Published in Genome Biol Evol on January 01, 2013
Intron Invasions Trace Algal Speciation and Reveal Nearly Identical Arctic and Antarctic Micromonas Populations. Mol Biol Evol (2015) 0.83
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC Genomics (2016) 0.81
Recurrent loss of specific introns during angiosperm evolution. PLoS Genet (2014) 0.79
Novel Introner-Like Elements in fungi Are Involved in Parallel Gains of Spliceosomal Introns. PLoS One (2015) 0.76
Evaluation of the mechanisms of intron loss and gain in the social amoebae Dictyostelium. BMC Evol Biol (2015) 0.76
Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PeerJ (2016) 0.75
mdRNA-Seq analysis of marine microbial communities from the northern Red Sea. Sci Rep (2016) 0.75
Circos: an information aesthetic for comparative genomics. Genome Res (2009) 40.02
Why genes in pieces? Nature (1978) 19.03
The origins of genome complexity. Science (2003) 12.25
Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci U S A (2006) 4.52
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res (2010) 4.39
The origins of eukaryotic gene structure. Mol Biol Evol (2005) 4.11
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science (2009) 4.05
Introns and the origin of nucleus-cytosol compartmentalization. Nature (2006) 3.16
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog (2012) 2.66
Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol (2005) 2.46
Intron evolution as a population-genetic process. Proc Natl Acad Sci U S A (2002) 2.37
Translational control of intron splicing in eukaryotes. Nature (2008) 2.15
Selfish DNA and the origin of introns. Nature (1985) 2.08
Complex early genes. Proc Natl Acad Sci U S A (2005) 1.88
The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Biol Direct (2006) 1.88
Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science (2010) 1.86
The evolution of spliceosomal introns. Curr Opin Genet Dev (2002) 1.84
Patterns of intron gain and loss in fungi. PLoS Biol (2004) 1.72
Birth of new spliceosomal introns in fungi by multiplication of introner-like elements. Curr Biol (2012) 1.67
Origin and evolution of spliceosomal introns. Biol Direct (2012) 1.65
Extensive, recent intron gains in Daphnia populations. Science (2009) 1.64
Both catalytic steps of nuclear pre-mRNA splicing are reversible. Science (2008) 1.62
The spliceosome: a flexible, reversible macromolecular machine. Trends Biochem Sci (2012) 1.56
A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. PLoS Comput Biol (2011) 1.40
Messenger RNA surveillance and the evolutionary proliferation of introns. Mol Biol Evol (2003) 1.36
Introns within ribosomal protein genes regulate the production and function of yeast ribosomes. Cell (2011) 1.25
ORCAE: online resource for community annotation of eukaryotes. Nat Methods (2012) 1.25
Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome. PLoS Genet (2008) 1.22
Mystery of intron gain: new data and new models. Trends Genet (2008) 1.22
On biased distribution of introns in various eukaryotes. Gene (2002) 1.18
Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage. Genome Biol (2012) 1.10
Evidence for extensive recent intron transposition in closely related fungi. Curr Biol (2011) 1.03
Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns. Genome Biol (2007) 1.01
Comparative analysis of information contents relevant to recognition of introns in many species. BMC Genomics (2011) 1.00
Identifying the mechanisms of intron gain: progress and trends. Biol Direct (2012) 0.98
A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. Mol Biol Evol (2007) 0.97
Phase distribution of spliceosomal introns: implications for intron origin. BMC Evol Biol (2006) 0.92
U12 type introns were lost at multiple occasions during evolution. BMC Genomics (2010) 0.87
Gene make-up: rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes. BMC Evol Biol (2013) 0.85
Ostreococcus tauri: seeing through the genes to the genome. Trends Genet (2007) 0.83
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (2007) 8.12
The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet (2010) 8.07
The European database on small subunit ribosomal RNA. Nucleic Acids Res (2002) 7.80
Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol (2005) 7.19
The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature (2008) 6.70
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res (2002) 6.43
A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One (2007) 5.62
The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci U S A (2002) 5.00
Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci U S A (2005) 5.00
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics (2004) 4.95
The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature (2011) 4.94
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (2007) 4.89
The Norway spruce genome sequence and conifer genome evolution. Nature (2013) 4.74
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet (2011) 4.65
Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci U S A (2006) 4.52
Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res (2003) 4.19
A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol (2002) 4.05
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science (2009) 4.05
Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci U S A (2004) 3.97
Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell (2002) 3.91
From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). Bioessays (2005) 3.91
The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature (2010) 3.60
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A (2007) 3.58
Genome duplication and the origin of angiosperms. Trends Ecol Evol (2005) 3.46
The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature (2011) 3.29
Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci U S A (2009) 3.13
Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proc Natl Acad Sci U S A (2004) 3.13
Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res (2002) 3.12
Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res (2004) 3.02
Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol (2003) 2.90
Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci U S A (2011) 2.84
Genome sequence of the recombinant protein production host Pichia pastoris. Nat Biotechnol (2009) 2.67
Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics (2009) 2.66
Evidence that rice and other cereals are ancient aneuploids. Plant Cell (2003) 2.62
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A (2006) 2.61
The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol (2006) 2.58
PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell (2009) 2.43
CATMA: a complete Arabidopsis GST database. Nucleic Acids Res (2003) 2.34
Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature (2013) 2.26
An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol Biol (2007) 2.17
The Mycobacterium tuberculosis regulatory network and hypoxia. Nature (2013) 2.04
Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol (2011) 1.98
Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol (2004) 1.94
Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol Syst Biol (2010) 1.91
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics (2008) 1.91
GenomeView: a next-generation genome browser. Nucleic Acids Res (2011) 1.91
Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol (2009) 1.90
Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev (2005) 1.87
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol (2006) 1.85
Genome-wide identification of potential plant E2F target genes. Plant Physiol (2005) 1.85
Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res (2007) 1.80
A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation. Dev Cell (2012) 1.72
EST data suggest that poplar is an ancient polyploid. New Phytol (2005) 1.70
i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics (2007) 1.68
Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations. Nucleic Acids Res (2003) 1.54
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res (2011) 1.51
Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol (2003) 1.50
Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res (2004) 1.48
SpliceMachine: predicting splice sites from high-dimensional local context representations. Bioinformatics (2004) 1.47
Choose your partners: dimerization in eukaryotic transcription factors. Trends Biochem Sci (2008) 1.43
Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis. Mol Biol Evol (2008) 1.40
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst Biol (2009) 1.40
Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Res (2005) 1.39
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. BMC Genomics (2013) 1.38
Module networks revisited: computational assessment and prioritization of model predictions. Bioinformatics (2009) 1.38
Investigating ancient duplication events in the Arabidopsis genome. J Struct Funct Genomics (2003) 1.38
Canalization without flux sensors: a traveling-wave hypothesis. Trends Plant Sci (2007) 1.36
Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biol (2009) 1.36
And then there were many: MADS goes genomic. Trends Plant Sci (2003) 1.35
How many genes are there in plants (... and why are they there)? Curr Opin Plant Biol (2007) 1.35
Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc Natl Acad Sci U S A (2013) 1.35
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics (2009) 1.34
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics (2010) 1.34
The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. Plant Cell (2013) 1.34
Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia. Clin Cancer Res (2012) 1.33
Automatic design of gene-specific sequence tags for genome-wide functional studies. Bioinformatics (2003) 1.33
AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol (2009) 1.33
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. BMC Bioinformatics (2007) 1.32
Large-scale event extraction from literature with multi-level gene normalization. PLoS One (2013) 1.30
The small RNA world of plants. New Phytol (2006) 1.25