Recurrent rewiring and emergence of RNA regulatory networks

Evolution and Biological Roles of Alternative 3′UTRs

(2016) Christine Mayr   TRENDS IN CELL BIOLOGY

Protein-RNA networks revealed through covalent RNA marks

(2015) Christopher P Lapointe et al.   NATURE METHODS

Metabolic regulation in model ascomycetes – adjusting similar genomes to different lifestyles

(2015) Malcolm Whiteway et al.   TRENDS IN GENETICS

RNA regulatory networks diversified through curvature of the PUF protein scaffold

(2015) Daniel Wilinski et al.   Nature Communications

Glucose-Regulated Phosphorylation of the PUF Protein Puf3 Regulates the Translational Fate of Its Bound mRNAs and Association with RNA Granules

(2015) Chien-Der Lee et al.   Cell Reports

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets

(2015) Gregory J. Hogan et al.   PLOS BIOLOGY

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Extensive Rewiring and Complex Evolutionary Dynamics in a C. elegans Multiparameter Transcription Factor Network

(2013) John S. Reece-Hoyes et al.   MOLECULAR CELL

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution

(2013) Christopher R. Baker et al.   SCIENCE

Correction: Evolutionary principles of modular gene regulation in yeasts

(2013) Dawn A Thompson et al.   eLife

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

(2013) Mallory A Freeberg et al.   GENOME BIOLOGY

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

Rewiring of Posttranscriptional RNA Regulons: Puf4p in Fungi as an Example

(2012) Huifeng Jiang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity

(2012) Zachary T. Campbell et al.   Cell Reports

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator

(2010) Aaron M. Kershner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Landscape of C. elegans 3'UTRs

(2010) M. Mangone et al.   SCIENCE

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

PUF proteins: repression, activation and mRNA localization

(2010) Tara Quenault et al.   TRENDS IN CELL BIOLOGY

Evolutionary Tinkering with Conserved Components of a Transcriptional Regulatory Network

(2010) Hugo Lavoie et al.   PLOS BIOLOGY

Roles of Puf proteins in mRNA degradation and translation

(2010) Melanie A. Miller et al.   Wiley Interdisciplinary Reviews-RNA

From elements to modules: regulatory evolution in Ascomycota fungi

(2009) Dana J Wohlbach et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Tools for Fungal Proteomics: Multifunctional Neurospora Vectors for Gene Replacement, Protein Expression and Protein Purification

(2009) S. Honda et al.   GENETICS

A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs

(2009) D. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

(2009) Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The GAIT system: a gatekeeper of inflammatory gene expression

(2009) Rupak Mukhopadhyay et al.   TRENDS IN BIOCHEMICAL SCIENCES

Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation

(2008) Hervé Hogues et al.   MOLECULAR CELL

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p

(2008) Matthew T Miller et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System

(2008) Alessia Galgano et al.   PLoS One