Published in Genome Biol on August 07, 2006
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
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The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet (2011) 2.16
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De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. Microb Cell Fact (2012) 1.62
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Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol (2014) 1.56
Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biol (2013) 1.46
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. Genome Biol (2013) 1.37
Draft genome sequence of adzuki bean, Vigna angularis. Sci Rep (2015) 1.37
Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation. Genome Biol (2012) 1.27
Conrad: gene prediction using conditional random fields. Genome Res (2007) 1.26
Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen. Genome Res (2013) 1.24
Transcriptomic responses of the softwood-degrading white-rot fungus Phanerochaete carnosa during growth on coniferous and deciduous wood. Appl Environ Microbiol (2011) 1.13
The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure. Nat Commun (2014) 1.10
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Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes. DNA Res (2013) 1.02
The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics (2014) 0.94
The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). Genome Biol Evol (2015) 0.92
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Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases. BMC Genomics (2014) 0.90
IMA Genome-F 2: Ceratocystis manginecans, Ceratocystis moniliformis, Diplodia sapinea: Draft genome sequences of Diplodia sapinea, Ceratocystis manginecans, and Ceratocystis moniliformis. IMA Fungus (2014) 0.89
Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genomics (2013) 0.88
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DIALIGN at GOBICS--multiple sequence alignment using various sources of external information. Nucleic Acids Res (2013) 0.87
Genome Sequencing of Multiple Isolates Highlights Subtelomeric Genomic Diversity within Fusarium fujikuroi. Genome Biol Evol (2015) 0.85
Genome sequence and virulence variation-related transcriptome profiles of Curvularia lunata, an important maize pathogenic fungus. BMC Genomics (2014) 0.85
Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques. PLoS One (2012) 0.85
DNA loss at the Ceratocystis fimbriata mating locus results in self-sterility. PLoS One (2014) 0.85
Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites. BMC Bioinformatics (2011) 0.84
IMA Genome-F 3: Draft genomes of Amanita jacksonii, Ceratocystis albifundus, Fusarium circinatum, Huntiella omanensis, Leptographium procerum, Rutstroemia sydowiana, and Sclerotinia echinophila. IMA Fungus (2014) 0.83
Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression. PLoS One (2014) 0.83
Diversity and evolution of myxozoan minicollagens and nematogalectins. BMC Evol Biol (2014) 0.83
Coral comparative genomics reveal expanded Hox cluster in the cnidarian-bilaterian ancestor. Integr Comp Biol (2012) 0.82
Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis. BMC Genomics (2012) 0.82
The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations. Genome Biol Evol (2014) 0.81
Genome survey sequencing and genetic background characterization of Gracilariopsis lemaneiformis (Rhodophyta) based on next-generation sequencing. PLoS One (2013) 0.81
Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. BMC Genomics (2014) 0.81
The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species. BMC Genomics (2014) 0.80
FRAMA: from RNA-seq data to annotated mRNA assemblies. BMC Genomics (2016) 0.80
IMA Genome-F 6: Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica and Penicillium freii DAOMC 242723. IMA Fungus (2016) 0.80
Increasing sequence search sensitivity with transitive alignments. PLoS One (2013) 0.79
Evolutionary signals of selection on cognition from the great tit genome and methylome. Nat Commun (2016) 0.79
Widespread Recurrent Patterns of Rapid Repeat Evolution in the Kinetochore Scaffold KNL1. Genome Biol Evol (2015) 0.79
ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection. Biomed Res Int (2013) 0.78
Automated alignment-based curation of gene models in filamentous fungi. BMC Bioinformatics (2014) 0.78
Draft Genome Sequence of Ochroconis constricta UM 578, Isolated from Human Skin Scraping. Genome Announc (2014) 0.78
Comparative genomics reveals convergent rates of evolution in ant-plant mutualisms. Nat Commun (2016) 0.78
Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp). RNA (2014) 0.78
Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment. BMC Bioinformatics (2014) 0.77
Improved rat genome gene prediction by integration of ESTs with RNA-Seq information. Bioinformatics (2014) 0.77
Comparative genomics of Taphrina fungi causing varying degrees of tumorous deformity in plants. Genome Biol Evol (2014) 0.77
Fruiting Body Formation in Volvariella volvacea Can Occur Independently of Its MAT-A-Controlled Bipolar Mating System, Enabling Homothallic and Heterothallic Life Cycles. G3 (Bethesda) (2016) 0.76
Phylogenomics-guided discovery of a novel conserved cassette of short linear motifs in BubR1 essential for the spindle checkpoint. Open Biol (2016) 0.76
