Published in RNA on June 19, 2008
The Norway spruce genome sequence and conifer genome evolution. Nature (2013) 4.74
Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Opin Plant Biol (2009) 3.18
Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci U S A (2008) 1.92
Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol (2010) 1.81
Next-generation sequencing identifies the natural killer cell microRNA transcriptome. Genome Res (2010) 1.75
Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics (2010) 1.74
Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development. PLoS Genet (2008) 1.31
Identification and characterization of maize microRNAs involved in the very early stage of seed germination. BMC Genomics (2011) 1.30
Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing. BMC Plant Biol (2012) 1.09
High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L.). PLoS One (2011) 1.02
Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing. BMC Genomics (2011) 1.02
Dynamic expression of small RNA populations in larch (Larix leptolepis). Planta (2012) 0.95
A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species. Plant Physiol (2013) 0.95
Evidence for small RNAs homologous to effector-encoding genes and transposable elements in the oomycete Phytophthora infestans. PLoS One (2012) 0.89
Comparative profiling of miRNA expression in developing seeds of high linoleic and high oleic safflower (Carthamus tinctorius L.) plants. Front Plant Sci (2013) 0.86
Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants. Plant Cell (2015) 0.85
Ancient Origin and Recent Innovations of RNA Polymerase IV and V. Mol Biol Evol (2015) 0.85
Deep sequencing discovery of novel and conserved microRNAs in wild type and a white-flesh mutant strawberry. Planta (2013) 0.84
Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway. Genome Biol Evol (2015) 0.82
Deciphering small noncoding RNAs during the transition from dormant embryo to germinated embryo in Larches (Larix leptolepis). PLoS One (2013) 0.81
Identification and Characterization of MicroRNAs in Ginkgo biloba var. epiphylla Mak. PLoS One (2015) 0.78
The pivotal role of small non-coding RNAs in the regulation of seed development. Plant Cell Rep (2017) 0.78
Identification and characterization of microRNAs from tree peony (Paeonia ostii) and their response to copper stress. PLoS One (2015) 0.77
Characterization and comparative profiling of the small RNA transcriptomes in two phases of flowering in Cymbidium ensifolium. BMC Genomics (2015) 0.77
Identification and expression profiles of sRNAs and their biogenesis and action-related genes in male and female cones of Pinus tabuliformis. BMC Genomics (2015) 0.76
Expression patterns of conserved microRNAs in the male gametophyte of loblolly pine (Pinus taeda). Plant Reprod (2014) 0.76
Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana). G3 (Bethesda) (2016) 0.76
An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers. Genome Biol Evol (2016) 0.76
Landscape of fluid sets of hairpin-derived 21-/24-nt-long small RNAs at seed set uncovers special epigenetic features in Picea glauca. Genome Biol Evol (2017) 0.75
Leaf Hydraulic Architecture and Stomatal Conductance: A Functional Perspective. Plant Physiol (2017) 0.75
MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol (2006) 14.44
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev (2006) 11.71
Elucidation of the small RNA component of the transcriptome. Science (2005) 8.66
Two classes of short interfering RNA in RNA silencing. EMBO J (2002) 8.54
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell (2005) 7.58
Epigenetic inheritance in plants. Nature (2007) 7.40
Methylation as a crucial step in plant microRNA biogenesis. Science (2005) 7.16
Heterochromatin and epigenetic control of gene expression. Science (2003) 7.12
RNAi-mediated pathways in the nucleus. Nat Rev Genet (2005) 6.55
Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science (2006) 6.33
Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nat Cell Biol (2004) 5.92
Structural basis for double-stranded RNA processing by Dicer. Science (2006) 5.86
Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet (2006) 5.81
DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2005) 5.16
RNA silencing genes control de novo DNA methylation. Science (2004) 5.11
Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol (2005) 4.98
Dicing and slicing: the core machinery of the RNA interference pathway. FEBS Lett (2005) 4.63
The diversity of RNA silencing pathways in plants. Trends Genet (2006) 4.32
Ferns diversified in the shadow of angiosperms. Nature (2004) 4.12
Common functions for diverse small RNAs of land plants. Plant Cell (2007) 3.30
On the origin and functions of RNA-mediated silencing: from protists to man. Curr Genet (2006) 3.05
Transposable elements and the evolution of genome size in eukaryotes. Genetica (2002) 3.00
RNAi-independent heterochromatin nucleation by the stress-activated ATF/CREB family proteins. Science (2004) 2.80
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res (2008) 2.70
Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr Opin Struct Biol (2006) 2.28
Evolution of DNA amounts across land plants (embryophyta). Ann Bot (2005) 2.26
The role of the RNAi machinery in heterochromatin formation. Cell (2005) 1.89
Extensive 3' modification of plant small RNAs is modulated by helper component-proteinase expression. Proc Natl Acad Sci U S A (2005) 1.82
The evolution and diversification of Dicers in plants. FEBS Lett (2006) 1.77
DNA methylation is independent of RNA interference in Neurospora. Science (2004) 1.66
RNA interference and heterochromatin in the fission yeast Schizosaccharomyces pombe. Trends Genet (2005) 1.47
DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold. Bioinformatics (2006) 1.21
Differential effects of heterochromatin protein 1 isoforms on mitotic chromosome distribution and growth in Dictyostelium discoideum. Eukaryot Cell (2006) 0.92
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
An obesity-associated gut microbiome with increased capacity for energy harvest. Nature (2006) 44.35
