sedman J, Luscombe NM.

Genome Biol. 2012 Jun 21;13(6):R55. doi: 10.1186/gb-2012-13-6-r55.

18.

The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex.

Conrad T, Cavalli FM, Holz H, Hallacli E, Kind J, Ilik I, Vaquerizas JM, Luscombe NM, Akhtar A.

Dev Cell. 2012 Mar 13;22(3):610-24. doi: 10.1016/j.devcel.2011.12.016.

19.

SpeCond: a method to detect condition-specific gene expression.

Cavalli FM, Bourgon R, Vaquerizas JM, Luscombe NM.

Genome Biol. 2011 Oct 18;12(10):R101. doi: 10.1186/gb-2011-12-10-r101. Erratum in: Genome Biol. 2011;12(12):413. Huber, Wolfgang [removed].

20.

How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome.

Vaquerizas JM, Teichmann SA, Luscombe NM.

Methods Mol Biol. 2012;786:3-19. doi: 10.1007/978-1-61779-292-2_1. Review.

PMID:
21938617
21.

Large-scale nuclear architecture and transcriptional control.

Vaquerizas JM, Akhtar A, Luscombe NM.

Subcell Biochem. 2011;52:279-95. doi: 10.1007/978-90-481-9069-0_13.

PMID:
21557088
22.

The nonspecific lethal complex is a transcriptional regulator in Drosophila.

Raja SJ, Charapitsa I, Conrad T, Vaquerizas JM, Gebhardt P, Holz H, Kadlec J, Fraterman S, Luscombe NM, Akhtar A.

Mol Cell. 2010 Jun 25;38(6):827-41. doi: 10.1016/j.molcel.2010.05.021.

23.

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets.

Reimand J, Vaquerizas JM, Todd AE, Vilo J, Luscombe NM.

Nucleic Acids Res. 2010 Aug;38(14):4768-77. doi: 10.1093/nar/gkq232. Epub 2010 Apr 12.

24.

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.

Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J.

Genome Res. 2010 Jun;20(6):861-73. doi: 10.1101/gr.100552.109. Epub 2010 Apr 8.

25.

Nuclear pore proteins nup153 and megator define transcriptionally active regions in the Drosophila genome.

Vaquerizas JM, Suyama R, Kind J, Miura K, Luscombe NM, Akhtar A.

PLoS Genet. 2010 Feb 12;6(2):e1000846. doi: 10.1371/journal.pgen.1000846.

26.

A census of human transcription factors: function, expression and evolution.

Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM.

Nat Rev Genet. 2009 Apr;10(4):252-63. doi: 10.1038/nrg2538. Review.

PMID:
19274049
27.

Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila.

Kind J, Vaquerizas JM, Gebhardt P, Gentzel M, Luscombe NM, Bertone P, Akhtar A.

Cell. 2008 May 30;133(5):813-28. doi: 10.1016/j.cell.2008.04.036.

29.

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes.

Conde L, Vaquerizas JM, Dopazo H, Arbiza L, Reumers J, Rousseau F, Schymkowitz J, Dopazo J.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W621-5.

30.

Next station in microarray data analysis: GEPAS.

Montaner D, Tárraga J, Huerta-Cepas J, Burguet J, Vaquerizas JM, Conde L, Minguez P, Vera J, Mukherjee S, Valls J, Pujana MA, Alloza E, Herrero J, Al-Shahrour F, Dopazo J.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W486-91.

31.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

Al-Shahrour F, Minguez P, Tárraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W472-6.

32.
33.

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.

Vaquerizas JM, Conde L, Yankilevich P, Cabezón A, Minguez P, Díaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W616-20.

34.

PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes.

Conde L, Vaquerizas JM, Ferrer-Costa C, de la Cruz X, Orozco M, Dopazo J.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W501-5.

35.

BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments.

Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W460-4.

36.

Highly specific and accurate selection of siRNAs for high-throughput functional assays.

Santoyo J, Vaquerizas JM, Dopazo J.

Bioinformatics. 2005 Apr 15;21(8):1376-82. Epub 2004 Dec 10.

PMID:
15591357
37.

DNMAD: web-based diagnosis and normalization for microarray data.

Vaquerizas JM, Dopazo J, Díaz-Uriarte R.

Bioinformatics. 2004 Dec 12;20(18):3656-8. Epub 2004 Jul 9.

PMID:
15247094
38.

New challenges in gene expression data analysis and the extended GEPAS.

Herrero J, Vaquerizas JM, Al-Shahrour F, Conde L, Mateos A, Díaz-Uriarte JS, Dopazo J.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W485-91.

39.

PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level.

Conde L, Vaquerizas JM, Santoyo J, Al-Shahrour F, Ruiz-Llorente S, Robledo M, Dopazo J.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W242-8.

40.

GEPAS: A web-based resource for microarray gene expression data analysis.

Herrero J, Al-Shahrour F, Díaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J.

Nucleic Acids Res. 2003 Jul 1;31(13):3461-7.

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