Published in Genome Res on September 01, 2003
Transposable elements and the evolution of regulatory networks. Nat Rev Genet (2008) 6.11
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res (2006) 3.41
Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol (2008) 2.91
Genomic duplication, fractionation and the origin of regulatory novelty. Genetics (2004) 2.22
A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics (2004) 1.94
Evolutionary strata on the X chromosomes of the dioecious plant Silene latifolia: evidence from new sex-linked genes. Genetics (2007) 1.88
Blueprint for a high-performance biomaterial: full-length spider dragline silk genes. PLoS One (2007) 1.81
Functional conservation of a root hair cell-specific cis-element in angiosperms with different root hair distribution patterns. Plant Cell (2006) 1.71
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet (2013) 1.68
Arabidopsis intragenomic conserved noncoding sequence. Proc Natl Acad Sci U S A (2007) 1.52
Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics (2008) 1.43
New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides. BMC Genomics (2008) 1.26
Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea. Plant Physiol (2006) 1.19
Conservation of noncoding microsatellites in plants: implication for gene regulation. BMC Genomics (2006) 1.19
Coordination of leaf development via regulation of KNOX1 genes. J Plant Res (2009) 1.17
DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes. Genetics (2005) 1.12
Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci U S A (2009) 1.12
A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol (2006) 1.10
Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids. Plant Cell (2011) 1.08
Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics. Genome Biol (2006) 1.08
Positive autoregulation of a KNOX gene is essential for shoot apical meristem maintenance in rice. Plant Cell (2011) 1.08
Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. Plant Cell (2012) 1.07
G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. Plant Cell (2007) 1.06
Unleashing the genome of brassica rapa. Front Plant Sci (2012) 0.98
Regulatory modules controlling maize inflorescence architecture. Genome Res (2013) 0.97
Regulation of SHOOT MERISTEMLESS genes via an upstream-conserved noncoding sequence coordinates leaf development. Proc Natl Acad Sci U S A (2007) 0.95
Comparative genomics of grasses promises a bountiful harvest. Plant Physiol (2009) 0.95
Plant spliceosomal introns: not only cut and paste. Curr Genomics (2008) 0.94
Identification and characterization of new long conserved noncoding sequences in vertebrates. Mamm Genome (2008) 0.93
Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes. Nucleic Acids Res (2011) 0.93
Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses. Front Plant Sci (2011) 0.93
Patterns of selective constraints in noncoding DNA of rice. BMC Evol Biol (2007) 0.91
The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences. BMC Genomics (2013) 0.91
Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. Genome Res (2012) 0.89
Regulation and a conserved intron sequence of liguleless3/4 knox class-I homeobox genes in grasses. Planta (2004) 0.85
Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis. Plant Cell (2014) 0.85
Functional analysis of DNA sequences controlling the expression of the rice OsCDPK2 gene. Planta (2005) 0.84
Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses. Front Plant Sci (2013) 0.83
Genetics of barley hooded suppression. Genetics (2004) 0.83
Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. BMC Genomics (2012) 0.81
Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning. Genome Biol Evol (2014) 0.79
New cis-regulatory elements in the Rht-D1b locus region of wheat. Funct Integr Genomics (2012) 0.79
Isolation and characterization of conserved non-coding sequences among rice (Oryza sativa L.) paralogous regions. Mol Genet Genomics (2008) 0.77
Transcriptional, posttranscriptional, and posttranslational regulation of SHOOT MERISTEMLESS gene expression in Arabidopsis determines gene function in the shoot apex. Plant Physiol (2014) 0.76
Plant noncoding RNA gene discovery by "single-genome comparative genomics". RNA (2011) 0.76
Inherited phenotype instability of inflorescence and floral organ development in homeotic barley double mutants and its specific modification by auxin inhibitors and 2,4-D. Ann Bot (2015) 0.75
GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates. Genome Biol Evol (2016) 0.75
Arabidopsis Motif Scanner. BMC Bioinformatics (2016) 0.75
The truth about mouse, human, worms and yeast. Hum Genomics (2004) 0.75
A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants. Plant Physiol (2016) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (2002) 21.26
Preservation of duplicate genes by complementary, degenerative mutations. Genetics (1999) 18.29
The probability of duplicate gene preservation by subfunctionalization. Genetics (2000) 10.27
Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science (2000) 10.14
Pseudoallelism and gene evolution. Cold Spring Harb Symp Quant Biol (1951) 10.02
Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet (2002) 9.16
An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing. Science (2001) 8.73
Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Genome Res (1997) 8.49
Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci U S A (1993) 7.47
rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res (2002) 7.33
DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A (1997) 7.08
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
Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res (2000) 6.18
Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet (2000) 5.88
