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Items: 17

1.

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.

Wyler E, Menegatti J, Franke V, Kocks C, Boltengagen A, Hennig T, Theil K, Rutkowski A, Ferrai C, Baer L, Kermas L, Friedel C, Rajewsky N, Akalin A, Dölken L, Grässer F, Landthaler M.

Genome Biol. 2017 Oct 31;18(1):209. doi: 10.1186/s13059-017-1329-5.

2.

RNA localization is a key determinant of neurite-enriched proteome.

Zappulo A, van den Bruck D, Ciolli Mattioli C, Franke V, Imami K, McShane E, Moreno-Estelles M, Calviello L, Filipchyk A, Peguero-Sanchez E, Müller T, Woehler A, Birchmeier C, Merino E, Rajewsky N, Ohler U, Mazzoni EO, Selbach M, Akalin A, Chekulaeva M.

Nat Commun. 2017 Sep 19;8(1):583. doi: 10.1038/s41467-017-00690-6.

3.

Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes.

Franke V, Ganesh S, Karlic R, Malik R, Pasulka J, Horvat F, Kuzman M, Fulka H, Cernohorska M, Urbanova J, Svobodova E, Ma J, Suzuki Y, Aoki F, Schultz RM, Vlahovicek K, Svoboda P.

Genome Res. 2017 Aug;27(8):1384-1394. doi: 10.1101/gr.216150.116. Epub 2017 May 18.

4.

Long non-coding RNA exchange during the oocyte-to-embryo transition in mice.

Karlic R, Ganesh S, Franke V, Svobodova E, Urbanova J, Suzuki Y, Aoki F, Vlahovicek K, Svoboda P.

DNA Res. 2017 Apr 1;24(2):219-220. doi: 10.1093/dnares/dsx008. No abstract available.

5.

Long non-coding RNA exchange during the oocyte-to-embryo transition in mice.

Karlic R, Ganesh S, Franke V, Svobodova E, Urbanova J, Suzuki Y, Aoki F, Vlahovicek K, Svoboda P.

DNA Res. 2017 Apr 1;24(2):129-141. doi: 10.1093/dnares/dsw058. Erratum in: DNA Res. 2017 Apr 1;24(2):219-220.

6.

Sculpting the Transcriptome During the Oocyte-to-Embryo Transition in Mouse.

Svoboda P, Franke V, Schultz RM.

Curr Top Dev Biol. 2015;113:305-49. doi: 10.1016/bs.ctdb.2015.06.004. Epub 2015 Jul 29. Review.

PMID:
26358877
7.

Maternal SIN3A regulates reprogramming of gene expression during mouse preimplantation development.

Jimenez R, Melo EO, Davydenko O, Ma J, Mainigi M, Franke V, Schultz RM.

Biol Reprod. 2015 Oct;93(4):89. doi: 10.1095/biolreprod.115.133504. Epub 2015 Sep 9.

8.

The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3' processing.

Abe K, Yamamoto R, Franke V, Cao M, Suzuki Y, Suzuki MG, Vlahovicek K, Svoboda P, Schultz RM, Aoki F.

EMBO J. 2015 Jun 3;34(11):1523-37. doi: 10.15252/embj.201490648. Epub 2015 Apr 20.

9.

Genomation: a toolkit to summarize, annotate and visualize genomic intervals.

Akalin A, Franke V, Vlahoviček K, Mason CE, Schübeler D.

Bioinformatics. 2015 Apr 1;31(7):1127-9. doi: 10.1093/bioinformatics/btu775. Epub 2014 Nov 21.

PMID:
25417204
10.

Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells.

Yukawa M, Akiyama T, Franke V, Mise N, Isagawa T, Suzuki Y, Suzuki MG, Vlahovicek K, Abe K, Aburatani H, Aoki F.

PLoS One. 2014 Mar 21;9(3):e92689. doi: 10.1371/journal.pone.0092689. eCollection 2014.

11.

Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs.

Godinic-Mikulcic V, Jaric J, Greber BJ, Franke V, Hodnik V, Anderluh G, Ban N, Weygand-Durasevic I.

Nucleic Acids Res. 2014 Apr;42(8):5191-201. doi: 10.1093/nar/gku164. Epub 2014 Feb 24.

12.

A cohesin-independent role for NIPBL at promoters provides insights in CdLS.

Zuin J, Franke V, van Ijcken WF, van der Sloot A, Krantz ID, van der Reijden MI, Nakato R, Lenhard B, Wendt KS.

PLoS Genet. 2014 Feb 13;10(2):e1004153. doi: 10.1371/journal.pgen.1004153. eCollection 2014 Feb.

13.

A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes.

Flemr M, Malik R, Franke V, Nejepinska J, Sedlacek R, Vlahovicek K, Svoboda P.

Cell. 2013 Nov 7;155(4):807-16. doi: 10.1016/j.cell.2013.10.001.

14.

A novel complex, RUNX1-MYEF2, represses hematopoietic genes in erythroid cells.

van Riel B, Pakozdi T, Brouwer R, Monteiro R, Tuladhar K, Franke V, Bryne JC, Jorna R, Rijkers EJ, van Ijcken W, Andrieu-Soler C, Demmers J, Patient R, Soler E, Lenhard B, Grosveld F.

Mol Cell Biol. 2012 Oct;32(19):3814-22. doi: 10.1128/MCB.05938-11. Epub 2012 Jul 16.

15.

The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner.

Sleutels F, Soochit W, Bartkuhn M, Heath H, Dienstbach S, Bergmaier P, Franke V, Rosa-Garrido M, van de Nobelen S, Caesar L, van der Reijden M, Bryne JC, van Ijcken W, Grootegoed JA, Delgado MD, Lenhard B, Renkawitz R, Grosveld F, Galjart N.

Epigenetics Chromatin. 2012 Jun 18;5(1):8. doi: 10.1186/1756-8935-5-8.

16.

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

Afgan E, Chapman B, Jadan M, Franke V, Taylor J.

Curr Protoc Bioinformatics. 2012 Jun;Chapter 11:Unit11.9. doi: 10.1002/0471250953.bi1109s38.

17.

Prediction of interacting protein residues using sequence and structure data.

Franke V, Sikić M, Vlahoviček K.

Methods Mol Biol. 2012;819:233-51. doi: 10.1007/978-1-61779-465-0_16.

PMID:
22183541

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