“Hypothesis for the Modern RNA World”: A pervasive Non-coding RNA-Based Genetic Regulation is a Prerequisite for the Emergence of Multicellular Complexity

The Multiple Origins of Complex Multicellularity

(2011) Andrew H. Knoll   Annual Review of Earth and Planetary Sciences

The Repatterning of Eukaryotic Genomes by Random Genetic Drift

(2011) Michael Lynch et al.   Annual Review of Genomics and Human Genetics

Pervasive transcription – Lessons from yeast

(2011) Mathieu Tisseur et al.   BIOCHIMIE

From snoRNA to miRNA: Dual function regulatory non-coding RNAs

(2011) Michelle S. Scott et al.   BIOCHIMIE

Computational discovery of human coding and non-coding transcripts with conserved splice sites

(2011) Dominic Rose et al.   BIOINFORMATICS

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

(2011) Philipp Kapranov et al.   BMC BIOLOGY

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Non-coding RNAs as regulators of embryogenesis

(2011) Andrea Pauli et al.   NATURE REVIEWS GENETICS

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project

(2011) Xinmeng Jasmine Mu et al.   NUCLEIC ACIDS RESEARCH

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

Response to “The Reality of Pervasive Transcription”

(2011) Harm van Bakel et al.   PLOS BIOLOGY

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

7SK snRNA: a noncoding RNA that plays a major role in regulating eukaryotic transcription

(2011) B. Matija Peterlin et al.   Wiley Interdisciplinary Reviews-RNA

MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis

(2010) M. D. Nodine et al.   GENES & DEVELOPMENT

Diverse Pathways Generate MicroRNA-like RNAs and Dicer-Independent Small Interfering RNAs in Fungi

(2010) Heng-Chi Lee et al.   MOLECULAR CELL

Enhancers make non-coding RNA

(2010) Bing Ren   NATURE

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

(2010) J. Mark Cock et al.   NATURE

Ancient animal microRNAs and the evolution of tissue identity

(2010) Foteini Christodoulou et al.   NATURE

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

The energetics of genome complexity

(2010) Nick Lane et al.   NATURE

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Shifts in metabolic scaling, production, and efficiency across major evolutionary transitions of life

(2010) J. P. DeLong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Benefits and costs of the grazer-induced colony formation inMicrocystis aeruginosa

(2009) Zhen Yang et al.   ANNALES DE LIMNOLOGIE-INTERNATIONAL JOURNAL OF LIMNOLOGY

Flower Evolution: The Origin and Subsequent Diversification of the Angiosperm Flower

(2009) Chelsea D. Specht et al.   Annual Review of Ecology Evolution and Systematics

MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion

(2009) Kevin J. Peterson et al.   BIOESSAYS

Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects

(2009) Francis Repoila et al.   BIOLOGY OF THE CELL

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Pervasive transcription constitutes a new level of eukaryotic genome regulation

(2009) Julia Berretta et al.   EMBO REPORTS

Long noncoding RNAs: functional surprises from the RNA world

(2009) J. E. Wilusz et al.   GENES & DEVELOPMENT

Conserved introns reveal novel transcripts in Drosophila melanogaster

(2009) M. Hiller et al.   GENOME RESEARCH

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

Biogenesis of small RNAs in animals

(2009) V. Narry Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MicroRNAs: key regulators of stem cells

(2009) Vamsi K. Gangaraju et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Early origin of the bilaterian developmental toolkit

(2009) D. H. Erwin   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"

(2009) V. Hampl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide evolutionary analysis of the noncoding RNA genes and noncoding DNA of Paramecium tetraurelia

(2009) C.-L. Chen et al.   RNA

Small RNAs Originated from Pseudogenes: cis- or trans-Acting?

(2009) Xingyi Guo et al.   PLoS Computational Biology

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

(2009) Ana C Marques et al.   GENOME BIOLOGY

The Origins of Multicellularity and the Early History of the Genetic Toolkit For Animal Development

(2008) Antonis Rokas   Annual Review of Genetics

MicroRNAs: components of an integrated system controlling cardiac development, physiology, and disease pathogenesis

(2008) G. Condorelli et al.   CARDIOVASCULAR RESEARCH

The evolution and functional diversification of animal microRNA genes

(2008) Na Liu et al.   CELL RESEARCH

The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks

(2008) Irma Lozada-Chávez et al.   JOURNAL OF MOLECULAR BIOLOGY

Arthropod 7SK RNA

(2008) A. R. Gruber et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive Evolution of Newly Emerged Micro-RNA Genes in Drosophila

(2008) J. Lu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

(2008) Nicole King et al.   NATURE

The birth and death of microRNA genes in Drosophila

(2008) Jian Lu et al.   NATURE GENETICS

Structurally different alleles of the ath-MIR824microRNA precursor are maintained at high frequency inArabidopsis thaliana

(2008) Juliette de Meaux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNAs and the advent of vertebrate morphological complexity

(2008) A. M. Heimberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Eukaryotic Genome as an RNA Machine

(2008) P. P. Amaral et al.   SCIENCE

The let-7 family of microRNAs

(2008) Sarah Roush et al.   TRENDS IN CELL BIOLOGY

Switching the light on plant riboswitches

(2008) Samuel E. Bocobza et al.   TRENDS IN PLANT SCIENCE

Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

(2007) T. Mourier et al.   GENOME RESEARCH