Evolutionary history of the grasses. Plant Physiol (2001) 5.22
Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res (1999) 4.50
A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell (2001) 4.36
Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res (2002) 4.25
Genome relationships: the grass model in current research. Plant Cell (2000) 3.25
DNA sequences required for anaerobic expression of the maize alcohol dehydrogenase 1 gene. Proc Natl Acad Sci U S A (1987) 3.06
Comparative sequence analysis of plant nuclear genomes:m microcolinearity and its many exceptions. Plant Cell (2000) 2.82
A conceptual framework for maize leaf development. Dev Biol (1992) 2.67
Maize Adh1. Annu Rev Genet (1985) 2.66
Enrichment of regulatory signals in conserved non-coding genomic sequence. Bioinformatics (2001) 2.27
Evolutionary strategies for the elucidation of cis and trans factors that regulate the developmental switching programs of the beta-like globin genes. Mol Phylogenet Evol (1996) 2.17
Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. Genome Res (2001) 2.04
Regulation of leaf initiation by the terminal ear 1 gene of maize. Nature (1998) 2.03
Mutator insertions in an intron of the maize knotted1 gene result in dominant suppressible mutations. Genetics (1994) 1.84
Regulatory elements and expression profiles. Curr Opin Struct Biol (1999) 1.65
Utility and distribution of conserved noncoding sequences in the grasses. Proc Natl Acad Sci U S A (2002) 1.61
Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell (2003) 1.55
Identification of a genetic element that controls the organ-specific expression of adh1 in maize. Genetics (1981) 1.45
The maize gene liguleless2 encodes a basic leucine zipper protein involved in the establishment of the leaf blade-sheath boundary. Genes Dev (1998) 1.34
Conservation of position and sequence of a novel, widely expressed gene containing the major human alpha-globin regulatory element. Genomics (1995) 1.31
In vivo footprinting reveals unique cis-elements and different modes of hypoxic induction in maize Adh1 and Adh2. Plant Cell (1991) 1.16
Using cauliflower to find conserved non-coding regions in Arabidopsis. Plant Physiol (2002) 1.08
Modeling DNA sequence-based cis-regulatory gene networks. Dev Biol (2002) 1.03
Constitutive and anaerobically induced DNase-I-hypersensitive sites in the 5' region of the maize Adh1 gene. Proc Natl Acad Sci U S A (1987) 1.00
Osmium tetroxide footprinting of a scaffold attachment region in the maize Adh1 promoter. Plant Mol Biol (1993) 0.90
Neuronal-specific gene expression--the interaction of both positive and negative transcriptional regulators. Prog Neurobiol (1996) 0.86
Cloning of maize ferredoxin III gene: presence of a unique repetitive nucleotide sequence within an intron found in the 5'-untranslated region. Plant Cell Physiol (1997) 0.79
Architecture of a plant promoter: S1 nuclease hypersensitive features of maize Adh1. Plant Mol Biol (1987) 0.77
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res (2009) 15.15
The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62
Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med (2011) 9.37
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
A high-throughput Arabidopsis reverse genetics system. Plant Cell (2002) 7.58
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Community-wide analysis of microbial genome sequence signatures. Genome Biol (2009) 3.96
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res (2006) 3.41
Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science (2012) 3.39
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res (2006) 3.33
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci U S A (2011) 2.97
Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol (2008) 2.91
Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol (2010) 2.90
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res (2012) 2.81
A geometric approach for classification and comparison of structural variants. Bioinformatics (2009) 2.79
How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J (2008) 2.76
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife (2013) 2.36
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol (2011) 2.33
Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. MBio (2013) 2.24
Genomic duplication, fractionation and the origin of regulatory novelty. Genetics (2004) 2.22
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci U S A (2010) 2.09
Initiation, establishment, and maintenance of heritable MuDR transposon silencing in maize are mediated by distinct factors. PLoS Biol (2006) 2.08
Biodiversity (Communications arising): maize transgene results in Mexico are artefacts. Nature (2002) 1.88
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun (2013) 1.80
Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat Genet (2005) 1.77
Large-scale structure-function analysis of the Arabidopsis RPM1 disease resistance protein. Plant Cell (2002) 1.72
Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. MBio (2013) 1.70
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome (2013) 1.69
Utility and distribution of conserved noncoding sequences in the grasses. Proc Natl Acad Sci U S A (2002) 1.61
Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci U S A (2011) 1.60
Astrophysical ionizing radiation and Earth: a brief review and census of intermittent intense sources. Astrobiology (2011) 1.60
Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci U S A (2010) 1.58
Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nat Commun (2013) 1.55
Heritable epigenetic variation among maize inbreds. PLoS Genet (2011) 1.54
Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PLoS One (2011) 1.52
