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19 items(s) found

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1.

Research highlight   Subscription Highly Accessed

Learning the language of post-transcriptional gene regulation

Stefanie Gerstberger, Markus Hafner, Thomas Tuschl Genome Biology 2013, 14:130 (23 August 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

RNA-binding proteins: Stefanie Gerstberger, Markus Hafner and Thomas Tuschl on the language of post-transcriptional gene regulation

2.

Research   Open Access Highly Accessed

Experimental characterization of the human non-sequence-specific nucleic acid interactome

Gerhard Dürnberger, Tilmann Bürckstümmer, Kilian Huber, Roberto Giambruno, Tobias Doerks, Evren Karayel, Thomas R Burkard, Ines Kaupe, André C Müller, Andreas Schönegger, Gerhard F Ecker, Hans Lohninger, Peer Bork, Keiryn L Bennett, Giulio Superti-Furga, Jacques Colinge Genome Biology 2013, 14:R81 (31 July 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A mass spectrometry and bioinformatics approach identifies human proteins that bind nucleic acids in a non-sequence-specific manner

3.

Software   Open Access

PARma: identification of microRNA target sites in AGO-PAR-CLIP data

Florian Erhard, Lars Dölken, Lukasz Jaskiewicz, Ralf Zimmer Genome Biology 2013, 14:R79 (29 July 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

A new software tool for the identification of microRNA target sites in AGO-PAR-CLIP data

4.

Research   Open Access

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

Mallory A Freeberg, Ting Han, James J Moresco, Andy Kong, Yu-Cheng Yang, Zhi Lu, John R Yates, John K Kim Genome Biology 2013, 14:R13 (14 February 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A study of the global binding of RNA binding proteins in yeast in response to stress

5.

Protein family review   Subscription

The ADAR protein family

Yiannis A Savva, Leila E Rieder, Robert A Reenan Genome Biology 2012, 13:252 (28 December 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

ADARs and RNA editing: a Protein Family Review by Robert Reenan and colleagues

6.

Research highlight   Subscription Highly Accessed

Dicer partners expand the repertoire of miRNA targets

Lukasz Jaskiewicz, Mihaela Zavolan Genome Biology 2012, 13:179 (29 November 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A Research Highlight by Lukasz Jaskiewicz and Mihaela Zavolan discusses how cofactors modify Dicer processing and, consequently, transcriptional networks

7.

Method   Open Access Highly Accessed

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule Genome Biology 2012, 13:R67 (3 August 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The CLIP and iCLIP methods are compared for their utility in determining RNA binding protein binding sites

8.

Research highlight   Free Highly Accessed

The greatest catch: big game fishing for mRNA-bound proteins

Christopher R Sibley, Jan Attig, Jernej Ule Genome Biology 2012, 13:163 (17 July 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Jernej Ule and colleagues highlight two recent studies that have identified many novel RNA-binding proteins

9.

Research   Open Access

Regulation of alternative splicing by the circadian clock and food related cues

Nicholas J McGlincy, Amandine Valomon, Johanna E Chesham, Elizabeth S Maywood, Michael H Hastings, Jernej Ule Genome Biology 2012, 13:R54 (21 June 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

An extensive analysis of how the circadian clock and the physiological cue of feeding regulates alternative splicing in mice

10.

Research   Open Access Highly Accessed

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

Minna-Liisa Änkö, Michaela Müller-McNicoll, Holger Brandl, Tomaz Curk, Crtomir Gorup, Ian Henry, Jernej Ule, Karla M Neugebauer Genome Biology 2012, 13:R17 (21 March 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

RNA-binding protein SRSF3 is the master regulator of a splicing network, and - together with SRSF4 - mysteriously regulates unsplicable histone transcripts

11.

Research highlight   Free

Maternal-to-zygotic transition: soma versus germline

Martine Simonelig Genome Biology 2012, 13:145 (22 February 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Martine Simonelig highlights our Research article on differences between the Drosophila maternal-to-zygotic transition in primordial germ cells and soma

12.

Research highlight   Free

Extensive regulation of NAGNAG alternative splicing: new tricks for the spliceosome?

Anke Busch, Klemens J Hertel Genome Biology 2012, 13:143 (22 February 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Anke Busch and Klemens Hertel highlight a recent RNA-seq study demonstrating that alternative tandem acceptor splicing is tissue-specifically regulated

13.

Research   Open Access

Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells

Najeeb U Siddiqui, Xiao Li, Hua Luo, Angelo Karaiskakis, Huayun Hou, Thomas Kislinger, J Timothy Westwood, Quaid Morris, Howard D Lipshitz Genome Biology 2012, 13:R11 (20 February 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Maternal-to-zygotic transition in Drosophila primordial germ cells is delayed relative to the soma and requires the RNA-binding protein Smaug

14.

Method   Open Access Highly Accessed

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

David L Corcoran, Stoyan Georgiev, Neelanjan Mukherjee, Eva Gottwein, Rebecca L Skalsky, Jack D Keene, Uwe Ohler Genome Biology 2011, 12:R79 (18 August 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A method for identifying RNA binding sites and miRNA target motifs from PAR-CLIP data

15.

Research   Open Access

Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins

Tanja Scherrer, Christian Femmer, Ralph Schiess, Ruedi Aebersold, André P Gerber Genome Biology 2011, 12:R3 (13 January 2011)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The RNA targets of the yeast zinc-finger RNA binding protein, Gis2p, are conserved in the human homolog, ZNF9.

16.

Research highlight   Free Highly Accessed

Metastasis suppression: a role of the Dice(r)

Scott Valastyan, Robert A Weinberg Genome Biology 2010, 11:141 (30 November 2010)

Abstract | Full text | PDF | PubMed

17.

Research   Open Access Highly Accessed

Genome-wide analysis of mRNA decay patterns during early Drosophila development

Stefan Thomsen, Simon Anders, Sarath Chandra Janga, Wolfgang Huber, Claudio R Alonso Genome Biology 2010, 11:R93 (21 September 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A study of mRNA decay in Drosophila embryos identifies maternally- and zygotically-encoded factors regulating mRNA degradation

18.

Protein family review   Free

The SR protein family

Peter J Shepard, Klemens J Hertel Genome Biology 2009, 10:242 (27 October 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The SR proteins are not only involved in pre-mRNA splicing but in mRNA export and the initiation of translation.

19.

Research   Open Access Highly Accessed

Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors

Margarida Gama-Carvalho, Nuno L Barbosa-Morais, Alexander S Brodsky, Pamela A Silver, Maria Carmo-Fonseca Genome Biology 2006, 7:R113 (30 November 2006)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A genome wide identification of mRNAs that were associated with the splicing factor subunit U2AF65 suggests that U2AF65 associates with specific subsets of spliced mRNAs and may be involved in novel cellular functions in addition to splicing.

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