Published in RNA on June 24, 2009
Evaluation of normalization methods in mammalian microRNA-Seq data. RNA (2012) 1.68
Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach. Genome Biol (2012) 1.31
The history and enduring contributions of planarians to the study of animal regeneration. Wiley Interdiscip Rev Dev Biol (2012) 1.28
The planarian flatworm: an in vivo model for stem cell biology and nervous system regeneration. Dis Model Mech (2010) 1.09
Discovery of novel human breast cancer microRNAs from deep sequencing data by analysis of pri-microRNA secondary structures. PLoS One (2011) 1.05
Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. PLoS One (2012) 1.04
Profiles of small non-coding RNAs in Schistosoma japonicum during development. PLoS Negl Trop Dis (2011) 1.02
Sex-biased expression of microRNAs in Schistosoma mansoni. PLoS Negl Trop Dis (2013) 0.98
Evolution of the let-7 microRNA family. RNA Biol (2012) 0.97
Substantial loss of conserved and gain of novel MicroRNA families in flatworms. Mol Biol Evol (2013) 0.96
Genome-wide approaches in the study of microRNA biology. Wiley Interdiscip Rev Syst Biol Med (2010) 0.95
A deep analysis of the small non-coding RNA population in Schistosoma japonicum eggs. PLoS One (2013) 0.95
Different miRNA expression profiles between human breast cancer tumors and serum. Front Genet (2014) 0.94
A critical appraisal of the use of microRNA data in phylogenetics. Proc Natl Acad Sci U S A (2014) 0.89
The miR-35-41 family of microRNAs regulates RNAi sensitivity in Caenorhabditis elegans. PLoS Genet (2012) 0.88
The CCR4-NOT complex mediates deadenylation and degradation of stem cell mRNAs and promotes planarian stem cell differentiation. PLoS Genet (2013) 0.84
microRNAs in parasites and parasite infection. RNA Biol (2013) 0.84
Identification of neoblast- and regeneration-specific miRNAs in the planarian Schmidtea mediterranea. RNA (2013) 0.81
Bioinformatic challenges of big data in non-coding RNA research. Front Genet (2012) 0.79
Loss of DNA mismatch repair imparts a selective advantage in planarian adult stem cells. PLoS One (2011) 0.78
Concise review: new frontiers in microRNA-based tissue regeneration. Stem Cells Transl Med (2014) 0.77
High-Throughput Profiling of Caenorhabditis elegans Starvation-Responsive microRNAs. PLoS One (2015) 0.76
Identification of microRNA genes in three opisthorchiids. PLoS Negl Trop Dis (2015) 0.75
Linkage of microRNA and proteome-based profiling data sets: a perspective for the priorization of candidate biomarkers in renal cell carcinoma? J Proteome Res (2011) 0.75
The miR-124 family of microRNAs is critical for regeneration of the brain and visual system in the planarian Schmidtea mediterranea. Development (2017) 0.75
Small RNAome sequencing delineates the small RNA landscape of pluripotent adult stem cells in the planarian Schmidtea mediterranea. Genom Data (2017) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature (2000) 39.31
RAS is regulated by the let-7 microRNA family. Cell (2005) 30.24
Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature (2000) 19.15
MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol (2005) 18.94
let-7 regulates self renewal and tumorigenicity of breast cancer cells. Cell (2007) 13.69
Getting to the root of miRNA-mediated gene silencing. Cell (2008) 7.17
SMEDWI-2 is a PIWI-like protein that regulates planarian stem cells. Science (2005) 3.83
Depletion of human micro-RNA miR-125b reveals that it is critical for the proliferation of differentiated cells but not for the down-regulation of putative targets during differentiation. J Biol Chem (2005) 3.33
Not your father's planarian: a classic model enters the era of functional genomics. Nat Rev Genet (2002) 3.06
Molecular analysis of stem cells and their descendants during cell turnover and regeneration in the planarian Schmidtea mediterranea. Cell Stem Cell (2008) 2.73
The Schmidtea mediterranea database as a molecular resource for studying platyhelminthes, stem cells and regeneration. Development (2002) 2.71
Planarian homologs of netrin and netrin receptor are required for proper regeneration of the central nervous system and the maintenance of nervous system architecture. Development (2005) 2.15
Isolation of planarian X-ray-sensitive stem cells by fluorescence-activated cell sorting. Dev Growth Differ (2006) 1.94