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature (2008) 38.13
Whole-genome sequencing and variant discovery in C. elegans. Nat Methods (2008) 31.92
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature (2010) 19.68
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods (2009) 18.41
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature (2009) 18.08
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (2009) 16.04
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res (2012) 15.90
Extending assembly of short DNA sequences to handle error. Bioinformatics (2007) 14.46
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature (2012) 14.33
Integrated genomic characterization of endometrial carcinoma. Nature (2013) 14.29
DNMT3A mutations in acute myeloid leukemia. N Engl J Med (2010) 14.07
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol (2003) 13.32
Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet (2009) 11.73
The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature (2012) 9.89
De novo gene disruptions in children on the autistic spectrum. Neuron (2012) 9.69
The origin and evolution of mutations in acute myeloid leukemia. Cell (2012) 9.66
Complete Khoisan and Bantu genomes from southern Africa. Nature (2010) 9.06
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat Genet (2004) 8.60
De novo transcriptome assembly with ABySS. Bioinformatics (2009) 8.38
Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature (2012) 8.03
Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature (2012) 7.76
Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat Genet (2012) 7.61
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Clonal architecture of secondary acute myeloid leukemia. N Engl J Med (2012) 6.71
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics (2010) 6.57
Next-generation tag sequencing for cancer gene expression profiling. Genome Res (2009) 6.50
Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res (2009) 6.42
Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell (2012) 6.09
Viral discovery and sequence recovery using DNA microarrays. PLoS Biol (2003) 5.95
The genome of a songbird. Nature (2010) 5.90
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
Mutation of FOXL2 in granulosa-cell tumors of the ovary. N Engl J Med (2009) 5.63
SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics (2011) 5.62
CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods (2011) 5.34
Modernizing reference genome assemblies. PLoS Biol (2011) 5.23
Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci U S A (2006) 5.13
Alternative expression analysis by RNA sequencing. Nat Methods (2010) 5.02
A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature (2012) 5.02
Novel mutations target distinct subgroups of medulloblastoma. Nature (2012) 4.82
MuSiC: identifying mutational significance in cancer genomes. Genome Res (2012) 4.73
Activating HER2 mutations in HER2 gene amplification negative breast cancer. Cancer Discov (2012) 4.72
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol (2011) 4.66
A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clin Cancer Res (2010) 4.61
ChIP-seq: welcome to the new frontier. Nat Methods (2007) 4.56
Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell (2012) 4.41
mrsFAST: a cache-oblivious algorithm for short-read mapping. Nat Methods (2010) 4.38
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A (2006) 4.18
Acquired copy number alterations in adult acute myeloid leukemia genomes. Proc Natl Acad Sci U S A (2009) 4.17
Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA (2011) 4.11
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A (2009) 4.09
Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One (2008) 4.03
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics (2010) 4.02
Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation. Blood (2010) 4.02
Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes. Nat Genet (2011) 4.02
Somatic mutations and germline sequence variants in the expressed tyrosine kinase genes of patients with de novo acute myeloid leukemia. Blood (2008) 3.89
Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts. Cell Rep (2013) 3.85
Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83
Distinct patterns of mutations occurring in de novo AML versus AML arising in the setting of severe congenital neutropenia. Blood (2007) 3.73
A burst of segmental duplications in the genome of the African great ape ancestor. Nature (2009) 3.63
Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol (2012) 3.62
Direct genomic selection. Nat Methods (2005) 3.61
In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res (2008) 3.55
Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat Genet (2013) 3.51
The genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat Genet (2013) 3.43
The genomics education partnership: successful integration of research into laboratory classes at a diverse group of undergraduate institutions. CBE Life Sci Educ (2010) 3.42
The next-generation sequencing revolution and its impact on genomics. Cell (2013) 3.35
The DNA sequence of human chromosome 7. Nature (2003) 3.18
A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell (2008) 3.10
The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression. Proc Natl Acad Sci U S A (2006) 3.07
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics (2006) 2.98
Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature (2010) 2.92
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics (2010) 2.90
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res (2008) 2.70
Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. JAMA (2011) 2.61
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol (2010) 2.60
PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Res (2007) 2.58
Association of age at diagnosis and genetic mutations in patients with neuroblastoma. JAMA (2012) 2.49
The Pediatric Cancer Genome Project. Nat Genet (2012) 2.49
Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma. Cancer Res (2008) 2.48