Published in PLoS One on February 15, 2013
How to interpret methylation sensitive amplified polymorphism (MSAP) profiles? BMC Genet (2014) 1.01
Rapid genomic DNA changes in allotetraploid fish hybrids. Heredity (Edinb) (2015) 0.86
Epigenetic control of mobile DNA as an interface between experience and genome change. Front Genet (2014) 0.79
MicroRNA profiles reveal female allotetraploid hybrid fertility. BMC Genet (2015) 0.75
AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res (1995) 45.26
The advantages and disadvantages of being polyploid. Nat Rev Genet (2005) 6.52
Hybrid speciation. Nature (2007) 6.52
Role for DNA methylation in the control of cell type specific maspin expression. Nat Genet (2002) 4.72
Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet (2009) 4.57
Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol (2007) 4.07
Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids. Plant Cell (2000) 3.83
The evolutionary consequences of polyploidy. Cell (2007) 3.80
Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res (1994) 3.76
Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics (2002) 3.67
Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes Dev (1997) 3.56
Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell (2007) 3.21
Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc Natl Acad Sci U S A (2001) 2.75
Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos Trans R Soc Lond B Biol Sci (2001) 2.66
Genome evolution and biodiversity in teleost fish. Heredity (Edinb) (2005) 2.65
Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol (2005) 2.53
Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol (2002) 2.41
Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proc Natl Acad Sci U S A (1998) 2.25
Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genet (1999) 2.23
Epigenetic phenomena and the evolution of plant allopolyploids. Mol Phylogenet Evol (2003) 1.95
Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Mol Genet Genomics (2002) 1.77
Changes in genomic methylation patterns during the formation of triploid asexual dandelion lineages. Mol Ecol (2009) 1.76
Aberrant methylation of the BRCA1 CpG island promoter is associated with decreased BRCA1 mRNA in sporadic breast cancer cells. Oncogene (1998) 1.74
Epigenetic silencing of maspin gene expression in human breast cancers. Int J Cancer (2000) 1.56
Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogenet Genome Res (2005) 1.48
Stable epigenetic effects impact adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae). Mol Biol Evol (2010) 1.42
Retrotransposon activation followed by rapid repression in introgressed rice plants. Genome (2000) 1.39
Methylation-related chromatin structure is associated with exclusion of transcription factors from and suppressed expression of the O-6-methylguanine DNA methyltransferase gene in human glioma cell lines. Mol Cell Biol (1994) 1.33
Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae). Mol Ecol (2010) 1.05
Distant hybridization leads to different ploidy fishes. Sci China Life Sci (2010) 1.05
Polyploid organisms. Sci China Life Sci (2012) 0.91
Variation in cytosine methylation patterns during ploidy level conversions in Eragrostis curvula. Plant Mol Biol (2009) 0.88
Novel genetic markers derived from the DNA fragments of Sox genes. Mol Cell Probes (2009) 0.87
Detecting differences in 5-methylcytosine using restriction enzyme isoschizomers: an endogenous control for complete digestion. Nucleic Acids Res (1995) 0.83
Snapshot of DNA methylation changes associated with hybridization in Xenopus. Physiol Genomics (2011) 0.82
Isolation and expression analysis of testicular type Sox9b in allotetraploid fish. Mar Biotechnol (NY) (2007) 0.78
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
Disability-adjusted life years (DALYs) for 291 diseases and injuries in 21 regions, 1990-2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet (2012) 41.47
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990-2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet (2012) 26.95
Enterotypes of the human gut microbiome. Nature (2011) 24.36
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy (2012) 20.08
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell (2010) 15.20
WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med (2009) 10.54
Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science (2010) 10.30
Increased methylation variation in epigenetic domains across cancer types. Nat Genet (2011) 8.92
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94
Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res (2008) 7.45
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med (2011) 7.11
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature (2011) 6.73
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62
Association of FKBP5 polymorphisms and childhood abuse with risk of posttraumatic stress disorder symptoms in adults. JAMA (2008) 6.60
