Published in Nucleic Acids Res on October 01, 2003
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82
The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res (2007) 14.24
Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res (2011) 11.32
The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res (2006) 8.26
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res (2011) 8.18
Annotating genomes with massive-scale RNA sequencing. Genome Biol (2008) 7.73
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44
Bioinformatics challenges of new sequencing technology. Trends Genet (2008) 5.34
Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol (2010) 5.33
Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics (2006) 4.54
Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci U S A (2006) 4.51
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet (2013) 4.20
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol (2005) 4.18
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol (2013) 4.04
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature (2012) 4.00
The institute for genomic research Osa1 rice genome annotation database. Plant Physiol (2005) 3.96
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol (2008) 3.73
The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res (2004) 3.30
Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa. PLoS Pathog (2007) 3.27
Using the Acropora digitifera genome to understand coral responses to environmental change. Nature (2011) 3.26
Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet (2008) 3.23
Selecting one of several mating types through gene segment joining and deletion in Tetrahymena thermophila. PLoS Biol (2013) 2.95
A beginner's guide to eukaryotic genome annotation. Nat Rev Genet (2012) 2.67
The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol (2005) 2.41
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics (2006) 2.41
Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biol (2011) 2.38
Genome wide analysis of Arabidopsis core promoters. BMC Genomics (2005) 2.24
Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res (2004) 2.19
Arabidopsis MPSS. An online resource for quantitative expression analysis. Plant Physiol (2004) 2.19
Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol (2009) 2.17
A non-EST-based method for exon-skipping prediction. Genome Res (2004) 2.15
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res (2009) 2.10
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Nucleic Acids Res (2011) 2.07
WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes. Nucleic Acids Res (2013) 1.95
An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res (2006) 1.90
Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol (2005) 1.86
Targeted discovery of novel human exons by comparative genomics. Genome Res (2007) 1.79
Genome-wide assembly and analysis of alternative transcripts in mouse. Genome Res (2005) 1.78
The genome of Eucalyptus grandis. Nature (2014) 1.76
Draft genome of the kiwifruit Actinidia chinensis. Nat Commun (2013) 1.72
Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology. DNA Res (2012) 1.69
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet (2013) 1.69
Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. Plant Cell (2009) 1.66
The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol (2012) 1.65
Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. Genome Res (2004) 1.63
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol (2014) 1.56
The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet Biol (2008) 1.56
Gene and alternative splicing annotation with AIR. Genome Res (2005) 1.55
A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics (2008) 1.55
Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS One (2008) 1.53
Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res (2005) 1.48
Approaches to Fungal Genome Annotation. Mycology (2011) 1.47
Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants. Plant Physiol (2005) 1.44
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res (2013) 1.44
Genome characterization of the oleaginous fungus Mortierella alpina. PLoS One (2011) 1.43
Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biol (2017) 1.43
The locust genome provides insight into swarm formation and long-distance flight. Nat Commun (2014) 1.42
The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. Genome Biol (2016) 1.42
Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta. Genome Biol (2013) 1.41
Global identification and characterization of transcriptionally active regions in the rice genome. PLoS One (2007) 1.41
Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. BMC Genomics (2008) 1.40
SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol (2010) 1.40
The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature (2015) 1.39
Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. BMC Biol (2017) 1.39
The Capsaspora genome reveals a complex unicellular prehistory of animals. Nat Commun (2013) 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
A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype. BMC Plant Biol (2014) 1.37
Sequence and structure of Brassica rapa chromosome A3. Genome Biol (2010) 1.35
Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics (2013) 1.35
The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun (2013) 1.32
An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics (2014) 1.32
Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evol Biol (2007) 1.30
RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics (2011) 1.27
Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun (2014) 1.26
Cassava genome from a wild ancestor to cultivated varieties. Nat Commun (2014) 1.25
Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biol Evol (2010) 1.24
The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants. Plant Physiol (2008) 1.24
Araport: the Arabidopsis information portal. Nucleic Acids Res (2014) 1.23
Databases and information integration for the Medicago truncatula genome and transcriptome. Plant Physiol (2005) 1.23
The transition from a phytopathogenic smut ancestor to an anamorphic biocontrol agent deciphered by comparative whole-genome analysis. Plant Cell (2013) 1.23
Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes. BMC Biol (2012) 1.23
Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus. PLoS Genet (2014) 1.21
Characterization of paralogous protein families in rice. BMC Plant Biol (2008) 1.19
Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. Genome Res (2005) 1.19
RNA interference targeting leucine aminopeptidase blocks hatching of Schistosoma mansoni eggs. Mol Biochem Parasitol (2009) 1.18
Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica. PLoS Genet (2013) 1.18
New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. PLoS Negl Trop Dis (2010) 1.17
The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Appl Environ Microbiol (2013) 1.16
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell (2014) 1.14
Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiol (2004) 1.14
Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics (2008) 1.14
