Published in Plant Mol Biol on January 01, 2002
Apollo: a sequence annotation editor. Genome Biol (2002) 10.77
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol (2005) 4.18
Computational gene prediction using multiple sources of evidence. Genome Res (2004) 2.58
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. Nucleic Acids Res (2004) 1.97
Genomic comparison of P-type ATPase ion pumps in Arabidopsis and rice. Plant Physiol (2003) 1.97
Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Res (2005) 0.92
Specific versus non-specific immune responses in an invertebrate species evidenced by a comparative de novo sequencing study. PLoS One (2012) 0.89
Targeted analysis of orthologous phytochrome A regions of the sorghum, maize, and rice genomes using comparative gene-island sequencing. Plant Physiol (2002) 0.83
A method for identifying alternative or cryptic donor splice sites within gene and mRNA sequences. Comparisons among sequences from vertebrates, echinoderms and other groups. BMC Genomics (2009) 0.76
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
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 genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
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
FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (2011) 13.71
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
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
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
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
Cloud computing and the DNA data race. Nat Biotechnol (2010) 7.81
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
How to map billions of short reads onto genomes. Nat Biotechnol (2009) 6.59
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol (2011) 6.23
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
The genome of woodland strawberry (Fragaria vesca). Nat Genet (2010) 5.86
Comparative genome assembly. Brief Bioinform (2004) 5.81
Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet (2011) 5.58
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
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
Bioinformatics challenges of new sequencing technology. Trends Genet (2008) 5.34
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A (2002) 5.28
The MaSuRCA genome assembler. Bioinformatics (2013) 5.07
Hierarchical scaffolding with Bambus. Genome Res (2004) 4.95
Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol (2002) 4.90
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (2007) 4.89
Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biol (2007) 4.80
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science (2005) 4.74
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol (2007) 4.27
Beware of mis-assembled genomes. Bioinformatics (2005) 4.14
DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics (2004) 3.74
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol (2008) 3.73
Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinformatics (2003) 3.50
Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics (2010) 3.38
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol (2004) 3.36
Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science (2005) 2.71
Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proc Natl Acad Sci U S A (2011) 2.62
Computational gene prediction using multiple sources of evidence. Genome Res (2004) 2.58
The value of complete microbial genome sequencing (you get what you pay for). J Bacteriol (2002) 2.58
Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature (2002) 2.49
JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics (2005) 2.37
Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol (2004) 2.36
GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics (2013) 2.24
Physiogenomic resources for rat models of heart, lung and blood disorders. Nat Genet (2006) 2.05
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions. Genome Biol (2006) 2.00
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol (2014) 1.90
Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. J Bacteriol (2011) 1.80
Automated correction of genome sequence errors. Nucleic Acids Res (2004) 1.80
Comprehensive DNA signature discovery and validation. PLoS Comput Biol (2007) 1.75
Between a chicken and a grape: estimating the number of human genes. Genome Biol (2010) 1.72
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res (2010) 1.72
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief Bioinform (2011) 1.70
GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Res (2003) 1.63
The complete genome sequence of Bacillus anthracis Ames "Ancestor". J Bacteriol (2008) 1.61
Detection and correction of false segmental duplications caused by genome mis-assembly. Genome Biol (2010) 1.54
The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol (2003) 1.52
Computational discovery of internal micro-exons. Genome Res (2003) 1.52
Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res (2005) 1.48
OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res (2008) 1.47
Sequencing and assembly of the 22-gb loblolly pine genome. Genetics (2014) 1.46
What are decision trees? Nat Biotechnol (2008) 1.39
2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates. PLoS One (2009) 1.32
Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics (2014) 1.32
Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. J Bacteriol (2010) 1.29
Clustering metagenomic sequences with interpolated Markov models. BMC Bioinformatics (2010) 1.28
The COMBREX project: design, methodology, and initial results. PLoS Biol (2013) 1.24
Insignia: a DNA signature search web server for diagnostic assay development. Nucleic Acids Res (2009) 1.23
Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas. PLoS One (2008) 1.22
A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biol Direct (2014) 1.20
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res (2011) 1.17
Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification. BMC Genomics (2010) 1.14
A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics (2007) 1.13
Do-it-yourself genetic testing. Genome Biol (2010) 1.06
Efficient decoding algorithms for generalized hidden Markov model gene finders. BMC Bioinformatics (2005) 1.05
Contamination in the draft of the human genome masquerades as lateral gene transfer. DNA Seq (2002) 1.00