Genome Biology | Tags

1.

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

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

Abstract | Provisional PDF | PubMed | Editor’s summary

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

2.

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

Florian Erhard, Lars Dolken, 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

3.

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

Shivendra Kishore, Andreas R Gruber, Dominik J Jedlinski, Afzal P Syed, Hadi Jorjani, Mihaela Zavolan Genome Biology 2013, 14:R45 (26 May 2013)

Abstract | Provisional PDF | PubMed | Editor’s summary

PAR-CLIP of snoRNA-associated proteins reveals the existence of extensive human loci that are processed into snoRNAs

4.

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.

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.

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.

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)

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

8.

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 | Editor’s summary

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

9.

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.

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.

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.

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)

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

13.

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)

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

14.

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.

15.

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

16.

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)

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

17.

The SR protein family

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

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

18.

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)

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.

	All
	1.	Research Experimental characterization of the human non-sequence-specific nucleic acid interactome Gerhard Duernberger, Tilmann Burckstummer, Kilian Huber, Roberto Giambruno, Tobias Doerks, Evren Karayel, Thomas R Burkard, Ines Kaupe, Andre C Muller, Andreas Schonegger, Gerhard F Ecker, Hans Lohninger, Peer Bork, Keiryn L Bennett, Giulio Superti-Furga, Jacques Colinge Genome Biology 2013, 14:R81 (31 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A mass spectrometry and bioinformatics approach identifies human proteins that bind nucleic acids in a non-sequence-specific manner
	2.	Software PARma: identification of microRNA target sites in Argonaute PAR-CLIP data Florian Erhard, Lars Dolken, 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
	3.	Research Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing Shivendra Kishore, Andreas R Gruber, Dominik J Jedlinski, Afzal P Syed, Hadi Jorjani, Mihaela Zavolan Genome Biology 2013, 14:R45 (26 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary PAR-CLIP of snoRNA-associated proteins reveals the existence of extensive human loci that are processed into snoRNAs
	4.	Research 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 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 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 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 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 \| Editor’s summary Jernej Ule and colleagues highlight two recent studies that have identified many novel RNA-binding proteins
	9.	Research 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 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 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 *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
	13.	Method 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
	14.	Research 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.
	15.	Research highlight 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
	16.	Research *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
	17.	Protein family review 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.
	18.	Research 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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