Arabidopsis intragenomic conserved noncoding sequence. Proc Natl Acad Sci U S A (2007) 1.52
Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics (2012) 1.49
Insights from the comparison of plant genome sequences. Annu Rev Plant Biol (2010) 1.47
A network of rice genes associated with stress response and seed development. Proc Natl Acad Sci U S A (2003) 1.47
Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. Microbiome (2014) 1.45
Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl Environ Microbiol (2009) 1.45
A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol (2008) 1.45
Horizontal transfer of a plant transposon. PLoS Biol (2006) 1.43
Grains of knowledge: genomics of model cereals. Genome Res (2005) 1.36
Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biol Evol (2012) 1.36
Causes of an ad 774-775 14C increase. Nature (2012) 1.35
Persisting viral sequences shape microbial CRISPR-based immunity. PLoS Comput Biol (2012) 1.32
Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Res (2006) 1.29
Whole-genome comparison of leucine-rich repeat extensins in Arabidopsis and rice. A conserved family of cell wall proteins form a vegetative and a reproductive clade. Plant Physiol (2003) 1.24
Systems of support to increase colorectal cancer screening and follow-up rates (SOS): design, challenges, and baseline characteristics of trial participants. Contemp Clin Trials (2010) 1.19
Transposed genes in Arabidopsis are often associated with flanking repeats. PLoS Genet (2010) 1.19
High-resolution mapping of open chromatin in the rice genome. Genome Res (2011) 1.19
The mop1 (mediator of paramutation1) mutant progressively reactivates one of the two genes encoded by the MuDR transposon in maize. Genetics (2005) 1.19
Conservation and molecular dissection of ROUGH SHEATH2 and ASYMMETRIC LEAVES1 function in leaf development. Proc Natl Acad Sci U S A (2003) 1.16
Phage mutations in response to CRISPR diversification in a bacterial population. Environ Microbiol (2012) 1.15
ZmDB, an integrated database for maize genome research. Nucleic Acids Res (2003) 1.14
Using genomic sequencing for classical genetics in E. coli K12. PLoS One (2011) 1.13
Mu killer causes the heritable inactivation of the Mutator family of transposable elements in Zea mays. Genetics (2003) 1.12
Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics (2011) 1.11
Epigenetic reprogramming during vegetative phase change in maize. Proc Natl Acad Sci U S A (2010) 1.10
Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids. Plant Cell (2011) 1.08
Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments. PLoS One (2013) 1.06
Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl Environ Microbiol (2012) 1.06
G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. Plant Cell (2007) 1.06
Structural variation analysis with strobe reads. Bioinformatics (2010) 1.05
Two evolutionarily distinct classes of paleopolyploidy. Mol Biol Evol (2013) 1.05
Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community. Environ Microbiol (2011) 1.04
Nonparticipation in a population-based trial to increase colorectal cancer screening. Am J Prev Med (2012) 1.04
Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. ISME J (2012) 1.03
A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes. PLoS Comput Biol (2011) 1.02
Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proc Natl Acad Sci U S A (2014) 1.01
Expression of a mutant maize gene in the ventral leaf epidermis is sufficient to signal a switch of the leaf's dorsoventral axis. Development (2002) 1.00
Ecological distribution and population physiology defined by proteomics in a natural microbial community. Mol Syst Biol (2010) 0.99
Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. BMC Genomics (2013) 0.98
Diversified microbiota of meconium is affected by maternal diabetes status. PLoS One (2013) 0.97
Long identical multispecies elements in plant and animal genomes. Proc Natl Acad Sci U S A (2012) 0.97
Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea (2013) 0.96
Metabolome-proteome differentiation coupled to microbial divergence. MBio (2010) 0.95
Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. Microbiome (2013) 0.95
Strobe sequence design for haplotype assembly. BMC Bioinformatics (2011) 0.94
Escape from preferential retention following repeated whole genome duplications in plants. Front Plant Sci (2012) 0.94
Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses. Front Plant Sci (2011) 0.93
Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics. MBio (2013) 0.93
Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics (2014) 0.92
A maize thiamine auxotroph is defective in shoot meristem maintenance. Plant Cell (2010) 0.90
Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points. Environ Microbiol (2014) 0.90
Evidence of function for conserved noncoding sequences in Arabidopsis thaliana. New Phytol (2011) 0.88
New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS". Appl Environ Microbiol (2013) 0.87
A position effect on the heritability of epigenetic silencing. PLoS Genet (2008) 0.87
Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities. Appl Environ Microbiol (2012) 0.86
New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake. Appl Environ Microbiol (2013) 0.85
Regulation and a conserved intron sequence of liguleless3/4 knox class-I homeobox genes in grasses. Planta (2004) 0.85
Prospective study of the progression of low-grade dysplasia in ulcerative colitis using current cancer surveillance guidelines. Inflamm Bowel Dis (2012) 0.85
The evolution of a high copy gene array in Arabidopsis. J Mol Evol (2010) 0.85
Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses. Front Plant Sci (2013) 0.83
Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules. PLoS One (2012) 0.82