The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians. RNA (2008) 1.87
The planarian Schmidtea mediterranea as a model for epigenetic germ cell specification: analysis of ESTs from the hermaphroditic strain. Proc Natl Acad Sci U S A (2005) 1.85
Planarian regeneration: its end is its beginning. Cell (2006) 1.81
nanos function is essential for development and regeneration of planarian germ cells. Proc Natl Acad Sci U S A (2007) 1.56
MicroRNAs from the Planarian Schmidtea mediterranea: a model system for stem cell biology. RNA (2006) 1.42
MicroRNAs and regeneration: Let-7 members as potential regulators of dedifferentiation in lens and inner ear hair cell regeneration of the adult newt. Biochem Biophys Res Commun (2007) 1.26
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci U S A (2008) 11.86
RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell (2009) 11.12
Divergent transcription from active promoters. Science (2008) 11.03
Expansion of the eukaryotic proteome by alternative splicing. Nature (2010) 8.84
A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells. Cell (2010) 7.51
Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Nat Neurosci (2011) 6.01
RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc Natl Acad Sci U S A (2007) 5.26
L1 retrotransposition in human neural progenitor cells. Nature (2009) 4.78
In vivo demonstration that alpha-synuclein oligomers are toxic. Proc Natl Acad Sci U S A (2011) 4.38
Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol (2010) 4.22
Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Mol Cell (2012) 3.96
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res (2004) 3.70
Identification of alternative splicing regulators by RNA interference in Drosophila. Proc Natl Acad Sci U S A (2004) 3.58
Transcriptional signature and memory retention of human-induced pluripotent stem cells. PLoS One (2009) 3.07
Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration. Proc Natl Acad Sci U S A (2013) 2.95
Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. Nat Neurosci (2012) 2.93
Genomewide characterization of non-polyadenylated RNAs. Genome Biol (2011) 2.92
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep (2012) 2.76
The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression. Cell (2007) 2.72
Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Res (2010) 2.69
Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics (2002) 2.54
The transcriptional diversity of 25 Drosophila cell lines. Genome Res (2010) 2.47
Diversity and dynamics of the Drosophila transcriptome. Nature (2014) 2.47
Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res (2010) 2.43
Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res (2010) 2.29
Dynamic integration of splicing within gene regulatory pathways. Cell (2013) 2.25
Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep (2012) 1.99
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Mol Cell (2012) 1.93
Cdk5 regulates accurate maturation of newborn granule cells in the adult hippocampus. PLoS Biol (2008) 1.92
The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians. RNA (2008) 1.87
A computational and experimental approach toward a priori identification of alternatively spliced exons. RNA (2004) 1.79
Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS Genet (2006) 1.71
Plant-derived flavanol (-)epicatechin enhances angiogenesis and retention of spatial memory in mice. J Neurosci (2007) 1.63
RS domains contact the pre-mRNA throughout spliceosome assembly. Trends Biochem Sci (2005) 1.59
Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Mol Cell (2013) 1.56
LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans. Nat Struct Mol Biol (2011) 1.51
Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol (2013) 1.49
ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43. Proc Natl Acad Sci U S A (2013) 1.48
Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci U S A (2010) 1.47
Misregulated RNA processing in amyotrophic lateral sclerosis. Brain Res (2012) 1.42
MicroRNAs from the Planarian Schmidtea mediterranea: a model system for stem cell biology. RNA (2006) 1.42
Exon-specific RNAi: a tool for dissecting the functional relevance of alternative splicing. RNA (2002) 1.41
Gene expression profiling of neural stem cells and their neuronal progeny reveals IGF2 as a regulator of adult hippocampal neurogenesis. J Neurosci (2012) 1.40