Aberrant excitatory neuronal activity and compensatory remodeling of inhibitory hippocampal circuits in mouse models of Alzheimer's disease. Neuron (2007) 6.60
Niemann-Pick C1 Like 1 protein is critical for intestinal cholesterol absorption. Science (2004) 6.19
Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist. Science (2010) 5.86
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73
Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62
Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58
Building the sequence map of the human pan-genome. Nat Biotechnol (2009) 5.53
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet (2010) 5.20
Structure of the human κ-opioid receptor in complex with JDTic. Nature (2012) 5.18
Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16
An inhibitor of mutant IDH1 delays growth and promotes differentiation of glioma cells. Science (2013) 5.10
JAK mutations in high-risk childhood acute lymphoblastic leukemia. Proc Natl Acad Sci U S A (2009) 4.98
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Hippo pathway inhibits Wnt signaling to restrain cardiomyocyte proliferation and heart size. Science (2011) 4.76
Influence of child abuse on adult depression: moderation by the corticotropin-releasing hormone receptor gene. Arch Gen Psychiatry (2008) 4.65
Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ (2011) 4.50
Rearrangement of CRLF2 in B-progenitor- and Down syndrome-associated acute lymphoblastic leukemia. Nat Genet (2009) 4.35
Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A (2012) 4.26
The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol (2010) 4.25
Regression of castrate-recurrent prostate cancer by a small-molecule inhibitor of the amino-terminus domain of the androgen receptor. Cancer Cell (2010) 4.16
KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics (2006) 4.15
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Dynamic T cell migration program provides resident memory within intestinal epithelium. J Exp Med (2010) 4.09
Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet (2012) 4.07
Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet (2010) 4.06
Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell (2012) 4.03
Essential roles of S-nitrosothiols in vascular homeostasis and endotoxic shock. Cell (2004) 3.98
Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature (2010) 3.95
Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nat Genet (2013) 3.87
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol (2012) 3.83
Plasma microRNA panel to diagnose hepatitis B virus-related hepatocellular carcinoma. J Clin Oncol (2011) 3.80
Comparative population genomics of maize domestication and improvement. Nat Genet (2012) 3.78
Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila. Science (2006) 3.77
Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet (2012) 3.74
Targeted inhibition of mutant IDH2 in leukemia cells induces cellular differentiation. Science (2013) 3.72
Sclerostin mediates bone response to mechanical unloading through antagonizing Wnt/beta-catenin signaling. J Bone Miner Res (2009) 3.69
Epidemiological evidence for the link between sleep duration and high blood pressure: a systematic review and meta-analysis. Sleep Med (2013) 3.68
Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet (2011) 3.66
TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. Brain (2010) 3.66
Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys. J Clin Invest (2009) 3.55
Clinical application of massively parallel sequencing-based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11,105 pregnancies with mixed risk factors. Prenat Diagn (2012) 3.54
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol (2011) 3.51
Structure of the human histamine H1 receptor complex with doxepin. Nature (2011) 3.48
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Acquired resistance to crizotinib from a mutation in CD74-ROS1. N Engl J Med (2013) 3.42
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol (2013) 3.41
Neuronal SIRT1 activation as a novel mechanism underlying the prevention of Alzheimer disease amyloid neuropathology by calorie restriction. J Biol Chem (2006) 3.40
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature (2013) 3.40
Adenosine A1 receptors mediate local anti-nociceptive effects of acupuncture. Nat Neurosci (2010) 3.38
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res (2010) 3.34
Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature (2011) 3.19
The draft genome of a diploid cotton Gossypium raimondii. Nat Genet (2012) 3.18
Structure of the human smoothened receptor bound to an antitumour agent. Nature (2013) 3.08
BioMart Central Portal: an open database network for the biological community. Database (Oxford) (2011) 3.03
A novel microRNA targeting HDAC5 regulates osteoblast differentiation in mice and contributes to primary osteoporosis in humans. J Clin Invest (2009) 3.03
Snap: an integrated SNP annotation platform. Nucleic Acids Res (2006) 2.99