The genomic mosaicism of hybrid speciation. Sci Adv (2017) 0.75
Draft Genome Sequence of the Basidiomycetous Fungus Flammulina velutipes TR19. Genome Announc (2016) 0.75
Draft Genome of the Scarab Beetle Oryctes borbonicus on La Réunion Island. Genome Biol Evol (2016) 0.75
Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area. BMC Genomics (2017) 0.75
Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles. BMC Genomics (2016) 0.75
Draft Genome of Toxocara canis, a Pathogen Responsible for Visceral Larva Migrans. Korean J Parasitol (2016) 0.75
Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum. PLoS One (2017) 0.75
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Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics (2003) 8.92
Integrating genomic homology into gene structure prediction. Bioinformatics (2001) 7.92
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
GeneID in Drosophila. Genome Res (2000) 6.61
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics (2004) 5.85
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics (2006) 5.23
An assessment of gene prediction accuracy in large DNA sequences. Genome Res (2000) 4.71
AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res (2006) 4.11
Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics (2003) 2.94
gff2ps: visualizing genomic annotations. Bioinformatics (2000) 2.69
Using database matches with for HMMGene for automated gene detection in Drosophila. Genome Res (2000) 2.52
EGASP: collaboration through competition to find human genes. Nat Methods (2005) 1.72
ExonHunter: a comprehensive approach to gene finding. Bioinformatics (2005) 1.55
Competition boosts bid to find human genes. Nature (2005) 0.93
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
Phylogenomics revives traditional views on deep animal relationships. Curr Biol (2009) 5.89
AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res (2004) 5.53
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics (2006) 5.23
Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol (2007) 4.66
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res (2005) 4.13
AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res (2006) 4.11
TICO: a tool for improving predictions of prokaryotic translation initiation sites. Bioinformatics (2005) 3.03
Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics (2003) 2.94
Fast and sensitive alignment of large genomic sequences. Proc IEEE Comput Soc Bioinform Conf (2002) 2.84
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes. BMC Bioinformatics (2006) 2.25
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms Mol Biol (2008) 2.07
Rhizobium sp. strain NGR234 possesses a remarkable number of secretion systems. Appl Environ Microbiol (2009) 2.07
The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. Nucleic Acids Res (2004) 1.88
DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics (2005) 1.87
The role of recombination in the emergence of a complex and dynamic HIV epidemic. Retrovirology (2010) 1.69
Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinformatics (2008) 1.64
jpHMM: improving the reliability of recombination prediction in HIV-1. Nucleic Acids Res (2009) 1.61
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. Nucleic Acids Res (2006) 1.58
Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites. BMC Bioinformatics (2004) 1.42
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics. BMC Bioinformatics (2009) 1.29
AGenDA: gene prediction by comparative sequence analysis. In Silico Biol (2002) 1.26
Identification of novel plant peroxisomal targeting signals by a combination of machine learning methods and in vivo subcellular targeting analyses. Plant Cell (2011) 1.09
AGenDA: homology-based gene prediction. Bioinformatics (2003) 1.08
MolabIS--an integrated information system for storing and managing molecular genetics data. BMC Bioinformatics (2011) 1.05
AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Res (2004) 1.00
jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus. Nucleic Acids Res (2012) 0.99
Divide-and-conquer multiple alignment with segment-based constraints. Bioinformatics (2003) 0.96
Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps. Algorithms Mol Biol (2008) 0.94
DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors. BMC Bioinformatics (2004) 0.93
DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS. Nucleic Acids Res (2010) 0.89
A min-cut algorithm for the consistency problem in multiple sequence alignment. Bioinformatics (2010) 0.88
DIALIGN at GOBICS--multiple sequence alignment using various sources of external information. Nucleic Acids Res (2013) 0.87
Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family. Algorithms Mol Biol (2008) 0.81
HIV classification using the coalescent theory. Bioinformatics (2010) 0.81
Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA. BMC Genomics (2008) 0.80
OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences. Nucleic Acids Res (2009) 0.79
Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC. Nucleic Acids Res (2005) 0.79
Detection of viral sequence fragments of HIV-1 subfamilies yet unknown. BMC Bioinformatics (2011) 0.78
5'TRU: identification and analysis of translationally regulative 5'untranslated regions in amino acid starved yeast cells. Mol Cell Proteomics (2011) 0.76
New journal: Algorithms for Molecular Biology. Algorithms Mol Biol (2006) 0.75