EST analysis reveals putative genes involved in glycyrrhizin biosynthesis. BMC Genomics (2010) 1.13
A field guide to whole-genome sequencing, assembly and annotation. Evol Appl (2014) 1.12
Formin homology 2 domains occur in multiple contexts in angiosperms. BMC Genomics (2004) 1.11
The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure. Nat Commun (2014) 1.10
Genome comparison using Gene Ontology (GO) with statistical testing. BMC Bioinformatics (2006) 1.10
Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biol (2011) 1.09
Integrating alternative splicing detection into gene prediction. BMC Bioinformatics (2005) 1.09
Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A (1988) 193.60
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature (2000) 70.33
A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res (1998) 22.69
Complementary DNA sequencing: expressed sequence tags and human genome project. Science (1991) 19.42
Ab initio gene finding in Drosophila genomic DNA. Genome Res (2000) 19.23
Database resources of the National Center for Biotechnology. Nucleic Acids Res (2003) 18.26
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res (2001) 8.44
Using GeneWise in the Drosophila annotation experiment. Genome Res (2000) 7.50
Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol (1994) 7.42
Alternative splicing and genome complexity. Nat Genet (2001) 7.30
Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res (2001) 7.27
Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. Annu Rev Genet (1998) 7.15
Computational inference of homologous gene structures in the human genome. Genome Res (2001) 6.96
Functional annotation of a full-length Arabidopsis cDNA collection. Science (2002) 6.15
Spidey: a tool for mRNA-to-genomic alignments. Genome Res (2001) 5.61
Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res (2001) 5.38
A tool for analyzing and annotating genomic sequences. Genomics (1997) 5.33
EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett (2000) 4.96
Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol (2002) 4.90
Sex-lethal, a Drosophila sex determination switch gene, exhibits sex-specific RNA splicing and sequence similarity to RNA binding proteins. Cell (1988) 4.52
A comparison of expressed sequence tags (ESTs) to human genomic sequences. Nucleic Acids Res (1997) 4.22
An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J (1993) 3.76
Positive autoregulation of sex-lethal by alternative splicing maintains the female determined state in Drosophila. Cell (1991) 3.43
Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics (2000) 3.14
Annotation of the Arabidopsis genome. Plant Physiol (2003) 3.06
STACK: Sequence Tag Alignment and Consensus Knowledgebase. Nucleic Acids Res (2001) 2.85
Comparison of gene indexing databases. Trends Genet (1999) 2.73
Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping. Plant Physiol (2003) 2.50
A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil. Plant Physiol (2000) 2.39
Analysis of EST-driven gene annotation in human genomic sequence. Genome Res (1998) 2.39
A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries. DNA Res (2000) 2.33
Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. Plant J (1996) 2.27
Regulation of flowering in Arabidopsis by an FLC homologue. Plant Physiol (2001) 2.19
The Arabidopsis splicing factor SR1 is regulated by alternative splicing. Plant Mol Biol (2000) 1.96
Computational discovery of internal micro-exons. Genome Res (2003) 1.52
Non-AUG initiation of AGAMOUS mRNA translation in Arabidopsis thaliana. Mol Cell Biol (1999) 1.47
Genomic sequence, splicing, and gene annotation. Am J Hum Genet (2000) 1.46
The Arabidopsis thaliana cDNA sequencing projects. FEBS Lett (1997) 1.29
Cloning and sequencing of cDNAs for hypothetical genes from chromosome 2 of Arabidopsis. Plant Physiol (2002) 1.27
Large-scale sequencing of plant genomes. Curr Opin Plant Biol (1998) 1.07
Multiple forms of formamidopyrimidine-DNA glycosylase produced by alternative splicing in Arabidopsis thaliana. J Photochem Photobiol B (2001) 1.06
Detection of Arabidopsis thaliana AtRAD1 cDNA variants and assessment of function by expression in a yeast rad1 mutant. Gene (2002) 1.03
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45
Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (2007) 47.63
Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS (2008) 18.69
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A (2005) 14.59
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (2011) 13.71
The TIGRFAMs database of protein families. Nucleic Acids Res (2003) 13.59
Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature (2005) 11.99
The genome of the African trypanosome Trypanosoma brucei. Science (2005) 11.48
GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res (2012) 11.33
Aggressive assembly of pyrosequencing reads with mates. Bioinformatics (2008) 11.01
Big data: The future of biocuration. Nature (2008) 10.81
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature (2003) 10.38
Searching for SNPs with cloud computing. Genome Biol (2009) 10.12
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science (2002) 9.83
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res (2006) 8.89
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods (2009) 8.15
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Cloud computing and the DNA data race. Nat Biotechnol (2010) 7.81
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature (2005) 7.74
Minimus: a fast, lightweight genome assembler. BMC Bioinformatics (2007) 7.65
The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science (2005) 7.61
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol (2002) 6.96
How to map billions of short reads onto genomes. Nat Biotechnol (2009) 6.59
Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol (2012) 6.27
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol (2011) 6.23
Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08
Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature (2008) 5.96
The genome of the blood fluke Schistosoma mansoni. Nature (2009) 5.94
Assembly of large genomes using second-generation sequencing. Genome Res (2010) 5.94
A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol (2009) 5.93
Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics (2004) 5.91
The genome of woodland strawberry (Fragaria vesca). Nat Genet (2010) 5.86
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
Comparative genome assembly. Brief Bioinform (2004) 5.81
The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci U S A (2003) 5.62
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol (2011) 5.60
Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet (2011) 5.58
High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics (2007) 5.56
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol (2005) 5.48
Genome sequencing and analysis of Aspergillus oryzae. Nature (2005) 5.47
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44
Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol (2014) 5.40
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Comparative genomics of trypanosomatid parasitic protozoa. Science (2005) 5.37