A regulator of Dscam mutually exclusive splicing fidelity. Nat Struct Mol Biol (2007) 1.35
RNA structure and the mechanisms of alternative splicing. Curr Opin Genet Dev (2011) 1.35
The origins and implications of Aluternative splicing. Trends Genet (2004) 1.35
Molecular biology: power sequencing. Nature (2008) 1.33
High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection. J Virol (2011) 1.28
microRNA-Seq reveals cocaine-regulated expression of striatal microRNAs. RNA (2011) 1.26
The genome of Anopheles darlingi, the main neotropical malaria vector. Nucleic Acids Res (2013) 1.16
Hippocampus-dependent learning is associated with adult neurogenesis in MRL/MpJ mice. Hippocampus (2009) 1.13
The iStem, a long-range RNA secondary structure element required for efficient exon inclusion in the Drosophila Dscam pre-mRNA. Mol Cell Biol (2005) 1.09
Enhancer-dependent 5'-splice site control of fruitless pre-mRNA splicing. J Biol Chem (2003) 1.08
Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing. Genes Dev (2003) 1.05
Tempo and mode of regulatory evolution in Drosophila. Genome Res (2014) 1.05
Probabilistic splicing of Dscam1 establishes identity at the level of single neurons. Cell (2013) 1.05
The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion. Annu Rev Biochem (2015) 1.04
Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. PLoS One (2012) 1.04
Competing RNA secondary structures are required for mutually exclusive splicing of the Dscam exon 6 cluster. RNA (2010) 1.04
The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus. Mol Microbiol (2014) 1.02
Characterization of U2AF(6), a splicing factor related to U2AF(35). Mol Cell Biol (2002) 1.01
Genomic imprinting absent in Drosophila melanogaster adult females. Cell Rep (2012) 1.00
Arginine/serine repeats are sufficient to constitute a splicing activation domain. Nucleic Acids Res (2003) 1.00
Stem cells: the good, bad and barely in control. Nat Med (2006) 0.98
Gene dosage-dependent rescue of HSP neurite defects in SPG4 patients' neurons. Hum Mol Genet (2013) 0.96
Programmable plasmid interference by the CRISPR-Cas system in Thermococcus kodakarensis. RNA Biol (2013) 0.96
Coordinate Nodal and BMP inhibition directs Baf60c-dependent cardiomyocyte commitment. Genes Dev (2013) 0.96
Genome-wide approaches in the study of microRNA biology. Wiley Interdiscip Rev Syst Biol Med (2010) 0.95
Massive expansions of Dscam splicing diversity via staggered homologous recombination during arthropod evolution. RNA (2009) 0.95
Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata. Nucleic Acids Res (2012) 0.94
Evidence for premature aging due to oxidative stress in iPSCs from Cockayne syndrome. Hum Mol Genet (2012) 0.94
Complex alternative splicing. Adv Exp Med Biol (2007) 0.94
Somatic mutations in SQSTM1 detected in affected tissues from patients with sporadic Paget's disease of bone. J Bone Miner Res (2009) 0.94
Alternative splicing in stem cell self-renewal and diferentiation. Adv Exp Med Biol (2010) 0.92
Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling. J Biol Chem (2013) 0.92
Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration. Dev Growth Differ (2012) 0.91
Splicing bioinformatics to biology. Genome Biol (2006) 0.91
Human cytomegalovirus infection of human embryonic stem cell-derived primitive neural stem cells is restricted at several steps but leads to the persistence of viral DNA. J Virol (2014) 0.91
Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases. Front Neurosci (2012) 0.91
Evolution of splicing regulatory networks in Drosophila. Genome Res (2014) 0.90
Multicellular self-assembled spheroidal model of the blood brain barrier. Sci Rep (2013) 0.90
Coordinated control of splicing and translation. Nat Struct Mol Biol (2005) 0.86
Sixty years of genome biology. Genome Biol (2013) 0.85
A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. Stem Cells Dev (2010) 0.85
Use of RNA interference to dissect the roles of trans-acting factors in alternative pre-mRNA splicing. Methods (2005) 0.85
New insights from existing sequence data: generating breakthroughs without a pipette. Mol Cell (2013) 0.84
Exon-specific RNA interference: a tool to determine the functional relevance of proteins encoded by alternatively spliced mRNAs. Methods Mol Biol (2005) 0.84
Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans. PLoS Genet (2013) 0.83