RNA-mediated gene regulation is less evolvable than transcriptional regulation
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Title
RNA-mediated gene regulation is less evolvable than transcriptional regulation
Authors
Keywords
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Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 115, Issue 15, Pages E3481-E3490
Publisher
Proceedings of the National Academy of Sciences
Online
2018-03-27
DOI
10.1073/pnas.1719138115
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- (2017) Ales Cvekl et al. Genome Biology and Evolution
- Structural properties of genotype–phenotype maps
- (2017) S. E. Ahnert Journal of the Royal Society Interface
- Alternative evolutionary histories in the sequence space of an ancient protein
- (2017) Tyler N. Starr et al. NATURE
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- (2017) Qin Cao et al. NATURE GENETICS
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- (2017) Alina Isakova et al. NATURE METHODS
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- (2017) Daniel Wilinski et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded
- (2017) Emily E. Wrenbeck et al. Nature Communications
- A thousand empirical adaptive landscapes and their navigability
- (2017) José Aguilar-Rodríguez et al. Nature Ecology & Evolution
- The Effect of Local Sequence Context on Mutational Bias of Genes Encoded on the Leading and Lagging Strands
- (2016) Jeremy W. Schroeder et al. CURRENT BIOLOGY
- Local fitness landscape of the green fluorescent protein
- (2016) Karen S. Sarkisyan et al. NATURE
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- (2016) Daniel Marbach et al. NATURE METHODS
- Genonets server—a web server for the construction, analysis and visualization of genotype networks
- (2016) Fahad Khalid et al. NUCLEIC ACIDS RESEARCH
- Network of epistatic interactions within a yeast snoRNA
- (2016) O. Puchta et al. SCIENCE
- The fitness landscape of a tRNA gene
- (2016) C. Li et al. SCIENCE
- The complete local genotype–phenotype landscape for the alternative splicing of a human exon
- (2016) Philippe Julien et al. Nature Communications
- Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability
- (2016) Sam F. Greenbury et al. PLoS Computational Biology
- High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop
- (2016) Chenxi Qiu et al. PLoS Genetics
- Environmental changes bridge evolutionary valleys
- (2016) B. Steinberg et al. Science Advances
- A global reference for human genetic variation
- (2015) Richard A. Gibbs et al. NATURE
- C2H2 zinc finger proteins greatly expand the human regulatory lexicon
- (2015) Hamed S Najafabadi et al. NATURE BIOTECHNOLOGY
- Recurrent somatic mutations in regulatory regions of human cancer genomes
- (2015) Collin Melton et al. NATURE GENETICS
- Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
- (2015) Nuala A. O'Leary et al. NUCLEIC ACIDS RESEARCH
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- (2015) Marjon G. J. de Vos et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2015) J. Rister et al. SCIENCE
- Pervasive degeneracy and epistasis in a protein-protein interface
- (2015) A. I. Podgornaia et al. SCIENCE
- Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets
- (2015) Gregory J. Hogan et al. PLOS BIOLOGY
- Dynamics of Transcription Factor Binding Site Evolution
- (2015) Murat Tuğrul et al. PLoS Genetics
- Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites
- (2015) Dave W Anderson et al. eLife
- Mechanisms of mutational robustness in transcriptional regulation
- (2015) Joshua L. Payne et al. Frontiers in Genetics
- Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
- (2014) Matthew T. Weirauch et al. CELL
- A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure
- (2014) S. F. Greenbury et al. Journal of the Royal Society Interface
- Genome-scale functional characterization of Drosophila developmental enhancers in vivo
- (2014) Evgeny Z. Kvon et al. NATURE
- Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes
- (2014) Jason D Buenrostro et al. NATURE BIOTECHNOLOGY
- Genome-wide analysis of noncoding regulatory mutations in cancer
- (2014) Nils Weinhold et al. NATURE GENETICS
- A census of human RNA-binding proteins
- (2014) Stefanie Gerstberger et al. NATURE REVIEWS GENETICS
- A unified design space of synthetic stripe-forming networks
- (2014) Yolanda Schaerli et al. Nature Communications
- RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
- (2014) Ian M Silverman et al. GENOME BIOLOGY
- Adaptive dynamics under development-based genotype–phenotype maps
- (2013) Isaac Salazar-Ciudad et al. NATURE
- A compendium of RNA-binding motifs for decoding gene regulation
- (2013) Debashish Ray et al. NATURE
- Genotype to phenotype: lessons from model organisms for human genetics
- (2013) Ben Lehner NATURE REVIEWS GENETICS
- Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges
- (2013) Michael T Lovci et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins
- (2013) Anton V. Persikov et al. NUCLEIC ACIDS RESEARCH
- Comprehensive experimental fitness landscape and evolutionary network for small RNA
- (2013) J. I. Jimenez et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- DNA-binding specificity changes in the evolution of forkhead transcription factors
- (2013) S. Nakagawa et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2013) I. Guerreiro et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2013) F. W. Huang et al. SCIENCE
- An expansive human regulatory lexicon encoded in transcription factor footprints
- (2012) Shane Neph et al. NATURE
- Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
- (2012) M. T. Maurano et al. SCIENCE
- Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
- (2012) Kevin Y Yip et al. GENOME BIOLOGY
- Tabix: fast retrieval of sequence features from generic TAB-delimited files
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- (2011) Svetlana Lebedeva et al. MOLECULAR CELL
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- (2011) Trevor Hinkley et al. NATURE GENETICS
- The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms
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- Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks
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- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients
- (2010) James Cotterell et al. Molecular Systems Biology
- Inducible gene expression: diverse regulatory mechanisms
- (2010) Vikki M. Weake et al. NATURE REVIEWS GENETICS
- Genotype-phenotype mapping and the end of the 'genes as blueprint' metaphor
- (2010) M. Pigliucci PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Rapid Construction of Empirical RNA Fitness Landscapes
- (2010) J. N. Pitt et al. SCIENCE
- Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same
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- RNA and Disease
- (2009) Thomas A. Cooper et al. CELL
- High-resolution DNA-binding specificity analysis of yeast transcription factors
- (2009) C. Zhu et al. GENOME RESEARCH
- Analysis of a complete DNA-protein affinity landscape
- (2009) W. Rowe et al. Journal of the Royal Society Interface
- Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
- (2009) Debashish Ray et al. NATURE BIOTECHNOLOGY
- A census of human transcription factors: function, expression and evolution
- (2009) Juan M. Vaquerizas et al. NATURE REVIEWS GENETICS
- RNA processing and its regulation: global insights into biological networks
- (2009) Donny D. Licatalosi et al. NATURE REVIEWS GENETICS
- Diversity and Complexity in DNA Recognition by Transcription Factors
- (2009) G. Badis et al. SCIENCE
- Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks
- (2009) João F. Matias Rodrigues et al. PLoS Computational Biology
- Neutralism and selectionism: a network-based reconciliation
- (2008) Andreas Wagner NATURE REVIEWS GENETICS
- RNA-binding proteins in human genetic disease
- (2008) Kiven E. Lukong et al. TRENDS IN GENETICS
- Robustness and evolvability: a paradox resolved
- (2007) A. Wagner PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
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