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Items: 18


A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.

McCorkindale AL, Wahle P, Werner S, Jungreis I, Menzel P, Shukla CJ, Abreu RLP, Irizarry RA, Meyer IM, Kellis M, Zinzen RP.

Development. 2019 Mar 28;146(6). pii: dev175265. doi: 10.1242/dev.175265.


Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis.

Menzel P, McCorkindale AL, Stefanov SR, Zinzen RP, Meyer IM.

RNA Biol. 2019 Jan;16(1):69-81. doi: 10.1080/15476286.2018.1558907. Epub 2019 Jan 20.


Determinants of promoter and enhancer transcription directionality in metazoans.

Ibrahim MM, Karabacak A, Glahs A, Kolundzic E, Hirsekorn A, Carda A, Tursun B, Zinzen RP, Lacadie SA, Ohler U.

Nat Commun. 2018 Oct 26;9(1):4472. doi: 10.1038/s41467-018-06962-z.


McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.

Hafez D, Karabacak A, Krueger S, Hwang YC, Wang LS, Zinzen RP, Ohler U.

Genome Biol. 2017 Oct 26;18(1):199. doi: 10.1186/s13059-017-1316-x.


The Drosophila embryo at single-cell transcriptome resolution.

Karaiskos N, Wahle P, Alles J, Boltengagen A, Ayoub S, Kipar C, Kocks C, Rajewsky N, Zinzen RP.

Science. 2017 Oct 13;358(6360):194-199. doi: 10.1126/science.aan3235. Epub 2017 Aug 31.


Putting chromatin in its place: the pioneer factor NeuroD1 modulates chromatin state to drive cell fate decisions.

Glahs A, Zinzen RP.

EMBO J. 2016 Jan 4;35(1):1-3. doi: 10.15252/embj.201593324. Epub 2015 Nov 13.


miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism.

Tattikota SG, Rathjen T, Hausser J, Khedkar A, Kabra UD, Pandey V, Sury M, Wessels HH, Mollet IG, Eliasson L, Selbach M, Zinzen RP, Zavolan M, Kadener S, Tschöp MH, Jastroch M, Friedländer MR, Poy MN.

J Biol Chem. 2015 Aug 14;290(33):20284-94. doi: 10.1074/jbc.M115.658625. Epub 2015 Jul 7.


A conserved role for Snail as a potentiator of active transcription.

Rembold M, Ciglar L, Yáñez-Cuna JO, Zinzen RP, Girardot C, Jain A, Welte MA, Stark A, Leptin M, Furlong EE.

Genes Dev. 2014 Jan 15;28(2):167-81. doi: 10.1101/gad.230953.113. Epub 2014 Jan 8.


Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP.

Bonn S, Zinzen RP, Perez-Gonzalez A, Riddell A, Gavin AC, Furlong EE.

Nat Protoc. 2012 Apr 26;7(5):978-94. doi: 10.1038/nprot.2012.049.


Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.

Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE.

Nat Genet. 2012 Jan 8;44(2):148-56. doi: 10.1038/ng.1064.


Combinatorial binding predicts spatio-temporal cis-regulatory activity.

Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE.

Nature. 2009 Nov 5;462(7269):65-70. doi: 10.1038/nature08531.


Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis.

Zinzen RP, Furlong EE.

Genome Biol. 2008;9(11):240. doi: 10.1186/gb-2008-9-11-240. Epub 2008 Nov 4. Review.


Evolution of the dorsal-ventral patterning network in the mosquito, Anopheles gambiae.

Goltsev Y, Fuse N, Frasch M, Zinzen RP, Lanzaro G, Levine M.

Development. 2007 Jul;134(13):2415-24. Epub 2007 May 23.


Enhancer responses to similarly distributed antagonistic gradients in development.

Zinzen RP, Papatsenko D.

PLoS Comput Biol. 2007 May;3(5):e84. Epub 2007 Mar 29.


Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.

Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, Young RA, Levine M.

Genes Dev. 2007 Feb 15;21(4):385-90.


Evolution of the ventral midline in insect embryos.

Zinzen RP, Cande J, Ronshaugen M, Papatsenko D, Levine M.

Dev Cell. 2006 Dec;11(6):895-902.


Computational models for neurogenic gene expression in the Drosophila embryo.

Zinzen RP, Senger K, Levine M, Papatsenko D.

Curr Biol. 2006 Jul 11;16(13):1358-65. Epub 2006 Jun 6.


Template requirements for telomerase translocation in Kluyveromyces lactis.

Underwood DH, Zinzen RP, McEachern MJ.

Mol Cell Biol. 2004 Jan;24(2):912-23.

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